Global repositioning of transcription start sites in a plant-fermenting bacterium

Nat Commun. 2016 Dec 16:7:13783. doi: 10.1038/ncomms13783.

Abstract

Bacteria respond to their environment by regulating mRNA synthesis, often by altering the genomic sites at which RNA polymerase initiates transcription. Here, we investigate genome-wide changes in transcription start site (TSS) usage by Clostridium phytofermentans, a model bacterium for fermentation of lignocellulosic biomass. We quantify expression of nearly 10,000 TSS at single base resolution by Capp-Switch sequencing, which combines capture of synthetically capped 5' mRNA fragments with template-switching reverse transcription. We find the locations and expression levels of TSS for hundreds of genes change during metabolism of different plant substrates. We show that TSS reveals riboswitches, non-coding RNA and novel transcription units. We identify sequence motifs associated with carbon source-specific TSS and use them for regulon discovery, implicating a LacI/GalR protein in control of pectin metabolism. We discuss how the high resolution and specificity of Capp-Switch enables study of condition-specific changes in transcription initiation in bacteria.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / genetics*
  • Bacteria / metabolism
  • Clostridium / genetics
  • Clostridium / metabolism
  • Fermentation*
  • Gene Expression Profiling
  • Genes, Bacterial / genetics
  • Pectins / metabolism
  • Plants / microbiology*
  • RNA, Messenger / genetics
  • Regulon / genetics
  • Sequence Analysis, DNA / methods
  • Transcription Initiation Site*
  • Transcription, Genetic

Substances

  • RNA, Messenger
  • Pectins