A sequence-based approach for prediction of CsrA/RsmA targets in bacteria with experimental validation in Pseudomonas aeruginosa.
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.
Department of Physics, University of Massachusetts Boston, Boston, MA 02125, USA.
Prajna R
PR
Kulkarni
Social Cognitive Networks Academic Research Center, and Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
Tao
T
Jia
School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK.
Sarah A
SA
Kuehne
Section of Infectious Diseases, Carilion Clinic/Virginia Tech Carilion School of Medicine/Jefferson College of Health Sciences, Roanoke, VA 24013, USA.
Thomas M
TM
Kerkering
School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK.
Elizabeth R
ER
Morris
School of Chemistry, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK.
Mark S
MS
Searle
School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK rahul.kulkarni@umb.edu.
Stephan
S
Heeb
Section of Infectious Diseases, Carilion Clinic/Virginia Tech Carilion School of Medicine/Jefferson College of Health Sciences, Roanoke, VA 24013, USA rahul.kulkarni@umb.edu.
Jayasimha
J
Rao
Department of Physics, University of Massachusetts Boston, Boston, MA 02125, USA rahul.kulkarni@umb.edu.
Rahul V
RV
Kulkarni
D000465:Algorithms; D001665:Binding Sites; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D012097:Repressor Proteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods*
C093587:CsrA protein, E coli; D029968:Escherichia coli Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D012097:Repressor Proteins