1
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Nicastro GG, Burroughs AM, Iyer L, Aravind L. Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems. Nucleic Acids Res 2023; 51:11479-11503. [PMID: 37889040 PMCID: PMC10681802 DOI: 10.1093/nar/gkad879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
While nucleic acid-targeting effectors are known to be central to biological conflicts and anti-selfish element immunity, recent findings have revealed immune effectors that target their building blocks and the cellular energy currency-free nucleotides. Through comparative genomics and sequence-structure analysis, we identified several distinct effector domains, which we named Calcineurin-CE, HD-CE, and PRTase-CE. These domains, along with specific versions of the ParB and MazG domains, are widely present in diverse prokaryotic immune systems and are predicted to degrade nucleotides by targeting phosphate or glycosidic linkages. Our findings unveil multiple potential immune systems associated with at least 17 different functional themes featuring these effectors. Some of these systems sense modified DNA/nucleotides from phages or operate downstream of novel enzymes generating signaling nucleotides. We also uncovered a class of systems utilizing HSP90- and HSP70-related modules as analogs of STAND and GTPase domains that are coupled to these nucleotide-targeting- or proteolysis-induced complex-forming effectors. While widespread in bacteria, only a limited subset of nucleotide-targeting effectors was integrated into eukaryotic immune systems, suggesting barriers to interoperability across subcellular contexts. This work establishes nucleotide-degrading effectors as an emerging immune paradigm and traces their origins back to homologous domains in housekeeping systems.
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Affiliation(s)
- Gianlucca G Nicastro
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
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2
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Warneke R, Garbers TB, Herzberg C, Aschenbrandt G, Ficner R, Stülke J. Ornithine is the central intermediate in the arginine degradative pathway and its regulation in Bacillus subtilis. J Biol Chem 2023; 299:104944. [PMID: 37343703 PMCID: PMC10404663 DOI: 10.1016/j.jbc.2023.104944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023] Open
Abstract
The Gram-positive bacterium Bacillus subtilis can utilize several proteinogenic and non-proteinogenic amino acids as sources of carbon, nitrogen, and energy. The utilization of the amino acids arginine, citrulline, and ornithine is catalyzed by enzymes encoded in the rocABC and rocDEF operons and by the rocG gene. The expression of these genes is controlled by the alternative sigma factor SigL. RNA polymerase associated with this sigma factor depends on ATP-hydrolyzing transcription activators to initiate transcription. The RocR protein acts as a transcription activator for the roc genes. However, the details of amino acid metabolism via this pathway are unknown. Here, we investigated the contributions of all enzymes of the Roc pathway to the degradation of arginine, citrulline, and ornithine. We identified the previously uncharacterized RocB protein as responsible for the conversion of citrulline to ornithine. In vitro assays with the purified enzyme suggest that RocB acts as a manganese-dependent N-carbamoyl-L-ornithine hydrolase that cleaves citrulline to form ornithine and carbamate. Moreover, the molecular effector that triggers transcription activation by RocR has not been unequivocally identified. Using a combination of transcription reporter assays and biochemical experiments, we demonstrate that ornithine is the molecular inducer of RocR activity. Taken together, our work suggests that binding of ATP to RocR triggers its hexamerization, and binding of ornithine then allows ATP hydrolysis and activation of roc gene transcription. Thus, ornithine is the central molecule of the roc degradative pathway as it is the common intermediate of arginine and citrulline degradation and the molecular effector of RocR.
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Affiliation(s)
- Robert Warneke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Tim Benedict Garbers
- Department of Molecular Structural Biology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Christina Herzberg
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Georg Aschenbrandt
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany.
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3
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Surrett ED, Guckes KR, Cousins S, Ruskoski TB, Cecere AG, Ludvik DA, Okafor CD, Mandel MJ, Miyashiro TI. Two enhancer binding proteins activate σ 54-dependent transcription of a quorum regulatory RNA in a bacterial symbiont. eLife 2023; 12:e78544. [PMID: 37145113 PMCID: PMC10162802 DOI: 10.7554/elife.78544] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
To colonize a host, bacteria depend on an ensemble of signaling systems to convert information about the various environments encountered within the host into specific cellular activities. How these signaling systems coordinate transitions between cellular states in vivo remains poorly understood. To address this knowledge gap, we investigated how the bacterial symbiont Vibrio fischeri initially colonizes the light organ of the Hawaiian bobtail squid Euprymna scolopes. Previous work has shown that the small RNA Qrr1, which is a regulatory component of the quorum-sensing system in V. fischeri, promotes host colonization. Here, we report that transcriptional activation of Qrr1 is inhibited by the sensor kinase BinK, which suppresses cellular aggregation by V. fischeri prior to light organ entry. We show that Qrr1 expression depends on the alternative sigma factor σ54 and the transcription factors LuxO and SypG, which function similar to an OR logic gate, thereby ensuring Qrr1 is expressed during colonization. Finally, we provide evidence that this regulatory mechanism is widespread throughout the Vibrionaceae family. Together, our work reveals how coordination between the signaling pathways underlying aggregation and quorum-sensing promotes host colonization, which provides insight into how integration among signaling systems facilitates complex processes in bacteria.
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Affiliation(s)
- Ericka D Surrett
- Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Kirsten R Guckes
- Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Shyan Cousins
- Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Terry B Ruskoski
- Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Andrew G Cecere
- Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Denise A Ludvik
- Department of Medical Microbiology and Immunology, University of Wisconsin-MadisonMadisonUnited States
| | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Mark J Mandel
- Department of Medical Microbiology and Immunology, University of Wisconsin-MadisonMadisonUnited States
| | - Tim I Miyashiro
- Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
- The Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State UniversityUniversity ParkUnited States
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4
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Martínez-Rodríguez L, López-Sánchez A, García-Alcaide A, Govantes F, Gallegos MT. FleQ, FleN and c-di-GMP coordinately regulate cellulose production in Pseudomonas syringae pv. tomato DC3000. Front Mol Biosci 2023; 10:1155579. [PMID: 37051327 PMCID: PMC10083355 DOI: 10.3389/fmolb.2023.1155579] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
The second messenger cyclic di-GMP (c-di-GMP) controls the transition between motility and sessility in many bacterial species by a variety of mechanisms, including the production of multiple exopolysaccharides. Pseudomonas syringae pv. tomato (Pto) DC3000 is a plant pathogenic bacteria able to synthesize acetylated cellulose under high c-di-GMP levels thanks to the expression of the wssABCDEFGHI operon. Increased cellulose production enhances air-liquid biofilm formation and generates a wrinkled colony phenotype on solid media. We previously showed that under low levels of c-di-GMP, the regulators FleQ and AmrZ bound to adjacent sequences at the wss promoter inhibiting its expression, but only FleQ responded to the presence of c-di-GMP by activating cellulose production. In the present work, we advance in the knowledge of this complex regulation in Pto DC3000 by shedding light over the role of FleN in this process. The distinctive features of this system are that FleN and FleQ are both required for repression and activation of the wss operon under low and high c-di-GMP levels, respectively. We have also identified three putative FleQ binding sites at the wss promoter and show that FleQ/FleN-ATP binds at those sites under low c-di-GMP levels, inducing a distortion of DNA, impairing RNA polymerase binding, and repressing wss transcription. However, binding of c-di-GMP induces a conformational change in the FleQ/FleN-ATP complex, which relieves the DNA distortion, allows promoter access to the RNA polymerase, and leads to activation of wss transcription. On the other hand, AmrZ is always bound at the wss promoter limiting its expression independently of FleQ, FleN and c-di-GMP levels.
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Affiliation(s)
| | - Aroa López-Sánchez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Andrea García-Alcaide
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Fernando Govantes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, Sevilla, Spain
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - María-Trinidad Gallegos
- Department of Soil and Plant Microbiology, Granada, Spain
- *Correspondence: María-Trinidad Gallegos,
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5
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Molecular Mechanism and Agricultural Application of the NifA-NifL System for Nitrogen Fixation. Int J Mol Sci 2023; 24:ijms24020907. [PMID: 36674420 PMCID: PMC9866876 DOI: 10.3390/ijms24020907] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Nitrogen-fixing bacteria execute biological nitrogen fixation through nitrogenase, converting inert dinitrogen (N2) in the atmosphere into bioavailable nitrogen. Elaborating the molecular mechanisms of orderly and efficient biological nitrogen fixation and applying them to agricultural production can alleviate the "nitrogen problem". Azotobacter vinelandii is a well-established model bacterium for studying nitrogen fixation, utilizing nitrogenase encoded by the nif gene cluster to fix nitrogen. In Azotobacter vinelandii, the NifA-NifL system fine-tunes the nif gene cluster transcription by sensing the redox signals and energy status, then modulating nitrogen fixation. In this manuscript, we investigate the transcriptional regulation mechanism of the nif gene in autogenous nitrogen-fixing bacteria. We discuss how autogenous nitrogen fixation can better be integrated into agriculture, providing preliminary comprehensive data for the study of autogenous nitrogen-fixing regulation.
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6
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Ye F, Gao F, Liu X, Buck M, Zhang X. Mechanisms of DNA opening revealed in AAA+ transcription complex structures. SCIENCE ADVANCES 2022; 8:eadd3479. [PMID: 36542713 PMCID: PMC9770992 DOI: 10.1126/sciadv.add3479] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter complex, where DNA is opened up. In bacteria, RNAP relies on σ factors for its promoter specificities. Using a special form of sigma factor (σ54), which forms a stable closed complex and requires its activator that belongs to the AAA+ ATPases (ATPases associated with diverse cellular activities), we obtained cryo-electron microscopy structures of transcription initiation complexes that reveal a previously unidentified process of DNA melting opening. The σ54 amino terminus threads through the locally opened up DNA and then becomes enclosed by the AAA+ hexameric ring in the activator-bound intermediate complex. Our structures suggest how ATP hydrolysis by the AAA+ activator could remove the σ54 inhibition while helping to open up DNA, using σ54 amino-terminal peptide as a pry bar.
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Affiliation(s)
- Fuzhou Ye
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, South Kensington SW7 2AZ, UK
| | - Forson Gao
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, South Kensington SW7 2AZ, UK
| | - Xiaojiao Liu
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, South Kensington SW7 2AZ, UK
| | - Martin Buck
- Department of Life Sciences, Imperial College London, South Kensington SW7 2AZ, UK
| | - Xiaodong Zhang
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, South Kensington SW7 2AZ, UK
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7
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Ma M, Garza AG, Lemon DJ, Caro EA, Ritchie L, Ryan C, Spearing VM, Murphy KA, Welch RD. Identifying the Gene Regulatory Network of the Starvation-Induced Transcriptional Activator Nla28. J Bacteriol 2022; 204:e0026522. [PMID: 36448789 PMCID: PMC9765219 DOI: 10.1128/jb.00265-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/24/2022] [Indexed: 12/03/2022] Open
Abstract
Myxococcus xanthus copes with starvation by producing fruiting bodies filled with dormant and stress-resistant spores. Here, we aimed to better define the gene regulatory network associated with Nla28, a transcriptional activator/enhancer binding protein (EBP) and a key regulator of the early starvation response. Previous work showed that Nla28 directly regulates EBP genes that are important for fruiting body development. However, the Nla28 regulatory network is likely to be much larger because hundreds of starvation-induced genes are downregulated in a nla28 mutant strain. To identify candidates for direct Nla28-mediated transcription, we analyzed the downregulated genes using a bioinformatics approach. Nine potential Nla28 target promoters (29 genes) were discovered. The results of in vitro promoter binding assays, coupled with in vitro and in vivo mutational analyses, suggested that the nine promoters along with three previously identified EBP gene promoters were indeed in vivo targets of Nla28. These results also suggested that Nla28 used tandem, imperfect repeats of an 8-bp sequence for promoter binding. Interestingly, eight of the new Nla28 target promoters were predicted to be intragenic. Based on mutational analyses, the newly identified Nla28 target loci contained at least one gene that was important for starvation-induced development. Most of these loci contained genes predicted to be involved in metabolic or defense-related functions. Using the consensus Nla28 binding sequence, bioinformatics, and expression profiling, 58 additional promoters and 102 genes were tagged as potential Nla28 targets. Among these putative Nla28 targets, functions, such as regulatory, metabolic, and cell envelope biogenesis, were assigned to many genes. IMPORTANCE In bacteria, starvation leads to profound changes in behavior and physiology. Some of these changes have economic and health implications because the starvation response has been linked to the formation of biofilms, virulence, and antibiotic resistance. To better understand how starvation contributes to changes in bacterial physiology and resistance, we identified the putative starvation-induced gene regulatory network associated with Nla28, a transcriptional activator from the bacterium Myxoccocus xanthus. We determined the mechanism by which starvation-responsive genes were activated by Nla28 and showed that several of the genes were important for the formation of a highly resistant cell type.
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Affiliation(s)
- Muqing Ma
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Anthony G. Garza
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - David J. Lemon
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Eduardo A. Caro
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Linnea Ritchie
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Charles Ryan
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | | | | | - Roy D. Welch
- Department of Biology, Syracuse University, Syracuse, New York, USA
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8
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Pacheco-Sánchez D, Marín P, Molina-Fuentes Á, Marqués S. Subtle sequence differences between two interacting σ 54 -dependent regulators lead to different activation mechanisms. FEBS J 2022; 289:7582-7604. [PMID: 35816183 PMCID: PMC10084136 DOI: 10.1111/febs.16576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/08/2022] [Accepted: 07/10/2022] [Indexed: 12/13/2022]
Abstract
In the strictly anaerobic nitrate reducing bacterium Aromatoleum anaerobium, degradation of 1,3-dihydroxybenzene (1,3-DHB, resorcinol) is controlled by two bacterial enhancer-binding proteins (bEBPs), RedR1 and RedR2, which regulate the transcription of three σ54 -dependent promoters controlling expression of the pathway. RedR1 and RedR2 are identical over their length except for their N-terminal tail which differ in sequence and length (six and eight residues, respectively), a single change in their N-terminal domain (NTD), and nine non-identical residues in their C-terminal domain (CTD). Their NTD is composed of a GAF and a PAS domain connected by a linker helix. We show that each regulator is controlled by a different mechanism: whilst RedR1 responds to the classical NTD-mediated negative regulation that is released by the presence of its effector, RedR2 activity is constitutive and controlled through interaction with BtdS, an integral membrane subunit of hydroxyhydroquinone dehydrogenase carrying out the second step in 1,3-DHB degradation. BtdS sequesters the RedR2 regulator to the membrane through its NTD, where a four-Ile track in the PAS domain, interrupted by a Thr in RedR1, and the N-terminal tail are involved. The presence of 1,3-DHB, which is metabolized to hydroxybenzoquinone, releases RedR2 from the membrane. Most bEBPs assemble into homohexamers to activate transcription; we show that hetero-oligomer formation between RedR1 and RedR2 is favoured over homo-oligomers. However, either an NTD-truncated version of RedR1 or a full-length RedR2 are capable of promoter activation on their own, suggesting they should assemble into homohexamers in vivo. We show that promoter DNA behaves as an allosteric effector through binding the CTD to control ΔNTD-RedR1 multimerization and activity. Overall, the regulation of the 1,3-DHB anaerobic degradation pathway can be described as a novel mode of bEBP activation and assembly.
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Affiliation(s)
- Daniel Pacheco-Sánchez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Patricia Marín
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Águeda Molina-Fuentes
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Silvia Marqués
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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9
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Hsieh ML, Kiel N, Jenkins L, Ng WL, Knipling L, Waters C, Hinton D. The Vibrio cholerae master regulator for the activation of biofilm biogenesis genes, VpsR, senses both cyclic di-GMP and phosphate. Nucleic Acids Res 2022; 50:4484-4499. [PMID: 35438787 PMCID: PMC9071405 DOI: 10.1093/nar/gkac253] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/11/2022] [Accepted: 03/30/2022] [Indexed: 01/07/2023] Open
Abstract
Vibrio cholerae biofilm formation/maintenance is controlled by myriad factors; chief among these are the regulator VpsR and cyclic di-guanosine monophosphate (c-di-GMP). VpsR has strong sequence similarity to enhancer binding proteins (EBPs) that activate RNA polymerase containing sigma factor σ54. However, we have previously shown that transcription from promoters within the biofilm biogenesis/maintenance pathways uses VpsR, c-di-GMP and RNA polymerase containing the primary sigma factor (σ70). Previous work suggested that phosphorylation of VpsR at a highly conserved aspartate, which is phosphorylated in other EBPs, might also contribute to activation. Using the biofilm biogenesis promoter PvpsL, we show that in the presence of c-di-GMP, either wild type or the phospho-mimic VpsR D59E activates PvpsL transcription, while the phospho-defective D59A variant does not. Furthermore, when c-di-GMP levels are low, acetyl phosphate (Ac∼P) is required for significant VpsR activity in vivo and in vitro. Although these findings argue that VpsR phosphorylation is needed for activation, we show that VpsR is not phosphorylated or acetylated by Ac∼P and either sodium phosphate or potassium phosphate, which are not phosphate donors, fully substitutes for Ac∼P. We conclude that VpsR is an unusual regulator that senses phosphate directly, rather than through phosphorylation, to aid in the decision to form/maintain biofilm.
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Affiliation(s)
- Meng-Lun Hsieh
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Niklas Kiel
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Lisa M Miller Jenkins
- Collaborative Protein Technology Resource, Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wai-Leung Ng
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Leslie Knipling
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher M Waters
- Correspondence may also be addressed to Christopher M. Waters. Tel: +1 517 884 5360; Fax: +1 517 355 6463;
| | - Deborah M Hinton
- To whom correspondence should be addressed. Tel: +1 301 496 9885; Fax: +1 301 402 0053;
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10
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Neuwald AF, Yang H, Tracy Nixon B. SPARC: Structural properties associated with residue constraints. Comput Struct Biotechnol J 2022; 20:1702-1715. [PMID: 35495120 PMCID: PMC9020082 DOI: 10.1016/j.csbj.2022.04.005] [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: 11/23/2021] [Revised: 03/22/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
SPARC facilitates the generation of plausible hypotheses regarding underlying biochemical mechanisms by structurally characterizing protein sequence constraints. Such constraints appear as residues co-conserved in functionally related subgroups, as subtle pairwise correlations (i.e., direct couplings), and as correlations among these sequence features or with structural features. SPARC performs three types of analyses. First, based on pairwise sequence correlations, it estimates the biological relevance of alternative conformations and of homomeric contacts, as illustrated here for death domains. Second, it estimates the statistical significance of the correspondence between directly coupled residue pairs and interactions at heterodimeric interfaces. Third, given molecular dynamics simulated structures, it characterizes interactions among constrained residues or between such residues and ligands that: (a) are stably maintained during the simulation; (b) undergo correlated formation and/or disruption of interactions with other constrained residues; or (c) switch between alternative interactions. We illustrate this for two homohexameric complexes: the bacterial enhancer binding protein (bEBP) NtrC1, which activates transcription by remodeling RNA polymerase (RNAP) containing σ54, and for DnaB helicase, which opens DNA at the bacterial replication fork. Based on the NtrC1 analysis, we hypothesize possible mechanisms for inhibiting ATP hydrolysis until ADP is released from an adjacent subunit and for coupling ATP hydrolysis to restructuring of σ54 binding loops. Based on the DnaB analysis, we hypothesize that DnaB 'grabs' ssDNA by flipping every fourth base and inserting it into cavities between subunits and that flipping of a DnaB-specific glutamine residue triggers ATP hydrolysis.
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Affiliation(s)
- Andrew F. Neuwald
- Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, 670 W. Baltimore Steet, Baltimore, MD 21201, USA,Corresponding author.
| | - Hui Yang
- Department of Biology. Penn State University, 304A Frear South Building, University Park, PA 16802
| | - B. Tracy Nixon
- Department of Biochemistry and Molecular Biology, 335 Frear South Building, University Park, PA 16802, USA
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11
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Allsopp LP, Collins ACZ, Hawkins E, Wood TE, Filloux A. RpoN/Sfa2-dependent activation of the Pseudomonas aeruginosa H2-T6SS and its cognate arsenal of antibacterial toxins. Nucleic Acids Res 2022; 50:227-243. [PMID: 34928327 PMCID: PMC8855297 DOI: 10.1093/nar/gkab1254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/26/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa uses three type six secretion systems (H1-, H2- and H3-T6SS) to manipulate its environment, subvert host cells and for microbial competition. These T6SS machines are loaded with a variety of effectors/toxins, many being associated with a specific VgrG. How P. aeruginosa transcriptionally coordinates the main T6SS clusters and the multiple vgrG islands spread through the genome is unknown. Here we show an unprecedented level of control with RsmA repressing most known T6SS-related genes. Moreover, each of the H2- and H3-T6SS clusters encodes a sigma factor activator (SFA) protein called, Sfa2 and Sfa3, respectively. SFA proteins are enhancer binding proteins necessary for the sigma factor RpoN. Using a combination of RNA-seq, ChIP-seq and molecular biology approaches, we demonstrate that RpoN coordinates the T6SSs of P. aeruginosa by activating the H2-T6SS but repressing the H1- and H3-T6SS. Furthermore, RpoN and Sfa2 control the expression of the H2-T6SS-linked VgrGs and their effector arsenal to enable very effective interbacterial killing. Sfa2 is specific as Sfa3 from the H3-T6SS cannot complement loss of Sfa2. Our study further delineates the regulatory mechanisms that modulate the deployment of an arsenal of T6SS effectors likely enabling P. aeruginosa to adapt to a range of environmental conditions.
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Affiliation(s)
- Luke P Allsopp
- Department of Life Sciences, MRC Centre for Molecular
Bacteriology and Infection, Imperial College London,
London, UK
- National Heart and Lung Institute, Imperial College
London, London, UK
| | - Alice C Z Collins
- National Heart and Lung Institute, Imperial College
London, London, UK
| | - Eleanor Hawkins
- Department of Life Sciences, MRC Centre for Molecular
Bacteriology and Infection, Imperial College London,
London, UK
| | - Thomas E Wood
- Department of Life Sciences, MRC Centre for Molecular
Bacteriology and Infection, Imperial College London,
London, UK
| | - Alain Filloux
- Department of Life Sciences, MRC Centre for Molecular
Bacteriology and Infection, Imperial College London,
London, UK
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12
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Ma X, Ma L, Huo YX. Reconstructing the transcription regulatory network to optimize resource allocation for robust biosynthesis. Trends Biotechnol 2021; 40:735-751. [PMID: 34895933 DOI: 10.1016/j.tibtech.2021.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022]
Abstract
An ideal microbial cell factory (MCF) should deliver maximal resources to production, which conflicts with the microbe's native growth-oriented resource allocation strategy and can therefore lead to early termination of the high-yield period. Reallocating resources from growth to production has become a critical factor in constructing robust MCFs. Instead of strengthening specific biosynthetic pathways, emerging endeavors are focused on rearranging the gene regulatory network to fundamentally reprogram the resource allocation pattern. Combining this idea with transcriptional regulation within the hierarchical regulatory network, this review discusses recent engineering strategies targeting the transcription machinery, module networks, regulatory edges, and bottom network layer. This global view will help to construct a production-oriented phenotype that fully harnesses the potential of MCFs.
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Affiliation(s)
- Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China
| | - Lianjie Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China; Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, People's Republic of China.
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13
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Yu C, Yang F, Xue D, Wang X, Chen H. The Regulatory Functions of σ 54 Factor in Phytopathogenic Bacteria. Int J Mol Sci 2021; 22:ijms222312692. [PMID: 34884502 PMCID: PMC8657755 DOI: 10.3390/ijms222312692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
σ54 factor (RpoN), a type of transcriptional regulatory factor, is widely found in pathogenic bacteria. It binds to core RNA polymerase (RNAP) and regulates the transcription of many functional genes in an enhancer-binding protein (EBP)-dependent manner. σ54 has two conserved functional domains: the activator-interacting domain located at the N-terminal and the DNA-binding domain located at the C-terminal. RpoN directly binds to the highly conserved sequence, GGN10GC, at the −24/−12 position relative to the transcription start site of target genes. In general, bacteria contain one or two RpoNs but multiple EBPs. A single RpoN can bind to different EBPs in order to regulate various biological functions. Thus, the overlapping and unique regulatory pathways of two RpoNs and multiple EBP-dependent regulatory pathways form a complex regulatory network in bacteria. However, the regulatory role of RpoN and EBPs is still poorly understood in phytopathogenic bacteria, which cause economically important crop diseases and pose a serious threat to world food security. In this review, we summarize the current knowledge on the regulatory function of RpoN, including swimming motility, flagella synthesis, bacterial growth, type IV pilus (T4Ps), twitching motility, type III secretion system (T3SS), and virulence-associated phenotypes in phytopathogenic bacteria. These findings and knowledge prove the key regulatory role of RpoN in bacterial growth and pathogenesis, as well as lay the groundwork for further elucidation of the complex regulatory network of RpoN in bacteria.
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Affiliation(s)
- Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (F.Y.)
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (F.Y.)
| | - Dingrong Xue
- National Engineering Laboratory of Grain Storage and Logistics, Academy of National Food and Strategic Reserves Administration, No. 11 Baiwanzhuang Street, Xicheng District, Beijing 100037, China;
| | - Xiuna Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (C.Y.); (F.Y.)
- Correspondence:
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14
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Sensing of intracellular Hcp levels controls T6SS expression in Vibrio cholerae. Proc Natl Acad Sci U S A 2021; 118:2104813118. [PMID: 34161288 DOI: 10.1073/pnas.2104813118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The type 6 secretion system (T6SS) is a bacterial weapon broadly distributed in gram-negative bacteria and used to kill competitors and predators. Featuring a long and double-tubular structure, this molecular machine is energetically costly to produce and thus is likely subject to diverse regulation strategies that are largely ill defined. In this study, we report a quantity-sensing control of the T6SS that down-regulates the expression of secreted components when they accumulate in the cytosol due to T6SS inactivation. Using Vibrio cholerae strains that constitutively express an active T6SS, we demonstrate that mRNA levels of secreted components, including the inner-tube protein component Hcp, were down-regulated in T6SS structural gene mutants while expression of the main structural genes remained unchanged. Deletion of both hcp gene copies restored expression from their promoters, while Hcp overexpression negatively impacted expression. We show that Hcp directly interacts with the RpoN-dependent T6SS regulator VasH, and deleting the N-terminal regulator domain of VasH abolishes this interaction as well as the expression difference of hcp operons between T6SS-active and inactive strains. We find that negative regulation of hcp also occurs in other V. cholerae strains and the pathogens Aeromonas dhakensis and Pseudomonas aeruginosa This Hcp-dependent sensing control is likely an important energy-conserving mechanism that enables T6SS-encoding organisms to quickly adjust T6SS expression and prevent wasteful build-up of its major secreted components in the absence of their efficient export out of the bacterial cell.
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15
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Mayer B, Schwan M, Oviedo-Bocanegra LM, Bange G, Thormann KM, Graumann PL. Dynamics of Bacterial Signal Recognition Particle at a Single Molecule Level. Front Microbiol 2021; 12:663747. [PMID: 33995327 PMCID: PMC8120034 DOI: 10.3389/fmicb.2021.663747] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/18/2021] [Indexed: 11/21/2022] Open
Abstract
We have studied the localization and dynamics of bacterial Ffh, part of the SRP complex, its receptor FtsY, and of ribosomes in the Gamma-proteobacterium Shewanella putrefaciens. Using structured illumination microscopy, we show that ribosomes show a pronounced accumulation at the cell poles, whereas SRP and FtsY are distributed at distinct sites along the cell membrane, but they are not accumulated at the poles. Single molecule dynamics can be explained by assuming that all three proteins/complexes move as three distinguishable mobility fractions: a low mobility/static fraction may be engaged in translation, medium-fast diffusing fractions may be transition states, and high mobility populations likely represent freely diffusing molecules/complexes. Diffusion constants suggest that SRP and FtsY move together with slow-mobile ribosomes. Inhibition of transcription leads to loss of static molecules and reduction of medium-mobile fractions, in favor of freely diffusing subunits, while inhibition of translation appears to stall the medium mobile fractions. Depletion of FtsY leads to aggregation of Ffh, but not to loss of the medium mobile fraction, indicating that Ffh/SRP can bind to ribosomes independently from FtsY. Heat maps visualizing the three distinct diffusive populations show that while static molecules are mostly clustered at the cell membrane, diffusive molecules are localized throughout the cytosol. The medium fast populations show an intermediate pattern of preferential localization, suggesting that SRP/FtsY/ribosome transition states may form within the cytosol to finally find a translocon.
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Affiliation(s)
- Benjamin Mayer
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Meike Schwan
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Luis M. Oviedo-Bocanegra
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Kai M. Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Peter L. Graumann
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
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16
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Multiple, short protein binding motifs in ORC1 and CDC6 control the initiation of DNA replication. Mol Cell 2021; 81:1951-1969.e6. [PMID: 33761311 DOI: 10.1016/j.molcel.2021.03.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/18/2021] [Accepted: 02/27/2021] [Indexed: 12/18/2022]
Abstract
The initiation of DNA replication involves cell cycle-dependent assembly and disassembly of protein complexes, including the origin recognition complex (ORC) and CDC6 AAA+ ATPases. We report that multiple short linear protein motifs (SLiMs) within intrinsically disordered regions (IDRs) in ORC1 and CDC6 mediate cyclin-CDK-dependent and independent protein-protein interactions, conditional on the cell cycle phase. A domain within the ORC1 IDR is required for interaction between the ORC1 and CDC6 AAA+ domains in G1, whereas the same domain prevents CDC6-ORC1 interaction during mitosis. Then, during late G1, this domain facilitates ORC1 destruction by a SKP2-cyclin A-CDK2-dependent mechanism. During G1, the CDC6 Cy motif cooperates with cyclin E-CDK2 to promote ORC1-CDC6 interactions. The CDC6 IDR regulates self-interaction by ORC1, thereby controlling ORC1 protein levels. Protein phosphatase 1 binds directly to a SLiM in the ORC1 IDR, causing ORC1 de-phosphorylation upon mitotic exit, increasing ORC1 protein, and promoting pre-RC assembly.
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17
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Ma M, Welch RD, Garza AG. The σ 54 system directly regulates bacterial natural product genes. Sci Rep 2021; 11:4771. [PMID: 33637792 PMCID: PMC7910581 DOI: 10.1038/s41598-021-84057-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023] Open
Abstract
Bacterial-derived polyketide and non-ribosomal peptide natural products are crucial sources of therapeutics and yet little is known about the conditions that favor activation of natural product genes or the regulatory machinery controlling their transcription. Recent findings suggest that the σ54 system, which includes σ54-loaded RNA polymerase and transcriptional activators called enhancer binding proteins (EBPs), might be a common regulator of natural product genes. Here, we explored this idea by analyzing a selected group of putative σ54 promoters identified in Myxococcus xanthus natural product gene clusters. We show that mutations in putative σ54-RNA polymerase binding regions and in putative Nla28 EBP binding sites dramatically reduce in vivo promoter activities in growing and developing cells. We also show in vivo promoter activities are reduced in a nla28 mutant, that Nla28 binds to wild-type fragments of these promoters in vitro, and that in vitro binding is lost when the Nla28 binding sites are mutated. Together, our results indicate that M. xanthus uses σ54 promoters for transcription of at least some of its natural product genes. Interestingly, the vast majority of experimentally confirmed and putative σ54 promoters in M. xanthus natural product loci are located within genes and not in intergenic sequences.
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Affiliation(s)
- Muqing Ma
- grid.264484.80000 0001 2189 1568Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244 USA
| | - Roy D. Welch
- grid.264484.80000 0001 2189 1568Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244 USA
| | - Anthony G. Garza
- grid.264484.80000 0001 2189 1568Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244 USA
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18
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Fiévet A, Merrouch M, Brasseur G, Eve D, Biondi EG, Valette O, Pauleta SR, Dolla A, Dermoun Z, Burlat B, Aubert C. OrpR is a σ 54 -dependent activator using an iron-sulfur cluster for redox sensing in Desulfovibrio vulgaris Hildenborough. Mol Microbiol 2021; 116:231-244. [PMID: 33595838 PMCID: PMC8359166 DOI: 10.1111/mmi.14705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 01/15/2023]
Abstract
Enhancer binding proteins (EBPs) are key players of σ54 -regulation that control transcription in response to environmental signals. In the anaerobic microorganism Desulfovibrio vulgaris Hildenborough (DvH), orp operons have been previously shown to be coregulated by σ54 -RNA polymerase, the integration host factor IHF and a cognate EBP, OrpR. In this study, ChIP-seq experiments indicated that the OrpR regulon consists of only the two divergent orp operons. In vivo data revealed that (i) OrpR is absolutely required for orp operons transcription, (ii) under anaerobic conditions, OrpR binds on the two dedicated DNA binding sites and leads to high expression levels of the orp operons, (iii) increasing the redox potential of the medium leads to a drastic down-regulation of the orp operons expression. Moreover, combining functional and biophysical studies on the anaerobically purified OrpR leads us to propose that OrpR senses redox potential variations via a redox-sensitive [4Fe-4S]2+ cluster in the sensory PAS domain. Overall, the study herein presents the first characterization of a new Fe-S redox regulator belonging to the σ54 -dependent transcriptional regulator family probably advantageously selected by cells adapted to the anaerobic lifestyle to monitor redox stress conditions.
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Affiliation(s)
| | | | | | - Danaé Eve
- Aix Marseille Univ, CNRS, LCB, Marseille, France
| | | | | | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO, REQUIMTE, Dept. Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Alain Dolla
- Aix Marseille Univ, Toulon Univ, CNRS, IRD, MIO, Marseille, France
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19
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Jessop M, Felix J, Gutsche I. AAA+ ATPases: structural insertions under the magnifying glass. Curr Opin Struct Biol 2021; 66:119-128. [PMID: 33246198 PMCID: PMC7973254 DOI: 10.1016/j.sbi.2020.10.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/19/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022]
Abstract
AAA+ ATPases are a diverse protein superfamily which power a vast number of cellular processes, from protein degradation to genome replication and ribosome biogenesis. The latest advances in cryo-EM have resulted in a spectacular increase in the number and quality of AAA+ ATPase structures. This abundance of new information enables closer examination of different types of structural insertions into the conserved core, revealing discrepancies in the current classification of AAA+ modules into clades. Additionally, combined with biochemical data, it has allowed rapid progress in our understanding of structure-functional relationships and provided arguments both in favour and against the existence of a unifying molecular mechanism for the ATPase activity and action on substrates, stimulating further intensive research.
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Affiliation(s)
- Matthew Jessop
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France.
| | - Jan Felix
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France.
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20
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Knittel V, Sadana P, Seekircher S, Stolle AS, Körner B, Volk M, Jeffries CM, Svergun DI, Heroven AK, Scrima A, Dersch P. RovC - a novel type of hexameric transcriptional activator promoting type VI secretion gene expression. PLoS Pathog 2020; 16:e1008552. [PMID: 32966346 PMCID: PMC7535981 DOI: 10.1371/journal.ppat.1008552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/05/2020] [Accepted: 08/01/2020] [Indexed: 12/05/2022] Open
Abstract
Type VI secretion systems (T6SSs) are complex macromolecular injection machines which are widespread in Gram-negative bacteria. They are involved in host-cell interactions and pathogenesis, required to eliminate competing bacteria, or are important for the adaptation to environmental stress conditions. Here we identified regulatory elements controlling the T6SS4 of Yersinia pseudotuberculosis and found a novel type of hexameric transcription factor, RovC. RovC directly interacts with the T6SS4 promoter region and activates T6SS4 transcription alone or in cooperation with the LysR-type regulator RovM. A higher complexity of regulation was achieved by the nutrient-responsive global regulator CsrA, which controls rovC expression on the transcriptional and post-transcriptional level. In summary, our work unveils a central mechanism in which RovC, a novel key activator, orchestrates the expression of the T6SS weapons together with a global regulator to deploy the system in response to the availability of nutrients in the species' native environment.
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Affiliation(s)
- Vanessa Knittel
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Pooja Sadana
- Young Investigator Group Structural Biology of Autophagy, Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stephanie Seekircher
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Anne-Sophie Stolle
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Germany
| | - Britta Körner
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Germany
| | - Marcel Volk
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Ann Kathrin Heroven
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andrea Scrima
- Young Investigator Group Structural Biology of Autophagy, Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Germany
- German Center for Infection Research, Baunschweig, Germany
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21
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Bylino OV, Ibragimov AN, Shidlovskii YV. Evolution of Regulated Transcription. Cells 2020; 9:E1675. [PMID: 32664620 PMCID: PMC7408454 DOI: 10.3390/cells9071675] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The genomes of all organisms abound with various cis-regulatory elements, which control gene activity. Transcriptional enhancers are a key group of such elements in eukaryotes and are DNA regions that form physical contacts with gene promoters and precisely orchestrate gene expression programs. Here, we follow gradual evolution of this regulatory system and discuss its features in different organisms. In eubacteria, an enhancer-like element is often a single regulatory element, is usually proximal to the core promoter, and is occupied by one or a few activators. Activation of gene expression in archaea is accompanied by the recruitment of an activator to several enhancer-like sites in the upstream promoter region. In eukaryotes, activation of expression is accompanied by the recruitment of activators to multiple enhancers, which may be distant from the core promoter, and the activators act through coactivators. The role of the general DNA architecture in transcription control increases in evolution. As a whole, it can be seen that enhancers of multicellular eukaryotes evolved from the corresponding prototypic enhancer-like regulatory elements with the gradually increasing genome size of organisms.
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Affiliation(s)
- Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
| | - Airat N. Ibragimov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (O.V.B.); (A.N.I.)
- I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia
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22
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Camarena L, Dreyfus G. Living in a Foster Home: The Single Subpolar Flagellum Fla1 of Rhodobacter sphaeroides. Biomolecules 2020; 10:E774. [PMID: 32429424 PMCID: PMC7277832 DOI: 10.3390/biom10050774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/14/2022] Open
Abstract
Rhodobacter sphaeroides is an α-proteobacterium that has the particularity of having two functional flagellar systems used for swimming. Under the growth conditions commonly used in the laboratory, a single subpolar flagellum that traverses the cell membrane, is assembled on the surface. This flagellum has been named Fla1. Phylogenetic analyses have suggested that this flagellar genetic system was acquired from an ancient γ-proteobacterium. It has been shown that this flagellum has components homologous to those present in other γ-proteobacteria such as the H-ring characteristic of the Vibrio species. Other features of this flagellum such as a straight hook, and a prominent HAP region have been studied and the molecular basis underlying these features has been revealed. It has also been shown that FliL, and the protein MotF, mainly found in several species of the family Rhodobacteraceae, contribute to remodel the amphipathic region of MotB, known as the plug, in order to allow flagellar rotation. In the absence of the plug region of MotB, FliL and MotF are dispensable. In this review we have covered the most relevant aspects of the Fla1 flagellum of this remarkable photosynthetic bacterium.
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Affiliation(s)
- Laura Camarena
- Depto. Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX 04510, Mexico
| | - Georges Dreyfus
- Depto. Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX 04510, Mexico
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