Generation and phenotyping of a collection of sRNA gene deletion mutants of the haloarchaeon Haloferax volcanii

PLoS One. 2014 Mar 17;9(3):e90763. doi: 10.1371/journal.pone.0090763. eCollection 2014.

Abstract

The haloarchaeon Haloferax volcanii was shown to contain 145 intergenic and 45 antisense sRNAs. In a comprehensive approach to unravel various biological roles of haloarchaeal sRNAs in vivo, 27 sRNA genes were selected and deletion mutants were generated. The phenotypes of these mutants were compared to that of the parent strain under ten different conditions, i.e. growth on four different carbon sources, growth at three different salt concentrations, and application of four different stress conditions. In addition, cell morphologies in exponential and stationary phase were observed. Furthermore, swarming of 17 mutants was analyzed. 24 of the 27 mutants exhibited a difference from the parent strain under at least one condition, revealing that haloarchaeal sRNAs are involved in metabolic regulation, growth under extreme conditions, regulation of morphology and behavior, and stress adaptation. Notably, 7 deletion mutants showed a gain of function phenotype, which has not yet been described for any other prokaryotic sRNA gene deletion mutant. Comparison of the transcriptomes of one sRNA gene deletion mutant and the parent strain led to the identification of differentially expressed genes. Genes for flagellins and chemotaxis were up-regulated in the mutant, in accordance with its gain of function swarming phenotype. While the deletion mutant analysis underscored that haloarchaeal sRNAs are involved in many biological functions, the degree of conservation is extremely low. Only 3 of the 27 genes are conserved in more than 10 haloarchaeal species. 22 of the 27 genes are confined to H. volcanii, indicating a fast evolution of haloarchaeal sRNA genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Biological / genetics
  • Energy Metabolism
  • Evolution, Molecular
  • Gene Deletion*
  • Gene Expression Profiling
  • Genes, Archaeal*
  • Haloferax volcanii / classification*
  • Haloferax volcanii / genetics*
  • Haloferax volcanii / growth & development
  • Haloferax volcanii / metabolism
  • Phenotype*
  • RNA, Archaeal*
  • Sodium Chloride / pharmacology
  • Stress, Physiological / drug effects
  • Stress, Physiological / genetics
  • Transcriptome

Substances

  • RNA, Archaeal
  • Sodium Chloride

Grants and funding

This work was funded by the German Research Council (Deutsche Forschungsgemeinschaft) through the Priority Program SPP1258 “Sensory and regulatory RNAs in prokaryotes” (grants DFG Ma1238/11-2 and So264/14-2). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.