Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria

BMC Genomics

Research Article

Marat D Kazanov¹  Eric I Sun²  Milton H Saier²  Pavel S Novichkov³  Dmitry A Rodionov⁴  Semen A Leyn⁴ 

[1] A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127994, Moscow, Russia;Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, 92093, La Jolla, CA, USA;Lawrence Berkeley National Laboratory, 94710, Berkeley, CA, USA;Sanford-Burnham Medical Research Institute, 92037, La Jolla, CA, USA;A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127994, Moscow, Russia;

关键词: RNA regulatory motif;    Riboswitch;    Regulon;    Gene function;    Comparative genomics;    Bacteria;   

DOI  :  10.1186/1471-2164-14-597

 received in 2013-05-23, accepted in 2013-08-30,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundIn silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels.An increasing number of riboswitches and other cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis.ResultsA comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs (including thiamin pyrophosphate and cobalamin riboswitches that control the cofactor metabolism) are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations.ConclusionsThe reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. The obtained genome-wide collection of reference RNA motif regulons is available in the RegPrecise database (http://regprecise.lbl.gov/).

【 授权许可】

Unknown   
© Sun et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.