1
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Liang F, Sun M, Xie L, Zhao X, Liu D, Zhao K, Zhang G. Recent advances and challenges in protein complex model accuracy estimation. Comput Struct Biotechnol J 2024; 23:1824-1832. [PMID: 38707538 PMCID: PMC11066466 DOI: 10.1016/j.csbj.2024.04.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024] Open
Abstract
Estimation of model accuracy plays a crucial role in protein structure prediction, aiming to evaluate the quality of predicted protein structure models accurately and objectively. This process is not only key to screening candidate models that are close to the real structure, but also provides guidance for further optimization of protein structures. With the significant advancements made by AlphaFold2 in monomer structure, the problem of single-domain protein structure prediction has been widely solved. Correspondingly, the importance of assessing the quality of single-domain protein models decreased, and the research focus has shifted to estimation of model accuracy of protein complexes. In this review, our goal is to provide a comprehensive overview of the reference and statistical metrics, as well as representative methods, and the current challenges within four distinct facets (Topology Global Score, Interface Total Score, Interface Residue-Wise Score, and Tertiary Residue-Wise Score) in the field of complex EMA.
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Affiliation(s)
| | | | - Lei Xie
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Xuanfeng Zhao
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Dong Liu
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Kailong Zhao
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Guijun Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
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2
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Hays M. Genetic conflicts in budding yeast: The 2μ plasmid as a model selfish element. Semin Cell Dev Biol 2024; 161-162:31-41. [PMID: 38598944 DOI: 10.1016/j.semcdb.2024.04.002] [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: 09/26/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Antagonistic coevolution, arising from genetic conflict, can drive rapid evolution and biological innovation. Conflict can arise both between organisms and within genomes. This review focuses on budding yeasts as a model system for exploring intra- and inter-genomic genetic conflict, highlighting in particular the 2-micron (2μ) plasmid as a model selfish element. The 2μ is found widely in laboratory strains and industrial isolates of Saccharomyces cerevisiae and has long been known to cause host fitness defects. Nevertheless, the plasmid is frequently ignored in the context of genetic, fitness, and evolution studies. Here, I make a case for further exploring the evolutionary impact of the 2μ plasmid as well as other selfish elements of budding yeasts, discuss recent advances, and, finally, future directions for the field.
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Affiliation(s)
- Michelle Hays
- Department of Genetics, Stanford University, Stanford, CA, United States.
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3
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Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA. An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense. Nat Commun 2024; 15:6955. [PMID: 39138193 PMCID: PMC11322646 DOI: 10.1038/s41467-024-51346-1] [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: 12/05/2023] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
The prevalence of multidrug resistant (MDR) bacterial infections continues to rise as the development of antibiotics needed to combat these infections remains stagnant. MDR enterococci are a major contributor to this crisis. A potential therapeutic approach for combating MDR enterococci is bacteriophage (phage) therapy, which uses lytic viruses to infect and kill pathogenic bacteria. While phages that lyse some strains of MDR enterococci have been identified, other strains display high levels of resistance and the mechanisms underlying this resistance are poorly defined. Here, we use a CRISPR interference (CRISPRi) screen to identify a genetic locus found on a mobilizable plasmid from Enterococcus faecalis involved in phage resistance. This locus encodes a putative serine recombinase followed by a Type IV restriction enzyme (TIV-RE) that we show restricts the replication of phage phi47 in vancomycin-resistant E. faecalis. We further find that phi47 evolves to overcome restriction by acquiring a missense mutation in a TIV-RE inhibitor protein. We show that this inhibitor, termed type IV restriction inhibiting factor A (tifA), binds and inactivates diverse TIV-REs. Overall, our findings advance our understanding of phage defense in drug-resistant E. faecalis and provide mechanistic insight into how phages evolve to overcome antiphage defense systems.
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Affiliation(s)
- Nathan P Bullen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Cydney N Johnson
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Shelby E Andersen
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Garima Arya
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Sonia R Marotta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Peter R Weigele
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA.
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4
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Deep A, Liang Q, Enustun E, Pogliano J, Corbett KD. Architecture and activation mechanism of the bacterial PARIS defence system. Nature 2024:10.1038/s41586-024-07772-8. [PMID: 39112702 DOI: 10.1038/s41586-024-07772-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 07/02/2024] [Indexed: 08/17/2024]
Abstract
Bacteria and their viruses (bacteriophages or phages) are engaged in an intense evolutionary arms race1-5. While the mechanisms of many bacterial antiphage defence systems are known1, how these systems avoid toxicity outside infection yet activate quickly after infection is less well understood. Here we show that the bacterial phage anti-restriction-induced system (PARIS) operates as a toxin-antitoxin system, in which the antitoxin AriA sequesters and inactivates the toxin AriB until triggered by the T7 phage counterdefence protein Ocr. Using cryo-electron microscopy, we show that AriA is related to SMC-family ATPases but assembles into a distinctive homohexameric complex through two oligomerization interfaces. In uninfected cells, the AriA hexamer binds to up to three monomers of AriB, maintaining them in an inactive state. After Ocr binding, the AriA hexamer undergoes a structural rearrangement, releasing AriB and allowing it to dimerize and activate. AriB is a toprim/OLD-family nuclease, the activation of which arrests cell growth and inhibits phage propagation by globally inhibiting protein translation through specific cleavage of a lysine tRNA. Collectively, our findings reveal the intricate molecular mechanisms of a bacterial defence system triggered by a phage counterdefence protein, and highlight how an SMC-family ATPase has been adapted as a bacterial infection sensor.
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Affiliation(s)
- Amar Deep
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Qishan Liang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Eray Enustun
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
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5
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Robins WP, Meader BT, Toska J, Mekalanos JJ. DdmABC-dependent death triggered by viral palindromic DNA sequences. Cell Rep 2024; 43:114450. [PMID: 39002129 DOI: 10.1016/j.celrep.2024.114450] [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: 05/08/2023] [Revised: 04/24/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024] Open
Abstract
Defense systems that recognize viruses provide important insights into both prokaryotic and eukaryotic innate immunity mechanisms. Such systems that restrict foreign DNA or trigger cell death have recently been recognized, but the molecular signals that activate many of these remain largely unknown. Here, we characterize one such system in pandemic Vibrio cholerae responsible for triggering cell density-dependent death (CDD) of cells in response to the presence of certain genetic elements. We show that the key component is the Lamassu DdmABC anti-phage/plasmid defense system. We demonstrate that signals that trigger CDD were palindromic DNA sequences in phages and plasmids that are predicted to form stem-loop hairpins from single-stranded DNA. Our results suggest that agents that damage DNA also trigger DdmABC activation and inhibit cell growth. Thus, any infectious process that results in damaged DNA, particularly during DNA replication, can in theory trigger DNA restriction and death through the DdmABC abortive infection system.
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Affiliation(s)
- William P Robins
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Bradley T Meader
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jonida Toska
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - John J Mekalanos
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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6
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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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7
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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 EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - 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 EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - 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 EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
| | - 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 EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
| | - 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 EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - 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 EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
| | - 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 EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
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8
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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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9
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Hossain AA, Pigli YZ, Baca CF, Heissel S, Thomas A, Libis VK, Burian J, Chappie JS, Brady SF, Rice PA, Marraffini LA. DNA glycosylases provide antiviral defence in prokaryotes. Nature 2024; 629:410-416. [PMID: 38632404 PMCID: PMC11078745 DOI: 10.1038/s41586-024-07329-9] [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: 05/19/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Bacteria have adapted to phage predation by evolving a vast assortment of defence systems1. Although anti-phage immunity genes can be identified using bioinformatic tools, the discovery of novel systems is restricted to the available prokaryotic sequence data2. Here, to overcome this limitation, we infected Escherichia coli carrying a soil metagenomic DNA library3 with the lytic coliphage T4 to isolate clones carrying protective genes. Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria. Our study highlights the benefits of screening unsequenced DNA and reveals prokaryotic DNA glycosylases as important players in the bacteria-phage arms race.
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Affiliation(s)
- Amer A Hossain
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Ying Z Pigli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Christian F Baca
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alexis Thomas
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Vincent K Libis
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Ján Burian
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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10
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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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11
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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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12
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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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13
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Agapov A, Baker KS, Bedekar P, Bhatia RP, Blower TR, Brockhurst MA, Brown C, Chong CE, Fothergill JL, Graham S, Hall JP, Maestri A, McQuarrie S, Olina A, Pagliara S, Recker M, Richmond A, Shaw SJ, Szczelkun MD, Taylor TB, van Houte S, Went SC, Westra ER, White MF, Wright R. Multi-layered genome defences in bacteria. Curr Opin Microbiol 2024; 78:102436. [PMID: 38368839 DOI: 10.1016/j.mib.2024.102436] [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: 11/14/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/20/2024]
Abstract
Bacteria have evolved a variety of defence mechanisms to protect against mobile genetic elements, including restriction-modification systems and CRISPR-Cas. In recent years, dozens of previously unknown defence systems (DSs) have been discovered. Notably, diverse DSs often coexist within the same genome, and some co-occur at frequencies significantly higher than would be expected by chance, implying potential synergistic interactions. Recent studies have provided evidence of defence mechanisms that enhance or complement one another. Here, we review the interactions between DSs at the mechanistic, regulatory, ecological and evolutionary levels.
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Affiliation(s)
- Aleksei Agapov
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Kate S Baker
- Department of Genetics, University of Cambridge, CB2 3EH, UK
| | - Paritosh Bedekar
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Rama P Bhatia
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Michael A Brockhurst
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Cooper Brown
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | | | - Joanne L Fothergill
- Dept of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
| | - Shirley Graham
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - James Pj Hall
- Dept of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
| | - Alice Maestri
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Stuart McQuarrie
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Anna Olina
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | | | - Mario Recker
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Anna Richmond
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Steven J Shaw
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS6 7YB, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS6 7YB, UK
| | - Tiffany B Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | | | - Sam C Went
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Edze R Westra
- ESI, Centre for Ecology and Conservation, University of Exeter, UK.
| | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Rosanna Wright
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
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14
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Wang J, Wang X, Yang K, Lu C, Fields B, Xu Y, Shen Q, Wei Z, Friman VP. Phage selection drives resistance-virulence trade-offs in Ralstonia solanacearum plant-pathogenic bacterium irrespective of the growth temperature. Evol Lett 2024; 8:253-266. [PMID: 38525025 PMCID: PMC10959482 DOI: 10.1093/evlett/qrad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 03/26/2024] Open
Abstract
While temperature has been shown to affect the survival and growth of bacteria and their phage parasites, it is unclear if trade-offs between phage resistance and other bacterial traits depend on the temperature. Here, we experimentally compared the evolution of phage resistance-virulence trade-offs and underlying molecular mechanisms in phytopathogenic Ralstonia solanacearum bacterium at 25 °C and 35 °C temperature environments. We found that while phages reduced R. solanacearum densities relatively more at 25 °C, no difference in the final level of phage resistance was observed between temperature treatments. Instead, small colony variants (SCVs) with increased growth rate and mutations in the quorum-sensing (QS) signaling receptor gene, phcS, evolved in both temperature treatments. Interestingly, SCVs were also phage-resistant and reached higher frequencies in the presence of phages. Evolving phage resistance was costly, resulting in reduced carrying capacity, biofilm formation, and virulence in planta, possibly due to loss of QS-mediated expression of key virulence genes. We also observed mucoid phage-resistant colonies that showed loss of virulence and reduced twitching motility likely due to parallel mutations in prepilin peptidase gene, pilD. Moreover, phage-resistant SCVs from 35 °C-phage treatment had parallel mutations in type II secretion system (T2SS) genes (gspE and gspF). Adsorption assays confirmed the role of pilD as a phage receptor, while no loss of adsorption was found with phcS or T2SS mutants, indicative of other downstream phage resistance mechanisms. Additional transcriptomic analysis revealed upregulation of CBASS and type I restriction-modification phage defense systems in response to phage exposure, which coincided with reduced expression of motility and virulence-associated genes, including pilD and type II and III secretion systems. Together, these results suggest that while phage resistance-virulence trade-offs are not affected by the growth temperature, they could be mediated through both pre- and postinfection phage resistance mechanisms.
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Affiliation(s)
- Jianing Wang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Xiaofang Wang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Keming Yang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Chunxia Lu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Bryden Fields
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Yangchun Xu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Zhong Wei
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
| | - Ville-Petri Friman
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, P.R. China
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Department of Biology, University of York, Wentworth Way, York , United Kingdom
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15
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Roy S, Adhikary H, D’Amours D. The SMC5/6 complex: folding chromosomes back into shape when genomes take a break. Nucleic Acids Res 2024; 52:2112-2129. [PMID: 38375830 PMCID: PMC10954462 DOI: 10.1093/nar/gkae103] [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: 11/13/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
High-level folding of chromatin is a key determinant of the shape and functional state of chromosomes. During cell division, structural maintenance of chromosome (SMC) complexes such as condensin and cohesin ensure large-scale folding of chromatin into visible chromosomes. In contrast, the SMC5/6 complex plays more local and context-specific roles in the structural organization of interphase chromosomes with important implications for health and disease. Recent advances in single-molecule biophysics and cryo-electron microscopy revealed key insights into the architecture of the SMC5/6 complex and how interactions connecting the complex to chromatin components give rise to its unique repertoire of interphase functions. In this review, we provide an integrative view of the features that differentiates the SMC5/6 complex from other SMC enzymes and how these enable dramatic reorganization of DNA folding in space during DNA repair reactions and other genome transactions. Finally, we explore the mechanistic basis for the dynamic targeting of the SMC5/6 complex to damaged chromatin and its crucial role in human health.
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Affiliation(s)
- Shamayita Roy
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Hemanta Adhikary
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
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16
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Roisné-Hamelin F, Liu HW, Taschner M, Li Y, Gruber S. Structural basis for plasmid restriction by SMC JET nuclease. Mol Cell 2024; 84:883-896.e7. [PMID: 38309275 DOI: 10.1016/j.molcel.2024.01.009] [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: 10/03/2023] [Revised: 12/06/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
DNA loop-extruding SMC complexes play crucial roles in chromosome folding and DNA immunity. Prokaryotic SMC Wadjet (JET) complexes limit the spread of plasmids through DNA cleavage, yet the mechanisms for plasmid recognition are unresolved. We show that artificial DNA circularization renders linear DNA susceptible to JET nuclease cleavage. Unlike free DNA, JET cleaves immobilized plasmid DNA at a specific site, the plasmid-anchoring point, showing that the anchor hinders DNA extrusion but not DNA cleavage. Structures of plasmid-bound JetABC reveal two presumably stalled SMC motor units that are drastically rearranged from the resting state, together entrapping a U-shaped DNA segment, which is further converted to kinked V-shaped cleavage substrate by JetD nuclease binding. Our findings uncover mechanical bending of residual unextruded DNA as molecular signature for plasmid recognition and non-self DNA elimination. We moreover elucidate key elements of SMC loop extrusion, including the motor direction and the structure of a DNA-holding state.
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Affiliation(s)
- Florian Roisné-Hamelin
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Hon Wing Liu
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Michael Taschner
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Yan Li
- 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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17
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Ipoutcha T, Racharaks R, Huttelmaier S, Wilson CJ, Ozer EA, Hartmann EM. A synthetic biology approach to assemble and reboot clinically relevant Pseudomonas aeruginosa tailed phages. Microbiol Spectr 2024; 12:e0289723. [PMID: 38294230 PMCID: PMC10913387 DOI: 10.1128/spectrum.02897-23] [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: 08/04/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024] Open
Abstract
The rise in the frequency of antibiotic resistance has made bacterial infections, specifically Pseudomonas aeruginosa, a cause for greater concern. Phage therapy is a promising solution that uses naturally isolated phages to treat bacterial infections. Ecological limitations, which stipulate a discrete host range and the inevitable evolution of resistance, may be overcome through a better understanding of phage biology and the utilization of engineered phages. In this study, we developed a synthetic biology approach to construct tailed phages that naturally target clinically relevant strains of Pseudomonas aeruginosa. As proof of concept, we successfully cloned and assembled the JG024 and DMS3 phage genomes in yeast using transformation-associated recombination cloning and rebooted these two phage genomes in two different strains of P. aeruginosa. We identified factors that affected phage reboot efficiency like the phage species or the presence of antiviral defense systems in the bacterial strain. We have successfully extended this method to two other phage species and observed that the method enables the reboot of phages that are naturally unable to infect the strain used for reboot. This research represents a critical step toward the construction of clinically relevant, engineered P. aeruginosa phages.IMPORTANCEPseudomonas aeruginosa is a bacterium responsible for severe infections and a common major complication in cystic fibrosis. The use of antibiotics to treat bacterial infections has become increasingly difficult as antibiotic resistance has become more prevalent. Phage therapy is an alternative solution that is already being used in some European countries, but its use is limited by the narrow host range due to the phage receptor specificity, the presence of antiviral defense systems in the bacterial strain, and the possible emergence of phage resistance. In this study, we demonstrate the use of a synthetic biology approach to construct and reboot clinically relevant P. aeruginosa tailed phages. This method enables a significant expansion of possibilities through the construction of engineered phages for therapy applications.
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Affiliation(s)
- Thomas Ipoutcha
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Ratanachat Racharaks
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Stefanie Huttelmaier
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Cole J. Wilson
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
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18
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Pradhan B, Deep A, König J, Baaske MD, Corbett KD, Kim E. Loop extrusion-mediated plasmid DNA cleavage by the bacterial SMC Wadjet complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.17.580791. [PMID: 38405785 PMCID: PMC10889018 DOI: 10.1101/2024.02.17.580791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes play pivotal roles in genome organization and maintenance across all domains of life. In prokaryotes, SMC family Wadjet complexes structurally resemble the widespread MukBEF genome-organizing complexes but serve a defensive role by inhibiting plasmid transformation. We previously showed that Wadjet specifically cleaves circular DNA; however, the molecular mechanism underlying DNA substrate recognition remains unclear. Here, we use in vitro single-molecule imaging to directly visualize DNA loop extrusion and plasmid cleavage by Wadjet. We find that Wadjet is a symmetric DNA loop extruder that simultaneously reels in DNA from both sides of a growing loop and that this activity requires a dimeric JetABC supercomplex containing two dimers of the JetC motor subunit. On surface-anchored plasmid DNAs, Wadjet extrudes the full length of a 44 kilobase pair plasmid, stalls, and then cleaves DNA. Our findings reveal the role of loop extrusion in the specific recognition and elimination of plasmids by Wadjet, and establish loop extrusion as an evolutionarily conserved mechanism among SMC complexes across kingdoms of life.
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Affiliation(s)
- Biswajit Pradhan
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA, USA
| | - Jessica König
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | | | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA, USA
- Department of Molecular Biology, University of California San Diego, La Jolla CA, USA
| | - Eugene Kim
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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19
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Kogay R, Wolf YI, Koonin EV. Defense systems and horizontal gene transfer in bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579689. [PMID: 38410456 PMCID: PMC10896350 DOI: 10.1101/2024.02.09.579689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages that generally impose fitness costs on their hosts. However, a substantial fraction of bacterial genes is involved in defense mechanisms that limit the propagation of MGEs, raising the possibility that they can actively restrict HGT. Here we examine whether defense systems curb HGT by exploring the connections between HGT rate and the presence of 73 defense systems in 12 bacterial species. We found that only 6 defense systems, 3 of which are different CRISPR-Cas subtypes, are associated with the reduced gene gain rate on the scale of species evolution. The hosts of such defense systems tend to have a smaller pangenome size and harbor fewer phage-related genes compared to genomes lacking these systems, suggesting that these defense mechanisms inhibit HGT by limiting the integration of prophages. We hypothesize that restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and 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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20
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Liu S, Liu H, Wang X, Shi L. The immune system of prokaryotes: potential applications and implications for gene editing. Biotechnol J 2024; 19:e2300352. [PMID: 38403433 DOI: 10.1002/biot.202300352] [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: 07/19/2023] [Revised: 11/30/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024]
Abstract
Gene therapy has revolutionized the treatment of genetic diseases. Spearheading this revolution are sophisticated genome editing methods such as TALENs, ZFNs, and CRISPR-Cas, which trace their origins back to prokaryotic immune systems. Prokaryotes have developed various antiviral defense systems to combat viral attacks and the invasion of genetic elements. The comprehension of these defense mechanisms has paved the way for the development of indispensable tools in molecular biology. Among them, restriction endonuclease originates from the innate immune system of bacteria. The CRISPR-Cas system, a widely applied genome editing technology, is derived from the prokaryotic adaptive immune system. Single-base editing is a precise editing tool based on CRISPR-Cas system that involves deamination of target base. It is worth noting that prokaryotes possess deamination enzymes as part of their defense arsenal over foreign genetic material. Furthermore, prokaryotic Argonauts (pAgo) proteins, also function in anti-phage defense, play an important role in complementing the CRISPR-Cas system by addressing certain limitations it may have. Recent studies have also shed light on the significance of Retron, a reverse transcription transposon previously showed potential in genome editing, has also come to light in the realm of prokaryotic immunity. These noteworthy findings highlight the importance of studying prokaryotic immune system for advancing genome editing techniques. Here, both the origin of prokaryotic immunity underlying aforementioned genome editing tools, and potential applications of deaminase, pAgo protein and reverse transcriptase in genome editing among prokaryotes were introduced, thus emphasizing the fundamental mechanism and significance of prokaryotic immunity.
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Affiliation(s)
- Siyang Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Hongling Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lei Shi
- School of Life Sciences, Chongqing University, Chongqing, China
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21
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Burke KA, Urick CD, Mzhavia N, Nikolich MP, Filippov AA. Correlation of Pseudomonas aeruginosa Phage Resistance with the Numbers and Types of Antiphage Systems. Int J Mol Sci 2024; 25:1424. [PMID: 38338703 PMCID: PMC10855318 DOI: 10.3390/ijms25031424] [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: 12/14/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Phage therapeutics offer a potentially powerful approach for combating multidrug-resistant bacterial infections. However, to be effective, phage therapy must overcome existing and developing phage resistance. While phage cocktails can reduce this risk by targeting multiple receptors in a single therapeutic, bacteria have mechanisms of resistance beyond receptor modification. A rapidly growing body of knowledge describes a broad and varied arsenal of antiphage systems encoded by bacteria to counter phage infection. We sought to understand the types and frequencies of antiphage systems present in a highly diverse panel of Pseudomonas aeruginosa clinical isolates utilized to characterize novel antibacterials. Using the web-server tool PADLOC (prokaryotic antiviral defense locator), putative antiphage systems were identified in these P. aeruginosa clinical isolates based on sequence homology to a validated and curated catalog of known defense systems. Coupling this host bacterium sequence analysis with host range data for 70 phages, we observed a correlation between existing phage resistance and the presence of higher numbers of antiphage systems in bacterial genomes. We were also able to identify antiphage systems that were more prevalent in highly phage-resistant P. aeruginosa strains, suggesting their importance in conferring resistance.
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Affiliation(s)
| | | | | | | | - Andrey A. Filippov
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (K.A.B.); (C.D.U.); (N.M.); (M.P.N.)
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22
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Burman N, Belukhina S, Depardieu F, Wilkinson RA, Skutel M, Santiago-Frangos A, Graham AB, Livenskyi A, Chechenina A, Morozova N, Zahl T, Henriques WS, Buyukyoruk M, Rouillon C, Shyrokova L, Kurata T, Hauryliuk V, Severinov K, Groseille J, Thierry A, Koszul R, Tesson F, Bernheim A, Bikard D, Wiedenheft B, Isaev A. Viral proteins activate PARIS-mediated tRNA degradation and viral tRNAs rescue infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573894. [PMID: 38260645 PMCID: PMC10802454 DOI: 10.1101/2024.01.02.573894] [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
Viruses compete with each other for limited cellular resources, and some viruses deliver defense mechanisms that protect the host from competing genetic parasites. PARIS is a defense system, often encoded in viral genomes, that is composed of a 53 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB). Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex. We use cryo-EM to determine the structure of this complex which explains how six molecules of AriA assemble into a propeller-shaped scaffold that coordinates three subunits of AriB. ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving the host tRNALys. Phage T5 subverts PARIS immunity through expression of a tRNALys variant that prevents PARIS-mediated cleavage, and thereby restores viral infection. Collectively, these data explain how AriA functions as an ATP-dependent sensor that detects viral proteins and activates the AriB toxin. PARIS is one of an emerging set of immune systems that form macromolecular complexes for the recognition of foreign proteins, rather than foreign nucleic acids.
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Affiliation(s)
- Nathaniel Burman
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Svetlana Belukhina
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow, Russia
| | - Florence Depardieu
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, 75015 Paris, France
| | - Royce A. Wilkinson
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Mikhail Skutel
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow, Russia
| | - Andrew Santiago-Frangos
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Ava B. Graham
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Alexei Livenskyi
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Chechenina
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow, Russia
| | - Natalia Morozova
- Peter the Great St Petersburg State Polytechnic University, St. Petersburg, Russia
| | - Trevor Zahl
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - William S. Henriques
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Murat Buyukyoruk
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Christophe Rouillon
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, 75015 Paris, France
| | - Lena Shyrokova
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Virus Centre, Lund University, Lund, Sweden
- Science for Life Laboratory, Lund, Sweden
| | | | - Justine Groseille
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
- Sorbonne Université, College Doctoral
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Florian Tesson
- Institut Pasteur, Université Paris Cité, Molecular Diversity of Microbes, 75015 Paris, France
| | - Aude Bernheim
- Institut Pasteur, Université Paris Cité, Molecular Diversity of Microbes, 75015 Paris, France
| | - David Bikard
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Synthetic Biology, 75015 Paris, France
| | - Blake Wiedenheft
- Montana State University, Bozeman, Department of Microbiology and Cell Biology, 59715 Montana, USA
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Center for Molecular and Cellular Biology, Moscow, Russia
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23
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Deep A, Liang Q, Enustun E, Pogliano J, Corbett KD. Architecture and infection-sensing mechanism of the bacterial PARIS defense system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573835. [PMID: 38260510 PMCID: PMC10802264 DOI: 10.1101/2024.01.02.573835] [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
Bacteria and the viruses that infect them (bacteriophages or phages) are engaged in an evolutionary arms race that has resulted in the development of hundreds of bacterial defense systems and myriad phage-encoded counterdefenses1-5. While the mechanisms of many bacterial defense systems are known1, how these systems avoid toxicity outside infection yet activate quickly upon sensing phage infection is less well understood. Here, we show that the bacterial Phage Anti-Restriction-Induced System (PARIS) operates as a toxin-antitoxin system, in which the antitoxin AriA sequesters and inactivates the toxin AriB until triggered by the T7 phage counterdefense protein Ocr. Using cryoelectron microscopy (cryoEM), we show that AriA is structurally similar to dimeric SMC-family ATPases but assembles into a distinctive homohexameric complex through two distinct oligomerization interfaces. In the absence of infection, the AriA hexamer binds up to three monomers of AriB, maintaining them in an inactive state. Ocr binding to the AriA-AriB complex triggers rearrangement of the AriA hexamer, releasing AriB and allowing it to dimerize and activate. AriB is a toprim/OLD-family nuclease whose activation arrests cell growth and inhibits phage propagation by globally inhibiting protein translation. Collectively, our findings reveal the intricate molecular mechanisms of a bacterial defense system that evolved in response to a phage counterdefense protein, and highlight how an SMC-family ATPase has been adapted as a bacterial infection sensor.
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Affiliation(s)
- Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA, USA
| | - Qishan Liang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla CA, USA
| | - Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California San Diego, La Jolla CA, USA
| | - Kevin D. Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA, USA
- Department of Molecular Biology, University of California San Diego, La Jolla CA, USA
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24
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Martínez-Alvarez L, Ramond JB, Vikram S, León-Sobrino C, Maggs-Kölling G, Cowan DA. With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities. Appl Environ Microbiol 2023; 89:e0062923. [PMID: 37971255 PMCID: PMC10734447 DOI: 10.1128/aem.00629-23] [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: 04/17/2023] [Accepted: 07/24/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.
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Affiliation(s)
- Laura Martínez-Alvarez
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
- Extreme Ecosystem Microbiomics & Ecogenomics (E²ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Surendra Vikram
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Carlos León-Sobrino
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | | | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
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25
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Tang D, Chen Y, Chen H, Jia T, Chen Q, Yu Y. Multiple enzymatic activities of a Sir2-HerA system cooperate for anti-phage defense. Mol Cell 2023; 83:4600-4613.e6. [PMID: 38096825 DOI: 10.1016/j.molcel.2023.11.010] [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: 06/08/2023] [Revised: 09/14/2023] [Accepted: 11/13/2023] [Indexed: 12/24/2023]
Abstract
In response to the persistent exposure to phage infection, bacteria have evolved diverse antiviral defense mechanisms. In this study, we report a bacterial two-component defense system consisting of a Sir2 NADase and a HerA helicase. Cryo-electron microscopy reveals that Sir2 and HerA assemble into a ∼1 MDa supramolecular octadecamer. Unexpectedly, this complex exhibits various enzymatic activities, including ATPase, NADase, helicase, and nuclease, which work together in a sophisticated manner to fulfill the antiphage function. Therefore, we name this defense system "Nezha" after a divine warrior in Chinese mythology who employs multiple weapons to defeat enemies. Our findings demonstrate that Nezha could sense phage infections, self-activate to arrest cell growth, eliminate phage genomes, and subsequently deactivate to allow for cell recovery. Collectively, Nezha represents a paradigm of sophisticated and multifaceted strategies bacteria use to defend against viral infections.
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Affiliation(s)
- Dongmei Tang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yijun Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tingting Jia
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiang Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Yamei Yu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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26
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Wallner B. Improved multimer prediction using massive sampling with AlphaFold in CASP15. Proteins 2023; 91:1734-1746. [PMID: 37548092 DOI: 10.1002/prot.26562] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
AlphaFold2 has revolutionized structure prediction by achieving high accuracy comparable to experimentally determined structures. However, there is still room for improvement, especially for challenging cases like multimers. A key to the success of AlphaFold is its ability to assess and rank its own predictions. Our basic idea for the Wallner group in CASP15 was to exploit this excellent scoring function in AlphaFold by massive sampling. To achieve this goal, we conducted AlphaFold runs using six different settings, using templates, without templates, and with an increased number of recycles for both multimer v1 and v2 weights. In all instances, we enabled dropout layers during inference, allowing for sampling of uncertainty and enhancing the diversity of the generated models. In total, 274 289 models were generated for the 38 targets in CASP15, with a median of 4810 models per target. Of these 38 targets, 10 were high quality, 11 were medium quality, 11 were acceptable, and only 6 were incorrect. The improvement over the baseline method, NBIS-AF2-multimer, is substantial, with the mean DockQ increasing from 0.43 to 0.56, with several targets showing a DockQ score increase of +0.6 units. Remarkable, considering Wallner and NBIS-AF2-multimer were using identical input data. The success can be attributed to the diversified sampling using dropout with different settings and, in particular, the use of multimer v1, which is much more susceptible to sampling compared with v2. The method is available here: http://wallnerlab.org/AFsample/.
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Affiliation(s)
- Björn Wallner
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
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27
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Studer G, Tauriello G, Schwede T. Assessment of the assessment-All about complexes. Proteins 2023; 91:1850-1860. [PMID: 37858934 DOI: 10.1002/prot.26612] [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: 05/03/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023]
Abstract
Predicting model quality is a fundamental component of any modeling procedure, and blind assessment of these methods constitutes a crucial aspect of the Critical Assessment of Protein Structure Prediction (CASP) experiment. Historically, the main focus was on assessing methods that predict global and per-residue accuracies in tertiary structure models. This focus shifted with the community's increased efforts in modeling complexes and assemblies. We asked the community to process the models from the CASP15 assembly category and provide estimates of the accuracy of the predicted quaternary structure, both globally and at the local interface level. Besides identifying remarkable accuracy of modeling groups in assessing their own predictions, we set up a benchmarking pipeline to highlight different aspects of quaternary structure models and introduced a simple consensus EMA method as baseline. While participating methods showed commendable performance, the baseline was difficult to surpass. It is important to point out that prediction performance varies for the individual CASP targets, highlighting potential areas of improvement and challenges ahead.
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Affiliation(s)
- Gabriel Studer
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Gerardo Tauriello
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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28
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Ozden B, Kryshtafovych A, Karaca E. The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15. Proteins 2023; 91:1636-1657. [PMID: 37861057 PMCID: PMC10873090 DOI: 10.1002/prot.26598] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 10/21/2023]
Abstract
In CASP15, 87 predictors submitted around 11 000 models on 41 assembly targets. The community demonstrated exceptional performance in overall fold and interface contact predictions, achieving an impressive success rate of 90% (compared to 31% in CASP14). This remarkable accomplishment is largely due to the incorporation of DeepMind's AF2-Multimer approach into custom-built prediction pipelines. To evaluate the added value of participating methods, we compared the community models to the baseline AF2-Multimer predictor. In over 1/3 of cases, the community models were superior to the baseline predictor. The main reasons for this improved performance were the use of custom-built multiple sequence alignments, optimized AF2-Multimer sampling, and the manual assembly of AF2-Multimer-built subcomplexes. The best three groups, in order, are Zheng, Venclovas, and Wallner. Zheng and Venclovas reached a 73.2% success rate over all (41) cases, while Wallner attained 69.4% success rate over 36 cases. Nonetheless, challenges remain in predicting structures with weak evolutionary signals, such as nanobody-antigen, antibody-antigen, and viral complexes. Expectedly, modeling large complexes also remains challenging due to their high memory compute demands. In addition to the assembly category, we assessed the accuracy of modeling interdomain interfaces in the tertiary structure prediction targets. Models on seven targets featuring 17 unique interfaces were analyzed. Best predictors achieved a 76.5% success rate, with the UM-TBM group being the leader. In the interdomain category, we observed that the predictors faced challenges, as in the case of the assembly category, when the evolutionary signal for a given domain pair was weak or the structure was large. Overall, CASP15 witnessed unprecedented improvement in interface modeling, reflecting the AI revolution seen in CASP14.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
| | - Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, USA
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
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29
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Kryshtafovych A, Rigden DJ. To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units. Proteins 2023; 91:1558-1570. [PMID: 37254889 PMCID: PMC10687315 DOI: 10.1002/prot.26533] [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: 03/10/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 06/01/2023]
Abstract
Processing of CASP15 targets into evaluation units (EUs) and assigning them to evolutionary-based prediction classes is presented in this study. The targets were first split into structural domains based on compactness and similarity to other proteins. Models were then evaluated against these domains and their combinations. The domains were joined into larger EUs if predictors' performance on the combined units was similar to that on individual domains. Alternatively, if most predictors performed better on the individual domains, then they were retained as EUs. As a result, 112 evaluation units were created from 77 tertiary structure prediction targets. The EUs were assigned to four prediction classes roughly corresponding to target difficulty categories in previous CASPs: TBM (template-based modeling, easy or hard), FM (free modeling), and the TBM/FM overlap category. More than a third of CASP15 EUs were attributed to the historically most challenging FM class, where homology or structural analogy to proteins of known fold cannot be detected.
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Affiliation(s)
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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30
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Oh H, Koo J, An SY, Hong SH, Suh JY, Bae E. Structural and functional investigation of GajB protein in Gabija anti-phage defense. Nucleic Acids Res 2023; 51:11941-11951. [PMID: 37897358 PMCID: PMC10681800 DOI: 10.1093/nar/gkad951] [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: 06/01/2023] [Revised: 09/13/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Bacteriophages (phages) are viruses that infect bacteria and archaea. To fend off invading phages, the hosts have evolved a variety of anti-phage defense mechanisms. Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB. GajA has been characterized experimentally as a sequence-specific DNA endonuclease. Although GajB was previously predicted to be a UvrD-like helicase, its function is unclear. Here, we report the results of structural and functional analyses of GajB. The crystal structure of GajB revealed a UvrD-like domain architecture, including two RecA-like core and two accessory subdomains. However, local structural elements that are important for the helicase function of UvrD are not conserved in GajB. In functional assays, GajB did not unwind or bind various types of DNA substrates. We demonstrated that GajB interacts with GajA to form a heterooctameric Gabija complex, but GajB did not exhibit helicase activity when bound to GajA. These results advance our understanding of the molecular mechanism underlying Gabija anti-phage defense and highlight the role of GajB as a component of a multi-subunit antiviral complex in bacteria.
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Affiliation(s)
- Hyejin Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - So Young An
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sung-Hyun Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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31
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Yáñez-Cuna FO, Koszul R. Insights in bacterial genome folding. Curr Opin Struct Biol 2023; 82:102679. [PMID: 37604045 DOI: 10.1016/j.sbi.2023.102679] [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: 04/03/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 08/23/2023]
Abstract
Chromosomes in all domains of life are well-defined structural entities with complex hierarchical organization. The regulation of this hierarchical organization and its functional interplay with gene expression or other chromosome metabolic processes such as repair, replication, or segregation is actively investigated in a variety of species, including prokaryotes. Bacterial chromosomes are typically gene-dense with few non-coding sequences and are organized into the nucleoid, a membrane-less compartment composed of DNA, RNA, and proteins (nucleoid-associated proteins or NAPs). The continuous improvement of imaging and genomic methods has put the organization of these Mb-long molecules at reach, allowing to disambiguate some of their highly dynamic properties and intertwined structural features. Here we review and discuss some of the recent advances in the field of bacterial chromosome organization.
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Affiliation(s)
- Fares Osam Yáñez-Cuna
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015, Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015, Paris, France.
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32
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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: 72] [Impact Index Per Article: 72.0] [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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33
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Akritidou K, Thurtle-Schmidt BH. OLD family nuclease function across diverse anti-phage defense systems. Front Microbiol 2023; 14:1268820. [PMID: 37840731 PMCID: PMC10568477 DOI: 10.3389/fmicb.2023.1268820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Bacteriophages constitute a ubiquitous threat to bacteria, and bacteria have evolved numerous anti-phage defense systems to protect themselves. These systems include well-studied phenomena such as restriction endonucleases and CRISPR, while emerging studies have identified many new anti-phage defense systems whose mechanisms are unknown or poorly understood. Some of these systems involve overcoming lysogenization defect (OLD) nucleases, a family of proteins comprising an ABC ATPase domain linked to a Toprim nuclease domain. Despite being discovered over 50 years ago, OLD nuclease function remained mysterious until recent biochemical, structural, and bioinformatic studies revealed that OLD nucleases protect bacteria by functioning in diverse anti-phage defense systems including the Gabija system and retrons. In this review we will highlight recent discoveries in OLD protein function and their involvement in multiple discrete anti-phage defense systems.
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34
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Ozden B, Kryshtafovych A, Karaca E. The Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: Insights from CASP15. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548341. [PMID: 37503072 PMCID: PMC10369898 DOI: 10.1101/2023.07.10.548341] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In CASP15, 87 predictors submitted around 11,000 models on 41 assembly targets. The community demonstrated exceptional performance in overall fold and interface contact prediction, achieving an impressive success rate of 90% (compared to 31% in CASP14). This remarkable accomplishment is largely due to the incorporation of DeepMind's AF2-Multimer approach into custom-built prediction pipelines. To evaluate the added value of participating methods, we compared the community models to the baseline AF2-Multimer predictor. In over 1/3 of cases the community models were superior to the baseline predictor. The main reasons for this improved performance were the use of custom-built multiple sequence alignments, optimized AF2-Multimer sampling, and the manual assembly of AF2-Multimer-built subcomplexes. The best three groups, in order, are Zheng, Venclovas and Wallner. Zheng and Venclovas reached a 73.2% success rate over all (41) cases, while Wallner attained 69.4% success rate over 36 cases. Nonetheless, challenges remain in predicting structures with weak evolutionary signals, such as nanobody-antigen, antibody-antigen, and viral complexes. Expectedly, modeling large complexes remains also challenging due to their high memory compute demands. In addition to the assembly category, we assessed the accuracy of modeling interdomain interfaces in the tertiary structure prediction targets. Models on seven targets featuring 17 unique interfaces were analyzed. Best predictors achieved the 76.5% success rate, with the UM-TBM group being the leader. In the interdomain category, we observed that the predictors faced challenges, as in the case of the assembly category, when the evolutionary signal for a given domain pair was weak or the structure was large. Overall, CASP15 witnessed unprecedented improvement in interface modeling, reflecting the AI revolution seen in CASP14.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
| | - Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, USA
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
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35
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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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36
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Abstract
Many cellular processes require large-scale rearrangements of chromatin structure. Structural maintenance of chromosomes (SMC) protein complexes are molecular machines that can provide structure to chromatin. These complexes can connect DNA elements in cis, walk along DNA, build and processively enlarge DNA loops and connect DNA molecules in trans to hold together the sister chromatids. These DNA-shaping abilities place SMC complexes at the heart of many DNA-based processes, including chromosome segregation in mitosis, transcription control and DNA replication, repair and recombination. In this Review, we discuss the latest insights into how SMC complexes such as cohesin, condensin and the SMC5-SMC6 complex shape DNA to direct these fundamental chromosomal processes. We also consider how SMC complexes, by building chromatin loops, can counteract the natural tendency of alike chromatin regions to cluster. SMC complexes thus control nuclear organization by participating in a molecular tug of war that determines the architecture of our genome.
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Affiliation(s)
- Claire Hoencamp
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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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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38
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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: 12] [Impact Index Per Article: 12.0] [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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39
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Dot EW, Thomason LC, Chappie JS. Everything OLD is new again: How structural, functional, and bioinformatic advances have redefined a neglected nuclease family. Mol Microbiol 2023; 120:122-140. [PMID: 37254295 DOI: 10.1111/mmi.15074] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 06/01/2023]
Abstract
Overcoming lysogenization defect (OLD) proteins are a conserved family of ATP-powered nucleases that function in anti-phage defense. Recent bioinformatic, genetic, and crystallographic studies have yielded new insights into the structure, function, and evolution of these enzymes. Here we review these developments and propose a new classification scheme to categorize OLD homologs that relies on gene neighborhoods, biochemical properties, domain organization, and catalytic machinery. This taxonomy reveals important similarities and differences between family members and provides a blueprint to contextualize future in vivo and in vitro findings. We also detail how OLD nucleases are related to PARIS and Septu anti-phage defense systems and discuss important mechanistic questions that remain unanswered.
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Affiliation(s)
- Elena Wanvig Dot
- Department of Molecular Medicine, Cornell University, Ithaca, New York, USA
| | - Lynn C Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, New York, USA
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40
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Georjon H, Tesson F, Shomar H, Bernheim A. Genomic characterization of the antiviral arsenal of Actinobacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001374. [PMID: 37531269 PMCID: PMC10482375 DOI: 10.1099/mic.0.001374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Phages are ubiquitous in nature, and bacteria with very different genomics, metabolisms, and lifestyles are subjected to their predation. Yet, the defence systems that allow bacteria to resist their phages have rarely been explored experimentally outside a very limited number of model organisms. Actinobacteria (Actinomycetota) are a phylum of GC-rich Gram-positive bacteria, which often produce an important diversity of secondary metabolites. Despite being ubiquitous in a wide range of environments, from soil to fresh and sea water but also the gut microbiome, relatively little is known about the anti-phage arsenal of Actinobacteria. In this work, we used DefenseFinder to systematically detect 131 anti-phage defence systems in 22803 fully sequenced prokaryotic genomes, among which are 2253 Actinobacteria of more than 700 species. We show that, like other bacteria, Actinobacteria encode many diverse anti-phage systems that are often encoded on mobile genetic elements. We further demonstrate that most detected defence systems are absent or rarer in Actinobacteria than in other bacteria, while a few rare systems are enriched (notably gp29-gp30 and Wadjet). We characterize the spatial distribution of anti-phage systems on Streptomyces chromosomes and show that some defence systems (e.g. RM systems) tend to be encoded in the core region, while others (e.g. Lamassu and Wadjet) are enriched towards the extremities. Overall, our results suggest that Actinobacteria might be a source of novel anti-phage systems and provide clues to characterize mechanistic aspects of known anti-phage systems.
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Affiliation(s)
- Héloïse Georjon
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, Inserm U1284, Paris, France
| | - Florian Tesson
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, Inserm U1284, Paris, France
- UMR 1137, IAME, Université de Paris, INSERM, Paris, France
| | - Helena Shomar
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, Inserm U1284, Paris, France
| | - Aude Bernheim
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, Inserm U1284, Paris, France
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41
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Lelkes E, Jemelková J, Holá M, Štefanovie B, Kolesár P, Vágnerová R, Dvořák Tomaštíková E, Pecinka A, Angelis KJ, Paleček JJ. Characterization of the conserved features of the NSE6 subunit of the Physcomitrium patens SMC5/6 complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1084-1099. [PMID: 37191775 DOI: 10.1111/tpj.16282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes are molecular machines ensuring chromatin organization at higher levels. They play direct roles in cohesion, condensation, replication, transcription, and DNA repair. Their cores are composed of long-armed SMC, kleisin, and kleisin-associated subunits. Additional factors, like NSE6 within SMC5/6, bind to SMC core complexes and regulate their activities. In the human HsNSE6/SLF2, we recently identified a new CANIN domain. Here we tracked down its sequence homology to lower plants, selected the bryophyte Physcomitrium patens, and analyzed PpNSE6 protein-protein interactions to explore its conservation in detail. We identified a previously unrecognized core sequence motif conserved from yeasts to humans within the NSE6 CANIN domain. This motif mediates the interaction between NSE6 and its NSE5 partner in yeasts and plants. In addition, the CANIN domain and its preceding PpNSE6 sequences bind both PpSMC5 and PpSMC6 arms. Interestingly, we mapped the PpNSE6-binding site at the PpSMC5 arm right next to the PpNSE2-binding surface. The position of NSE6 at SMC arms suggests its role in the regulation of SMC5/6 dynamics. Consistent with the regulatory role of NSE6 subunits, Ppnse6 mutant lines were viable and sensitive to the DNA-damaging drug bleomycin and lost a large portion of rDNA copies. These moss mutants also exhibited reduced growth and developmental aberrations. Altogether, our data showed the conserved function of the NSE6 subunit and architecture of the SMC5/6 complex across species.
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Affiliation(s)
- Edit Lelkes
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Jitka Jemelková
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Marcela Holá
- Institute of Experimental Botany, Czech Academy of Sciences, Na Karlovce 1, 16000, Prague, Czech Republic
| | - Barbora Štefanovie
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Peter Kolesár
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Radka Vágnerová
- Institute of Experimental Botany, Czech Academy of Sciences, Na Karlovce 1, 16000, Prague, Czech Republic
| | - Eva Dvořák Tomaštíková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Karel J Angelis
- Institute of Experimental Botany, Czech Academy of Sciences, Na Karlovce 1, 16000, Prague, Czech Republic
| | - Jan J Paleček
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
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42
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Mariano G, Blower TR. Conserved domains can be found across distinct phage defence systems. Mol Microbiol 2023; 120:45-53. [PMID: 36840376 PMCID: PMC10952713 DOI: 10.1111/mmi.15047] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023]
Abstract
Bacteria are continuously exposed to predation from bacteriophages (phages) and, in response, have evolved a broad range of defence systems. These systems can prevent the replication of phages and other mobile genetic elements (MGE). Defence systems are often encoded together in genomic loci defined as "defence islands", a tendency that has been extensively exploited to identify novel antiphage systems. In the last few years, >100 new antiphage systems have been discovered, and some display homology to components of the immune systems of plants and animals. In many instances, prediction tools have found domains with similar predicted functions present as different combinations within distinct antiphage systems. In this Perspective Article, we review recent reports describing the discovery and the predicted domain composition of several novel antiphage systems. We discuss several examples of similar protein domains adopted by different antiphage systems, including domains of unknown function (DUFs), domains involved in nucleic acid recognition and degradation, and domains involved in NAD+ depletion. We further discuss the potential evolutionary advantages that could have driven the independent acquisition of these domains by different antiphage systems.
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Affiliation(s)
- Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
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43
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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: 26] [Impact Index Per Article: 26.0] [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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44
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Bürmann F, Löwe J. Structural biology of SMC complexes across the tree of life. Curr Opin Struct Biol 2023; 80:102598. [PMID: 37104976 PMCID: PMC10512200 DOI: 10.1016/j.sbi.2023.102598] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/20/2023] [Accepted: 03/26/2023] [Indexed: 04/29/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes guard and organize the three-dimensional structure of chromosomal DNA across the tree of life. Many SMC functions can be explained by an inherent motor activity that extrudes large DNA loops while the complexes move along their substrate. Here, we review recent structural insights into the architecture and conservation of these molecular machines, their interaction with DNA, and the conformational changes that are linked to their ATP hydrolysis cycle.
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Affiliation(s)
- Frank Bürmann
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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45
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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: 25] [Impact Index Per Article: 25.0] [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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46
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Sparks IL, Derbyshire KM, Jacobs WR, Morita YS. Mycobacterium smegmatis: The Vanguard of Mycobacterial Research. J Bacteriol 2023; 205:e0033722. [PMID: 36598232 PMCID: PMC9879119 DOI: 10.1128/jb.00337-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The genus Mycobacterium contains several slow-growing human pathogens, including Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium avium. Mycobacterium smegmatis is a nonpathogenic and fast growing species within this genus. In 1990, a mutant of M. smegmatis, designated mc2155, that could be transformed with episomal plasmids was isolated, elevating M. smegmatis to model status as the ideal surrogate for mycobacterial research. Classical bacterial models, such as Escherichia coli, were inadequate for mycobacteria research because they have low genetic conservation, different physiology, and lack the novel envelope structure that distinguishes the Mycobacterium genus. By contrast, M. smegmatis encodes thousands of conserved mycobacterial gene orthologs and has the same cell architecture and physiology. Dissection and characterization of conserved genes, structures, and processes in genetically tractable M. smegmatis mc2155 have since provided previously unattainable insights on these same features in its slow-growing relatives. Notably, tuberculosis (TB) drugs, including the first-line drugs isoniazid and ethambutol, are active against M. smegmatis, but not against E. coli, allowing the identification of their physiological targets. Furthermore, Bedaquiline, the first new TB drug in 40 years, was discovered through an M. smegmatis screen. M. smegmatis has become a model bacterium, not only for M. tuberculosis, but for all other Mycobacterium species and related genera. With a repertoire of bioinformatic and physical resources, including the recently established Mycobacterial Systems Resource, M. smegmatis will continue to accelerate mycobacterial research and advance the field of microbiology.
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Affiliation(s)
- Ian L. Sparks
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Keith M. Derbyshire
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yasu S. Morita
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
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47
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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: 20] [Impact Index Per Article: 10.0] [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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48
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Konishi K, Yasutake Y, Muramatsu S, Murata S, Yoshida K, Ishiya K, Aburatani S, Sakasegawa SI, Tamura T. Disruption of SMC-related genes promotes recombinant cholesterol esterase production in Burkholderia stabilis. Appl Microbiol Biotechnol 2022; 106:8093-8110. [PMID: 36399168 DOI: 10.1007/s00253-022-12277-3] [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: 07/15/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
Burkholderia stabilis strain FERMP-21014 secretes cholesterol esterase (BsChe), which is used in clinical settings to determine serum cholesterol levels. Previously, we constructed an expression plasmid with an endogenous constitutive promoter to enable the production of recombinant BsChe. In this study, we obtained one mutant strain with 13.1-fold higher BsChe activity than the wild type, using N-methyl-N'-nitro-N-nitrosoguanidine as a mutagen. DNA-sequencing analysis revealed that the strain had lost chromosome 3 (∆Chr3), suggesting that the genes hindering BsChe production may be encoded on Chr3. We also identified common mutations in the functionally unknown BSFP_068720/30 genes in the top 10 active strains generated during transposon mutagenesis. As BSFP_068720/30/40 comprised an operon on Chr3, we created the BSFP_068720/30/40 disruption mutant and confirmed that each disruption mutant containing the expression plasmid exhibited ~ 16.1-fold higher BsChe activity than the wild type. Quantitative PCR showed that each disruption mutant and ΔChr3 had a ~ 9.4-fold higher plasmid copy number than the wild type. Structural prediction models indicate that BSFP_068730/40 is structurally homologous to the structural maintenance of chromosomes (SMC) protein MukBE, which is responsible for chromosome segregation during cell division. Conversely, BSFP_068720/30/40 disruption did not lead to a Chr3 drop-out. These results imply that BSFP_068720/30/40 is not a SMC protein but is involved in destabilizing foreign plasmids to prevent the influx of genetic information from the environment. In conclusion, the disruption of BSFP_068720/30/40 improved plasmid stability and copy number, resulting in exceptionally high BsChe production. KEY POINTS: • Disruption of BSFP_068720/30/40 enabled mass production of Burkholderia Che/Lip. • BSFP_068730/40 is an SMC protein homolog not involved in chromosome retention. • BSFP_068720/30/40 is likely responsible for the exclusion of exogenous plasmids.
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Affiliation(s)
- Kenji Konishi
- Asahi Kasei Pharma Corporation, Shizuoka, 410-2321, Japan.,Laboratory of Molecular Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yoshiaki Yasutake
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, 169-8555, Japan
| | | | - Satomi Murata
- Asahi Kasei Pharma Corporation, Shizuoka, 410-2321, Japan
| | - Keitaro Yoshida
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan
| | - Koji Ishiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan
| | - Sachiyo Aburatani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan
| | | | - Tomohiro Tamura
- Laboratory of Molecular Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan. .,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.
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