CrfA, a small noncoding RNA regulator of adaptation to carbon starvation in Caulobacter crescentus

J Bacteriol. 2010 Sep;192(18):4763-75. doi: 10.1128/JB.00343-10. Epub 2010 Jul 2.

Abstract

Small noncoding regulatory RNAs (sRNAs) play a key role in the posttranscriptional regulation of many bacterial genes. The genome of Caulobacter crescentus encodes at least 31 sRNAs, and 27 of these sRNAs are of unknown function. An overexpression screen for sRNA-induced growth inhibition along with sequence conservation in a related Caulobacter species led to the identification of a novel sRNA, CrfA, that is specifically induced upon carbon starvation. Twenty-seven genes were found to be strongly activated by CrfA accumulation. One-third of these target genes encode putative TonB-dependent receptors, suggesting CrfA plays a role in the surface modification of C. crescentus, facilitating the uptake of nutrients during periods of carbon starvation. The mechanism of CrfA-mediated gene activation was investigated for one of the genes predicted to encode a TonB-dependent receptor, CC3461. CrfA functions to stabilize the CC3461 transcript. Complementarity between a region of CrfA and the terminal region of the CC3461 5'-untranslated region (5'-UTR) and also the behavior of a deletion of this region and a site-specific base substitution and a 3-base deletion in the CrfA complementary sequence suggest that CrfA binds to a stem-loop structure upstream of the CC3461 Shine-Dalgarno sequence and stabilizes the transcript.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 5' Untranslated Regions / genetics
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Blotting, Northern
  • Carbon / metabolism
  • Caulobacter crescentus / genetics
  • Caulobacter crescentus / metabolism*
  • Gene Expression Regulation, Bacterial / genetics
  • Gene Expression Regulation, Bacterial / physiology
  • Molecular Sequence Data
  • Nucleic Acid Amplification Techniques
  • Oligonucleotide Array Sequence Analysis
  • Polymerase Chain Reaction
  • Promoter Regions, Genetic / genetics
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism*
  • RNA, Untranslated / genetics
  • RNA, Untranslated / metabolism*
  • Sequence Homology, Amino Acid

Substances

  • 5' Untranslated Regions
  • Bacterial Proteins
  • RNA, Bacterial
  • RNA, Untranslated
  • Carbon