Modification of the RpoS network with a synthetic small RNA

Nucleic Acids Res. 2013 Sep;41(17):8332-40. doi: 10.1093/nar/gkt604. Epub 2013 Jul 9.

Abstract

Translation of the sigma factor RpoS is activated by DsrA, RprA and ArcA, three small non-coding sRNAs (sRNA) that expose the ribosome-binding site (RBS) by opening up an inhibitory loop. In the RpoS network, no sRNAs have been found to pair with the RBS, a most common sRNA target site in bacteria. Here, we generate Ribo-0, an artificial sRNA, which represses rpoS translation by pairing with the RBS. Ribo-0 bypasses the RNA chaperon Hfq but requires the RBS to be loosely blocked. Ribo-0 interacts with DsrA and reshapes the RpoS network. Specifically, in the intact RpoS network, DsrA activates rpoS translation by freeing up the RBS. In the modified RpoS network where Ribo-0 is introduced, the DsrA-caused RBS exposure facilitates Ribo-0 binding, thereby strengthening Ribo-0 inhibition. In other words, Ribo-0 changes DsrA from an activator to an accomplice for repressing rpoS translation. This work presents an artificial mechanism of rpoS regulation, reveals mutual effects of native and synthetic players and demonstrates genetic context-dependency of their functions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Gene Expression Regulation*
  • Gene Library
  • Gene Regulatory Networks
  • Host Factor 1 Protein / metabolism
  • Protein Biosynthesis*
  • RNA, Messenger / metabolism
  • RNA, Small Untranslated / chemistry
  • RNA, Small Untranslated / metabolism*
  • Sigma Factor / genetics*
  • Sigma Factor / metabolism

Substances

  • Bacterial Proteins
  • Host Factor 1 Protein
  • RNA, Messenger
  • RNA, Small Untranslated
  • Sigma Factor
  • sigma factor KatF protein, Bacteria