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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.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-385) contains supplementary material, which is available to authorized users.

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