Bacteriophage T4 Head: Structure, Assembly, and Genome Packaging

Rao, Venigalla B.; Fokine, Andrei; Fang, Qianglin; Shao, Qianqian

doi:10.3390/v15020527

Cited by 19 publications

(14 citation statements)

References 142 publications

(254 reference statements)

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“…We hypothesize that this may result from stabilizing effects that Hoc potentially exerts on gp23 hexamers, particularly under external pressure. These observations may shed new light on the possible role of Hoc—previously considered only marginally involved in providing stability—again highlighting how different elements in the complex structure of T4 capsid contribute to its overall fitness: while Soc trimers form a molecular cage that may reinforce the phage head against the internal pressure of tightly packed genetic material ( 10 , 30 ), resisting external pressure appears to require a different mechanism. External pressure and flow conditions may to some extent resemble gut conditions in the area of intensive peristaltic movements, but this problem requires further studies.…”

Section: Discussionmentioning

confidence: 93%

“…While gp23 hexamers form the surface lattice, gp24 builds 11 pentameric vertices of the bacteriophage T4 capsid. These two proteins share ~21% amino acid sequence identity ( 6 ) and 31% sequence similarity ( 29 ) and gp24 is postulated to be a gp23 derivative, originating from a gene duplication and subsequent sequence divergence and optimization ( 30 ). Moreover, specialized vertex protein likely is a relatively recent evolutionary addition, given the fact that spontaneously occurring specific mutations in gp23 quite easily allow for a functional substitution of gp24 ( 7 ), bypassing the otherwise lethal effect of gp24 deficiencies.…”

Section: Discussionmentioning

confidence: 99%

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Evolution of the T4 phage virion is driven by selection pressure from non-bacterial factors

Majewska,

Miernikiewicz,

Szymczak

et al. 2023

Microbiol Spectr

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Bacteriophages colonize animal and human bodies, propagating on sensitive bacteria that are symbionts, commensals, or pathogens of animals and humans. T4-like phages are dependent on abundant symbionts such as Escherichia coli , commonly present in animal and human gastrointestinal (GI) tracts. Bacteriophage T4 is one of the most complex viruses, and its intricate structure, particularly the capsid head protecting the phage genome, likely contributes substantially to the overall phage fitness in diverse environments. We investigated how individual head proteins—gp24, Hoc, and Soc—affect T4 phage survival under pressure from non-bacterial factors. We constructed a panel of T4 phage variants defective in these structural proteins: T4∆Soc, T4∆24byp24, T4∆Hoc∆Soc, T4∆Hoc∆24byp24, T4∆Soc∆24byp24, and T4∆Hoc∆Soc∆24byp24 (byp = bypass). These variants were investigated for their sensitivity to selected environmental conditions relevant to the microenvironment of the GI tract, including pH, temperature, and digestive enzymes. The simple and “primitive” structure of the phage capsid (∆24byp24) was significantly less stable at low pH and more sensitive to inactivation by digestive enzymes, and the simultaneous lack of gp24 and Soc resulted in a notable decrease in phage activity at 37°C. Gp24 was also found to be highly resistant to thermal and chemical denaturation. Thus, gp24, which was acquired relatively late in evolution, seems to play a key role in T4 withstanding environmental conditions, including those related to the animal/human GI tract, and Soc is a molecular glue that enhances this protective effect. IMPORTANCE Bacteriophages are important components of animal and human microbiota, particularly in the gastrointestinal tract, where they dominate the viral community and contribute to shaping microbial balance. However, interactions with bacterial hosts are not the only element of the equation in phage survival—phages inhabiting the GI tract are constantly exposed to increased temperature, pH fluctuations, or digestive enzymes, which raises the question of whether and how the complex structure of phage capsids contributes to their persistence in the specific microenvironment of human/animal bodies. Here we address this phage-centric perspective, identifying the role of individual head proteins in T4 phage survival in GI tract conditions. The selection pressure driving the evolution of T4-like phages could have come from the external environment that affects phage virions with increased temperature and variable pH; it is possible that in the local microenvironment along the GI tract, the phage benefits from stability-protecting proteins.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Evolution of the T4 phage virion is driven by selection pressure from non-bacterial factors

Majewska,

Miernikiewicz,

Szymczak

et al. 2023

Microbiol Spectr

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“…Assembly of the tails and heads of Myoviridae phages proceeds via independent pathways and are joined together to form infectious virions [ 43 ]. Bacteriophage T4 is the most thoroughly investigated member of the Myoviridae family, whose assembly pathway is well-established [ 11 , 44 ]. Based on the structural similarity between the XM1 and T4 virions, we propose the following assembly pathway for phage XM1, which is analogous to that of T4.…”

Section: Resultsmentioning

confidence: 99%

“…Once the prohead is assembled, the protease digests the major scaffolding protein and cleaves off the N-terminal region of MCP [ 43 , 44 ]. The degradation products escape from the prohead’s interior to liberate a place for genomic DNA.…”

Section: Resultsmentioning

confidence: 99%

Structure of Vibrio Phage XM1, a Simple Contractile DNA Injection Machine

Wang,

Fokine,

Guo

et al. 2023

Viruses

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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.

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“…Procapsids (virion precursors without DNA) are assembled from the dodecameric portal via the addition of MCP hexons and pentons [38]. This process is promoted by scaffolding proteins that have been proposed to establish bridges between capsid MCPs [39,40].…”

Section: The Procapsid Scaffolding Proteinmentioning

confidence: 99%

Partial Atomic Model of the Tailed Lactococcal Phage TP901-1 as Predicted by AlphaFold2: Revelations and Limitations

Mahony,

Goulet,

van Sinderen

et al. 2023

Viruses

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Bacteria are engaged in a constant battle against preying viruses, called bacteriophages (or phages). These remarkable nano-machines pack and store their genomes in a capsid and inject it into the cytoplasm of their bacterial prey following specific adhesion to the host cell surface. Tailed phages possessing dsDNA genomes are the most abundant phages in the bacterial virosphere, particularly those with long, non-contractile tails. All tailed phages possess a nano-device at their tail tip that specifically recognizes and adheres to a suitable host cell surface receptor, being proteinaceous and/or saccharidic. Adhesion devices of tailed phages infecting Gram-positive bacteria are highly diverse and, for the majority, remain poorly understood. Their long, flexible, multi-domain-encompassing tail limits experimental approaches to determine their complete structure. We have previously shown that the recently developed protein structure prediction program AlphaFold2 can overcome this limitation by predicting the structures of phage adhesion devices with confidence. Here, we extend this approach and employ AlphaFold2 to determine the structure of a complete phage, the lactococcal P335 phage TP901-1. Herein we report the structures of its capsid and neck, its extended tail, and the complete adhesion device, the baseplate, which was previously partially determined using X-ray crystallography.

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Bacteriophage T4 Head: Structure, Assembly, and Genome Packaging

Cited by 19 publications

References 142 publications

Evolution of the T4 phage virion is driven by selection pressure from non-bacterial factors

Evolution of the T4 phage virion is driven by selection pressure from non-bacterial factors

Structure of Vibrio Phage XM1, a Simple Contractile DNA Injection Machine

Partial Atomic Model of the Tailed Lactococcal Phage TP901-1 as Predicted by AlphaFold2: Revelations and Limitations

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