- Research article
- Open Access
Assessment of CcpA-mediated catabolite control of gene expression in Bacillus cereusATCC 14579
© van der Voort et al; licensee BioMed Central Ltd. 2008
- Received: 19 October 2007
- Accepted: 16 April 2008
- Published: 16 April 2008
The catabolite control protein CcpA is a transcriptional regulator conserved in many Gram-positives, controlling the efficiency of glucose metabolism. Here we studied the role of Bacillus cereus ATCC 14579 CcpA in regulation of metabolic pathways and expression of enterotoxin genes by comparative transcriptome analysis of the wild-type and a ccpA-deletion strain.
Comparative analysis revealed the growth performance and glucose consumption rates to be lower in the B. cereus ATCC 14579 ccpA deletion strain than in the wild-type. In exponentially grown cells, the expression of glycolytic genes, including a non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase that mediates conversion of D-glyceraldehyde 3-phosphate to 3-phospho-D-glycerate in one single step, was down-regulated and expression of gluconeogenic genes and genes encoding the citric acid cycle was up-regulated in the B. cereus ccpA deletion strain. Furthermore, putative CRE-sites, that act as binding sites for CcpA, were identified to be present for these genes. These results indicate CcpA to be involved in the regulation of glucose metabolism, thereby optimizing the efficiency of glucose catabolism. Other genes of which the expression was affected by ccpA deletion and for which putative CRE-sites could be identified, included genes with an annotated function in the catabolism of ribose, histidine and possibly fucose/arabinose and aspartate. Notably, expression of the operons encoding non-hemolytic enterotoxin (Nhe) and hemolytic enterotoxin (Hbl) was affected by ccpA deletion, and putative CRE-sites were identified, which suggests catabolite repression of the enterotoxin operons to be CcpA-dependent.
The catabolite control protein CcpA in B. cereus ATCC 14579 is involved in optimizing the catabolism of glucose with concomitant repression of gluconeogenesis and alternative metabolic pathways. Furthermore, the results point to metabolic control of enterotoxin gene expression and suggest that CcpA-mediated glucose sensing provides an additional mode of control in moderating the expression of the nhe and hbl operons in B. cereus ATCC 14579.
- Glutamate Dehydrogenase
- Citric Acid Cycle
- Fumarate Hydratases
- Amino Acid Catabolism
- Gluconeogenic Gene
Bacillus cereus is an important Gram-positive, spore-forming food-borne pathogen. Many strains cause either an emetic or a diarrhoeal type of disease. The production of emetic toxin in foods, also referred to as cereulide, may cause nausea and vomiting. The diarrhoeal type of disease is associated with the production of enterotoxins in the intestines and may involve Nhe, Hbl and CytK [1–3]. Food-borne disease caused by B. cereus is generally characterized by mild symptoms. However, recently more severe cases with a lethal outcome have been described [4, 5]. B. cereus can also be the causative agent of other diseases, such as periodontitis, fulminant endophthalmitis, and meningitis in immuno-compromised patients [1, 6–8]. B. cereus is ubiquitously found in the environment, including in soil. Therefore, the transfer to food is not surprising and causes many problems . In nutrient-rich environments, such as food, B. cereus shows low generation times putatively gaining advantage from its capacity to use various carbohydrates and proteinaceous substrates . The regulation of gene expression plays an important role in the efficient selection of the preferred carbon and energy source for growth. Annotation of the genome of B. cereus ATCC 14579 predicted the regulation of gene expression to be highly complex involving over two hundred transcriptional regulators managing its 5370 open reading frames (ORFs) [9, 10]. One of these putative regulators is the catabolite control protein CcpA, which is a member of the LacI-family of transcriptional regulators. CcpA and the regulatory mechanism of the catabolite repression are highly conserved in low-GC Gram-positives . B. cereus ATCC 14579 CcpA shows 77% identity with B. subtilis CcpA. Furthermore, CcpA in B. subtilis has been shown to have a role in optimizing glucose metabolism and the underlying regulatory mechanisms have recently been reviewed [12–14]. Regulation of gene expression by CcpA is mediated by its binding to DNA at a specific cis-binding sequence, the Catabolite Responsive Element (CRE) [14–16].
In recent years the regulon of B. subtilis CcpA has been studied extensively by transcriptome analyses, revealing genes and operons under direct and indirect control of CcpA [17–20]. Furthermore, Moreno et al.  showed a clear correlation between the glucose-repressed genes and the presence of predicted CRE-sites. Moreover, they showed CcpA-mediated glucose-independent regulation of expression . Other organisms for which the role of CcpA in carbon metabolism was established are Lactobacillus acidophilus  and Lactococcus lactis . Recently, a role for CcpA in the control of virulence of Staphylococcus aureus , Streptococcus pneumoniae , and Clostridium perfringens was reported  and reviewed .
Notably, comparative genomics of the different species of the B. cereus group revealed reduced capacity to metabolize carbohydrates and increased potential for protein metabolism as compared to B. subtilis [28, 29]. Here we report on the role of CcpA in regulation of metabolism and virulence in B. cereus ATCC 14579.
Growth and glucose utilization of the ccpAdeletion strain compared to the wild-type
Overview of the transcriptome data
Expression ratios of six randomly chosen genes with significantly altered expression in the ccpA deletion strain (cggR, acoR, gapB, ymfC, fruR and odhA) were quantified using qPCR. Expression ratios obtained by microarray analysis were compared to ratios obtained by qPCR. The tested genes showed the same trend in expression, with differential expression only slightly more pronounced in qPCR experiments, a feature observed before in such comparisons . This indicates the microarray platform to be suited for gene expression analysis (for qPCR data see Additional file 1).
Identification of the B. cereus CRE-site consensus and in silicoanalysis
Analysis of genes differentially expressed in the ccpAdeletion strain
Genes involved in B. cereus ATCC14579 glucose metabolism and their putative CRE-sites
PTS system, glucose-specific IIABC component
Phosphocarrier protein HPr
Central glycolytic genes regulator
NADP-dependent glyceraldehyde-3-P dehydrogenase
Pyruvate dehydrogenase (acetyl-transferring)
Pyruvate dehydrogenase (acetyl-transferring)
Acetolactate synthase large subunit
Citric acid cycle
Isocitrate dehydrogenase [NADP]
Succinate-CoA ligase (ADP-forming)
Succinate-CoA ligase (ADP-forming)
Phosphoenolpyruvate carboxykinase (ATP)
One of the glycolytic genes found to be expressed lower in the ccpA deletion strain was yfmT. This gene encodes a non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), for which 2 putative CRE-sites could be identified. We propose to rename yfmT as gapN, since this gene shows similarity with gapN of the other members of the B. cereus group, and with gapN of B. halodurans, Streptococci and Clostridia . Notably, the gene is lacking in B. subtilis [29, 33]. Next to the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase, two phosphorylating glyceraldehyde-3-phosphate dehydrogenases encoding genes (gapA and gapB) are present on the B. cereus ATCC 14579 genome. The function of GAPN in microbial metabolism is yet unclear. Recently, Asanuma and Hino (2006) showed a role for CcpA in expression control of gapN in Streptococcus bovis and proposed that NADPH is provided by GAPN activity for NADPH-dependent biosynthetic reactions, thereby maintaining an optimal redox balance at the same time. However, in hyperthermophilic archaea GAPN has been shown to play a role in accelerating glycolysis as it can produce 3-phospho-D-glycerate from D-glyceraldehyde 3-phosphate in a one-step reaction, instead of two steps. As a putative drawback, ATP is not produced in this one-step reaction. The exact role of GAPN in B. cereus metabolism remains to be elucidated.
The gluconeogenic genes expressed higher in the ccpA deletion strain included ywjI and gapB. The ywjI gene is part of the putative murA2-ywjI operon and is annotated as a fructose-1,6-bisphosphatase. The ywjI gene of B. subtilis, that shows similarity to ywjI of B. cereus, is annotated to be a fructose-1,6-bisphosphatase, as a member of the glpX-family. The other annotated fructose-1,6-bisphosphatase gene for B. subtilis, fbp, which is no member of the glpX-family, is not regulated by CcpA and deletion of this gene seems to have no effect on gluconeogenesis . A corresponding fbp homologue appears to be absent in B. cereus. However, on the B. cereus genome two members of the glpX-family of fructose-1,6-bisphosphatases are present, of which ywjI expression was found to be affected by ccpA deletion, accordingly a putative CRE-site was identified in the promoter region of its operon. The gapB gene encodes a NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase. Three putative CRE-sites were identified for gapB in B. cereus (Table 1). In contrast, no CRE-sites were identified for gapB in B. subtilis, and its expression was shown to be only indirectly affected by ccpA deletion . Furthermore, gluconeogenesis in B. subtilis was shown to be regulated by the transcriptional regulator CcpN [37, 38]. CcpN is also present on the genome of B. cereus ATCC 14579 and putative CcpN binding sites can be found in front of the gluconeogenic genes encoding GapB and PckA . Combined with our results this would point to dual control of the expression of gluconeogenic genes in B. cereus by CcpN and CcpA.
Glutamate is a product of protein and amino acid catabolism and acts as link between nitrogen and carbon metabolism, mediated by glutamate synthase and glutamate dehydrogenase, as described for B. subtilis [46, 47]. The B. subtilis genome contains a glutamate synthase (gltAB) and two glutamate dehydrogenases (rocG and gudB) of which the GudB dehydrogenase appears to be inactive . Glutamate biosynthesis in B. subtilis has recently been shown to be tightly regulated by interaction of RocG and GltC , but these genes are not encoded on the B. cereus genome. The microbial glutamate synthases generally belong to the NADPH-GltS family of glutamate synthases and are encoded by two genes . In the glutamate synthase reaction L-glutamate is produced from L-glutamine and 2-oxoglutarate, with the latter compound derived from the citric acid cycle . The gltAB operon of B. subtilis is suggested to be regulated by CcpA [46, 50]. On the genome of B. cereus ATCC 14579 only one glutamate synthase gene (gltA) is present and its expression at various phases of growth is similar in the wild-type and its ccpA deletion strain, indicating that its expression is not regulated by CcpA. Moreover, it is unclear to which family of glutamate synthases GltA of B. cereus belongs. Interestingly, gudB was the only gene present on the genome of B. cereus encoding a glutamate dehydrogenase, and its expression was observed to be clearly higher in the ccpA deletion strain (Table 1). Glutamate dehydrogenase is responsible for the reaction from L-glutamate to 2-oxoglutarate linking L-glutamate to the citric acid cycle . Higher expression of gudB in the ccpA deletion strain compared to the wild-type, together with the fact that it is the only glutamate dehydrogenase annotated on the genome of B. cereus suggests that GudB is the active glutamate dehydrogenase for B. cereus. This is supported by the fact that the 9-bp sequence, encoding the 3 amino acids causing the inactivity of GudB in B. subtilis , are absent in the gudB sequence of B. cereus ATCC 14579. Two putative CRE-sites in front of and one within gudB were identified pointing to CcpA-controlled expression in B. cereus.
B. subtilis contains a large number of carbohydrate catabolic pathways , whereas the number of these pathways is limited in B. cereus. The observed deficiency of the B. subtilis ccpA deletion strain in growth with ammonium as the sole nitrogen-source, has been attributed to the regulation of the gltAB genes by CcpA [46, 50] and the read-through transcription of the rocG gene . The lack of regulation of gltA in B. cereus by CcpA, together with a similarity to the B. subtilis gltA of only 46%, offers an explanation for the observation that the ccpA deletion strain of B. cereus is able to grow with ammonium as the sole nitrogen source (data not shown), conceivably with GudB as the active glutamate dehydrogenase.
The role of CcpA in optimisation of glucose metabolism is apparent, since glycolytic enzymes were expressed lower and expression of genes encoding citric acid cycle enzymes was shown to be higher in the ccpA deletion strain compared to the wild-type. Up-regulation in the ccpA deletion strain was found for ~30 genes encoding enzymes involved in protein, peptide and amino acid metabolism (see Additional file 1). This is seemingly in contrast with the proposed preferred use of proteinaceous substrates for growth of B. cereus, a hypothesis put forward by Ivanova et al. . This hypothesis was supported by the annotation of a large number of genes encoding proteolytic enzymes, a multiplicity of peptide and amino acid transporters, and a large variety of amino acid degradation pathways. However, under the conditions tested glucose is used as the carbon and energy source (Fig. 1) and genes encoding enzymes involved in protein, peptide and amino acid catabolism appear to be subject to catabolite repression, indicating that under the conditions tested, glycolysis rather than protein catabolism is the preferred energy generation route of B. cereus ATCC 14579.
CcpA-mediated catabolite control of enterotoxin gene expression in B. cereus
B. cereus ATCC 14579 catabolite control protein CcpA is involved in optimizing the catabolism of glucose with concomitant repression of a range of metabolic pathways. Furthermore, CcpA-mediated glucose sensing is shown to provide an additional mode of control in moderating the expression of the nhe- and hbl-operon in this human pathogen.
Bacterial strains, culture media, growth conditions, and genetic methods
B. cereus ATCC 14579 and its ccpA deletion strain FM1403 were cultured in brain heart infusion broth (BHI, Becton and Dickinson, The Netherlands) medium at 30°C, with shaking at 200 rpm. The growth of the culture was monitored by measurement of the optical density at OD600. D-glucose concentrations were measured by use of a D-glucose measuring kit (Boehringer). Growth experiments and glucose measurements were performed in three fold. Plasmid DNAs were purified from E. coli with a Qiaprep Spin Miniprep kit (Westburg, Leusden, The Netherlands). Pwo polymerase (Roche Diagnostics, Almere, The Netherlands) was used for PCR generated fragments that were used in cloning and Taq polymerase (Fermentas, Amersfoort, The Netherlands) was used in control PCRs. E. coli HB101/pRK24  was used as the donor host in conjugation experiments. The antibiotics used were ampicillin (Sigma, Zwijndrecht, The Netherlands) at a concentration of 50 μg/ml, kanamycin (Sigma) at a concentration of 70 μg/ml, erythromycin (Sigma) at a concentration of 150 μg/ml (for E. coli) or 5 μg/ml (for B. cereus), spectinomycin (Sigma) at a concentration of 100 μg/ml, and polymyxin B (VWR, Amsterdam, The Netherlands) at a concentration of 50 μg/ml for counter-selection against E. coli upon conjugation.
Construction of ccpAdeletion strain
To construct a double cross-over deletion strain of ccpA, an ~3.5-kb PCR product, comprising ccpA and 1-kb flanking regions was obtained by use of forward primer ccpAKOsacIforw (TCgagctcAGATTACGTTGATGTTATTC) and reverse primer ccpAKOxbaIrev (TGtctagaAGAAGAAGAAAAAGAGGAAGAAAT). This PCR product was cloned into pGemT-easy (Promega, Leiden, The Netherlands) according to the manufacturer's protocol resulting in pGemTccpA. Subsequently, an erythromycin-resistance cassette amplified from pUC18ERY  with forward primer ErycasFBsrGI (TCtgtacaGTCCGCAAAAGAAAAACG) and reverse primer ErycasRClaI (TCatcgatCATACCTAATAATTTATCTAC) was cloned into pGemTccpA after digesting both with Bsp1407I (BsrGI) and Bsu15I (ClaI) (Fermentas). The insert of the resulting plasmid, comprising the 1-kb flanking regions and the erythromycin-resistance cassette was cloned into the conjugal vector pATΔS28  by digestion of the insert and the vector with XbaI and SacI (Fermentas). The resulting plasmid pATΔCcpAery was isolated from DH5α and transformed into E. coli HB101/pRK24. The resulting strain was used in a conjugation experiment with B. cereus ATCC 14579 following established procedures . Transconjugants were obtained by selection for spectinomycin sensitivity and erythromycin resistance and one was analysed in comparison with the wild-type strain. PCR and Southern Blot analysis confirmed the deletion of ccpA by double homologous recombination (data not shown). The B. cereus ccpA deletion strain was designated B. cereus FM1403.
RNA was extracted from both the ccpA deletion strain and the wild-type at four time points in the growth curve at OD600 of 0.2, 0.8, 4 and 8 which corresponds to early-exponential, mid-exponential, transition and stationary phase of growth from two independent cultures per phase by using RNAwiz (Ambion, Huntingdon, United Kingdom) according to the manufacturers protocol. Residual DNA from the RNA preparations was enzymatically removed by using TURBO DNA-free (Ambion). Extracted RNA samples were stored in 70% EtOH, 0.3 M sodium acetate buffer (pH 5.2) at -80°C.
Microarray construction and transcriptome analysis
Amplicon based DNA-microarrays were constructed for B. cereus ATCC 14579 as described for L. lactis IL1403 [64, 65] with modifications as detailed below. Amplicons were designed on 5199 genes selected from the 5311 annotated genes (ORFs smaller than 80-bp were omitted) on the genome of B. cereus ATCC 14579 . To reduce cross-hybridization between probe and target DNA sequences the amplicons had sizes of 70 – 700-bp (depending on gene sizes) and comprised the most unique part of a gene. The amplicons were synthesized by EuroGentec (Seraing, Belgium) in two amplification steps. In the first amplification step, primers were used with a unique tag-sequence for B. cereus ATCC 14579 (forward primers were extended with the sequence: 5'-TCGGGCAGCTGCTCC-3'; and reverse primers with the sequence: 5'-TGGCGCCCCTAGATG-3'). Two copies of each amplicon were present per array, resulting in microarrays comprising 10398 spots.
Normalized expression data (Feature Extract, Agilent) for each spot was used in a statistical analysis. The biological replicate experiments were merged with the web-supported VAMPIRE microarray suite, based on a Bayesian frame work. Furthermore, VAMPIRE calculated p-values for individual spots and subsequently used this p-value to identify statistically differentially expressed spots between compared growth conditions by use of a false discovery rate (FDR) of 0.05 as a threshold [66, 67]. In addition, only ORFs of which both individual spots passed the FDR based threshold were considered to be putatively differentially regulated. Expression ratios per ORF were established by calculating the average of the log-values of individual spots. This value (R) was then used to calculate the average expression ratio (10R) per ORF. Finally, only ORFs that showed a change in expression of at least 2-fold (up/down) were considered to be differentially expressed. Microarray data are submitted to the GEO database with accession number: GSE7843.
To determine gene similarity, homology and gene context NCBI BLAST and the ERGO database were used , while KEGG  was used for assessment of metabolic functions and pathways. Whether succeeding genes were part of one operon was determined according to operon prediction as performed by .
Definition and identification of B. cereusCRE-site
The 350-bp upstream and 150-bp downstream sequences of the translation start of genes identified by the array experiments to be significantly higher expressed in the ccpA deletion strain compared to the wild-type strain for early- and mid-exponential growth were analyzed with AlignACE 3.1 , which searches the input sequences for stretches of nucleotides which align between the different input sequences. The 13-bp CRE-sites identified by AlignACE were aligned with MUSCLE 3.6  and a Hidden Markov Model (HMM) was constructed with the HMMER package . The HMM was used to search CRE-sites in the complete genome sequence of B. cereus ATCC 14579 , and not only the 350-bp upstream and 150-bp downstream sequences significantly higher expressed genes in the ccpA deletion strain. Subsequently, to analyse whether the B. cereus consensus was longer than 13-bp, the obtained sites after the HMM search were extended to 18-bp, as has been the reported length for B. subtilis . The resulting extended CRE-sites were again aligned using MUSCLE 3.6 . This alignment was subsequently visualized with WebLogo  and a iteration HMM search was performed on the B. cereus ATCC 14579 sequence  to identify all putative CRE-sites confirming to the new alignment in the B. cereus ATCC 14579 genome.
Financial support was received from the IOP Genomics Program of Senter Novem (grant IGE1018). The authors would like to thank Mark de Been and Christof Francke (Centre for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands) for their bioinformatics input, and Anne de Jong for his efforts in construction of the DNA microarrays.
- Kotiranta A, Lounatmaa K, Haapasalo M: Epidemiology and pathogenesis of Bacillus cereus infections. Microbes Infect. 2000, 2 (2): 189-198. 10.1016/S1286-4579(00)00269-0.View ArticlePubMedGoogle Scholar
- Schoeni JL, Wong AC: Bacillus cereus food poisoning and its toxins. J Food Prot. 2005, 68 (3): 636-648.PubMedGoogle Scholar
- Granum PE, Lund T: Bacillus cereus and its food poisoning toxins. FEMS Microbiol Lett. 1997, 157 (2): 223-228. 10.1111/j.1574-6968.1997.tb12776.x.View ArticlePubMedGoogle Scholar
- Lund T, De Buyser ML, Granum PE: A new cytotoxin from Bacillus cereus that may cause necrotic enteritis. Mol Microbiol. 2000, 38 (2): 254-261. 10.1046/j.1365-2958.2000.02147.x.View ArticlePubMedGoogle Scholar
- Dierick K, Van Coillie E, Swiecicka I, Meyfroidt G, Devlieger H, Meulemans A, Hoedemaekers G, Fourie L, Heyndrickx M, Mahillon J: Fatal family outbreak of Bacillus cereus-associated food poisoning. J Clin Microbiol. 2005, 43 (8): 4277-4279. 10.1128/JCM.43.8.4277-4279.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Drobniewski FA: Bacillus cereus and related species. Clin Microbiol Rev. 1993, 6 (4): 324-338.PubMed CentralPubMedGoogle Scholar
- Gaur AH, Patrick CC, McCullers JA, Flynn PM, Pearson TA, Razzouk BI, Thompson SJ, Shenep JL: Bacillus cereus bacteremia and meningitis in immunocompromised children. Clin Infect Dis. 2001, 32 (10): 1456-1462. 10.1086/320154.View ArticlePubMedGoogle Scholar
- Hilliard NJ, Schelonka RL, Waites KB: Bacillus cereus bacteremia in a preterm neonate. J Clin Microbiol. 2003, 41 (7): 3441-3444. 10.1128/JCM.41.7.3441-3444.2003.PubMed CentralView ArticlePubMedGoogle Scholar
- Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E, Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N: Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature. 2003, 423 (6935): 87-91. 10.1038/nature01582.View ArticlePubMedGoogle Scholar
- Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N: The ERGO genome analysis and discovery system. Nucleic Acids Res. 2003, 31 (1): 164-171. 10.1093/nar/gkg148.PubMed CentralView ArticlePubMedGoogle Scholar
- Warner JB, Lolkema JS: CcpA-dependent carbon catabolite repression in bacteria. Microbiol Mol Biol Rev. 2003, 67 (4): 475-490. 10.1128/MMBR.67.4.475-490.2003.PubMed CentralView ArticlePubMedGoogle Scholar
- Titgemeyer F, Hillen W: Global control of sugar metabolism: a gram-positive solution. Antonie Van Leeuwenhoek. 2002, 82 (1-4): 59-71. 10.1023/A:1020628909429.View ArticlePubMedGoogle Scholar
- Bruckner R, Titgemeyer F: Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. FEMS Microbiol Lett. 2002, 209 (2): 141-148.View ArticlePubMedGoogle Scholar
- Stulke J, Hillen W: Regulation of carbon catabolism in Bacillus species. Annu Rev Microbiol. 2000, 54: 849-880. 10.1146/annurev.micro.54.1.849.View ArticlePubMedGoogle Scholar
- Miwa Y, Nakata A, Ogiwara A, Yamamoto M, Fujita Y: Evaluation and characterization of catabolite-responsive elements (cre) of Bacillus subtilis. Nucleic Acids Res. 2000, 28 (5): 1206-1210. 10.1093/nar/28.5.1206.PubMed CentralView ArticlePubMedGoogle Scholar
- Deutsher J, Galinier A, Martin-Verstraete I: Carbohydrate uptake and metabolism. Bacillus subtilis and its closest relatives: form genes to cells. Edited by: Sonenshein AL. 2002, Washington, D.C. , ASM Press, 129-150.View ArticleGoogle Scholar
- Yoshida K, Kobayashi K, Miwa Y, Kang CM, Matsunaga M, Yamaguchi H, Tojo S, Yamamoto M, Nishi R, Ogasawara N, Nakayama T, Fujita Y: Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucleic Acids Res. 2001, 29 (3): 683-692. 10.1093/nar/29.3.683.PubMed CentralView ArticlePubMedGoogle Scholar
- Blencke HM, Homuth G, Ludwig H, Mader U, Hecker M, Stulke J: Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 2003, 5 (2): 133-149. 10.1016/S1096-7176(03)00009-0.View ArticlePubMedGoogle Scholar
- Lorca GL, Chung YJ, Barabote RD, Weyler W, Schilling CH, Saier MH: Catabolite repression and activation in Bacillus subtilis: dependency on CcpA, HPr, and HprK. J Bacteriol. 2005, 187 (22): 7826-7839. 10.1128/JB.187.22.7826-7839.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Lulko AT, Buist G, Kok J, Kuipers OP: Transcriptome analysis of temporal regulation of carbon metabolism by CcpA in Bacillus subtilis reveals additional target genes. J Mol Microbiol Biotechnol. 2007, 12 (1-2): 82-95. 10.1159/000096463.View ArticlePubMedGoogle Scholar
- Moreno MS, Schneider BL, Maile RR, Weyler W, Saier MH: Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses. Mol Microbiol. 2001, 39 (5): 1366-1381. 10.1111/j.1365-2958.2001.02328.x.View ArticlePubMedGoogle Scholar
- 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 U S A. 2006, 103 (10): 3816-3821. 10.1073/pnas.0511287103.PubMed CentralView ArticlePubMedGoogle Scholar
- Zomer AL, Buist G, Larsen R, Kok J, Kuipers OP: Time-resolved determination of the CcpA regulon of Lactococcus lactis subsp. cremoris MG1363. J Bacteriol. 2007, 189 (4): 1366-1381. 10.1128/JB.01013-06.PubMed CentralView ArticlePubMedGoogle Scholar
- Seidl K, Stucki M, Ruegg M, Goerke C, Wolz C, Harris L, Berger-Bachi B, Bischoff M: Staphylococcus aureus CcpA affects virulence determinant production and antibiotic resistance. Antimicrob Agents Chemother. 2006, 50 (4): 1183-1194. 10.1128/AAC.50.4.1183-1194.2006.PubMed CentralView ArticlePubMedGoogle Scholar
- Iyer R, Baliga NS, Camilli A: Catabolite control protein A (CcpA) contributes to virulence and regulation of sugar metabolism in Streptococcus pneumoniae. J Bacteriol. 2005, 187 (24): 8340-8349. 10.1128/JB.187.24.8340-8349.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Varga J, Stirewalt VL, Melville SB: The CcpA protein is necessary for efficient sporulation and enterotoxin gene (cpe) regulation in Clostridium perfringens. J Bacteriol. 2004, 186 (16): 5221-5229. 10.1128/JB.186.16.5221-5229.2004.PubMed CentralView ArticlePubMedGoogle Scholar
- Deutscher J, Herro R, Bourand A, Mijakovic I, Poncet S: P-Ser-HPr--a link between carbon metabolism and the virulence of some pathogenic bacteria. Biochim Biophys Acta. 2005, 1754 (1-2): 118-125.View ArticlePubMedGoogle Scholar
- Rasko DA, Altherr MR, Han CS, Ravel J: Genomics of the Bacillus cereus group of organisms. FEMS Microbiol Rev. 2005, 29 (2): 303-329. 10.1016/j.femsre.2004.12.005.PubMedGoogle Scholar
- Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Danchin A, et al: The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997, 390 (6657): 249-256. 10.1038/36786.View ArticlePubMedGoogle Scholar
- van Schaik W, van der Voort M, Molenaar D, Moezelaar R, de Vos WM, Abee T: Identification of the sigmaB regulon of Bacillus cereus and conservation of sigmaB-regulated genes in low-GC-content gram-positive bacteria. J Bacteriol. 2007, 189 (12): 4384-4390. 10.1128/JB.00313-07.PubMed CentralView ArticlePubMedGoogle Scholar
- Price MN, Huang KH, Alm EJ, Arkin AP: A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res. 2005, 33 (3): 880-892. 10.1093/nar/gki232.PubMed CentralView ArticlePubMedGoogle Scholar
- Makita Y, Nakao M, Ogasawara N, Nakai K: DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res. 2004, 32 (Database issue): D75-77. 10.1093/nar/gkh074.PubMed CentralView ArticlePubMedGoogle Scholar
- Iddar A, Valverde F, Assobhei O, Serrano A, Soukri A: Widespread occurrence of non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase among gram-positive bacteria. Int Microbiol. 2005, 8 (4): 251-258.PubMedGoogle Scholar
- Ahmed H, Ettema TJ, Tjaden B, Geerling AC, van der Oost J, Siebers B: The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation. Biochem J. 2005, 390 (Pt 2): 529-540.PubMed CentralView ArticlePubMedGoogle Scholar
- Fujita Y, Yoshida K, Miwa Y, Yanai N, Nagakawa E, Kasahara Y: Identification and expression of the Bacillus subtilis fructose-1, 6-bisphosphatase gene (fbp). J Bacteriol. 1998, 180 (16): 4309-4313.PubMed CentralPubMedGoogle Scholar
- Ludwig H, Rebhan N, Blencke HM, Merzbacher M, Stulke J: Control of the glycolytic gapA operon by the catabolite control protein A in Bacillus subtilis: a novel mechanism of CcpA-mediated regulation. Mol Microbiol. 2002, 45 (2): 543-553. 10.1046/j.1365-2958.2002.03034.x.View ArticlePubMedGoogle Scholar
- Servant P, Le Coq D, Aymerich S: CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of Bacillus subtilis gluconeogenic genes. Mol Microbiol. 2005, 55 (5): 1435-1451. 10.1111/j.1365-2958.2005.04473.x.View ArticlePubMedGoogle Scholar
- Licht A, Brantl S: Transcriptional repressor CcpN from Bacillus subtilis compensates asymmetric contact distribution by cooperative binding. J Mol Biol. 2006, 364 (3): 434-448. 10.1016/j.jmb.2006.09.021.View ArticlePubMedGoogle Scholar
- Debarbouille M, Gardan R, Arnaud M, Rapoport G: Role of bkdR, a transcriptional activator of the sigL-dependent isoleucine and valine degradation pathway in Bacillus subtilis. J Bacteriol. 1999, 181 (7): 2059-2066.PubMed CentralPubMedGoogle Scholar
- Tam le T, Eymann C, Antelmann H, Albrecht D, Hecker M: Global gene expression profiling of Bacillus subtilis in response to ammonium and tryptophan starvation as revealed by transcriptome and proteome analysis. J Mol Microbiol Biotechnol. 2007, 12 (1-2): 121-130. 10.1159/000096467.View ArticlePubMedGoogle Scholar
- Tojo S, Satomura T, Morisaki K, Deutscher J, Hirooka K, Fujita Y: Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA, CodY and TnrA. Mol Microbiol. 2005, 56 (6): 1560-1573.View ArticlePubMedGoogle Scholar
- Shivers RP, Sonenshein AL: Bacillus subtilis ilvB operon: an intersection of global regulons. Mol Microbiol. 2005, 56 (6): 1549-1559.View ArticlePubMedGoogle Scholar
- Samuel J, Luo Y, Morgan PM, Strynadka NC, Tanner ME: Catalysis and binding in L-ribulose-5-phosphate 4-epimerase: a comparison with L-fuculose-1-phosphate aldolase. Biochemistry. 2001, 40 (49): 14772-14780. 10.1021/bi011252v.View ArticlePubMedGoogle Scholar
- Lorca G, Winnen B, Saier MH: Identification of the L-aspartate transporter in Bacillus subtilis. J Bacteriol. 2003, 185 (10): 3218-3222. 10.1128/JB.185.10.3218-3222.2003.PubMed CentralView ArticlePubMedGoogle Scholar
- Satomura T, Shimura D, Asai K, Sadaie Y, Hirooka K, Fujita Y: Enhancement of glutamine utilization in Bacillus subtilis through the GlnK-GlnL two-component regulatory system. J Bacteriol. 2005, 187 (14): 4813-4821. 10.1128/JB.187.14.4813-4821.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Wacker I, Ludwig H, Reif I, Blencke HM, Detsch C, Stulke J: The regulatory link between carbon and nitrogen metabolism in Bacillus subtilis: regulation of the gltAB operon by the catabolite control protein CcpA. Microbiology. 2003, 149 (Pt 10): 3001-3009. 10.1099/mic.0.26479-0.View ArticlePubMedGoogle Scholar
- Belitsky BR, Sonenshein AL: Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol. 1998, 180 (23): 6298-6305.PubMed CentralPubMedGoogle Scholar
- Commichau FM, Herzberg C, Tripal P, Valerius O, Stulke J: A regulatory protein-protein interaction governs glutamate biosynthesis in Bacillus subtilis: the glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol. 2007, 65 (3): 642-654. 10.1111/j.1365-2958.2007.05816.x.View ArticlePubMedGoogle Scholar
- Vanoni MA, Curti B: Glutamate synthase: a complex iron-sulfur flavoprotein. Cell Mol Life Sci. 1999, 55 (4): 617-638. 10.1007/s000180050319.View ArticlePubMedGoogle Scholar
- Faires N, Tobisch S, Bachem S, Martin-Verstraete I, Hecker M, Stulke J: The catabolite control protein CcpA controls ammonium assimilation in Bacillus subtilis. J Mol Microbiol Biotechnol. 1999, 1 (1): 141-148.PubMedGoogle Scholar
- Struck J, Sizer IW: The substrate specificity of glutamic acid dehydrogenase. Arch Biochem Biophys. 1960, 86: 260-266. 10.1016/0003-9861(60)90415-X.View ArticlePubMedGoogle Scholar
- Lindback T, Fagerlund A, Rodland MS, Granum PE: Characterization of the Bacillus cereus Nhe enterotoxin. Microbiology. 2004, 150 (Pt 12): 3959-3967. 10.1099/mic.0.27359-0.View ArticlePubMedGoogle Scholar
- Ryan PA, Macmillan JD, Zilinskas BA: Molecular cloning and characterization of the genes encoding the L1 and L2 components of hemolysin BL from Bacillus cereus. J Bacteriol. 1997, 179 (8): 2551-2556.PubMed CentralPubMedGoogle Scholar
- Bron PA, Grangette C, Mercenier A, de Vos WM, Kleerebezem M: Identification of Lactobacillus plantarum genes that are induced in the gastrointestinal tract of mice. J Bacteriol. 2004, 186 (17): 5721-5729. 10.1128/JB.186.17.5721-5729.2004.PubMed CentralView ArticlePubMedGoogle Scholar
- Hooper LV, Gordon JI: Glycans as legislators of host-microbial interactions: spanning the spectrum from symbiosis to pathogenicity. Glycobiology. 2001, 11 (2): 1R-10R. 10.1093/glycob/11.2.1R.View ArticlePubMedGoogle Scholar
- Ouhib O, Clavel T, Schmitt P: The production of Bacillus cereus enterotoxins is influenced by carbohydrate and growth rate. Curr Microbiol. 2006, 53 (3): 222-226. 10.1007/s00284-006-0094-6.View ArticlePubMedGoogle Scholar
- Duport C, Zigha A, Rosenfeld E, Schmitt P: Control of enterotoxin gene expression in Bacillus cereus F4430/73 involves the redox-sensitive ResDE signal transduction system. J Bacteriol. 2006, 188 (18): 6640-6651. 10.1128/JB.00702-06.PubMed CentralView ArticlePubMedGoogle Scholar
- Zigha A, Rosenfeld E, Schmitt P, Duport C: The redox regulator Fnr is required for fermentative growth and enterotoxin synthesis in Bacillus cereus F4430/73. J Bacteriol. 2007, 189 (7): 2813-2824. 10.1128/JB.01701-06.PubMed CentralView ArticlePubMedGoogle Scholar
- Gohar M, Okstad OA, Gilois N, Sanchis V, Kolsto AB, Lereclus D: Two-dimensional electrophoresis analysis of the extracellular proteome of Bacillus cereus reveals the importance of the PlcR regulon. Proteomics. 2002, 2 (6): 784-791. 10.1002/1615-9861(200206)2:6<784::AID-PROT784>3.0.CO;2-R.View ArticlePubMedGoogle Scholar
- Trieu-Cuot P, Carlier C, Poyart-Salmeron C, Courvalin P: Shuttle vectors containing a multiple cloning site and a lacZ alpha gene for conjugal transfer of DNA from Escherichia coli to gram-positive bacteria. Gene. 1991, 102 (1): 99-104. 10.1016/0378-1119(91)90546-N.View ArticlePubMedGoogle Scholar
- van Kranenburg R, Marugg JD, van S, Willem NJ, de Vos WM: Molecular characterization of the plasmid-encoded eps gene cluster essential for exopolysaccharide biosynthesis in Lactococcus lactis. Mol Microbiol. 1997, 24 (2): 387-397. 10.1046/j.1365-2958.1997.3521720.x.View ArticlePubMedGoogle Scholar
- Trieu-Cuot P, Carlier C, Poyart-Salmeron C, Courvalin P: A pair of mobilizable shuttle vectors conferring resistance to spectinomycin for molecular cloning in Escherichia coli and in gram-positive bacteria. Nucleic Acids Res. 1990, 18 (14): 4296-10.1093/nar/18.14.4296.PubMed CentralView ArticlePubMedGoogle Scholar
- Bron S: Plasmids. Molecular biological methods for Bacillus. Edited by: Harwood CR, Cutting SM. 1990, Chichester , John Wiley & Sons Ltd., 75-174.Google Scholar
- Kuipers OP, de Jong A, Baerends RJ, van Hijum SA, Zomer AL, Karsens HA, den Hengst CD, Kramer NE, Buist G, Kok J: Transcriptome analysis and related databases of Lactococcus lactis. Antonie Van Leeuwenhoek. 2002, 82 (1-4): 113-122. 10.1023/A:1020691801251.View ArticlePubMedGoogle Scholar
- van Hijum SA, de Jong A, Baerends RJ, Karsens HA, Kramer NE, Larsen R, den Hengst CD, Albers CJ, Kok J, Kuipers OP: A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics. 2005, 6 (1): 77-10.1186/1471-2164-6-77.PubMed CentralView ArticlePubMedGoogle Scholar
- Hsiao A, Ideker T, Olefsky JM, Subramaniam S: VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Res. 2005, 33 (Web Server issue): W627-632. 10.1093/nar/gki443.PubMed CentralView ArticlePubMedGoogle Scholar
- Hsiao A, Worrall DS, Olefsky JM, Subramaniam S: Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes. Bioinformatics. 2004, 20 (17): 3108-3127. 10.1093/bioinformatics/bth371.View ArticlePubMedGoogle Scholar
- Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006, 34 (Database issue): D354-357. 10.1093/nar/gkj102.PubMed CentralView ArticlePubMedGoogle Scholar
- Roth FP, Hughes JD, Estep PW, Church GM: Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol. 1998, 16 (10): 939-945. 10.1038/nbt1098-939.View ArticlePubMedGoogle Scholar
- Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004, 5: 113-10.1186/1471-2105-5-113.PubMed CentralView ArticlePubMedGoogle Scholar
- Durbin R, Eddy SR, Krogh A, Mitchison G: Biological sequence analysis: probabilistic models of proteins and nucleic acids. 1998, Cambridge,United Kingdom , Cambridge University PressView ArticleGoogle Scholar
- Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome Res. 2004, 14 (6): 1188-1190. 10.1101/gr.849004.PubMed CentralView ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. 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.