Revisiting intrinsic transcription termination in mycobacteria: U-tract downstream of secondary structure is dispensable for termination

Biochem Biophys Res Commun. 2020 Jan 29;522(1):226-232. doi: 10.1016/j.bbrc.2019.11.062. Epub 2019 Nov 20.

Abstract

In Escherichia coli, G/C-rich hairpin structure followed by a U-tract in the 3' region of the nascent RNA are crucial determinants for intrinsic or factor independent transcription termination. In mycobacteria, there is a scarcity of such intrinsic terminators. However, secondary structures having G/C-rich stem devoid of any U's or with suboptimal U-tracts were identified earlier as terminators and found to be functional both in vitro and in vivo. Two different observations - that a mycobacterial RNA polymerase (RNAP) does not function at intrinsic terminators devoid of U-tracts and the identification of an altogether new motif for termination in mycobacteria necessitated re-examining a number of putative terminators for their function as terminators. When these in silico identified non-canonical terminators were subjected to experimental validation, they were found to dissociate RNA from the elongating RNAP. Termination is observed when the U-tracts were reduced, or totally absent both in vitro and in vivo. Our results, thus indicate that the presence of U-tract following the G/C-rich stem in an intrinsic terminator may not be an essential determinant for transcription termination in mycobacteria.

Keywords: Gene expression; Intrinsic termination; Mycobacteria; RNA polymerase; Transcription.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Gene Expression Regulation, Bacterial*
  • Humans
  • Mycobacterium / chemistry
  • Mycobacterium / genetics*
  • Mycobacterium Infections / microbiology
  • Nucleic Acid Conformation
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / genetics*
  • Terminator Regions, Genetic
  • Transcription, Genetic*

Substances

  • RNA, Bacterial