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Rybina AA, Glushak RA, Bessonova TA, Dakhnovets AI, Rudenko AY, Ozhiganov RM, Kaznadzey AD, Tutukina MN, Gelfand MS. Phylogeny and structural modeling of the transcription factor CsqR (YihW) from Escherichia coli. Sci Rep 2024; 14:7852. [PMID: 38570624 PMCID: PMC10991401 DOI: 10.1038/s41598-024-58492-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/29/2024] [Indexed: 04/05/2024] Open
Abstract
CsqR (YihW) is a local transcription factor that controls expression of yih genes involved in degradation of sulfoquinovose in Escherichia coli. We recently showed that expression of the respective gene cassette might be regulated by lactose. Here, we explore the phylogenetic and functional traits of CsqR. Phylogenetic analysis revealed that CsqR had a conserved Met25. Western blot demonstrated that CsqR was synthesized in the bacterial cell as two protein forms, 28.5 (CsqR-l) and 26 kDa (CsqR-s), the latter corresponding to start of translation at Met25. CsqR-s was dramatically activated during growth with sulfoquinovose as a sole carbon source, and displaced CsqR-l in the stationary phase during growth on rich medium. Molecular dynamic simulations revealed two possible states of the CsqR-s structure, with the interdomain linker being represented by either a disordered loop or an ɑ-helix. This helix allowed the hinge-like motion of the N-terminal domain resulting in a switch of CsqR-s between two conformational states, "open" and "compact". We then modeled the interaction of both CsqR forms with putative effectors sulfoquinovose, sulforhamnose, sulfoquinovosyl glycerol, and lactose, and revealed that they all preferred the same pocket in CsqR-l, while in CsqR-s there were two possible options dependent on the linker structure.
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Affiliation(s)
- Anna A Rybina
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205.
| | - Roman A Glushak
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Tatiana A Bessonova
- Institute of Cell Biophysics RAS (Federal Research Center "Pushchino Scientific Center for Biological Research RAS"), Pushchino, Russia, 142290
| | | | - Alexander Yu Rudenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Ratislav M Ozhiganov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Anna D Kaznadzey
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
| | - Maria N Tutukina
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
- Institute of Cell Biophysics RAS (Federal Research Center "Pushchino Scientific Center for Biological Research RAS"), Pushchino, Russia, 142290
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
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2
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Duarte-Velázquez I, de la Mora J, Ramírez-Prado JH, Aguillón-Bárcenas A, Tornero-Gutiérrez F, Cordero-Loreto E, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Muñoz-Carranza SR, Romero-González OE, Cardoso-Reyes LR, Rodríguez-Ojeda RA, Mora-Montes HM, Vargas-Maya NI, Padilla-Vaca F, Franco B. Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships. PeerJ 2022; 10:e13772. [PMID: 35880217 PMCID: PMC9308461 DOI: 10.7717/peerj.13772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/01/2022] [Indexed: 01/17/2023] Open
Abstract
Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history.
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Affiliation(s)
- Isabel Duarte-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Javier de la Mora
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autonoma de Mexico, Mexico City, México
| | | | - Alondra Aguillón-Bárcenas
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fátima Tornero-Gutiérrez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Eugenia Cordero-Loreto
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fernando Anaya-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Itzel Páramo-Pérez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Ángeles Rangel-Serrano
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | | | - Luis Rafael Cardoso-Reyes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | - Héctor Manuel Mora-Montes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Naurú Idalia Vargas-Maya
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Felipe Padilla-Vaca
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Bernardo Franco
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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3
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Kobayashi I, Mochizuki K, Teramoto J, Imamura S, Takaya K, Ishihama A, Shimada T. Transcription Factor SrsR (YgfI) Is a Novel Regulator for the Stress-Response Genes in Stationary Phase in Escherichia coli K-12. Int J Mol Sci 2022; 23:ijms23116055. [PMID: 35682733 PMCID: PMC9181523 DOI: 10.3390/ijms23116055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 02/04/2023] Open
Abstract
Understanding the functional information of all genes and the biological mechanism based on the comprehensive genome regulation mechanism is an important task in life science. YgfI is an uncharacterized LysR family transcription factor in Escherichia coli. To identify the function of YgfI, the genomic SELEX (gSELEX) screening was performed for YgfI regulation targets on the E. coli genome. In addition, regulatory and phenotypic analyses were performed. A total of 10 loci on the E. coli genome were identified as the regulatory targets of YgfI with the YgfI binding activity. These predicted YgfI target genes were involved in biofilm formation, hydrogen peroxide resistance, and antibiotic resistance, many of which were expressed in the stationary phase. The TCAGATTTTGC sequence was identified as an YgfI box in in vitro gel shift assay and DNase-I footprinting assays. RT-qPCR analysis in vivo revealed that the expression of YgfI increased in the stationary phase. Physiological analyses suggested the participation of YgfI in biofilm formation and an increase in the tolerability against hydrogen peroxide. In summary, we propose to rename ygfI as srsR (a stress-response regulator in stationary phase).
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Affiliation(s)
- Ikki Kobayashi
- School of Agriculture, Meiji University, Kawasaki 214-8571, Kanagawa, Japan;
| | - Kenji Mochizuki
- Micro-Nano Technology Research Center, Hosei University, Koganei 184-0003, Tokyo, Japan; (K.M.); (J.T.)
| | - Jun Teramoto
- Micro-Nano Technology Research Center, Hosei University, Koganei 184-0003, Tokyo, Japan; (K.M.); (J.T.)
| | - Sousuke Imamura
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi 180-8585, Tokyo, Japan; (S.I.); (K.T.)
| | - Kazuhiro Takaya
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino-shi 180-8585, Tokyo, Japan; (S.I.); (K.T.)
| | - Akira Ishihama
- Micro-Nano Technology Research Center, Hosei University, Koganei 184-0003, Tokyo, Japan; (K.M.); (J.T.)
- Correspondence: (A.I.); (T.S.)
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, Kawasaki 214-8571, Kanagawa, Japan;
- Correspondence: (A.I.); (T.S.)
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4
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Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC. Persistence and plasticity in bacterial gene regulation. Nat Methods 2021; 18:1499-1505. [PMID: 34824476 DOI: 10.1038/s41592-021-01312-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/24/2021] [Indexed: 11/09/2022]
Abstract
Organisms orchestrate cellular functions through transcription factor (TF) interactions with their target genes, although these regulatory relationships are largely unknown in most species. Here we report a high-throughput approach for characterizing TF-target gene interactions across species and its application to 354 TFs across 48 bacteria, generating 17,000 genome-wide binding maps. This dataset revealed themes of ancient conservation and rapid evolution of regulatory modules. We observed rewiring, where the TF sensing and regulatory role is maintained while the arrangement and identity of target genes diverges, in some cases encoding entirely new functions. We further integrated phenotypic information to define new functional regulatory modules and pathways. Finally, we identified 242 new TF DNA binding motifs, including a 70% increase of known Escherichia coli motifs and the first annotation in Pseudomonas simiae, revealing deep conservation in bacterial promoter architecture. Our method provides a versatile tool for functional characterization of genetic pathways in prokaryotes and eukaryotes.
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Affiliation(s)
- Leo A Baumgart
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ji Eun Lee
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Asaf Salamov
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David J Dilworth
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hyunsoo Na
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew Mingay
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew J Blow
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu Zhang
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuko Yoshinaga
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris G Daum
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ronan C O'Malley
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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5
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Díaz-Rodríguez M, Lithgow-Serrano O, Guadarrama-García F, Tierrafría VH, Gama-Castro S, Solano-Lira H, Salgado H, Rinaldi F, Méndez-Cruz CF, Collado-Vides J. Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194753. [PMID: 34461312 PMCID: PMC10155859 DOI: 10.1016/j.bbagrm.2021.194753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/12/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
The number of published papers in biomedical research makes it rather impossible for a researcher to keep up to date. This is where manually curated databases contribute facilitating the access to knowledge. However, the structure required by databases strongly limits the type of valuable information that can be incorporated. Here, we present Lisen&Curate, a curation system that facilitates linking sentences or part of sentences (both considered sources) in articles with their corresponding curated objects, so that rich additional information of these objects is easily available to users. These sources are going to be offered both within RegulonDB and a new database, L-Regulon. To show the relevance of our work, two senior curators performed a curation of 31 articles on the regulation of transcription initiation of E. coli using Lisen&Curate. As a result, 194 objects were curated and 781 sources were recorded. We also found that these sources are useful to develop automatic approaches to detect objects in articles by observing word frequency patterns and by carrying out an open information extraction task. Sources may help to elaborate a controlled vocabulary of experimental methods. Finally, we discuss our ecosystem of interconnected applications, RegulonDB, L-Regulon, and Lisen&Curate, to facilitate the access to knowledge on regulation of transcription initiation in bacteria. We see our proposal as the starting point to change the way experimentalists connect a piece of knowledge with its evidence using RegulonDB.
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Affiliation(s)
- Martín Díaz-Rodríguez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n Col. Chamilpa, 62210 Cuernavaca, Mor., Mexico
| | - Oscar Lithgow-Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n Col. Chamilpa, 62210 Cuernavaca, Mor., Mexico; Dalle Molle Institute for Artificial Intelligence Research, IDSIA USI-SUPSI, Polo universitario Lugano-Campus Est, Via la Santa 1, CH-6962 Lugano, Switzerland
| | - Francisco Guadarrama-García
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n Col. Chamilpa, 62210 Cuernavaca, Mor., Mexico
| | - Víctor H Tierrafría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n Col. Chamilpa, 62210 Cuernavaca, Mor., Mexico
| | - Socorro Gama-Castro
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n Col. Chamilpa, 62210 Cuernavaca, Mor., Mexico
| | - Hilda Solano-Lira
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n Col. Chamilpa, 62210 Cuernavaca, Mor., Mexico
| | - Heladia Salgado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n Col. Chamilpa, 62210 Cuernavaca, Mor., Mexico
| | - Fabio Rinaldi
- Dalle Molle Institute for Artificial Intelligence Research, IDSIA USI-SUPSI, Polo universitario Lugano-Campus Est, Via la Santa 1, CH-6962 Lugano, Switzerland; Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Carlos-Francisco Méndez-Cruz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n Col. Chamilpa, 62210 Cuernavaca, Mor., Mexico.
| | - Julio Collado-Vides
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n Col. Chamilpa, 62210 Cuernavaca, Mor., Mexico; Department of Biomedical Engineering, Boston University, 44 Cummington Mall Room 403, 02215 Boston, MA, USA; Center for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
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6
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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7
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Ishihama A, Shimada T. Hierarchy of transcription factor network in Escherichia coli K-12: H-NS-mediated silencing and Anti-silencing by global regulators. FEMS Microbiol Rev 2021; 45:6312496. [PMID: 34196371 DOI: 10.1093/femsre/fuab032] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022] Open
Abstract
Transcriptional regulation for genome expression determines growth and adaptation of single-cell bacteria that are directly exposed to environment. The transcriptional apparatus in Escherichia coli K-12 is composed of RNA polymerase core enzyme and two groups of its regulatory proteins, seven species of promoter-recognition subunit sigma and about 300 species of transcription factors. The identification of regulatory targets for all these regulatory proteins is critical toward understanding the genome regulation as a whole. For this purpose, we performed a systematic search in vitro of the whole set of binding sites for each factor by gSELEX system. This review summarizes the accumulated knowledge of regulatory targets for more than 150 TFs from E. coli K-12. Overall TFs could be classified into four families: nucleoid-associated bifunctional TFs; global regulators; local regulators; and single-target regulators, in which the regulatory functions remain uncharacterized for the nucleoid-associated TFs. Here we overview the regulatory targets of two nucleoid-associated TFs, H-NS and its paralog StpA, both together playing the silencing role of a set of non-essential genes. Participation of LeuO and other global regulators have been indicated for the anti-silencing. Finally, we propose the hierarchy of TF network as a key framework of the bacterial genome regulation.
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Affiliation(s)
- Akira Ishihama
- Hosei University, Research Institute for Micro-Nano Technology, Koganei, Tokyo 184-0003, Japan
| | - Tomohiro Shimada
- Meiji University, School of Agriculture, Kawasaki, Kanagawa 214-8571, Japan
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8
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Thomas GH. Microbial Musings - September 2020. MICROBIOLOGY-SGM 2020; 166:794-796. [PMID: 32993848 PMCID: PMC7654740 DOI: 10.1099/mic.0.000978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Anzai T, Imamura S, Ishihama A, Shimada T. Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility. Microb Genom 2020; 6. [PMID: 32975502 PMCID: PMC7660256 DOI: 10.1099/mgen.0.000442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The transcription factor PdhR has been recognized as the master regulator of the pyruvate catabolism pathway in Escherichia coli, including both NAD-linked oxidative decarboxylation of pyruvate to acetyl-CoA by PDHc (pyruvate dehydrogenase complex) and respiratory electron transport of NADH to oxygen by Ndh-CyoABCD enzymes. To identify the whole set of regulatory targets under the control of pyruvate-sensing PdhR, we performed genomic SELEX (gSELEX) screening in vitro. A total of 35 PdhR-binding sites were identified along the E. coli K-12 genome, including previously identified targets. Possible involvement of PdhR in regulation of the newly identified target genes was analysed in detail by gel shift assay, RT-qPCR and Northern blot analysis. The results indicated the participation of PdhR in positive regulation of fatty acid degradation genes and negative regulation of cell mobility genes. In fact, GC analysis indicated an increase in free fatty acids in the mutant lacking PdhR. We propose that PdhR is a bifunctional global regulator for control of a total of 16–23 targets, including not only the genes involved in central carbon metabolism but also some genes for the surrounding pyruvate-sensing cellular pathways such as fatty acid degradation and flagella formation. The activity of PdhR is controlled by pyruvate, the key node between a wide variety of metabolic pathways, including generation of metabolic energy and cell building blocks.
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Affiliation(s)
- Takumi Anzai
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Akira Ishihama
- Micro-Nanotechnology Research Center, Hosei University, Koganei, Tokyo, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
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10
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Ogasawara H, Ishizuka T, Hotta S, Aoki M, Shimada T, Ishihama A. Novel regulators of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli K-12. Microbiology (Reading) 2020; 166:880-890. [DOI: 10.1099/mic.0.000947] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Under stressful conditions,
Escherichia coli
forms biofilm for survival by sensing a variety of environmental conditions. CsgD, the master regulator of biofilm formation, controls cell aggregation by directly regulating the synthesis of Curli fimbriae. In agreement of its regulatory role, as many as 14 transcription factors (TFs) have so far been identified to participate in regulation of the csgD promoter, each monitoring a specific environmental condition or factor. In order to identify the whole set of TFs involved in this typical multi-factor promoter, we performed in this study ‘promoter-specific transcription-factor’ (PS-TF) screening in vitro using a set of 198 purified TFs (145 TFs with known functions and 53 hitherto uncharacterized TFs). A total of 48 TFs with strong binding to the csgD promoter probe were identified, including 35 known TFs and 13 uncharacterized TFs, referred to as Y-TFs. As an attempt to search for novel regulators, in this study we first analysed a total of seven Y-TFs, including YbiH, YdcI, YhjC, YiaJ, YiaU, YjgJ and YjiR. After analysis of curli fimbriae formation, LacZ-reporter assay, Northern-blot analysis and biofilm formation assay, we identified at least two novel regulators, repressor YiaJ (renamed PlaR) and activator YhjC (renamed RcdB), of the csgD promoter.
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Affiliation(s)
- Hiroshi Ogasawara
- Academic Assembly School of Humanities and Social Sciences Institute of Humanities, Shinshu University, Asahi 3-1-1, Matsumoto, 390–8621, Japan
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Toshiyuki Ishizuka
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Shuhei Hotta
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Michiko Aoki
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, 1-1-1 Higashi Mita, Tama-ku, Kawasaki, Kanagawa 214–8571, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
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