1
|
Nguyen TVP, Wu Y, Yao T, Trinh JT, Zeng L, Chemla YR, Golding I. Coinfecting phages impede each other's entry into the cell. Curr Biol 2024; 34:2841-2853.e18. [PMID: 38878771 PMCID: PMC11233250 DOI: 10.1016/j.cub.2024.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/15/2024] [Accepted: 05/16/2024] [Indexed: 06/25/2024]
Abstract
The developmental choice made by temperate phages, between cell death (lysis) and viral dormancy (lysogeny), is influenced by the relative abundance of viruses and hosts in the environment. The paradigm for this abundance-driven decision is phage lambda of E. coli, whose propensity to lysogenize increases with the number of viruses coinfecting the same bacterium. It is believed that lambda uses this number to infer whether phages or bacteria outnumber each other. However, this interpretation is premised on an accurate mapping between the extracellular phage-to-bacteria ratio and the intracellular multiplicity of infection (MOI). Here, we show this premise to be faulty. By simultaneously labeling phage capsids and genomes, we find that, while the number of phages landing on each cell reliably samples the population ratio, the number of phages entering the cell does not. Single-cell infections, performed in a microfluidic device and interpreted using a stochastic model, reveal that the probability and rate of phage entry decrease with the number of adsorbed phages. This decrease reflects an MOI-dependent perturbation to host physiology caused by phage attachment, as evidenced by compromised membrane integrity and loss of membrane potential. The dependence of entry dynamics on the surrounding medium results in a strong impact on the infection outcome, while the protracted entry of coinfecting phages increases the heterogeneity in infection outcome at a given MOI. Our findings in lambda, and similar results we obtained for phages T5 and P1, demonstrate the previously unappreciated role played by entry dynamics in determining the outcome of bacteriophage infection.
Collapse
Affiliation(s)
- Thu Vu Phuc Nguyen
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuchen Wu
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Tianyou Yao
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Jimmy T Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Yann R Chemla
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ido Golding
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
| |
Collapse
|
2
|
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
|
3
|
Cingolani G, Iglesias S, Hou CF, Lemire S, Soriaga A, Kyme P. Cryo-EM analysis of Pseudomonas phage Pa193 structural components. RESEARCH SQUARE 2024:rs.3.rs-4189479. [PMID: 38659960 PMCID: PMC11042391 DOI: 10.21203/rs.3.rs-4189479/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The World Health Organization has designated Pseudomonas aeruginosa as a critical pathogen for the development of new antimicrobials. Bacterial viruses, or bacteriophages, have been used in various clinical settings, commonly called phage therapy, to address this growing public health crisis. Here, we describe a high-resolution structural atlas of a therapeutic, contractile-tailed Pseudomonas phage, Pa193. We used bioinformatics, proteomics, and cryogenic electron microscopy single particle analysis to identify, annotate, and build atomic models for 21 distinct structural polypeptide chains forming the icosahedral capsid, neck, contractile tail, and baseplate. We identified a putative scaffolding protein stabilizing the interior of the capsid 5-fold vertex. We also visualized a large portion of Pa193 ~ 500 Å long tail fibers and resolved the interface between the baseplate and tail fibers. The work presented here provides a framework to support a better understanding of phages as biomedicines for phage therapy and inform engineering opportunities.
Collapse
|
4
|
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
|
5
|
Nguyen TVP, Wu Y, Yao T, Trinh JT, Zeng L, Chemla YR, Golding I. CO-INFECTING PHAGES IMPEDE EACH OTHER'S ENTRY INTO THE CELL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543643. [PMID: 37333217 PMCID: PMC10274716 DOI: 10.1101/2023.06.05.543643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Bacteriophage lambda tunes its propensity to lysogenize based on the number of viral genome copies inside the infected cell. Viral self-counting is believed to serve as a way of inferring the abundance of available hosts in the environment. This interpretation is premised on an accurate mapping between the extracellular phage-to-bacteria ratio and the intracellular multiplicity of infection (MOI). However, here we show this premise to be untrue. By simultaneously labeling phage capsids and genomes, we find that, while the number of phages landing on each cell reliably samples the population ratio, the number of phages entering the cell does not. Single-cell infections, followed in a microfluidic device and interpreted using a stochastic model, reveal that the probability and rate of individual phage entries decrease with MOI. This decrease reflects an MOI-dependent perturbation to host physiology caused by phage landing, evidenced by compromised membrane integrity and loss of membrane potential. The dependence of phage entry dynamics on the surrounding medium is found to result in a strong impact of environmental conditions on the infection outcome, while the protracted entry of co-infecting phages increases the cell-to-cell variability in infection outcome at a given MOI. Our findings demonstrate the previously unappreciated role played by entry dynamics in determining the outcome of bacteriophage infection.
Collapse
Affiliation(s)
- Thu Vu Phuc Nguyen
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX 77030, USA
| | - Yuchen Wu
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Tianyou Yao
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Jimmy T. Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Yann R. Chemla
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Ido Golding
- Department of Physics, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Houston, TX 77030, USA
- Department of Microbiology, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| |
Collapse
|
6
|
Fan F, Li X, Pang B, Zhang C, Li Z, Zhang L, Li J, Zhang J, Yan M, Liang W, Kan B. The outer-membrane protein TolC of Vibrio cholerae serves as a second cell-surface receptor for the VP3 phage. J Biol Chem 2017; 293:4000-4013. [PMID: 29259138 DOI: 10.1074/jbc.m117.805689] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/14/2017] [Indexed: 12/17/2022] Open
Abstract
Receptor recognition is a key step in the initiation of phage infection. Previously, we found that VP3, the T7 family phage of the Vibrio cholerae serogroup O1 biotype El Tor, can adsorb the core oligosaccharide (OS) of lipopolysaccharides of V. cholerae However, some wildtype strains of V. cholerae possessing the intact OS gene cluster still have VP3 binding but are resistant to VP3 infection. Moreover, an OS gene-deletion mutant still exhibits weak VP3 binding, suggesting multiple factors are possibly involved in VP3 binding to V. cholerae Here, we report that the outer-membrane protein TolC of V. cholerae is involved in the host adsorption of VP3. We observed that TolC directly interacts with the VP3 tail fiber protein gp44 and its C-terminal domains, and we also found that three amino acid residues in the outside loops of TolC, at positions 78, 290, and 291, are critical for binding to gp44. Among the VP3-resistant wildtype V. cholerae strains, frequent amino acid residue mutations were observed in the loops around the sites 78, 290, and 291, which were predicted to be exposed to the cell surface. These findings reveal a co-receptor-binding mechanism for VP3 infection of V. cholerae and that both outer-membrane TolC and OS are necessary for successful VP3 infection of V. cholerae We conclude that mutations on the outside loops of the receptor may confer V. cholerae strains with VP3 phage resistance, enabling these strains to survive in environments containing VP3 or related phages.
Collapse
Affiliation(s)
- Fenxia Fan
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Xu Li
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Bo Pang
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Cheng Zhang
- the National Institute of Biological Sciences, Beijing 102206, China
| | - Zhe Li
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Lijuan Zhang
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Jie Li
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Jingyun Zhang
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Meiying Yan
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206
| | - Weili Liang
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206.,the Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang 310003, and
| | - Biao Kan
- From the State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, .,the Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang 310003, and
| |
Collapse
|
7
|
Mahony J, Alqarni M, Stockdale S, Spinelli S, Feyereisen M, Cambillau C, Sinderen DV. Functional and structural dissection of the tape measure protein of lactococcal phage TP901-1. Sci Rep 2016; 6:36667. [PMID: 27824135 PMCID: PMC5099701 DOI: 10.1038/srep36667] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/18/2016] [Indexed: 01/22/2023] Open
Abstract
The tail tape measure protein (TMP) of tailed bacteriophages (also called phages) dictates the tail length and facilitates DNA transit to the cell cytoplasm during infection. Here, a thorough mutational analysis of the TMP from lactococcal phage TP901-1 (TMPTP901-1) was undertaken. We generated 56 mutants aimed at defining TMPTP901-1 domains that are essential for tail assembly and successful infection. Through analysis of the derived mutants, we determined that TP901-1 infectivity requires the N-terminal 154 aa residues, the C-terminal 60 residues and the first predicted hydrophobic region of TMPTP901-1 as a minimum. Furthermore, the role of TMPTP901-1 in tail length determination was visualized by electron microscopic imaging of TMP-deletion mutants. The inverse linear correlation between the extent of TMPTP901-1-encoding gene deletions and tail length of the corresponding virion provides an estimate of TMPTP901-1 regions interacting with the connector or involved in initiator complex formation. This study represents the most thorough characterisation of a TMP from a Gram-positive host-infecting phage and provides essential advances to understanding its role in virion assembly, morphology and infection.
Collapse
Affiliation(s)
- Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Mona Alqarni
- School of Microbiology, University College Cork, Cork, Ireland
| | - Stephen Stockdale
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Marseille, France
| | | | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Marseille, France
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| |
Collapse
|
8
|
Cumby N, Reimer K, Mengin-Lecreulx D, Davidson AR, Maxwell KL. The phage tail tape measure protein, an inner membrane protein and a periplasmic chaperone play connected roles in the genome injection process ofE. coliphage HK97. Mol Microbiol 2015; 96:437-47. [DOI: 10.1111/mmi.12918] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2014] [Indexed: 01/21/2023]
Affiliation(s)
- Nichole Cumby
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
- Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto Ontario Canada
| | - Kelly Reimer
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
- Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto Ontario Canada
| | - Dominique Mengin-Lecreulx
- Laboratoire des Enveloppes Bactériennes et Antibiotiques; IBBMC; UMR 8619 CNRS; Université Paris Sud; Orsay Cedex France
| | - Alan R. Davidson
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
- Department of Biochemistry; University of Toronto; Toronto Ontario Canada
| | - Karen L. Maxwell
- Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto Ontario Canada
| |
Collapse
|
9
|
Stockdale SR, Mahony J, Courtin P, Chapot-Chartier MP, van Pijkeren JP, Britton RA, Neve H, Heller KJ, Aideh B, Vogensen FK, van Sinderen D. The lactococcal phages Tuc2009 and TP901-1 incorporate two alternate forms of their tail fiber into their virions for infection specialization. J Biol Chem 2013; 288:5581-90. [PMID: 23300085 PMCID: PMC3581408 DOI: 10.1074/jbc.m112.444901] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/07/2013] [Indexed: 01/04/2023] Open
Abstract
Lactococcal phages Tuc2009 and TP901-1 possess a conserved tail fiber called a tail-associated lysin (referred to as Tal(2009) for Tuc2009, and Tal(901-1) for TP901-1), suspended from their tail tips that projects a peptidoglycan hydrolase domain toward a potential host bacterium. Tal(2009) and Tal(901-1) can undergo proteolytic processing mid-protein at the glycine-rich sequence GG(S/N)SGGG, removing their C-terminal structural lysin. In this study, we show that the peptidoglycan hydrolase of these Tal proteins is an M23 peptidase that exhibits D-Ala-D-Asp endopeptidase activity and that this activity is required for efficient infection of stationary phase cells. Interestingly, the observed proteolytic processing of Tal(2009) and Tal(901-1) facilitates increased host adsorption efficiencies of the resulting phages. This represents, to the best of our knowledge, the first example of tail fiber proteolytic processing that results in a heterogeneous population of two phage types. Phages that possess a full-length tail fiber, or a truncated derivative, are better adapted to efficiently infect cells with an extensively cross-linked cell wall or infect with increased host-adsorption efficiencies, respectively.
Collapse
Affiliation(s)
| | | | - Pascal Courtin
- INRA, UMR1319 Micalis, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | | | - Jan-Peter van Pijkeren
- the Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Robert A. Britton
- the Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Horst Neve
- the Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany, and the Department of Food Science
| | - Knut J. Heller
- the Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany, and the Department of Food Science
| | | | | | - Douwe van Sinderen
- From the Department of Microbiology and
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| |
Collapse
|
10
|
Abstract
Sixty years after Hershey and Chase showed that nucleic acid is the major component of phage particles that is ejected into cells, we still do not fully understand how the process occurs. Advances in electron microscopy have revealed the structure of the condensed DNA confined in a phage capsid, and the mechanisms and energetics of packaging a phage genome are beginning to be better understood. Condensing DNA subjects it to high osmotic pressure, which has been suggested to provide the driving force for its ejection during infection. However, forces internal to a phage capsid cannot, alone, cause complete genome ejection into cells. Here, we describe the structure of the DNA inside mature phages and summarize the current models of genome ejection, both in vitro and in vivo.
Collapse
Affiliation(s)
- Ian J Molineux
- Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
| | | |
Collapse
|
11
|
Abstract
Correct host cell recognition is important in the replication cycle for any virus, including bacterial viruses. This essential step should occur before the bacteriophage commits to transfer its genomic material into the host. In this chapter we will discuss the proteins and mechanisms bacteriophages use for receptor recognition (just before full commitment to infection) and nucleic acid injection, which occurs just after commitment. Some bacteriophages use proteins of the capsid proper for host cell recognition, others use specialised spikes or fibres. Usually, several identical recognition events take place, and the information that a suitable host cell has been encountered is somehow transferred to the part of the bacteriophage capsid involved in nucleic acid transfer. The main part of the capsids of bacteriophages stay on the cell surface after transferring their genome, although a few specialised proteins move with the DNA, either forming a conduit, protecting the nucleic acids after transfer and/or functioning in the process of transcription and translation.
Collapse
Affiliation(s)
- Carmela Garcia-Doval
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CSIC), c/Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | | |
Collapse
|
12
|
Davidson AR, Cardarelli L, Pell LG, Radford DR, Maxwell KL. Long noncontractile tail machines of bacteriophages. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:115-42. [PMID: 22297512 DOI: 10.1007/978-1-4614-0980-9_6] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this chapter, we describe the structure, assembly, function, and evolution of the long, noncontractile tail of the siphophages, which comprise ∼60% of the phages on earth. We place -particular emphasis on features that are conserved among all siphophages, and trace evolutionary connections between these phages and myophages, which possess long contractile tails. The large number of high-resolution structures of tail proteins solved recently coupled to studies of tail-related complexes by electron microscopy have provided many new insights in this area. In addition, the availability of thousands of phage and prophage genome sequences has allowed the delineation of several large families of tail proteins that were previously unrecognized. We also summarize current knowledge pertaining to the mechanisms by which siphophage tails recognize the bacterial cell surface and mediate DNA injection through the cell envelope. We show that phages infecting Gram-positive and Gram-negative bacteria possess distinct families of proteins at their tail tips that are involved in this process. Finally, we speculate on the evolutionary advantages provided by long phage tails.
Collapse
Affiliation(s)
- Alan R Davidson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | | | | | | | | |
Collapse
|
13
|
Chang JT, Schmid MF, Haase-Pettingell C, Weigele PR, King JA, Chiu W. Visualizing the structural changes of bacteriophage Epsilon15 and its Salmonella host during infection. J Mol Biol 2010; 402:731-40. [PMID: 20709082 PMCID: PMC3164490 DOI: 10.1016/j.jmb.2010.07.058] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 07/26/2010] [Accepted: 07/29/2010] [Indexed: 01/12/2023]
Abstract
The efficient mechanism by which double-stranded DNA bacteriophages deliver their chromosome across the outer membrane, cell wall, and inner membrane of Gram-negative bacteria remains obscure. Advances in single-particle electron cryomicroscopy have recently revealed details of the organization of the DNA injection apparatus within the mature virion for various bacteriophages, including epsilon15 (ɛ15) and P-SSP7. We have used electron cryotomography and three-dimensional subvolume averaging to capture snapshots of ɛ15 infecting its host Salmonella anatum. These structures suggest the following stages of infection. In the first stage, the tailspikes of ɛ15 attach to the surface of the host cell. Next, ɛ15's tail hub attaches to a putative cell receptor and establishes a tunnel through which the injection core proteins behind the portal exit the virion. A tube spanning the periplasmic space is formed for viral DNA passage, presumably from the rearrangement of core proteins or from cellular components. This tube would direct the DNA into the cytoplasm and protect it from periplasmic nucleases. Once the DNA has been injected into the cell, the tube and portal seals, and the empty bacteriophage remains at the cell surface.
Collapse
Affiliation(s)
- Juan T. Chang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael F. Schmid
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Peter R. Weigele
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan A. King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
14
|
Literature Alerts. J Microencapsul 2008. [DOI: 10.3109/02652048609021802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
15
|
Literature Alerts. J Microencapsul 2008. [DOI: 10.3109/02652048609031578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
16
|
Gurnev PA, Oppenheim AB, Winterhalter M, Bezrukov SM. Docking of a Single Phage Lambda to its Membrane Receptor Maltoporin as a Time-resolved Event. J Mol Biol 2006; 359:1447-55. [PMID: 16697410 DOI: 10.1016/j.jmb.2006.04.034] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Revised: 03/27/2006] [Accepted: 04/10/2006] [Indexed: 10/24/2022]
Abstract
We have been able to observe the first step in bacteriophage infection, the docking of phage lambda to its membrane receptor maltoporin, at the single-particle level. High-resolution conductance recording from a single trimeric maltoporin channel reconstituted into a planar lipid bilayer has allowed detection of the simultaneous and irreversible interaction of the phage tail with all three monomers of the receptor. The formation of a phage-maltoporin complex affects the channel transport properties. Our analysis demonstrates that phage attaches symmetrically to all three receptor monomers. The statistics of sugar binding to the phage-receptor complex on the side opposite to phage docking show that the monomers of maltoporin still bind sugar independently, with the kinetic constants expected from those of the phage-free receptor. This finding suggests that phage docking does not distort the structure of the receptor, and that the phage-binding regions are close to, but do not overlap with, the sugar-binding domains of the maltoporin monomers. However, ion fluxes through the pores of maltoporin in the phage-receptor complex share a new common pathway. We expect that the present study contributes to the current needs for structural information on the functional complexes involved in intercellular recognition.
Collapse
Affiliation(s)
- Philip A Gurnev
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | |
Collapse
|
17
|
Molineux IJ. Fifty-three years since Hershey and Chase; much ado about pressure but which pressure is it? Virology 2006; 344:221-9. [PMID: 16364752 DOI: 10.1016/j.virol.2005.09.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Accepted: 09/10/2005] [Indexed: 11/30/2022]
Abstract
The events that occur at the initiation of phage infection are discussed, from adsorption through DNA ejection from the virion into the cell. A new model for DNA translocation is described that not only overcomes difficulties associated with previous models of DNA ejection but also provides a mechanism by which both single-stranded genomes and internal phage proteins can be transported from the virion into the cell cytoplasm.
Collapse
Affiliation(s)
- Ian J Molineux
- Molecular Genetics and Microbiology, Institute for Cell and Molecular Biology, The University of Texas, Austin, TX 78712, USA.
| |
Collapse
|
18
|
Geller BL, Ngo HT, Mooney DT, Su P, Dunn N. Lactococcal 936-Species Phage Attachment to Surface of Lactococcus lactis. J Dairy Sci 2005; 88:900-7. [PMID: 15738223 DOI: 10.3168/jds.s0022-0302(05)72756-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The interactions of the 936-species phages sk1, jj50, and 64 with the cell surface of Lactococcus lactis LM0230 were analyzed. Cell envelopes (walls + plasma membrane), cell wall, or plasma membrane from L. lactis ssp. lactis LM0230 each inactivated the phages in vitro. However, other 936-species phages kh and P008, which do not infect strain LM0230, were not inactivated by any of the subcellular fractions. Treating cell walls or plasma membrane with the cell wall hydrolase mutanolysin eliminated inactivation of phage sk1. This suggested that intact cell wall fragments were required for inactivation. A role for plasma membrane in phage sk1 inactivation was further investigated. Boiling, washing in 2 M KCl, 8 M urea, or 0.1 M Na(2)CO(3)/pH 11, or treating the plasma membrane with proteases did not reduce adsorption or inactivation of phage. Adding lipoteichoic acid or antibodies to lipoteichoic acid did not reduce inactivation of phage in a mixture with membrane, suggesting that lipoteichoic acid was not involved. Inactivation by envelopes or cell wall correlated with ejection of DNA from the phage sk1 capsid. Although calcium is required for plaque formation, it was not required for adsorption, inactivation, or ejection of phage DNA by envelopes or cell wall. The results suggest that at least for phages sk1, jj50, and 64, adsorption and phage DNA injection into the host does not require a host membrane protein or lipoteichoic acid, and that cell wall components are sufficient for these initial steps of phage infection.
Collapse
Affiliation(s)
- B L Geller
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA.
| | | | | | | | | |
Collapse
|
19
|
Kemp P, Gupta M, Molineux IJ. Bacteriophage T7 DNA ejection into cells is initiated by an enzyme-like mechanism. Mol Microbiol 2004; 53:1251-65. [PMID: 15306026 DOI: 10.1111/j.1365-2958.2004.04204.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a normal infection about 850 bp of the bacteriophage T7 genome is ejected into the cell, the remainder of the genome is internalized through transcription by Escherichia coli and then T7 RNA polymerase. Rates of T7 DNA internalization by the E. coli enzyme in vivo are constant across the whole genome. As expected for an enzyme-catalysed reaction, rates vary with temperature and can be fitted to Arrhenius kinetics. Phage virions containing a mutant gp16, a protein known to be ejected from the phage capsid into the cell at the initiation of infection, allow complete entry of the T7 genome in the absence of transcription. The kinetics of DNA ejection from such a mutant virion into the bacterial cytoplasm have also been measured at different temperatures in vivo. Between 15 and 43 degrees C the entire 40 kb T7 genome is translocated into the cell at a constant rate that is characteristic for each temperature, and the temperature-dependence of DNA translocation rates can be fitted to Arrhenius kinetics. The data are consistent with the idea that transcription-independent DNA translocation from the T7 virion is also enzyme-catalysed. The proton motive force is necessary for this mode of DNA translocation, because collapsing the membrane potential while the T7 genome is entering the cell abruptly halts further DNA transfer.
Collapse
Affiliation(s)
- Priscilla Kemp
- Section of Molecular Genetics and Microbiology, and Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712-1095, USA
| | | | | |
Collapse
|
20
|
Kivelä HM, Daugelavicius R, Hankkio RH, Bamford JKH, Bamford DH. Penetration of membrane-containing double-stranded-DNA bacteriophage PM2 into Pseudoalteromonas hosts. J Bacteriol 2004; 186:5342-54. [PMID: 15292135 PMCID: PMC490941 DOI: 10.1128/jb.186.16.5342-5354.2004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The icosahedral bacteriophage PM2 has a circular double-stranded DNA (dsDNA) genome and an internal lipid membrane. It is the only representative of the Corticoviridae family. How the circular supercoiled genome residing inside the viral membrane is translocated into the gram-negative marine Pseudoalteromonas host has been an intriguing question. Here we demonstrate that after binding of the virus to an abundant cell surface receptor, the protein coat is most probably dissociated. During the infection process, the host cell outer membrane becomes transiently permeable to lipophilic gramicidin D molecules proposing fusion with the viral membrane. One of the components of the internal viral lipid core particle is the integral membrane protein P7, with muralytic activity that apparently aids the process of peptidoglycan penetration. Entry of the virion also causes a limited depolarization of the cytoplasmic membrane. These phenomena differ considerably from those observed in the entry process of bacteriophage PRD1, a dsDNA virus, which uses its internal membrane to make a cell envelope-penetrating tubular structure.
Collapse
Affiliation(s)
- Hanna M Kivelä
- Faculty of Biosciences and Institute of Biotechnology, University of Helsinki, Finland
| | | | | | | | | |
Collapse
|
21
|
Abstract
Gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. Although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. This review summarizes the development in the field since our previous review (H. Nikaido and M. Vaara, Microbiol. Rev. 49:1-32, 1985) was published. With the discovery of protein channels, structural knowledge enables us to understand in molecular detail how porins, specific channels, TonB-linked receptors, and other proteins function. We are now beginning to see how the export of large proteins occurs across the outer membrane. With our knowledge of the lipopolysaccharide-phospholipid asymmetric bilayer of the outer membrane, we are finally beginning to understand how this bilayer can retard the entry of lipophilic compounds, owing to our increasing knowledge about the chemistry of lipopolysaccharide from diverse organisms and the way in which lipopolysaccharide structure is modified by environmental conditions.
Collapse
Affiliation(s)
- Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202, USA.
| |
Collapse
|
22
|
Abstract
Viruses occur throughout the biosphere. Cells of Eukarya, Bacteria, and Archaea are infected by a variety of viruses that considerably outnumber the host cells. Although viruses have adapted to different host systems during evolution and many different viral strategies have developed, certain similarities can be found. Viruses encounter common problems during their entry process into the host cells, and similar strategies seem to ensure, for example, that the movement toward the site of replication and the translocation through the host membrane occur. The penetration of the host cell's external envelope involves, across the viral world, either fusion between two membranes, channel formation through the host envelope, disruption of the membrane vesicle, or a combination of these events. Endocytic-type events may occur during the entry of a bacterial virus as well as during the entry of an animal virus; the same applies for membrane fusion.
Collapse
Affiliation(s)
- Minna M Poranen
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Finland.
| | | | | |
Collapse
|
23
|
Berrier C, Bonhivers M, Letellier L, Ghazi A. High-conductance channel induced by the interaction of phage lambda with its receptor maltoporin. FEBS Lett 2000; 476:129-33. [PMID: 10913599 DOI: 10.1016/s0014-5793(00)01705-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Bacteriophage lambda that binds to liposomes bears its receptor maltoporin (LamB) and is able to inject its DNA into the internal space. During this process, the liposomes are permeabilized, suggesting that a transmembrane channel has formed (Roessner and Ihler (1986) J. Biol. Chem. 261, 386-390). This pore possibly constitutes the pathway used by lambda DNA to cross the membrane. We reconstituted purified LamB from Shigella in liposomes that were incubated with lambda phages. Addition of this mixture to a bilayer chamber resulted in the incorporation in planar bilayers of high-conductance channels whose conductance, kinetics and voltage dependence were totally different from those of maltoporin channels.
Collapse
Affiliation(s)
- C Berrier
- UMR CNRS 8619, Bât. 430, Université Paris-Sud, 91405 Cedex, Orsay, France
| | | | | | | |
Collapse
|
24
|
Szabò I, Bàthori G, Tombola F, Brini M, Coppola A, Zoratti M. DNA translocation across planar bilayers containing Bacillus subtilis ion channels. J Biol Chem 1997; 272:25275-82. [PMID: 9312144 DOI: 10.1074/jbc.272.40.25275] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The mechanisms by which genetic material crosses prokaryotic membranes are incompletely understood. We have developed a new methodology to study the translocation of genetic material via pores in a reconstituted system, using techniques from electrophysiology and molecular biology. We report here that planar bilayer membranes become permeable to double-stranded DNA (kilobase range) if Bacillus subtilis membrane vesicles containing high conductance channels have been fused into them. The translocation is an electrophoretic process, since it does not occur if a transmembrane electrical field opposing the movement of DNA, a polyanion, is applied. It is not an aspecific permeation through the phospholipid bilayer, since it does not take place if no proteins have been incorporated into the membrane. The transport is also not due simply to the presence of polypeptides in the membrane, since it does not occur if the latter contains gramicidin A or a eukaryotic, multi-protein vesicle fraction exhibiting 30-picosiemens anion-selective channel activity. The presence of DNA alters the behavior of the bacterial channels, indicating that it interacts with the pores and may travel through their lumen. These results support the idea that DNA translocation may take place through proteic pores and suggest that some of the high conductance bacterial channels observed in electrophysiological experiments may be constituents of the DNA translocating machinery in these organisms.
Collapse
Affiliation(s)
- I Szabò
- CNR Unit for the Study of Biomembranes, Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | | | | | | | | | | |
Collapse
|
25
|
George SK, Najera L, Sandoval R, Ihler GM. Beta-galactosidase fused to the hydrophobic domain of cytochrome b5 spontaneously associates with liposomes. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1061:26-32. [PMID: 1899801 DOI: 10.1016/0005-2736(91)90264-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Since liver microsomal cytochrome b5 spontaneously associates with liposomes and membranes by means of its C-terminal hydrophobic domain (HP), chimeric proteins containing HP prepared by genetic fusion might also spontaneously associate with liposomes or cellular membranes. Synthetic DNA corresponding to the hydrophobic domain of cytochrome b5 was enzymatically fused in-frame to cloned DNA corresponding to the C-terminus of the Escherichia coli enzyme, beta-galactosidase. This protein, LacZ:HP, synthesized in E. coli and purified from a crude E. coli membrane extract, was shown to spontaneously associated with liposomes, as does cytochrome b5. Association is rapid and stable in the presence of salt and high pH and the fusion protein behaves as an integral membrane protein. LacZ:HP can be readily and extensively purified from crude extracts by association with liposomes and this procedure may provide a convenient purification scheme for proteins not otherwise readily purified, for example polypeptides from cloned gene fragments to be used for antibody production. These hybrid proteins may represent a new potentially useful class of polypeptides capable of hydrophobic interactions with membranes.
Collapse
Affiliation(s)
- S K George
- Department of Medical Biochemistry and Genetics, Texas A & M College of Medicine, College Station 77843
| | | | | | | |
Collapse
|
26
|
Padan E, Schuldiner S. Intracellular pH and membrane potential as regulators in the prokaryotic cell. J Membr Biol 1987; 95:189-98. [PMID: 3295250 DOI: 10.1007/bf01869481] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
27
|
Determination of the relative molal heat content of dipalmitoylphosphatidylcholine vesicles in various physical states. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0166-6622(87)80206-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|