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Zeng X, Huang M, Sun QX, Peng YJ, Xu X, Tang YB, Zhang JY, Yang Y, Zhang CC. A c-di-GMP binding effector controls cell size in a cyanobacterium. Proc Natl Acad Sci U S A 2023; 120:e2221874120. [PMID: 36947515 PMCID: PMC10068817 DOI: 10.1073/pnas.2221874120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial signaling molecule. It is also a critical player in the regulation of cell size and cell behaviors such as cell aggregation and phototaxis in cyanobacteria, which constitute an important group of prokaryotes for their roles in the ecology and evolution of the Earth. However, c-di-GMP receptors have never been revealed in cyanobacteria. Here, we report the identification of a c-di-GMP receptor, CdgR, from the filamentous cyanobacterium Anabaena PCC 7120. Crystal structural analysis and genetic studies demonstrate that CdgR binds c-di-GMP at the dimer interface and this binding is required for the control of cell size in a c-di-GMP-dependent manner. Different functions of CdgR, in ligand binding and signal transmission, could be separated genetically, allowing us to dissect its molecular signaling functions. The presence of the apo-form of CdgR triggers cell size reduction, consistent with the similar effects observed with a decrease of c-di-GMP levels in cells. Furthermore, we found that CdgR exerts its function by interacting with a global transcription factor DevH, and this interaction was inhibited by c-di-GMP. The lethal effect triggered by conditional depletion of DevH or by the production of several point-mutant proteins of CdgR in cells indicates that this signaling pathway plays critical functions in Anabaena. Our studies revealed a mechanism of c-di-GMP signaling in the control of cell size, an important and complex trait for bacteria. CdgR is highly conserved in cyanobacteria, which will greatly expand our understanding of the roles of c-di-GMP signaling in these organisms.
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Affiliation(s)
- Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Min Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Qing-Xue Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Ye-Jun Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Xiaomei Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Yun-Bin Tang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Institut AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei430070, People’s Republic of China
- Innovation Academy for Seed Design Chinese Academy of Sciences, Beijing100049, People’s Republic of China
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ComFC mediates transport and handling of single-stranded DNA during natural transformation. Nat Commun 2022; 13:1961. [PMID: 35414142 PMCID: PMC9005727 DOI: 10.1038/s41467-022-29494-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
The ComFC protein is essential for natural transformation, a process that plays a major role in the spread of antibiotic resistance genes and virulence factors across bacteria. However, its role remains largely unknown. Here, we show that Helicobacter pylori ComFC is involved in DNA transport through the cell membrane, and is required for the handling of the single-stranded DNA once it is delivered into the cytoplasm. The crystal structure of ComFC includes a zinc-finger motif and a putative phosphoribosyl transferase domain, both necessary for the protein's in vivo activity. Furthermore, we show that ComFC is a membrane-associated protein with affinity for single-stranded DNA. Our results suggest that ComFC provides the link between the transport of the transforming DNA into the cytoplasm and its handling by the recombination machinery.
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Pilloni G, Cao F, Ruhmel M, Mishra P. Proteins identified through predictive metagenomics as potential biomarkers for the detection of microbiologically influenced corrosion. J Ind Microbiol Biotechnol 2022; 49:kuab068. [PMID: 34543407 PMCID: PMC9113181 DOI: 10.1093/jimb/kuab068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/11/2021] [Indexed: 01/04/2023]
Abstract
The unpredictability of microbial growth and subsequent localized corrosion of steel can cause significant cost for the oil and gas industry, due to production downtime, repair, and replacement. Despite a long tradition of academic research and industrial experience, microbial corrosion is not yet fully understood and thus not effectively controlled. In particular, biomarkers suitable for diagnosing microbial corrosion which abstain from the detection of the classic signatures of sulfate-reducing bacteria are urgently required. In this study, a natural microbial community was enriched anaerobically with carbon steel coupons and in the presence of a variety of physical and chemical conditions. With the characterization of the microbiome and of its functional properties inferred through predictive metagenomics, a series of proteins were identified as biomarkers in the water phase that could be correlated directly to corrosion. This study provides an opportunity for the further development of a protein-based biomarker approach for effective and reliable microbial corrosion detection and monitoring in the field.
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Affiliation(s)
- Giovanni Pilloni
- Corporate Strategic Research, ExxonMobil Research and Engineering Company, Annandale, NJ 08801, USA
| | - Fang Cao
- Corporate Strategic Research, ExxonMobil Research and Engineering Company, Annandale, NJ 08801, USA
| | - Megan Ruhmel
- Corporate Strategic Research, ExxonMobil Research and Engineering Company, Annandale, NJ 08801, USA
| | - Pooja Mishra
- Corporate Strategic Research, ExxonMobil Research and Engineering Company, Annandale, NJ 08801, USA
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De Santis M, Hahn J, Dubnau D. ComEB protein is dispensable for the transformation but must be translated for the optimal synthesis of comEC. Mol Microbiol 2021; 116:71-79. [PMID: 33527432 DOI: 10.1111/mmi.14690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/05/2023]
Abstract
We show that the ComEB protein is not required for transformation in Bacillus subtilis, despite its expression from within the comE operon under competence control, nor is it required for the correct polar localization of ComGA. We show further that the synthesis of the putative channel protein ComEC is translationally coupled to the upstream comEB open reading frame, so that the translation of comEB and a suboptimal ribosomal-binding site embedded in its sequence are needed for proper comEC expression. Translational coupling appears to be a common mechanism in three major competence operons for the adjustment of protein amounts independent of transcriptional control, probably ensuring the correct stoichiometries for assembly of the transformation machinery. comEB and comFC, respectively, encode cytidine deaminase and a protein resembling type 1 phosphoribosyl transferases and we speculate that nucleotide scavenging proteins are produced under competence control for efficient reutilization of the products of degradation of the non-transforming strand during DNA uptake.
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Affiliation(s)
- Micaela De Santis
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Jeanette Hahn
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - David Dubnau
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
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5
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Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell. Proc Natl Acad Sci U S A 2018; 115:12465-12470. [PMID: 30455297 PMCID: PMC6298092 DOI: 10.1073/pnas.1807709115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Phylogenetic evidence suggests that the invasion and proliferation of retroelements, selfish mobile genetic elements that copy and paste themselves within a host genome, was one of the early evolutionary events in the emergence of eukaryotes. Here we test the effects of this event by determining the pressures retroelements exert on simple genomes. We transferred two retroelements, human LINE-1 and the bacterial group II intron Ll.LtrB, into bacteria, and find that both are functional and detrimental to growth. We find, surprisingly, that retroelement lethality and proliferation are enhanced by the ability to perform eukaryotic-like nonhomologous end-joining (NHEJ) DNA repair. We show that the only stable evolutionary consequence in simple cells is maintenance of retroelements in low numbers, suggesting how retrotransposition rates and costs in early eukaryotes could have been constrained to allow proliferation. Our results suggest that the interplay between NHEJ and retroelements may have played a fundamental and previously unappreciated role in facilitating the proliferation of retroelements, elements of which became the ancestors of the spliceosome components in eukaryotes.
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Chilton SS, Falbel TG, Hromada S, Burton BM. A Conserved Metal Binding Motif in the Bacillus subtilis Competence Protein ComFA Enhances Transformation. J Bacteriol 2017; 199:e00272-17. [PMID: 28559293 PMCID: PMC5512226 DOI: 10.1128/jb.00272-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/18/2017] [Indexed: 02/05/2023] Open
Abstract
Genetic competence is a process in which cells are able to take up DNA from their environment, resulting in horizontal gene transfer, a major mechanism for generating diversity in bacteria. Many bacteria carry homologs of the central DNA uptake machinery that has been well characterized in Bacillus subtilis It has been postulated that the B. subtilis competence helicase ComFA belongs to the DEAD box family of helicases/translocases. Here, we made a series of mutants to analyze conserved amino acid motifs in several regions of B. subtilis ComFA. First, we confirmed that ComFA activity requires amino acid residues conserved among the DEAD box helicases, and second, we show that a zinc finger-like motif consisting of four cysteines is required for efficient transformation. Each cysteine in the motif is important, and mutation of at least two of the cysteines dramatically reduces transformation efficiency. Further, combining multiple cysteine mutations with the helicase mutations shows an additive phenotype. Our results suggest that the helicase and metal binding functions are two distinct activities important for ComFA function during transformation.IMPORTANCE ComFA is a highly conserved protein that has a role in DNA uptake during natural competence, a mechanism for horizontal gene transfer observed in many bacteria. Investigation of the details of the DNA uptake mechanism is important for understanding the ways in which bacteria gain new traits from their environment, such as drug resistance. To dissect the role of ComFA in the DNA uptake machinery, we introduced point mutations into several motifs in the protein sequence. We demonstrate that several amino acid motifs conserved among ComFA proteins are important for efficient transformation. This report is the first to demonstrate the functional requirement of an amino-terminal cysteine motif in ComFA.
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Affiliation(s)
- Scott S Chilton
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Tanya G Falbel
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
| | - Susan Hromada
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
| | - Briana M Burton
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA
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Diallo A, Foster HR, Gromek KA, Perry TN, Dujeancourt A, Krasteva PV, Gubellini F, Falbel TG, Burton BM, Fronzes R. Bacterial transformation: ComFA is a DNA-dependent ATPase that forms complexes with ComFC and DprA. Mol Microbiol 2017; 105:741-754. [DOI: 10.1111/mmi.13732] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Amy Diallo
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
- Université Pierre et Marie Curie; Paris France
| | | | | | - Thomas N. Perry
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
| | - Annick Dujeancourt
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
| | - Petya V. Krasteva
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
| | - Francesca Gubellini
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
| | | | | | - Rémi Fronzes
- Institut Pasteur, G5 Groupe Biologie Structurale de la Sécrétion Bactérienne; Paris France
- CNRS, UMR3528, Institut Pasteur; 25-28 rue du Docteur Roux, Paris F-75015 France
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Matthey N, Blokesch M. The DNA-Uptake Process of Naturally Competent Vibrio cholerae. Trends Microbiol 2015; 24:98-110. [PMID: 26614677 DOI: 10.1016/j.tim.2015.10.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/05/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
The sophisticated DNA-uptake machinery used during natural transformation is still poorly characterized, especially in Gram-negative bacteria where the transforming DNA has to cross two membranes as well as the peptidoglycan layer before entering the cytoplasm. The DNA-uptake machinery was hypothesized to take the form of a pseudopilus, which, upon repeated cycles of extension and retraction, would pull external DNA towards the cell surface or into the periplasmic space, followed by translocation across the cytoplasmic membrane. In this review, we summarize recent advances on the DNA-uptake machinery of V. cholerae, highlighting the presence of an extended competence-induced pilus and the contribution of a conserved DNA-binding protein that acts as a ratchet and reels DNA into the periplasm.
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Affiliation(s)
- Noémie Matthey
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Station 19, EPFL-SV-UPBLO, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Station 19, EPFL-SV-UPBLO, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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