Identification of over ten thousand candidate structured RNAs in viruses and phages
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...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023004257 |
| _version_ | 1797384088292687872 |
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| author | Brayon J. Fremin Ami S. Bhatt Nikos C. Kyrpides |
| author_facet | Brayon J. Fremin Ami S. Bhatt Nikos C. Kyrpides |
| author_sort | Brayon J. Fremin |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T21:30:27Z |
| format | Article |
| id | doaj.art-be9567633c1e4d73b698bdfa81e4fbfa |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:30:27Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-be9567633c1e4d73b698bdfa81e4fbfa2023-12-21T07:32:30ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012156305639Identification of over ten thousand candidate structured RNAs in viruses and phagesBrayon J. Fremin0Ami S. Bhatt1Nikos C. Kyrpides2Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Corresponding authors at: Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.Blood and Marrow Transplantation) and Genetics, Stanford University, Stanford, CA, USA; Department of Medicine (Hematology, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USADepartment of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Lead Contact, USA; Corresponding authors at: Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.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.http://www.sciencedirect.com/science/article/pii/S2001037023004257PhageCandidate structured RNAsComparative genomics |
| spellingShingle | Brayon J. Fremin Ami S. Bhatt Nikos C. Kyrpides Identification of over ten thousand candidate structured RNAs in viruses and phages Computational and Structural Biotechnology Journal Phage Candidate structured RNAs Comparative genomics |
| title | Identification of over ten thousand candidate structured RNAs in viruses and phages |
| title_full | Identification of over ten thousand candidate structured RNAs in viruses and phages |
| title_fullStr | Identification of over ten thousand candidate structured RNAs in viruses and phages |
| title_full_unstemmed | Identification of over ten thousand candidate structured RNAs in viruses and phages |
| title_short | Identification of over ten thousand candidate structured RNAs in viruses and phages |
| title_sort | identification of over ten thousand candidate structured rnas in viruses and phages |
| topic | Phage Candidate structured RNAs Comparative genomics |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023004257 |
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