High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs

DSpace/Manakin Repository

High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs

Citable link to this page


Title: High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs
Author: Teonadi, Hidayat; Livny, Miron; Livny, Jonathan; Waldor, Matthew K

Note: Order does not necessarily reflect citation order of authors.

Citation: Livny, Jonathan, Hidayat Teonadi, Miron Livny, and Matthew K. Waldor. 2008. High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS ONE 3(9): e3197.
Full Text & Related Files:
Abstract: Background: Diverse bacterial genomes encode numerous small non-coding RNAs (sRNAs) that regulate myriad biological processes. While bioinformatic algorithms have proven effective in identifying sRNA-encoding loci, the lack of tools and infrastructure with which to execute these computationally demanding algorithms has limited their utilization. Genome-wide predictions of sRNA-encoding genes have been conducted in less than 3% of all sequenced bacterial strains, leading to critical gaps in current annotations. The relative paucity of genome-wide sRNA prediction represents a critical gap in current annotations of bacterial genomes and has limited examination of larger issues in sRNA biology, such as sRNA evolution. Methodology/Principal Findings: We have developed and deployed SIPHT, a high throughput computational tool that utilizes workflow management and distributed computing to effectively conduct kingdom-wide predictions and annotations of intergenic sRNA-encoding genes. Candidate sRNA-encoding loci are identified based on the presence of putative Rho-independent terminators downstream of conserved intergenic sequences, and each locus is annotated for several features, including conservation in other species, association with one of several transcription factor binding sites and homology to any of over 300 previously identified sRNAs and cis-regulatory RNA elements. Using SIPHT, we conducted searches for putative sRNA-encoding genes in all 932 bacterial replicons in the NCBI database. These searches yielded nearly 60% of previously confirmed sRNAs, hundreds of previously annotated cis-encoded regulatory RNA elements such as riboswitches, and over 45,000 novel candidate intergenic loci. Conclusions/Significance: Candidate loci were identified across all branches of the bacterial evolutionary tree, suggesting a central and ubiquitous role for RNA-mediated regulation among bacterial species. Annotation of candidate loci by SIPHT provides clues into the potential biological function of thousands of previously confirmed and candidate regulatory RNAs and affords new insights into the evolution of bacterial riboregulation.
Published Version: doi://10.1371/journal.pone.0003197
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527527/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:10198688
Downloads of this work:

Show full Dublin Core record

This item appears in the following Collection(s)


Search DASH

Advanced Search