1
|
Sigal N, Lichtenstein-Wolfheim R, Schlussel S, Azulay G, Borovok I, Holdengraber V, Elad N, Wolf SG, Zalk R, Zarivach R, Frank GA, Herskovits AA. Specialized Listeria monocytogenes produce tailocins to provide a population-level competitive growth advantage. Nat Microbiol 2024:10.1038/s41564-024-01793-9. [PMID: 39300324 DOI: 10.1038/s41564-024-01793-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 07/23/2024] [Indexed: 09/22/2024]
Abstract
Tailocins are phage tail-like bacteriocins produced by various bacterial species to kill kin competitors. Given that tailocin release is dependent upon cell lysis, regulation of tailocin production at the single-cell and population level remains unclear. Here we used flow cytometry, competition assays and structural characterization of tailocin production in a human bacterial pathogen, Listeria monocytogenes. We revealed that a specialized subpopulation, constituting less than 1% of the total bacterial population, differentiates to produce, assemble and store thousands of tailocin particles. Tailocins are packed in a highly ordered manner, clustered in a liquid crystalline phase that occupies a substantial volume of the cell. Tailocin production confers a competitive growth advantage for the rest of the population. This study provides molecular insights into tailocin production as a form of altruism, showing how cell specialization within bacterial populations can confer competitive advantages at the population level.
Collapse
Affiliation(s)
- Nadejda Sigal
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rotem Lichtenstein-Wolfheim
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shai Schlussel
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Gil Azulay
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ilya Borovok
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Nadav Elad
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Ran Zalk
- Ilse Katz Institute for Nanotechnology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Gabriel A Frank
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anat A Herskovits
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| |
Collapse
|
2
|
Xu Y, Liu B, Jiao N, Liu J, Chen F. New evidence supports the prophage origin of RcGTA. Appl Environ Microbiol 2024; 90:e0043424. [PMID: 39189727 PMCID: PMC11409702 DOI: 10.1128/aem.00434-24] [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: 03/06/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024] Open
Abstract
Gene transfer agents (GTAs) are phage-like entities that package and transfer random host genome fragments between prokaryotes. RcGTA, produced by Rhodobacter capsulatus, is hypothesized to originate from a prophage ancestor. Most of the evidence supporting this hypothesis came from the finding of RcGTA-like genes in phages. More than 75% of the RcGTA genes have a phage homolog. However, only a few RcGTA homologs have been identified in a (pro)phage genome, leaving the hypothesis that GTAs evolved from prophages through gene loss with only weak evidence. We herein report the discovery of an inducible prophage (vB_MseS-P1) from a Mesorhizobium sediminum strain that contains the largest number (12) of RcGTA homologs found in a phage genome to date. We also identified three putative prophages and two prophage remnants harboring 12-14 RcGTA homologs in a Methylobacterium nodulans strain. The protein remote homology detection also revealed more RcGTA homologs from other phages than we previously thought. Moreover, the head-tail gene architecture of these newly discovered prophage-related elements closely resembles that of RcGTA. Furthermore, vB_MseS-P1 virions have structural proteins similar to RcGTA particles. Close phylogenetic relationships between certain prophage genes and RcGTA-like genes in Alphaproteobacteria further support the shared ancestry between RcGTA and prophages. Our findings provide new relatively direct evidence of the origin of RcGTA from a prophage progenitor.IMPORTANCEGTAs are important genetic elements in certain groups of bacteria and contribute to the genetic diversification, evolution, and ecological adaptation of bacteria. RcGTA, a common type of GTA, is known to package and transfer random fragments of the bacterial genome to recipient cells. However, the origin of RcGTA is still elusive. It has been hypothesized that RcGTA evolved from a prophage ancestor through gene loss. However, the few RcGTA homologs identified in a (pro)phage genome leave the hypothesis lacking direct evidence. This study uncovers the presence of a large number of RcGTA homologs in an inducible prophage and several putative prophages. The similar head-tail gene architecture and structural protein compositions of these newly discovered prophage-related elements and RcGTA further demonstrate an unprecedentedly observed close evolutionary relationship between prophages and RcGTA. Together, our findings provide more direct evidence supporting the origin of RcGTA from prophage.
Collapse
Affiliation(s)
- Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China
| | - Binbin Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Nianzhi Jiao
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| |
Collapse
|
3
|
Valentová L, Füzik T, Nováček J, Hlavenková Z, Pospíšil J, Plevka P. Structure and replication of Pseudomonas aeruginosa phage JBD30. EMBO J 2024:10.1038/s44318-024-00195-1. [PMID: 39143239 DOI: 10.1038/s44318-024-00195-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/10/2024] [Accepted: 07/24/2024] [Indexed: 08/16/2024] Open
Abstract
Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosa via the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment.
Collapse
Affiliation(s)
- Lucie Valentová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zuzana Hlavenková
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jakub Pospíšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| |
Collapse
|
4
|
Sonani RR, Esteves NC, Scharf BE, Egelman EH. Cryo-EM structure of flagellotropic bacteriophage Chi. Structure 2024; 32:856-865.e3. [PMID: 38614087 PMCID: PMC11246221 DOI: 10.1016/j.str.2024.03.011] [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: 01/07/2024] [Revised: 02/08/2024] [Accepted: 03/19/2024] [Indexed: 04/15/2024]
Abstract
The flagellotropic bacteriophage χ (Chi) infects bacteria via the flagellar filament. Despite years of study, its structural architecture remains partly characterized. Through cryo-EM, we unveil χ's nearly complete structure, encompassing capsid, neck, tail, and tail tip. While the capsid and tail resemble phage YSD1, the neck and tail tip reveal new proteins and their arrangement. The neck shows a unique conformation of the tail tube protein, forming a socket-like structure for attachment to the neck. The tail tip comprises four proteins, including distal tail protein (DTP), two baseplate hub proteins (BH1P and BH2P), and tail tip assembly protein (TAP) exhibiting minimal organization compared to other siphophages. Deviating from the consensus in other siphophages, DTP in χ forms a trimeric assembly, reducing tail symmetry from 6-fold to 3-fold at the tip. These findings illuminate the previously unexplored structural organization of χ's neck and tail tip.
Collapse
Affiliation(s)
- Ravi R Sonani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | | | - Birgit E Scharf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.
| |
Collapse
|
5
|
Bardy P, MacDonald CI, Kirchberger PC, Jenkins HT, Botka T, Byrom L, Alim NT, Traore DA, König HC, Nicholas TR, Chechik M, Hart SJ, Turkenburg JP, Blaza JN, Beatty JT, Fogg PC, Antson AA. A stargate mechanism of Microviridae genome delivery unveiled by cryogenic electron tomography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598214. [PMID: 38915634 PMCID: PMC11195240 DOI: 10.1101/2024.06.11.598214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Single-stranded DNA bacteriophages of the Microviridae family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut microbiome, where their diversity has been linked to various chronic health disorders. Despite the clear importance of microviruses, little is known about the molecular mechanism of host infection. Here, we have characterized an exceptionally large microvirus, Ebor, and provide crucial insights into long-standing mechanistic questions. Cryogenic electron microscopy of Ebor revealed a capsid with trimeric protrusions that recognise lipopolysaccharides on the host surface. Cryogenic electron tomography of the host cell colonized with virus particles demonstrated that the virus initially attaches to the cell via five such protrusions, located at the corners of a single pentamer. This interaction triggers a stargate mechanism of capsid opening along the 5-fold symmetry axis, enabling delivery of the virus genome. Despite variations in specific virus-host interactions among different Microviridae family viruses, structural data indicate that the stargate mechanism of infection is universally employed by all members of the family. Startlingly, our data reveal a mechanistic link for the opening of relatively small capsids made out of a single jelly-roll fold with the structurally unrelated giant viruses.
Collapse
Affiliation(s)
- Pavol Bardy
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| | - Conor I.W. MacDonald
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Paul C. Kirchberger
- Department of Microbiology & Molecular Genetics, Oklahoma State University, US
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| | - Tibor Botka
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Lewis Byrom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Nawshin T.B. Alim
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - Daouda A.K. Traore
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, The Netherlands
| | - Hannah C. König
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - Tristan R. Nicholas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| | - Samuel J. Hart
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - James N. Blaza
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| | - J. Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - Paul C.M. Fogg
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| |
Collapse
|
6
|
Tran NT, Le TBK. Control of a gene transfer agent cluster in Caulobacter crescentus by transcriptional activation and anti-termination. Nat Commun 2024; 15:4749. [PMID: 38834569 PMCID: PMC11150451 DOI: 10.1038/s41467-024-49114-2] [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: 11/19/2023] [Accepted: 05/23/2024] [Indexed: 06/06/2024] Open
Abstract
Gene Transfer Agents (GTAs) are phage-like particles that cannot self-multiply and be infectious. Caulobacter crescentus, a bacterium best known as a model organism to study bacterial cell biology and cell cycle regulation, has recently been demonstrated to produce bona fide GTA particles (CcGTA). Since C. crescentus ultimately die to release GTA particles, the production of GTA particles must be tightly regulated and integrated with the host physiology to prevent a collapse in cell population. Two direct activators of the CcGTA biosynthetic gene cluster, GafY and GafZ, have been identified, however, it is unknown how GafYZ controls transcription or how they coordinate gene expression of the CcGTA gene cluster with other accessory genes elsewhere on the genome for complete CcGTA production. Here, we show that the CcGTA gene cluster is transcriptionally co-activated by GafY, integration host factor (IHF), and by GafZ-mediated transcription anti-termination. We present evidence that GafZ is a transcription anti-terminator that likely forms an anti-termination complex with RNA polymerase, NusA, NusG, and NusE to bypass transcription terminators within the 14 kb CcGTA cluster. Overall, we reveal a two-tier regulation that coordinates the synthesis of GTA particles in C. crescentus.
Collapse
Affiliation(s)
- Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
| |
Collapse
|
7
|
Craske MW, Wilson JS, Fogg PCM. Gene transfer agents: structural and functional properties of domesticated viruses. Trends Microbiol 2024:S0966-842X(24)00133-1. [PMID: 38806321 DOI: 10.1016/j.tim.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Horizontal exchange of DNA between bacteria and archaea is prevalent and has major potential implications for genome evolution, plasticity, and population fitness. Several transfer mechanisms have been identified, including gene transfer agents (GTAs). GTAs are intricately regulated domesticated viruses that package host DNA into virus-like capsids and transfer this DNA throughout the bacterial community. Several important advances have recently been made in our understanding of these unusual particles. In this review, we highlight some of these findings, primarily for the model GTA produced by Rhodobacter capsulatus but also for newly identified GTA producers. We provide key insights into these important genetic elements, including the differences between GTAs from their ancestral bacteriophages, their regulation and control, and their elusive evolutionary function.
Collapse
Affiliation(s)
| | - Jason S Wilson
- Biology Department, University of York, York YO10 5DD, UK; York Structural Biology Laboratory (YSBL), University of York, York YO10 5DD, UK
| | - Paul C M Fogg
- Biology Department, University of York, York YO10 5DD, UK; York Biomedical Research Institute (YBRI), University of York, York YO10 5NG, UK.
| |
Collapse
|
8
|
Ge X, Wang J. Structural mechanism of bacteriophage lambda tail's interaction with the bacterial receptor. Nat Commun 2024; 15:4185. [PMID: 38760367 PMCID: PMC11101478 DOI: 10.1038/s41467-024-48686-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
Bacteriophage infection, a pivotal process in microbiology, initiates with the phage's tail recognizing and binding to the bacterial cell surface, which then mediates the injection of viral DNA. Although comprehensive studies on the interaction between bacteriophage lambda and its outer membrane receptor, LamB, have provided rich information about the system's biochemical properties, the precise molecular mechanism remains undetermined. This study revealed the high-resolution cryo-electron microscopy (cryo-EM) structures of the bacteriophage lambda tail complexed with its irreversible Shigella sonnei 3070 LamB receptor and the closed central tail fiber. These structures reveal the complex processes that trigger infection and demonstrate a substantial conformational change in the phage lambda tail tip upon LamB binding. Providing detailed structures of bacteriophage lambda infection initiation, this study contributes to the expanding knowledge of lambda-bacterial interaction, which holds significance in the fields of microbiology and therapeutic development.
Collapse
Affiliation(s)
- Xiaofei Ge
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, PR China
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, PR China.
| |
Collapse
|
9
|
Banks EJ, Le TBK. Co-opting bacterial viruses for DNA exchange: structure and regulation of gene transfer agents. Curr Opin Microbiol 2024; 78:102431. [PMID: 38309246 DOI: 10.1016/j.mib.2024.102431] [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: 11/23/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
Horizontal gene transfer occurs via a range of mechanisms, including transformation, conjugation and bacteriophage transduction. Gene transfer agents (GTAs) are an alternative, less-studied route for interbacterial DNA exchange. Encoded within bacterial or archaeal genomes, GTAs assemble into phage-like particles that selflessly package and transmit host DNA to recipient bacteria. Several unique features distinguish GTAs from canonical phages such as an inability to self-replicate, thus producing non-infectious particles. GTAs are also deeply integrated into the physiology of the host cell and are maintained under tight host-regulatory control. Recent advances in understanding the structure and regulation of GTAs have provided further insights into a DNA transfer mechanism that is proving increasingly widespread across the bacterial tree of life.
Collapse
Affiliation(s)
- Emma J Banks
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK.
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK.
| |
Collapse
|
10
|
Zhang JT, Liu XY, Li Z, Wei XY, Song XY, Cui N, Zhong J, Li H, Jia N. Structural basis for phage-mediated activation and repression of bacterial DSR2 anti-phage defense system. Nat Commun 2024; 15:2797. [PMID: 38555355 PMCID: PMC10981675 DOI: 10.1038/s41467-024-47177-9] [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: 11/11/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Silent information regulator 2 (Sir2) proteins typically catalyze NAD+-dependent protein deacetylation. The recently identified bacterial Sir2 domain-containing protein, defense-associated sirtuin 2 (DSR2), recognizes the phage tail tube and depletes NAD+ to abort phage propagation, which is counteracted by the phage-encoded DSR anti-defense 1 (DSAD1), but their molecular mechanisms remain unclear. Here, we determine cryo-EM structures of inactive DSR2 in its apo form, DSR2-DSAD1 and DSR2-DSAD1-NAD+, as well as active DSR2-tube and DSR2-tube-NAD+ complexes. DSR2 forms a tetramer with its C-terminal sensor domains (CTDs) in two distinct conformations: CTDclosed or CTDopen. Monomeric, rather than oligomeric, tail tube proteins preferentially bind to CTDclosed and activate Sir2 for NAD+ hydrolysis. DSAD1 binding to CTDopen allosterically inhibits tube binding and tube-mediated DSR2 activation. Our findings provide mechanistic insight into DSR2 assembly, tube-mediated DSR2 activation, and DSAD1-mediated inhibition and NAD+ substrate catalysis in bacterial DSR2 anti-phage defense systems.
Collapse
Affiliation(s)
- Jun-Tao Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xiao-Yu Liu
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Zhuolin Li
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xin-Yang Wei
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xin-Yi Song
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Ning Cui
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
- Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 518055, Shenzhen, China
- Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Jirui Zhong
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- Biomedicial Department, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Hongchun Li
- Research Center for Computer-Aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- Biomedicial Department, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ning Jia
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China.
- Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 518055, Shenzhen, China.
- Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, 518055, Shenzhen, China.
| |
Collapse
|
11
|
Kogay R, Zhaxybayeva O. Co-evolution of gene transfer agents and their alphaproteobacterial hosts. J Bacteriol 2024; 206:e0039823. [PMID: 38240570 PMCID: PMC10883770 DOI: 10.1128/jb.00398-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/19/2023] [Indexed: 02/23/2024] Open
Abstract
Gene transfer agents (GTAs) are enigmatic elements that resemble small viruses and are known to be produced during nutritional stress by some bacteria and archaea. The production of GTAs is regulated by quorum sensing, under which a small fraction of the population acts as GTA producers, while the rest becomes GTA recipients. In contrast to canonical viruses, GTAs cannot propagate themselves because they package pieces of the producing cell's genome. In alphaproteobacteria, GTAs are mostly vertically inherited and reside in their hosts' genomes for hundreds of millions of years. While GTAs' ability to transfer genetic material within a population and their long-term preservation suggest an increased fitness of GTA-producing microbes, the associated benefits and type of selection that maintains GTAs are poorly understood. By comparing rates of evolutionary change in GTA genes to the rates in gene families abundantly present across 293 alphaproteobacterial genomes, we detected 59 gene families that likely co-evolve with GTA genes. These gene families are predominantly involved in stress response, DNA repair, and biofilm formation. We hypothesize that biofilm formation enables the physical proximity of GTA-producing cells, limiting GTA-derived benefits only to a group of closely related cells. We further conjecture that the population structure of biofilm-forming sub-populations ensures that the trait of GTA production is maintained despite the inevitable rise of "cheating" genotypes. Because release of GTA particles kills the producing cell, maintenance of GTAs is an exciting example of social evolution in a microbial population.IMPORTANCEGene transfer agents (GTAs) are viruses domesticated by some archaea and bacteria as vehicles for carrying pieces of the host genome. Produced under certain environmental conditions, GTA particles can deliver DNA to neighboring, closely related cells. The function of GTAs remains uncertain. While making GTAs is suicidal for a cell, GTA-encoding genes are widespread in genomes of alphaproteobacteria. Such GTA persistence implies functional benefits but raises questions about how selection maintains this lethal trait. By showing that GTA genes co-evolve with genes involved in stress response, DNA repair, and biofilm formation, we provide support for the hypothesis that GTAs facilitate DNA exchange during the stress conditions and present a model for how GTAs persist in biofilm-forming bacterial populations despite being lethal.
Collapse
Affiliation(s)
- Roman Kogay
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
| |
Collapse
|
12
|
Wang C, Duan J, Gu Z, Ge X, Zeng J, Wang J. Architecture of the bacteriophage lambda tail. Structure 2024; 32:35-46.e3. [PMID: 37918400 DOI: 10.1016/j.str.2023.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/21/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023]
Abstract
Bacteriophage lambda has a double-stranded DNA genome and a long, flexible, non-contractile tail encoded by a contiguous block of 11 genes downstream of the head genes. The tail allows host recognition and delivery of viral DNA from the head shell to the cytoplasm of the infected cell. Here, we present a high-resolution structure of the tail complex of bacteriophage lambda determined by cryoelectron microscopy. Most component proteins of the lambda tail were determined at the atomic scale. The structure sheds light on the molecular organization of the extensively studied tail of bacteriophage lambda.
Collapse
Affiliation(s)
- Chang Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
| | - Jinsong Duan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
| | - Zhiwei Gu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
| | - Xiaofei Ge
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
| | - Jianwei Zeng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China.
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China.
| |
Collapse
|
13
|
Brown C, Agarwal A, Luque A. pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells. Bioinformatics 2024; 40:btad761. [PMID: 38113434 PMCID: PMC10786678 DOI: 10.1093/bioinformatics/btad761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 11/01/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023] Open
Abstract
SUMMARY pyCapsid is a Python package developed to facilitate the characterization of the dynamics and quasi-rigid mechanical units of protein shells and other protein complexes. The package was developed in response to the rapid increase of high-resolution structures, particularly capsids of viruses, requiring multiscale biophysical analyses. Given a protein shell, pyCapsid generates the collective vibrations of its amino-acid residues, identifies quasi-rigid mechanical regions associated with the disassembly of the structure, and maps the results back to the input proteins for interpretation. pyCapsid summarizes the main results in a report that includes publication-quality figures. AVAILABILITY AND IMPLEMENTATION pyCapsid's source code is available under MIT License on GitHub. It is compatible with Python 3.8-3.10 and has been deployed in two leading Python package-management systems, PIP and Conda. Installation instructions and tutorials are available in the online documentation and in the pyCapsid's YouTube playlist. In addition, a cloud-based implementation of pyCapsid is available as a Google Colab notebook. pyCapsid Colab does not require installation and generates the same report and outputs as the installable version. Users can post issues regarding pyCapsid in the repository's issues section.
Collapse
Affiliation(s)
- Colin Brown
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Department of Physics, San Diego State University, San Diego, CA 92116, United States
| | - Anuradha Agarwal
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Computational Science Research Center, San Diego State University, San Diego, CA 92116, United States
| | - Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Computational Science Research Center, San Diego State University, San Diego, CA 92116, United States
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92116, United States
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
| |
Collapse
|
14
|
Xiong Y, Ma K, Zou X, Liang Y, Zheng K, Wang T, Zhang H, Dong Y, Wang Z, Liu Y, Shao H, McMinn A, Wang M. Vibrio cyclitrophicus phage encoding gene transfer agent fragment, representing a novel viral family. Virus Res 2024; 339:199270. [PMID: 37972855 PMCID: PMC10694778 DOI: 10.1016/j.virusres.2023.199270] [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: 07/19/2023] [Revised: 11/11/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Vibrio is a prevalent bacterial genus in aquatic environments and exhibits diverse metabolic capabilities, playing a vital role in marine biogeochemical cycles. This study isolated a novel virus infecting Vibrio cyclitrophicus, vB_VviC_ZQ26, from coastal waters near Qingdao, China. The vB_VviC_ZQ26 comprises a linear double-stranded DNA genome with a length of 42,982 bp and a G + C content of 43.21 %, encoding 72 putative open reading frames (ORFs). Transmission electron microscope characterization indicates a siphoviral-morphology of vB_VviC_ZQ26. Nucleic-acids-wide analysis indicates a tetranucleotide frequency deviation for genomic segments encoding putative gene transfer agent protein (GTA) and coil-containing protein, implying divergent origins occurred in different parts of viral genomes. Phylogenetic and genome-content-based analysis suggest that vB_VviC_ZQ26 represents a novel vibriophage-specific family designated as Coheviridae. From the result of biogeographic analysis, Coheviridae is mainly colonized in the temperate and tropical epipelagic zones. This study describes a novel vibriophage infecting V. cyclitrophicus, shedding light on the evolutionary divergence of different parts of the viral genome and its ecological footprint in marine environments.
Collapse
Affiliation(s)
- Yao Xiong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Keran Ma
- Haide College, Ocean University of China, Qingdao, China
| | - Xiao Zou
- Xiangdong Hospital, Hunan Normal University, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Centre for Marine Studies, Qingdao, China.
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Tiancong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hong Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yue Dong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ziyue Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China; Haide College, Ocean University of China, Qingdao, China; UMT-OUC Joint Centre for Marine Studies, Qingdao, China; The Affiliated Hospital of Qingdao University, Qingdao, China.
| |
Collapse
|
15
|
Rūmnieks J, Füzik T, Tārs K. Structure of the Borrelia Bacteriophage φBB1 Procapsid. J Mol Biol 2023; 435:168323. [PMID: 37866476 DOI: 10.1016/j.jmb.2023.168323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all B. burgdorferi isolates carry a prophage φBB1 as resident circular plasmids. Like its host, the φBB1 phage is quite distinctive and shares little sequence similarity with other known bacteriophages. We expressed φBB1 head morphogenesis proteins in Escherichia coli which resulted in assembly of homogeneous prolate procapsid structures and used cryo-electron microscopy to determine the three-dimensional structure of these particles. The φBB1 procapsids consist of 415 copies of the major capsid protein and an equal combined number of three homologous capsid decoration proteins that form trimeric knobs on the outside of the particle. One of the end vertices of the particle is occupied by a portal assembled from twelve copies of the portal protein. The φBB1 scaffolding protein is entirely α-helical and has an elongated shape with a small globular domain in the middle. Within the tubular section of the procapsid, the internal scaffold is built of stacked rings, each composed of 32 scaffolding protein molecules, which run in opposite directions from both caps with a heterogeneous part in the middle. Inside the portal-containing cap, the scaffold is organized asymmetrically with ten scaffolding protein molecules bound to the portal. The φBB1 procapsid structure provides better insight into the vast structural diversity of bacteriophages and presents clues of how elongated bacteriophage particles might be assembled.
Collapse
Affiliation(s)
- Jānis Rūmnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, 1067 Riga, Latvia.
| | - Tibor Füzik
- Structural Virology, Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, 1067 Riga, Latvia; Faculty of Biology, University of Latvia, Jelgavas 1, 1004 Riga, Latvia
| |
Collapse
|
16
|
Mahony J, Goulet A, van Sinderen D, Cambillau C. Partial Atomic Model of the Tailed Lactococcal Phage TP901-1 as Predicted by AlphaFold2: Revelations and Limitations. Viruses 2023; 15:2440. [PMID: 38140681 PMCID: PMC10747895 DOI: 10.3390/v15122440] [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: 11/10/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Bacteria are engaged in a constant battle against preying viruses, called bacteriophages (or phages). These remarkable nano-machines pack and store their genomes in a capsid and inject it into the cytoplasm of their bacterial prey following specific adhesion to the host cell surface. Tailed phages possessing dsDNA genomes are the most abundant phages in the bacterial virosphere, particularly those with long, non-contractile tails. All tailed phages possess a nano-device at their tail tip that specifically recognizes and adheres to a suitable host cell surface receptor, being proteinaceous and/or saccharidic. Adhesion devices of tailed phages infecting Gram-positive bacteria are highly diverse and, for the majority, remain poorly understood. Their long, flexible, multi-domain-encompassing tail limits experimental approaches to determine their complete structure. We have previously shown that the recently developed protein structure prediction program AlphaFold2 can overcome this limitation by predicting the structures of phage adhesion devices with confidence. Here, we extend this approach and employ AlphaFold2 to determine the structure of a complete phage, the lactococcal P335 phage TP901-1. Herein we report the structures of its capsid and neck, its extended tail, and the complete adhesion device, the baseplate, which was previously partially determined using X-ray crystallography.
Collapse
Affiliation(s)
- Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
| | - Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université—CNRS, UMR 7255, 13009 Marseille, France;
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
| | - Christian Cambillau
- School of Microbiology & APC Microbiome Ireland, University College Cork, T12 K8AF Cork, Ireland;
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université—CNRS, UMR 7255, 13009 Marseille, France;
| |
Collapse
|
17
|
Xiao H, Tan L, Tan Z, Zhang Y, Chen W, Li X, Song J, Cheng L, Liu H. Structure of the siphophage neck-Tail complex suggests that conserved tail tip proteins facilitate receptor binding and tail assembly. PLoS Biol 2023; 21:e3002441. [PMID: 38096144 PMCID: PMC10721106 DOI: 10.1371/journal.pbio.3002441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
Siphophages have a long, flexible, and noncontractile tail that connects to the capsid through a neck. The phage tail is essential for host cell recognition and virus-host cell interactions; moreover, it serves as a channel for genome delivery during infection. However, the in situ high-resolution structure of the neck-tail complex of siphophages remains unknown. Here, we present the structure of the siphophage lambda "wild type," the most widely used, laboratory-adapted fiberless mutant. The neck-tail complex comprises a channel formed by stacked 12-fold and hexameric rings and a 3-fold symmetrical tip. The interactions among DNA and a total of 246 tail protein molecules forming the tail and neck have been characterized. Structural comparisons of the tail tips, the most diversified region across the lambda and other long-tailed phages or tail-like machines, suggest that their tail tip contains conserved domains, which facilitate tail assembly, receptor binding, cell adsorption, and DNA retaining/releasing. These domains are distributed in different tail tip proteins in different phages or tail-like machines. The side tail fibers are not required for the phage particle to orient itself vertically to the surface of the host cell during attachment.
Collapse
Affiliation(s)
- Hao Xiao
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Le Tan
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China
| | - Zhixue Tan
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China
| | - Yewei Zhang
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China
| | - Wenyuan Chen
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China
| | - Xiaowu Li
- School of Electronics and Information Engineering, Hunan University of Science and Engineering, Yongzhou, China
| | - Jingdong Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lingpeng Cheng
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China
| | - Hongrong Liu
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha, China
| |
Collapse
|
18
|
Zhu D, Cao D, Zhang X. Virus structures revealed by advanced cryoelectron microscopy methods. Structure 2023; 31:1348-1359. [PMID: 37797619 DOI: 10.1016/j.str.2023.09.008] [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: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions.
Collapse
Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
19
|
Su Y, Zhang W, Liang Y, Wang H, Liu Y, Zheng K, Liu Z, Yu H, Ren L, Shao H, Sung YY, Mok WJ, Wong LL, Zhang YZ, McMinn A, Wang M. Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m. Microbiol Spectr 2023; 11:e0191223. [PMID: 37728551 PMCID: PMC10580944 DOI: 10.1128/spectrum.01912-23] [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: 05/06/2023] [Accepted: 08/04/2023] [Indexed: 09/21/2023] Open
Abstract
Viruses play crucial roles in the ecosystem by modulating the host community structure, mediating biogeochemical cycles, and compensating for the metabolism of host cells. Mariana Trench, the world's deepest hadal habitat, harbors a variety of unique microorganisms that have adapted to its extreme conditions of low temperatures, high pressure, and nutrient scarcity. However, our knowledge about isolated hadal phage strains in the hadal trench is still limited. This study reported the discovery of a temperate phage, vB_HmeY_H4907, infecting Halomonas meridiana H4907, isolated from surface sediment from the Mariana Trench at a depth of 8,900 m. To our best knowledge, it is the deepest isolated siphovirus from the ocean. Its 40,452 bp linear dsDNA genome has 57.64% GC content and 55 open reading frames, and it is highly homologous to its host. Phylogenetic analysis and average nucleotide sequence identification reveal that vB_HmeY_H4907 is separated from the isolated phages and represents a new family, Suviridae, with eight predicted proviruses and six uncultured viral genomes. They are widely distributed in the ocean, suggesting a prevalence of this viral family in the deep sea. These findings expand our understanding of the phylogenetic diversity and genomic features of hadal lysogenic phages, provide essential information for further studies of phage-host interactions and evolution, and may reveal new insights into the lysogenic lifestyles of viruses inhabiting the hadal ocean. IMPORTANCE Halomonas phage vB_HmeY_H4907 is the deepest isolated siphovirus from the ocean, and it represents a novel abundant viral family in the ocean. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral family, namely, Suviridae.
Collapse
Affiliation(s)
- Yue Su
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Wenjing Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
| | - Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ziqi Liu
- Department of Integrated Global Studies, School of Integrated Arts and Sciences, Hiroshima University, Hiroshima, Japan
| | - Hao Yu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Linyi Ren
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- UMT-OUC Joint Academic Centre for Marine Studies, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
20
|
Abstract
A massive number of microorganisms, belonging to different species, continuously divide inside the guts of animals and humans. The large size of these communities and their rapid division times imply that we should be able to watch microbial evolution in the gut in real time, in a similar manner to what has been done in vitro. Here, we review recent findings on how natural selection shapes intrahost evolution (also known as within-host evolution), with a focus on the intestines of mice and humans. The microbiota of a healthy host is not as static as initially thought from the information measured at only one genomic marker. Rather, the genomes of each gut-colonizing species can be highly dynamic, and such dynamism seems to be related to the microbiota species diversity. Genetic and bioinformatic tools, and analysis of time series data, allow quantification of the selection strength on emerging mutations and horizontal transfer events in gut ecosystems. The drivers and functional consequences of gut evolution can now begin to be grasped. The rules of this intrahost microbiota evolution, and how they depend on the biology of each species, need to be understood for more effective development of microbiota therapies to help maintain or restore host health.
Collapse
Affiliation(s)
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
| |
Collapse
|
21
|
Mariani F, Galvan EM. Staphylococcus aureus in Polymicrobial Skinand Soft Tissue Infections: Impact of Inter-Species Interactionsin Disease Outcome. Antibiotics (Basel) 2023; 12:1164. [PMID: 37508260 PMCID: PMC10376372 DOI: 10.3390/antibiotics12071164] [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: 06/14/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Polymicrobial biofilms provide a complex environment where co-infecting microorganisms can behave antagonistically, additively, or synergistically to alter the disease outcome compared to monomicrobial infections. Staphylococcus aureus skin and soft tissue infections (Sa-SSTIs) are frequently reported in healthcare and community settings, and they can also involve other bacterial and fungal microorganisms. This polymicrobial aetiology is usually found in chronic wounds, such as diabetic foot ulcers, pressure ulcers, and burn wounds, where the establishment of multi-species biofilms in chronic wounds has been extensively described. This review article explores the recent updates on the microorganisms commonly found together with S. aureus in SSTIs, such as Pseudomonas aeruginosa, Escherichia coli, Enterococcus spp., Acinetobacter baumannii, and Candida albicans, among others. The molecular mechanisms behind these polymicrobial interactions in the context of infected wounds and their impact on pathogenesis and antimicrobial susceptibility are also revised.
Collapse
Affiliation(s)
- Florencia Mariani
- Laboratorio de Patogénesis Bacteriana, Departamento de Investigaciones Bioquímicas y Farmacéuticas, Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Hidalgo 775, Buenos Aires C1405, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires A4400, Argentina
| | - Estela Maria Galvan
- Laboratorio de Patogénesis Bacteriana, Departamento de Investigaciones Bioquímicas y Farmacéuticas, Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD), Universidad Maimónides, Hidalgo 775, Buenos Aires C1405, Argentina;
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires A4400, Argentina
| |
Collapse
|
22
|
Huang Y, Sun H, Wei S, Cai L, Liu L, Jiang Y, Xin J, Chen Z, Que Y, Kong Z, Li T, Yu H, Zhang J, Gu Y, Zheng Q, Li S, Zhang R, Xia N. Structure and proposed DNA delivery mechanism of a marine roseophage. Nat Commun 2023; 14:3609. [PMID: 37330604 PMCID: PMC10276861 DOI: 10.1038/s41467-023-39220-y] [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: 09/12/2022] [Accepted: 06/02/2023] [Indexed: 06/19/2023] Open
Abstract
Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene delivery. Here, we report the atomic capsid and in-situ structures of the tail machine of the marine siphophage, vB_DshS-R4C (R4C), which infects Roseobacter. The R4C virion, comprising 12 distinct structural protein components, has a unique five-fold vertex of the icosahedral capsid that allows genome delivery. The specific position and interaction pattern of the tail tube proteins determine the atypical long rigid tail of R4C, and further provide negative charge distribution within the tail tube. A ratchet mechanism assists in DNA transmission, which is initiated by an absorption device that structurally resembles the phage-like particle, RcGTA. Overall, these results provide in-depth knowledge into the intact structure and underlining DNA delivery mechanism for the ecologically important siphophages.
Collapse
Affiliation(s)
- Yang Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Hui Sun
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Liqin Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Yanan Jiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Jiabao Xin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Zhenqin Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Yuqiong Que
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Zhibo Kong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Tingting Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Hai Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Ying Gu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Qingbing Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
- Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen, 361102, China.
| |
Collapse
|
23
|
Huet A, Oh B, Maurer J, Duda RL, Conway JF. A symmetry mismatch unraveled: How phage HK97 scaffold flexibly accommodates a 12-fold pore at a 5-fold viral capsid vertex. SCIENCE ADVANCES 2023; 9:eadg8868. [PMID: 37327331 PMCID: PMC10275583 DOI: 10.1126/sciadv.adg8868] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/12/2023] [Indexed: 06/18/2023]
Abstract
Tailed bacteriophages and herpesviruses use a transient scaffold to assemble icosahedral capsids with hexameric capsomers on the faces and pentameric capsomers at all but one vertex where a 12-fold portal is thought to nucleate the assembly. How does the scaffold orchestrate this step? We have determined the portal vertex structure of the bacteriophage HK97 procapsid, where the scaffold is a domain of the major capsid protein. The scaffold forms rigid helix-turn-strand structures on the interior surfaces of all capsomers and is further stabilized around the portal, forming trimeric coiled-coil towers, two per surrounding capsomer. These 10 towers bind identically to 10 of 12 portal subunits, adopting a pseudo-12-fold organization that explains how the symmetry mismatch is managed at this early step.
Collapse
Affiliation(s)
- Alexis Huet
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bonnie Oh
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josh Maurer
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert L. Duda
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - James F. Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
24
|
Fallon AM, Carroll EM. Virus-like Particles from Wolbachia-Infected Cells May Include a Gene Transfer Agent. INSECTS 2023; 14:516. [PMID: 37367332 DOI: 10.3390/insects14060516] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023]
Abstract
Wolbachia are obligate intracellular bacteria that occur in insects and filarial worms. Strains that infect insects have genomes that encode mobile genetic elements, including diverse lambda-like prophages called Phage WO. Phage WO packages an approximately 65 kb viral genome that includes a unique eukaryotic association module, or EAM, that encodes unusually large proteins thought to mediate interactions between the bacterium, its virus, and the eukaryotic host cell. The Wolbachia supergroup B strain, wStri from the planthopper Laodelphax striatellus, produces phage-like particles that can be recovered from persistently infected mosquito cells by ultracentrifugation. Illumina sequencing, assembly, and manual curation of DNA from two independent preparations converged on an identical 15,638 bp sequence that encoded packaging, assembly, and structural proteins. The absence of an EAM and regulatory genes defined for Phage WO from the wasp, Nasonia vitripennis, was consistent with the possibility that the 15,638 bp sequence represents an element related to a gene transfer agent (GTA), characterized by a signature head-tail region encoding structural proteins that package host chromosomal DNA. Future investigation of GTA function will be supported by the improved recovery of physical particles, electron microscopic examination of potential diversity among particles, and rigorous examination of DNA content by methods independent of sequence assembly.
Collapse
Affiliation(s)
- Ann M Fallon
- Department of Entomology, University of Minnesota, 1980 Folwell Ave., St. Paul, MN 55108, USA
| | - Elissa M Carroll
- Department of Entomology, University of Minnesota, 1980 Folwell Ave., St. Paul, MN 55108, USA
| |
Collapse
|
25
|
Alim NTB, Koppenhöfer S, Lang AS, Beatty JT. Extracellular Polysaccharide Receptor and Receptor-Binding Proteins of the Rhodobacter capsulatus Bacteriophage-like Gene Transfer Agent RcGTA. Genes (Basel) 2023; 14:genes14051124. [PMID: 37239483 DOI: 10.3390/genes14051124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
A variety of prokaryotes produce a bacteriophage-like gene transfer agent (GTA), and the alphaproteobacterial Rhodobacter capsulatus RcGTA is a model GTA. Some environmental isolates of R. capsulatus lack the ability to acquire genes transferred by the RcGTA (recipient capability). In this work, we investigated the reason why R. capsulatus strain 37b4 lacks recipient capability. The RcGTA head spike fiber and tail fiber proteins have been proposed to bind extracellular oligosaccharide receptors, and strain 37b4 lacks a capsular polysaccharide (CPS). The reason why strain 37b4 lacks a CPS was unknown, as was whether the provision of a CPS to 37b4 would result in recipient capability. To address these questions, we sequenced and annotated the strain 37b4 genome and used BLAST interrogations of this genome sequence to search for homologs of genes known to be needed for R. capsulatus recipient capability. We also created a cosmid-borne genome library from a wild-type strain, mobilized the library into 37b4, and used the cosmid-complemented strain 37b4 to identify genes needed for a gain of function, allowing for the acquisition of RcGTA-borne genes. The relative presence of CPS around a wild-type strain, 37b4, and cosmid-complemented 37b4 cells was visualized using light microscopy of stained cells. Fluorescently tagged head spike fiber and tail fiber proteins of the RcGTA particle were created and used to measure the relative binding to wild-type and 37b4 cells. We found that strain 37b4 lacks recipient capability because of an inability to bind RcGTA; the reason it is incapable of binding is that it lacks CPS, and the absence of CPS is due to the absence of genes previously shown to be needed for CPS production in another strain. In addition to the head spike fiber, we found that the tail fiber protein also binds to the CPS.
Collapse
Affiliation(s)
- Nawshin T B Alim
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sonja Koppenhöfer
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - J Thomas Beatty
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| |
Collapse
|
26
|
Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA. Structural atlas of a human gut crassvirus. Nature 2023; 617:409-416. [PMID: 37138077 PMCID: PMC10172136 DOI: 10.1038/s41586-023-06019-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/27/2023] [Indexed: 05/05/2023]
Abstract
CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals1-4. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses4,5. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss0016, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.
Collapse
Affiliation(s)
- Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
| | - Andrey N Shkoporov
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ekaterina V Khokhlova
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
| |
Collapse
|
27
|
d’Acapito A, Roret T, Zarkadas E, Mocaër PY, Lelchat F, Baudoux AC, Schoehn G, Neumann E. Structural Study of the Cobetia marina Bacteriophage 1 (Carin-1) by Cryo-EM. J Virol 2023; 97:e0024823. [PMID: 36943070 PMCID: PMC10134823 DOI: 10.1128/jvi.00248-23] [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: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 03/23/2023] Open
Abstract
Most of studied bacteriophages (phages) are terrestrial viruses. However, marine phages are shown to be highly involved in all levels of oceanic regulation. They are, however, still largely overlooked by the scientific community. By inducing cell lysis on half of the bacterial population daily, their role and influence on the bacterial biomass and evolution, as well as their impact in the global biogeochemical cycles, is undeniable. Cobetia marina virus 1 (Carin-1) is a member of the Podoviridae family infecting the γ-protoabacteria C. marina. Here, we present the almost complete, nearly-atomic resolution structure of Carin-1 comprising capsid, portal, and tail machineries at 3.5 Å, 3.8 Å and 3.9 Å, respectively, determined by cryo-electron microscopy (cryo-EM). Our experimental results, combined with AlphaFold2 (AF), allowed us to obtain the nearly-atomic structure of Carin-1 by fitting and refining the AF atomic models in the high resolution cryo-EM map, skipping the bottleneck of de-novo manual building and speeding up the structure determination process. Our structural results highlighted the T7-like nature of Carin1, as well as several novel structural features like the presence of short spikes on the capsid, reminiscent those described for Rhodobacter capsulatus gene transfer agent (RcGTA). This is, to our knowledge, the first time such assembly is described for a bacteriophage, shedding light into the common evolution and shared mechanisms between gene transfer agents and phages. This first full structure determined for a marine podophage allowed to propose an infection mechanism different than the one proposed for the archetypal podophage T7. IMPORTANCE Oceans play a central role in the carbon cycle on Earth and on the climate regulation (half of the planet's CO2 is absorbed by phytoplankton photosynthesis in the oceans and just as much O2 is liberated). The understanding of the biochemical equilibriums of marine biology represents a major goal for our future. By lysing half of the bacterial population every day, marine bacteriophages are key actors of these equilibriums. Despite their importance, these marine phages have, so far, only been studied a little and, in particular, structural insights are currently lacking, even though they are fundamental for the understanding of the molecular mechanisms of their mode of infection. The structures described in our manuscript allow us to propose an infection mechanism that differs from the one proposed for the terrestrial T7 virus, and might also allow us to, in the future, better understand the way bacteriophages shape the global ecosystem.
Collapse
Affiliation(s)
| | - Thomas Roret
- Station Biologique de Roscoff (SBR), CNRS FR2424, Sorbonne Université, Roscoff, France
| | | | - Pierre-Yves Mocaër
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
| | | | - Anne-Claire Baudoux
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, France
| | - Guy Schoehn
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | |
Collapse
|
28
|
Cambillau C, Goulet A. Exploring Host-Binding Machineries of Mycobacteriophages with AlphaFold2. J Virol 2023; 97:e0179322. [PMID: 36916948 PMCID: PMC10062164 DOI: 10.1128/jvi.01793-22] [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: 11/18/2022] [Accepted: 02/17/2023] [Indexed: 03/16/2023] Open
Abstract
Although more than 12,000 bacteriophages infecting mycobacteria (mycobacteriophages) have been isolated so far, there is a knowledge gap on their structure-function relationships. Here, we have explored the architecture of host-binding machineries from seven representative mycobacteriophages of the Siphoviridae family infecting Mycobacterium smegmatis, Mycobacterium abscessus, and Mycobacterium tuberculosis, using AlphaFold2 (AF2). AF2 enables confident structural analyses of large and flexible biological assemblies resistant to experimental methods, thereby opening new avenues to shed light on phage structure and function. Our results highlight the modularity and structural diversity of siphophage host-binding machineries that recognize host-specific receptors at the onset of viral infection. Interestingly, the studied mycobacteriophages' host-binding machineries present unique features compared with those of phages infecting other Gram-positive actinobacteria. Although they all assemble the classical Dit (distal tail), Tal (tail-associated lysin), and receptor-binding proteins, five of them contain two potential additional adhesion proteins. Moreover, we have identified brush-like domains formed of multiple polyglycine helices which expose hydrophobic residues as potential receptor-binding domains. These polyglycine-rich domains, which have been observed in only five native proteins, may be a hallmark of mycobacteriophages' host-binding machineries, and they may be more common in nature than expected. Altogether, the unique composition of mycobacteriophages' host-binding machineries indicate they might have evolved to bind to the peculiar mycobacterial cell envelope, which is rich in polysaccharides and mycolic acids. This work provides a rational framework to efficiently produce recombinant proteins or protein domains and test their host-binding function and, hence, to shed light on molecular mechanisms used by mycobacteriophages to infect their host. IMPORTANCE Mycobacteria include both saprophytes, such as the model system Mycobacterium smegmatis, and pathogens, such as Mycobacterium tuberculosis and Mycobacterium abscessus, that are poorly responsive to antibiotic treatments and pose a global public health problem. Mycobacteriophages have been collected at a very large scale over the last decade, and they have proven to be valuable tools for mycobacteria genetic manipulation, rapid diagnostics, and infection treatment. Yet, molecular mechanisms used by mycobacteriophages to infect their host remain poorly understood. Therefore, exploring the structural diversity of mycobacteriophages' host-binding machineries is important not only to better understand viral diversity and bacteriophage-host interactions, but also to rationally develop biotechnological tools. With the powerful protein structure prediction software AlphaFold2, which was publicly released a year ago, it is now possible to gain structural and functional insights on such challenging assemblies.
Collapse
Affiliation(s)
- Christian Cambillau
- School of Microbiology, University College Cork, Cork, Ireland
- AlphaGraphix, Formiguères, France
| | - Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologie, CNRS and Aix-Marseille Université, Marseille, France
| |
Collapse
|
29
|
Linares R, Arnaud CA, Effantin G, Darnault C, Epalle NH, Boeri Erba E, Schoehn G, Breyton C. Structural basis of bacteriophage T5 infection trigger and E. coli cell wall perforation. SCIENCE ADVANCES 2023; 9:eade9674. [PMID: 36961893 PMCID: PMC10038345 DOI: 10.1126/sciadv.ade9674] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Most bacteriophages present a tail allowing host recognition, cell wall perforation, and viral DNA channeling from the capsid to the infected bacterium cytoplasm. The majority of tailed phages bear a long flexible tail (Siphoviridae) at the tip of which receptor binding proteins (RBPs) specifically interact with their host, triggering infection. In siphophage T5, the unique RBP is located at the extremity of a central fiber. We present the structures of T5 tail tip, determined by cryo-electron microscopy before and after interaction with its E. coli receptor, FhuA, reconstituted into nanodisc. These structures bring out the important conformational changes undergone by T5 tail tip upon infection, which include bending of T5 central fiber on the side of the tail tip, tail anchoring to the membrane, tail tube opening, and formation of a transmembrane channel. The data allow to detail the first steps of an otherwise undescribed infection mechanism.
Collapse
|
30
|
Podgorski JM, Freeman K, Gosselin S, Huet A, Conway JF, Bird M, Grecco J, Patel S, Jacobs-Sera D, Hatfull G, Gogarten JP, Ravantti J, White SJ. A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability. Structure 2023; 31:282-294.e5. [PMID: 36649709 PMCID: PMC10071307 DOI: 10.1016/j.str.2022.12.012] [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: 09/13/2022] [Revised: 10/31/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023]
Abstract
Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. After the genome packaging at near-crystalline densities, the capsid is subjected to a major expansion and stabilization step that allows it to withstand environmental stresses and internal high pressure. Several different mechanisms for stabilizing the capsid have been structurally characterized, but how these mechanisms have evolved is still not understood. Using cryo-EM structure determination of 10 capsids, structural comparisons, phylogenetic analyses, and Alphafold predictions, we have constructed a detailed structural dendrogram describing the evolution of capsid structural stability within the actinobacteriophages. We show that the actinobacteriophage major capsid proteins can be classified into 15 groups based upon their HK97-fold.
Collapse
Affiliation(s)
- Jennifer M Podgorski
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Krista Freeman
- Clapp Hall, Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Sophia Gosselin
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Alexis Huet
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - James F Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mary Bird
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - John Grecco
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Shreya Patel
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Deborah Jacobs-Sera
- Clapp Hall, Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Graham Hatfull
- Clapp Hall, Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Johann Peter Gogarten
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06268-3125, USA
| | - Janne Ravantti
- University of Helsinki, Molecular and Integrative Biosciences Research Programme, Helsinki, Finland
| | - Simon J White
- Biology/Physics Building, Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA.
| |
Collapse
|
31
|
Abstract
Viruses are highly abundant and the main predator of microorganisms. Microorganisms of each domain of life are infected by dedicated viruses. Viruses infecting archaea are genomically and structurally highly diverse. Archaea are undersampled for viruses in comparison with bacteria and eukaryotes. Consequently, the infection mechanisms of archaeal viruses are largely unknown, and most available knowledge stems from viruses infecting a select group of archaea, such as crenarchaea. We employed Haloferax tailed virus 1 (HFTV1) and its host, Haloferax gibbonsii LR2-5, to study viral infection in euryarchaea. We found that HFTV1, which has a siphovirus morphology, is virulent, and interestingly, viral particles adsorb to their host several orders of magnitude faster than most studied haloarchaeal viruses. As the binding site for infection, HFTV1 uses the cell wall component surface (S)-layer protein. Electron microscopy of infected cells revealed that viral particles often made direct contact with their heads to the cell surface, whereby the virion tails were perpendicular to the surface. This seemingly unfavorable orientation for genome delivery might represent a first reversible contact between virus and cell and could enhance viral adsorption rates. In a next irreversible step, the virion tail is orientated toward the cell surface for genome delivery. With these findings, we uncover parallels between entry mechanisms of archaeal viruses and those of bacterial jumbo phages and bacterial gene transfer agents. IMPORTANCE Archaeal viruses are the most enigmatic members of the virosphere. These viruses infect ubiquitous archaea and display an unusually high structural and genetic diversity. Unraveling their mechanisms of infection will shed light on the question if entry and egress mechanisms are highly conserved between viruses infecting a single domain of life or if these mechanisms are dependent on the morphology of the virus and the growth conditions of the host. We studied the entry mechanism of the tailed archaeal virus HFTV1. This showed that despite "typical" siphovirus morphology, the infection mechanism is different from standard laboratory models of tailed phages. We observed that particles bound first with their head to the host cell envelope, and, as such, we discovered parallels between archaeal viruses and nonmodel bacteriophages. This work contributes to a better understanding of entry mechanisms of archaeal viruses and a more complete view of microbial viruses in general.
Collapse
|
32
|
Agnello E, Pajak J, Liu X, Kelch BA. Conformational dynamics control assembly of an extremely long bacteriophage tail tube. J Biol Chem 2023; 299:103021. [PMID: 36791911 PMCID: PMC10034513 DOI: 10.1016/j.jbc.2023.103021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Tail tube assembly is an essential step in the lifecycle of long-tailed bacteriophages. Limited structural and biophysical information has impeded an understanding of assembly and stability of their long, flexible tail tubes. The hyperthermophilic phage P74-26 is particularly intriguing as it has the longest tail of any known virus (nearly 1 μm) and is the most thermostable known phage. Here, we use structures of the P74-26 tail tube along with an in vitro system for studying tube assembly kinetics to propose the first molecular model for the tail tube assembly of long-tailed phages. Our high-resolution cryo-EM structure provides insight into how the P74-26 phage assembles through flexible loops that fit into neighboring rings through tight "ball-and-socket"-like interactions. Guided by this structure, and in combination with mutational, light scattering, and molecular dynamics simulations data, we propose a model for the assembly of conserved tube-like structures across phage and other entities possessing tail tube-like proteins. We propose that formation of a full ring promotes the adoption of a tube elongation-competent conformation among the flexible loops and their corresponding sockets, which is further stabilized by an adjacent ring. Tail assembly is controlled by the cooperative interaction of dynamic intraring and interring contacts. Given the structural conservation among tail tube proteins and tail-like structures, our model can explain the mechanism of high-fidelity assembly of long, stable tubes.
Collapse
Affiliation(s)
- Emily Agnello
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester Massachusetts, USA
| | - Joshua Pajak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester Massachusetts, USA
| | - Xingchen Liu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester Massachusetts, USA
| | - Brian A Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester Massachusetts, USA.
| |
Collapse
|
33
|
Zhu J, Yang F, Du K, Wei ZL, Wu QF, Chen Y, Li WF, Li Q, Zhou CZ. Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer. ENVIRONMENTAL MICROBIOME 2023; 18:3. [PMID: 36639816 PMCID: PMC9837993 DOI: 10.1186/s40793-023-00461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date. RESULTS Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0 kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the α-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and α-proteobacteria. CONCLUSION In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.
Collapse
Affiliation(s)
- Jie Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Feng Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Kang Du
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Zi-Lu Wei
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Qing-Fa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Yuxing Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Wei-Fang Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Qiong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| |
Collapse
|
34
|
Selection for Translational Efficiency in Genes Associated with Alphaproteobacterial Gene Transfer Agents. mSystems 2022; 7:e0089222. [PMID: 36374047 PMCID: PMC9765227 DOI: 10.1128/msystems.00892-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Gene transfer agents (GTAs) are virus-like elements that are encoded by some bacterial and archaeal genomes. The production of GTAs can be induced by carbon depletion and results in host lysis and the release of virus-like particles that contain mostly random fragments of the host DNA. The remaining members of a GTA-producing population act as GTA recipients by producing proteins needed for GTA-mediated DNA acquisition. Here, we detected a codon usage bias toward codons with more readily available tRNAs in the RcGTA-like GTA genes of alphaproteobacterial genomes. Such bias likely improves the translational efficacy during GTA gene expression. While the strength of codon usage bias fluctuates substantially among individual GTA genes and across taxonomic groups, it is especially pronounced in Sphingomonadales, whose members are known to inhabit nutrient-depleted environments. By screening genomes for gene families with trends in codon usage biases similar to those in GTA genes, we found a gene that likely encodes head completion protein in some GTAs where it appeared missing, and 13 genes previously not implicated in the GTA life cycle. The latter genes are involved in various molecular processes, including the homologous recombination and transport of scarce organic matter. Our findings provide insights into the role of selection for translational efficiency in the evolution of GTA genes and outline genes that are potentially involved in the previously hypothesized integration of GTA-delivered DNA into the host genome. IMPORTANCE Horizontal gene transfer (HGT) is a fundamental process that drives evolution of microorganisms. HGT can result in a rapid dissemination of beneficial genes within and among microbial communities and can be achieved via multiple mechanisms. One peculiar HGT mechanism involves viruses "domesticated" by some bacteria and archaea (their hosts). These so-called gene transfer agents (GTAs) are encoded in hosts' genomes, produced under starvation conditions, and cannot propagate themselves as viruses. We show that GTA genes are under selection to improve the efficiency of their translation when the host activates GTA production. The selection is especially pronounced in bacteria that occupy nutrient-depleted environments. Intriguingly, several genes involved in incorporation of DNA into a genome are under similar selection pressure, suggesting that they may facilitate the integration of GTA-delivered DNA into the host genome. Our findings underscore the potential importance of GTAs as a mechanism of HGT under nutrient-limited conditions, which are widespread in microbial habitats.
Collapse
|
35
|
Langille E, Bottaro CS, Lang AS. Purification of Functional Gene Transfer Agents Using Two-Step Preparative Monolithic Chromatography. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:194-203. [PMID: 36793882 PMCID: PMC9917305 DOI: 10.1089/phage.2022.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background Gene transfer agents (GTAs) are phage-like particles that transfer cellular genomic DNA between cells. A hurdle faced in studying GTA function and interactions with cells is the difficulty in obtaining pure and functional GTAs from cultures. Materials and Methods We used a novel two-step method for purification of GTAs from R. capsulatus by monolithic chromatography. Results Our efficient and simple process had advantages compared to previous approaches. The purified GTAs retained gene transfer activity and the packaged DNA could be used for further studies. Conclusions This method is applicable to GTAs produced by other species and small phages, and could be useful for therapeutic applications.
Collapse
Affiliation(s)
- Evan Langille
- Department of Chemistry and Memorial University of Newfoundland, St. John's, Canada
- Department of Biology, Memorial University of Newfoundland, St. John's, Canada
| | - Christina S. Bottaro
- Department of Chemistry and Memorial University of Newfoundland, St. John's, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Canada
| |
Collapse
|
36
|
CryoEM structure and assembly mechanism of a bacterial virus genome gatekeeper. Nat Commun 2022; 13:7283. [PMID: 36435855 PMCID: PMC9701221 DOI: 10.1038/s41467-022-34999-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/15/2022] [Indexed: 11/28/2022] Open
Abstract
Numerous viruses package their dsDNA genome into preformed capsids through a portal gatekeeper that is subsequently closed. We report the structure of the DNA gatekeeper complex of bacteriophage SPP1 (gp612gp1512gp166) in the post-DNA packaging state at 2.7 Å resolution obtained by single particle cryo-electron microscopy. Comparison of the native SPP1 complex with assembly-naïve structures of individual components uncovered the complex program of conformational changes leading to its assembly. After DNA packaging, gp15 binds via its C-terminus to the gp6 oligomer positioning gp15 subunits for oligomerization. Gp15 refolds its inner loops creating an intersubunit β-barrel that establishes different types of contacts with six gp16 subunits. Gp16 binding and oligomerization is accompanied by folding of helices that close the portal channel to keep the viral genome inside the capsid. This mechanism of assembly has broad functional and evolutionary implications for viruses of the prokaryotic tailed viruses-herpesviruses lineage.
Collapse
|
37
|
DNA Gyrase Inhibitors Increase the Frequency of Bacteriophage-like RcGTA-Mediated Gene Transfer in Rhodobacter capsulatus. Genes (Basel) 2022; 13:genes13112071. [DOI: 10.3390/genes13112071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
Rhodobacter capsulatus produces a bacteriophage-like particle called the gene transfer agent (RcGTA) that mediates horizontal gene transfer. RcGTA particles transfer random ~4.5-kb fragments of genomic DNA that integrate into recipient genomes by allelic replacement. This work addresses the effect of sub-inhibitory concentrations of antibiotics on gene transfer by RcGTA. A transduction assay was developed to test the effects of various substances on gene transfer. Using this assay, low concentrations of DNA gyrase inhibitors were found to increase the frequency of gene transfer. Novobiocin was studied in more detail, and it was found that this antibiotic did not influence the production or release of RcGTA but instead appeared to act on the recipient cells. The target of novobiocin in other species has been shown to be the GyrB subunit of DNA gyrase (a heterotetramer of 2GyrA and 2GyrB). R. capsulatus encodes GyrA and GyrB homologues, and a GyrB overexpression plasmid was created and found to confer resistance to novobiocin. The presence of the overexpression plasmid in recipient cells greatly diminished the novobiocin-mediated increase in gene transfer, confirming that this effect is due to the binding of novobiocin by GyrB. The results of this work show that antibiotics affect gene transfer in R. capsulatus and may be relevant to microbial genetic exchange in natural ecosystems.
Collapse
|
38
|
Russo CJ, Dickerson JL, Naydenova K. Cryomicroscopy in situ: what is the smallest molecule that can be directly identified without labels in a cell? Faraday Discuss 2022; 240:277-302. [PMID: 35913392 PMCID: PMC9642008 DOI: 10.1039/d2fd00076h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/09/2022] [Indexed: 01/09/2023]
Abstract
Electron cryomicroscopy (cryoEM) has made great strides in the last decade, such that the atomic structure of most biological macromolecules can, at least in principle, be determined. Major technological advances - in electron imaging hardware, data analysis software, and cryogenic specimen preparation technology - continue at pace and contribute to the exponential growth in the number of atomic structures determined by cryoEM. It is now conceivable that within the next decade we will have structures for hundreds of thousands of unique protein and nucleic acid molecular complexes. But the answers to many important questions in biology would become obvious if we could identify these structures precisely inside cells with quantifiable error. In the context of an abundance of known structures, it is appropriate to consider the current state of electron cryomicroscopy for frozen specimens prepared directly from cells, and try to answer to the question of the title, both now and in the foreseeable future.
Collapse
Affiliation(s)
- Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Joshua L Dickerson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Katerina Naydenova
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| |
Collapse
|
39
|
Lang AS. Virus-derived gene transfer agents benefit host cells by providing templates for DNA repair. PLoS Biol 2022; 20:e3001874. [PMID: 36346786 PMCID: PMC9642860 DOI: 10.1371/journal.pbio.3001874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The potential benefits of producing gene transfer agents (GTAs) have long been speculated. A new study in PLOS Biology shows that DNA transfer by these phage-like elements allows cells with DNA damage to perform DNA repair and survive.
Collapse
Affiliation(s)
- Andrew S. Lang
- Department of Biology, Memorial University, St. John’s, Newfoundland and Labrador, Canada
- * E-mail:
| |
Collapse
|
40
|
Expansion of Known Rhodobacter capsulatus Bacteriophage Diversity with 24 Additional Genomes. Microbiol Resour Announc 2022; 11:e0087922. [DOI: 10.1128/mra.00879-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the genome sequences of 24 newly discovered bacteriophages that infect
Rhodobacter capsulatus
, a model for photosynthesis and horizontal gene transfer studies. All have substantial relatedness to previously reported siphovirus bacteriophages. Most are categorized in known clusters (RcB, RcC, RcD, and RcF), with one forming a new cluster, RcG.
Collapse
|
41
|
Gozzi K, Tran NT, Modell JW, Le TBK, Laub MT. Prophage-like gene transfer agents promote Caulobacter crescentus survival and DNA repair during stationary phase. PLoS Biol 2022; 20:e3001790. [PMID: 36327213 PMCID: PMC9632790 DOI: 10.1371/journal.pbio.3001790] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/09/2022] [Indexed: 11/05/2022] Open
Abstract
Gene transfer agents (GTAs) are prophage-like entities found in many bacterial genomes that cannot propagate themselves and instead package approximately 5 to 15 kbp fragments of the host genome that can then be transferred to related recipient cells. Although suggested to facilitate horizontal gene transfer (HGT) in the wild, no clear physiological role for GTAs has been elucidated. Here, we demonstrate that the α-proteobacterium Caulobacter crescentus produces bona fide GTAs. The production of Caulobacter GTAs is tightly regulated by a newly identified transcription factor, RogA, that represses gafYZ, the direct activators of GTA synthesis. Cells lacking rogA or expressing gafYZ produce GTAs harboring approximately 8.3 kbp fragment of the genome that can, after cell lysis, be transferred into recipient cells. Notably, we find that GTAs promote the survival of Caulobacter in stationary phase and following DNA damage by providing recipient cells a template for homologous recombination-based repair. This function may be broadly conserved in other GTA-producing organisms and explain the prevalence of this unusual HGT mechanism.
Collapse
Affiliation(s)
- Kevin Gozzi
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ngat T. Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Joshua W. Modell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Tung B. K. Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| |
Collapse
|
42
|
Kogay R, Koppenhöfer S, Beatty JT, Kuhn JH, Lang AS, Zhaxybayeva O. Formal recognition and classification of gene transfer agents as viriforms. Virus Evol 2022; 8:veac100. [PMID: 36381234 PMCID: PMC9662315 DOI: 10.1093/ve/veac100] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/10/2022] [Accepted: 10/14/2022] [Indexed: 06/19/2024] Open
Abstract
Morphological and genetic features strongly suggest that gene transfer agents (GTAs) are caudoviricete-derived entities that have evolved in concert with cellular genomes to such a degree that they should not be considered viruses. Indeed, GTA particles resemble caudoviricete virions, but, in contrast to caudoviricetes (or any viruses), GTAs can encapsidate at best only part of their own genomes, are induced solely in small subpopulations of prokaryotic host cells, and are transmitted vertically as part of cellular genomes during replication and division. Therefore, the lifecycles of GTAs are analogous to virus-derived entities found in the parasitoid wasps, which have recently been recognized as non-virus entities and therefore reclassified as viriforms. We evaluated three distinct, independently exapted GTA groups, for which the genetic basis for GTA particle production has been established. Based on the evidence, we outline a classification scheme for these viriforms.
Collapse
Affiliation(s)
- Roman Kogay
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, USA
| | | | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John’s, NL A1C 5S7, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, USA
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John’s, NL A1C 5S7, Canada
| |
Collapse
|
43
|
Loss of the Rhodobacter capsulatus Serine Acetyl Transferase Gene, cysE1, Impairs Gene Transfer by Gene Transfer Agents and Biofilm Phenotypes. Appl Environ Microbiol 2022; 88:e0094422. [PMID: 36098534 PMCID: PMC9552610 DOI: 10.1128/aem.00944-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilms are widespread in the environment, where they allow bacterial species to survive adverse conditions. Cells in biofilms are densely packed, and this proximity is likely to increase the frequency of horizontal gene transfer. Gene transfer agents (GTAs) are domesticated viruses with the potential to spread any gene between bacteria. GTA production is normally restricted to a small subpopulation of bacteria, and regulation of GTA loci is highly coordinated, but the environmental conditions that favor GTA production are poorly understood. Here, we identified a serine acetyltransferase gene, cysE1, in Rhodobacter capsulatus that is required for optimal receipt of GTA DNA, accumulation of extracellular polysaccharide, and biofilm formation. The cysE1 gene is directly downstream of the core Rhodobacter-like GTA (RcGTA) structural gene cluster and upregulated in an RcGTA overproducer strain, although it is expressed on a separate transcript. The data we present suggest that GTA production and biofilm are coregulated, which could have important implications for the study of rapid bacterial evolution and understanding the full impact of GTAs in the environment. IMPORTANCE Direct exchange of genes between bacteria leads to rapid evolution and is the major factor underlying the spread of antibiotic resistance. Gene transfer agents (GTAs) are an unusual but understudied mechanism for genetic exchange that are capable of transferring any gene from one bacterium to another, and therefore, GTAs are likely to be important factors in genome plasticity in the environment. Despite the potential impact of GTAs, our knowledge of their regulation is incomplete. In this paper, we present evidence that elements of the cysteine biosynthesis pathway are involved in coregulation of various phenotypes required for optimal biofilm formation by Rhodobacter capsulatus and successful infection by the archetypal RcGTA. Establishing the regulatory mechanisms controlling GTA-mediated gene transfer is a key stepping stone to allow a full understanding of their role in the environment and wider impact.
Collapse
|
44
|
Abstract
Alteromonas is an opportunistic marine bacterium that persists in the global ocean and has important ecological significance. However, current knowledge about the diversity and ecology of alterophages (phages that infect Alteromonas) is lacking. Here, three similar phages infecting Alteromonas macleodii ATCC 27126T were isolated and physiologically characterized. Transmission electron microscopy revealed Siphoviridae morphology, with an oblate icosahedral head and a long noncontractile tail. Notably, these members displayed a small burst size (15–19 plaque-forming units/cell) yet an extensively broad host spectrum when tested on 175 Alteromonas strains. Such unique infection kinetics are potentially associated with discrepancies in codon usage bias from the host tRNA inventory. Phylogenetic analysis indicated that the three phages are closely evolutionarily related; they clustered at the species level and represent a novel genus. Three auxiliary metabolic genes with roles in nucleotide metabolism and putative biofilm dispersal were found in these phage genomes, which revealed important biogeochemical significance of these alterophages in marine ecosystems. Our isolation and characterization of these novel phages expand the current understanding of alterophage diversity, evolution, and phage–host interactions. IMPORTANCE The marine bacterium Alteromonas is prevalent in the global ocean with crucial ecological significance; however, little is known about the diversity and evolution of its bacteriophages that profoundly affect the bacterial communities. Our study characterized a novel genus of three newly isolated Alteromonas phages that exhibited a distinct infection strategy of broad host spectrum and small burst size. This strategy is likely a consequence of the viral trade-off between virulence and lysis profiles during phage–host coevolution, and our work provides new insight into viral evolution and infection strategies.
Collapse
|
45
|
Shkoporov AN, Turkington CJ, Hill C. Mutualistic interplay between bacteriophages and bacteria in the human gut. Nat Rev Microbiol 2022; 20:737-749. [PMID: 35773472 DOI: 10.1038/s41579-022-00755-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 12/12/2022]
Abstract
Bacteriophages (phages) are often described as obligate predators of their bacterial hosts, and phage predation is one of the leading forces controlling the density and distribution of bacterial populations. Every 48 h half of all bacteria on Earth are killed by phages. Efficient killing also forms the basis of phage therapy in humans and animals and the use of phages as food preservatives. In turn, bacteria have a plethora of resistance systems against phage attack, but very few bacterial species, if any, have entirely escaped phage predation. However, in complex communities and environments such as the human gut, this antagonistic model of attack and counter-defence does not fully describe the scope of phage-bacterium interactions. In this Review, we explore some of the more mutualistic aspects of phage-bacterium interactions in the human gut, and we suggest that the relationship between phages and their bacterial hosts in the gut is best characterized not as a fight to the death between enemies but rather as a mutualistic relationship between partners.
Collapse
Affiliation(s)
- Andrey N Shkoporov
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland. .,Department of Medicine, University College Cork, Cork, Ireland.
| | | | - Colin Hill
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland.
| |
Collapse
|
46
|
George EE, Tashyreva D, Kwong WK, Okamoto N, Horák A, Husnik F, Lukeš J, Keeling PJ. Gene Transfer Agents in Bacterial Endosymbionts of Microbial Eukaryotes. Genome Biol Evol 2022; 14:6615375. [PMID: 35738252 PMCID: PMC9254644 DOI: 10.1093/gbe/evac099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/14/2022] Open
Abstract
Gene transfer agents (GTAs) are virus-like structures that package and transfer prokaryotic DNA from donor to recipient prokaryotic cells. Here, we describe widespread GTA gene clusters in the highly reduced genomes of bacterial endosymbionts from microbial eukaryotes (protists). Homologs of the GTA capsid and portal complexes were initially found to be present in several highly reduced alphaproteobacterial endosymbionts of diplonemid protists (Rickettsiales and Rhodospirillales). Evidence of GTA expression was found in polyA-enriched metatranscriptomes of the diplonemid hosts and their endosymbionts, but due to biases in the polyA-enrichment methods, levels of GTA expression could not be determined. Examining the genomes of closely related bacteria revealed that the pattern of retained GTA head/capsid complexes with missing tail components was common across Rickettsiales and Holosporaceae (Rhodospirillales), all obligate symbionts with a wide variety of eukaryotic hosts. A dN/dS analysis of Rickettsiales and Holosporaceae symbionts revealed that purifying selection is likely the main driver of GTA evolution in symbionts, suggesting they remain functional, but the ecological function of GTAs in bacterial symbionts is unknown. In particular, it is unclear how increasing horizontal gene transfer in small, largely clonal endosymbiont populations can explain GTA retention, and, therefore, the structures may have been repurposed in endosymbionts for host interactions. Either way, their widespread retention and conservation in endosymbionts of diverse eukaryotes suggests an important role in symbiosis.
Collapse
Affiliation(s)
- Emma E George
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada
| | - Daria Tashyreva
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Waldan K Kwong
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Instituto Gulbenkian de Ciência, 6, 2780-156 Oeiras, Portugal
| | - Noriko Okamoto
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Hakai Institute, Quadra Island, British Columbia, Canada
| | - Aleš Horák
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.,University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Filip Husnik
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.,University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Patrick J Keeling
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada
| |
Collapse
|
47
|
Abstract
Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.
Collapse
|
48
|
Benler S, Koonin EV. Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes. Front Mol Biosci 2022; 9:821197. [PMID: 35402511 PMCID: PMC8987985 DOI: 10.3389/fmolb.2022.821197] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
Prokaryotic genomes are replete with mobile genetic elements (MGE) that span a continuum of replication autonomy. On numerous occasions during microbial evolution, diverse MGE lose their autonomy altogether but, rather than being quickly purged from the host genome, assume a new function that benefits the host, rendering the immobilized MGE subject to purifying selection, and resulting in its vertical inheritance. This mini-review highlights the diversity of the repurposed (exapted) MGE as well as the plethora of cellular functions that they perform. The principal contribution of the exaptation of MGE and their components is to the prokaryotic functional systems involved in biological conflicts, and in particular, defense against viruses and other MGE. This evolutionary entanglement between MGE and defense systems appears to stem both from mechanistic similarities and from similar evolutionary predicaments whereby both MGEs and defense systems tend to incur fitness costs to the hosts and thereby evolve mechanisms for survival including horizontal mobility, causing host addiction, and exaptation for functions beneficial to the host. The examples discussed demonstrate that the identity of an MGE, overall mobility and relationship with the host cell (mutualistic, symbiotic, commensal, or parasitic) are all factors that affect exaptation.
Collapse
Affiliation(s)
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
49
|
David Hou CF, Swanson NA, Li F, Yang R, Lokareddy RK, Cingolani G. Cryo-EM structure of a kinetically trapped dodecameric portal protein from the Pseudomonas-phage PaP3. J Mol Biol 2022; 434:167537. [DOI: 10.1016/j.jmb.2022.167537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/09/2022] [Accepted: 03/04/2022] [Indexed: 10/18/2022]
|
50
|
Tall tails: cryo-electron microscopy of phage tail DNA ejection conduits. Biochem Soc Trans 2022; 50:459-22W. [PMID: 35129586 PMCID: PMC9022992 DOI: 10.1042/bst20210799] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
The majority of phages, viruses that infect prokaryotes, inject their genomic material into their host through a tubular assembly known as a tail. Despite the genomic diversity of tailed phages, only three morphological archetypes have been described: contractile tails of Myoviridae-like phages; short non-contractile tails of Podoviridae-like phages; and long and flexible non-contractile tails of Siphoviridae-like phages. While early cryo-electron microscopy (cryo-EM) work elucidated the organisation of the syringe-like injection mechanism of contractile tails, the intrinsic flexibility of the long non-contractile tails prevented high-resolution structural determination. In 2020, four cryo-EM structures of Siphoviridae-like tail tubes were solved and revealed common themes and divergences. The central tube is structurally conserved and homologous to the hexameric rings of the tail tube protein (TTP) also found in contractile tails, bacterial pyocins, and type VI secretion systems. The interior surface of the tube presents analogous motifs of negatively charged amino acids proposed to facilitate ratcheting of the DNA during genome ejection. The lack of a conformational change upon genome ejection implicates the tape measure protein in triggering genome release. A distinctive feature of Siphoviridae-like tails is their flexibility. This results from loose inter-ring connections that can asymmetrically stretch on one side to allow bending and flexing of the tube without breaking. The outer surface of the tube differs greatly and may be smooth or rugged due to additional Ig-like domains in TTP. Some of these variable domains may contribute to adsorption of the phage to prokaryotic and eukaryotic cell surfaces affecting tropism and virulence.
Collapse
|