Identification of Structural and Morphogenesis Genes of Pseudoalteromonas phage RIO-1 and Placement within the Evolutionary History of Podoviridae

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HMM–HMM comparisons find homologous virion proteins across diverse phages

Text by Stephen C. Hardies and Byung Cheol Cho


Pseudoalteromonas phage φRIO1 is a marine bacteriophage isolated as part of a project to improve the understanding of the diversity of phages in the marine ecosystem. Initial characterization indicated that it has classic podoviral morphology but by sequence analysis it belongs to a thinly populated branch of Podoviridae only anciently related to T7 and other better known phages. Proteomic analysis by mass spectrometry and advanced bioinformatic analysis was conducted to clarify the relationship of φRIO1 virion proteins to T7. Homologs were established for all of the head, tail, and internal virion proteins of T7, each related to T7 at some ancient time. This result clarified that the peculiar strategy of T7 to extend a transient tail structure, sometimes called an injection needle, at the time of infection was an ancient invention. Interestingly, the same methodology identified additional homologs of these structures throughout most of Podoviridae.


One of us, Stephen C. Hardies, characterized one of the φRIO1 relatives, VpV262, about 10 years ago. It was necessary at the time to use PSIBLAST together with limiting the search database based on posited synteny to establish homology between VpV262 head structure proteins and those of T7. The most that could be said of the tail structure proteins was that there was an array of genes of suitable size in the expected genomic position. Since the tail defines that a phage is a podovirus, it has been a goal since then to break through the divergence barrier and understand the relationship of the tail proteins between diverse podoviruses. The reduced database strategy, with more related phages and an improved profile method in the form of HHPRED, has now accomplished that goal. While relating the tail structures of φRIO1- and T7-related phages, that approach went further to find homologs in other diverged branches of Podoviridae. This has made it possible to collate structural and functional evidence gained from different phages into a single model, which can be envisioned as having components conserved from the initial invention of the short tail with injection needle, and other components that tend to undergo modification. Perhaps most surprisingly, the protein comprising the tip of the injection needle has been modified to inject into the cytoplasm a virion RNA polymerase in some podoviruses, and a DNA modifying activity in others. Probably not coincidentally, both of those activities may act on the phage DNA during entry.



Figure legend

SDS-PAGE of φRIO-1 virions indicating gel position of specific φRIO-1 proteins detected by mass spectrometry. (A) Molecular weight markers. (B) φRIO-1 virions. The slice where maximum number of spectra assigned for each gene product is indicated.

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Left: Stephen C. Hardies. Right: Byung Cheol Cho.

About the research

Identification of Structural and Morphogenesis Genes of Pseudoalteromonas phage RIO-1 and Placement within the Evolutionary History of Podoviridae

Stephen C. Hardies, Julie A. Thomas, Lindsay Black, Susan T. Weintraub, Chung Y. Hwang, Byung C. Cho

Virology, Volume 489, February 2016, Pages 116–127