Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria

BMC Genomics

Research Article

Natalia V Sernova¹  Marat D Kazanov¹  Aaron A Best²  Pavel S Novichkov³  Dmitry A Rodionov⁴  Dmitry A Ravcheev⁴ 

[1] A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127994, Moscow, Russia;Department of Biology, Hope College, 49423, Holland, MI, 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: Transcriptional regulatory network;    Comparative genomics;    Carbohydrate metabolism;    Lactobacillaceae;    Streptococcaceae;    Lactic acid bacteria;    Regulon;    Transcription factor;   

DOI  :  10.1186/1471-2164-14-94

 received in 2012-11-16, accepted in 2013-02-08,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundGenome scale annotation of regulatory interactions and reconstruction of regulatory networks are the crucial problems in bacterial genomics. The Lactobacillales order of bacteria collates various microorganisms having a large economic impact, including both human and animal pathogens and strains used in the food industry. Nonetheless, no systematic genome-wide analysis of transcriptional regulation has been previously made for this taxonomic group.ResultsA comparative genomics approach was used for reconstruction of transcriptional regulatory networks in 30 selected genomes of lactic acid bacteria. The inferred networks comprise regulons for 102 orthologous transcription factors (TFs), including 47 novel regulons for previously uncharacterized TFs. Numerous differences between regulatory networks of the Streptococcaceae and Lactobacillaceae groups were described on several levels. The two groups are characterized by substantially different sets of TFs encoded in their genomes. Content of the inferred regulons and structure of their cognate TF binding motifs differ for many orthologous TFs between the two groups. Multiple cases of non-orthologous displacements of TFs that control specific metabolic pathways were reported.ConclusionsThe reconstructed regulatory networks substantially expand the existing knowledge of transcriptional regulation in lactic acid bacteria. In each of 30 studied genomes the obtained regulatory network contains on average 36 TFs and 250 target genes that are mostly involved in carbohydrate metabolism, stress response, metal homeostasis and amino acids biosynthesis. The inferred networks can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. All reconstructed regulons are captured within the Streptococcaceae and Lactobacillaceae collections in the RegPrecise database (http://regprecise.lbl.gov).

【 授权许可】

Unknown   
© Ravcheev 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.