Open Access Research article

Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions

Chris J Stubben, Sofiya N Micheva-Viteva, Yulin Shou, Sarah K Buddenborg, John M Dunbar and Elizabeth Hong-Geller*

  • * Corresponding author: Elizabeth Hong-Geller ehong@lanl.gov

  • † Equal contributors

Author Affiliations

Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA

For all author emails, please log on.

BMC Genomics 2014, 15:385  doi:10.1186/1471-2164-15-385

Published: 19 May 2014

Abstract

Background

Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with downstream target mRNAs to attenuate translation of mRNA into protein at the post-transcriptional level. In response to specific environmental changes, sRNAs can modulate the expression levels of target genes, thus enabling adaptation of cellular physiology.

Results

We profiled sRNA expression in the Gram-negative bacteria Burkholderia thailandensis cultured under 54 distinct growth conditions using a Burkholderia-specific microarray that contains probe sets to all intergenic regions greater than 90 bases. We identified 38 novel sRNAs and performed experimental validation on five sRNAs that play a role in adaptation of Burkholderia to cell stressors. In particular, the trans-encoded BTH_s1 and s39 exhibited differential expression profiles dependent on growth phase and cell stimuli, such as antibiotics and serum. Furthermore, knockdown of the highly-expressed BTH_s39 by antisense transcripts reduced B. thailandensis cell growth and attenuated host immune response upon infection, indicating that BTH_s39 functions in bacterial metabolism and adaptation to the host. In addition, expression of cis-encoded BTH_s13 and s19 found in the 5′ untranslated regions of their cognate genes correlated with tight regulation of gene transcript levels. This sRNA-mediated downregulation of gene expression may be a conserved mechanism of post-transcriptional gene dosage control.

Conclusions

These studies provide a broad analysis of differential Burkholderia sRNA expression profiles and illustrate the complexity of bacterial gene regulation in response to different environmental stress conditions.

Keywords:
Small RNAs; Burkholderia; Microarray; Stress conditions; Bacterial adaptation; Gene expression