Viral Small Terminase: A Divergent Structural Framework for a Conserved Biological Function

Lokareddy, Ravi K.; Hou, Chun-Feng David; Li, Fenglin; Yang, Ruoyu; Cingolani, Gino

doi:10.3390/v14102215

Cited by 20 publications

(13 citation statements)

References 120 publications

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“…Perhaps GpsA and GpsB function together or separately as a PLE-specific TerS (Figure 6C). In line with this prediction, bioinformatic analysis hints that GpsB may have a DNA-binding motif, a feature expected of TerS proteins (31). Alternatively, GpsA and/or GpsB could modulate Gpi’s binding to TerL, selectively removing Gpi to allow ICP1’s TerS to package PLE genomes (Figure 6C).…”

Section: Discussionmentioning

confidence: 82%

“…Satellites interfere with late gene expression (18,32,50), inhibit phage-sized capsid assembly (12,(51)(52)(53), and interfere with genome packaging (7)(8)(9). Interestingly, despite the notable structural dissimilarity of TerSs (31), other phage satellites target phage TerSs. In fact, this variable target can limit the satellites' ability to interfere with other phages (8).…”

Section: Data Availabilitymentioning

confidence: 99%

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A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread

Boyd,

Seed

2024

Preprint

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ICP1, a lytic bacteriophage of Vibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs dependence on ICP1s DNA replication machinery, and virion components results in inhibition of ICP1s lifecycle. PLEs are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLEs indiscriminate genome packaging inhibitor. Gpi binds to ICP1s large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpis negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1s pac site as a backup strategy to ensure genome packaging. PLEs pac site mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA, and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1s lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.

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Section: Discussionmentioning

confidence: 82%

Section: Data Availabilitymentioning

confidence: 99%

A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread

Boyd,

Seed

2024

Preprint

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“…PhageTerm analysis for the genome ends detected long direct terminal repeats (2298 bp). All three phage genomes were dsDNA ( Figure 5 ), which were confirmed by cutting with restriction endonucleases, and included ORFs encoding small and large terminase subunits, which are hallmark genes for tailed dsDNA bacteriophages that package their genomes into a preformed procapsid [ 29 , 30 ]. Although Lumi is a unique phage, ORF searches with Blastp suggested that Lumi shares some similar ORFs with the Achromobacter phage JWF, a siphovirus originating from sewage [ 31 , 32 ].…”

Section: Resultsmentioning

confidence: 99%

Three Phages from a Boreal Lake during Ice Cover Infecting Xylophilus, Caulobacter, and Polaromonas Species

Laanto

Oksanen

2023

Viruses

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Although the important role of microbes in freshwater is well understood, studies on phage–host systems in such environments during ice cover are completely lacking. Here, we describe the isolation and characterization of three new bacteriophages infecting Xylophilus sp., Caudobacter sp., and Polaromonas sp. from freshwater samples taken under the ice cover of Lake Konnevesi, Finland. Lumi, Kuura, and Tiera bacteriophages have tailed icosahedral virions and double-stranded DNA. Lumi is a siphophage with a genome of 80,496 bp, and Kuura and Tiera are podophages, and their genomes are 43,205 and 45,327 bp in length, resembling viruses in the class Caudoviricetes. Their host ranges were very limited among the winter-isolated bacterial strains from Konnevesi, each infecting only their own hosts. They can infect efficiently at 4 °C, showing that they are adapted to living in lake water under ice cover. Analysis of the viral genome sequences showed that a significant number of the gene products of each virus are unique, indicating that there is unexplored viral diversity in freshwaters. To our knowledge, Lumi and Tiera are the first phages isolated on the Xylophilus sp. and Polaromonas sp. strains, allowing their exploitation in further studies of freshwater bacterial–phage interactions.

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“…An interaction with gp17 through its C-terminal domain would lead to the formation of TerS-TerL complex that then proceeds with DNA cleavage and insertion of DNA end into the portal channel to initiate packaging. Though models have been proposed in which DNA passes through the TerS channel and may even be threaded during DNA translocation, the evidence is not consistent with such models [ 88 , 89 ]. Mutations of residues that line the channel, including partial or complete deletion of one of the channel helices, do not lead to loss of DNA binding in vitro or cause lethality in vivo.…”

Section: Genome Packagingmentioning

confidence: 99%

Bacteriophage T4 Head: Structure, Assembly, and Genome Packaging

Rao

Fokine

Fang

et al. 2023

Viruses

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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.

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Viral Small Terminase: A Divergent Structural Framework for a Conserved Biological Function

Cited by 20 publications

References 120 publications

A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread

A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread

Three Phages from a Boreal Lake during Ice Cover Infecting Xylophilus, Caulobacter, and Polaromonas Species

Bacteriophage T4 Head: Structure, Assembly, and Genome Packaging

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