1
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Loeff L, Adams DW, Chanez C, Stutzmann S, Righi L, Blokesch M, Jinek M. Molecular mechanism of plasmid elimination by the DdmDE defense system. Science 2024; 385:188-194. [PMID: 38870273 DOI: 10.1126/science.adq0534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
Seventh-pandemic Vibrio cholerae strains contain two pathogenicity islands that encode the DNA defense modules DdmABC and DdmDE. In this study, we used cryogenic electron microscopy to determine the mechanistic basis for plasmid defense by DdmDE. The helicase-nuclease DdmD adopts an autoinhibited dimeric architecture. The prokaryotic Argonaute protein DdmE uses a DNA guide to target plasmid DNA. The structure of the DdmDE complex, validated by in vivo mutational studies, shows that DNA binding by DdmE triggers disassembly of the DdmD dimer and loading of monomeric DdmD onto the nontarget DNA strand. In vitro studies indicate that DdmD translocates in the 5'-to-3' direction, while partially degrading the plasmid DNA. These findings provide critical insights into the mechanism of DdmDE systems in plasmid elimination.
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Affiliation(s)
- Luuk Loeff
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - David W Adams
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Christelle Chanez
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Sandrine Stutzmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laurie Righi
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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2
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Liu T, Gao X, Chen R, Tang K, Liu Z, Wang P, Wang X. A nuclease domain fused to the Snf2 helicase confers antiphage defence in coral-associated Halomonas meridiana. Microb Biotechnol 2024; 17:e14524. [PMID: 38980956 PMCID: PMC11232893 DOI: 10.1111/1751-7915.14524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024] Open
Abstract
The coral reef microbiome plays a vital role in the health and resilience of reefs. Previous studies have examined phage therapy for coral pathogens and for modifying the coral reef microbiome, but defence systems against coral-associated bacteria have received limited attention. Phage defence systems play a crucial role in helping bacteria fight phage infections. In this study, we characterized a new defence system, Hma (HmaA-HmaB-HmaC), in the coral-associated Halomonas meridiana derived from the scleractinian coral Galaxea fascicularis. The Swi2/Snf2 helicase HmaA with a C-terminal nuclease domain exhibits antiviral activity against Escherichia phage T4. Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. Additionally, HmaA homologues are present in ~1000 bacterial and archaeal genomes. The high frequency of HmaA helicase in Halomonas strains indicates the widespread presence of these phage defence systems, while the insertion of defence genes in the hma region confirms the existence of a defence gene insertion hotspot. These findings offer insights into the diversity of phage defence systems in coral-associated bacteria and these diverse defence systems can be further applied into designing probiotics with high-phage resistance.
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Affiliation(s)
- Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Gao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ziyao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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3
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Ledvina HE, Whiteley AT. Conservation and similarity of bacterial and eukaryotic innate immunity. Nat Rev Microbiol 2024; 22:420-434. [PMID: 38418927 DOI: 10.1038/s41579-024-01017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Pathogens are ubiquitous and a constant threat to their hosts, which has led to the evolution of sophisticated immune systems in bacteria, archaea and eukaryotes. Bacterial immune systems encode an astoundingly large array of antiviral (antiphage) systems, and recent investigations have identified unexpected similarities between the immune systems of bacteria and animals. In this Review, we discuss advances in our understanding of the bacterial innate immune system and highlight the components, strategies and pathogen restriction mechanisms conserved between bacteria and eukaryotes. We summarize evidence for the hypothesis that components of the human immune system originated in bacteria, where they first evolved to defend against phages. Further, we discuss shared mechanisms that pathogens use to overcome host immune pathways and unexpected similarities between bacterial immune systems and interbacterial antagonism. Understanding the shared evolutionary path of immune components across domains of life and the successful strategies that organisms have arrived at to restrict their pathogens will enable future development of therapeutics that activate the human immune system for the precise treatment of disease.
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Affiliation(s)
- Hannah E Ledvina
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Aaron T Whiteley
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
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4
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Rakibova Y, Dunham DT, Seed KD, Freddolino L. Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae. mSphere 2024:e0001124. [PMID: 38920383 DOI: 10.1128/msphere.00011-24] [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: 01/08/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches they occupy. H-NS, the histone-like nucleoid structuring protein, is the best-studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs. IMPORTANCE New strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until they are needed. H-NS is the best-studied xenogeneic silencer; it is one of the nucleoid-associated proteins (NAPs) in gamma-proteobacteria and is responsible for the proper regulation of HAEs within the bacterial transcriptional network. We studied the effects of H-NS and other NAPs on the HAEs of a clinical isolate of V. cholerae. Importantly, we found that H-NS partners with a small and poorly characterized protein, TsrA, to help domesticate new HAEs involved in bacterial survival and in causing disease. A proper understanding of the regulatory state in emerging isolates of V. cholerae will provide improved therapies against new isolates of the pathogen.
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Affiliation(s)
- Yulduz Rakibova
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Drew T Dunham
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Lydia Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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5
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Vento JM, Durmusoglu D, Li T, Patinios C, Sullivan S, Ttofali F, van Schaik J, Yu Y, Wang Y, Barquist L, Crook N, Beisel CL. A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria. Mol Cell 2024:S1097-2765(24)00481-7. [PMID: 38936361 DOI: 10.1016/j.molcel.2024.06.003] [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: 09/13/2023] [Revised: 04/10/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic biological chassis. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here, we report imitating methylation patterns rapidly in TXTL (IMPRINT), a generalized, rapid, and scalable approach based on cell-free transcription-translation (TXTL) to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes TXTL to express DNA methyltransferases from a bacterium's restriction-modification systems. The expressed methyltransferases then methylate DNA in vitro to match the bacterium's DNA methylation pattern, circumventing restriction and enhancing transformation. With IMPRINT, we efficiently multiplex methylation by diverse DNA methyltransferases and enhance plasmid transformation in gram-negative and gram-positive bacteria. We also develop a high-throughput pipeline that identifies the most consequential methyltransferases, and we apply IMPRINT to screen a ribosome-binding site library in a hard-to-transform Bifidobacterium. Overall, IMPRINT can enhance DNA transformation, enabling the use of sophisticated genetic manipulation tools across the bacterial world.
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Affiliation(s)
- Justin M Vento
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Tianyu Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Constantinos Patinios
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Sean Sullivan
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Fani Ttofali
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - John van Schaik
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Yanyan Wang
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany; Department of Biology, University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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6
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Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, Bikard D, Hall AR, Sørensen SJ, Pinilla-Redondo R. Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans. Cell Host Microbe 2024; 32:875-886.e9. [PMID: 38754416 DOI: 10.1016/j.chom.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 03/05/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Plasmid-encoded type IV-A CRISPR-Cas systems lack an acquisition module, feature a DinG helicase instead of a nuclease, and form ribonucleoprotein complexes of unknown biological functions. Type IV-A3 systems are carried by conjugative plasmids that often harbor antibiotic-resistance genes and their CRISPR array contents suggest a role in mediating inter-plasmid conflicts, but this function remains unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 system co-opts the type I-E adaptation machinery from its host, Klebsiella pneumoniae (K. pneumoniae), to update its CRISPR array. Furthermore, we reveal that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By silencing plasmid core functions, type IV-A3 impacts the horizontal transfer and stability of targeted plasmids, supporting its role in plasmid competition. Our findings shed light on the mechanisms and ecological function of type IV-A3 systems and demonstrate their practical efficacy for countering antibiotic resistance in clinically relevant strains.
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Affiliation(s)
- Fabienne Benz
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, Paris 75015, France; Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France; Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Sarah Camara-Wilpert
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Katharina G Wandera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Rimvydė Čepaitė
- Life Sciences Center - European Molecular Biology Laboratory (LSC-EMBL) Partnership for Genome Editing Technologies, Vilnius University - Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Manuel Ares-Arroyo
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | | | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Johannes A Kuehn
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Silvana Gloor
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Mario Rodríguez Mestre
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Mònica Aguilà-Sans
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Lorrie Maccario
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lennart Randau
- Department of Biology, Philipps Universität Marburg, Marburg, Germany; SYNMIKRO, Center for Synthetic Microbiology, Marburg, Germany
| | - Patrick Pausch
- Life Sciences Center - European Molecular Biology Laboratory (LSC-EMBL) Partnership for Genome Editing Technologies, Vilnius University - Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany; Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Jonas Stenløkke Madsen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Synthetic Biology, Paris 75015, France
| | - Alex R Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Søren Johannes Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
| | - Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
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7
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Otto SB, Servajean R, Lemopoulos A, Bitbol AF, Blokesch M. Interactions between pili affect the outcome of bacterial competition driven by the type VI secretion system. Curr Biol 2024; 34:2403-2417.e9. [PMID: 38749426 DOI: 10.1016/j.cub.2024.04.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 06/06/2024]
Abstract
The bacterial type VI secretion system (T6SS) is a widespread, kin-discriminatory weapon capable of shaping microbial communities. Due to the system's dependency on contact, cellular interactions can lead to either competition or kin protection. Cell-to-cell contact is often accomplished via surface-exposed type IV pili (T4Ps). In Vibrio cholerae, these T4Ps facilitate specific interactions when the bacteria colonize natural chitinous surfaces. However, it has remained unclear whether and, if so, how these interactions affect the bacterium's T6SS-mediated killing. In this study, we demonstrate that pilus-mediated interactions can be harnessed by T6SS-equipped V. cholerae to kill non-kin cells under liquid growth conditions. We also show that the naturally occurring diversity of pili determines the likelihood of cell-to-cell contact and, consequently, the extent of T6SS-mediated competition. To determine the factors that enable or hinder the T6SS's targeted reduction of competitors carrying pili, we developed a physics-grounded computational model for autoaggregation. Collectively, our research demonstrates that T4Ps involved in cell-to-cell contact can impose a selective burden when V. cholerae encounters non-kin cells that possess an active T6SS. Additionally, our study underscores the significance of T4P diversity in protecting closely related individuals from T6SS attacks through autoaggregation and spatial segregation.
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Affiliation(s)
- Simon B Otto
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Richard Servajean
- Laboratory of Computational Biology and Theoretical Biophysics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Alexandre Lemopoulos
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anne-Florence Bitbol
- Laboratory of Computational Biology and Theoretical Biophysics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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8
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Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature 2024; 630:961-967. [PMID: 38740055 DOI: 10.1038/s41586-024-07515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation1. Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET)2. Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE-guide-target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.
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Affiliation(s)
- Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Institute of Science and Technology Austria (ISTA), Klosterneuberg, Austria.
| | - Delisa A Ramos
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | - Caiden Ingram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA
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9
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Zongo PD, Cabanel N, Royer G, Depardieu F, Hartmann A, Naas T, Glaser P, Rosinski-Chupin I. An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages. Nat Commun 2024; 15:4093. [PMID: 38750030 PMCID: PMC11096173 DOI: 10.1038/s41467-024-48219-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: 02/08/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024] Open
Abstract
Plasmids carrying antibiotic resistance genes (ARG) are the main mechanism of resistance dissemination in Enterobacterales. However, the fitness-resistance trade-off may result in their elimination. Chromosomal integration of ARGs preserves resistance advantage while relieving the selective pressure for keeping costly plasmids. In some bacterial lineages, such as carbapenemase producing sequence type ST38 Escherichia coli, most ARGs are chromosomally integrated. Here we reproduce by experimental evolution the mobilisation of the carbapenemase blaOXA-48 gene from the pOXA-48 plasmid into the chromosome. We demonstrate that this integration depends on a plasmid-induced fitness cost, a mobile genetic structure embedding the ARG and a novel antiplasmid system ApsAB actively involved in pOXA-48 destabilization. We show that ApsAB targets high and low-copy number plasmids. ApsAB combines a nuclease/helicase protein and a novel type of Argonaute-like protein. It belongs to a family of defense systems broadly distributed among bacteria, which might have a strong ecological impact on plasmid diffusion.
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Affiliation(s)
- Pengdbamba Dieudonné Zongo
- Ecology and Evolution of Antibiotic Resistance Unit, Institut Pasteur, Paris, France
- Sorbonne Université, Paris, France
- Université Paris Cité, Paris, France
| | - Nicolas Cabanel
- Ecology and Evolution of Antibiotic Resistance Unit, Institut Pasteur, Paris, France
- Université Paris Cité, Paris, France
| | - Guilhem Royer
- Ecology and Evolution of Antibiotic Resistance Unit, Institut Pasteur, Paris, France
- Université Paris Cité, Paris, France
| | - Florence Depardieu
- Université Paris Cité, Paris, France
- Synthetic Biology Unit, Institut Pasteur, Paris, France
| | - Alain Hartmann
- UMR AgroEcologie 1347, INRAe, Université Bourgogne Franche-Comté, Dijon, France
| | - Thierry Naas
- Team ReSIST, INSERM UMR 1184, Paris-Saclay University, Le Kremlin-Bicêtre, France
- Department of Bacteriology-Hygiene, Bicêtre Hospital, APHP, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Institut Pasteur, Paris, France
- Université Paris Cité, Paris, France
| | - Isabelle Rosinski-Chupin
- Ecology and Evolution of Antibiotic Resistance Unit, Institut Pasteur, Paris, France.
- Université Paris Cité, Paris, France.
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10
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Zheng L, Shen J, Chen R, Hu Y, Zhao W, Leung ELH, Dai L. Genome engineering of the human gut microbiome. J Genet Genomics 2024; 51:479-491. [PMID: 38218395 DOI: 10.1016/j.jgg.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The human gut microbiome, a complex ecosystem, significantly influences host health, impacting crucial aspects such as metabolism and immunity. To enhance our comprehension and control of the molecular mechanisms orchestrating the intricate interplay between gut commensal bacteria and human health, the exploration of genome engineering for gut microbes is a promising frontier. Nevertheless, the complexities and diversities inherent in the gut microbiome pose substantial challenges to the development of effective genome engineering tools for human gut microbes. In this comprehensive review, we provide an overview of the current progress and challenges in genome engineering of human gut commensal bacteria, whether executed in vitro or in situ. A specific focus is directed towards the advancements and prospects in cargo DNA delivery and high-throughput techniques. Additionally, we elucidate the immense potential of genome engineering methods to enhance our understanding of the human gut microbiome and engineer the microorganisms to enhance human health.
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Affiliation(s)
- Linggang Zheng
- Dr Neher's Biophysics Laboratory for Innovative Drug Discovery/State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Juntao Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ruiyue Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yucan Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Elaine Lai-Han Leung
- Cancer Center, Faculty of Health Science, University of Macau, Macau 999078, China; MOE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China.
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Yang QE, Ma X, Li M, Zhao M, Zeng L, He M, Deng H, Liao H, Rensing C, Friman VP, Zhou S, Walsh TR. Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages. Nat Commun 2024; 15:3654. [PMID: 38688912 PMCID: PMC11061290 DOI: 10.1038/s41467-024-48006-9] [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: 09/08/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
The horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen (Klebsiella pneumoniae) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella-specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms.
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Affiliation(s)
- Qiu E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaodan Ma
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Minchun Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengshi Zhao
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingshuang Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Minzhen He
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hui Deng
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ville-Petri Friman
- Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Timothy R Walsh
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, OX1 3RE, UK.
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12
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Martínez M, Rizzuto I, Molina R. Knowing Our Enemy in the Antimicrobial Resistance Era: Dissecting the Molecular Basis of Bacterial Defense Systems. Int J Mol Sci 2024; 25:4929. [PMID: 38732145 PMCID: PMC11084316 DOI: 10.3390/ijms25094929] [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: 03/20/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Bacteria and their phage adversaries are engaged in an ongoing arms race, resulting in the development of a broad antiphage arsenal and corresponding viral countermeasures. In recent years, the identification and utilization of CRISPR-Cas systems have driven a renewed interest in discovering and characterizing antiphage mechanisms, revealing a richer diversity than initially anticipated. Currently, these defense systems can be categorized based on the bacteria's strategy associated with the infection cycle stage. Thus, bacterial defense systems can degrade the invading genetic material, trigger an abortive infection, or inhibit genome replication. Understanding the molecular mechanisms of processes related to bacterial immunity has significant implications for phage-based therapies and the development of new biotechnological tools. This review aims to comprehensively cover these processes, with a focus on the most recent discoveries.
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Affiliation(s)
| | | | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física Blas Cabrera, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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13
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Bedore AM, Waters CM. Plasmid-free cheater cells commonly evolve during laboratory growth. Appl Environ Microbiol 2024; 90:e0231123. [PMID: 38446071 PMCID: PMC11022567 DOI: 10.1128/aem.02311-23] [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: 12/20/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, extracellular beta-lactamases produced by resistant cells that subsequently degrade penicillin and related antibiotics allow neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show in multiple bacterial species that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface-grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss was still observed. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.IMPORTANCEPlasmids are routinely used in microbiology as readouts of cell biology or tools to manipulate cell function. Central to these studies is the assumption that all cells in an experiment contain the plasmid. Plasmid maintenance in a host cell typically depends on a plasmid-encoded antibiotic resistance marker, which provides a selective advantage when the plasmid-containing cell is grown in the presence of antibiotic. Here, we find that growth of plasmid-containing bacteria on a surface and to a lesser extent in liquid culture in the presence of three distinct antibiotic families leads to the evolution of a significant number of plasmid-free cells, which rely on the resistance mechanisms of the plasmid-containing cells. This process generates a heterogenous population of plasmid-free and plasmid-containing bacteria, an outcome which could confound further experimentation.
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Affiliation(s)
- Amber M. Bedore
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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14
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Gomez JB, Waters CM. A Vibrio cholerae Type IV restriction system targets glucosylated 5-hydroxyl methyl cytosine to protect against phage infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588314. [PMID: 38617239 PMCID: PMC11014532 DOI: 10.1101/2024.04.05.588314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A major challenge faced by Vibrio cholerae is constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation, V. cholerae has evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized more were encoded in V. cholerae given the relative paucity of phage that have been isolated which infect this species. Using a V. cholerae genomic library, we identified a Type IV restriction system consisting of two genes within a 16kB region of the Vibrio pathogenicity island-2 that we name TgvA and TgvB (Type I-embedded gmrSD-like system of VPI-2). We show that both TgvA and TgvB are required for defense against T2, T4, and T6 by targeting glucosylated 5-hydroxymethylcytosine (5hmC). T2 or T4 phages that lose the glucose modification are resistant to TgvAB defense but exhibit a significant evolutionary tradeoff becoming susceptible to other Type IV restriction systems that target unglucosylated 5hmC. We show that additional phage defense genes are encoded in VPI-2 that protect against other phage like T3, secΦ18, secΦ27 and λ. Our study uncovers a novel Type IV restriction system in V. cholerae, increasing our understanding of the evolution and ecology of V. cholerae while highlighting the evolutionary interplay between restriction systems and phage genome modification.
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Affiliation(s)
- Jasper B Gomez
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Christopher M Waters
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
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15
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Cossart P, Hacker J, Holden DH, Normark S, Vogel J. Meeting report 'Microbiology 2023: from single cell to microbiome and host', an international interacademy conference in Würzburg. MICROLIFE 2024; 5:uqae008. [PMID: 38665235 PMCID: PMC11044969 DOI: 10.1093/femsml/uqae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
On September 20-22 September 2023, the international conference 'Microbiology 2023: from single cell to microbiome and host' convened microbiologists from across the globe for a very successful symposium, showcasing cutting-edge research in the field. Invited lecturers delivered exceptional presentations covering a wide range of topics, with a major emphasis on phages and microbiomes, on the relevant bacteria within these ecosystems, and their multifaceted roles in diverse environments. Discussions also spanned the intricate analysis of fundamental bacterial processes, such as cell division, stress resistance, and interactions with phages. Organized by four renowned Academies, the German Leopoldina, the French Académie des sciences, the Royal Society UK, and the Royal Swedish Academy of Sciences, the symposium provided a dynamic platform for experts to share insights and discoveries, leaving participants inspired and eager to integrate new knowledge into their respective projects. The success of Microbiology 2023 prompted the decision to host the next quadrennial academic meeting in Sweden. This choice underscores the commitment to fostering international collaboration and advancing the frontiers of microbiological knowledge. The transition to Sweden promises to be an exciting step in the ongoing global dialogue and specific collaborations on microbiology, a field where researchers will continue to push the boundaries of knowledge, understanding, and innovation not only in health and disease but also in ecology.
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Affiliation(s)
| | - Jörg Hacker
- German National Academy of Science Leopoldina, Jägerberg 1, D-06108 Halle, Germany
| | - David H Holden
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Flowers Building, South Kensington Campus, Exhibition Road, Imperial College London, London SW7 2AZ, United Kingdom
| | - Staffan Normark
- Karolinska Institute, Tumor-och-cellbiologi, C1 Microbial Pathogenesis, 17177 Stockholm, Sweden
| | - Jörg Vogel
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str2/Gebaude D15; É. D-97080 Würzburg, Germany
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16
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Richard E, Darracq B, Littner E, Millot GA, Conte V, Cokelaer T, Engelstädter J, Rocha EPC, Mazel D, Loot C. Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons. PLoS Genet 2024; 20:e1011231. [PMID: 38578806 PMCID: PMC11023631 DOI: 10.1371/journal.pgen.1011231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/17/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
Integrons are adaptive devices that capture, stockpile, shuffle and express gene cassettes thereby sampling combinatorial phenotypic diversity. Some integrons called sedentary chromosomal integrons (SCIs) can be massive structures containing hundreds of cassettes. Since most of these cassettes are non-expressed, it is not clear how they remain stable over long evolutionary timescales. Recently, it was found that the experimental inversion of the SCI of Vibrio cholerae led to a dramatic increase of the cassette excision rate associated with a fitness defect. Here, we question the evolutionary sustainability of this apparently counter selected genetic context. Through experimental evolution, we find that the integrase is rapidly inactivated and that the inverted SCI can recover its original orientation by homologous recombination between two insertion sequences (ISs) present in the array. These two outcomes of SCI inversion restore the normal growth and prevent the loss of cassettes, enabling SCIs to retain their roles as reservoirs of functions. These results illustrate a nice interplay between gene orientation, genome rearrangement, bacterial fitness and demonstrate how integrons can benefit from their embedded ISs.
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Affiliation(s)
- Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Eloi Littner
- Sorbonne Université, ED515, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
| | - Gael A. Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Valentin Conte
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, Plateforme Technologique Biomics, Paris, France
| | - Jan Engelstädter
- School of the Environment, The University of Queensland, Brisbane, Australia
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
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17
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Kogay R, Wolf YI, Koonin EV. Defence systems and horizontal gene transfer in bacteria. Environ Microbiol 2024; 26:e16630. [PMID: 38643972 PMCID: PMC11034907 DOI: 10.1111/1462-2920.16630] [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: 02/09/2024] [Accepted: 04/05/2024] [Indexed: 04/23/2024]
Abstract
Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.
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Affiliation(s)
- Roman Kogay
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
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18
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Rakibova Y, Dunham DT, Seed KD, Freddolino PL. Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573743. [PMID: 38260642 PMCID: PMC10802314 DOI: 10.1101/2023.12.30.573743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in the different environmental niches it occupies. H-NS, the histone-like nucleoid structuring protein, is the best studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently discovered HAEs encoding for phage defense systems, we show that a lack of H-NS causes a robust increase in the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity. We also identified a few sites that are affected by TsrA independently of H-NS, suggesting TsrA may act with diverse regulatory mechanisms. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently discovered HAEs. Importance New strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until they are needed. H-NS is the best-studied xenogeneic silencer; it is one of the nucleoid-associated proteins (NAPs) in gamma-proteobacteria and is responsible for the proper regulation of HAEs within the bacterial transcriptional network. We studied the effects of H-NS and other NAPs on the HAEs of a clinical isolate of V. cholerae. Importantly, we found that H-NS partners with a small and poorly characterized protein, TsrA, to help domesticate new HAEs involved in bacterial survival and in causing disease. Proper understanding of the regulatory state in emerging isolates of V. cholerae will provide improved therapies against new isolates of the pathogen.
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Affiliation(s)
- Yulduz Rakibova
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Drew T. Dunham
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kimberley D. Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - P. Lydia Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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19
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Costa AR, van den Berg DF, Esser JQ, Muralidharan A, van den Bossche H, Bonilla BE, van der Steen BA, Haagsma AC, Fluit AC, Nobrega FL, Haas PJ, Brouns SJJ. Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa. SCIENCE ADVANCES 2024; 10:eadj0341. [PMID: 38394193 PMCID: PMC10889362 DOI: 10.1126/sciadv.adj0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Prokaryotes encode multiple distinct anti-phage defense systems in their genomes. However, the impact of carrying a multitude of defense systems on phage resistance remains unclear, especially in a clinical context. Using a collection of antibiotic-resistant clinical strains of Pseudomonas aeruginosa and a broad panel of phages, we demonstrate that defense systems contribute substantially to defining phage host range and that overall phage resistance scales with the number of defense systems in the bacterial genome. We show that many individual defense systems target specific phage genera and that defense systems with complementary phage specificities co-occur in P. aeruginosa genomes likely to provide benefits in phage-diverse environments. Overall, we show that phage-resistant phenotypes of P. aeruginosa with at least 19 phage defense systems exist in the populations of clinical, antibiotic-resistant P. aeruginosa strains.
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Affiliation(s)
- Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Daan F. van den Berg
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Jelger Q. Esser
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Aswin Muralidharan
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Halewijn van den Bossche
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Boris Estrada Bonilla
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Baltus A. van der Steen
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Anna C. Haagsma
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Ad C. Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Stan J. J. Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
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20
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Pfeifer E, Rocha EPC. Phage-plasmids promote recombination and emergence of phages and plasmids. Nat Commun 2024; 15:1545. [PMID: 38378896 PMCID: PMC10879196 DOI: 10.1038/s41467-024-45757-3] [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: 08/23/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Phages and plasmids are regarded as distinct types of mobile genetic elements that drive bacterial evolution by horizontal gene transfer. However, the distinction between both types is blurred by the existence of elements known as prophage-plasmids or phage-plasmids, which transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here, we study gene flow between the three types of elements. We show that the gene repertoire of phage-plasmids overlaps with those of phages and plasmids. By tracking recent recombination events, we find that phage-plasmids exchange genes more frequently with plasmids than with phages, and that direct gene exchange between plasmids and phages is less frequent in comparison. The results suggest that phage-plasmids can mediate gene flow between plasmids and phages, including exchange of mobile element core functions, defense systems, and antibiotic resistance. Moreover, a combination of gene transfer and gene inactivation may result in the conversion of elements. For example, gene loss turns P1-like phage-plasmids into integrative prophages or into plasmids (that are no longer phages). Remarkably, some of the latter have acquired conjugation-related functions to became mobilisable by conjugation. Thus, our work indicates that phage-plasmids can play a key role in the transfer of genes across mobile elements within their hosts, and can act as intermediates in the conversion of one type of element into another.
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Affiliation(s)
- Eugen Pfeifer
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015, Paris, France.
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015, Paris, France.
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21
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Gerdes K. Diverse genetic contexts of HicA toxin domains propose a role in anti-phage defense. mBio 2024; 15:e0329323. [PMID: 38236063 PMCID: PMC10865869 DOI: 10.1128/mbio.03293-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Toxin-antitoxin (TA) modules are prevalent in prokaryotic genomes, often in substantial numbers. For instance, the Mycobacterium tuberculosis genome alone harbors close to 100 TA modules, half of which belong to a singular type. Traditionally ascribed multiple biological roles, recent insights challenge these notions and instead indicate a predominant function in phage defense. TAs are often located within Defense Islands, genomic regions that encode various defense systems. The analysis of genes within Defense Islands has unveiled a wide array of systems, including TAs that serve in anti-phage defense. Prokaryotic cells are equipped with anti-phage Viperins that, analogous to their mammalian counterparts, inhibit viral RNA transcription. Additionally, bacterial Structural Maintenance of Chromosome (SMC) proteins combat plasmid intrusion by recognizing foreign DNA signatures. This study undertakes a comprehensive bioinformatics analysis of genetic elements encoding the HicA double-stranded RNA-binding domain, complemented by protein structure modeling. The HicA toxin domains are found in at least 14 distinct contexts and thus exhibit a remarkable genetic diversity. Traditional bicistronic TA operons represent eight of these contexts, while four are characterized by monocistronic operons encoding fused HicA domains. Two contexts involve hicA adjacent to genes that encode bacterial Viperins. Notably, genes encoding RelE toxins are also adjacent to Viperin genes in some instances. This configuration hints at a synergistic enhancement of Viperin-mediated anti-phage action by HicA and RelE toxins. The discovery of a HicA domain merged with an SMC domain is compelling, prompting further investigation into its potential roles.IMPORTANCEProkaryotic organisms harbor a multitude of toxin-antitoxin (TA) systems, which have long puzzled scientists as "genes in search for a function." Recent scientific advancements have shed light on the primary role of TAs as anti-phage defense mechanisms. To gain an overview of TAs it is important to analyze their genetic contexts that can give hints on function and guide future experimental inquiries. This article describes a thorough bioinformatics examination of genes encoding the HicA toxin domain, revealing its presence in no fewer than 14 unique genetic arrangements. Some configurations notably align with anti-phage activities, underscoring potential roles in microbial immunity. These insights robustly reinforce the hypothesis that HicA toxins are integral components of the prokaryotic anti-phage defense repertoire. The elucidation of these genetic contexts not only advances our understanding of TAs but also contributes to a paradigm shift in how we perceive their functionality within the microbial world.
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Affiliation(s)
- Kenn Gerdes
- Kenn Gerdes is an independent researcher with the residence, Voldmestergade, Copenhagen, Denmark
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22
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Ryan MP, Carraro N, Slattery S, Pembroke JT. Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria. Crit Rev Microbiol 2024; 50:105-126. [PMID: 36634159 DOI: 10.1080/1040841x.2022.2161870] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.
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Affiliation(s)
- Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon, Limerick, Ireland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shannon Slattery
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
| | - J Tony Pembroke
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
- Bernal Institute, University of Limerick, Ireland
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23
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Doan A, Chatterjee S, Kothapalli R, Khan Z, Sen S, Kedei N, Jha JK, Chattoraj DK, Ramachandran R. The replication enhancer crtS depends on transcription factor Lrp for modulating binding of initiator RctB to ori2 of Vibrio cholerae. Nucleic Acids Res 2024; 52:708-723. [PMID: 38000366 PMCID: PMC10810183 DOI: 10.1093/nar/gkad1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Replication of Vibrio cholerae chromosome 2 (Chr2) initiates when the Chr1 locus, crtS (Chr2 replication triggering site) duplicates. The site binds the Chr2 initiator, RctB, and the binding increases when crtS is complexed with the transcription factor, Lrp. How Lrp increases the RctB binding and how RctB is subsequently activated for initiation by the crtS-Lrp complex remain unclear. Here we show that Lrp bends crtS DNA and possibly contacts RctB, acts that commonly promote DNA-protein interactions. To understand how the crtS-Lrp complex enhances replication, we isolated Tn-insertion and point mutants of RctB, selecting for retention of initiator activity without crtS. Nearly all mutants (42/44) still responded to crtS for enhancing replication, exclusively in an Lrp-dependent manner. The results suggest that the Lrp-crtS controls either an essential function or more than one function of RctB. Indeed, crtS modulates two kinds of RctB binding to the origin of Chr2, ori2, both of which we find to be Lrp-dependent. Some point mutants of RctB that are optimally modulated for ori2 binding without crtS still remained responsive to crtS and Lrp for replication enhancement. We infer that crtS-Lrp functions as a unit, which has an overarching role, beyond controlling initiator binding to ori2.
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Affiliation(s)
- Alexander Doan
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Soniya Chatterjee
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Roopa Kothapalli
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zaki Khan
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shaanit Sen
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noemi Kedei
- Collaborative Protein Technology Resource, OSTP, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jyoti K Jha
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dhruba K Chattoraj
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Revathy Ramachandran
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- College of Medicine, Mohammed Bin Rashid University, Dubai, UAE
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24
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Loot C, Millot GA, Richard E, Littner E, Vit C, Lemoine F, Néron B, Cury J, Darracq B, Niault T, Lapaillerie D, Parissi V, Rocha EPC, Mazel D. Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites. Nat Microbiol 2024; 9:228-240. [PMID: 38172619 DOI: 10.1038/s41564-023-01548-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
Integrons are genetic elements involved in bacterial adaptation which capture, shuffle and express genes encoding adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Using computational and molecular genetic approaches, here we demonstrate that the integrase also catalyses cassette integration into bacterial genomes outside of its known att sites. Once integrated, these cassettes can be expressed if located near bacterial promoters and can be excised at the integration point or outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 105 independent integration events revealed a very large genomic integration landscape. We identified consensus recombination sequences, named attG sites, which differ greatly in sequence and structure from classical att sites. These results unveil an alternative route for dissemination of adaptive functions in bacteria and expand the role of integrons in bacterial evolution.
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Affiliation(s)
- Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France.
| | - Gael A Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Eloi Littner
- Sorbonne Université, Collège Doctoral, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Microbial Evolutionary Genomics, Paris, France
| | - Claire Vit
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Bertrand Néron
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Jean Cury
- Université Paris-Saclay, Inria, Laboratoire de Recherche en Informatique, CNRS UMR 8623, Orsay, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Théophile Niault
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Delphine Lapaillerie
- Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS UMR 5234, Département de Sciences Biologiques et Médicales, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Vincent Parissi
- Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS UMR 5234, Département de Sciences Biologiques et Médicales, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
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25
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Patel KM, Seed KD. Sporadic phage defense in epidemic Vibrio cholerae mediated by the toxin-antitoxin system DarTG is countered by a phage-encoded antitoxin mimic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571748. [PMID: 38168179 PMCID: PMC10760071 DOI: 10.1101/2023.12.14.571748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Bacteria and their viral predators (phages) are constantly evolving to subvert one another. Many bacterial immune systems that inhibit phages are encoded on mobile genetic elements that can be horizontally transmitted to diverse bacteria. Despite the pervasive appearance of immune systems in bacteria, it is not often known if these immune systems function against phages that the host encounters in nature. Additionally, there are limited examples demonstrating how these phages counter-adapt to such immune systems. Here, we identify clinical isolates of the global pathogen Vibrio cholerae harboring a novel genetic element encoding the bacterial immune system DarTG and reveal the immune system's impact on the co-circulating lytic phage ICP1. We show that DarTG inhibits ICP1 genome replication, thus preventing ICP1 plaquing. We further characterize the conflict between DarTG-mediated defense and ICP1 by identifying an ICP1-encoded protein that counters DarTG and allows ICP1 progeny production. Finally, we identify this protein as a functional antitoxin that abrogates the toxin DarT likely through direct interactions. Following the detection of the DarTG system in clinical V. cholerae isolates, we observed a rise in ICP1 isolates with the functional antitoxin. These data highlight the use of surveillance of V. cholerae and its lytic phages to understand the co-evolutionary arms race between bacteria and their phages in nature.
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Affiliation(s)
- Kishen M Patel
- Infectious Diseases and Immunity Graduate Group, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
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26
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Niault T, Czarnecki J, Lambérioux M, Mazel D, Val ME. Cell cycle-coordinated maintenance of the Vibrio bipartite genome. EcoSal Plus 2023; 11:eesp00082022. [PMID: 38277776 PMCID: PMC10729929 DOI: 10.1128/ecosalplus.esp-0008-2022] [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] [Indexed: 01/28/2024]
Abstract
To preserve the integrity of their genome, bacteria rely on several genome maintenance mechanisms that are co-ordinated with the cell cycle. All members of the Vibrio family have a bipartite genome consisting of a primary chromosome (Chr1) homologous to the single chromosome of other bacteria such as Escherichia coli and a secondary chromosome (Chr2) acquired by a common ancestor as a plasmid. In this review, we present our current understanding of genome maintenance in Vibrio cholerae, which is the best-studied model for bacteria with multi-partite genomes. After a brief overview on the diversity of Vibrio genomic architecture, we describe the specific, common, and co-ordinated mechanisms that control the replication and segregation of the two chromosomes of V. cholerae. Particular attention is given to the unique checkpoint mechanism that synchronizes Chr1 and Chr2 replication.
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Affiliation(s)
- Théophile Niault
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Jakub Czarnecki
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| | - Morgan Lambérioux
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Didier Mazel
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| | - Marie-Eve Val
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
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27
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Yin H, Wang H, Wang M, Shi B. The interaction between extracellular polymeric substances and corrosion products in pipes shaped different bacterial communities and the effects of micropollutants. WATER RESEARCH 2023; 247:120822. [PMID: 37950951 DOI: 10.1016/j.watres.2023.120822] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/13/2023]
Abstract
There are growing concerns over the effects of micropollutants on biofilms formation and antibiotic resistance gene (ARGs) transmission in drinking water distribution pipes. However, there was no reports about the influence of the interaction between extracellular polymeric substances (EPS) and corrosion products on biofilms formation. Our results indicated that the abundance of quorum sensing (QS)-related genes, polysaccharide and amino acids biosynthesis genes of EPS was 6747-8055 TPM, 2221-2619 TPM, and 1461-1535 TPM in biofilms of cast iron pipes, respectively, which were higher than that of stainless steel pipes. The two-dimensional correlation spectroscopy (2D-COS) analysis of attenuated total reflectance-Fourier transform infrared spectrometry (ATR-FTIR) results indicated that polysaccharide of EPS was more easily adsorbed onto the corrosion products of cast iron pipes. Therefore, more human pathogenic bacteria (HPB) carrying ARGs were formed in biofilms of cast iron pipes. The amide I and amide II components and phosphate moieties of EPS were more susceptible to the corrosion products of stainless steel pipes. Thus, more bacteria genera carrying mobile genetic elements (MGE)-ARG were formed in biofilms of stainless steel pipes due to more abundance of QS-related genes, amino acids biosynthesis genes of EPS and the functional genes related to lipid metabolism. The enrichment of dimethyl phthalate (DMP), perfluorooctanoic acid (PFOA) and sulfadiazine (SUL) in corrosion products induced upregulation of QS and EPS-related genes, which promoted bacteria carrying different ARGs growth in biofilms, inducing more microbial risks.
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Affiliation(s)
- Hong Yin
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Haibo Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Min Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Baoyou Shi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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28
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Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:656-668. [PMID: 37794696 PMCID: PMC10667661 DOI: 10.1111/1758-2229.13203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid-encoded genes is similar to that of chromosome-encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.
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Affiliation(s)
- Fabian Nies
- Institute of General MicrobiologyKiel UniversityKielGermany
| | - Tanita Wein
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | | | - Benjamin L. Springstein
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Biological Sciences FacultyPontifical Catholic University of ChileSantiagoChile
| | - Claudia Taubenheim
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Department of Internal Medicine IIUniversity Medical Center Schleswig‐HolsteinKielGermany
| | - Tal Dagan
- Institute of General MicrobiologyKiel UniversityKielGermany
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29
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Severin GB, Ramliden MS, Ford KC, Van Alst AJ, Sanath-Kumar R, Decker KA, Hsueh BY, Chen G, Yoon SH, Demey LM, O'Hara BJ, Rhoades CR, DiRita VJ, Ng WL, Waters CM. Activation of a Vibrio cholerae CBASS anti-phage system by quorum sensing and folate depletion. mBio 2023; 14:e0087523. [PMID: 37623317 PMCID: PMC10653837 DOI: 10.1128/mbio.00875-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/13/2023] [Indexed: 08/26/2023] Open
Abstract
IMPORTANCE To counteract infection with phage, bacteria have evolved a myriad of molecular defense systems. Some of these systems initiate a process called abortive infection, in which the infected cell kills itself to prevent phage propagation. However, such systems must be inhibited in the absence of phage infection to prevent spurious death of the host. Here, we show that the cyclic oligonucleotide based anti-phage signaling system (CBASS) accomplishes this by sensing intracellular folate molecules and only expressing this system in a group. These results enhance our understanding of the evolution of the seventh Vibrio cholerae pandemic and more broadly how bacteria defend themselves against phage infection.
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Affiliation(s)
- Geoffrey B. Severin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Miriam S. Ramliden
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Kathryne C. Ford
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Andrew J. Van Alst
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Ram Sanath-Kumar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Kaitlin A. Decker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Brian Y. Hsueh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Gong Chen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Soo Hun Yoon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Lucas M. Demey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Brendan J. O'Hara
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Christopher R. Rhoades
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Victor J. DiRita
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Wai-Leung Ng
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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30
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Georjon H, Bernheim A. The highly diverse antiphage defence systems of bacteria. Nat Rev Microbiol 2023; 21:686-700. [PMID: 37460672 DOI: 10.1038/s41579-023-00934-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 09/14/2023]
Abstract
Bacteria and their viruses have coevolved for billions of years. This ancient and still ongoing arms race has led bacteria to develop a vast antiphage arsenal. The development of high-throughput screening methods expanded our knowledge of defence systems from a handful to more than a hundred systems, unveiling many different molecular mechanisms. These findings reveal that bacterial immunity is much more complex than previously thought. In this Review, we explore recently discovered bacterial antiphage defence systems, with a particular focus on their molecular diversity, and discuss the ecological and evolutionary drivers and implications of the existing diversity of antiphage defence mechanisms.
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Affiliation(s)
- Héloïse Georjon
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France
| | - Aude Bernheim
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France.
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31
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Lassalle F, Al-Shalali S, Al-Hakimi M, Njamkepo E, Bashir IM, Dorman MJ, Rauzier J, Blackwell GA, Taylor-Brown A, Beale MA, Cazares A, Al-Somainy AA, Al-Mahbashi A, Almoayed K, Aldawla M, Al-Harazi A, Quilici ML, Weill FX, Dhabaan G, Thomson NR. Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen. Nat Microbiol 2023; 8:1787-1798. [PMID: 37770747 PMCID: PMC10539172 DOI: 10.1038/s41564-023-01472-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Since 2016, Yemen has been experiencing the largest cholera outbreak in modern history. Multidrug resistance (MDR) emerged among Vibrio cholerae isolates from cholera patients in 2018. Here, to characterize circulating genotypes, we analysed 260 isolates sampled in Yemen between 2018 and 2019. Eighty-four percent of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sub-lineage T13, whereas 16% were non-toxigenic, from divergent non-7PET lineages. Treatment of severe cholera with macrolides between 2016 and 2019 coincided with the emergence and dominance of T13 subclones carrying an incompatibility type C (IncC) plasmid harbouring an MDR pseudo-compound transposon. MDR plasmid detection also in endemic non-7PET V. cholerae lineages suggested genetic exchange with 7PET epidemic strains. Stable co-occurrence of the IncC plasmid with the SXT family of integrative and conjugative element in the 7PET background has major implications for cholera control, highlighting the importance of genomic epidemiological surveillance to limit MDR spread.
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Affiliation(s)
- Florent Lassalle
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
| | | | | | - Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | | | - Matthew J Dorman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- Churchill College, Cambridge, UK
| | - Jean Rauzier
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | - Grace A Blackwell
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- EMBL-EBI, Hinxton, UK
| | - Alyce Taylor-Brown
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Mathew A Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Adrián Cazares
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Khaled Almoayed
- National Centre of Public Health Laboratories, Sana'a, Yemen
| | - Mohammed Aldawla
- Ministry of Public Health, Infection Control Unit, Sana'a, Yemen
| | | | - Marie-Laure Quilici
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | - Ghulam Dhabaan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
- London School of Hygiene and Tropical Medicine, London, UK.
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Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
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Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
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Weisberg AJ, Chang JH. Mobile Genetic Element Flexibility as an Underlying Principle to Bacterial Evolution. Annu Rev Microbiol 2023; 77:603-624. [PMID: 37437216 DOI: 10.1146/annurev-micro-032521-022006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Mobile genetic elements are key to the evolution of bacteria and traits that affect host and ecosystem health. Here, we use a framework of a hierarchical and modular system that scales from genes to populations to synthesize recent findings on mobile genetic elements (MGEs) of bacteria. Doing so highlights the role that emergent properties of flexibility, robustness, and genetic capacitance of MGEs have on the evolution of bacteria. Some of their traits can be stored, shared, and diversified across different MGEs, taxa of bacteria, and time. Collectively, these properties contribute to maintaining functionality against perturbations while allowing changes to accumulate in order to diversify and give rise to new traits. These properties of MGEs have long challenged our abilities to study them. Implementation of new technologies and strategies allows for MGEs to be analyzed in new and powerful ways.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
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Dorado-Morales P, Lambérioux M, Mazel D. Unlocking the potential of microbiome editing: A review of conjugation-based delivery. Mol Microbiol 2023. [PMID: 37658686 DOI: 10.1111/mmi.15147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023]
Abstract
In recent decades, there has been a rapid increase in the prevalence of multidrug-resistant pathogens, posing a challenge to modern antibiotic-based medicine. This has highlighted the need for novel treatments that can specifically affect the target microorganism without disturbing other co-inhabiting species, thus preventing the development of dysbiosis in treated patients. Moreover, there is a pressing demand for tools to effectively manipulate complex microbial populations. One of the approaches suggested to address both issues was to use conjugation as a tool to modify the microbiome by either editing the genome of specific bacterial species and/or the removal of certain taxonomic groups. Conjugation involves the transfer of DNA from one bacterium to another, which opens up the possibility of introducing, modifying or deleting specific genes in the recipient. In response to this proposal, there has been a significant increase in the number of studies using this method for gene delivery in bacterial populations. This MicroReview aims to provide a detailed overview on the use of conjugation for microbiome engineering, and at the same time, to initiate a discussion on the potential, limitations and possible future directions of this approach.
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Affiliation(s)
- Pedro Dorado-Morales
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, et CNRS, UMR3525, Paris, France
| | - Morgan Lambérioux
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, et CNRS, UMR3525, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université de Paris, Unité Plasticité du Génome Bactérien, et CNRS, UMR3525, Paris, France
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Liu HW, Roisné-Hamelin F, Gruber S. SMC-based immunity against extrachromosomal DNA elements. Biochem Soc Trans 2023; 51:1571-1583. [PMID: 37584323 PMCID: PMC10586767 DOI: 10.1042/bst20221395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023]
Abstract
SMC and SMC-like complexes promote chromosome folding and genome maintenance in all domains of life. Recently, they were also recognized as factors in cellular immunity against foreign DNA. In bacteria and archaea, Wadjet and Lamassu are anti-plasmid/phage defence systems, while Smc5/6 and Rad50 complexes play a role in anti-viral immunity in humans. This raises an intriguing paradox - how can the same, or closely related, complexes on one hand secure the integrity and maintenance of chromosomal DNA, while on the other recognize and restrict extrachromosomal DNA? In this minireview, we will briefly describe the latest understanding of each of these complexes in immunity including speculations on how principles of SMC(-like) function may explain how the systems recognize linear or circular forms of invading DNA.
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Affiliation(s)
- Hon Wing Liu
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Florian Roisné-Hamelin
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
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Cheng R, Huang F, Lu X, Yan Y, Yu B, Wang X, Zhu B. Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense. Cell Host Microbe 2023; 31:1331-1344.e5. [PMID: 37480847 DOI: 10.1016/j.chom.2023.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/03/2023] [Accepted: 06/27/2023] [Indexed: 07/24/2023]
Abstract
The Gabija complex is a prokaryotic antiviral system consisting of the GajA and GajB proteins. GajA was identified as a DNA nicking endonuclease but the functions of GajB and the complex remain unknown. Here, we show that synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense against virulent bacteriophages. The antiviral activity of GajA requires GajB, which senses DNA termini produced by GajA to hydrolyze (d)A/(d)GTP, depleting essential nucleotides. This ATPase activity of Gabija complex is only activated upon DNA binding. GajA binds to GajB to form stable complexes in vivo and in vitro. However, a functional Gabija complex requires a molecular ratio between GajB and GajA below 1:1, indicating stoichiometric regulation of the DNA/nucleotide processing complex. Thus, the Gabija system exhibits distinct and efficient antiviral defense through sequential sensing and activation of nucleotide depletion and DNA cleavage, causing a cascade suicide effect.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518063, China
| | - Xueling Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yan Yan
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Bingbing Yu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xionglue Wang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518063, China.
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37
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Dewan I, Uecker H. A mathematician's guide to plasmids: an introduction to plasmid biology for modellers. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001362. [PMID: 37505810 PMCID: PMC10433428 DOI: 10.1099/mic.0.001362] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.
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Affiliation(s)
- Ian Dewan
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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38
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Mayo-Muñoz D, Pinilla-Redondo R, Birkholz N, Fineran PC. A host of armor: Prokaryotic immune strategies against mobile genetic elements. Cell Rep 2023; 42:112672. [PMID: 37347666 DOI: 10.1016/j.celrep.2023.112672] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023] Open
Abstract
Prokaryotic adaptation is strongly influenced by the horizontal acquisition of beneficial traits via mobile genetic elements (MGEs), such as viruses/bacteriophages and plasmids. However, MGEs can also impose a fitness cost due to their often parasitic nature and differing evolutionary trajectories. In response, prokaryotes have evolved diverse immune mechanisms against MGEs. Recently, our understanding of the abundance and diversity of prokaryotic immune systems has greatly expanded. These defense systems can degrade the invading genetic material, inhibit genome replication, or trigger abortive infection, leading to population protection. In this review, we highlight these strategies, focusing on the most recent discoveries. The study of prokaryotic defenses not only sheds light on microbial evolution but also uncovers novel enzymatic activities with promising biotechnological applications.
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Affiliation(s)
- David Mayo-Muñoz
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Rafael Pinilla-Redondo
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Bioprotection Aotearoa, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Bioprotection Aotearoa, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.
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39
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Gao Z, Feng Y. Bacteriophage strategies for overcoming host antiviral immunity. Front Microbiol 2023; 14:1211793. [PMID: 37362940 PMCID: PMC10286901 DOI: 10.3389/fmicb.2023.1211793] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023] Open
Abstract
Phages and their bacterial hosts together constitute a vast and diverse ecosystem. Facing the infection of phages, prokaryotes have evolved a wide range of antiviral mechanisms, and phages in turn have adopted multiple tactics to circumvent or subvert these mechanisms to survive. An in-depth investigation into the interaction between phages and bacteria not only provides new insight into the ancient coevolutionary conflict between them but also produces precision biotechnological tools based on anti-phage systems. Moreover, a more complete understanding of their interaction is also critical for the phage-based antibacterial measures. Compared to the bacterial antiviral mechanisms, studies into counter-defense strategies adopted by phages have been a little slow, but have also achieved important advances in recent years. In this review, we highlight the numerous intracellular immune systems of bacteria as well as the countermeasures employed by phages, with an emphasis on the bacteriophage strategies in response to host antiviral immunity.
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40
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Walton MG, Cubillejo I, Nag D, Withey JH. Advances in cholera research: from molecular biology to public health initiatives. Front Microbiol 2023; 14:1178538. [PMID: 37283925 PMCID: PMC10239892 DOI: 10.3389/fmicb.2023.1178538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/14/2023] [Indexed: 06/08/2023] Open
Abstract
The aquatic bacterium Vibrio cholerae is the etiological agent of the diarrheal disease cholera, which has plagued the world for centuries. This pathogen has been the subject of studies in a vast array of fields, from molecular biology to animal models for virulence activity to epidemiological disease transmission modeling. V. cholerae genetics and the activity of virulence genes determine the pathogenic potential of different strains, as well as provide a model for genomic evolution in the natural environment. While animal models for V. cholerae infection have been used for decades, recent advances in this area provide a well-rounded picture of nearly all aspects of V. cholerae interaction with both mammalian and non-mammalian hosts, encompassing colonization dynamics, pathogenesis, immunological responses, and transmission to naïve populations. Microbiome studies have become increasingly common as access and affordability of sequencing has improved, and these studies have revealed key factors in V. cholerae communication and competition with members of the gut microbiota. Despite a wealth of knowledge surrounding V. cholerae, the pathogen remains endemic in numerous countries and causes sporadic outbreaks elsewhere. Public health initiatives aim to prevent cholera outbreaks and provide prompt, effective relief in cases where prevention is not feasible. In this review, we describe recent advancements in cholera research in these areas to provide a more complete illustration of V. cholerae evolution as a microbe and significant global health threat, as well as how researchers are working to improve understanding and minimize impact of this pathogen on vulnerable populations.
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Affiliation(s)
| | | | | | - Jeffrey H. Withey
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
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41
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Molina-Quiroz RC, Silva-Valenzuela CA. Interactions of Vibrio phages and their hosts in aquatic environments. Curr Opin Microbiol 2023; 74:102308. [PMID: 37062175 DOI: 10.1016/j.mib.2023.102308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 04/18/2023]
Abstract
Bacteriophages (phages) are viruses that specifically infect bacteria. These viruses were discovered a century ago and have been used as a model system in microbial genetics and molecular biology. In order to survive, bacteria have to quickly adapt to phage challenges in their natural settings. In turn, phages continuously develop/evolve mechanisms for battling host defenses. A deeper understanding of the arms race between bacteria and phages is essential for the rational design of phage-based prophylaxis and therapies to prevent and treat bacterial infections. Vibrio species and their phages (vibriophages) are a suitable model to study these interactions. Phages are highly ubiquitous in aquatic environments and Vibrio are waterborne bacteria that must survive the constant attack by phages for successful transmission to their hosts. Here, we review relevant literature from the past two years to delve into the molecular interactions of Vibrio species and their phages in aquatic niches.
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Affiliation(s)
- Roberto C Molina-Quiroz
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts Medical Center and Tufts University, Boston, MA, USA
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42
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Chen Y, Zeng Z, She Q, Han W. The abortive infection functions of CRISPR-Cas and Argonaute. Trends Microbiol 2023; 31:405-418. [PMID: 36463018 DOI: 10.1016/j.tim.2022.11.005] [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: 09/15/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]
Abstract
CRISPR-Cas and prokaryotic Argonaute (pAgo) are nucleic acid (NA)-guided defense systems that protect prokaryotes against the invasion of mobile genetic elements. Previous studies established that they are directed by NA fragments (guides) to recognize invading complementary NA (targets), and that they cleave the targets to silence the invaders. Nevertheless, growing evidence indicates that many CRISPR-Cas and pAgo systems exploit the abortive infection (Abi) strategy to confer immunity. The CRISPR-Cas and pAgo Abi systems typically sense invaders using the NA recognition ability and activate various toxic effectors to kill the infected cells to prevent the invaders from spreading. This review summarizes the diverse mechanisms of these CRISPR-Cas and pAgo systems, and highlights their critical roles in the arms race between microbes and invaders.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, 266237, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China.
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Horne T, Orr VT, Hall JP. How do interactions between mobile genetic elements affect horizontal gene transfer? Curr Opin Microbiol 2023; 73:102282. [PMID: 36863168 DOI: 10.1016/j.mib.2023.102282] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 03/03/2023]
Abstract
Horizontal gene transfer is central to bacterial adaptation and is facilitated by mobile genetic elements (MGEs). Increasingly, MGEs are being studied as agents with their own interests and adaptations, and the interactions MGEs have with one another are recognised as having a powerful effect on the flow of traits between microbes. Collaborations and conflicts between MGEs are nuanced and can both promote and inhibit the acquisition of new genetic material, shaping the maintenance of newly acquired genes and the dissemination of important adaptive traits through microbiomes. We review recent studies that shed light on this dynamic and oftentimes interlaced interplay, highlighting the importance of genome defence systems in mediating MGE-MGE conflicts, and outlining the consequences for evolutionary change, that resonate from the molecular to microbiome and ecosystem levels.
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Affiliation(s)
- Tanya Horne
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Victoria T Orr
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - James Pj Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.
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Balasubramanian D, López-Pérez M, Almagro-Moreno S. Cholera Dynamics and the Emergence of Pandemic Vibrio cholerae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:127-147. [PMID: 36792874 DOI: 10.1007/978-3-031-22997-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Cholera is a severe diarrheal disease caused by the aquatic bacterium Vibrio cholerae. Interestingly, to date, only one major clade has emerged to cause pandemic disease in humans: the clade that encompasses the strains from the O1 and O139 serogroups. In this chapter, we provide a comprehensive perspective on the virulence factors and mobile genetic elements (MGEs) associated with the emergence of pandemic V. cholerae strains and highlight novel findings such as specific genomic background or interactions between MGEs that explain their confined distribution. Finally, we discuss pandemic cholera dynamics contextualizing them within the evolution of the bacterium.
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Affiliation(s)
- Deepak Balasubramanian
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA
| | - Mario López-Pérez
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, USA.
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Norfolk WA, Lipp EK. Use and Evaluation of a pES213-Derived Plasmid for the Constitutive Expression of gfp Protein in Pathogenic Vibrios: a Tagging Tool for In Vitro Studies. Microbiol Spectr 2023; 11:e0249022. [PMID: 36507673 PMCID: PMC9927583 DOI: 10.1128/spectrum.02490-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/20/2022] [Indexed: 12/14/2022] Open
Abstract
Insertion of green fluorescent protein (GFP) into bacterial cells for constitutive expression is a powerful tool for the localization of species of interest within complex mixtures. Here, we demonstrate and evaluate the efficacy of the pES213-derived donor plasmid pVSV102 (gfp Knr) as a conjugative tool for the tagging of Vibrio and related species (termed vibrios). Using a triparental mating assay assisted by the helper plasmid pEVS104 (tra trb Knr), we successfully tagged 12 species within the Vibrionaceae family representing 8 of the proposed clades. All transconjugant strains demonstrated bright fluorescence and were readily differentiable within complex mixtures of nontagged cells. Plasmid retention was assessed using persistence and subculture experimentation. Persistence experiments evaluated plasmid loss over time for nonsubcultured samples inoculated into antibiotic-free media and sterile artificial seawater, whereas subculture trials evaluated plasmid loss following one to four subculture passages. Strong plasmid retention (≥80%) was observed in persistence experiments for all transconjugant strains for up to 48 h in both antibiotic-free media and artificial seawater with the exception of Vibrio cholerae, which showed a substantial decline in media after 24 h. Subculturing experiments also demonstrated strong plasmid stability, with all transconjugant strains showing ≥80% retention after four subculture passages. The results of this research suggest that pVSV102 is a stable GFP plasmid for the tagging of a broad range of vibrios. IMPORTANCE Prior research has suggested that the use of Aliivibrio fischeri-derived donor plasmids with the pES213 origin of replication may provide increased plasmid stability for the tagging of vibrios compared to Escherichia coli-derived p15A plasmids. Here, we present a structured protocol for conjugation-based tagging of vibrios using the pES213-derived plasmid pVSV102 and evaluate the plasmid stability of tagged strains. These methods and the resulting transconjugant strains provide important standardized tools to facilitate experimentation requiring the use of traceable vibrio strains. Furthermore, the determination of the species-specific plasmid stability provides an estimation of the anticipated level of plasmid loss under the given set of culture conditions. This estimation can be used to reduce the occurrence of experimental biases introduced by plasmid drift.
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Affiliation(s)
- William A. Norfolk
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, USA
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, USA
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DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage. Mol Cell 2022; 82:4727-4740.e6. [PMID: 36525956 DOI: 10.1016/j.molcel.2022.11.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/31/2022] [Accepted: 11/16/2022] [Indexed: 12/23/2022]
Abstract
Structural maintenance of chromosome (SMC) complexes fold DNA by loop extrusion to support chromosome segregation and genome maintenance. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA. Here, we show that JetABCD restricts circular plasmids with an upper size limit of about 100 kb, whereas a linear plasmid evades restriction. Purified JetABCD complexes cleave circular DNA molecules, regardless of the DNA helical topology; cleavage is DNA sequence nonspecific and depends on the SMC ATPase. A cryo-EM structure reveals a distinct JetABC dimer-of-dimers geometry, with the two SMC dimers facing in opposite direction-rather than the same as observed with MukBEF. We hypothesize that JetABCD is a DNA-shape-specific endonuclease and propose the "total extrusion model" for DNA cleavage exclusively when extrusion of an entire plasmid has been completed by a JetABCD complex. Total extrusion cannot be achieved on the larger chromosome, explaining how self-DNA may evade processing.
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When bacteria are phage playgrounds: interactions between viruses, cells, and mobile genetic elements. Curr Opin Microbiol 2022; 70:102230. [PMID: 36335712 DOI: 10.1016/j.mib.2022.102230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/23/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Studies of viral adaptation have focused on the selective pressures imposed by hosts. However, there is increasing evidence that interactions between viruses, cells, and other mobile genetic elements are determinant to the success of infections. These interactions are often associated with antagonism and competition, but sometimes involve cooperation or parasitism. We describe two key types of interactions - defense systems and genetic regulation - that allow the partners of the interaction to destroy or control the others. These interactions evolve rapidly by genetic exchanges, including among competing partners. They are sometimes followed by functional diversification. Gene exchanges also facilitate the emergence of cross-talk between elements in the same bacterium. In the end, these processes produce multilayered networks of interactions that shape the outcome of viral infections.
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Deep A, Gu Y, Gao YQ, Ego KM, Herzik MA, Zhou H, Corbett KD. The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA. Mol Cell 2022; 82:4145-4159.e7. [PMID: 36206765 PMCID: PMC9637719 DOI: 10.1016/j.molcel.2022.09.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/19/2022] [Accepted: 09/06/2022] [Indexed: 11/06/2022]
Abstract
Self versus non-self discrimination is a key element of innate and adaptive immunity across life. In bacteria, CRISPR-Cas and restriction-modification systems recognize non-self nucleic acids through their sequence and their methylation state, respectively. Here, we show that the Wadjet defense system recognizes DNA topology to protect its host against plasmid transformation. By combining cryoelectron microscopy with cross-linking mass spectrometry, we show that Wadjet forms a complex similar to the bacterial condensin complex MukBEF, with a novel nuclease subunit similar to a type II DNA topoisomerase. Wadjet specifically cleaves closed-circular DNA in a reaction requiring ATP hydrolysis by the structural maintenance of chromosome (SMC) ATPase subunit JetC, suggesting that the complex could use DNA loop extrusion to sense its substrate's topology, then specifically activate the nuclease subunit JetD to cleave plasmid DNA. Overall, our data reveal how bacteria have co-opted a DNA maintenance machine to specifically recognize and destroy foreign DNAs through topology sensing.
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Affiliation(s)
- Amar Deep
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yong-Qi Gao
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kaori M Ego
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark A Herzik
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Huilin Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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Koopal B, Mutte SK, Swarts DC. A long look at short prokaryotic Argonautes. Trends Cell Biol 2022:S0962-8924(22)00239-2. [DOI: 10.1016/j.tcb.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/23/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
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Adade NE, Aniweh Y, Mosi L, Valvano MA, Duodu S, Ahator SD. Comparative analysis of Vibrio cholerae isolates from Ghana reveals variations in genome architecture and adaptation of outbreak and environmental strains. Front Microbiol 2022; 13:998182. [PMID: 36312941 PMCID: PMC9608740 DOI: 10.3389/fmicb.2022.998182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022] Open
Abstract
Recurrent epidemics of cholera denote robust adaptive mechanisms of Vibrio cholerae for ecological shifting and persistence despite variable stress conditions. Tracking the evolution of pathobiological traits requires comparative genomic studies of isolates from endemic areas. Here, we investigated the genetic differentiation among V. cholerae clinical and environmental isolates by highlighting the genomic divergence associated with gene decay, genome plasticity, and the acquisition of virulence and adaptive traits. The clinical isolates showed high phylogenetic relatedness due to a higher frequency of shared orthologs and fewer gene variants in contrast to the evolutionarily divergent environmental strains. Divergence of the environmental isolates is linked to extensive genomic rearrangements in regions containing mobile genetic elements resulting in numerous breakpoints, relocations, and insertions coupled with the loss of virulence determinants acf, zot, tcp, and ctx in the genomic islands. Also, four isolates possessed the CRISPR-Cas systems with spacers specific for Vibrio phages and plasmids. Genome synteny and homology analysis of the CRISPR-Cas systems suggest horizontal acquisition. The marked differences in the distribution of other phage and plasmid defense systems such as Zorya, DdmABC, DdmDE, and type-I Restriction Modification systems among the isolates indicated a higher propensity for plasmid or phage disseminated traits in the environmental isolates. Our results reveal that V. cholerae strains undergo extensive genomic rearrangements coupled with gene acquisition, reflecting their adaptation during ecological shifts and pathogenicity.
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Affiliation(s)
- Nana Eghele Adade
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
- Department of Microbiology, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Yaw Aniweh
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Lydia Mosi
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Miguel A. Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
| | - Samuel Duodu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Samuel Duodu,
| | - Stephen Dela Ahator
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Stephen Dela Ahator,
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