Global transcriptome response in Lactobacillus sakei during growth on ribose

  • Anette McLeod1, 2Email author,

    Affiliated with

    • Lars Snipen2,

      Affiliated with

      • Kristine Naterstad1 and

        Affiliated with

        • Lars Axelsson1

          Affiliated with

          BMC Microbiology201111:145

          DOI: 10.1186/1471-2180-11-145

          Received: 9 February 2011

          Accepted: 24 June 2011

          Published: 24 June 2011

          Abstract

          Background

          Lactobacillus sakei is valuable in the fermentation of meat products and exhibits properties that allow for better preservation of meat and fish. On these substrates, glucose and ribose are the main carbon sources available for growth. We used a whole-genome microarray based on the genome sequence of L. sakei strain 23K to investigate the global transcriptome response of three L. sakei strains when grown on ribose compared with glucose.

          Results

          The function of the common regulated genes was mostly related to carbohydrate metabolism and transport. Decreased transcription of genes encoding enzymes involved in glucose metabolism and the L-lactate dehydrogenase was observed, but most of the genes showing differential expression were up-regulated. Especially transcription of genes directly involved in ribose catabolism, the phosphoketolase pathway, and in alternative fates of pyruvate increased. Interestingly, the methylglyoxal synthase gene, which encodes an enzyme unique for L. sakei among lactobacilli, was up-regulated. Ribose catabolism seems closely linked with catabolism of nucleosides. The deoxyribonucleoside synthesis operon transcriptional regulator gene was strongly up-regulated, as well as two gene clusters involved in nucleoside catabolism. One of the clusters included a ribokinase gene. Moreover, hprK encoding the HPr kinase/phosphatase, which plays a major role in the regulation of carbon metabolism and sugar transport, was up-regulated, as were genes encoding the general PTS enzyme I and the mannose-specific enzyme II complex (EIIman). Putative catabolite-responsive element (cre) sites were found in proximity to the promoter of several genes and operons affected by the change of carbon source. This could indicate regulation by a catabolite control protein A (CcpA)-mediated carbon catabolite repression (CCR) mechanism, possibly with the EIIman being indirectly involved.

          Conclusions

          Our data shows that the ribose uptake and catabolic machinery in L. sakei is highly regulated at the transcription level. A global regulation mechanism seems to permit a fine tuning of the expression of enzymes that control efficient exploitation of available carbon sources.

          Background

          The Lactobacillus sakei species belongs to the lactic acid bacteria (LAB), a group of Gram-positive organisms with a low G+C content which produce lactic acid as the main end product of carbohydrate fermentation. This trait has, throughout history, made LAB suitable for production of food. Acidification suppresses the growth and survival of undesirable spoilage bacteria and human pathogens. L. sakei is naturally associated with the meat and fish environment, and is important in the meat industry where it is used as starter culture for sausage fermentation [1, 2]. The bacterium shows great potential as a protective culture and biopreservative to extend storage life and ensure microbial safety of meat and fish products [36]. The genome sequence of L. sakei strain 23K has revealed a metabolic repertoire which reflects the bacterium's adaption to meat products and the ability to flexibly use meat components [7]. Only a few carbohydrates are available in meat and fish, and L. sakei can utilize mainly glucose and ribose for growth, a utilization biased in favour of glucose [79]. The species has been observed as a transient member of the human gastrointestinal tract (GIT) [10, 11], and ribose may be described as a commonly accessible carbon source in the gut environment [12]. Transit through the GIT of axenic mice gave mutant strains which grow faster on ribose compared with glucose [13].

          Glucose is primarily transported and phosphorylated by the phosphoenolpyruvate (PEP)-dependent carbohydrate phosphotransferase system (PTS). A phosphorylation cascade is driven from PEP through the general components enzyme I (EI) and the histidine protein (HPr), then via the mannose-specific enzyme II complex (EIIman) to the incoming sugar. Moreover, glucose is fermented through glycolysis leading to lactate [7, 8, 14]. Ribose transport and subsequent phosphorylation are induced by the ribose itself and mediated by a ribose transporter (RbsU), a D-ribose pyranase (RbsD), and a ribokinase (RbsK) encoded by rbsUDK, respectively. These genes form an operon with rbsR which encodes the local repressor RbsR [15, 16]. The phosphoketolase pathway (PKP) is used for pentose fermentation ending with lactate and other end products [8, 17]. L. sakei also has the ability to catabolize arginine, which is abundant in meat, and to catabolize the nucleosides inosine and adenine, a property which is uncommon among lactobacilli [7, 18].

          By proteomics, we recently identified proteins involved in ribose catabolism and the PKP to be over-expressed during growth on ribose compared with glucose, while several glycolytic enzymes were less expressed. Moreover, also enzymes involved in pyruvate- and glycerol/glycerolipid metabolism were over-expressed on ribose [19]. Bacteria often use carbon catabolite repression (CCR) in order to control hierarchical utilization of different carbon sources. In low G+C content Gram-positive bacteria, the dominant CCR pathway is mediated by the three main components: (1) catabolite control protein A (CcpA) transcriptional regulator; (2) the histidine protein (HPr); and (3) catabolite-responsive element (cre) DNA sites located in proximity to catabolic genes and operons, which are bound by CcpA [2023]. The HPr protein has diverse regulatory functions in carbon metabolism depending on its phosphorylation state. In response to high throughput through glycolysis, the enzyme is phosphorylated at Ser46 by HPr kinase/phosphorylase (HPrK/P). This gives P-Ser-HPr which can bind to CcpA and convert it into its DNA-binding-competent conformation. However, when the concentration of glycolytic intermediates drop, the HPrK/P dephosphorylates P-Ser-HPr [20, 2224]. Under low glucose concentrations, HPr is phosphorylated by E1 of the PTS at His15 to give P-His-HPr, which has a catalytic function in the PTS and regulatory functions by phosphorylation of catabolic enzymes and transcriptional regulators with a PTS regulation domain (PRD). Several P-EIIBs also phosphorylate different types of non-PTS proteins and regulate their activities [2022]. Evidence for regulatory processes resembling glucose repression was shown both during lactose utilization [25] and catabolism of arginine [26, 27] in L. sakei. A cre site has been reported upstream of the rbs operon [28], thus CcpA could likely be acting on the rbs operon as well as other catabolic genes and operons in this bacterium.

          In the present study, we use a microarray representing the L. sakei 23K genome and an additional set of sequenced L. sakei genes, to investigate the global transcriptome response of three L. sakei strains when grown on ribose compared with glucose. Moreover, we predict the frequency of cre sites presumed to be involved in CCR in the L. sakei 23K genome sequence. Our objective was to identify differentially expressed genes between growth on the two sugars, and to increase the understanding of how the primary metabolism is regulated.

          Methods

          Bacterial strains, media and growth conditions

          L. sakei 23K is a plasmid-cured sausage isolate [29], and its complete genome sequence has been published [7]. L. sakei LS 25 is a commercial starter culture strain for salami sausage [30]. L. sakei MF1053 originates from fermented fish (Norwegian "rakfisk") [9]. The strains were maintained at -80°C in MRS broth (Oxoid) supplemented with 20% glycerol. Growth experiments were performed in a defined medium for lactobacilli [31] supplemented with 0.5% glucose (DMLG) or 0.5% ribose + 0.02% glucose (DMLRg) as described previously [19]. Samples were extracted at three different days from independent DMLG and DMLRg cultures from each strain grown at 30°C to mid-exponential phase (OD600 = 0.5-0.6) for a total of three sample sets (parallels).

          Microarrays

          The microarrays used have been described by Nyquist et al. [32], and a description is available at http://​migale.​jouy.​inra.​fr/​sakei/​Supplement.​html/​. 70-mer oligonucleotide probes representing the L. sakei strain 23K genome and an additional set of sequenced L. sakei genes were printed in three copies onto epoxy glass slides (Corning).

          RNA extraction

          Total RNA extraction was performed using the RNeasy Protect Mini Prep Kit (Qiagen) as described by Rud et al. [33]. The concentration and purity of the total RNA was analysed using NanoDrop ND-1000 (NanoDrop Technologies), and the quality using Agilent 2100 Bioanalyzer (Agilent Technologies). Sample criteria for further use in the transcriptome analysis were A260/A280 ratio superior to 1.9 and 23S/16S RNA ratio superior to 1.6.

          cDNA synthesis, labeling, and hybridization

          cDNA was synthesized and labeled with the Fairplay III Microarray Labeling Kit (Stratagene, Agilent Technologies) as described previously [34]. After labeling, unincorporated dyes were removed from the samples using the QIAQuick PCR purification kit (Qiagen). The following prehybridization, hybridization, washing, and drying of the arrays were performed in a Tecan HS 400 Pro hybridization station (Tecan) as described by Nyquist et al. [32]. For studying the carbon effects, samples from DMLG and DMLRg were co-hybridized for each of the three strains. Separate hybridizations were performed for each strain on all three biological parallels. In order to remove potential biases associated with labelling and subsequent scanning, a replicate hybridization was performed for each strain for one of the three parallels, where the Cy3 and Cy5 dyes (GE Healthcare) used during cDNA synthesis were swapped. The hybridized arrays were scanned at wavelengths 532 nm (Cy3) and 635 nm (Cy5) with a Tecan scanner LS (Tecan). GenePix Pro 6.0 (Molecular Devices) was used for image analysis, and spots were excluded based on slide or morphology abnormalities.

          Microarray data analysis

          Downstream analysis was done by the Limma package http://​www.​bioconductor.​org in the R computing environment http://​www.​r-project.​org. Pre-processing and normalization followed a standard procedure using methods described by Smyth & Speed [35], and testing for differential expressed genes were done by using a linear mixed model as described by Smyth [36]. A mixed-model approach was chosen to adequately describe between-array variation and still utilize probe-replicates (three replicates of each probe in each array). An empirical Bayes smoothing of gene-wise variances was conducted according to Smyth et al. [37], and for each gene the p-value was adjusted to control the false discovery rate (FDR), hence all p-values displayed are FDR-adjusted (often referred to as q-values in the literature).

          Validation of microarray data by qRT-PCR analysis

          The microarray results were validated on selected regulated genes for the LS 25 strain by quantitative real-time reverse transcriptase PCR (qRT-PCR) performed as described previously [38]. Primers and probes (Additional file 1, Table S3) were designed using Primer Express 3.0 (Applied Biosystems). Relative gene expression was calculated by the ΔC T method, using the DNA gyrase subunit alpha gene (gyrA) as the endogenous reference gene.

          Microarray accession numbers

          The microarray data have been deposited in the Array Express database http://​www.​ebi.​ac.​uk/​arrayexpress/​ under the accession numbers A-MEXP-1166 (array design) and E-MEXP-2892 (experiment).

          Sequence analysis

          A prediction of cre sites in the L. sakei 23K genome sequence (GeneBank acc. no. CR936503.1), both strands, was performed based on the consensus sequence TGWNANCGNTNWCA (W = A/T, N = A/T/G/C), confirmed in Gram-positive bacteria [39]. We made a search with the consensus sequence described by the regular expression T-G-[AT]-X-A-X-C-G-X-T-X-[AT]-C-A, allowing up to two mismatches in the conserved positions except for the two center position, highlighted in boldface. All computations were done in R http://​www.​r-project.​org.

          Results and Discussion

          Selection of L. sakei strains and growth conditions

          We have previously investigated L. sakei strain variation [9], and used proteomics to study the bacterium's primary metabolism [19], providing us with a basis for choosing strains with interesting differences for further studies. The starter culture strain LS 25 showed the fastest growth rates in a variety of media, and together with strain MF1053 from fish, it fermented the highest number of carbohydrates [9]. The LS 25 strain belongs to the L. sakei subsp. sakei, whereas the 23K and MF1053 strains belong to L. sakei subsp. carnosus [9, 19]. By identification of differentially expressed proteins caused by the change of carbon source from glucose to ribose, LS 25 seemed to down-regulate the glycolytic pathway more efficiently than other strains during growth on ribose [19]. For these reasons, LS 25 and MF1053 were chosen in addition to 23K for which the microarray is based on. Nyquist et al. [32] recently investigated the genomes of various L. sakei strains compared to the sequenced strain 23K by comparative genome hybridization (CGH) using the same microarray as in the present study. A large part of the 23K genes belongs to a common gene pool invariant in the species, and the status for each gene on the array is known for all the three strains [32].

          As glucose is the preferred sugar, L. sakei grows faster when glucose is utilized as the sole carbon source compared with ribose [8, 9, 15]. However, glucose stimulates ribose uptake and a possible co-metabolism of these two sugars present in meat and fish has been suggested, a possibility that give the organism an advantage in competition with other microbiota [15, 16, 40]. To obtain comparable 2-DE gels between samples issued from bacteria grown on the two carbohydrates in our recent proteomic analysis, growth on ribose was enhanced by adding small amounts of glucose [19]. For the present transcriptome analysis we therefore chose the same growth conditions.

          Global gene expression patterns

          A microarray representing the L. sakei 23K genome and an additional set of sequenced L. sakei genes was used for studying the effect of carbon source on the transcriptome of L. sakei strains 23K, MF1053 and LS 25. Genes displaying a significant differential expression with a log2 ratio > 0.5 or < -0.5 were classified into functional categories according to the L. sakei 23K genome database http://​migale.​jouy.​inra.​fr/​sakei/​genome-server and are listed in Table 1. The 23K strain showed differential expression for 364 genes within these limits, MF1053 and LS 25 for 223 and 316 genes, respectively. Among these, 88, 47 and 82, respectively, were genes belonging to the category of genes of 'unknown' function. Eighty three genes, the expression of which varied depending on the carbon source, were common to the three strains, among which 52 were up-regulated and 31 down-regulated during growth on ribose (Figure 1). The function of these common regulated genes was mostly related to carbohydrate transport and metabolism (34 genes, Table 1). The reliability of the microarray results was assessed by qRT-PCR analysis using selected regulated genes in the LS 25 strain. As shown in Table S4 in the additional material (Additional file 1), the qRT-PCR results were in agreement with the data obtained by the microarrays.
          Table 1

          Genes with significant differential expression in three L. sakei strains grown on ribose compared with glucose, FDR adjusted p-value less than 0.01 and log2 of > 0.5 or < -0.5 (log2 values > 1.0 or < -1.0 are shown in bold).

          Gene locus

          Gene

          Description

          23K

          MF1053

          LS 25

          Carbohydrate transport and metabolism

          Transport/binding of carbohydrates

          LSA0185*

          galP

          Galactose:cation symporter

          1.2

           

          1.7

          LSA0200*

          rbsU

          Ribose transport protein

          2.8

          3.5

          4.3

          LSA0353*

          lsa0353

          Putative cellobiose-specific PTS, enzyme IIB

          3.6

          1.3

          2.5

          LSA0449*

          manL

          Mannose-specific PTS, enzyme IIAB

          2.1

          2.5

          1.5

          LSA0450*

          manN

          Mannose-specific PTS, enzyme IIC

          1.9

          2.0

          1.4

          LSA0451*

          manM

          Mannose-specific PTS, enzyme IID

          2.4

          1.0

          2.1

          LSA0651*

          glpF

          Glycerol uptake facilitator protein, MIP family

          3.4

          4.7

          3.4

          LSA1050*

          fruA

          Fructose-specific PTS, enzyme IIABC

            

          0.9

          LSA1204*

          lsa1204

          Putative sugar transporter

           

          1.1

           

          LSA1457*

          lsa1457

          Putative cellobiose-specific PTS, enzyme IIC

           

          2.3

           

          LSA1462*

          ptsI

          PTS, enzyme I

          0.8

          1.7

          0.9

          LSA1463*

          ptsH

          Phosphocarrier protein HPr (histidine protein)

           

          1.2

          0.9

          LSA1533

          lsa1533

          Putative cellobiose-specific PTS, enzyme IIA

           

          2.5

          2.1

          LSA1690

          lsa1690

          Putative cellobiose-specific PTS, enzyme IIC

          0.9

            

          LSA1792*

          scrA

          Sucrose-specific PTS, enzyme IIBCA

          0.8

           

          1.1

          Metabolism of carbohydrates and related molecules

          LSA0123*

          lsa0123

          Putative sugar kinase, ROK family

          1.2

            

          LSA0198

          ack1

          Acetate kinase (acetokinase)

          1.7

           

          1.3

          LSA0254*

          lsa0254

          Putative carbohydrate kinase

          2.4

          0.8

          1.8

          LSA0292*

          budC

          Acetoin reductase (acetoin dehydrogenase) (meso-2,3-butanediol dehydrogenase)

          3.4

          2.3

          3.4

          LSA0444

          lsa0444

          Putative malate dehydrogenase

          3.4

          D

          2.1

          LSA0516

          hprK

          Hpr kinase/phosphorylase

          2.0

          1.6

          1.2

          LSA0664*

          loxL1N

          L-lactate oxidase (N-terminal fragment), degenerate

          1.2

           

          0.7

          LSA0665*

          loxLI

          L-lactate oxidase (central fragment), degenerate

          1.0

            

          LSA0666*

          loxL1C

          L-lactate oxidase (C-terminal fragment), degenerate

          1.0

            

          LSA0974*

          pflB

          Formate C-acetyltransferase (pyruvate formate-lyase) (formate acetyltransferase)

          4.0

            

          LSA0981

          aldB

          Acetolactate decarboxylase (alpha-acetolactate decarboxylase)

           

          0.6

          1.9

          LSA0982

          als

          Acetolactate synthase (alpha-acetolactate synthase)

            

          1.9

          LSA0983

          lsa0983

          Putative aldose-1 epimerase

          0.6

            

          LSA1032

          pyk

          Pyruvate kinase

           

          -0.7

           

          LSA1080

          lsa1080

          Myo-inositol monophosphatase

          0.6

           

          0.8

          LSA1082

          pdhD

          Pyruvate dehydrogenase complex, E3 component, dihydrolipoamide dehydrogenase

          2.8

          2.5

          2.1

          LSA1083

          pdhC

          Puruvate dehydrogenase complex, E2 component, dihydrolipoamide acetyltransferase

          3.4

          3.7

          2.7

          LSA1084

          pdhB

          Pyruvate dehydrogenase complex, E1 component, beta subunit

          3.2

          3.3

          2.2

          LSA1085

          pdhA

          Pyruvate dehydrogenase complex, E1 component, alpha subunit

          2.9

          3.5

          2.4

          LSA1141*

          ppdK

          Pyruvate phosphate dikinase

          1.0

           

          0.9

          LSA1188*

          pox1

          Pyruvate oxidase

          2.3

          3.1

          2.1

          LSA1298

          ack2

          Acetate kinase (acetokinase)

          1.1

          0.9

          0.9

          LSA1343*

          eutD

          Phosphate acetyltransferase (phosphotransacetylase)

          2.0

          1.0

          1.6

          LSA1381

          lsa1381

          Putative acylphosphatase

          -0.6

          -0.5

           

          LSA1399*

          loxL2

          L-lactate oxidase

          3.4

          U

           

          LSA1630

          lsa1630

          Putative sugar kinase, ROK family

          -0.6

           

          -0.6

          LSA1640*

          nanA

          N-acetylneuraminate lyase

          2.0

           

          D

          LSA1641*

          nanE

          N-acylglucosamine/mannosamine-6-phosphate 2-epimerase

          0.9

           

          D

          LSA1643*

          lsa1643

          Putative sugar kinase, ROK family

          1.8

            

          LSA1668

          ack3

          Acetate kinase (acetokinase)

          -0.7

           

          -1.1

          LSA1830*

          pox2

          Pyruvate oxidase

          0.7

            

          Intermediary metabolism

          LSA0255*

          lsa0255

          Putative phosphoribosyl isomerase

          2.0

          1.0

          1.6

          Specific carbohydrate metabolic pathway

          LSA0201*

          rbsD

          D-ribose pyranase

          2.5

          2.5

          3.4

          LSA0202*

          rbsK

          Ribokinase

          3.0

          3.9

          4.3

          LSA0289*

          xpk

          Xylulose-5-phosphate phosphoketolase

          3.2

          2.3

          2.6

          LSA0297

          gntZ

          6-phosphogluconate dehydrogenase

          -1.2

          -0.9

          -1.7

          LSA0298

          gntK

          Gluconokinase

          -0.8

            

          LSA0381

          zwf

          Glucose-6-phosphate 1-dehydrogenase

          -0.6

          -0.6

          -0.6

          LSA0649*

          glpK

          Glycerol kinase

          3.4

          4.8

          2.1

          LSA0650*

          glpD

          Glycerol-3-phosphate dehydrogenase

          2.3

          2.2

          2.0

          LSA0764*

          galK

          Galactokinase

          1.1

          0.7

          1.8

          LSA0765*

          galE1

          UDP-glucose 4-epimerase

            

          1.2

          LSA0766*

          galT

          Galactose-1-phosphate uridylyltransferase

          1.2

          0.8

          2.0

          LSA0767*

          galM

          Aldose 1-epimerase (mutarotase)

          1.3

           

          2.0

          LSA1146*

          manA

          Mannose-6-phosphate isomerase

          1.4

          1.3

          1.5

          LSA1531

          lsa1531

          Putative beta-glucosidase

           

          0.7

          0.9

          LSA1588

          nagA

          N-acetylglucosamine-6-phosphate deacetylase

          0.6

            

          LSA1685

          rpiA

          Ribose 5-phosphate epimerase (ribose 5-phosphate isomerase)

           

          1.1

          0.8

          LSA1710*

          lacM

          Beta-galactosidase, small subunit (lactase, small subunit)

          3.3

           

          1.2

          LSA1711*

          lacL

          Beta-galactosidase, large subunit (lactase, large subunit)

          3.0

          1.5

          1.7

          LSA1790*

          scrK

          Fructokinase

           

          1.0

          1.1

          LSA1791*

          dexB

          Glucan 1,6-alpha-glucosidase (dextran glucosidase)

            

          1.1

          LSA1795

          melA

          Alpha-galactosidase (melibiase)

            

          -0.6

          Glycolytic pathway

          LSA0131

          gpm2

          Phosphoglycerate mutase

           

          0.7

           

          LSA0206

          gpm3

          Phosphoglycerate mutase

          -0.7

          -0.8

          -0.9

          LSA0609*

          gloAC

          Lactoylglutathione lyase (C-terminal fragment), authentic frameshift

          1.1

           

          0.7

          LSA0803

          gpm4

          Phosphoglycerate mutase

          0.5

           

          0.5

          LSA1033

          pfk

          6-phosphofructokinase

          -0.6

          -1.1

          -0.5

          LSA1157

          mgsA

          Methylglyoxal synthase

          2.3

          1.4

          1.7

          LSA1179

          pgi

          Glucose-6-phosphate isomerase

          0.5

            

          LSA1527

          fba

          Fructose-bisphosphate aldolase

          -1.0

          -0.7

          -1.1

          LSA1606

          ldhL

          L-lactate dehydrogenase

          -1.0

          -0.9

          -1.5

          Nucleotide transport and metabolism

          Transport/binding of nucleosides, nucleotides, purines and pyrimidines

          LSA0013

          lsa0013

          Putative nucleobase:cation symporter

          -0.9

           

          -1.5

          LSA0055

          lsa0055

          Putative thiamine/thiamine precursor:cation symporter

            

          1.6

          LSA0064

          lsa0064

          Putative nucleobase:cation symporter

           

          -0.8

           

          LSA0259

          lsa0259

          Pyrimidine-specific nucleoside symporter

          1.5

           

          1.3

          LSA0798*

          lsa0798

          Pyrimidine-specific nucleoside symporter

          3.5

          2.2

          1.7

          LSA0799*

          lsa0799

          Putative purine transport protein

          4.4

          2.7

          2.9

          LSA1210

          lsa1210

          Putative cytosine:cation symporter (C-terminal fragment), authentic frameshift

          -0.8

           

          -0.6

          LSA1211

          lsa1211

          Putative cytosine:cation symporter (N-terminal fragment), authentic frameshit

          -1.1

           

          -0.9

          Metabolism of nucleotides and nucleic acids

          LSA0010

          lsa0010

          Putative nucleotide-binding phosphoesterase

            

          -0.6

          LSA0023

          lsa0023

          Putative ribonucleotide reductase (NrdI-like)

          -0.5

          D

          D

          LSA0063

          purA

          Adenylosuccinate synthetase (IMP-aspartate ligase)

           

          -0.8

           

          LSA0139

          guaA

          Guanosine monophosphate synthase (glutamine amidotransferase)

           

          -0.5

          -0.8

          LSA0252

          iunH1

          Inosine-uridine preferring nucleoside hydrolase

          2.6

          2.6

          1.8

          LSA0446

          pyrDB

          Putative dihydroorotate oxidase, catalytic subunit

            

          0.9

          LSA0489

          lsa0489

          Putative metal-dependent phosphohydrolase precursor

          0.5

            

          LSA0533*

          iunH2

          Inosine-uridine preferring nucleoside hydrolase

          1.2

            

          LSA0785

          lsa0785

          Putative NCAIR mutase, PurE-related protein

          -2.3

           

          -1.3

          LSA0795*

          deoC

          2 Deoxyribose-5 phosphate aldolase

          4.0

          2.1

          2.2

          LSA0796*

          deoB

          Phosphopentomutase (phosphodeoxyribomutase)

          5.5

          4.1

          3.2

          LSA0797*

          deoD

          Purine-nucleoside phosphorylase

          4.5

          2.6

          1.9

          LSA0801*

          pdp

          Pyrimidine-nucleoside phosphorylase

          1.8

            

          LSA0940

          nrdF

          Ribonucleoside-diphosphate reductase, beta chain

           

          1.0

          0.6

          LSA0941

          nrdE

          Ribonucleoside-diphosphate reductase, alpha chain

           

          1.0

          0.6

          LSA0942

          nrdH

          Ribonucleotide reductase, NrdH-redoxin

           

          1.1

           

          LSA0950

          pyrR

          Bifunctional protein: uracil phosphoribosyltransferase and pyrimidine operon transcriptional regulator

          -0.6

            

          LSA0993

          rnhB

          Ribonuclease HII (RNase HII)

            

          0.6

          LSA1018

          cmk

          Cytidylate kinase

            

          0.6

          LSA1097

          lsa1097

          Putative ADP-ribose phosphorylase, NUDIX family

          0.5

            

          LSA1352

          lsa1352

          Putative phosphomethylpyrimidine kinase

          -0.8

            

          LSA1651

          lsa1651

          Putative purine phosphoribosyltransferase, PRT family

           

          0.8

           

          LSA1661

          lsa1661

          Putative nucleotide hydrolase, NUDIX family

           

          -0.5

           

          LSA1805

          dgk

          Deoxyguanosine kinase

          -1.0

           

          -0.8

          Transcription

          Transcription regulation

          LSA0130

          lsa0130

          Putative transcriptional regulator, LacI family

          -0.6

            

          LSA0132

          lsa0132

          Putative transcriptional regulator, MarR family

          -0.6

            

          LSA0161

          lsa0161

          Putative transcriptional regulator, ArsR family

          -0.6

            

          LSA0186

          lsa0186

          Putative transcriptional regulator, LytR family

           

          0.8

          0.6

          LSA0203

          rbsR

          Ribose operon transcriptional regulator, LacI family

          1.7

            

          LSA0217

          lsa0217

          Putative thiosulfate sulfurtransferase with a ArsR-HTH domain, rhodanese family

           

          -1.0

          -0.7

          LSA0229

          lsa0229

          Putative transcriptional regulator, MerR family (N-terminal fragment), authentic frameshift

          -0.5

            

          LSA0269

          lsa0269

          Putative transcriptional regulator, TetR family

            

          -0.6

          LSA0293

          lsa0293

          Putative DNA-binding protein, XRE family

            

          -0.6

          LSA0356

          rex1

          Redox-sensing transcriptional repressor, Rex

          -0.8

          -0.5

          -0.9

          LSA0603

          cggR

          Glycolytic genes regulator

           

          -0.6

          -0.6

          LSA0669

          lsa0669

          Putative transcription regulator, TetR family

           

          -0.6

           

          LSA0783

          lsa0783

          Putative transcriptional regulator, Fnr/Crp Family

          -0.6

            

          LSA0800

          deoR

          Deoxyribonucleoside synthesis operon transcriptional regulator, GntR family

          3.8

          2.1

          1.9

          LSA0835

          lsa0835

          Putative DNA-binding protein, XRE family

          -0.6

            

          LSA0848

          rex

          Redox-sensing transcriptional repressor, Rex

          1.6

          0.7

           

          LSA0972

          lsa0972

          Putative transcriptional regulator, LysR family

          0.9

            

          LSA1201

          lsa1201

          Putative transcriptional regulator, GntR family

          1.4

          D

          D

          LSA1322

          glnR

          Glutamine synthetase transcriptional regulator, MerR family

          -1.4

          -1.3

           

          LSA1351

          lsa1351

          Putative transcritional regulator with aminotransferase domain, GntR family

           

          -0.5

          -0.6

          LSA1434

          lsa1434

          Putative transcriptional regulator, DUF24 family (related to MarR/PadR families)

          -0.8

            

          LSA1449

          spxA

          Transcriptional regulator Spx

          1.0

           

          0.6

          LSA1521

          lsa1521

          Putative transcriptional regulator, TetR family

          0.6

            

          LSA1554

          lsa1554

          Putative transcriptional regulator, LacI family

          -0.7

          -0.9

          -0.5

          LSA1587

          lsa1587

          Putative transcriptional regulator, GntR family

          0.6

            

          LSA1611

          lsa1611

          Putative DNA-binding protein, PemK family

           

          -0.5

          -0.7

          LSA1653

          lsa1653

          Putative transcriptional regulator, MarR family

            

          -0.6

          LSA1692

          lsa1692

          Putative transcriptional regulator, GntR family

          0.7

           

          0.7

          CoEnzyme transport and metabolism

          Metabolism of coenzymes and prostethic groups

          LSA0041

          panE

          2-dehydropantoate 2-reductase

           

          0.8

           

          LSA0057

          thiE

          Thiamine-phosphate pyrophosphorylase (thiamine-phosphate synthase)

            

          1.9

          LSA0058

          thiD

          Phosphomethylpyrimidine kinase (HMP-phosphate kinase)

            

          1.4

          LSA0059

          thiM

          Hydroxyethylthiazole kinase (4-methyl-5-beta-hydroxyethylthiazole kinase)

          1.0

           

          1.8

          LSA0183

          lsa0183

          Putative hydrolase, isochorismatase/nicotamidase family

          -0.7

            

          LSA0840

          lsa0840

          Putative glutamate-cysteine ligase

          0.6

            

          LSA0947

          fhs

          Formate-tetrahydrofolate ligase (formyltetrahydrofolate synthetase)

          0.6

            

          LSA0980

          lsa0980

          Putative hydroxymethylpyrimidine/phosphomethylpyrimidine kinase, PfkB family

          0.6

            

          LSA1101

          folK

          2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase

          0.6

          U

           

          LSA1614

          acpS

          Holo-[acyl-carrier protein] synthase (holo-ACP synthase) (4'-phosphopantetheine transferase AcpS)

          -1.0

          -0.9

          -0.9

          LSA1664

          lsa1664

          Putative dihydrofolate reductase

          1.6

          1.1

          1.5

          Energy production and conversion

          Membrane bioenergetics (ATP synthase)

          LSA1125

          atpC

          H(+)-transporting two-sector ATPase (ATP synthase), epsilon subunit

          0.6

            

          LSA1126

          atpD

          H(+)-transporting two-sector ATPase (ATP synthase), beta subunit

            

          0.6

          LSA1127

          atpG

          H(+)-transporting two-sector ATPase (ATP synthase), gamma subunit

            

          0.8

          LSA1128

          atpA

          H(+)-transporting two-sector ATPase (ATP synthase), alpha subunit

            

          0.6

          LSA1129

          atpH

          H(+)-transporting two-sector ATPase (ATP synthase), delta subunit

            

          0.6

          LSA1130

          atpF

          H(+)-transporting two-sector ATPase (ATP synthase), B subunit

            

          0.5

          LSA1131

          atpE

          H(+)-transporting two-sector ATPase (ATP synthase), C subunit

            

          0.7

          Inorganic ion transport and metabolism

          Transport/binding of inorganic ions

          LSA0029

          lsa0029

          Putative ion Mg(2+)/Co(2+) transport protein, hemolysinC-family

            

          -0.7

          LSA0134

          lsa0134

          Putative Na(+)/H(+) antiporter

            

          -0.6

          LSA0180

          mtsC

          Manganese ABC transporter, ATP-binding subunit

          -0.8

            

          LSA0181

          mtsB

          Manganese ABC transporter, membrane-spanning subunit

          -0.8

           

          -1.0

          LSA0182

          mtsA

          Manganese ABC transporter, substrate-binding lipoprotein precursor

          -0.7

           

          -0.6

          LSA0246

          mntH1

          Mn(2+)/Fe(2+) transport protein

          -0.9

           

          -1.3

          LSA0283

          lsa0283

          Putative zinc/iron ABC transporter, ATP-binding subunit

            

          -0.5

          LSA0284

          lsa0284

          Putative zinc/iron ABC transporter, membrane-spanning subunit

            

          -0.6

          LSA0399

          lsa0399

          Iron(III)-compound ABC transporter, substrate-binding lipoprotein precursor

          1.1

          0.9

           

          LSA0400

          lsa0400

          Iron(III)-compound ABC transporter, ATP-binding subunit

           

          0.7

           

          LSA0401

          lsa0401

          Iron(III)-compound ABC transporter, membrane-spanning subunit

            

          0.5

          LSA0402

          lsa0402

          Iron(III)-compound ABC transporter, membrane-spanning subunit

          0.5

           

          0.6

          LSA0503

          pstC

          Phosphate ABC transporter, membrane-spanning subunit

          0.5

            

          LSA0504

          pstA

          Phosphate ABC transporter, membrane-spanning subunit

          0.6

            

          LSA0781

          lsa0781

          Putative cobalt ABC transporter, membrane-spanning/permease subunit

          -0.9

            

          LSA0782

          lsa0782

          Putative cobalt ABC transporter, membrane-spanning/permease subunit

          -2.1

            

          LSA1166

          lsa1166

          Putative potassium transport protein

          0.7

            

          LSA1440

          cutC

          Copper homeostasis protein, CutC family

          -0.6

            

          LSA1460

          atkB

          Copper-transporting P-type ATPase

          0.6

            

          LSA1638

          lsa1638

          Putative large conductance mechanosensitive channel

           

          -1.0

          -0.8

          LSA1645

          lsa1645

          Putative Na(+)/(+) antiporter

          1.4

           

          D

          LSA1699

          mntH2

          Mn(2+)/Fe(2+) transport protein

            

          -0.6

          LSA1703

          lsa1703

          Putative Na(+)/H(+) antiporter

          -1.2

            

          LSA1704

          lsa1704

          Putative calcium-transporting P-type ATPase

            

          -0.8

          LSA1735

          lsa1735

          Putative cobalt ABC transporter, membrane-spanning subunit

            

          -0.6

          LSA1736

          lsa1736

          Putative cobalt ABC transporter, ATP-binding subunit

          -0.6

            

          LSA1737

          lsa1737

          Putative cobalt ABC transporter, ATP-binding subunit

          -0.7

            

          LSA1838

          lsa1838

          Putative metal ion ABC transporter, membrane-spanning subunit

            

          -0.5

          LSA1839

          lsa1839

          Putative metal ion ABC transporter, substrate-binding lipoprotein precursor

            

          -0.6

          Amino acid transport and metabolism

          Transport/binding of amino acids

          LSA0125

          lsa0125

          Putative amino acid/polyamine transport protein

          0.6

            

          LSA0189

          lsa0189

          Putative amino acid/polyamine transport protein

            

          -0.7

          LSA0311

          lsa0311

          Putative glutamate/aspartate:cation symporter

          -1.1

           

          -1.0

          LSA1037

          lsa1037

          Putative amino acid/polyamine transport protein

          1.0

          0.8

          0.5

          LSA1219

          lsa1219

          Putative cationic amino acid transport protein

          0.7

            

          LSA1415

          lsa1415

          Putative amino acid/polyamine transport protein

          1.1

           

          0.7

          LSA1424

          lsa1424

          Putative L-aspartate transport protein

          -1.4

          -0.9

          -1.2

          LSA1435

          lsa1435

          Putative amino acid:H(+) symporter

          1.0

           

          0.8

          LSA1496

          lsa1496

          Putative glutamine/glutamate ABC transporter, ATP-binding subunit

           

          1.2

           

          LSA1497

          lsa1497

          Putative glutamine/glutamate ABC transporter, membrane-spanning/substrate-binding subunit precursor

           

          0.7

           

          Transport/binding of proteins/peptides

          LSA0702

          oppA

          Oligopeptide ABC transporter, substrate-binding lipoprotein precursor

           

          1.3

          1.0

          LSA0703

          oppB

          Oligopeptide ABC transporter, membrane-spanning subunit

           

          0.8

          0.8

          LSA0704

          oppC

          Oligopeptide ABC transporter, membrane-spanning subunit

           

          1.8

          1.0

          LSA0705

          oppD

          Oligopeptide ABC transporter, ATP-binding subunit

           

          1.2

          1.1

          LSA0706

          oppF

          Oligopeptide ABC transporter, ATP-binding subunit

           

          1.2

          1.2

          Protein fate

          LSA0053

          pepO

          Endopeptidase O

          0.6

            

          LSA0133

          pepR

          Prolyl aminopeptidase

          1.5

            

          LSA0226

          pepN

          Aminopeptidase N (lysyl-aminopeptidase-alanyl aminopeptidase)

            

          -0.7

          LSA0285

          pepF1

          Oligoendopeptidase F1

            

          -0.7

          LSA0320

          pepD3

          Dipeptidase D-type (U34 family)

           

          -0.8

          -0.5

          LSA0424

          pepV

          Xaa-His dipeptidase V (carnosinase)

          1.6

            

          LSA0643

          pepX

          X-Prolyl dipeptidyl-aminopeptidase

          0.6

            

          LSA0888

          pepT

          Tripeptide aminopeptidase T

          0.6

            

          LSA1522

          pepS

          Aminopeptidase S

          0.5

            

          LSA1686

          pepC1N

          Cysteine aminopeptidase C1 (bleomycin hydrolase) (N-terminal fragment), authentic frameshift

           

          1.6

           

          LSA1688

          pepC2

          Cysteine aminopeptidase C2 (bleomycin hydrolase)

           

          0.7

           

          LSA1689

          lsa1689

          Putative peptidase M20 family

          1.0

           

          1.1

          Metabolism of amino acids and related molecules

          LSA0220_c

          dapE

          Succinyl-diaminopimelate desuccinylase

          -1.4

           

          -1.5

          LSA0316

          sdhB

          L-serine dehydratase, beta subunit (L-serine deaminase)

          -0.7

            

          LSA0370*

          arcA

          Arginine deiminase (arginine dihydrolase)

          1.9

            

          LSA0372*

          arcC

          Carbamate kinase

          0.5

            

          LSA0463

          lsa0463

          Putative 2-hydroxyacid dehydrogenase

          -0.7

            

          LSA0509

          kbl

          2-amino-3-ketobutyrate coenzyme A ligase (glycine acetyltransferase)

          1.5

            

          LSA0510

          lsa0510

          L-threonine dehydrogenase (N-terminal fragment), authentic frameshift

          2.0

          0.5

           

          LSA0572*

          tdcB

          Threonine deaminase (threonine ammonia-lyase, threonine dehydratase, IlvA homolog)

          2.2

           

          1.7

          LSA0922

          serA

          D-3-phosphoglycerate dehydrogenase

          0.9

            

          LSA1134

          glyA

          Glycine/Serine hydroxymethyltransferase

           

          0.7

           

          LSA1321

          glnA

          Glutamate-ammonia ligase (glutamine synthetase)

          -1.3

          -1.0

           

          LSA1484

          mvaS

          Hydroxymethylglutaryl-CoA synthase

          -0.7

          -0.6

          -0.7

          LSA1693

          asnA2

          L-asparaginase

          0.8

            

          Lipid transport and metabolism

          Metabolism of lipids

          LSA0045

          cfa

          Cyclopropane-fatty-acyl-phospholipid synthase

          -1.3

          -1.4

          -1.4

          LSA0644

          lsa0644

          Putative acyl-CoA thioester hydrolase

          0.6

            

          LSA0812

          fabZ1

          (3R)-hydroxymyristoyl-[acyl-carrier protein] dehydratase

           

          -0.7

          0.5

          LSA0813

          fabH

          3-oxoacyl-[acyl carrier protein] synthetase III

            

          0.6

          LSA0814

          acpP

          Acyl carrier protein

            

          0.6

          LSA0815

          fabD

          Malonyl-CoA:ACP transacylase

           

          -0.7

          0.7

          LSA0816

          fabG

          3-oxoacyl-acyl carrier protein reductase

           

          -0.7

           

          LSA0817

          fabF

          3-oxoacyl-[acyl carrier protein] synthetase II

           

          -0.7

           

          LSA0819

          fabZ

          (3R)-hydroxymyristoyl-[acyl carrier proetin] dehydratase

            

          0.7

          LSA0820

          accC

          Acetyl-CoA carboxylase (biotin carbooxylase subunit)

           

          -0.7

           

          LSA0821

          accD

          Acetyl-CoA carboxylase (carboxyl transferase beta subunit)

            

          0.8

          LSA0822

          accA

          Acetyl-CoA carboxylase (carboxyl transferase alpha subunit)

            

          0.6

          LSA0823

          fabI

          Enoyl [acyl carrier protein] reductase

            

          0.9

          LSA0891

          lsa0891

          Putative lipase/esterase

          1.2

            

          LSA1485

          mvaA

          Hydroxymethylglutaryl-CoA reductase

          -0.5

            

          LSA1493

          lsa1493

          Putative diacylglycerol kinase

          -0.6

          -0.9

          -0.7

          LSA1652

          ipk

          4-diphosphocytidyl-2-C-methyl-D-erythritol kinase

          -0.6

           

          -0.7

          Secondary metabolites transport and metabolism

          Transport/binding proteins and lipoproteins

          LSA0046

          lsa0046

          Putative transport protein

          -1.0

          -0.6

          -1.3

          LSA0089

          lsa0089

          Putative drug transport protein

          -2.1

          -0.9

          -0.8

          LSA0094

          lsa0094

          Putative transport protein, Major Facilitator Super (MFS) family transporter

          -0.7

           

          -0.7

          LSA0095

          lsa0095

          Putative transport protein

          1.3

          0.5

           

          LSA0128

          lsa0128

          Putative antimicrobial peptide ABC exporter, membrane-spanning/permease subunit

            

          -0.5

          LSA0187

          lsa0187

          Putative drug-resistance ABC transporter, two ATP-binding subunits

           

          0.7

           

          LSA0219_b

          lsa0219_b

          Putative cyanate transport protein

          -0.6

            

          LSA0232

          lmrA

          Multidrug ABC exporter, ATP-binding and membrane-spanning/permease subunits

          -0.7

           

          -0.7

          LSA0270

          lsa0270

          Putative multidrug ABC exporter, membrane-spanning/permease subunit

          -0.7

            

          LSA0271

          lsa0271

          Putative multidrug ABC exporter, ATP-binding subunit

          -0.7

           

          -0.6

          LSA0272

          lsa0272

          Putative multidrug ABC exporter, ATP-binding and membrane-spanning/permease subunits

          -0.6

           

          -0.6

          LSA0308

          lsa0308

          Putative drug:H(+) antiporter

            

          -0.7

          LSA0376

          lsa0376

          Putative transport protein

          0.7

            

          LSA0420

          lsa0420

          Putative drug:H(+) antiporter (N-terminal fragment), authentic frameshift

          -0.8

           

          -1.1

          LSA0469

          lsa0469

          Putative drug:H(+) antiporter

          -0.6

           

          -0.5

          LSA0788

          lsa0788

          Putative facilitator protein, MIP family

          -2.6

            

          LSA0936

          lsa0936

          Putative drug ABC exporter, membrane-spanning/permease subunit

          1.1

            

          LSA0937

          lsa0937

          Putative drug ABC exporter, membrane-spanning/permease subunit

          1.3

            

          LSA0938

          lsa0938

          Putative drug ABC exporter, ATP-binding subunit

          1.2

            

          LSA0963

          lsa0963

          Integral membrane protein, hemolysin III related

             

          LSA1088

          lsa1088

          Putative multidrug ABC exporter, ATP-binding and membrane-spanning/permease subunits

          0.5

            

          LSA1261

          lsa1261

          Putative autotransport protein

          0.5

            

          LSA1340

          lsa1340

          Putative transport protein

           

          -0.7

           

          LSA1366

          lsa1366

          Putative ABC exporter, ATP-binding subunit

          -0.8

           

          -1.0

          LSA1367

          lsa1367

          Putative ABC exporter, membrane-spanning/permease subunit

          -0.8

          -0.5

          -0.8

          LSA1420

          lsa1417

          Putative lipase/esterase

           

          -1.1

           

          LSA1621

          lsa1621

          Putative drug:H(+) antiporter

           

          -1.1

           

          LSA1642

          lsa1642

          Putative Solute:Na(+) symporter

          3.4

          1.8

          D

          LSA1872

          lsa1872

          Putative drug:H(+) antiporter

           

          0.7

           

          LSA1878

          lsa1878

          Putative drug resistance ABC transporter, two ATP-binding subunits

          -0.6

            

          Detoxification

          LSA0772

          lsa0772

          Hypothetical protein (TelA, telluric resistance family)

          1.0

           

          0.7

          LSA1317

          lsa1317

          Putative chromate reductase

          0.6

          -0.7

           

          LSA1450

          lsa1450

          Putative metal-dependent hydrolase (beta-lactamase family III)

            

          0.6

          LSA1776

          lsa1776

          Putative 4-carboxymuconolactone decarboxylase

          0.6

           

          D

          Translation, ribosomal structure and biogenesis

          Translation initiation

          LSA1135

          lsa1135

          Putative translation factor, Sua5 family

           

          0.7

          0.6

          Translation elongation

          LSA0251

          efp1

          Elongation factor P (EF-P)

          0.5

            

          LSA1063

          tuf

          Elongation factor Tu (EF-Tu)

          0.6

            

          Ribosomal proteins

          LSA0011

          rplI

          50S Ribosomal protein L9

            

          -0.8

          LSA0266

          rpsN

          30S ribosomal protein S14

           

          0.7

          -0.5

          LSA0494

          lsa0494

          30S ribosomal interface protein S30EA

          1.7

            

          LSA0696

          rpmB

          50S ribosomal protein L28

            

          0.8

          LSA1017

          rpsA

          30S Ribosomal protein S1

          0.9

           

          0.6

          LSA1333

          rpmG

          50S ribosomal protein L33

            

          0.6

          LSA1666

          rplL

          50S ribosomal protein L7/L12

          -0.6

            

          LSA1676

          rpmG2

          50S ribosomal protein L33

            

          -0.6

          LSA1750

          rplF

          50S ribosomal protein L6

           

          0.6

           

          LSA1755

          rpsQ

          30S ribosomal protein S17

           

          0.5

           

          LSA1761

          rplB

          50S ribosomal protein L2

           

          0.6

           

          LSA1765

          rpsJ

          30S ribosomal protein S10

          -0.7

            

          Protein synthesis

          LSA0377

          tgt

          Queuine tRNA-ribosyltransferase

          -0.6

            

          LSA1546

          gatB

          Glutamyl-tRNA amidotransferase, subunit B

           

          -0.5

           

          LSA1547

          gatA

          Glutamyl-tRNA amidotransferase, subunit A

          -0.5

           

          -0.5

          RNA restriction and modification

          LSA0437

          lsa0437

          Hypothetical protein with an RNA-binding domain

          -0.7

            

          LSA0443

          lsa0443

          Putative single-stranded mRNA endoribonuclease

          2.7

           

          1.9

          LSA0738

          dtd

          D-tyrosyl-tRNA(tyr) deacylase

          0.5

            

          LSA0794

          trmU

          tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase

           

          -0.9

           

          LSA1534

          lsa1534

          Putative ATP-dependent RNA helicase

           

          0.9

           

          LSA1615

          lsa1615

          Putative ATP-dependent RNA helicase

          -0.7

          -0.8

          -1.0

          LSA1723

          truA

          tRNA pseudouridylate synthase A (pseudouridylate synthase I)

          -0.7

           

          -0.6

          LSA1880

          trmE

          tRNA modification GTPase trmE

          -0.7

            

          Aminoacyl-tRNA synthetases

          LSA0880

          glyQ

          Glycyl-tRNA synthetase, alpha subunit

           

          0.7

           

          LSA0881

          glyS

          Glycyl-tRNA synthetase, beta subunit

           

          0.7

           

          LSA1400

          thrS

          Threonyl-tRNA synthetase

          0.6

            

          LSA1681

          cysS

          Cysteinyl-tRNA synthetase

          -0.6

            

          DNA replication, recombination and repair

          DNA replication

          LSA0221

          lsa0221

          Putative transcriptional regulator, LysR family (C-terminal fragment), degenerate

          -0.8

          -0.9

          -1.1

          LSA0976

          parE

          Topoisomerase IV, subunit B

           

          0.5

           

          Transposon and IS

          LSA1152_a

          tnpA3-ISLsa1

          Transposase of ISLsa1 (IS30 family)

          -0.6

            

          Phage-related function

          LSA1292

          lsa1292

          Putative prophage protein

          0.6

            

          LSA1788

          lsa1788

          Putative phage-related 1,4-beta-N-acetyl muramidase (cell wall hydrolase)

          -1.0

          D

          D

          DNA recombination and repair

          LSA0076

          lsa0076

          Putative DNA invertase (plasmidic resolvase)

          -1.1

          -1.5

          -1.4

          LSA0366

          ruvA

          Holliday junction DNA helicase RuvA

            

          -0.5

          LSA0382

          dinP

          DNA-damage-inducible protein P

          -0.5

            

          LSA0487

          recA

          DNA recombinase A

          -0.8

           

          -1.1

          LSA0523

          uvrB

          Excinuclease ABC, subunit B

          -0.7

           

          -0.5

          LSA0524

          uvrA1

          Excinuclease ABC, subunit A

          -1.2

           

          -0.7

          LSA0910

          rexAN

          ATP-dependent exonuclease, subunit A (N-terminal fragment), authentic frameshift

          0.6

            

          LSA0911

          rexAC

          ATP-dependent exonuclease, subunit A (C-terminal fragment), authentic frameshift

          0.7

            

          LSA0912

          lsa0912

          Putative ATP-dependent helicase, DinG family

          0.6

           

          0.8

          LSA1162

          lsa1162

          DNA-repair protein (SOS response UmuC-like protein)

           

          0.8

          -0.6

          LSA1405

          fpg

          Formamidopyrimidine-DNA glycosylase

          -0.5

          -0.6

          -0.6

          LSA1477

          recX

          Putative regulatory protein, RecX family

          -0.6

            

          LSA1843

          ogt

          Methylated-DNA-protein-cysteine S-methyltransferase

          -0.6

            

          DNA restriction and modification

          LSA0143

          lsa0143

          Putative adenine-specific DNA methyltransferase

          -0.7

          D

          D

          LSA0921

          lsa0921

          Putative adenine-specific DNA methyltransferase

          0.8

            

          LSA1299

          lsa1299

          Putative adenine-specific DNA methyltransferase

          0.9

          0.7

          1.2

          Information pathways

          LSA0326

          lsa0326

          Putative DNA helicase

           

          -0.6

          U

          DNA packaging and segregation

          LSA0135

          lsa0135

          Hypothetical integral membrane protein, similar to CcrB

            

          -0.6

          LSA1015

          hbsU

          Histone-like DNA-binding protein HU

          1.0

           

          0.9

          Cell division and chromosome partitioning

          Cell division

          LSA0755

          divIVA

          Cell-division initiation protein (septum placement)

            

          0.5

          LSA0845

          lsa0845

          Putative negative regulator of septum ring formation

          0.7

           

          0.6

          LSA1118

          lsa1118

          Rod-shape determining protein

           

          0.6

          0.5

          LSA1597

          ftsH

          ATP-dependent zinc metalloendopeptidase FtsH (cell division protein FtsH)

            

          -0.6

          LSA1879

          gidA

          Cell division protein GidA

          -0.6

            

          Cell envelope biogenesis, outer membrane

          Cell wall

          LSA0280

          murE

          UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase

          -0.6

          -0.6

          -0.7

          LSA0621

          pbp2A

          Bifunctional glycolsyltransferase/transpeptidase penicillin binding protein 2A

            

          0.7

          LSA0648

          lsa0648

          Putative penicillin-binding protein precursor (beta-lactamase class C)

            

          1.0

          LSA0862

          lsa0862

          N-acetylmuramoyl-L-alanine amidase precursor (cell wall hydrolase) (autolysin)

          0.6

           

          0.8

          LSA0917

          pbp1A

          Bifunctional glycosyltransferase/transpeptidase penicillin-binding protein 1A

            

          0.5

          LSA1123

          murA1

          UDP-N-acetylglucosamine 1-carboxyvinyltransferase I

           

          -0.5

           

          LSA1334

          pbp2B2

          Bifuntional dimerisation/transpeptidase penicillin-binding protein 2B

           

          0.7

          0.7

          LSA1437

          lsa1437

          N-acetylmuramoyl-L-alanine amidase precursor (cell wall hydrolase) (autolysin)

           

          -0.7

           

          LSA1441

          bacA

          Putative undecaprenol kinase (bacitracine resistance protein A)

           

          0.6

           

          LSA1613

          alr

          Alanine racemase

          -0.8

          -0.9

          -0.7

          LSA1616

          murF

          UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase

            

          -0.5

          Cell envelope and cellular processes

            

          LSA0162

          lsa0162

          Putative Bifunctional glycosyl transferase, family 8

           

          -1.2

          -1.5

          LSA1246

          lsa1246

          Putative glycosyl transferase, family 2

           

          -0.9

           

          LSA1558

          lsa1558

          Putative extracellular N-acetylmuramoyl-L-alanine amidase precursor (cell wall hydrolase/Lysosyme subfamily 2)

            

          -0.6

          Cell motility and secretion

          Protein secretion

          LSA0948

          lspA

          Signal peptidase II (lipoprotein signal peptidase) (prolipoprotein signal peptidase)

            

          0.5

          LSA1884

          oxaA2

          Membrane protein chaperone oxaA

            

          -0.6

          Signal transduction

          Signal transduction

          LSA0561

          sppKN

          Two-component system, sensor histidine kinase, (SppK fragment), degenerate

           

          0.5

           

          LSA0692

          lsa0692

          Putative serine/threonine protein kinase

           

          0.5

          0.6

          LSA1384

          lsa1384

          Two-component system, response regulator

           

          0.5

           

          Post translational modifications, protein turnover, chaperones

          Protein folding

          LSA0050

          lsa0050

          Putative molecular chaperone, small heat shock protein, Hsp20 family

            

          -0.7

          LSA0082

          htrA

          Serine protease HtrA precursor, trypsin family

           

          -0.6

           

          LSA0207

          clpL

          ATPase/chaperone ClpL, putative specificity factor for ClpP protease

          0.6

            

          LSA0358

          groS

          Co-chaperonin GroES (10 kD chaperonin) (protein Cpn10)

            

          -0.5

          LSA0359

          groEL

          Chaperonin GroEL (60 kDa chaperonin) (protein Cpn60)

            

          -0.5

          LSA0436

          lsa0436

          Putative peptidylprolyl isomerase (peptidylprolyl cis-trans isomerase) (PPIase)

            

          -0.6

          LSA0984

          hslU

          ATP-dependent Hsl protease, ATP-binding subunit HslU

          0.7

           

          0.7

          LSA1465

          clpE

          ATPase/chaperone ClpE, putative specificity factor for ClpP protease

          -0.7

          -0.6

          -0.6

          LSA1618

          htpX

          Membrane metalloprotease, HtpX homolog

           

          0.8

           

          Adaption to atypical conditions

          LSA0170

          lsa0170

          Putative general stress protein

          0.5

           

          -1.5

          LSA0247

          usp2

          Similar to universal stress protein, UspA family

            

          -0.5

          LSA0264

          lsa0264

          Putative glycine/betaine/carnitine/choline transport protein

          -0.6

           

          -0.6

          LSA0513

          lsa0513

          Putative stress-responsive transcriptional regulator

           

          -0.8

           

          LSA0552

          lsa0552

          Organic hydroperoxide resistance protein

           

          0.6

           

          LSA0616

          lsa0616

          Putative glycine/betaine/carnitine/choline ABC transporter, ATP-binding subunit

          0.9

            

          LSA0617

          lsa0617

          Putative glycine/betaine/carnitine/choline ABC transporter, membrane-spanning subunit

          1.3

            

          LSA0618

          lsa0618

          Putative glycine/betaine/carnitine/choline ABC transporter, substrate-binding lipoprotein

          0.6

            

          LSA0619

          lsa0619

          Putative glycine/betaine/carnitine/choline ABC transporter, membrane-spanning subunit

          1.5

          0.5

           

          LSA0642

          usp3

          Similar to universal stress protein, UspA

          0.9

            

          LSA0768

          csp1

          Similar to cold shock protein, CspA family

          2.1

          0.6

          1.8

          LSA0836

          usp6

          Similar to universal stress protein, UspA family

          0.6

            

          LSA0946

          csp4

          Similar to cold shock protein, CspA family

          0.6

            

          LSA1110

          lsa1110

          Putative NifU-homolog involved in Fe-S cluster assembly

           

          0.6

           

          LSA1111

          lsa1111

          Putative cysteine desulfurase (class-V aminotransferase, putative SufS protein homologue)

           

          0.7

           

          LSA1173

          usp4

          Similar to universal stress protein, UspA family

          1.5

          -2.1

           

          LSA1694

          lsa1694

          Putative glycine/betaine/carnitine ABC transporter, substrate binding lipoprotein precursor

          -1.7

           

          -1.1

          LSA1695

          lsa1695

          Putative glycine/betaine/carnitine ABC transporter, membrane-spanning subunit

          -2.1

          -2.0

          -1.9

          LSA1696

          lsa1696

          Putative glycine/betaine/carnitine ABC transporter, ATP-binding subunit

          -1.6

           

          -0.9

          LSA1870

          lsa1870

          Putative glycine betaine/carnitine/choline ABC transporter, ATP-binding subunit

          -0.6

           

          -0.6

          Protein modification

          LSA0865

          lsa0865

          Putative protein methionine sulfoxide reductase

           

          -0.6

           

          LSA0866

          msrA

          Protein methionine sulfoxide reductase

           

          -0.7

           

          LSA0934

          lplA

          Lipoate-protein ligase

          1.6

          1.4

          1.0

          LSA0973

          pflA

          Pyruvate formate-lyase activating enzyme

          1.7

            

          General function prediction only

          Miscellaneous

          LSA0030

          lsa0030

          Putative aldo/keto reductase (oxidoreductase)

           

          -0.7

          -0.8

          LSA0120

          lsa0120

          Putative GTP-binding protein

          -0.5

            

          LSA0164

          lsa0164

          Putative serine/tyrosine protein phosphatase

          0.2

          -1.1

          -1.2

          LSA0165

          lsa0165

          Putative oxidoreductase, short chain dehydrogenase/reductase family

           

          -0.9

          -1.2

          LSA0218

          trxA1

          Thioredoxin

           

          -0.9

           

          LSA0258

          lsa0258

          Putative iron-containing alcohol dehydrogenase

          1.6

          0.5

          1.6

          LSA0260

          lsa0260

          Putative aldo/keto reductase (oxidoreductase)

          1.9

          1.2

          1.7

          LSA0312

          lsa0312

          Putative NADH oxidase

          -0.9

           

          -1.0

          LSA0324

          lsa0324

          Putative hydrolase, haloacid dehalogenase family (N-terminal fragment), authentic frameshift

          1.9

            

          LSA0325

          lsa0325

          Putative hydrolase, haloacid dehalogenase family (C-terminal fragment), authentic frameshift

          1.8

            

          LSA0350

          lsa0350

          Putative N-acetyltransferase, GNAT family

          -0.5

            

          LSA0369

          lsa0369

          Putative N-acetyltransferase, GNAT family

          -0.5

           

          -0.5

          LSA0384

          lsa0384

          Putative phosphoesterase, DHH family

          -0.5

            

          LSA0403

          lsa0403

          Putative thioredoxin reductase

           

          0.9

           

          LSA0447

          lsa0447

          Putative hydrolase, haloacid dehalogenase family

            

          0.6

          LSA0475

          lsa0475

          Putative N-acetyltransferase, GNAT family

           

          -0.6

           

          LSA0520

          trxB2

          Thioredoxin reductase

          -0.8

            

          LSA0575

          npr

          NADH peroxidase

          1.0

          U

           

          LSA0802

          nox

          NADH oxidase

          1.5

            

          LSA0806

          lsa0806

          Putative N-acetyltransferase, GNAT family

          0.6

            

          LSA0831

          lsa0831

          Putative nitroreductase (oxidoreductase)

           

          1.6

           

          LSA0896

          sodA

          Iron/Manganese superoxide dismutase

          3.4

          1.7

          1.7

          LSA0925

          adh

          Putative zinc-containg alcohol dehydrogenase (oxidoreductase)

          0.5

            

          LSA0971

          ppa

          Inorganic pyrophosphatase (pyrophosphate phosphohydrolase)

          0.7

            

          LSA0994

          lsa0994

          Putative GTP-binding protein

            

          0.6

          LSA1016

          engA

          Putative GTP-binding protein

          0.6

           

          0.7

          LSA1045

          obgE

          Putative GTP-binding protein

          0.6

            

          LSA1153

          lsa1153

          Hypothetical protein, CAAX protease family

          0.5

            

          LSA1311

          lsa1311

          Hypothetical protein containing a possible heme/steroid binding domain

          0.7

          -0.6

           

          LSA1320

          lsa1320

          Putative NADPH-quinone oxidoreductase

           

          -0.8

           

          LSA1345

          lsa1345

          Putative hydrolase, haloacid dehalogenase family

          0.5

            

          LSA1349

          lsa1349

          Putative N-acetyltransferase, GNAT family

           

          -0.5

           

          LSA1365

          lsa1365

          Hypothetical protein

           

          -0.5

          -0.7

          LSA1368

          lsa1368

          Hypothetical protein

          0.9

           

          0.6

          LSA1371

          lsa1371

          Hypothetical membrane protein

          0.6

            

          LSA1395

          lsa1395

          Putative zinc-containing alcohol dehydrogenase (oxidoreductase)

          0.9

            

          LSA1427

          lsa1427

          Putative hydrolase, haloacid dehalogenase

          1.3

           

          0.6

          LSA1472

          lsa1472

          Putative N-acetyl transferase, GNAT family

          0.6

            

          LSA1535

          lsa1535

          Putative oxidoreductase

          0.5

          1.1

          0.7

          LSA1553

          lsa1553

          Putative hydrolase, haloacid dehalogenase family

          -0.6

            

          LSA1559

          lsa1559

          Putative oxidoreductase

          0.6

          1.1

          0.7

          LSA1702

          lsa1702

          Putative zinc-containing alcohol dehydrogenase (oxidoreductase)

          1.1

            

          LSA1712

          lsa1712

          Putative nitroreductase (oxidoreductase)

           

          -0.7

          -0.8

          LSA1832

          lsa1832

          Putative zinc-containing alcohol dehydrogenase (oxidoreductase)

           

          1.0

           

          LSA1835

          lsa1835

          Putative zinc-containing alcohol dehydrogenase (oxidoreductase)

          -0.7

           

          -1.0

          LSA1867

          lsa1867

          Putative acetyltransferase, isoleucine patch superfamily

          -0.5

          -0.6

          -0.7

          LSA1871

          gshR

          Glutathione reductase

          -0.6

            

          Unknown

          Proteins of unknown function that are similar to other proteins

          LSA0018

          lsa0018

          Hypothetical protein

           

          0.5

           

          LSA0027

          lsa0027

          Hypothetical protein

            

          -1.1

          LSA0028

          lsa0028

          Hypothetical protein, DegV family

          -0.5

            

          LSA0044

          lsa0044

          Hypothetical protein

            

          -0.7

          LSA0061

          lsa0061

          Hypothetical extracellular protein precursor

          -0.5

            

          LSA0106

          lsa0106

          Hypothetical cell surface protein precursor

          0.5

            

          LSA0160

          lsa0160

          Hypothetical protein

          -0.7

            

          LSA0166

          lsa0166

          Hypothetical Integral membrane protein

            

          -1.2

          LSA0190

          lsa0190

          Hypothetical integral membrane protein

          -0.7

           

          -0.6

          LSA0191

          lsa0191

          Hypothetical integral membrane protein

          -0.6

           

          -0.6

          LSA0199

          lsa0199

          Hypothetical protein

          1.1

          1.0

          1.1

          LSA0208

          lsa0208

          Hypothetical integral membrane protein

          0.7

            

          LSA0235

          lsa0235

          Hypothetical extracellular protein precursor

          2.1

          1.6

          1.7

          LSA0236

          lsa0236

          Hypothetical extracellular peptide precursor

          2.0

          1.3

          1.5

          LSA0244

          lsa0244

          Hypothetical integral membrane protein

            

          -0.5

          LSA0245

          lsa0245

          Hypothetical lipoprotein precursor

          -0.9

          -1.0

          -1.1

          LSA0249

          lsa0249

          Hypothetical protein

          1.1

          1.0

           

          LSA0263

          lsa0263

          Hypothetical integral membrane protein

          -0.6

           

          -0.9

          LSA0300

          lsa0300

          Hypothetical protein

            

          0.7

          LSA0315

          lsa0315

          Hypothetical protein

          -0.7

            

          LSA0319

          lsa0319

          Hypothetical protein

           

          -0.8

          -0.8

          LSA0323

          lsa0323

          Hypothetical protein

            

          -0.5

          LSA0337

          lsa0337

          Hypothetical protein

          -0.7

            

          LSA0348

          lsa0348

          Hypothetical integral membrane protein

          -0.9

           

          -0.7

          LSA0352

          lsa0352

          Hypothetical integral membrane protein

          -0.6

            

          LSA0354

          lsa0354

          Hypothetical integral membrane protein

            

          -1.1

          LSA0388

          lsa0388

          Hypothetical protein

           

          -0.6

           

          LSA0389

          lsa0389

          Hypothetical protein

           

          -0.7

          -0.7

          LSA0390

          lsa0390

          Hypothetical protein

           

          -0.5

           

          LSA0409

          lsa0409

          Hypothetical integral membrane protein

            

          -0.8

          LSA0418

          lsa0418

          Hypothetical protein

            

          -0.8

          LSA0464

          lsa0464

          Hypothetical protein

           

          -0.6

           

          LSA0470

          lsa0470

          Hypothetical protein

          0.9

           

          0.7

          LSA0512

          lsa0512

          Hypothetical protein

           

          -0.6

           

          LSA0515

          lsa0515

          Hypothetical integral membrane protein

           

          -0.5

           

          LSA0536

          lsa0536

          Hypothetical protein

           

          0.7

           

          LSA0716

          lsa0716

          Hypothetical protein

            

          0.6

          LSA0752

          lsa0752

          Hypothetical protein

          0.5

           

          0.6

          LSA0757

          lsa0757

          Hypothetical protein

           

          0.8

           

          LSA0773

          lsa0773

          Hypothetical protein

          0.9

           

          0.6

          LSA0784

          lsa0784

          Hypothetical protein

          -2.6

            

          LSA0786

          lsa0786

          Hypothetical protein

          -2.0

            

          LSA0787

          lsa0787

          Hypothetical protein

          -1.7

            

          LSA0790

          lsa0790

          Hypothetical protein, ATP utilizing enzyme PP-loop family

          -2.5

            

          LSA0827

          lsa0827

          Hypothetical lipoprotein precursor

          0.8

           

          U

          LSA0828

          lsa0828

          Hypothetical protein

          0.7

            

          LSA0829

          lsa0829

          Hypothetical integral membrane protein

            

          0.5

          LSA0874

          lsa0874

          Hypothetical protein

          0.5

            

          LSA0901

          lsa0901

          Hypothetical protein

            

          0.5

          LSA0913

          lsa0913

          Hypothetical extracellular protein precursor

          0.5

           

          0.7

          LSA0919

          lsa0919

          Hypothetical protein

            

          0.7

          LSA0933

          lsa0933

          Hypothetical protein

          0.6

           

          0.6

          LSA0961

          lsa0961

          Hypothetical protein, DegV family

           

          -0.5

           

          LSA0968

          lsa0968

          Hypothetical integral membrane protein

          0.7

            

          LSA0977

          lsa0977

          Hypothetical integral membrane protein

          0.7

           

          0.8

          LSA0987

          lsa0987

          Hypotehtical protein, GidA family (C-terminal fragment)

          0.5

            

          LSA0996

          lsa0996

          Hypothetical protein

            

          0.5

          LSA1003

          lsa1003

          Hypothetical protein

          2.0

           

          1.2

          LSA1005

          lsa1005

          Hypothetical membrane protein

          0.9

          0.6

          0.7

          LSA1008

          lsa1008

          Putative extracellular chitin-binding protein precursor

           

          0.9

          1.2

          LSA1027

          lsa1027

          Hypothetical protein

            

          0.6

          LSA1047

          lsa1047

          Hypothetical protein

          3.5

          1.2

          1.3

          LSA1064

          lsa1064

          Hypothetical protein

          0.5

           

          0.7

          LSA1075

          lsa1075

          Hypothetical protein

            

          0.5

          LSA1078

          lsa1078

          Hypothetical protein

            

          0.6

          LSA1081

          lsa1081

          Hypothetical protein

          1.0

           

          1.0

          LSA1091

          lsa1091

          Hypothetical protein

            

          0.6

          LSA1096

          lsa1096

          Hypothetical protein

          0.6

            

          LSA1124

          lsa1124

          Hypothetical protein

           

          -0.7

           

          LSA1154

          lsa1154

          Hypothetical protein

          0.6

           

          0.6

          LSA1158

          lsa1158

          Hypothetical protein

          1.7

          1.4

           

          LSA1189

          lsa1189

          Hypothetical integral membrane protein

          -1.6

           

          -1.1

          LSA1282

          lsa1282

          Hypothetical protein

           

          -0.5

           

          LSA1296

          lsa1296

          Hypothetical integral membrane protein

           

          -1.2

          -0.8

          LSA1342

          lsa1342

          Hypothetical protein

           

          -0.7

           

          LSA1346

          lsa1346

          Hypothetical protein

          0.8

            

          LSA1350

          lsa1350

          Hypothetical protein

           

          -0.6

          -1.0

          LSA1353

          lsa1353

          Hypothetical integral membrane protein

          -0.9

          -0.5

           

          LSA1446

          lsa1446

          Hypothetical protein

          -0.6

          -0.6

          -0.7

          LSA1466

          lsa1466

          Hypothetical protein

          0.6

            

          LSA1467

          lsa1467

          Hypothetical protein

           

          -0.6

          -1.1

          LSA1524

          lsa1524

          Hypothetical protein

          0.7

            

          LSA1540

          lsa1540

          Hypothetical extracellular protein precursor

          0.7

            

          LSA1563

          lsa1563

          Hypothetical integral membrane protein

           

          -0.6

          -0.6

          LSA1610

          lsa1610

          Hypothetical integral membrane protein

          -0.7

           

          -0.9

          LSA1617

          lsa1617

          Hypothetical protein

            

          -0.7

          LSA1620

          lsa1620

          Hypothetical protein

            

          -0.6

          LSA1623

          lsa1623

          Hypothetical integral membrane protein

          -0.5

           

          -0.6

          LSA1637

          lsa1637

          Hypothetical integral membrane protein, TerC family

          -1.7

          -1.0

          -1.6

          LSA1644

          lsa1644

          Hypothetical protein

          1.7

           

          D

          LSA1649

          lsa1649

          Hypothetical extracellular protein precursor

            

          -0.5

          LSA1659

          lsa1659

          Hypothetical protein

          -0.5

            

          LSA1662

          lsa1662

          Hypothetical protein

          -1.0

          -0.6

          -0.7

          LSA1663

          lsa1663

          Hypothetical protein

          -0.8

            

          LSA1678

          lsa1678

          Hypothetical protein

          -0.6

            

          LSA1680

          lsa1680

          Hypothetical protein

          -0.6

            

          LSA1716

          lsa1716

          Hypothetical protein

           

          -0.5

           

          LSA1822

          lsa1822

          Hypothetical protein

            

          -0.5

          LSA1828

          lsa1828

          Hypothetical integral membrane protein

          0.6

          0.7

           

          LSA1850

          lsa1850

          Hypothetical protein

           

          -0.6

           

          LSA1876

          lsa1876

          Hypothetical integral membrane protein

            

          -0.6

          LSA1877

          lsa1877

          Hypothetical protein

            

          -0.6

          Proteins of unknown function only similar to other proteins from the same organism

          LSA1159

          lsa1159

          Hypothetical cell surface protein precursor

          2.0

           

          0.5

          LSA1165

          lsa1165

          Hypothetical cell surface protein precursor

          1.8

            

          LSA1700

          lsa1700

          Hypothetical protein

          2.1

          0.8

           

          LSA1814

          lsa1814

          Hypothetical protein

            

          -0.5

          Proteins of unknown function. without similarity to other proteins

          LSA0065

          lsa0065

          Hypothetical integral membrane protein

          -0.5

            

          LSA0093

          lsa0093

          Hypothetical integral membrane protein

          -0.9

           

          -1.2

          LSA0121

          lsa0121

          Hypothetical small peptide

          -0.7

          -0.6

          -0.5

          LSA0163

          lsa0163

          Hypothetical protein

           

          -1.1

          -1.3

          LSA0167

          lsa0167

          Hypothetical protein

            

          -1.4

          LSA0168

          lsa0168

          Hypothetical protein

            

          -1.4

          LSA0188

          lsa0188

          Hypothetical small peptide

            

          -0.8

          LSA0256_a

          lsa0256_a

          Hypothetical protein

          2.3

          1.0

          2.2

          LSA0257

          lsa0257

          Hypothetical protein

          1.4

            

          LSA0281

          lsa0281

          Hypothetical lipoprotein precursor

           

          -0.5

          -0.6

          LSA0301

          lsa0301

          Hypothetical protein

            

          0.6

          LSA0334

          lsa0334

          Hypothetical extracellular protein precursor

          1.1

            

          LSA0339

          lsa0339

          Hypothetical protein

          -0.5

            

          LSA0378

          lsa0378

          Hypothetical protein

          -0.7

            

          LSA0514

          lsa0514

          Hypothetical small extracellular protein precursor

           

          -0.8

           

          LSA0534

          lsa0534

          Hypothetical cell surface protein precursor (with LPQTG sorting signal)

          1.0

           

          D

          LSA0576

          lsa0576

          Hypothetical protein

          0.5

          D

           

          LSA0641

          lsa0641

          Hypothetical extracellular peptide precursor

           

          -0.5

           

          LSA0647

          lsa0647

          Hypothetical extracellular protein precursor

          0.6

            

          LSA0667

          lsa0667

          Hypothetical protein

          1.0

           

          0.9

          LSA0753

          lsa0753

          Hypothetical integral membrane protein

            

          0.5

          LSA0789

          lsa0789

          Hypothetical protein

          -1.9

            

          LSA0837

          lsa0837

          Hypothetical protein

          1.2

          1.3

          1.4

          LSA0885

          lsa0885

          Hypothetical protein

          1.8

            

          LSA0902

          lsa0902

          Hypothetical protein

          0.7

          D

           

          LSA0945

          lsa0945

          Hypothetical protein

            

          0.9

          LSA1019

          lsa1019

          Hypothetical cell surface protein precursor

            

          0.8

          LSA1035

          lsa1035

          Hypothetical small integral membrane protein

            

          0.6

          LSA1086

          lsa1086

          hypothetical protein

          0.8

           

          0.5

          LSA1104

          lsa1104

          Hypothetical protein

          -0.5

            

          LSA1155

          lsa1155

          Hypothetical integral membrane protein

          0.5

            

          LSA1174

          lsa1174

          Hypothetical protein

          1.0

            

          LSA1176

          lsa1176

          Hypothetical protein

           

          -1.0

          U

          LSA1319

          lsa1319

          Hypothetical small protein

           

          -0.8

           

          LSA1408

          lsa1408

          Hypothetical protein

            

          0.6

          LSA1464

          lsa1464

          Hypothetical protein

          -0.6

            

          LSA1478

          lsa1478

          Hypothetical protein

          -0.7

          -0.6

          -0.6

          LSA1480

          lsa1480

          Hypothetical membrane protein

          0.5

          D

           

          LSA1524

          lsa1524

          Hypothetical protein

          0.8

            

          LSA1539

          lsa1539

          Hypothetical protein

          0.9

            

          LSA1713

          lsa1713

          Hypothtical small peptide

            

          -0.6

          LSA1787

          lsa1787

          Hypothetical cell surface protein precursor

          -0.5

          U

           

          LSA1820

          lsa1820

          Hypothetical cell surface protein precursor

            

          -0.6

          LSA1821

          lsa1821

          Hypothetical cell surface protein precursor

           

          -0.6

           

          LSA1845

          lsa1845

          Hypothetical small protein

           

          0.8

           

          LSA1848

          lsa1848

          Hypothetical protein

            

          -0.5

          LSA1851

          lsa1851

          Hypothetical extracellular small protein

          -0.6

           

          -0.7

          LSA1883

          lsa1883

          Hypothetical small protein

          1.2

           

          1.5

          Bacteriocin associated genes

          SKP0001

          sppIP

          Bacteriocin sakacin P inducing peptide

          D

          0.5

          D

          SKP0006

          sppT

          Sakacin P ABC transporter

          D

          0.6

          D

          SKP0007

          sppE

          Sakacin P accesory transport protein

          D

          0.6

          D

          The microarray used has been described previously [32]. Asterix (*) relates the gene to Table 2. D and U refer to genes classified as 'divergent' and 'uncertain', respectively, by CGH analysis [32]. Genes encoding proteins with a change in expression according to McLeod et al. [19], are underlined.

          http://static-content.springer.com/image/art%3A10.1186%2F1471-2180-11-145/MediaObjects/12866_2011_1438_Fig1_HTML.jpg
          Figure 1

          Venn diagram showing the number of unique and common up- and down-regulated genes inL. sakeistrains 23K, MF1053 and LS 25 when grown on ribose compared with glucose.

          Several of the up-regulated genes are located in operons, an organisation believed to provide the advantage of coordinated regulation. In addition, in order to discriminate genes induced by growth on ribose from those repressed by glucose (submitted to CCR mediated by CcpA), a search of the complete genome sequence of L. sakei 23K [7] was undertaken, with the aim to identify putative cre sites. The search revealed 1962 hits, most of which did not have any biological significance considering their unsuitable location in relation to promoters. Relief of CcpA-mediated CCR likely occur for many of the up-regulated genes in the category of carbohydrate transport and metabolism. Putative cre sites were identified in their promoter region, as well as for some genes involved in nucleoside and amino acid transport and metabolism (Table 2). In the other gene categories, the presences of putative cre sites were rare. With regard to gene product, the L. sakei genome shares high level of conservation with Lactobacillus plantarum [7], and high similarity of catabolic operon organization. The role of CcpA in CCR in L. plantarum has been established, and was shown to mediate regulation of the pox genes encoding pyruvate oxidases [41, 42]. During growth on ribose, L. plantarum induces a similar set of genes as observed in the present study, and putative cre sites were identified in the upstream region of several genes involved [33].
          Table 2

          Putative cre sites present in the promoter region of some L. sake i genes up-regulated in the present study.

          Gene locus

          Gene

          cre site sequencea

          Positionb

          Co-transcribed genes/operonc

          Gene locus

          LSA0123

          lsa0123

          TGAAAGCGTTACAA

          -93

            

          LSA0185

          galP

          GAACATCGTTATCA

          -46

            

          LSA0200

          rbsU

          GTAAACCGTTTTCA

          -113

          rbsUDK

          LSA0200-0202

          LSA0254

          lsa0254

          TGTAAGCGTTTTAT

          -56

          lsa0254-lsa0255-lsa0256_a

          LSA0254-0256_a

          LSA0289

          xpk

          CTATTACGATGACA

          -8

            

          LSA0292

          budC

          TGTAACCGTTTTAA

          -51

            

          LSA0353

          lsa0353

          AGAAAGCGCTTATA

          -102

            

          LSA0370

          arcA

          TGAAAGCGATTACC

          -58

          arcA-arcB e -arcC-arcT e -arcD e

          LSA0370-0374

          LSA0449

          manL

          TGTTAGCGTTTTTA

          -56

          manL-manM-manN

          LSA0449-0451

          LSA0533

          iunH2

          AAAAAGCGTTCACA

          -35

            

          LSA0572

          tdcB

          TGAAAACGTTCTAA

          -134

            

          LSA0608

          Glo AN

          TGTAACCGTTTTAA

          -100

          gloAN-gloAC

          LSA0608-0609

          LSA0649

          glpK

          AGGAAACGTTTTCC

          -42

          glpK-glpD-glpF

          LSA0649-0651

          LSA0664

          loxL1

          AGAAAGCGAGTACA

          -82

          loxL1N-loxLI-loxL1C

          LSA0664-0666

          LSA0764

          galK

          TGAAAGCGATTAAT

          -30

          galK-galE1-galT-galM

          LSA0764-0767

          LSA0795

          deoC

          TGAAAGCGTTAACA

          -33

          deoC-deoB-deoD-lsa0798-lsa0799-deoR-pdp

          LSA0795-0801

          LSA0974

          pflB

          TACGAACGCTTACA

          -147

          pflB-pflA

          LSA0974-0973

          LSA1048

          fruR e

          TGTAAACGATGACA

          -39

          fruR e -fruK e -fruA

          LSA1048-1050

          LSA1141

          ppdK

          GGTTATCGATAAAA

          -29

            

          LSA1146

          manA

          CGAAATCGCTTTAA

          -98

            

          LSA1188

          pox1

          TGTAATCGATTTCA

          -88

            

          LSA1204

          lsa1204

          TGTAATCGTTTTTT

          -127

            

          LSA1343

          eutD

          GTAAAACGCTCTCA

          -94

            

          LSA1399

          loxL2

          TGTAAACGATTTCA

          -42

            

          LSA1457

          lsa1457

          TGATAACGCTTACA

          -85

            

          LSA1463d

          ptsH

          TGAAAGCGGTATAG

          -161

          ptsHI

          LSA1463-1462

          LSA1641

          nanE

          TGTAAGCGGTTAAT

          -85

          nanE-nanA

          LSA1641-1640

          LSA1643

          lsa1643

          TGATAACGCTTACA

          -31

            

          LSA1651

          lsa1651

          GGTAAGCGGTTAAA

          -148

            

          LSA1711

          lacL

          TGAAACCGTTTTAA

          -36

          lacL-lacM

          LSA1711-1710

          LSA1792

          scrA

          TGTAAACGGTTGTA

          -78

          scrA-dexB-scrK

          LSA1792-1790

          LSA1830

          pox2

          TTGTAACGCTTACA

          -70

            

          The identification is based on the genome sequence of L. sakei strain 23K, and the consensus sequence TGWNANCG NTNWCA (W = A/T, N = A/T/G/C), confirmed in Gram-positive bacteria [39] was used in the search, allowing up to two mismatches (underlined) in the conserved positions except for the two center positions, highlighted in boldface.

          a mismatch to consensus sequence is underlined

          b position of cre in relation to the start codon

          c suggested co-transcribed genes or genes organized in an operon

          dcre in preceding gene encoding hypothetical protein

          e gene not regulated in this study

          Ribose catabolism and PKP

          Confirming its major role in ribose transport and utilization in L. sakei, and in agreement with previous findings [16], our microarray data revealed a strong up-regulation (Table 1; log2 = 2.8-4.3) of rbsUDK. The genes encoding an additional putative carbohydrate kinase belonging to the ribokinase family and a putative phosphoribosyl isomerase, lsa0254 and lsa0255, respectively, previously suggested to be involved in catabolism of ribose in L. sakei [7], were induced in all the strains (Table 1). Recent CGH studies revealed that some L. sakei strains which were able to grow on ribose did not harbour the rbsK gene, whereas lsa0254 was present in all strains investigated [32]. This second ribokinase could therefore function as the main ribokinase in some L. sakei strains. The rbsK sequence could also differ considerably from that of 23K in these strains. The PKP showed an obvious induction with an up-regulation (2.2-3.2) of the xpk gene encoding the key enzyme xylulose-5-phosphate phosphoketolase (Xpk). This enzyme connects the upper part of the PKP to the lower part of glycolysis by converting xylulose-5-phosphate into glyceraldehyde-3-phosphate and acetyl-phosphate. Acetyl-phosphate is then converted to acetate and ATP by acetate kinase (Ack). Supporting our results, previous proteomic analysis showed an over-expression of RbsK, RbsD and Xpk during growth on ribose [15, 16, 19]. The induction of ribose transport and phosphorylation, and increased phosphoketolase and acetate kinase activities were previously observed during growth on ribose [15]. Three genes encoding Ack are present in the 23K genome [7], as well as in MF1053 and LS 25 [32]. A preferential expression of different ack genes for the acetate kinase activity seem to exist. The ack2 gene was up-regulated in all the strains, while ack1 was up-regulated and ack3 down-regulated in 23K and LS 25 (Table 1). An illustration of the metabolic pathways with genes affected by the change of carbon source from glucose to ribose in L. sakei is shown in Figure 2.
          http://static-content.springer.com/image/art%3A10.1186%2F1471-2180-11-145/MediaObjects/12866_2011_1438_Fig2_HTML.jpg
          Figure 2

          Overview of the glycolysis, phosphoketolase pathway and nucleoside catabolic pathway affected by the change of carbon source from glucose to ribose in threeL. sakeistrains in this study. Genes which expression is up- or down-regulated are indicated with upward and downward pointing arrows, respectively, and are listed in Table 1. Black arrows indicate regulation in all three strains, and grey arrows indicate regulation in one or two strains. Schematic representation of CcpA-mediated CCR pathway is shown in the upper right corner. EII, enzyme II of the phosphotransferase system (PTS); EI, enzyme I, HPr, Histidine-containing protein; T, transport protein; P, phosphate; HPrK/P, HPr kinase/phosphatase; G6P, glucose-6-phosphate; F6P; fructose-6-phosphate; FBP, fructose-1,6-bisphosphate; G3P, glyceraldehyde-3-phosphate; DHAP, dihydroxyacetone phosphate; Gly3P, glycerol-3-phosphate; X5P, xylulose-5-phosphate; 1,3PG, 1,3-phosphoglycerate; 3PG, 3-phosphoglycerate; 2PG, 2-phosphoglycerate; PEP, phosphoenolepyruvate; glk, glucokinase; pgi, phosphoglucoisomerase; fbp, fructose-1,6-bisphosphatase; tpi, triose-phosphate isomerase; gap, glyceraldehyde-3-phosphate dehydrogenase; pgk, phosphoglycerate kinase; eno, enolase; rpi, ribose-5-phosphate isomerase; rpe, ribulose-phosphate 3-epimerase.

          As a consequence of the pentose-induced PKP, genes involved in PKP-metabolism of glucose, such as gntZ, gntK and zwf, were down-regulated (Table 1, Figure 2). The glycolytic pathway was clearly repressed, supporting previous findings [15, 19]. Among these genes were pfk (0.5-1.1) encoding 6-phosphofructokinase (Pfk), and fba (0.7-1.1) coding for fructose-bisphosphate aldolase, both acting at the initial steps of glycolysis. In addition, gpm3 encoding one of the five phosphoglycerate mutases present in the 23K genome, acting in the lower part of glycolysis, was also down-regulated (0.7-0.9). MF1053 down-regulated pyk (0.7) encoding pyruvate kinase (Pyk) that competes for PEP with the PTS (Figure 2). Its activity results in the production of pyruvate and ATP, and it is of major importance in glycolysis and energy production in the cell. MF1053 also showed a stronger down-regulation of pfk than the other strains (Table 1). Similar to several other lactobacilli, pfk is transcribed together with pyk [43, 44], and in many microorganisms the glycolytic flux depends on the activity of the two enzymes encoded from this operon [43, 45]. At the protein level, we previously observed both Pfk and Pyk expressed at a lower level for all the three strains [19], however this was not confirmed at the level of gene expression for 23K and LS 25. We could also not confirm the lower protein expression of glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase and enolase previously seen in LS 25 [19]. The latter three enzymes are encoded from the central glycolytic operon (cggR-gap-pgk-tpi-eno) together with triose-phosphate isomerase and the putative central glycolytic genes regulator (CggR) [46]. Besides the cggR gene being down-regulated in MF1053 and LS 25, no change in gene expression was seen of these central glycolytic genes. Thus at the transcription level it is not obvious that the LS 25 strain down-regulate the glycolytic pathway more efficiently than the other strains, as previously suggested [19].

          Interestingly, all the strains showed an induction (1.4-2.3) of mgsA encoding methylglyoxal synthase, which catalyzes the conversion of dihydroxyacetone-phosphate to methylglyoxal (Figure 2). The presence of this gene is uncommon among LAB and so far a unique feature among the sequenced lactobacilli. The methylglyoxal pathway represents an energetically unfavourable bypass to the glycolysis. In E. coli, this bypass occurs as a response to phosphate starvation or uncontrolled carbohydrate metabolism, and enhanced ribose uptake was shown to lead to the accumulation of methylglyoxal [47, 48]. As suggested by Chaillou et al. [7], such flexibility in the glycolytic process in L. sakei may reflect the requirement to deal with glucose starvation or to modulate carbon flux during co-metabolism of alternative carbon sources. Breakdown of methylglyoxal is important as it is toxic to the cells [49]. An induction of the lsa1158 gene contiguous with mgsA was seen for 23K and MF1053. This gene encodes a hypothetical protein, also suggested as a putative oxidoreductase, which may reduce methylglyoxal to lactaldehyde [7]. However, no induction of the adhE (lsa0379) gene encoding an iron-containing aldehyde dehydrogenase suggested to further reduce lactaldehyde to L-lactate [7] was seen. By CGH [32]lsa1158 and adhE were present in all the L. sakei strains investigated, whereas mgsA was lacking in some strains, indicating that the MgsA function is not vital.

          Pyruvate metabolism

          Pyruvate is important in both glycolysis and PKP. It can be converted into lactate by the NAD-dependent L-lactate dehydrogenase, which regenerates NAD+ and maintains the redox balance. This enzyme is encoded by the ldhL gene which was down-regulated (0.7-1.4) in all three strains, in accordance with previous findings [50], and the down-regulation was strongest for the LS 25 strain. At the protein level, only LS 25 showed a lower expression of this enzyme during growth on ribose [19]. Genes responsible for alternative fates of pyruvate (Figure 2) were highly induced in all the strains, however with some interesting strain variation (Table 1). The shift in pyruvate metabolism can benefit the bacteria by generating ATP, or by gaining NAD+ for maintaining the redox balance and may lead to various end products in addition to lactate [51].

          In all the strains, a strongly up-regulated (2.1-3.0) pox1 gene was observed, and in 23K an up-regulated pox2 (0.7), encoding pyruvate oxidases which under aerobic conditions convert pyruvate to acetyl-phosphate with hydrogen peroxide (H2O2) and CO2 as side products. Accumulation of peroxide ultimately leads to aerobic growth arrest [52]. H2O2 belongs to a group of compounds known as reactive oxygen species and reacts readily with metal ions to yield hydroxyl radicals that damage DNA, proteins and membranes [53]. Remarkable differences in redox activities exist among Lactobacillus species and L. sakei is among those extensively well equipped to cope with changing oxygen conditions, as well as dealing effectively with toxic oxygen byproducts [7]. 23K up-regulated npr (1.0) encoding NADH peroxidase which decomposes low concentrations of H2O2 to H2O and O2, and all the strains up-regulated the sodA gene (1.7-3.4) encoding a superoxide dismutase which produces hydrogen peroxide from superoxide (O2 -). Various oxidoreductases showed an up-regulation in all the strains (Table 1), indicating the need for the bacterium to maintain its redox balance.

          The pdhABCD gene cluster encoding components of the pyruvate dehydrogenase enzyme complex (PDC) which transforms pyruvate into acetyl-CoA and CO2 were among the strongly up-regulated (2.1-3.7) genes. The eutD gene encoding a phosphate acetyltransferase which further forms acetyl-phosphate from acetyl-CoA was also induced (1.0-2.0). Pyruvate can be transformed to acetolactate by acetolactate synthase and further to acetoin by acetolactate decarboxylase, before 2,3-butanediol may be formed by an acetoin recuctase (Figure 2). While the budC gene encoding the acetoin reductase showed a strong up-regulation in all three strains, the als-aldB operon was only strongly up-regulated in LS 25 (1.9). Pyruvate formate lyase produces acetyl-CoA and formate from pyruvate. Only in 23K, the pflAB genes encoding formate C-acetyltransferase and its activating enzyme involved in formate formation were strongly up-regulated (4.0 and 1.7, respectively). This strain was the only one to strongly induce L-lactate oxidase encoding genes which are responsible for conversion of lactate to acetate when oxygen is present (Table 1). In 23K and LS 25, the ppdK gene coding for the pyruvate phosphate dikinase involved in regenerating PEP, was induced, as was also lsa0444 encoding a putative malate dehydrogenase that catalyzes the conversion of malate into oxaloacetate using NAD+ and vice versa (Table 1).

          During growth on ribose, L. sakei was shown to require thiamine (vitamine B1) [15]. The E1 component subunit α of the PDC, as well as Pox and Xpk, require thiamine pyrophosphate, the active form of thiamine, as a coenzyme [54]. This could explain the induction of the thiMDE operon and lsa0055 in LS 25, as well as lsa0980 in 23K, encoding enzymes involved in thiamine uptake and biosynthesis (Table 1). The up-regulation of lsa1664 (1.1-1.6) encoding a putative dihydrofolate reductase involved in biosynthesis of riboflavin (vitamin B2) in all the strains could indicate a requirement for flavin nucleotides as enzyme cofactors. Riboflavin is the precursor for flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) redox cofactors in flavoproteins, and the E3 component of PDC as well as glycerol-3-phosphate dehydrogenase encoded from the up-regulated glpD, are among enzymes requiring FAD. Another cofactor which seems to be important during growth on ribose is lipoate, essential of the E2 component of the PDC. An up-regulation of lplA (1.0 - 1.6) encoding lipoate-protein ligase, which facilitates attachment of the lipoyl moiety to metabolic enzyme complexes, was seen in all the strains, allowing the bacterium to scavenge extracellular lipoate [55, 56].

          Nucleoside catabolism

          The L. sakei genome contains a multiplicity of catabolic genes involved in exogenous nucleoside salvage pathways, and the bacterium has been shown to catabolize inosine and adenosine for energy [7]. Three iunH genes are present in the 23K genome, which encode inosine-uridine preferring nucleoside hydrolases responsible for conversion of inosine to ribose and purine base. The iunH1 gene was up-regulated in all the strains when grown on ribose (1.8-2.6), as was also the iunH2 gene in 23K (1.2). The deoC gene encodes a deoxyribose-phosphate aldolase, and is located in an operon structure preceding the genes deoB, deoD, lsa0798, lsa0799, deoR and pdp which encode phosphopentomutase, purine nucleoside phosphorylase, pyrimidine-specific nucleoside symporter, a putative purine transport protein, the deoxyribonucleoside synthesis operon transcriptional regulator (DeoR), and a pyrimidine-nucleoside phosphorylase, respectively. The complete operon was induced in all the strains, except for pdp only induced in 23K (Table 1). The phosphorylases catalyze cleavage of ribonucleosides and deoxyribonucleosides to the free base pluss ribose-1-phosphate or deoxyribose-1-phosphate. The bases are further utilized in nucleotide synthesis or as nitrogen sources. The pentomutase converts ribose-1-phosphate or deoxyribose-1-phosphate to ribose-5-phosphate or deoxyribose-5-phosphate, respectively, which can be cleaved by the aldolase to glyceraldehyde-3-phosphate and acetaldehyde. Glyceraldehyde-3-phosphate enters the glycolysis, while a putative iron containing alcohol dehydrogenase, encoded by lsa0258 up-regulated in all the strains (0.5-1.6), could further reduce acetaldehyde to ethanol (Figure 2). The obvious induced nucleoside catabolism at the level of gene expression was not seen by proteomic analysis [19].

          Genes involved in glycerol/glycerolipid/fatty acid metabolism

          During growth on ribose, a strong induction of the glpKDF operon encoding glycerol kinase (GlpK), glycerol-3-phosphate dehydrogenase (GlpD), and glycerol uptake facilitator protein was observed (Table 1), which is in correlation with the over-expression of GlpD and GlpK seen by proteomic analysis [19]. GlpD is FADH2 linked and converts glycerol-3-phosphate to dihydroxyacetone-phosphate. An over-expression of GlpD was also reported when L. sakei was exposed to low temperature [57]. A glpD mutant showed enhanced survival at low temperature, and it was suggested that this was a result of the glycerol metabolism being redirected into phosphatidic acid synthesis which leads to membrane phospholipid biosynthesis [57]. Nevertheless, a down-regulation was observed of the lsa1493 gene (0.6-0.9) encoding a putative diacylglycerol kinase involved in the synthesis of phosphatidic acid, and of cfa (1.3-1.4) encoding cyclopropane-fatty-acyl-phospholipid synthase directly linked to modifications in the bacterial membrane fatty acid composition that reduce membrane fluidity and helps cells adapt to their environment [58]. Interestingly, LS 25 up-regulated several genes (LSA0812-0823), including accD and accA encoding the α- and ß-subunits of the multi-subunit acetyl-CoA carboxylase (Table 1). This is a biotin-dependent enzyme that catalyzes the irreversible carboxylation of acetyl-CoA to produce malonyl-CoA, an essential intermediate in fatty acid biosynthesis. In B. subtilis, the malonyl-CoA relieves repression of the fab genes [59]. We observed that also acpP, fabZ1, fabH, fabD and fabI (Table 1) encoding enzymes involved in fatty acid biosynthesis were induced in LS 25. The altered flux to malonyl-CoA may be a result of the decreased glycolytic rate. MF1053, on the other hand, showed a down-regulation of several genes in the same gene cluster. A higher level of acetate is produced when the bacterium utilizes ribose, and acetate lowers the pH and has a higher antimicrobial effect than lactate. Changes in the phospholipid composition could be a response to changes in intracellular pH. Protons need to be expelled at a higher rate when the pH drops. The LS 25 strain which showed faster growth rates than the other strains [9], was the only strain to up-regulate the F0F1 ATP synthase (Table 1), which at the expense of ATP expels protons during low pH.

          Regulation mechanisms

          Little is known about the regulation of catabolic pathways in L. sakei. Starting from ribose uptake, the rbs operon may be both relieved from repression and ribose induced. Presumably, a dual regulation of this operon by two opposite mechanisms, substrate induction by ribose and CCR by glucose may occur in L. sakei. The ccpA gene was not regulated, consistent with this gene commonly showing constitutive expression in lactobacilli [42, 60]. The local repressor RbsR is homologous with CcpA, both belonging to the same LacI/GalR family of transcriptional regulators. RbsR was proposed to bind a cre-like consensus sequence located close to a putative CcpA cre site, both preceding rbsU [28]. RbsR in the Gram-positive soil bacterium Corynebacterium glutamicum was shown to bind a cre-like sequence, and using microarrays, the transcription of no other genes but the rbs operon was affected positively in an rbsR deletion mutant. It was concluded that RbsR influences the expression of only the rbs operon [61]. Similarily, in the L. sakei sequence, no other candidate members of RbsR regulation could be found [28]. However, experiments are needed to confirm RbsR binding in

          L. sakei. In Bacillus subtilis, RbsR represent a novel interaction partner of P-Ser-HPr in a similar fashion to CcpA [62]. The P-Ser-HPr interaction is possible also in L. sakei as the bacterium exhibits HPr-kinase/phosphatase activity.

          A putative cre site is present in the promoter of lsa0254 encoding the second ribokinase (Table 2), and this gene is preceeded by the opposite oriented gene lsa0253 encoding a transcriptional regulator with a sugar binding domain which belongs to the GntR family. This family of transcriptional regulators, as well as the LacI family which RbsR and CcpA belong to, are among the families to which regulators involved in carbohydrate uptake or metabolism usually belong [63]. The GntR-type regulator could possibly be involved in regulating the expression of the second ribokinase, or of the inosine-uridine preferring nucleoside hydrolase encoding iunH1 gene which is located further upstream of lsa0254. C. glutamicum possesses an operon encoding a ribokinase, a uridine transporter, and a uridine-preferring nucleoside hydrolase which is co-controlled by a local repressor together with the RbsR repressor of the rbs operon [60, 61, 64]. It is possible that such co-control could exist also in L. sakei. Ribose as well as nucleosides are products of the degradation of organic materials such as DNA, RNA and ATP. The simultaneous expression of the rbs and deo operons as well as the other genes involved in ribose and nucleoside catabolism (Figure 2) allows the bacterium to access the different substrates simultaneously and use both ribose as well as nucleosides as carbon and energy source. DeoR shows 51% identity to the B. subtilis DeoR repressor protein [65, 66]. Genes encoding deoxyribose-phosphate aldolase, nucleoside uptake protein and pyrimidine nucleoside phosphorylase in B. subtilis are organized in a dra-nupC-pdp operon followed by deoR, and ribose was shown to release DeoR from DNA binding and thus repression of the operon genes are alleviated [6567]. The B. subtilis pentomutase and purine-nucleoside phosphorylase are encoded from a drm-pupG operon which is not negatively regulated by DeoR, though both operons are subject to CcpA mediated CCR [65, 66, 68]. As a cre site is found preceding the L. sakei deoC (Table 2), the operon could be regulated by CcpA as well. It is interesting that deoR is the only strongly induced transcriptional regulator gene in all three strains, and the encoded regulator has sigma (σ) factor activity. We can only speculate whether it could function as activator of transcription on some of the regulated genes in this study.

          Expression of the Xpk encoding gene of Lactobacillus pentosus was reported to be induced by sugars fermented through the PKP and repressed by glucose mediated by CcpA [69]. Indeed, the cre site overlapping ATG start codon of L. sakei xpk (Table 2) indicates relief of CcpA-mediated CCR during growth on ribose. Also for several genes involved in alternative fates of pyruvate, putative cre sites were present (Table 2).

          Several genes and operons involved in transport and metabolism of various carbohydrates such as mannose, galactose, fructose, lactose, cellobiose, N-acetylglucosamine, including putative sugar kinases and PTSs, were induced during growth on ribose (Table 1), and as shown in Table 2, putative cre sites are located in the promoter region of many of these up-regulated genes and operons. 23K showed an up-regulation of genes involved in the arginine deiminase pathway, and 23K and LS 25 showed an up-regulated threonine deaminase (Table 1). The arcA and tdcB both have putative cre sites in their promoter regions (Table 2). Thus ribose seems to induce a global regulation of carbon metabolism in L. sakei.

          A putative cre site precedes the glp operon (Table 2), suggesting regulation mediated by CcpA. However, regulation of the L. sakei GlpK may also occur by an inducer exclusion-based CcpA-independent CCR mechanism as described in enterococci and B. subtilis [70, 71], and as previously suggested by Stentz et al. [15]. By this mechanism, glycerol metabolism is regulated by PEP-dependent, EI- and HPr-catalyzed phosphorylation of GlpK in response to the presence or absence of a PTS substrate. In the absence of a PTS sugar, GlpK is phosphorylated by P-His-HPr at a conserved histidyl residue, forming the active P-GlpK form, whereas during growth on a PTS sugar, phosphoryl transfer flux through the PTS is high, concentration of P-His-HPr is low, and GlpK is present in a less active dephospho form [20, 70, 71]. This conserved histidyl residue (His232) is present in L. sakei GlpK [20], and Stentz et al. [15] reported that whereas L. sakei can grow poorly on glycerol, this growth was abolished in ptsI mutants.

          Mannose-PTS

          As mentioned in the introduction, the PTS plays a central role, in both the uptake of a number of carbohydrates and regulatory mechanisms [2022]. Encoding the general components, ptsH showed an up-regulation in MF1053 and LS 25 (1.2 and 0.9, respectively), while all the strains up-regulated ptsI (0.8-1.7). The manLMN operon encoding the EIIman complex was surprisingly strongly up-regulated during growth on ribose in all the strains (Table 1). By proteomic analysis, no regulation of the PTS enzymes was seen [19]. The expression of HPr and EI in L. sakei during growth on glucose or ribose was previously suggested to be constitutive [14], and in other lactobacilli, the EIIman complex was reported to be consistently highly expressed, regardless of carbohydrate source [7274]. Notably, PEP-dependent phosphorylation of PTS sugars has been detected in ribose-grown cells, indicating that the EIIman complex is active, and since no transport and phosphorylation via EIIman occurs, the complex is phosphorylated, while it is unphosphorylated in the presence of the substrates of the EIIman complex [8, 73]. The stimulating effect exerted by small amounts of glucose on ribose uptake in L. sakei, which has also been reported in other lactobacilli [74, 75], was suggested to be caused by dephosphorylation of the PTS proteins in the presence of glucose, as a ptsI mutant lacking EI, as well as P-His-HPr, was shown to enhance ribose uptake [15, 16, 76]. Stentz et al. [15] observed that a L. sakei mutant (strain RV52) resistant to 2 deoxy-D-glucose, a glucose toxic analog transported by EIIman, and thus assumed to be affected in the EIIman, did not show the same enhanced uptake [15]. It was concluded that EIIman is not involved in the PTS-mediated regulation of ribose metabolism in L. sakei. The mutation was though not reported verified by sequencing [15], and other mutations could be responsible for the observed phenotype. The L. sakei EIIABman, EIICman and EIIDman show 72, 81, and 82% identity, respectively, with the same enzymes in L. casei, in which mutations rendering the EIIman complex inactive were shown to derepress rbs genes, resulting in a loss of the preferential use of glucose over ribose [75]. Furthermore, in L. pentosus, EIIman was shown to provide a strong signal to the CcpA-dependent repression pathway [73]. The hprK gene encoding HPrK/P which controls the phosphorylation state of HPr was strongly up-regulated (1.2-2.0) in all three strains. HPrK/P dephosphorylates P-Ser-HPr when the concentration of glycolytic intermediates drop, which is likely the situation during growth on ribose [20, 22, 24].

          Numerous genes encoding hypothetical proteins with unknown function were also found to be differentially expressed (Table 1), as well as several other genes belonging to various functional categories. For most of these, their direct connection with ribose metabolism is unknown, and is likely an indirect effect.

          Conclusions

          The ability to ferment meat and fish is related to the capacity of the bacterium to rapidly take up the available carbohydrates and other components for growth. The importance of this process, especially to the meat industry, stimulates research aimed at understanding the mechanisms for transport and metabolism of these compounds, with the ultimate goal to be able to select improved strains. Genome-wide transcriptome analyses with DNA microarrays efficiently allowed the identification of genes differentially expressed between growth on the two carbohydrates which L. sakei can utilize from these substrates. Moreover, microarrays were a powerful tool to increase the understanding of the bacterium's primary metabolism and revealed a global regulatory mechanism. In summary, the ribose uptake and catabolic machinery is highly regulated at the transcription level, and it is closely linked with catabolism of nucleosides. A global regulation mechanism seems to permit a fine tuning of the expression of enzymes that control efficient exploitation of available carbon sources.

          Abbreviations

          PKP: 

          phosphoketolase pathway

          PEP: 

          phosphoenolpyruvate

          PTS: 

          PEP-dependent carbohydrate phosphotransferase system

          CCR: 

          carbon catabolite repression

          cre

          catabolite responsive element

          RbsK: 

          ribokinase

          RbsD: 

          D-Ribose pyranase

          Xpk: 

          xylulose-5-phosphate phosphoketolase

          Ack: 

          Acetate kinase

          Pfk: 

          6-phosphofructokinase

          Pyk: 

          pyruvate kinase

          PDC: 

          pyruvate dehydrogenase complex

          GlpD: 

          glycerol-3-phosphate dehydrogenase

          GlpK: 

          glycerol kinase

          EII: 

          enzyme II

          EI: 

          enzyme I

          HPr: 

          histidine protein

          HPrK/P: 

          HPr kinase/phosphatase

          DeoR: 

          deoxyribonucleoside synthesis operon transcriptional regulator

          Declarations

          Acknowledgements and funding

          This work was financially supported by Grant 159058/I10 from the Norwegian Research Council. The authors would like to thank Monique Zagorec for helpful suggestions and critically reading the manuscript. We also thank Margrete Solheim, Mari Christine Brekke, and Signe Marie Drømtorp for their assistance during the experiments, and Hallgeir Bergum, the Norwegian Microarray Consortium (NMC), for printing the microarray slides.

          Authors’ Affiliations

          (1)
          Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research
          (2)
          Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences

          References

          1. Hammes WP, Bantleon A, Min S: Lactic acid bacteria in meat fermentation. FEMS Microbiol Rev 1990, 87:165–174.View Article
          2. Hammes WP, Hertel C: New developments in meat starter cultures. Meat Science 1998, 49:125–138.View Article
          3. Bredholt S, Nesbakken T, Holck A: Protective cultures inhibit growth of Listeria monocytogenes and Escherichia coli O157:H7 in cooked, sliced, vacuum- and gas-packaged meat. Int J Food Microbiol 1999, 53:43–52.PubMedView Article
          4. Bredholt S, Nesbakken T, Holck A: Industrial application of an antilisterial strain of Lactobacillus sakei as a protective culture and its effect on the sensory acceptability of cooked, sliced, vacuum-packaged meats. Int J Food Microbiol 2001, 66:191–196.PubMedView Article
          5. Katikou P, Georgantelis D, Paleologos EK, Ambrosiadis I, Kontominas MG: Relation of biogenic amines' formation with microbiological and sensory attributes in Lactobacillus -inoculated vacuum-packed rainbow trout ( Oncorhynchus mykiss ) fillets. J Agric Food Chem 2006, 54:4277–4283.PubMedView Article
          6. Vermeiren L, Devlieghere F, Debevere J: Evaluation of meat born lactic acid bacteria as protective cultures for biopreservation of cooked meat products. Int J Food Microbiol 2004, 96:149–164.PubMedView Article
          7. Chaillou S, Champomier-Vergès MC, Cornet M, Crutz-Le Coq AM, Dudez AM, Martin V, Beaufils S, Darbon-Rongere E, Bossy R, Loux V, Zagorec M: The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23 K. Nat Biotechnol 2005, 23:1527–1533.PubMedView Article
          8. Lauret R, Morel-Deville F, Berthier F, Champomier-Vergès M, Postma P, Ehrlich SD, Zagorec M: Carbohydrate utilization in Lactobacillus sake . Appl Environ Microbiol 1996, 62:1922–1927.PubMed
          9. McLeod A, Nyquist OL, Snipen L, Naterstad K, Axelsson L: Diversity of Lactobacillus sakei strains investigated by phenotypic and genotypic methods. Syst Appl Microbiol 2008, 31:393–403.PubMedView Article
          10. Chiaramonte F, Blugeon S, Chaillou S, Langella P, Zagorec M: Behavior of the meat-borne bacterium Lactobacillus sakei during its transit through the gastrointestinal tracts of axenic and conventional mice. Appl Environ Microbiol 2009, 75:4498–4505.PubMedView Article
          11. Dal Bello F, Walter J, Hammes WP, Hertel C: Increased complexity of the species composition of lactic acid bacteria in human feces revealed by alternative incubation condition. Microb Ecol 2003, 45:455–463.PubMedView Article
          12. Walker A, Cerdeno-Tarraga A, Bentley S: Faecal matters. Nat Rev Microbiol 2006, 4:572–573.PubMedView Article
          13. Chiaramonte F, Anglade P, Baraige F, Gratadoux JJ, Langella P, Champomier-Vergès MC, Zagorec M: Analysis of Lactobacillus sakei mutants selected after adaptation to the gastrointestinal tract of axenic mice. Appl Environ Microbiol 2010, 76:2932–2939.PubMedView Article
          14. Stentz R, Lauret R, Ehrlich SD, Morel-Deville F, Zagorec M: Molecular cloning and analysis of the ptsHI operon in Lactobacillus sake . Appl Environ Microbiol 1997, 63:2111–2116.PubMed
          15. Stentz R, Cornet M, Chaillou S, Zagorec M: Adaption of Lactobacillus sakei to meat: a new regulatory mechanism of ribose utilization? INRA, EDP Sciences 2001, 81:131–138.
          16. Stentz R, Zagorec M: Ribose utilization in Lactobacillus sakei : analysis of the regulation of the rbs operon and putative involvement of a new transporter. J Mol Microbiol Biotechnol 1999, 1:165–173.PubMed
          17. Torriani S, Clementi F, Vancanneyt M, Hoste B, Dellaglio F, Kersters K: Differentiation of Lactobacillus plantarum , L. pentosus and L. paraplantarum species by RAPD-PCR and AFLP. Syst Appl Microbiol 2001, 24:554–560.PubMedView Article
          18. Claesson MJ, van Sinderen D, O'Toole PW: The genus Lactobacillus - a genomic basis for understanding its diversity. FEMS Microbiol Lett 2007, 269:22–28.PubMedView Article
          19. McLeod A, Zagorec M, Champomier-Vergès MC, Naterstad K, Axelsson L: Primary metabolism in Lactobacillus sakei food isolates by proteomic analysis. BMC Microbiol 2010, 10:120.PubMedView Article
          20. Deutscher J, Francke C, Postma PW: How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 2006, 70:939–1031.PubMedView Article
          21. Stulke J, Hillen W: Carbon catabolite repression in bacteria. Curr Opin Microbiol 1999, 2:195–201.PubMedView Article
          22. Titgemeyer F, Hillen W: Global control of sugar metabolism: a gram-positive solution. Antonie Van Leeuwenhoek 2002, 82:59–71.PubMedView Article
          23. Fujita Y: Carbon catabolite control of the metabolic network in Bacillus subtilis . Biosci Biotechnol Biochem 2009, 73:245–259.PubMedView Article
          24. Schumacher MA, Allen GS, Diel M, Seidel G, Hillen W, Brennan RG: Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P. Cell 2004, 118:731–741.PubMedView Article
          25. Obst M, Hehn R, Vogel RF, Hammes WP: Lactose metabolism in Lactobacillus curvatus and Lactobacillus sake . FEMS Microbiol Lett 1992, 97:209–214.View Article
          26. Montel MC, Champomier MC: Arginine catabolism in Lactobacillus sake isolated from meat. Appl Environ Microbiol 1987, 53:2683–2685.PubMed
          27. Zuniga M, Champomier-Vergès M, Zagorec M, Pérez-Martinez G: Structural and functional analysis of the gene cluster encoding the enzymes of the arginine deiminase pathway of Lactobacillus sake . J Bacteriol 1998, 180:4154–4159.PubMed
          28. Rodionov DA, Mironov AA, Gelfand MS: Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria. FEMS Microbiol Lett 2001, 205:305–314.PubMedView Article
          29. Berthier F, Zagorec M, Champomier-Vergès MC, Ehrlich SD, Morel-Deville F: Efficient transformation of Lactobacillus sake by electroporation. Microbiol 1996, 142:1273–1279.View Article
          30. Hagen BF, Næs H, Holck AL: Meat starters have individual requirements for Mn2+. Meat Science 2000, 55:161–168.View Article
          31. Møretrø T, Hagen BF, Axelsson L: A new, completely defined medium for meat lactobacilli. J Appl Microbiol 1998, 85:715–722.View Article
          32. Nyquist OL, McLeod A, Brede DA, Snipen L, Nes IF: Comparative genomics of Lactobacillus sakei with emphasis on strains from meat. Mol Genet Genomics 2011, 285:297–311.PubMedView Article
          33. Rud I, Naterstad K, Bongers RS, Molenaar D, Kleerebezem M, Axelsson L: Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis. Microbial Biotechnology 2011, 4:345–356.PubMedView Article
          34. Vebø HC, Solheim M, Snipen L, Nes IF, Brede DA: Comparative genomic analysis of pathogenic and probiotic Enterococcus faecalis isolates, and their transcriptional responses to growth in human urine. PLoS One 2010, 5:e12489.PubMedView Article
          35. Smyth GK, Speed T: Normalization of cDNA microarray data. Methods 2003, 31:265–273.PubMedView Article
          36. Smyth GK: Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:Article3.PubMed
          37. Smyth GK, Michaud J, Scott HS: Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005, 21:2067–2075.PubMedView Article
          38. Rode TM, Møretrø T, Langsrud S, Langsrud O, Vogt G, Holck A: Responses of Staphylococcus aureus exposed to HCl and organic acid stress. Can J Microbiol 2010, 56:777–792.PubMedView Article
          39. Weickert MJ, Chambliss GH: Site-directed mutagenesis of a catabolite repression operator sequence in Bacillus subtilis . Proc Natl Acad Sci USA 1990, 87:6238–6242.PubMedView Article
          40. Champomier-Vergès MC, Chaillou S, Cornet M, Zagorec M: Erratum to " Lactobacillus sakei : recent developments and future prospects". Res Microbiol 2002, 153:115–123.PubMedView Article
          41. Lorquet F, Goffin P, Muscariello L, Baudry JB, Ladero V, Sacco M, Kleerebezem M, Hols P: Characterization and functional analysis of the poxB gene, which encodes pyruvate oxidase in Lactobacillus plantarum . J Bacteriol 2004, 186:3749–3759.PubMedView Article
          42. Muscariello L, Marasco R, De Felice M, Sacco M: The functional ccpA gene is required for carbon catabolite repression in Lactobacillus plantarum . Appl Environ Microbiol 2001, 67:2903–2907.PubMedView Article
          43. Branny P, De La Torre F, Garel JR: Cloning, sequencing, and expression in Escherichia coli of the gene coding for phosphofructokinase in Lactobacillus bulgaricus . J Bacteriol 1993, 175:5344–5349.PubMed
          44. Viana R, Perez-Martinez G, Deutscher J, Monedero V: The glycolytic genes pfk and pyk from Lactobacillus casei are induced by sugars transported by the phosphoenolpyruvate:sugar phosphotransferase system and repressed by CcpA. Arch Microbiol 2005, 183:385–393.PubMedView Article
          45. Kandler O: Carbohydrate metabolism in lactic acid bacteria. Antonie Van Leeuwenhoek 1983, 49:209–224.PubMedView Article
          46. Naterstad K, Rud I, Kvam I, Axelsson L: Characterisation of the gap operon from Lactobacillus plantarum and Lactobacillus sakei . Curr Microbiol 2007, 54:180–185.PubMedView Article
          47. Kim I, Kim E, Yoo S, Shin D, Min B, Song J, Park C: Ribose utilization with an excess of mutarotase causes cell death due to accumulation of methylglyoxal. J Bacteriol 2004, 186:7229–7235.PubMedView Article
          48. Weber J, Kayser A, Rinas U: Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. II. Dynamic response to famine and feast, activation of the methylglyoxal pathway and oscillatory behaviour. Microbiology 2005, 151:707–716.PubMedView Article
          49. Totemeyer S, Booth NA, Nichols WW, Dunbar B, Booth IR: From famine to feast: the role of methylglyoxal production in Escherichia coli . Mol Microbiol 1998, 27:553–562.PubMedView Article
          50. Malleret C, Lauret R, Ehrlich SD, Morel-Deville F, Zagorec M: Disruption of the sole ldhL gene in Lactobacillus sakei prevents the production of both L- and D-lactate. Microbiology 1998, 144:3327–3333.PubMedView Article
          51. Axelsson L: Lactic acid bacteria: classification and physiology. In Lactic acid bacteria: microbiological and functional aspects. Third revised and expanded edition. Edited by: Salminen S, von Wright A, Ouwehand A. New York, USA: Marcel Dekker, Inc./CRC Press; 2004:1–66.
          52. Condon S: Responses of lactic acid bacteria to oxygen. FEMS Microbiol Rev 1987, 46:269–280.View Article
          53. Fridovich I: The biology of oxygen radicals. Science 1978, 201:875–880.PubMedView Article
          54. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS: Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem 2002, 277:48949–48959.PubMedView Article
          55. Jordan A, Reichard P: Ribonucleotide reductases. Annu Rev Biochem 1998, 67:71–98.PubMedView Article
          56. Keeney KM, Stuckey JA, O'Riordan MX: LplA1-dependent utilization of host lipoyl peptides enables Listeria cytosolic growth and virulence. Mol Microbiol 2007, 66:758–770.PubMedView Article
          57. Marceau A, Zagorec M, Chaillou S, Mera T, Champomier-Vergès MC: Evidence for involvement of at least six proteins in adaptation of Lactobacillus sakei to cold temperatures and addition of NaCl. Appl Environ Microbiol 2004, 70:7260–7268.PubMedView Article
          58. Grogan DW, Cronan JE Jr: Cyclopropane ring formation in membrane lipids of bacteria. Microbiol Mol Biol Rev 1997, 61:429–441.PubMed
          59. Schujman GE, Guerin M, Buschiazzo A, Schaeffer F, Llarrull LI, Reh G, Vila AJ, Alzari PM, de Mendoza D: Structural basis of lipid biosynthesis regulation in Gram-positive bacteria. Embo J 2006, 25:4074–4083.PubMedView Article
          60. Mahr K, Hillen W, Titgemeyer F: Carbon catabolite repression in Lactobacillus pentosus : analysis of the ccpA region. Appl Environ Microbiol 2000, 66:277–283.PubMedView Article
          61. Nentwich SS, Brinkrolf K, Gaigalat L, Huser AT, Rey DA, Mohrbach T, Marin K, Puhler A, Tauch A, Kalinowski J: Characterization of the LacI-type transcriptional repressor RbsR controlling ribose transport in Corynebacterium glutamicum ATCC 13032. Microbiology 2009, 155:150–164.PubMedView Article
          62. Muller W, Horstmann N, Hillen W, Sticht H: The transcription regulator RbsR represents a novel interaction partner of the phosphoprotein HPr-Ser46-P in Bacillus subtilis . Febs J 2006, 273:1251–1261.PubMedView Article
          63. Perez-Rueda E, Collado-Vides J: The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res 2000, 28:1838–1847.PubMedView Article
          64. Brinkrolf K, Ploger S, Solle S, Brune I, Nentwich SS, Huser AT, Kalinowski J, Puhler A, Tauch A: The LacI/GalR family transcriptional regulator UriR negatively controls uridine utilization of Corynebacterium glutamicum by binding to catabolite-responsive element ( cre )-like sequences. Microbiology 2008, 154:1068–1081.PubMedView Article
          65. Saxild HH, Andersen LN, Hammer K: dra-nupC-pdp operon of Bacillus subtilis : nucleotide sequence, induction by deoxyribonucleosides, and transcriptional regulation by the deoR -encoded DeoR repressor protein. J Bacteriol 1996, 178:424–434.PubMed
          66. Zeng X, Saxild HH: Identification and characterization of a DeoR-specific operator sequence essential for induction of dra-nupC-pdp operon expression in Bacillus subtilis . J Bacteriol 1999, 181:1719–1727.PubMed
          67. Zeng X, Saxild HH, Switzer RL: Purification and characterization of the DeoR repressor of Bacillus subtilis . J Bacteriol 2000, 182:1916–1922.PubMedView Article
          68. Schuch R, Garibian A, Saxild HH, Piggot PJ, Nygaard P: Nucleosides as a carbon source in Bacillus subtilis : characterization of the drm-pupG operon. Microbiology 1999, 145:2957–2966.PubMed
          69. Posthuma CC, Bader R, Engelmann R, Postma PW, Hengstenberg W, Pouwels PH: Expression of the xylulose 5-phosphate phosphoketolase gene, xpkA , from Lactobacillus pentosus MD363 is induced by sugars that are fermented via the phosphoketolase pathway and is repressed by glucose mediated by CcpA and the mannose phosphoenolpyruvate phosphotransferase system. Appl Environ Microbiol 2002, 68:831–837.PubMedView Article
          70. Charrier V, Buckley E, Parsonage D, Galinier A, Darbon E, Jaquinod M, Forest E, Deutscher J, Claiborne A: Cloning and sequencing of two enterococcal glpK genes and regulation of the encoded glycerol kinases by phosphoenolpyruvate-dependent, phosphotransferase system-catalyzed phosphorylation of a single histidyl residue. J Biol Chem 1997, 272:14166–14174.PubMedView Article
          71. Darbon E, Servant P, Poncet S, Deutscher J: Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P-GlpK dephosphorylation control Bacillus subtilis glpFK expression. Mol Microbiol 2002, 43:1039–1052.PubMedView Article
          72. Barrangou R, Azcarate-Peril MA, Duong T, Conners SB, Kelly RM, Klaenhammer TR: Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays. Proc Natl Acad Sci USA 2006, 103:3816–3821.PubMedView Article
          73. Chaillou S, Postma PW, Pouwels PH: Contribution of the phosphoenolpyruvate:mannose phosphotransferase system to carbon catabolite repression in Lactobacillus pentosus . Microbiology 2001, 147:671–679.PubMed
          74. Veyrat A, Gosalbes MJ, Perez-Martinez G: Lactobacillus curvatus has a glucose transport system homologous to the mannose family of phosphoenolpyruvate-dependent phosphotransferase systems. Microbiology 1996, 142:3469–3477.PubMedView Article
          75. Veyrat A, Monedero V, Perez-Martinez G: Glucose transport by the phosphoenolpyruvate:mannose phosphotransferase system in Lactobacillus casei ATCC 393 and its role in carbon catabolite repression. Microbiology 1994, 140:1141–1149.PubMedView Article
          76. Viana R, Monedero V, Dossonnet V, Vadeboncoeur C, Perez-Martinez G, Deutscher J: Enzyme I and HPr from Lactobacillus casei : their role in sugar transport, carbon catabolite repression and inducer exclusion. Mol Microbiol 2000, 36:570–584.PubMedView Article

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          This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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