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Viruses
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Phage Structural Biology
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Phage Structural Biology

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Bacterial Viruses".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 18655

Special Issue Editors

Prof. Dr. Wen Jiang

E-Mail Website
Guest Editor
Department of Biological Sciences, Hockmeyer Hall of Structural Biology, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-1971, USA
Interests: cryo-EM; phage
Dr. Matthew Lowell Baker

E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, McGovern Medical School at The University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
Interests: cryo-EM; cryoET; computational modeling; image processing; cancer immunotherapy; membrane proteins; macromolecular structure

Special Issue Information

Dear Colleagues,

Bacteriophages are among the most diverse and abundant life forms on earth. Since the discovery of phages about a hundred years ago, studies of phages have led to numerous breakthroughs from the original use as treatments for bacterial infections to the more recent bacterial CRISPR defense system against phage infections. With the advances in structural biology methods, we have now gained significant insights into the structure and function of many phage systems. Here, we call for contributions to a Special Issue on Phage Structural Biology to highlight cutting-edge structural studies of all phages and all aspects of phage biology, including but not limited to the structures and dynamics of phage head/tail and host factors during phage assembly, maturation, DNA packaging, attachment to host cells, DNA translocation into host cells, replication inside host cells, and release of progeny phage particles.

Prof. Dr. Wen Jiang
Dr. Matthew Lowell Baker
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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Published Papers (6 papers)

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Research

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20 pages, 12369 KiB  
Article
Structure of Vibrio Phage XM1, a Simple Contractile DNA Injection Machine
by Zhiqing Wang, Andrei Fokine, Xinwu Guo, Wen Jiang, Michael G. Rossmann, Richard J. Kuhn, Zhu-Hua Luo and Thomas Klose
Viruses 2023, 15(8), 1673; https://doi.org/10.3390/v15081673 - 31 Jul 2023
Cited by 12 | Viewed by 2485
Abstract
Antibiotic resistance poses a growing risk to public health, requiring new tools to combat pathogenic bacteria. Contractile injection systems, including bacteriophage tails, pyocins, and bacterial type VI secretion systems, can efficiently penetrate cell envelopes and become potential antibacterial agents. Bacteriophage XM1 is a [...] Read more.
Antibiotic resistance poses a growing risk to public health, requiring new tools to combat pathogenic bacteria. Contractile injection systems, including bacteriophage tails, pyocins, and bacterial type VI secretion systems, can efficiently penetrate cell envelopes and become potential antibacterial agents. Bacteriophage XM1 is a dsDNA virus belonging to the Myoviridae family and infecting Vibrio bacteria. The XM1 virion, made of 18 different proteins, consists of an icosahedral head and a contractile tail, terminated with a baseplate. Here, we report cryo-EM reconstructions of all components of the XM1 virion and describe the atomic structures of 14 XM1 proteins. The XM1 baseplate is composed of a central hub surrounded by six wedge modules to which twelve spikes are attached. The XM1 tail contains a fewer number of smaller proteins compared to other reported phage baseplates, depicting the minimum requirements for building an effective cell-envelope-penetrating machine. We describe the tail sheath structure in the pre-infection and post-infection states and its conformational changes during infection. In addition, we report, for the first time, the in situ structure of the phage neck region to near-atomic resolution. Based on these structures, we propose mechanisms of virus assembly and infection. Full article
(This article belongs to the Special Issue Phage Structural Biology)
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26 pages, 4026 KiB  
Article
A Multimodal Approach towards Genomic Identification of Protein Inhibitors of Uracil-DNA Glycosylase
by Wael Muselmani, Naail Kashif-Khan, Claire Bagnéris, Rosalia Santangelo, Mark A. Williams and Renos Savva
Viruses 2023, 15(6), 1348; https://doi.org/10.3390/v15061348 - 10 Jun 2023
Viewed by 2331
Abstract
DNA-mimicking proteins encoded by viruses can modulate processes such as innate cellular immunity. An example is Ung-family uracil-DNA glycosylase inhibition, which prevents Ung-mediated degradation via the stoichiometric protein blockade of the Ung DNA-binding cleft. This is significant where uracil-DNA is a key determinant [...] Read more.
DNA-mimicking proteins encoded by viruses can modulate processes such as innate cellular immunity. An example is Ung-family uracil-DNA glycosylase inhibition, which prevents Ung-mediated degradation via the stoichiometric protein blockade of the Ung DNA-binding cleft. This is significant where uracil-DNA is a key determinant in the replication and distribution of virus genomes. Unrelated protein folds support a common physicochemical spatial strategy for Ung inhibition, characterised by pronounced sequence plasticity within the diverse fold families. That, and the fact that relatively few template sequences are biochemically verified to encode Ung inhibitor proteins, presents a barrier to the straightforward identification of Ung inhibitors in genomic sequences. In this study, distant homologs of known Ung inhibitors were characterised via structural biology and structure prediction methods. A recombinant cellular survival assay and in vitro biochemical assay were used to screen distant variants and mutants to further explore tolerated sequence plasticity in motifs supporting Ung inhibition. The resulting validated sequence repertoire defines an expanded set of heuristic sequence and biophysical signatures shared by known Ung inhibitor proteins. A computational search of genome database sequences and the results of recombinant tests of selected output sequences obtained are presented here. Full article
(This article belongs to the Special Issue Phage Structural Biology)
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12 pages, 13673 KiB  
Article
In Situ Structures of the Ultra-Long Extended and Contracted Tail of Myoviridae Phage P1
by Fan Yang, Liwen Wang, Junquan Zhou, Hao Xiao and Hongrong Liu
Viruses 2023, 15(6), 1267; https://doi.org/10.3390/v15061267 - 29 May 2023
Cited by 5 | Viewed by 3264
Abstract
The Myoviridae phage tail is a common component of contractile injection systems (CISs), essential for exerting contractile function and facilitating membrane penetration of the inner tail tube. The near-atomic resolution structures of the Myoviridae tail have been extensively studied, but the dynamic conformational [...] Read more.
The Myoviridae phage tail is a common component of contractile injection systems (CISs), essential for exerting contractile function and facilitating membrane penetration of the inner tail tube. The near-atomic resolution structures of the Myoviridae tail have been extensively studied, but the dynamic conformational changes before and after contraction and the associated molecular mechanism are still unclear. Here, we present the extended and contracted intact tail-structures of Myoviridae phage P1 by cryo-EM. The ultra-long tail of P1, 2450 Å in length, consists of a neck, a tail terminator, 53 repeated tail sheath rings, 53 repeated tube rings, and a baseplate. The sheath of the contracted tail shrinks by approximately 55%, resulting in the separation of the inner rigid tail tube from the sheath. The extended and contracted tails were further resolved by local reconstruction at 3.3 Å and 3.9 Å resolutions, respectively, allowing us to build the atomic models of the tail terminator protein gp24, the tube protein BplB, and the sheath protein gp22 for the extended tail, and of the sheath protein gp22 for the contracted tail. Our atomic models reveal the complex interaction network in the ultra-long Myoviridae tail and the novel conformational changes of the tail sheath between extended and contracted states. Our structures provide insights into the contraction and stabilization mechanisms of the Myoviridae tail. Full article
(This article belongs to the Special Issue Phage Structural Biology)
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12 pages, 4704 KiB  
Article
Assembly and Capsid Expansion Mechanism of Bacteriophage P22 Revealed by High-Resolution Cryo-EM Structures
by Hao Xiao, Junquan Zhou, Fan Yang, Zheng Liu, Jingdong Song, Wenyuan Chen, Hongrong Liu and Lingpeng Cheng
Viruses 2023, 15(2), 355; https://doi.org/10.3390/v15020355 - 26 Jan 2023
Cited by 12 | Viewed by 3827
Abstract
The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid undergoes extensive structural rearrangement and expansion to become the mature capsid. Bacteriophage P22 is an established model system used to [...] Read more.
The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid undergoes extensive structural rearrangement and expansion to become the mature capsid. Bacteriophage P22 is an established model system used to study virus maturation. Here, we report the cryo-electron microscopy structures of procapsid, empty procapsid, empty mature capsid, and mature capsid of phage P22 at resolutions of 2.6 Å, 3.9 Å, 2.8 Å, and 3.0 Å, respectively. The structure of the procapsid allowed us to build an accurate model of the coat protein gp5 and the C-terminal region of the scaffolding protein gp8. In addition, interactions among the gp5 subunits responsible for procapsid assembly and stabilization were identified. Two C-terminal α-helices of gp8 were observed to interact with the coat protein in the procapsid. The amino acid interactions between gp5 and gp8 in the procapsid were consistent with the results of previous biochemical studies involving mutant proteins. Our structures reveal hydrogen bonds and salt bridges between the gp5 subunits in the procapsid and the conformational changes of the gp5 domains involved in the closure of the local sixfold opening and a thinner capsid shell during capsid maturation. Full article
(This article belongs to the Special Issue Phage Structural Biology)
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13 pages, 2174 KiB  
Article
Structural Insights into the Chaperone-Assisted Assembly of a Simplified Tail Fiber of the Myocyanophage Pam3
by Zi-Lu Wei, Feng Yang, Bo Li, Pu Hou, Wen-Wen Kong, Jie Wang, Yuxing Chen, Yong-Liang Jiang and Cong-Zhao Zhou
Viruses 2022, 14(10), 2260; https://doi.org/10.3390/v14102260 - 14 Oct 2022
Cited by 6 | Viewed by 2617
Abstract
At the first step of phage infection, the receptor-binding proteins (RBPs) such as tail fibers are responsible for recognizing specific host surface receptors. The proper folding and assembly of tail fibers usually requires a chaperone encoded by the phage genome. Despite extensive studies [...] Read more.
At the first step of phage infection, the receptor-binding proteins (RBPs) such as tail fibers are responsible for recognizing specific host surface receptors. The proper folding and assembly of tail fibers usually requires a chaperone encoded by the phage genome. Despite extensive studies on phage structures, the molecular mechanism of phage tail fiber assembly remains largely unknown. Here, using a minimal myocyanophage, termed Pam3, isolated from Lake Chaohu, we demonstrate that the chaperone gp25 forms a stable complex with the tail fiber gp24 at a stoichiometry of 3:3. The 3.1-Å cryo-electron microscopy structure of this complex revealed an elongated structure with the gp25 trimer embracing the distal moieties of gp24 trimer at the center. Each gp24 subunit consists of three domains: the N-terminal α-helical domain required for docking to the baseplate, the tumor necrosis factor (TNF)-like and glycine-rich domains responsible for recognizing the host receptor. Each gp25 subunit consists of two domains: a non-conserved N-terminal β-sandwich domain that binds to the TNF-like and glycine-rich domains of the fiber, and a C-terminal α-helical domain that mediates trimerization/assembly of the fiber. Structural analysis enabled us to propose the assembly mechanism of phage tail fibers, in which the chaperone first protects the intertwined and repetitive distal moiety of each fiber subunit, further ensures the proper folding of these highly plastic structural elements, and eventually enables the formation of the trimeric fiber. These findings provide the structural basis for the design and engineering of phage fibers for biotechnological applications. Full article
(This article belongs to the Special Issue Phage Structural Biology)
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Review

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19 pages, 9114 KiB  
Review
Recent Advances in Structural Studies of Single-Stranded RNA Bacteriophages
by Jirapat Thongchol, Zachary Lill, Zachary Hoover and Junjie Zhang
Viruses 2023, 15(10), 1985; https://doi.org/10.3390/v15101985 - 23 Sep 2023
Cited by 6 | Viewed by 3099
Abstract
Positive-sense single-stranded RNA (ssRNA) bacteriophages (phages) were first isolated six decades ago. Since then, extensive research has been conducted on these ssRNA phages, particularly those infecting E. coli. With small genomes of typically 3–4 kb that usually encode four essential proteins, ssRNA [...] Read more.
Positive-sense single-stranded RNA (ssRNA) bacteriophages (phages) were first isolated six decades ago. Since then, extensive research has been conducted on these ssRNA phages, particularly those infecting E. coli. With small genomes of typically 3–4 kb that usually encode four essential proteins, ssRNA phages employ a straightforward infectious cycle involving host adsorption, genome entry, genome replication, phage assembly, and host lysis. Recent advancements in metagenomics and transcriptomics have led to the identification of ~65,000 sequences from ssRNA phages, expanding our understanding of their prevalence and potential hosts. This review article illuminates significant investigations into ssRNA phages, with a focal point on their structural aspects, providing insights into the various stages of their infectious cycle. Full article
(This article belongs to the Special Issue Phage Structural Biology)
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