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22 pages, 865 KiB

Open AccessReview

Bridging Classical Methodologies in Salmonella Investigation with Modern Technologies: A Comprehensive Review

by Steven Ray Kitchens, Chengming Wang and Stuart B. Price

Microorganisms 2024, 12(11), 2249; https://doi.org/10.3390/microorganisms12112249 - 7 Nov 2024

Cited by 2 | Viewed by 2861

Advancements in genomics and machine learning have significantly enhanced the study of Salmonella epidemiology. Whole-genome sequencing has revolutionized bacterial genomics, allowing for detailed analysis of genetic variation and aiding in outbreak investigations and source tracking. Short-read sequencing technologies, such as those provided by Illumina, have been instrumental in generating draft genomes that facilitate serotyping and the detection of antimicrobial resistance. Long-read sequencing technologies, including those from Pacific Biosciences and Oxford Nanopore Technologies, offer the potential for more complete genome assemblies and better insights into genetic diversity. In addition to these sequencing approaches, machine learning techniques like decision trees and random forests provide powerful tools for pattern recognition and predictive modeling. Importantly, the study of bacteriophages, which interact with Salmonella, offers additional layers of understanding. Phages can impact Salmonella population dynamics and evolution, and their integration into Salmonella genomics research holds promise for novel insights into pathogen control and epidemiology. This review revisits the history of Salmonella and its pathogenesis and highlights the integration of these modern methodologies in advancing our understanding of Salmonella. Full article

(This article belongs to the Special Issue Salmonella Infections: Trends and Updates)

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20 pages, 12369 KiB

Open AccessEditor’s ChoiceArticle

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 13 | Viewed by 2791

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 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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30 pages, 10878 KiB

Open AccessReview

Bacteriophage T4 Head: Structure, Assembly, and Genome Packaging

by Venigalla B. Rao, Andrei Fokine, Qianglin Fang and Qianqian Shao

Viruses 2023, 15(2), 527; https://doi.org/10.3390/v15020527 - 14 Feb 2023

Cited by 25 | Viewed by 10722

Abstract

Bacteriophage (phage) T4 has served as an extraordinary model to elucidate biological structures and mechanisms. Recent discoveries on the T4 head (capsid) structure, portal vertex, and genome packaging add a significant body of new literature to phage biology. Head structures in unexpanded and expanded conformations show dramatic domain movements, structural remodeling, and a ~70% increase in inner volume while creating high-affinity binding sites for the outer decoration proteins Soc and Hoc. Small changes in intercapsomer interactions modulate angles between capsomer planes, leading to profound alterations in head length. The in situ cryo-EM structure of the symmetry-mismatched portal vertex shows the remarkable structural morphing of local regions of the portal protein, allowing similar interactions with the capsid protein in different structural environments. Conformational changes in these interactions trigger the structural remodeling of capsid protein subunits surrounding the portal vertex, which propagate as a wave of expansion throughout the capsid. A second symmetry mismatch is created when a pentameric packaging motor assembles at the outer “clip” domains of the dodecameric portal vertex. The single-molecule dynamics of the packaging machine suggests a continuous burst mechanism in which the motor subunits adjusted to the shape of the DNA fire ATP hydrolysis, generating speeds as high as 2000 bp/s. Full article

(This article belongs to the Special Issue Phage Assembly Pathways - to the Memory of Lindsay Black)

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11 pages, 3221 KiB

Open AccessArticle

The M13 Phage Assembly Machine Has a Membrane-Spanning Oligomeric Ring Structure

by Maximilian Haase, Lutz Tessmer, Lilian Köhnlechner and Andreas Kuhn

Viruses 2022, 14(6), 1163; https://doi.org/10.3390/v14061163 - 27 May 2022

Cited by 5 | Viewed by 4894

Abstract

Bacteriophage M13 assembles its progeny particles in the inner membrane of the host. The major component of the assembly machine is G1p and together with G11p it generates an oligomeric structure with a pore-like inner cavity and an ATP hydrolysing domain. This allows the formation of the phage filament, which assembles multiple copies of the membrane-inserted major coat protein G8p around the extruding single-stranded circular DNA. The phage filament then passes through the G4p secretin that is localized in the outer membrane. Presumably, the inner membrane G1p/G11p and the outer G4p form a common complex. To unravel the structural details of the M13 assembly machine, we purified G1p from infected E. coli cells. The protein was overproduced together with G11p and solubilized from the membrane as a multimeric complex with a size of about 320 kDa. The complex revealed a pore-like structure with an outer diameter of about 12 nm, matching the dimensions of the outer membrane G4p secretin. The function of the M13 assembly machine for phage generation and secretion is discussed. Full article

(This article belongs to the Special Issue Phage Assembly Pathways - to the Memory of Lindsay Black)

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36 pages, 28617 KiB

Open AccessArticle

Evolution of Phage Tail Sheath Protein

by Peter Evseev, Mikhail Shneider and Konstantin Miroshnikov

Viruses 2022, 14(6), 1148; https://doi.org/10.3390/v14061148 - 26 May 2022

Cited by 13 | Viewed by 4694

Abstract

Sheath proteins comprise a part of the contractile molecular machinery present in bacteriophages with myoviral morphology, contractile injection systems, and the type VI secretion system (T6SS) found in many Gram-negative bacteria. Previous research on sheath proteins has demonstrated that they share common structural features, even though they vary in their size and primary sequence. In this study, 112 contractile phage tail sheath proteins (TShP) representing different groups of bacteriophages and archaeal viruses with myoviral morphology have been modelled with the novel machine learning software, AlphaFold 2. The obtained structures have been analysed and conserved and variable protein parts and domains have been identified. The common core domain of all studied sheath proteins, including viral and T6SS proteins, comprised both N-terminal and C-terminal parts, whereas the other parts consisted of one or several moderately conserved domains, presumably added during phage evolution. The conserved core appears to be responsible for interaction with the tail tube protein and assembly of the phage tail. Additional domains may have evolved to maintain the stability of the virion or for adsorption to the host cell. Evolutionary relations between TShPs representing distinct viral groups have been proposed using a phylogenetic analysis based on overall structural similarity and other analyses. Full article

(This article belongs to the Special Issue Phage Assembly Pathways - to the Memory of Lindsay Black)

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26 pages, 1474 KiB

Open AccessReview

Filamentous Bacteriophage: Biology, Phage Display and Nanotechnology Applications

by Jasna Rakonjac, Nicholas J. Bennett, Julian Spagnuolo, Dragana Gagic and Marjorie Russel

Curr. Issues Mol. Biol. 2011, 13(2), 51-76; https://doi.org/10.21775/cimb.013.051 - 18 Apr 2011

Cited by 267 | Viewed by 3697

Abstract

Filamentous bacteriophage, long and thin filaments that are secreted from the host cells without killing them, have been an antithesis to the standard view of head-and-tail bacterial killing machines. Episomally replicating filamentous phage Ff of Escherichia coli provide the majority of information about the principles and mechanisms of filamentous phage infection, episomal replication and assembly. Chromosomally- integrated "temperate" filamentous phage have complex replication and integration, which are currently under active investigation. The latter are directly or indirectly implicated in diseases caused by bacterial pathogens Vibrio cholerae, Pseudomonas aeruginosa and Neisseria meningitidis. In the first half of the review, both the Ff and temperate phage are described and compared. A large section of the review is devoted to an overview of phage display technology and its applications in nanotechnology. Full article

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