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.


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


  • Bacterial Proteins
  • RNA, Untranslated

Grant support

The financial support by the National Natural Science Foundation of China (No. 31100081) and Scientific Research Foundation of Nanjing Forestry University for Introduction of High Level Talents (YJ2012-03) is gratefully acknowledged, as well as the financial support given by the Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions. This study was further supported by the Natural Science Foundation of Jiangsu Province (No. BK20151514).