Abstract
BackgroundThe sRNAs of bacterial pathogens are known to be involved in various cellular roles including environmental adaptation as well as regulation of virulence and pathogenicity. It is expected that sRNAs may also have similar functions for Burkholderia pseudomallei, a soil bacterium that can adapt to diverse environmental conditions, which causes the disease melioidosis and is also able to infect a wide variety of hosts.ResultsBy integrating several proven sRNA prediction programs into a computational pipeline, available Burkholderia spp. genomes were screened to identify sRNA gene candidates. Orthologous sRNA candidates were then identified via comparative analysis. From the total prediction, 21 candidates were found to have Rfam homologs. RT-PCR and sequencing of candidate sRNA genes of unknown functions revealed six putative sRNAs which were highly conserved in Burkholderia spp. and two that were unique to B. pseudomallei present in a normal culture conditions transcriptome. The validated sRNAs include potential cis-acting elements associated with the modulation of methionine metabolism and one B. pseudomallei-specific sRNA that is expected to bind to the Hfq protein.ConclusionsThe use of the pipeline developed in this study and subsequent comparative analysis have successfully aided in the discovery and shortlisting of sRNA gene candidates for validation. This integrated approach identified 29 B. pseudomallei sRNA genes - of which 21 have Rfam homologs and 8 are novel.
Highlights
Small RNAs are known to function as regulatory or catalytic molecules in bacteria with sequences normally ranging from ~50-250 nt in length and located in the intergenic regions (IGRs) [1,2]
We report the development of a computational pipeline that integrated successful sRNA prediction programs to identify candidate sRNA genes in B. pseudomallei and subsequent validation by Reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing
Pipeline development and performance assessment Several computational approaches for sRNA discovery have been used on various bacterial genomes to successfully identify and validate tens to hundreds of putative sRNA genes (Table 1)
Summary
Small RNAs (sRNAs) are known to function as regulatory or catalytic molecules in bacteria with sequences normally ranging from ~50-250 nt in length and located in the intergenic regions (IGRs) [1,2]. SRNAs have been associated with regulatory networks that modulate the adherence to, and invasion into the host cell [17,18], environmental adaptation [19,20] as well as virulence and pathogenicity [17,18,20,21,22,23]. The sRNAs of bacterial pathogens are known to be involved in various cellular roles including environmental adaptation as well as regulation of virulence and pathogenicity. It is expected that sRNAs may have similar functions for Burkholderia pseudomallei, a soil bacterium that can adapt to diverse environmental conditions, which causes the disease melioidosis and is able to infect a wide variety of hosts
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