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Suvorova IA, Gelfand MS. Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content. Front Microbiol 2021; 12:675815. [PMID: 34177859 PMCID: PMC8222616 DOI: 10.3389/fmicb.2021.675815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
The IclR-family is a large group of transcription factors (TFs) regulating various biological processes in diverse bacteria. Using comparative genomics techniques, we have identified binding motifs of IclR-family TFs, reconstructed regulons and analyzed their content, finding co-occurrences between the regulated COGs (clusters of orthologous genes), useful for future functional characterizations of TFs and their regulated genes. We describe two main types of IclR-family motifs, similar in sequence but different in the arrangement of the half-sites (boxes), with GKTYCRYW3-4RYGRAMC and TGRAACAN1-2TGTTYCA consensuses, and also predict that TFs in 32 orthologous groups have binding sites comprised of three boxes with alternating direction, which implies two possible alternative modes of dimerization of TFs. We identified trends in site positioning relative to the translational gene start, and show that TFs in 94 orthologous groups bind tandem sites with 18-22 nucleotides between their centers. We predict protein-DNA contacts via the correlation analysis of nucleotides in binding sites and amino acids of the DNA-binding domain of TFs, and show that the majority of interacting positions and predicted contacts are similar for both types of motifs and conform well both to available experimental data and to general protein-DNA interaction trends.
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Affiliation(s)
- Inna A Suvorova
- Institute for Information Transmission Problems of Russian Academy of Sciences (The Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems of Russian Academy of Sciences (The Kharkevich Institute), Moscow, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
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2
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Barnes SL, Belliveau NM, Ireland WT, Kinney JB, Phillips R. Mapping DNA sequence to transcription factor binding energy in vivo. PLoS Comput Biol 2019; 15:e1006226. [PMID: 30716072 PMCID: PMC6375646 DOI: 10.1371/journal.pcbi.1006226] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 02/14/2019] [Accepted: 11/06/2018] [Indexed: 11/18/2022] Open
Abstract
Despite the central importance of transcriptional regulation in biology, it has proven difficult to determine the regulatory mechanisms of individual genes, let alone entire gene networks. It is particularly difficult to decipher the biophysical mechanisms of transcriptional regulation in living cells and determine the energetic properties of binding sites for transcription factors and RNA polymerase. In this work, we present a strategy for dissecting transcriptional regulatory sequences using in vivo methods (massively parallel reporter assays) to formulate quantitative models that map a transcription factor binding site’s DNA sequence to transcription factor-DNA binding energy. We use these models to predict the binding energies of transcription factor binding sites to within 1 kBT of their measured values. We further explore how such a sequence-energy mapping relates to the mechanisms of trancriptional regulation in various promoter contexts. Specifically, we show that our models can be used to design specific induction responses, analyze the effects of amino acid mutations on DNA sequence preference, and determine how regulatory context affects a transcription factor’s sequence specificity. It has been said that we live in the “genomic era,” a time where we can readily sequence full genomes at will. However, it remains difficult to interpret much of the information within a genome. This is especially true of non-coding sequences such as promoters, which contain a number of features such as transcription factor binding sites that determine how genes are regulated. There is no straightforward regulatory “code” that tells us how transcription factor binding sites are organized within a promoter. In this work we examine how DNA sequence determines one of the most important features of a promoter, the strength with which a transcription factor binds to its DNA binding site. We discuss an approach to modeling DNA sequence-specific transcription factor binding energies in vivo using a massively parellel reporter assay. We develop models that allow us to predict the binding energy between a transcription factor and a mutated version of its binding site. We then show that this modeling technique can be used to address a number of scientific and design questions, such as engineering the behavior of genetic circuit elements or examining how transcription factors and their binding sites co-evolve.
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Affiliation(s)
- Stephanie L. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Nathan M. Belliveau
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - William T. Ireland
- Department of Physics, California Institute of Technology, Pasadena, California, United States of America
| | - Justin B. Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Department of Physics, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
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3
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Stolze Y, Bremges A, Maus I, Pühler A, Sczyrba A, Schlüter A. Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants. Microb Biotechnol 2017; 11:667-679. [PMID: 29205917 PMCID: PMC6011919 DOI: 10.1111/1751-7915.12982] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/23/2017] [Accepted: 10/23/2017] [Indexed: 11/26/2022] Open
Abstract
Biogas production is performed anaerobically by complex microbial communities with key species driving the process. Hence, analyses of their in situ activities are crucial to understand the process. In a previous study, metagenome sequencing and subsequent genome binning for different production‐scale biogas plants (BGPs) resulted in four genome bins of special interest, assigned to the phyla Thermotogae, Fusobacteria, Spirochaetes and Cloacimonetes, respectively, that were genetically analysed. In this study, metatranscriptome sequencing of the same BGP samples was conducted, enabling in situ transcriptional activity determination of these genome bins. For this, mapping of metatranscriptome reads on genome bin sequences was performed providing transcripts per million (TPM) values for each gene. This approach revealed an active sugar‐based metabolism of the Thermotogae and Spirochaetes bins and an active amino acid‐based metabolism of the Fusobacteria and Cloacimonetes bins. The data also hint at syntrophic associations of the four corresponding species with methanogenic Archaea.
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Affiliation(s)
- Yvonne Stolze
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Andreas Bremges
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany.,Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Alexander Sczyrba
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany.,Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
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Lee CM, Monson RE, Adams RM, Salmond GPC. The LacI-Family Transcription Factor, RbsR, Is a Pleiotropic Regulator of Motility, Virulence, Siderophore and Antibiotic Production, Gas Vesicle Morphogenesis and Flotation in Serratia. Front Microbiol 2017; 8:1678. [PMID: 28955306 PMCID: PMC5601083 DOI: 10.3389/fmicb.2017.01678] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/21/2017] [Indexed: 11/21/2022] Open
Abstract
Gas vesicles (GVs) are proteinaceous, gas-filled organelles used by some bacteria to enable upward movement into favorable air/liquid interfaces in aquatic environments. Serratia sp. ATCC39006 (S39006) was the first enterobacterium discovered to produce GVs naturally. The regulation of GV assembly in this host is complex and part of a wider regulatory network affecting various phenotypes, including antibiotic biosynthesis. To identify new regulators of GVs, a comprehensive mutant library containing 71,000 insertion mutants was generated by random transposon mutagenesis and 311 putative GV-defective mutants identified. Three of these mutants were found to have a transposon inserted in a LacI family transcription regulator gene (rbsR) of the putative ribose operon. Each of these rbsR mutants was GV-defective; no GVs were visible by phase contrast microscopy (PCM) or transmission electron microscopy (TEM). GV deficiency was caused by the reduction of gvpA1 and gvrA transcription (the first genes of the two contiguous operons in the GV gene locus). Our results also showed that a mutation in rbsR was highly pleiotropic; the production of two secondary metabolites (carbapenem and prodigiosin antibiotics) was abolished. Interestingly, the intrinsic resistance to the carbapenem antibiotic was not affected by the rbsR mutation. In addition, the production of a siderophore, cellulase and plant virulence was reduced in the mutant, whereas it exhibited increased swimming and swarming motility. The RbsR protein was predicted to bind to regions upstream of at least 18 genes in S39006 including rbsD (the first gene of the ribose operon) and gvrA. Electrophoretic mobility shift assays (EMSA) confirmed that RbsR bound to DNA sequences upstream of rbsD, but not gvrA. The results of this study indicate that RbsR is a global regulator that affects the modulation of GV biogenesis, but also with complex pleiotropic physiological impacts in S39006.
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Hehemann JH, Truong LV, Unfried F, Welsch N, Kabisch J, Heiden SE, Junker S, Becher D, Thürmer A, Daniel R, Amann R, Schweder T. Aquatic adaptation of a laterally acquired pectin degradation pathway in marine gammaproteobacteria. Environ Microbiol 2017; 19:2320-2333. [PMID: 28276126 DOI: 10.1111/1462-2920.13726] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 03/03/2017] [Accepted: 03/05/2017] [Indexed: 01/09/2023]
Abstract
Mobile genomic islands distribute functional traits between microbes and habitats, yet it remains unclear how their proteins adapt to new environments. Here we used a comparative phylogenomic and proteomic approach to show that the marine bacterium Pseudoalteromonas haloplanktis ANT/505 acquired a genomic island with a functional pathway for pectin catabolism. Bioinformatics and biochemical experiments revealed that this pathway encodes a series of carbohydrate-active enzymes including two multi-modular pectate lyases, PelA and PelB. PelA is a large enzyme with a polysaccharide lyase family 1 (PL1) domain and a carbohydrate esterase family 8 domain, and PelB contains a PL1 domain and two carbohydrate-binding domains of family 13. Comparative phylogenomic analyses indicate that the pathway was most likely acquired from terrestrial microbes, yet we observed multi-modular orthologues only in marine bacteria. Proteomic experiments showed that P. haloplanktis ANT/505 secretes both pectate lyases into the environment in the presence of pectin. These multi-modular enzymes may therefore represent a marine innovation that enhances physical interaction with pectins to reduce loss of substrate and enzymes by diffusion. Our results revealed that marine bacteria can catabolize pectin, and highlight enzyme fusion as a potential adaptation that may facilitate microbial consumption of polymeric substrates in aquatic environments.
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Affiliation(s)
- Jan-Hendrik Hehemann
- MARUM, Center for Marine Environmental Sciences at the University of Bremen, Leobener Strasse, Bremen, D-28359, Germany.,Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Le Van Truong
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Institute of Biotechnology, Vietnamese Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Frank Unfried
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany.,Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Norma Welsch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Johannes Kabisch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany.,Department of Biology, Computer-aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, Darmstadt, D-64287, Germany
| | - Stefan E Heiden
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Sabryna Junker
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, D-17487, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, D-17487, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory (G2L), Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory (G2L), Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Thomas Schweder
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
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6
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Korostelev YD, Zharov IA, Mironov AA, Rakhmaininova AB, Gelfand MS. Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors. PLoS One 2016; 11:e0162681. [PMID: 27690309 PMCID: PMC5045206 DOI: 10.1371/journal.pone.0162681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 08/26/2016] [Indexed: 11/25/2022] Open
Abstract
The large and increasing volume of genomic data analyzed by comparative methods provides information about transcription factors and their binding sites that, in turn, enables statistical analysis of correlations between factors and sites, uncovering mechanisms and evolution of specific protein-DNA recognition. Here we present an online tool, Prot-DNA-Korr, designed to identify and analyze crucial protein-DNA pairs of positions in a family of transcription factors. Correlations are identified by analysis of mutual information between columns of protein and DNA alignments. The algorithm reduces the effects of common phylogenetic history and of abundance of closely related proteins and binding sites. We apply it to five closely related subfamilies of the MerR family of bacterial transcription factors that regulate heavy metal resistance systems. We validate the approach using known 3D structures of MerR-family proteins in complexes with their cognate DNA binding sites and demonstrate that a significant fraction of correlated positions indeed form specific side-chain-to-base contacts. The joint distribution of amino acids and nucleotides hence may be used to predict changes of specificity for point mutations in transcription factors.
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Affiliation(s)
- Yuriy D. Korostelev
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994
- Department of Bioengineering and Bioinformatics, Moscow State University, 1-73 Vorobievy Gory, Moscow, Russia, 119991
| | - Ilya A. Zharov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994
| | - Andrey A. Mironov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994
- Department of Bioengineering and Bioinformatics, Moscow State University, 1-73 Vorobievy Gory, Moscow, Russia, 119991
| | - Alexandra B. Rakhmaininova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994
| | - Mikhail S. Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 19-1 Bolshoy Karetny pereulok, Moscow, Russia, 127994
- Department of Bioengineering and Bioinformatics, Moscow State University, 1-73 Vorobievy Gory, Moscow, Russia, 119991
- * E-mail:
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7
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He J, Guo X, Sun L, Wang K, Yao H. Networks analysis of genes and microRNAs in human Wilms' tumors. Oncol Lett 2016; 12:3579-3585. [PMID: 27900039 DOI: 10.3892/ol.2016.5102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/12/2016] [Indexed: 01/12/2023] Open
Abstract
Wilms' tumor (WT) is a common kidney cancer. To date, the expression of genes [transcription factors (TFs), target genes and host genes] and microRNAs (miRNAs/miRs) in WTs has captured the attention of biologists, while the regulatory association between the genes and miRNAs remains unclear. In the present study, TFs, miRNAs, target genes and host genes were considered as key factors in the construction of three levels of regulatory networks, namely, the differentially-expressed network, the related network and the global network. The four factors had three types of association, including the regulation of miRNAs by TFs, the targeting of the target genes by miRNAs and the location of miRNAs at host genes. The differentially-expressed network is the most important of the three networks, and only involves the differentially-expressed genes and miRNAs; with the exception of host genes, those elements all behave abnormally when a WT occurs, which suggests that the differentially-expressed network can accurately reveal the pathogenesis of WTs. E2F3, for example, is overexpressed in WTs, and it regulates hsa-let-7a, hsa-let-7a-1, hsa-miR-106b, among others. Meanwhile, E2F3 is targeted by hsa-miR-106b, hsa-miR-17 and hsa-miR-20a. If the regulatory network can be used to adjust those factors to a normal level, there may be a chance to cure patients with WTs. WT-associated factors were placed into the related network; this network is useful for understanding the regulatory pathways of genes and miRNA in WTs. The networks provide a novel perspective in order to study the inner interactions of genes and miRNAs. The present study provides authoritative data and regulatory pathway analysis in order to partially elucidate the pathogenesis of WT, and thus supplies biologists with a basis for future research.
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Affiliation(s)
- Jimin He
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, P.R. China; Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Xiaoxin Guo
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, P.R. China; Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Linlin Sun
- Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin 130012, P.R. China; College of Software, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Kuhao Wang
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, P.R. China; Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin 130012, P.R. China
| | - Haiying Yao
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, P.R. China; Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun, Jilin 130012, P.R. China
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8
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Suvorova IA, Korostelev YD, Gelfand MS. GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution. PLoS One 2015; 10:e0132618. [PMID: 26151451 PMCID: PMC4494728 DOI: 10.1371/journal.pone.0132618] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/16/2015] [Indexed: 12/03/2022] Open
Abstract
The GntR family of transcription factors (TFs) is a large group of proteins present in diverse bacteria and regulating various biological processes. Here we use the comparative genomics approach to reconstruct regulons and identify binding motifs of regulators from three subfamilies of the GntR family, FadR, HutC, and YtrA. Using these data, we attempt to predict DNA-protein contacts by analyzing correlations between binding motifs in DNA and amino acid sequences of TFs. We identify pairs of positions with high correlation between amino acids and nucleotides for FadR, HutC, and YtrA subfamilies and show that the most predicted DNA-protein interactions are quite similar in all subfamilies and conform well to the experimentally identified contacts formed by FadR from E. coli and AraR from B. subtilis. The most frequent predicted contacts in the analyzed subfamilies are Arg-G, Asn-A, Asp-C. We also analyze the divergon structure and preferred site positions relative to regulated genes in the FadR and HutC subfamilies. A single site in a divergon usually regulates both operons and is approximately in the middle of the intergenic area. Double sites are either involved in the co-operative regulation of both operons and then are in the center of the intergenic area, or each site in the pair independently regulates its own operon and tends to be near it. We also identify additional candidate TF-binding boxes near palindromic binding sites of TFs from the FadR, HutC, and YtrA subfamilies, which may play role in the binding of additional TF-subunits.
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Affiliation(s)
- Inna A. Suvorova
- Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia
- * E-mail:
| | - Yuri D. Korostelev
- Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia
| | - Mikhail S. Gelfand
- Research and Training Center on Bioinformatics, Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
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9
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Vujanac M, Iyer VS, Sengupta M, Ajdic D. Regulation of Streptococcus mutans PTS Bio by the transcriptional repressor NigR. Mol Oral Microbiol 2015; 30:280-94. [PMID: 25580872 DOI: 10.1111/omi.12093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2014] [Indexed: 11/29/2022]
Abstract
Streptococcus mutans is implicated in human dental caries, and the carbohydrate metabolism of this organism plays an important role in the formation of this disease. Carbohydrate transport and metabolism are essential for the survival of S. mutans in the oral cavity. It is known that a unique phosphoenolpyruvate-sugar phosphotransferase system PTS(B) (io) of S. mutans UA159 is expressed in sucrose-grown biofilms (Mol Oral Microbiol 28: 2013; 114). In this study we analyzed the transcriptional regulation of the operon (O(B) (io) ) encoding the PTS(B) (io) and showed that it was repressed by NigR, a LacI-like transcriptional regulator. Using electro-mobility shift assay, we described two operators to which NigR bound with different affinities. We also identified the transcriptional start site and showed that one of the operators overlaps with the promoter and presumably represses initiation of transcription. Mutational analyses revealed the key nucleotides in the operators required for high-affinity binding of NigR. PTS(B) (io) is expressed in S. mutans biofilms so understanding its regulation may provide improved strategies for caries treatment and prevention.
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Affiliation(s)
- M Vujanac
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - V S Iyer
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - M Sengupta
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - D Ajdic
- Miller School of Medicine, University of Miami, Miami, FL, USA
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10
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Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov PS, Gelfand MS, Rodionov DA. Comparative genomics and evolution of regulons of the LacI-family transcription factors. Front Microbiol 2014; 5:294. [PMID: 24966856 PMCID: PMC4052901 DOI: 10.3389/fmicb.2014.00294] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 05/28/2014] [Indexed: 12/31/2022] Open
Abstract
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 the function and evolution of LacI-TFs, we performed genomics-based reconstruction and comparative analysis of their regulons. For over 1300 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, as well as 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 the LacI protein family. The obtained genomic collection of in silico reconstructed LacI-TF 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 bacterial lineages.
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Affiliation(s)
- Dmitry A Ravcheev
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Matvei S Khoroshkin
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Olga N Laikova
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Olga V Tsoy
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia ; Faculty of Bioengineering and Bioinformatics, Moscow State University Moscow, Russia
| | - Natalia V Sernova
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Svetlana A Petrova
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia ; Faculty of Bioengineering and Bioinformatics, Moscow State University Moscow, Russia
| | | | - Pavel S Novichkov
- Lawrence Berkeley National Laboratory, Genomics Division Berkeley, CA, USA
| | - Mikhail S Gelfand
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Dmitry A Rodionov
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia ; Department of Bioinformatics, Sanford-Burnham Medical Research Institute La Jolla, CA, USA
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The LacI-Type transcriptional regulator AraR acts as an L-arabinose-responsive repressor of L-arabinose utilization genes in Corynebacterium glutamicum ATCC 31831. J Bacteriol 2014; 196:2242-54. [PMID: 24706742 DOI: 10.1128/jb.01655-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Corynebacterium glutamicum ATCC 31831 araBDA operon consists of three l-arabinose catabolic genes, upstream of which the galM, araR, and araE genes are located in opposite orientation. araR encodes a LacI-type transcriptional regulator that negatively regulates the l-arabinose-inducible expression of araBDA and araE (encoding an l-arabinose transporter), through a mechanism that has yet to be identified. Here we show that the AraR protein binds in vitro to three sites: one upstream of araBDA and two upstream of araE. We verify that a 16-bp consensus palindromic sequence is essential for binding of AraR, using a series of mutations introduced upstream of araB in electrophoretic mobility shift assays. Moreover, the DNA-binding activity of AraR is reduced by l-arabinose. We employ quantitative reverse transcription-PCR (qRT-PCR) analyses using various mutant strains deficient in l-arabinose utilization genes to demonstrate that the prominent upregulation of araBDA and araE within 5 min of l-arabinose supplementation is dependent on the uptake but independent of the catabolism of l-arabinose. Similar expression patterns, together with the upregulation by araR disruption without l-arabinose, are evident with the apparent galM-araR operon, although attendant changes in expression levels are much smaller than those realized with the expression of araBDA and araE. The AraR-binding site upstream of araB overlaps the -10 region of the divergent galM promoter. These observations indicate that AraR acts as a transcriptional repressor of araBDA, araE, and galM-araR and that l-arabinose acts as an intracellular negative effector of the AraR-dependent regulation.
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Baumgart M, Luder K, Grover S, Gätgens C, Besra GS, Frunzke J. IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria. BMC Biol 2013; 11:122. [PMID: 24377418 PMCID: PMC3899939 DOI: 10.1186/1741-7007-11-122] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/17/2013] [Indexed: 11/10/2022] Open
Abstract
Background The development of new drugs against tuberculosis and diphtheria is focused on disrupting the biogenesis of the cell wall, the unique architecture of which confers resistance against current therapies. The enzymatic pathways involved in the synthesis of the cell wall by these pathogens are well understood, but the underlying regulatory mechanisms are largely unknown. Results Here, we characterize IpsA, a LacI-type transcriptional regulator conserved among Mycobacteria and Corynebacteria that plays a role in the regulation of cell wall biogenesis. IpsA triggers myo-inositol formation by activating ino1, which encodes inositol phosphate synthase. An ipsA deletion mutant of Corynebacterium glutamicum cultured on glucose displayed significantly impaired growth and presented an elongated cell morphology. Further studies revealed the absence of inositol-derived lipids in the cell wall and a complete loss of mycothiol biosynthesis. The phenotype of the C. glutamicum ipsA deletion mutant was complemented to different extend by homologs from Corynebacterium diphtheriae (dip1969) and Mycobacterium tuberculosis (rv3575), indicating the conserved function of IpsA in the pathogenic species. Additional targets of IpsA with putative functions in cell wall biogenesis were identified and IpsA was shown to bind to a conserved palindromic motif within the corresponding promoter regions. Myo-inositol was identified as an effector of IpsA, causing the dissociation of the IpsA-DNA complex in vitro. Conclusions This characterization of IpsA function and of its regulon sheds light on the complex transcriptional control of cell wall biogenesis in the mycolata taxon and generates novel targets for drug development.
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Affiliation(s)
| | | | | | | | | | - Julia Frunzke
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, 52425 Jülich, Germany.
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Tsoy OV, Pyatnitskiy MA, Kazanov MD, Gelfand MS. Evolution of transcriptional regulation in closely related bacteria. BMC Evol Biol 2012; 12:200. [PMID: 23039862 PMCID: PMC3735044 DOI: 10.1186/1471-2148-12-200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 09/26/2012] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The exponential growth of the number of fully sequenced genomes at varying taxonomic closeness allows one to characterize transcriptional regulation using comparative-genomics analysis instead of time-consuming experimental methods. A transcriptional regulatory unit consists of a transcription factor, its binding site and a regulated gene. These units constitute a graph which contains so-called "network motifs", subgraphs of a given structure. Here we consider genomes of closely related Enterobacteriales and estimate the fraction of conserved network motifs and sites as well as positions under selection in various types of non-coding regions. RESULTS Using a newly developed technique, we found that the highest fraction of positions under selection, approximately 50%, was observed in synvergon spacers (between consecutive genes from the same strand), followed by ~45% in divergon spacers (common 5'-regions), and ~10% in convergon spacers (common 3'-regions). The fraction of selected positions in functional regions was higher, 60% in transcription factor-binding sites and ~45% in terminators and promoters. Small, but significant differences were observed between Escherichia coli and Salmonella enterica. This fraction is similar to the one observed in eukaryotes.The conservation of binding sites demonstrated some differences between types of regulatory units. In E. coli, strains the interactions of the type "local transcriptional factor gene" turned out to be more conserved in feed-forward loops (FFLs) compared to non-motif interactions. The coherent FFLs tend to be less conserved than the incoherent FFLs. A natural explanation is that the former imply functional redundancy. CONCLUSIONS A naïve hypothesis that FFL would be highly conserved turned out to be not entirely true: its conservation depends on its status in the transcriptional network and also from its usage. The fraction of positions under selection in intergenic regions of bacterial genomes is roughly similar to that of eukaryotes. Known regulatory sites explain 20±5% of selected positions.
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Affiliation(s)
- Olga V Tsoy
- Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, Moscow 127994, Russia
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On the search for design principles in biological systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 751:183-93. [PMID: 22821459 DOI: 10.1007/978-1-4614-3567-9_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The search for basic concepts and underlying principles was at the core of the systems approach to science and technology. This approach was somehow abandoned in mainstream biology after its initial proposal, due to the rise and success of molecular biology. This situation has changed. The accumulated knowledge of decades of molecular studies in combination with new technological advances, while further highlighting the intricacies of natural systems, is also bringing back the quest-for-principles research program. Here, I present two lessons that I derived from my own quest: the importance of studying biological information processing to identify common principles in seemingly unrelated contexts and the adequacy of using known design principles at one level of biological organization as a valuable tool to help recognizing principles at an alternative one. These and additional lessons should contribute to the ultimate goal of establishing principles able to integrate the many scales of biological complexity.
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Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression. Curr Opin Biotechnol 2012; 23:689-94. [DOI: 10.1016/j.copbio.2011.12.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 12/14/2011] [Accepted: 12/15/2011] [Indexed: 01/06/2023]
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Bréchemier-Baey D, Domínguez-Ramírez L, Plumbridge J. The linker sequence, joining the DNA-binding domain of the homologous transcription factors, Mlc and NagC, to the rest of the protein, determines the specificity of their DNA target recognition inEscherichia coli. Mol Microbiol 2012; 85:1007-19. [DOI: 10.1111/j.1365-2958.2012.08158.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Hall BM, Vaughn EE, Begaye AR, Cordes MHJ. Reengineering Cro protein functional specificity with an evolutionary code. J Mol Biol 2011; 413:914-28. [PMID: 21945527 DOI: 10.1016/j.jmb.2011.08.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 08/13/2011] [Accepted: 08/29/2011] [Indexed: 11/17/2022]
Abstract
Cro proteins from different lambdoid bacteriophages are extremely variable in their target consensus DNA sequences and constitute an excellent model for evolution of transcription factor specificity. We experimentally tested a bioinformatically derived evolutionary code relating switches between pairs of amino acids at three recognition helix sites in Cro proteins to switches between pairs of nucleotide bases in the cognate consensus DNA half-sites. We generated all eight possible code variants of bacteriophage λ Cro and used electrophoretic mobility shift assays to compare binding of each variant to its own putative cognate site and to the wild-type cognate site; we also tested the wild-type protein against all eight DNA sites. Each code variant showed stronger binding to its putative cognate site than to the wild-type site, except some variants containing proline at position 27; each also bound its cognate site better than wild-type Cro bound the same site. Most code variants, however, displayed poorer affinity and specificity than wild-type λ Cro. Fluorescence anisotropy assays on λ Cro and the triple code variant (PSQ) against the two cognate sites confirmed the switch in specificity and showed larger apparent effects on binding affinity and specificity. Bacterial one-hybrid assays of λ Cro and PSQ against libraries of sequences with a single randomized half-site showed the expected switches in specificity at two of three coded positions and no clear switches in specificity at noncoded positions. With a few caveats, these results confirm that the proposed Cro evolutionary code can be used to reengineer Cro specificity.
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Affiliation(s)
- Branwen M Hall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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Porcheron G, Kut E, Canepa S, Maurel MC, Schouler C. Regulation of fructooligosaccharide metabolism in an extra-intestinal pathogenic Escherichia coli strain. Mol Microbiol 2011; 81:717-33. [PMID: 21692876 DOI: 10.1111/j.1365-2958.2011.07725.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A gene cluster involved in the metabolism of prebiotic short-chain fructooligosaccharides (scFOS) has recently been identified in the extra-intestinal avian pathogenic Escherichia coli strain BEN2908. This gene cluster, called the fos locus, plays a major role in the initiation stage of chicken intestinal colonization. This locus is composed of six genes organized as an operon encoding a sugar transporter and enzymes involved in scFOS metabolism, and of a divergently transcribed gene encoding a transcriptional regulator, FosR, belonging to the LacI/GalR family. To decipher the regulation of scFOS metabolism, we monitored the fos operon promoter activity using a luciferase reporter gene assay. We demonstrated that the expression of fos genes is repressed by FosR, controlled by catabolite repression and induced in the presence of scFOS. Using electrophoretic mobility shift assays and surface plasmon resonance experiments, we showed that FosR binds to two operator sequences of the fos operon promoter region. This binding to DNA was inhibited in the presence of scFOS, especially by GF2. We then propose a model of scFOS metabolism regulation in a pathogenic bacterium, which will help to identify the environmental conditions required for fos gene expression and to understand the role of this locus in intestinal colonization.
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Affiliation(s)
- Gaëlle Porcheron
- INRA, UR1282 Infectiologie Animale et Santé Publique, F-37380 Nouzilly, France
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