Identification of over ten thousand candidate structured RNAs in viruses and phages

Fremin, Brayon J.; Bhatt, Ami S.; Kyrpides, Nikos C.

doi:10.1016/j.csbj.2023.11.010

Title: Identification of over ten thousand candidate structured RNAs in viruses and phages

Journal Article · 06 November 2023 · Computational and Structural Biotechnology Journal

DOI: https://doi.org/10.1016/j.csbj.2023.11.010 · OSTI ID:2280938

Fremin, Brayon J. ^[1]; Bhatt, Ami S. ^[2]; Kyrpides, Nikos C. ^[1]

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint Genome Institute; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
Stanford University, CA (United States)

Structured RNAs play crucial roles in viruses, exerting influence over both viral and host gene expression. However, the extensive diversity of structured RNAs and their ability to act in cis or trans positions pose challenges for predicting and assigning their functions. While comparative genomics approaches have successfully predicted candidate structured RNAs in microbes on a large scale, similar efforts for viruses have been lacking. In this study, we screened over 5 million DNA and RNA viral sequences, resulting in the prediction of 10,006 novel candidate structured RNAs. These predictions are widely distributed across taxonomy and ecosystem. We found transcriptional evidence for 206 of these candidate structured RNAs in the human fecal microbiome. These candidate RNAs exhibited evidence of nucleotide covariation, indicative of selective pressure maintaining the predicted secondary structures. Our analysis revealed a diverse repertoire of candidate structured RNAs, encompassing a substantial number of putative tRNAs or tRNA-like structures, Rho-independent transcription terminators, and potentially cis-regulatory structures consistently positioned upstream of genes. In summary, our findings shed light on the extensive diversity of structured RNAs in viruses, offering a valuable resource for further investigations into their functional roles and implications in viral gene expression and pave the way for a deeper understanding of the intricate interplay between viruses and their hosts at the molecular level.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health; Sloan Foundation; Damon Runyon Clinical Investigator Award

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2280938

Journal Information:: Computational and Structural Biotechnology Journal, Journal Name: Computational and Structural Biotechnology Journal Vol. 21; ISSN 2001-0370

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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phage

Title: Identification of over ten thousand candidate structured RNAs in viruses and phages

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