The small RNA RybA regulates the aromatic amino acid biosynthesis under oxidative stress

The small RNA RybA regulates the aromatic amino acid biosynthesis under oxidative stress

Kirstin Gerstle¹, Kristin Klätschke² and Nicolas Piganeau¹

¹University of Hamburg, Institute of Biochemistry and Molecular Biology, Group Prof. Hahn,

Martin-Luther-King-Platz 6, 20146 Hamburg , Germany

²University Medical Center Hamburg, Department of Clinical Chemistry/Central Laboratories, Eppendorf Martinistr. 52, 20246 Hamburg, Germany

Abstract

In bacteria the adaptive response to extern stimuli is often regulated by small RNAs (sRNA).Most act through base pairing with a target mRNA thereby regulating translation and/or mRNA stability. Alternatively they also may sequester a target protein and inhibit its function. No function could be attributed to 40 out of the 79 sRNAs confirmed in E. coli to date. We set out to decipher the function of one of these orphan sRNAs. RybA was discovered in 2001 by Wassarman et al. by comparative genomic. It is conserved between Escherichia coli, Salmonella typhimurium and Klebsiella pneumonia. During this study the authors observed that RybA does not seem to bind to Hfq, a cofactor required for most antisense sRNAs for function. Furthermore RybA seems to be present in at least two forms of roughly 300 and 200 nt (Wassarman et al. Genes Dev. 2001; 15(13):1637-1651).

We further characterized RybA and determined its expression pattern under different growth conditions and its 5’and 3’ ends. Using microarray and northern analysis we show that under oxidative stress RybA regulates key genes in the TyrR and CusR regulons, involved in the metabolism of aromatic amino acids and copper transport respectively. Former experiments by Yang et .al. indicate that the CusR regulon might be under the control of TyrR, presumably the direct target of RybA (Yang J et al. J Bacteriol. 2007; 189(16):6080-4.).

The physiological implications of this regulation remain speculative. The down regulation of aromatic amino acids synthesis might lead to an increase in the cellular concentration of chorismate. Chorismate is also a precursor of ubiquinone, which is involved in the defense against oxidative stress in the cytoplasmic membrane.

We are currently investigating the genetic pathway underlying the regulation of the TyrR regulon by RybA.