A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa

Kulkarni, Prajna R.; Jia, Tao; Kuehne, Sarah H.; Kerkering, Thomas M.; Morris, Elizabeth R.; Searle, Mark S.; Heeb, Stephan; Rao, Jayasimha; Kulkarni, Rahul V.

Abstract

CsrA/RsmA homologs are an extensive family of ribonucleic acid (RNA)-binding proteins that function as global post-transcriptional regulators controlling important cellular processes such as secondary metabolism, motility, biofilm formation and the production and secretion of virulence factors in diverse bacterial species. While direct messenger RNA binding by CsrA/RsmA has been studied in detail for some genes, it is anticipated that there are numerous additional, as yet undiscovered, direct targets that mediate its global regulation. To assist in the discovery of these targets, we propose a sequence-based approach to predict genes directly regulated by these regulators. In this work, we develop a computer code (CSRA TARGET) implementing this approach, which leads to predictions for several novel targets in Escherichia coli and Pseudomonas aeruginosa. The predicted targets in other bacteria, specifically Salmonella enterica serovar Typhimurium, Pectobacterium carotovorum and Legionella pneumophila, also include global regulators that control virulence in these pathogens, unraveling intricate indirect regulatory roles for CsrA/RsmA.We have experimentally validated four predicted RsmA targets in P. aeruginosa. The sequence-based approach developed in this work can thus lead to several testable predictions for direct targets of CsrA homologs, thereby complementing and accelerating efforts to unravel global regulation by this important family of proteins.

Citation

Kulkarni, P. R., Jia, T., Kuehne, S. H., Kerkering, T. M., Morris, E. R., Searle, M. S., Heeb, S., Rao, J., & Kulkarni, R. V. (in press). A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa. Nucleic Acids Research, 42(11), https://doi.org/10.1093/nar/gku309

• Journal Article Type: Article
• Acceptance Date: Mar 28, 2014
• Online Publication Date: Apr 29, 2014
• Deposit Date: Jul 11, 2016
• Publicly Available Date: Jul 11, 2016
• Journal: Nucleic Acids Research
• Print ISSN: 0305-1048
• Electronic ISSN: 1362-4962
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 42
• Issue: 11
• DOI: https://doi.org/10.1093/nar/gku309
• Public URL: https://nottingham-repository.worktribe.com/output/726454
• Publisher URL: http://nar.oxfordjournals.org/content/42/11/6811
• Contract Date: Jul 11, 2016