Research article

Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species

Nicolas González¹ , Stephan Heeb² , Claudio Valverde^1,4 , Elisabeth Kay^1,5 , Cornelia Reimmann¹ , Thomas Junier³ and Dieter Haas¹

¹Département de Microbiologie Fondamentale, Biophore, Université de Lausanne, CH-1015 Lausanne, Switzerland

²Institute of Infection, Immunity and Inflammation, Center for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK

³Department of Genetic Medicine and Development, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland

⁴Departamento de Ciencia y Tecnología, Programa Interacciones Biológicas, Universidad Nacional de Quilmes, Saenz Peña 352, Bernal B1876BXD, Argentina

⁵UMR5163/CNRS-UJF, Institut Jean-Roget, Grenoble, France

author email corresponding author email

BMC Genomics 2008, 9:167doi:10.1186/1471-2164-9-167

Published:	13 April 2008

Abstract

Background

Small RNAs (sRNAs) are widespread among bacteria and have diverse regulatory roles. Most of these sRNAs have been discovered by a combination of computational and experimental methods. In Pseudomonas aeruginosa, a ubiquitous Gram-negative bacterium and opportunistic human pathogen, the GacS/GacA two-component system positively controls the transcription of two sRNAs (RsmY, RsmZ), which are crucial for the expression of genes involved in virulence. In the biocontrol bacterium Pseudomonas fluorescens CHA0, three GacA-controlled sRNAs (RsmX, RsmY, RsmZ) regulate the response to oxidative stress and the expression of extracellular products including biocontrol factors. RsmX, RsmY and RsmZ contain multiple unpaired GGA motifs and control the expression of target mRNAs at the translational level, by sequestration of translational repressor proteins of the RsmA family.

Results

A combined computational and experimental approach enabled us to identify 14 intergenic regions encoding sRNAs in P. aeruginosa. Eight of these regions encode newly identified sRNAs. The intergenic region 1698 was found to specify a novel GacA-controlled sRNA termed RgsA. GacA regulation appeared to be indirect. In P. fluorescens CHA0, an RgsA homolog was also expressed under positive GacA control. This 120-nt sRNA contained a single GGA motif and, unlike RsmX, RsmY and RsmZ, was unable to derepress translation of the hcnA gene (involved in the biosynthesis of the biocontrol factor hydrogen cyanide), but contributed to the bacterium's resistance to hydrogen peroxide. In both P. aeruginosa and P. fluorescens the stress sigma factor RpoS was essential for RgsA expression.

Conclusion

The discovery of an additional sRNA expressed under GacA control in two Pseudomonas species highlights the complexity of this global regulatory system and suggests that the mode of action of GacA control may be more elaborate than previously suspected. Our results also confirm that several GGA motifs are required in an sRNA for sequestration of the RsmA protein.