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Dmitry A Rodionov - One of the best experts on this subject based on the ideXlab platform.
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novel metabolic pathways and Regulons for hexuronate utilization in proteobacteria
Journal of Bacteriology, 2018Co-Authors: J T Bouvier, Natalia V Sernova, Salehe Ghasempur, Irina A Rodionova, Nawar Alobaidi, Matthew W. Vetting, Steven C Almo, John A Gerlt, Dmitry A RodionovAbstract:ABSTRACT We used comparative genomics to reconstruct d-galacturonic and d-glucuronic acid catabolic pathways and associated transcriptional Regulons involving the tripartite ATP-independent periplasmic (TRAP) family transporters that bind hexuronates in proteobacteria. The reconstructed catabolic network involves novel transcription factors, catabolic enzymes, and transporters for utilization of both hexuronates and aldarates (d-glucarate and meso-galactarate). The reconstructed Regulons for a novel GntR family transcription factor, GguR, include the majority of hexuronate/aldarate utilization genes in 47 species from the Burkholderiaceae, Comamonadaceae, Halomonadaceae, and Pseudomonadaceae families. GudR, GulR, and UdhR are additional local regulators of some hexuronate/aldarate utilization genes in some of the above-mentioned organisms. The predicted DNA binding motifs of GguR and GudR regulators from Ralstonia pickettii and Polaromonas were validated by in vitro binding assays. Genes from the GulR- and GguR-controlled loci were differentially expressed in R. pickettii grown on hexuronates and aldarates. By a combination of bioinformatics and experimental techniques we identified a novel variant of the oxidative pathway for hexuronate utilization, including two previously uncharacterized subfamilies of lactone hydrolases (UxuL and UxuF). The genomic context of respective genes and reconstruction of associated pathways suggest that both enzymes catalyze the conversion of d-galactaro- and d-glucaro-1,5-lactones to the ring-opened aldarates. The activities of the purified recombinant enzymes, UxuL and UxuF, from four proteobacterial species were directly confirmed and kinetically characterized. The inferred novel aldarate-specific transporter from the tripartite tricarboxylate transporter (TTT) family transporter TctC was confirmed to bind d-glucarate in vitro. This study expands our knowledge of bacterial carbohydrate catabolic pathways by identifying novel families of catabolic enzymes, transcriptional regulators, and transporters. IMPORTANCE Hexuronate catabolic pathways and their transcriptional networks are highly variable among different bacteria. We identified novel transcriptional regulators that control the hexuronate and aldarate utilization genes in four families of proteobacteria. By Regulon reconstruction and genome context analysis we identified several novel components of the common hexuronate/aldarate utilization pathways, including novel uptake transporters and catabolic enzymes. Two novel families of lactonases involved in the oxidative pathway of hexuronate catabolism were characterized. Novel transcriptional Regulons were validated via in vitro binding assays and gene expression studies with Polaromonas and Ralstonia species. The reconstructed catabolic pathways are interconnected with each other metabolically and coregulated via the GguR Regulons in proteobacteria.
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Comparative genomics and evolution of transcriptional Regulons in Proteobacteria
Microbial genomics, 2016Co-Authors: Semen A Leyn, Inna A. Suvorova, Pavel S. Novichkov, Alexey E Kazakov, Dmitry A. Ravcheev, Vita V. Stepanova, Dmitry A RodionovAbstract:Comparative genomics approaches are broadly used for analysis of transcriptional regulation in bacterial genomes. In this work, we identified binding sites and reconstructed Regulons for 33 orthologous groups of transcription factors (TFs) in 196 reference genomes from 21 taxonomic groups of Proteobacteria. Overall, we predict over 10 600 TF binding sites and identified more than 15 600 target genes for 1896 TFs constituting the studied orthologous groups of regulators. These include a set of orthologues for 21 metabolism-associated TFs from Escherichia coli and/or Shewanella that are conserved in five or more taxonomic groups and several additional TFs that represent non-orthologous substitutions of the metabolic regulators in some lineages of Proteobacteria. By comparing gene contents of the reconstructed Regulons, we identified the core, taxonomy-specific and genome-specific TF Regulon members and classified them by their metabolic functions. Detailed analysis of ArgR, TyrR, TrpR, HutC, HypR and other amino-acid-specific Regulons demonstrated remarkable differences in regulatory strategies used by various lineages of Proteobacteria. The obtained genomic collection of in silico reconstructed TF Regulons contains a large number of new regulatory interactions that await future experimental validation. The collection provides a framework for future evolutionary studies of transcriptional regulatory networks in Bacteria. It can be also used for functional annotation of putative metabolic transporters and enzymes that are abundant in the reconstructed Regulons.
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Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota
Journal of Bacteriology, 2015Co-Authors: Semen A Leyn, Irina A Rodionova, Dmitry A RodionovAbstract:ABSTRACT Autotrophic microorganisms are able to utilize carbon dioxide as their only carbon source, or, alternatively, many of them can grow heterotrophically on organics. Different variants of autotrophic pathways have been identified in various lineages of the phylum Crenarchaeota. Aerobic members of the order Sulfolobales utilize the hydroxypropionate-hydroxybutyrate cycle (HHC) to fix inorganic carbon, whereas anaerobic Thermoproteales use the dicarboxylate-hydroxybutyrate cycle (DHC). Knowledge of transcriptional regulation of autotrophic pathways in Archaea is limited. We applied a comparative genomics approach to predict novel autotrophic Regulons in the Crenarchaeota. We report identification of two novel DNA motifs associated with the autotrophic pathway genes in the Sulfolobales (HHC box) and Thermoproteales (DHC box). Based on genome context evidence, the HHC box Regulon was attributed to a novel transcription factor from the TrmB family named HhcR. Orthologs of HhcR are present in all Sulfolobales genomes but were not found in other lineages. A predicted HHC box regulatory motif was confirmed by in vitro binding assays with the recombinant HhcR protein from Metallosphaera yellowstonensis. For the DHC box Regulon, we assigned a different potential regulator, named DhcR, which is restricted to the order Thermoproteales. DhcR in Thermoproteus neutrophilus (Tneu_0751) was previously identified as a DNA-binding protein with high affinity for the promoter regions of two autotrophic operons. The global HhcR and DhcR Regulons reconstructed by comparative genomics were reconciled with available omics data in Metallosphaera and Thermoproteus spp. The identified Regulons constitute two novel mechanisms for transcriptional control of autotrophic pathways in the Crenarchaeota. IMPORTANCE Little is known about transcriptional regulation of carbon dioxide fixation pathways in Archaea. We previously applied the comparative genomics approach for reconstruction of DtxR family Regulons in diverse lineages of Archaea. Here, we utilize similar computational approaches to identify novel regulatory motifs for genes that are autotrophically induced in microorganisms from two lineages of Crenarchaeota and to reconstruct the respective Regulons. The predicted novel Regulons in archaeal genomes control the majority of autotrophic pathway genes and also other carbon and energy metabolism genes. The HhcR Regulon was experimentally validated by DNA-binding assays in Metallosphaera spp. Novel Regulons described for the first time in this work provide a basis for understanding the mechanisms of transcriptional regulation of autotrophic pathways in Archaea.
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Comparative Genomics of Transcriptional Regulation of Methionine Metabolism in Proteobacteria
PLOS ONE, 2014Co-Authors: Semen A Leyn, Inna A. Suvorova, Tatiana D. Kholina, Sofia S. Sherstneva, Pavel S. Novichkov, Michael S Gelfand, Dmitry A RodionovAbstract:Methionine metabolism and uptake genes in Proteobacteria are controlled by a variety of RNA and DNA regulatory systems. We have applied comparative genomics to reconstruct Regulons for three known transcription factors, MetJ, MetR, and SahR, and three known riboswitch motifs, SAH, SAM-SAH, and SAM_alpha, in ∼200 genomes from 22 taxonomic groups of Proteobacteria. We also identified two novel Regulons: a SahR-like transcription factor SamR controlling various methionine biosynthesis genes in the Xanthomonadales group, and a potential RNA regulatory element with terminator-antiterminator mechanism controlling the metX or metZ genes in beta-proteobacteria. For each analyzed regulator we identified the core, taxon-specific and genome-specific Regulon members. By analyzing the distribution of these regulators in bacterial genomes and by comparing their Regulon contents we elucidated possible evolutionary scenarios for the regulation of the methionine metabolism genes in Proteobacteria.
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Comparative Genomics of DtxR Family Regulons for Metal Homeostasis in Archaea
Journal of Bacteriology, 2014Co-Authors: Semen A Leyn, Dmitry A RodionovAbstract:The DtxR family consists of metal-dependent transcription factors (DtxR-TFs) that regulate the expression of genes involved in metal homeostasis in the cell. The majority of characterized DtxR-TFs belong to Bacteria. In the current work, we applied a comparative genomics approach to predict DNA-binding sites and reconstruct Regulons for DtxR-TFs in Archaea. As a result, we inferred 575 candidate binding sites for 139 DtxR-TFs in 77 genomes from 15 taxonomic orders. Novel DNA motifs of archaeal DtxR-TFs that have a common palindromic structure were classified into 10 distinct groups. By combining functional Regulon reconstructions with phylogenetic analysis, we selected 28 DtxR-TF clades and assigned them metal specificities and regulator names. The reconstructed FetR (ferrous iron), MntR (manganese), and ZntR (zinc) Regulons largely contain known or putative metal uptake transporters from the FeoAB, NRAMP, ZIP, and TroA families. A novel family of putative iron transporters (named Irt), including multiple FetR-regulated paralogs, was identified in iron-oxidizing Archaea from the Sulfolobales order. The reconstructed DtxR-TF Regulons were reconciled with available transcriptomics data in Archaeoglobus, Halobacterium, and Thermococcus spp.
Mikhail S Gelfand - One of the best experts on this subject based on the ideXlab platform.
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Comparative genomics and evolution of Regulons of the LacI-family transcription factors
Frontiers in Microbiology, 2014Co-Authors: Dmitry A. Ravcheev, Natalia V Sernova, Pavel S. Novichkov, Olga N Laikova, Mikhail S Gelfand, Matvei S. Khoroshkin, Olga V. Tsoy, Svetlana A. Petrova, Aleksandra B. Rakhmaninova, Dmitry A RodionovAbstract:DNA-binding transcription factors (TFs) are essential components of transcriptional regulatory networks in Bacteria. LacI-family TFs (LacI-TFs) are broadly distributed among certain lineages of bacteria. The majority of characterized LacI-TFs sense sugar effectors and regulate carbohydrate utilization genes. The comparative genomics approaches enable in silico identification of TF-binding sites and Regulon reconstruction. To study function and evolution of LacI-TFs, we performed genomics-based reconstruction and comparative analysis of their Regulons. For over 1,300 LacI-TFs from over 270 bacterial genomes, we predicted their cognate DNA-binding motifs and identified target genes. Using the genome context and metabolic subsystem analyses of reconstructed Regulons we tentatively assigned functional roles and predicted candidate effectors for 78% and 67% of the analyzed LacI-TFs, respectively. Nearly 90% of the studied LacI-TFs are local regulators of sugar utilization pathways, whereas the remaining 125 global regulators control large and diverse sets of metabolic genes. The global LacI-TFs include the previously known regulators CcpA in Firmicutes, FruR in Enterobacteria, and PurR in Gammaproteobacteria, and the three novel regulators, GluR, GapR, and PckR, that are predicted to control the central carbohydrate metabolism in three lineages of Alphaproteobacteria. Phylogenetic analysis of regulators combined with the reconstructed Regulons provides a model of evolutionary diversification of LacI-TFs. The obtained genomic collection of in silico reconstructed Regulons in Bacteria is available in the RegPrecise database (http://regprecise.lbl.gov). It provides a framework for future structural and functional classification of the LacI protein family and identification of molecular determinants of the DNA and ligand specificity. The inferred Regulons can be also used for functional gene annotation and reconstruction of sugar catabolic networks in diverse bacteria.
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Genome-Wide Analysis of Cell Type-Specific Gene Transcription during Spore Formation in Clostridium difficile
PLoS Genetics, 2013Co-Authors: Laure Saujet, Mikhail S Gelfand, Fátima C Pereira, Monica Serrano, Olga Soutourina, Marc Monot, Pavel V Shelyakin, Bruno Dupuy, Adriano O Henriques, Isabelle Martin-verstraeteAbstract:Clostridium difficile, a Gram positive, anaerobic, spore-forming bacterium is an emergent pathogen and the most common cause of nosocomial diarrhea. Although transmission of C. difficile is mediated by contamination of the gut by spores, the regulatory cascade controlling spore formation remains poorly characterized. During Bacillus subtilis sporulation, a cascade of four sigma factors, s F and s G in the forespore and s E and s K in the mother cell governs compartment-specific gene expression. In this work, we combined genome wide transcriptional analyses and promoter mapping to define the C. difficile s F , s E , s G and s K Regulons. We identified about 225 genes under the control of these sigma factors: 25 in the s F Regulon, 97 s E-dependent genes, 50 s G-governed genes and 56 genes under s K control. A significant fraction of genes in each Regulon is of unknown function but new candidates for spore coat proteins could be proposed as being synthesized under s E or s K control and detected in a previously published spore proteome. SpoIIID of C. difficile also plays a pivotal role in the mother cell line of expression repressing the transcription of many members of the s E Regulon and activating sigK expression. Global analysis of developmental gene expression under the control of these sigma factors revealed deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We showed that the expression of the s E Regulon in the mother cell was not strictly under the control of s F despite the fact that the forespore product SpoIIR was required for the processing of pros E. In addition, the s K Regulon was not controlled by s G in C. difficile in agreement with the lack of pros K processing. This work is one key step to obtain new insights about the diversity and evolution of the sporulation process among Firmicutes.
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Comparative genomics of the dormancy Regulons in mycobacteria.
Journal of Bacteriology, 2011Co-Authors: Anna Gerasimova, Inna Dubchak, Adam Paul Arkin, Alexey E Kazakov, Mikhail S GelfandAbstract:In response to stresses, Mycobacterium cells become dormant. This process is regulated by the DosR transcription factor. In Mycobacterium tuberculosis, the dormancy Regulon is well characterized and contains the dosR gene itself and dosS and dosT genes encoding DosR kinases, nitroreductases (acg; Rv3131), diacylglycerol acyltransferase (DGAT) (Rv3130c), and many universal stress proteins (USPs). In this study, we apply comparative genomic analysis to characterize the DosR Regulons in nine Mycobacterium genomes, Rhodococcus sp. RHA1, Nocardia farcinica, and Saccharopolyspora erythraea. The Regulons are highly labile, containing eight core gene groups (regulators, kinases, USPs, DGATs, nitroreductases, ferredoxins, heat shock proteins, and the orthologs of the predicted kinase [Rv2004c] from M. tuberculosis) and 10 additional genes with more restricted taxonomic distribution that are mostly involved in anaerobic respiration. The largest Regulon is observed in M. marinum and the smallest in M. abscessus. Analysis of large gene families encoding USPs, nitroreductases, and DGATs demonstrates a mosaic distribution of regulated and nonregulated members, suggesting frequent acquisition and loss of DosR-binding sites.
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regpredict an integrated system for Regulon inference in prokaryotes by comparative genomics approach
Nucleic Acids Research, 2010Co-Authors: Pavel S. Novichkov, Adam Paul Arkin, Dmitry A Rodionov, Elena S Novichkova, Mikhail S Gelfand, Elena D Stavrovskaya, Alexey E Kazakov, Andrey A Mironov, Inna DubchakAbstract:RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial Regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of Regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large Regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) Regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel Regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate Regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov.
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regprecise a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
Nucleic Acids Research, 2010Co-Authors: Pavel S. Novichkov, Inna Dubchak, Adam Paul Arkin, Olga N Laikova, Elena S Novichkova, Mikhail S Gelfand, Dmitry A RodionovAbstract:The RegPrecise database (http://regprecise.lbl.gov) was developed for capturing, visualization and analysis of predicted transcription factor Regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic approach. A significant number of highquality inferences of transcriptional regulatory interactions have been already accumulated for diverse taxonomic groups of bacteria. The reconstructed Regulons include transcription factors, their cognate DNA motifs and regulated genes/ operons linked to the candidate transcription factor binding sites. The RegPrecise allows for browsing the Regulon collections for: (i) conservation of DNA binding sites and regulated genes for a particular Regulon across diverse taxonomic lineages; (ii) sets of Regulons for a family of transcription factors; (iii) repertoire of Regulons in a particular taxonomic group of species; (iv) Regulons associated with a metabolic pathway or a biological process in various genomes. The initial release of the database includes 11500 candidate binding sites for 400 orthologous groups of transcription factors from over 350 prokaryotic genomes. Majority of these data are represented by genomewide Regulon reconstructions in Shewanella and Streptococcus genera and a large-scale prediction of Regulons for the LacI family of transcription factors. Another section in the database represents the results of accurate Regulon propagation to the closely related genomes.
John D Helmann - One of the best experts on this subject based on the ideXlab platform.
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bacillus subtilis extracytoplasmic function ecf sigma factors and defense of the cell envelope
Current Opinion in Microbiology, 2016Co-Authors: John D HelmannAbstract:Bacillus subtilis provides a model for investigation of the bacterial cell envelope, the first line of defense against environmental threats. Extracytoplasmic function (ECF) sigma factors activate genes that confer resistance to agents that threaten the integrity of the envelope. Although their individual Regulons overlap, σW is most closely associated with membrane-active agents, σX with cationic antimicrobial peptide resistance, and σV with resistance to lysozyme. Here, I highlight the role of the σM Regulon, which is strongly induced by conditions that impair peptidoglycan synthesis and includes the core pathways of envelope synthesis and cell division, as well as stress-inducible alternative enzymes. Studies of these cell envelope stress responses provide insights into how bacteria acclimate to the presence of antibiotics.
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the bacillus subtilis σm Regulon and its contribution to cell envelope stress responses
Molecular Microbiology, 2008Co-Authors: Warawan Eiamphungporn, John D HelmannAbstract:Summary The Bacillus subtilis extracytoplasmic function (ECF) σM factor is activated by cell envelope stress elicited by antibiotics, and by acid, heat, ethanol and superoxide stresses. Here, we have used several complementary approaches to identify genes controlled by σM. In many cases, expression is only partially dependent on σM because of both overlapping promoter recognition with other ECF σ factors and the presence of additional promoter elements. Genes regulated by σM have a characteristic pattern of induction in response to cell envelope-acting antibiotics as evidenced by hierarchical clustering analysis. σM also contributes to the expression of the Spx transcription factor and thereby indirectly regulates genes of the Spx Regulon. Cell envelope stress responses also include Regulons controlled by σW, σB and several two-component regulatory systems (e.g. LiaRS, YycFG, BceRS). Activation of the σM Regulon increases expression of proteins functioning in transcriptional control, cell wall synthesis and shape determination, cell division, DNA damage monitoring, recombinational repair and detoxification.
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the bacillus subtilis extracytoplasmic function σx factor regulates modification of the cell envelope and resistance to cationic antimicrobial peptides
Journal of Bacteriology, 2004Co-Authors: John D HelmannAbstract:Bacillus subtilis contains seven extracytoplasmic-function σ factors that activate partially overlapping Regulons. We here identify four additional members of the σX Regulon, pbpX (penicillin-binding protein), ywnJ, the dlt operon (d-alanylation of teichoic acids), and the pss ybfM psd operon (phosphatidylethanolamine biosynthesis). Modification of teichoic acids by esterification with d-alanine and incorporation of phosphatidylethanolamine into the cell membrane have a common consequence: in both cases positively charged amino groups are introduced into the cell envelope. The resulting reduction in the net negative charge of the cell envelope has been previously implicated as a resistance mechanism specific for cationic antimicrobial peptides. Consistent with this notion, we find that both sigX and dltA mutants are more sensitive to nisin than wild-type cells. We conclude that activation of the σX Regulon serves to alter cell surface properties to provide protection against antimicrobial peptides.
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defining the bacillus subtilis σw Regulon a comparative analysis of promoter consensus search run off transcription macroarray analysis roma and transcriptional profiling approaches
Journal of Molecular Biology, 2002Co-Authors: Min Cao, Phil A Kobel, Maud M Morshedi, Chris Paddon, John D HelmannAbstract:The Bacillus subtilis extracytoplasmic function (ECF) sigma factor sigma(W) controls a large Regulon that is strongly induced by alkali shock. To define the physiological role of sigma(W) we have sought to identify the complete set of genes under sigma(W) control. Previously, we described a promoter consensus search procedure to identify sigma(W) controlled genes. Herein, we introduce a novel method to identify additional target promoters: run-off transcription followed by macroarray analysis (ROMA). We compare the resulting list of targets with those identified in conventional transcriptional profiling studies and using the consensus search approach. While transcriptional profiling identifies genes that are strongly dependent on sigma(W) for in vivo expression, some sigma(W)-dependent promoters are not detected due to the masking effects of other promoter elements, overlapping recognition with other ECF sigma factors, or both. Taken together, the consensus search, ROMA, and transcriptional profiling approaches establish a minimum of 30 promoter sites (controlling approximately 60 genes) as direct targets for activation by sigma(W). Significantly, no single approach identifies more than approximately 80% of the Regulon so defined. We therefore suggest that a combination of two or more complementary approaches be employed in studies seeking to achieve maximal coverage when defining bacterial Regulons. Our results indicate that sigma(W) controls genes that protect the cell against agents that impair cell wall biosynthesis but fail to reveal any connection to operons likely to function in adaptation to alkaline growth conditions. This is consistent with the observation that a sigW mutant is unaffected in its ability to survive alkali shock. We conclude that in B. subtilis sudden imposition of alkali stress activates the sigma(W) stress response, perhaps by impairing the ability of the cell wall biosynthetic machinery to function.
Fitnat H Yildiz - One of the best experts on this subject based on the ideXlab platform.
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regulation of rugosity and biofilm formation in vibrio cholerae comparison of vpst and vpsr Regulons and epistasis analysis of vpst vpsr and hapr
Journal of Bacteriology, 2007Co-Authors: Sinem Beyhan, Kivanc Bilecen, Sofie R Salama, Catharina Casperlindley, Fitnat H YildizAbstract:Vibrio cholerae undergoes phenotypic variation that generates two morphologically different variants, termed smooth and rugose. The transcriptional profiles of the two variants differ greatly, and many of the differentially regulated genes are controlled by a complex regulatory circuitry that includes the transcriptional regulators VpsR, VpsT, and HapR. In this study, we identified the VpsT Regulon and compared the VpsT and VpsR Regulons to elucidate the contribution of each positive regulator to the rugose variant transcriptional profile and associated phenotypes. We have found that although the VpsT and VpsR Regulons are very similar, the magnitude of the gene regulation accomplished by each regulator is different. We also determined that cdgA, which encodes a GGDEF domain protein, is partially responsible for the altered vps gene expression between the vpsT and vpsR mutants. Analysis of epistatic relationships among hapR, vpsT, and vpsR with respect to a whole-genome expression profile, colony morphology, and biofilm formation revealed that vpsR is epistatic to hapR and vpsT. Expression of virulence genes was increased in a vpsR hapR double mutant relative to a hapR mutant, suggesting that VpsR negatively regulates virulence gene expression in the hapR mutant. These results show that a complex regulatory interplay among VpsT, VpsR, HapR, and GGDEF/EAL family proteins controls transcription of the genes required for Vibrio polysaccharide and virulence factor production in V. cholerae.
Oscar P Kuipers - One of the best experts on this subject based on the ideXlab platform.
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The Regulation of the AdcR Regulon in Streptococcus pneumoniae Depends Both on Zn(2+)- and Ni(2+)-Availability.
Frontiers in Cellular and Infection Microbiology, 2015Co-Authors: Irfan Manzoor, Sulman Shafeeq, Muhammad Afzal, Oscar P KuipersAbstract:By using a transcriptomic approach, we have elucidated the effect of Ni2+ on the global gene expression of S. pneumoniae D39 by identifying several differentially expressed genes/operons in the presence of a high extracellular concentration of Ni2+. The genes belonging to the AdcR Regulon (adcRCBA, adcAII-phtD, phtA, phtB, and phtE) and the PsaR Regulon (pcpA, prtA, and psaBCA) were highly upregulated in the presence of Ni2+. We have further studied the role of Ni2+ in the regulation of the AdcR Regulon by using ICP-MS analysis, electrophoretic mobility shift assays and transcriptional lacZ-reporter studies, and demonstrate that Ni2+ is directly involved in the derepression of the AdcR Regulon via the Zn2+-dependent repressor AdcR, and has an opposite effect on the expression of the AdcR Regulon compared to Zn2+.
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Maltose-Dependent Transcriptional Regulation of the mal Regulon by MalR in Streptococcus pneumoniae.
PLOS ONE, 2015Co-Authors: Muhammad Afzal, Sulman Shafeeq, Irfan Manzoor, Oscar P KuipersAbstract:The maltose Regulon (mal Regulon) has previously been shown to consist of the mal gene cluster (malMP, malXCD and malAR operons) in Streptococcus pneumoniae. In this study, we have further elucidated the complete mal Regulon in S. pneumoniae D39 using microarray analyses and β-galactosidase assays. In addition to the mal gene cluster, the complete mal Regulon of S. pneumoniae D39 consists of a pullulanase (PulA), a glucosidase (DexB), a glucokinase (RokB), a PTS component (PtsG) and an amylase (AmyA2). Our microarray studies and β-galactosidase assays further showed that the LacI-family transcriptional regulator MalR represses the expression of the mal Regulon in the absence of maltose. Furthermore, the role of the pleiotropic transcriptional regulator CcpA in the regulation of the mal Regulon in the presence of maltose was explored. Our microarray analysis with a ΔccpA strain showed that CcpA only represses the expression of the malXCD operon and the pulA gene in the presence of maltose. Hence, we extend the mal Regulon now consisting of pulA, dexB, rokB, ptsG and amyA2 in addition to malMP, malXCD and malAR operons.
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pepper a webserver for prediction of prokaryote promoter elements and Regulons
BMC Genomics, 2012Co-Authors: Anne De Jong, Hilco Pietersma, Martijn Cordes, Oscar P KuipersAbstract:Background: Accurate prediction of DNA motifs that are targets of RNA polymerases, sigma factors and transcription factors (TFs) in prokaryotes is a difficult mission mainly due to as yet undiscovered features in DNA sequences or structures in promoter regions. Improved prediction and comparison algorithms are currently available for identifying transcription factor binding sites (TFBSs) and their accompanying TFs and Regulon members. Results: We here extend the current databases of TFs, TFBSs and Regulons with our knowledge on Lactococcus lactis and developed a webserver for prediction, mining and visualization of prokaryote promoter elements and Regulons via a novel concept. This new approach includes an all-in-one method of data mining for TFs, TFBSs, promoters, and Regulons for any bacterial genome via a user-friendly webserver. We demonstrate the power of this method by mining WalRK Regulons in Lactococci and Streptococci and, vice versa, use L. lactis Regulon data (CodY) to mine closely related species. Conclusions: The PePPER webserver offers, besides the all-in-one analysis method, a toolbox for mining for Regulons, promoters and TFBSs and accommodates a new L. lactis Regulon database in addition to already existing Regulon data. Identification of putative Regulons and full annotation of intergenic regions in any bacterial genome on the basis of existing knowledge on a related organism can now be performed by biologists and it can be done for a wide range of Regulons. On the basis of the PePPER output, biologist can design experiments to further verify the existence and extent of the proposed Regulons. The PePPER webserver is freely accessible at http://pepper.molgenrug.nl.
