dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42

PLoS One. 2015 Nov 5;10(11):e0142002. doi: 10.1371/journal.pone.0142002. eCollection 2015.

Abstract

Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments. In order to better understand the molecular mechanisms of bacteria-plant symbiosis, we have systematically analyzed the primary transcriptome of strain FZB42 grown under rhizosphere-mimicking conditions using differential RNA sequencing (dRNA-seq). Our analysis revealed 4,877 transcription start sites for protein-coding genes, identified genes differentially expressed under different growth conditions, and corrected many previously mis-annotated genes. We also identified a large number of riboswitches and cis-encoded antisense RNAs, as well as trans-encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus. Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacillus / genetics*
  • Bacterial Proteins / genetics
  • Gene Expression Regulation, Bacterial / genetics
  • Genome, Bacterial / genetics*
  • Plant Roots / microbiology*
  • Plants / microbiology*
  • RNA, Untranslated / genetics*
  • Rhizobium / genetics*
  • Rhizosphere
  • Sequence Analysis, RNA / methods
  • Symbiosis / genetics
  • Transcription Initiation Site / physiology
  • Transcriptome / genetics

Substances

  • Bacterial Proteins
  • RNA, Untranslated