Identification and validation of sRNAs in Edwardsiella tarda S08

PLoS One. 2017 Mar 7;12(3):e0172783. doi: 10.1371/journal.pone.0172783. eCollection 2017.

Abstract

Bacterial small non-coding RNAs (sRNAs) are known as novel regulators involved in virulence, stress responsibility, and so on. Recently, a lot of new researches have highlighted the critical roles of sRNAs in fine-tune gene regulation in both prokaryotes and eukaryotes. Edwardsiella tarda (E. tarda) is a gram-negative, intracellular pathogen that causes edwardsiellosis in fish. Thus far, no sRNA has been reported in E. tarda. The present study represents the first attempt to identify sRNAs in E. tarda S08. Ten sRNAs were validated by RNA sequencing and quantitative PCR (qPCR). ET_sRNA_1 and ET_sRNA_2 were homolous to tmRNA and GcvB, respectively. However, the other candidate sRNAs have not been reported till now. The cellular abundance of 10 validated sRNA was detected by qPCR at different growth phases to monitor their biosynthesis. Nine candidate sRNAs were expressed in the late-stage of exponential growth and stationary stages of growth (36~60 h). And the expression of the nine sRNAs was growth phase-dependent. But ET_sRNA_10 was almost expressed all the time and reached the highest peak at 48 h. Their targets were predicted by TargetRNA2 and each sRNA target contains some genes that directly or indirectly relate to virulence. These results preliminary showed that sRNAs probably play a regulatory role of virulence in E. tarda.

MeSH terms

  • Animals
  • Computational Biology / methods
  • Edwardsiella tarda / genetics*
  • Edwardsiella tarda / isolation & purification
  • Flatfishes / microbiology
  • Gene Expression Regulation, Bacterial
  • Nucleic Acid Conformation
  • Promoter Regions, Genetic
  • RNA, Small Untranslated / chemistry
  • RNA, Small Untranslated / genetics*
  • Sequence Analysis, RNA
  • Virulence / genetics

Substances

  • RNA, Small Untranslated

Grants and funding

The project was supported by The National Natural Science Foundation of China (41306165), The Natural Science Foundation of Jiangsu Province (BK20140442), A Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions, China Postdoctoral Foundation Funding (2011M501169) and the fifth-batch “521 High-Level Talent Education Project of Lianyungang”.