Exploring biogenesis and functions of 3'UTR-derived small regulatory RNAs

• Applicant: Professor Dr. Jörg Vogel
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms
• Term: from 2015 to 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 278016524

• Final Report Year: 2020

Final Report Abstract

Our discoveries with the CpxQ and SdhX sRNAs have very robustly shown that the 3′ regions of mRNA genes constitute a large reservoir from which the Hfq network recruits new sRNAs to rewire gene expression at the post-transcriptional level. Through our studies of these two 3’UTR-derived sRNAs, we have firmly established the general principle of their biogenesis by RNase E and that they fulfill as important and conserved functions in bacterial cells as do sRNAs transcribed from otherwise “empty” intergenic regions. The short SdhX sRNA variant identified by us lends itself to being exploited both, as a molecular platform for functional seed regions and as a prime candidate for the outstanding high-resolution structure of Hfq with a sRNA.

Publications

• (2020) Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica. EcoSal Plus 9 (1) 1-24
  Hör, Jens; Matera, Gianluca; Vogel, Jörg; Gottesman, Susan; Storz, Gisela
  (See online at https://doi.org/10.1128/ecosalplus.ESP-0030-2019)
• (2016) A 3’UTR derived small RNA provides the regulatory noncoding arm of the inner membrane stress response. Molecular Cell 61:352-363
  Chao Y, Vogel J
  (See online at https://doi.org/10.1016/j.molcel.2015.12.023)
• (2017) Molecular mechanism of mRNA repression in trans by a ProQ-dependent small RNA. EMBO Journal 36(8):1029-1045
  Smirnov A, Wang C, Drewry LL, Vogel J
  (See online at https://doi.org/10.15252/embj.201696127)
• (2019) Functional expansion of a TCA cycle operon mRNA by a 3’ end-derived small RNA. Nucleic Acids Research 47(4):2075-2088
  Miyakoshi M, Matera G, Maki K, Sone Y, Vogel J
  (See online at https://doi.org/10.1093/nar/gky1243)
• (2019) The major RNA-binding protein ProQ impacts virulence gene expression in Salmonella Typhimurium. mBio 10(1) pii:e02504-18
  Westermann AJ, Venturini E, Sellin ME, Förstner KU, Hardt WD, Vogel J
  (See online at https://doi.org/10.1128/mBio.02504-18)
• (2020) The conserved 3’ UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration. Nucleic Acids Research 48(4):2126–2143
  Wang C, Chao Y, Matera G, Gao Q, Vogel J
  (See online at https://doi.org/10.1093/nar/gkz1168)