The MarR-like protein PchR (YvmB) regulates expression of genes involved in pulcherriminic acid biosynthesis and in the initiation of sporulation in Bacillus subtilis
© The Author(s). 2016
Received: 24 May 2016
Accepted: 7 August 2016
Published: 20 August 2016
Cyclodipeptides and their derivatives constitute a large class of peptide natural products with noteworthy biological activities. In some yeasts and bacterial species, pulcherriminic acid derived from cyclo-L-leucyl-L-leucyl is excreted and chelates free ferric ions to form the pulcherrimin. In Bacillus subtilis, the enzymes YvmC and CypX are known to be involved in pulcherriminic acid biosynthesis. However, the mechanisms controlling the transcription of the yvmC-cypX operon are still unknown.
In this work, we demonstrated that the B. subtilis YvmB MarR-like regulator is the major transcription factor controlling yvmC-cypX expression. A comprehensive quantitative proteomic analysis revealed a wide and prominent effect of yvmB deletion on proteins involved in cellular processes depending on iron availability. In addition, expression of yvmB depends on iron availability. Further analysis with real-time in vivo transcriptional profiling allowed us to define the YvmB regulon. We identified yvmBA, yvmC-cypX and yvnB for negative regulation and yisI for positive regulation. In combination with genetic approaches, gel mobility shift assays indicated that a 14-bp palindromic motif constitutes the YvmB binding site. It was unexpected that YvmB controls expression of yisI, whose encoding protein plays a negative role in the regulation of the sporulation initiation pathway. YvmB appears as an additional regulatory element into the cell’s decision to grow or sporulate.
Our findings reveal a possible role of the B. subtilis YvmB regulator in the regulatory networks connected to iron metabolism and to the control of proper timing of sporulation. YvmB was renamed as PchR controlling the pulcherriminic acid biosynthetic pathway of B. subtilis.
Cyclodipeptides and their derivatives constitute a large class of secondary metabolites that are mainly synthesized by microorganisms. The biological role of theses peptide natural products is mostly unknown but such compounds are of interest due to their potential antibacterial, antifungal, antitumoral or antiinflammatory activities. Cyclodipeptides from Pseudomonas aeruginosa exhibit cytotoxic properties towards human tumor cells , albonoursin produced by Actinomyces tumemacerans present antibacterial activities [2–4] whereas mycocyclosin may be essential for Mycobacterium tuberculosis viability [5, 6]. Some yeasts and bacterial Bacillus species synthesize pulcherriminic acid that is derived from cyclo-L-leucyl-L-leucyl (cLL) [7–10]. Pulcherriminic acid is secreted in the growth medium and chelates ferric ions by a non-enzymatic reaction to form an extracellular red pigment, the pulcherrimin. In Metschnikowia pulcherrimina strains, pulcherrimin appears to be involved in their antagonistic effects on the other microorganisms by depletion of iron in the growth medium [11–13]. In Bacillus subtilis, the enzymes involved in pulcherriminic acid synthesis were more recently identified. The cyclodipeptide synthase YvmC utilizes charged leucyl tRNAs as substrate to catalyze the formation of cLL [14, 15]. The gene downstream of yvmC, cypX, encodes a cytochrome P450, which is implicated in transformation of cLL into pulcherriminic acid .
The extended bacterial MarR family of transcriptional regulators is involved in the regulation of various cellular processes such as regulation of response to antibiotics, aromatic compounds and oxidative stress agents [17–22]. They can also play a crucial role in virulence factor production, enabling the pathogenic bacteria to adapt to host environments [23–26]. The majority of MarR family members have been characterized as transcriptional repressors although a few examples of transcriptional activators have also been reported [27–29]. They function as homodimers and bind inverted repeat nucleic sequence [30–32]. A genomic locus generally consists of divergently oriented genes encoding the MarR homolog and the gene(s) under its control. By binding to a specific site in the intergenic regions between divergently transcribed genes, the MarR homolog represses transcription of both . Another defining feature of MarR homologs is their response to specific ligands. In absence of ligand, specific DNA binding occurs, most often resulting in repression of the transcription, while binding of the ligand results in attenuated DNA binding and hence de-repressed gene expression . For many MarR-type homologues, as well as for many transcription factors, the natural ligand is still unknown.
The objective of this study was to identify the mechanisms of regulation of the pulcherriminic acid biosynthetic pathway in the soil bacterium B. subtilis. We demonstrated that the uncharacterized B. subtilis YvmB MarR-type regulator is the major regulator controlling expression of the yvmCcypX operon. In combination with genetic approaches, gel mobility shift assays allowed us to define a palindromic motif that constitutes the YvmB-binding site. We also characterized the YvmB regulon, which is composed of four transcriptional units. In addition, a comprehensive quantitative proteomic analysis showed significant repercussions of yvmB deletion for proteins associated to various cellular processes such as metabolism, translation, stress response and biosynthesis of cell wall.
Identification of YvmB as repressor of yvmC-cypX and yvmBA
Pairwise alignment of the amino acid sequence of YvmB with proteins from databases, reveals similarity in the secondary structures between YvmB and other characterized MarR regulators (Additional file 1: Figure S1).
Bacillus subtilis strains used in this study
(Nicolas et al. 2012 )
trpC2 cypX’::lacZ erm
amyE::pyvmB’-lacZ cat ΔyvmB::aphA3
amyE::pyvmB’-lacZ cat ΔccpA::spc
amyE::pAyvmC’-lacZ cat ΔyvmB::aphA3
trpC2 cypX’::lacZ erm ΔyvmB::aphA3
amyE::pA*yvmC’-lacZ cat ΔyvmB::aphA3
amyE::pCyvmC’-lacZ cat ΔyvmB::aphA3
amyE::pByvmC’-lacZ cat ΔyvmB::aphA3
yvnB’-luc cat ΔyvmB::aphA3
yisI’-luc cat ΔyvmB::aphA3
Expression of yvmB is repressed by CcpA in stationary growth phase
Expression of yvmB was proposed to be subject to repression by glucose by direct binding of the carbon metabolism regulator CcpA to a cre site, which overlaps the −35 region . Therefore, we investigated expression of the yvmB-promoter-lacZ fusion in a ccpA mutant. Expression of yvmB was up-regulated in ΔccpA cells upon the stationary growth phase (Fig. 3c). This result confirmed that CcpA acts as negative regulator of yvmB expression. Therefore, yvmB expression undergoes a dual regulation by YvmB and CcpA depending on growth phase.
Transcription of yvmB is induced by iron starvation
Pulcherriminic acid is known to be secreted in the growth medium and to chelate ferric ions. Here, we examined the effect of iron starvation on cypX::lacZ expression. The BFS815 strain (Table 1) was cultivated in LB medium and a sample was spread onto solid medium containing X-gal. A drop of 10 mM bipyridyl, a specific iron chelator, was deposited at the center of the plate. After incubation, a white ring was observed around the bipyridyl drop (Additional file 2: Figure S2) which indicates that iron starvation does not induce yvmC-cypX expression. We further tested the effect of iron starvation on the yvmB-promoter-lacZ fusion (strain BSAS108) using the same experimental procedure. Remarkably, a characteristic blue ring was observed around the bipyridyl drop (Additional file 2: Figure S2) indicating that iron deficiency induces yvmB expression.
Effect of yvmB deletion on B. subtilis proteome
Proteins up- or down-regulated in a B. subtilis yvmB mutant
ΔyvmB vs wta
Carbon metabolism and transport
Citrate synthase 2
Phosphocarrier protein HPr of the PTS
Iron metabolism/electron transport/respiration
Cytochrome P450, cLL dipeptide oxidase
FeS cluster assembly protein
Putative NADH dehydrogenase
Amino acid/nitrogen/nucleotides metabolism
CTP synthase (NH3, glutamine)
Purine nucleoside phosphorylase
Cell wall synthesis/lipid metabolism
Similar to tetrahydrodipicolinate succinylase
Enoyl-[acyl-carrier-protein] reductase [NADH]
50S ribosomal protein L7/L12
30S ribosomal protein S8
Transcription factor and their control
MRP family regulator
Cold-shock protein, molecular chaperone
putative Pit accessory protein
DNA-binding protein HU 1
Proteomic analysis of a yvmB mutant confirmed a 24- and 13-fold enhanced production of the YvmB primary targets, CypX and YvmA. It also revealed a wide and prominent effect on proteins associated with carbon metabolism, translation, stress response and biosynthesis of cell wall. Remarkably, several of these proteins have a function related to metal ions metabolism. Shifts in metabolic pathways particularly occur in response to iron availability [35, 36]. CitB and CitZ are down-regulated in a yvmB mutant. Both proteins are known to be less synthesized under conditions of iron limitation [37–39]. Moreover, the down-regulated ribosomal proteins RplL and RpsH belong to the stringent response, which could be initiated by iron limitation . Iron participates in many metabolic processes related to electron transfer and redox state of the cell, as well as to pH homeostasis [36, 41]. Interestingly, proteins involved in FeS cluster assembly and in respiration, like SufD and Ndh, respectively, are more abundant in a yvmB mutant. In the same line, a yvmB mutant shows increased level of the ferredoxin-dependent reductase YumC, which is involved in electron transport. The up-regulated protein KatA is part of the iron-dependent peroxide stress response mediated by PerR, which is activated when aerobically growing cells enter the stationary phase . Most of the PerR regulon was shown to be repressed when cells are exposed to high levels of iron . Up-regulated MurAA, YkuQ and PgcA are related to cell wall synthesis and lipid biosynthesis. Membrane structure remodeling can result from interaction of ferric ion with external membrane phospholipids bilayer [43–45]. Therefore, deletion of yvmB induces disruptions of proteins involved in cellular processes that depend on iron availability.
Determination of the YvmB recognition site in the yvmC promoter
Detection of several regions involved in the control of yvmB by YvmB
A second set of luc fusions was constructed. Expression of the pDyvmB fusion was not detected whereas the pEyvmB fusion was 10-fold up-regulated in entry to stationary phase (Fig. 6b). Therefore, the −60 to −23 region was also involved in yvmB repression. Remarkably, this region overlaps a 60-bp imperfect palindromic sequence that we named palindrome II (Fig. 6c). The short pFyvmB fusion, without palindrome I nor palindrome II, was fully depressed in entry to stationary phase (Fig. 6b) showing a cumulative repressive effect of palindromes I and II. Remarkably, the pFyvmB fusion yielded a very high and transient induction probably due to the repressive effect of CcpA in stationary phase, as shown above (Fig. 3c).
Definition of a YvmB box consensus and prediction of YvmB boxes within the whole-genome sequence
We used this YvmB box consensus to search putative YvmB boxes within the B. subtilis whole-genome sequence, less than 500 bp upstream of a translational start and in a define promoter region according to Nicolas et al. . This allowed the identification of 5 highly similar motifs preceding the yckD, yisI, yvnB, yxnA and ndhF genes (Fig. 7b). The corresponding proteins were not detected in our proteomic analysis. However, we assumed that YvmB could be involved in the transcriptional regulation of these 5 genes. By contrast, no evident YvmB box-like motif was detected upstream of the transcriptional units encoding proteins differentially abundant in the yvmB mutant suggesting an indirect effect of yvmB deletion.
Interaction of YvmB with the yvmB, yvnB and yisI promoter regions
His-tagged YvmB protein was overproduced in E. coli and purified in a single step by Ni-chelate affinity chromatography to greater than 95 % homogeneity, as revealed by SDS-PAGE (Additional file 6: Figure S4). A sample of the purified protein was fractionated by chromatography on a gel-filtration column. The YvmBHis-tag protein eluted as a major peak with an apparent molecular mass of 45 ± 5 kDa (Additional file 6: Figure S4). As the YvmBHis-tag polypeptide has a molecular mass of 19.2 kDa, this means that the native protein is most likely a dimer.
Gel shift assays were also performed with a DNA fragment corresponding to the yvnB, yisI, yxnA, ndhF, yckD promoter regions (Additional file 7: Table S3). Fragments (110 bp long) carrying putative YvmB boxes in the centre were subjected to gel retardation analysis with YvmBHis-tag. No interaction was detected with probes corresponding to yxnA, ndhF and yckD promoter regions (data not shown). Binding of YvmBHis-tag to the P-yvnB and P-yisI probes resulted in shifts, for which we determined the apparent dissociation constant at 25 nM and 2.5 nM, respectively (Fig. 8c and d). It should be noted that a minor second protein-DNA complex formed in the presence of 100 nM YvmBHis-tag and probe P-yvnB. This could be due to the presence of a degenerated YvmB motif (GTTTACTGGGTAAT) located 119 bp upstream of yvnB. To conclude, the predicted YvmB box upstream of yvnB and yisI appears functional for YvmB binding in vitro. We assumed that YvmB could be involved in the transcriptional regulation of yisI and yvnB.
Dual role of YvmB as repressor of yvnB and as activator of yisI
We also tested the activity of YvmB as transcriptional regulator of the yisI gene, which encodes a protein involved in the sporulation process. We constructed a transcriptional fusion between the promoter region of yisI and the luciferase gene in wild-type and ΔyvmB cells. Expression of the yisI fusion is 2-fold down-regulated in ΔyvmB cells in the stationary growth phase in LB and DSM media (Fig. 9c and d). Thus, YvmB positively regulates yisI expression.
Subsequently, we used the MEME standard bioinformatic method  to redefine the YvmB box consensus from the YvmB box sequences upstream of the yvmB, yvmC, yvnB and yisI promoter regions. The resulting new YvmB consensus sequence exhibited an inverted repeat sequence with highly conserved nucleotides at the external positions 1, 2, 3, 12, 13 and 14 and in the mid-positions 5 and 6 (Fig. 7c).
In this study, we identified the B. subtilis YvmB uncharacterized MarR-like protein as the main negative regulator of the pulcherriminic acid biosynthetic pathway. To our knowledge, this is the first report of the molecular and genetic mechanisms involved in the regulation of this pathway in microorganisms. Our genetic analysis, gel-shift assays and computational analysis highlight a 14-bp core perfect inverted repeat, which likely defines the YvmB binding site in the yvmC-cypX operator region. This motif overlaps the −10 promoter element of the yvmC target gene, as previously described for MarR-type regulators DNA-binding sites . In addition, our work led to the identification of the YvmB regulon, which extends to yvmBA (divergent from yvmC), yvnB and yisI genes. A sequence analysis of the YvmB boxes using the MEME suite produced a consensus composed of highly conserved nucleotides at the external positions 1, 2, 3, 12, 13 and 14 and at the mid-positions 5 and 6 (Fig. 7c). As these nucleotides are also present in the unbound YvmB boxes preceding the yckD, yxnA and ndhF genes, the local sequence environment might also be important for the specific DNA binding of YvmB.
The regulation of yvmB expression is complex since the activity of its promoter is modulated by at least two transcriptional regulators, CcpA and YvmB. CcpA seems to act as repressor of yvmB expression in the stationary growth phase while YvmB represses its own expression. Autoregulation is a characteristic of the MarR-like repressor . We showed that YvmB binds specifically to three regions containing a YvmB box. The three YvmB boxes play a cumulative effect in yvmB repression. In addition, preliminary analysis of the purified YvmBHis-tag protein by analytical chromatography suggests that YvmB is a dimer in the absence of the effector. The nature of the metabolite controlling YvmB repressor activity by binding to DNA remains to be clarified. Remarkably, expression of yvmB is also up-regulated in response to iron starvation. Our results support the existence of an auxiliary transcriptional mechanism, independent of YvmB, to control yvmB expression in response to iron availability.
An unexpected finding is the activation of the yisI gene by YvmB during entry into the stationary growth phase. To our knowledge there are few examples of MarR-like regulator showing a dual role as a repressor and an activator . Remarkably, the YisI protein is an aspartyl-phosphate phosphatase, which specifically dephosphorylates the sporulation transcription factor Spo0A-P and negatively regulates the sporulation initiation pathway in order to control the proper timing of sporulation . It is known that the yisI gene is expressed mainly during the transition phase between exponential and stationary phase, its induction is dependent upon the presence of Spo0A . By our proteomic analysis, two proteins of the Spo0A regulon are induced in a yvmB mutant. These are represented by the RocD ornithine aminotransferase and the Tkt transketolase, which might be due to a difference in phosphorylated/unphosphorylated form of the Spo0A regulator in a yvmB mutant. Therefore, YvmB appears an additional regulatory element into the cell’s decision to grow or sporulate. A database search revealed that yvmBA, yvmC-cypX and yisI genes are present in B. licheniformis and Bacillus thuringiensis, suggesting the functional conservation of the role of YvmB in pulcherriminic acid synthesis and in sporulation in other Bacilli.
The exact role of pulcherriminic acid produced by B. subtilis is still unclear. Expression of yvmC-cypX is not up-regulated in response to iron deficiency in agreement with Kupfer et al., who showed that similar amounts of pulcherriminic acid were detected in the presence of both low and high concentrations of ferric ions . Since pulcherrimin is a large nondiffusible complex [8, 9, 49], mechanism of iron depletion is different from the mechanisms operating in microbes that release siderophores into the environment for iron acquisition. Our comprehensive quantitative proteomic analysis revealed that yvmB deletion induces changes of proteins involved in cellular processes depending on iron availability. However, we did not identify evident YvmB-box motifs upstream of the transcriptional units encoding these proteins. We assume that chelation of external iron by pulcherriminic acid could disrupt iron-dependent processes that can explain the wide indirect cellular changes into ΔyvmB cells.
Here, we demonstrated that YvmB controls expression of the yvmA and yvnB genes, which encodes a putative permease and a putative metallophosphatase, respectively. In M. pulcherrimina, pulcherrimin is involved in antimicrobial effects by depletion of iron in the growth medium [11–13]. M. pulcherrimina also secretes lytic enzymes such as chitinase that may contribute to the overall antagonistic effects of related M. pulcherrimina strains . The role of YvmA and YvnB in potential antagonist effects of pulcherrimin produced by B. subtilis deserve further studies.
This study allowed to identify the mechanism of regulation of the genes involved in the biosynthesis of pulcherriminic acid in B. subtilis. We identified the uncharacterized YvmB MarR-like protein as the main regulator of the yvmCcypX operon. Additionally, we defined the YvmB regulon comprising at least four transcriptional units. Our results also highlight a complex impact of YvmB on cellular processes depending on iron availability and on the regulation of the initiation of sporulation. Further studies will be required to investigate the role of the genes controlled by YvmB.
Bacterial strains and growth conditions
The B. subtilis strains used in this work are listed in Table 1. B. subtilis strains are derivatives of the BaSysBio reference strain BSB1 which is a tryptophan-prototrophic (trp+) 168 strain . Escherichia coli strains used were TG1 (Lab strain) for plasmid construction and ER2566 (New England Biolabs) for protein expression and purification. B. subtilis cells were grown in Luria-Bertani (LB) medium or in MS medium containing 62 mM K2HPO4, 44 mM KH2PO4, 17 mM trisodium citrate, 11 mM K2SO4, 0.4 % glucose, 0.06 % L-glutamine, 0.01 % L-tryptophane, 0.1 % casamino acids, 2 mM MgSO4, 1 mM CaCl2, 100 μM FeCl3 citrate, 112 μM ZnCl2; 5 μM MnCl2; 2.5 μM CuCl2. E. coli cells were propagated in LB medium. Antibiotics were added at the following concentrations when required: 100 μg ampicillin ml−1; 5 μg chloramphenicol ml−1; 100 μg spectinomycin ml−1; 5 μg kanamycin ml−1; 10 μg erythromycin ml−1. Solid media were prepared by addition of 20 g Agar noble l−1 (Difco). Standard procedures were used to transform E. coli  and B. subtilis .
The loss of amylase activity was detected as described by Stülke et al. . β-galactosidase specific activity was measured as described by Miller  with cell extracts obtained by lysozyme treatment. One unit of β-galactosidase activity was defined as the amount of enzyme that produces 1 nmol o-nitrophenol min−1 at 28 °C. The mean values of three independent experiments are presented. Standard deviations were less than 20 % of the mean.
DNA manipulations and cloning procedures were performed as described elsewhere . Restriction enzymes, Pfu DNA polymerase and phage T4 DNA ligase were used as recommended by the manufacturer (Biolabs). DNA fragments were purified from agarose gels using the QIAquick kit (Qiagen).
Construction of plasmids and strains
The BSAS82 yvmB mutant was constructed by homologous replacement of the YvmB coding sequence with a kanamycin resistance gene (aphA3) using a joining PCR technique . The aphA3 gene was first amplified. The region upstream of the yvmB gene (nucleotide −990 to +52 relative to the translational start site) was amplified by PCR with a 24 bp aphA3 fragment at its 3′ end. The region downstream of yvmB (nucleotides +421 to +1495) was amplified with a 24 bp aphA3 fragment at its 5′ end. The three DNA fragments were combined and then a PCR reaction was performed with the two external oligonucleotides. The final product, corresponding to the two regions flanking yvmB with the inserted aphA3 cassette in between, was purified from a gel and used to transform B. subtilis. Integration and deletion were confirmed by PCR and verified by DNA sequencing.
The inactivation of the cypX locus while creating a lacZ fusion (strain BFS815) was done within the framework of a European project on the functional analysis of the genome of B. subtilis (see http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi).
Plasmid pAC6  allowed the construction of a transcriptional fusion between the promoter region of yvmB (nucleotides −291 to +9 relative to the translational start site) and the promoterless lacZ gene. The yvmB promoter region was amplified by PCR, with the creation of EcoRI and BamHI sites. The PCR product was inserted into pAC6. The resulting plasmid was linearized with ScaI, which allowed the insertion of the transcriptional lacZ fusion as a single copy at the amyE locus (Table 1). The same procedure was used to construct a series of transcriptional fusions between the promoter region of yvmC and the lacZ gene.
To construct transcriptional fusions between the promoter region of yvmB, yvnB and yisI and the luc reporter gene, we used the assembly Gibson’s procedure  as previously described . The PUC18cm-luc plasmid was used as template to amplify the luc reporter gene. The sequences of the resulting constructs were verified by DNA sequencing.
For the detection of luciferase activity, strains were first grown in LB medium to an optical density at 600 nm (OD600) of 2. Cells were then centrifuged and resuspended in fresh minimal medium, adjusting all the cultures to an OD600 of 2. These pre-cultures were then diluted 20 fold in fresh minimal medium and 200 μl was distributed in each of two wells in a 96-well black plate (Corning). 10 μl of luciferin were added to each well to reach a final concentration of 1.5 mg/ml (4.7 mM). The cultures were incubated at 37 °C with agitation in a PerkinElmer Envision 2104 Multilabel Reader equipped with an enhanced sensitivity photomultiplier for luminometry. The temperature of the clear plastic lid was maintained at 38 °C to avoid condensation. Relative Luminescence Unit (RLU) and OD600 were measured at 5 min intervals.
Four independent cultures of each B. subtilis strains were grown in 500 mL of LB medium to an OD600 of 0.8. Cultures were harvested by centrifugation (6000 × g, 10 min, 4 °C) and washed twice with a cold low-salt buffer (150 mM NaCl, 10 mM Tris, 0.5 mM EDTA, pH 7.5). Resuspended bacteria were mechanically disrupted by a passage through a One Shot Cell Disrupter (Constant Systems Ltd., Warwickshire, UK) at 2.7 Kbar. Cell lysates were centrifuged (27 000 × g, 20 min, 4 °C) and resulting supernatants were treated to ultracentrifugation (100 000 × g, 1 h, 4 °C). Cytoplasmic fractions were considered as the soluble parts after a single ultracentrifugation step, while the remaining pellets were designated as crude membrane fraction. After resuspension in Bis-Tris NaCl buffer (50 mM bis-tris, 50 mM NaCl, pH7.2) followed by ultra-centrifugation (100 000 × g, 1 h, 4 °C), pellets were resuspended overnight in 150 μL resuspension buffer (20 mM Tris–HCl, 10 mM EDTA, pH7.5) and then added of 1 volume of SDS-PAGE sample buffer (125 mM Tris–HCl pH6.8, 20 % v/v glycerol, 10 % w/v SDS, 5 % β-mercaptoethanol). Protein concentration was determined by NanoDrop. All the samples were loaded on a 10 % NuPAGE Bis-Tris Gels (Invitrogen).
Tryptic digestion in gel
All Coomassie-stained protein sample detected on SDS-PAGE were cut in small pieces and washed twice with 0.2 % TFA-50 % acetonitrile. The protein disulfide bridges were reduced by DTT 10 mM for one hour at 56 °C and resulting reduced cysteine were alkylated by iodoacetamide (50 mM) for 1 h at room temperature into darkness before the step of enzymatic digestion performed by adding 500 ng of sequencing grade modified trypsin (Promega) diluted in 25 mM NH4HCO3 for 18 h at 37 °C for each protein sample. Tryptic peptides were recovered by washing the gel pieces twice in 0.2 % TFA-50 % acetonitrile and once in 100 % acetonitrile and the supernatant was evaporated to dryness. The peptides were then resuspended in 25 μL of precolumn loading buffer (0.05 % trifluoroacetic acid (TFA) and 5 % acetonitrile (ACN) in H2O), prior to LC-MS/MS analysis.
Peptide and protein identification
LC-MS/MS analysis was performed NanoLC-Ultra Eksigent (SCIEX) system connected to Q-Exactive mass spectrometer (ThermoFisher) by nanoelectrospray ion source. Tryptic peptide mixtures (4 μl) were loaded at flow rate 7.5 μl min−1 onto precolumn Biosphere C18, 5 μm, 20 mm, 100 μm i.d.; NanoSeparations, Nieuwkoop, NL). After 3 min, the precolumn was connected with the separating nanocolumn PepMap100C18, 3 μm, 500 mm, 75 μm i.d.; Dionex), and the linear gradient was started from 5 to 35 % of buffer B (0.1 % formic acid, 100 % acetonitrile) in buffer A (0.1 % formic acid, 5 % acetonitrile) at 300 nl min−1 during 120 min for a running time of 130 min with washing and equilibration steps. Ionization was performed on liquid junction with a spray voltage of 1.5 kV applied to an uncoated capillary probe (PicoTip EMITER 10-μm tip inner diameter; New Objective). Peptides ions were automatically analyzed in positive mode by the data-dependent method as follows: full MS scan (m/z 400 to 1400, resolution 70,000 at m/z 400) and MS/MS on the 12 most abundant precursors (resolution 17,500 at m/z 400). In the present study only +2 and +3 charged peptides were subjected to MS/MS experiments with an exclusion window of 40 sec, in HCD fragmentation mode with a normalized collision energy fixed to 26 %. The lock mass option was activated on m/z dimethylcyclosiloxan 445.12003.
The raw data produced on Q-Exactive mass spectrometer were first converted in mzXML file with msconvert (http://proteowizard.sourceforge.net, version 3.0.3706), and protein identification was performed with X!Tandem software (X! Tandem Sledgehammer 2013.09.01.1; http://www.thegpm.org) against a protein database of B. subtilis 168 (downloaded to ftp://ftp.ebi.ac.uk/pub/databases/integr8/last_release/fasta/proteomes contain 4253 proteins associated to a classical proteomic contaminant database). The X!Tandem search parameters were as follows: trypsin specificity with two missed cleavage, fixed alkylation of cysteine (+57.0215), and variable oxidation of methionine (+15.9949). The mass tolerance was fixed to 10 ppm for precursor ions and 0.02 Da for fragment ions. For all proteins identified with a protein E-value of < 0.01 in the first step, we searched for additional peptides to reinforce identification using similar parameters except that semitryptic peptides and protein N-terminal acetylations were accepted. All results for each analysis were merged with an homemade program written in java: (X!tandempipeline version 3.3.1; http://pappso.inra.fr/bioinfo/xtandempipeline/). The final search results were filtered by using a multiple threshold filter applied at the protein level and consisting of a Log10 protein E-value lower than −2.6 identified with a minimum of two different peptides sequences, detected in at least one analysis, with a peptide E-value lower than 0.05.
Relative quantification of peptides and proteins
Control quality of data, normalization, filtration and statistical analysis were performed by using MassChroqR (http://pappso.inra.fr/bioinfo/masschroqr/). The peaks showing a width greater than 100 s or instability in retention time (RT standard deviation greater than 20 s) were filtered out. Only proteins quantified with at least two specific and repeatable peptides were analyzed. Unspecific peptides were discarded. Repeatable peptides were those which were presents in at least 7 of 8 samples. Missing values were imputed by linear regression according to the values of the other peptides of the same protein. Data were normalized to compensate for global variations between LC-MS: for each LC–MS the normalization factor was the median value of the ratios of peptide intensities to their intensity in a reference LC-MS. Protein values were computed by adding the normalized values of their specific and repeatable peptides. The proteins whose number of peaks was significantly different (with a minimum difference of 5 peaks between the mutant and the wild type) were determined by using the Kruskal-Wallis test (Additional file 9: Figure S6, Additional file 10: Figure S7, Additional file 11: Figure S8 and Additional file 12: Figure S9). A one-way ANOVA model was used to analyze changes, with the genotype as a fixed effect. A protein was considered as significantly variable when the p-value was < 0.05 (Additional file 4: Table S2).
Purification of YvmB6His
His-tagged YvmB was over-produced as a soluble protein and purified using plasmid pJ411 (DNA2.0) and E. coli strain ER2566. ER2566 carries a chromosomal copy of the T7 RNA polymerase gene inserted into the lacZ gene, and thus is under the control of the lac promoter. The yvmB gene was amplified by PCR using a forward primer (5′-gggcatatgtctgatttgacaaaacagatg-3′) which contains a 5′ NdeI site and a reverse primer (5′-gggctcgagttaatggtgatggtgatggtgctttacaggtttgtctggagt-3′) which contains a His-tag followed by a XhoI site. The amplified fragment was digested with NdeI/XhoI and ligated NdeI/XhoI digested-pJ411 vector to construct plasmid pJ411-yvmB, which encodes a fusion protein containing YvmB followed by a hexa-his-tag. This plasmid was introduced into E. coli strain ER2566. Transformants were grown in 30 μg kanamycin ml−1 LB medium at 30 °C to an OD600 of 0.8. The expression of the yvmB gene was induced by adding 0.5 mM IPTG (isopropyl-β-D-thiogalactopyranoside). The cells were then incubated for an additional 3 h before they were harvested. The cell pellet was resuspended in 1 M NaCl-50 mM Tris–HCl (pH 8.0) and was broken by sonication (Bioblock Sientific, Vibra-CellTM 72408). The cell lysate was clarified by centrifugation for 90 min. at 40 000 rpm to remove cell debris. Purification was performed by stepwise elution with linear imidazole gradient (20 to 400 mM) from a Ni-affinity column. After sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the fractions, the fraction containing the protein was dialyzed against against 50 mM Tris–HCl (pH 8.0)-0.4 M NaCl-1 mM DTT-50 % glycerol, and stored at −20 °C.
Denaturing gel electrophoresis
The SDS-polyacrylamide gels electrophoresis (PAGE) were 13.5 % acrylamide. The samples were loaded after being mixed with the sample buffer (125 mM Tris–HCl, 10 % glycerol, 0.1 % bromophenol blue, 2 % SDS, 1 mM DTT) with 10 min. boiling at 90 °C. Electrophoresis were done in Tris-Glycine buffer for 4 to 6 h at 15 mA.
Gel mobility shift assay
Sequences of PCR primer pairs are shown in Additional file 7: Table S3. The Cy5 5′-labeled oligodeoxynucleotides were purchased from Eurofins Genomics (Ebersberg, Germany). PCRs were performed on DNA using Ex Taq Polimerase (Takara). Amplified fragments were gel-purified using Wizard Kit (Promega). A further PCR was run using the purified fragment as template. Electrophoretic mobility shift assay was carried out by mixing 50 ng of the desired Cy5-labelled purified DNA with a 5× binding buffer (100 mM Tris pH 8, 0.5 M KCl, 2.5 mM dithiothreitol, 25 mM MgCl2, 0.25 mg/ml BSA, 0.25 mg/ml poly(dIdC)) to a final volume of 20 μL. Different amounts of purified His-tagged YvmB were used in the reactions to obtain a clear shifted DNA band compared to the control without protein. After incubation of the reaction mixture for 20 min at 30 °C, the shift reaction was loaded onto a 6 or 10 % native polyacrylamide gel (depending on the fragment size) and run for 1 h 45 min. at 150 V. The migration of the DNA bands was visualized by a Bio-Rad Chemidoc imager with Image Lab software (Cy5-based blot protocol).
LC-MS/MS analyses were performed on the Plateforme d’Analyse Protéomique de Paris Sud-Ouest (PAPPSO). We are grateful to Stephen McGovern for his technical assistance. We thank Dr Philippe Noirot for the financial support.
This research received funding from the European Union, Marie Curie ITN AMBER, 317338.
Availability of data and materials
All supporting data are included in the main paper and in the additional supporting files.
PR and SA conceived and designed the experiments and analyzed the data. SA drafted the manuscript. AAF and AG participated in the design of the experiments and in the analyses of the data. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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