1
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Chechik M, Greive SJ, Antson AA, Jenkins HT. Structural basis for DNA recognition by a viral genome-packaging machine. Proc Natl Acad Sci U S A 2024; 121:e2406138121. [PMID: 39116131 PMCID: PMC11331095 DOI: 10.1073/pnas.2406138121] [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: 03/25/2024] [Accepted: 07/09/2024] [Indexed: 08/10/2024] Open
Abstract
DNA recognition is critical for assembly of double-stranded DNA viruses, particularly for the initiation of packaging the viral genome into the capsid. The key component that recognizes viral DNA is the small terminase protein. Despite prior studies, the molecular mechanism for DNA recognition remained elusive. Here, we address this question by identifying the minimal site in the bacteriophage HK97 genome specifically recognized by the small terminase and determining the structure of this complex by cryoEM. The circular small terminase employs an entirely unexpected mechanism in which DNA transits through the central tunnel, and sequence-specific recognition takes place as it emerges. This recognition stems from a substructure formed by the N- and C-terminal segments of two adjacent protomers which are unstructured when DNA is absent. Such interaction ensures continuous engagement of the small terminase with DNA, enabling it to slide along the DNA while simultaneously monitoring its sequence. This mechanism allows locating and instigating packaging initiation and termination precisely at the specific cos sequence.
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Affiliation(s)
- Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, YorkYO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, YorkYO10 5NG, United Kingdom
| | - Sandra J. Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, YorkYO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, YorkYO10 5NG, United Kingdom
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, YorkYO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, YorkYO10 5NG, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, YorkYO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, YorkYO10 5NG, United Kingdom
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2
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Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
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Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
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3
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Gu Z, Wu K, Wang J. Structural morphing in the viral portal vertex of bacteriophage lambda. J Virol 2024; 98:e0006824. [PMID: 38661364 PMCID: PMC11092355 DOI: 10.1128/jvi.00068-24] [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: 01/10/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
The portal protein of tailed bacteriophage plays essential roles in various aspects of capsid assembly, motor assembly, genome packaging, connector formation, and infection processes. After DNA packaging is complete, additional proteins are assembled onto the portal to form the connector complex, which is crucial as it bridges the mature head and tail. In this study, we report high-resolution cryo-electron microscopy (cryo-EM) structures of the portal vertex from bacteriophage lambda in both its prohead and mature virion states. Comparison of these structures shows that during head maturation, in addition to capsid expansion, the portal protein undergoes conformational changes to establish interactions with the connector proteins. Additionally, the independently assembled tail undergoes morphological alterations at its proximal end, facilitating its connection to the head-tail joining protein and resulting in the formation of a stable portal-connector-tail complex. The B-DNA molecule spirally glides through the tube, interacting with the nozzle blade region of the middle-ring connector protein. These insights elucidate a mechanism for portal maturation and DNA translocation within the phage lambda system. IMPORTANCE The tailed bacteriophages possess a distinct portal vertex that consists of a ring of 12 portal proteins associated with a 5-fold capsid shell. This portal protein is crucial in multiple stages of virus assembly and infection. Our research focused on examining the structures of the portal vertex in both its preliminary prohead state and the fully mature virion state of bacteriophage lambda. By analyzing these structures, we were able to understand how the portal protein undergoes conformational changes during maturation, the mechanism by which it prevents DNA from escaping, and the process of DNA spirally gliding.
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Affiliation(s)
- Zhiwei Gu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kexun Wu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
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Huang D, Xia R, Chen C, Liao J, Chen L, Wang D, Alvarez PJJ, Yu P. Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. Trends Microbiol 2024:S0966-842X(24)00042-8. [PMID: 38433027 DOI: 10.1016/j.tim.2024.02.002] [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: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rong Xia
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengyi Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Linxing Chen
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dongsheng Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314100, China.
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Mukherjee A, Kizziah JL, Hawkins NC, Nasef MO, Parker LK, Dokland T. Structure of the Portal Complex from Staphylococcus aureus Pathogenicity Island 1 Transducing Particles In Situ and In Isolation. J Mol Biol 2024; 436:168415. [PMID: 38135177 PMCID: PMC10923094 DOI: 10.1016/j.jmb.2023.168415] [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: 10/24/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal itself, produced by overexpression, and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.
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Affiliation(s)
- Amarshi Mukherjee
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - James L Kizziah
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - N'Toia C Hawkins
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Mohamed O Nasef
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Laura K Parker
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Terje Dokland
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Dasgupta S, Thomas JA, Ray K. Mechanism of Viral DNA Packaging in Phage T4 Using Single-Molecule Fluorescence Approaches. Viruses 2024; 16:192. [PMID: 38399968 PMCID: PMC10893049 DOI: 10.3390/v16020192] [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: 12/29/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the mechanisms responsible for DNA translocation. Over the last fifteen years, single-molecule fluorescence technologies have been applied to study viral nucleic acid packaging using the robust and flexible T4 in vitro packaging system in conjunction with genetic, biochemical, and structural analyses. In this review, we discuss the novel findings from these studies, including that the T4 genome was determined to be packaged as an elongated loop via the colocalization of dye-labeled DNA termini above the portal structure. Packaging efficiency of the TerL motor was shown to be inherently linked to substrate structure, with packaging stalling at DNA branches. The latter led to the design of multiple experiments whose results all support a proposed torsional compression translocation model to explain substrate packaging. Evidence of substrate compression was derived from FRET and/or smFRET measurements of stalled versus resolvase released dye-labeled Y-DNAs and other dye-labeled substrates relative to motor components. Additionally, active in vivo T4 TerS fluorescent fusion proteins facilitated the application of advanced super-resolution optical microscopy toward the visualization of the initiation of packaging. The formation of twin TerS ring complexes, each expected to be ~15 nm in diameter, supports a double protein ring-DNA synapsis model for the control of packaging initiation, a model that may help explain the variety of ring structures reported among pac site phages. The examination of the dynamics of the T4 packaging motor at the single-molecule level in these studies demonstrates the value of state-of-the-art fluorescent tools for future studies of complex viral replication mechanisms.
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Affiliation(s)
- Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Julie A. Thomas
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA;
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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Hawkins DEDP, Godwin OC, Antson AA. Viral Genomic DNA Packaging Machinery. Subcell Biochem 2024; 104:181-205. [PMID: 38963488 DOI: 10.1007/978-3-031-58843-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Tailed double-stranded DNA bacteriophage employs a protein terminase motor to package their genome into a preformed protein shell-a system shared with eukaryotic dsDNA viruses such as herpesviruses. DNA packaging motor proteins represent excellent targets for antiviral therapy, with Letermovir, which binds Cytomegalovirus terminase, already licensed as an effective prophylaxis. In the realm of bacterial viruses, these DNA packaging motors comprise three protein constituents: the portal protein, small terminase and large terminase. The portal protein guards the passage of DNA into the preformed protein shell and acts as a protein interaction hub throughout viral assembly. Small terminase recognises the viral DNA and recruits large terminase, which in turn pumps DNA in an ATP-dependent manner. Large terminase also cleaves DNA at the termination of packaging. Multiple high-resolution structures of each component have been resolved for different phages, but it is only more recently that the field has moved towards cryo-EM reconstructions of protein complexes. In conjunction with highly informative single-particle studies of packaging kinetics, these structures have begun to inspire models for the packaging process and its place among other DNA machines.
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Affiliation(s)
- Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
| | - Owen C Godwin
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Structural Biology, The Francis Crick Institute, London, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
- Structural Biology, The Francis Crick Institute, London, UK.
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8
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Mukherjee A, Kizziah JL, Hawkins NC, Nasef MO, Parker LK, Dokland T. Structure of the portal complex from Staphylococcus aureus pathogenicity island 1 transducing particles in situ and in solution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.557803. [PMID: 37786723 PMCID: PMC10541612 DOI: 10.1101/2023.09.18.557803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal in solution and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.
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Affiliation(s)
| | | | | | - Mohamed O. Nasef
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Laura K. Parker
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Terje Dokland
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
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9
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Chechik M, Greive SJ, Antson AA, Jenkins HT. Structure of HK97 small terminase:DNA complex unveils a novel DNA binding mechanism by a circular protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549218. [PMID: 37503206 PMCID: PMC10370121 DOI: 10.1101/2023.07.17.549218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
DNA recognition is critical for assembly of double-stranded DNA viruses, in particular for the initiation of packaging the viral genome into the capsid. DNA packaging has been extensively studied for three archetypal bacteriophage systems: cos, pac and phi29. We identified the minimal site within the cos region of bacteriophage HK97 specifically recognised by the small terminase and determined a cryoEM structure for the small terminase:DNA complex. This nonameric circular protein utilizes a previously unknown mechanism of DNA binding. While DNA threads through the central tunnel, unexpectedly, DNA-recognition is generated at its exit by a substructure formed by the N- and C-terminal segments of two adjacent protomers of the terminase which are unstructured in the absence of DNA. Such interaction ensures continuous engagement of the small terminase with DNA, allowing sliding along DNA while simultaneously checking the DNA sequence. This mechanism allows locating and instigating packaging initiation and termination precisely at the cos site.
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Affiliation(s)
- Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | | | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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