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首页> 外文期刊>BMC Genomics >Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs
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Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs

机译：新发现的伯克霍尔德氏菌保守和伯克霍尔德氏菌假mallei独特sRNA的计算发现和RT-PCR验证

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Background 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 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. Results By 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. Conclusions The 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.
机译：背景技术已知细菌病原体的sRNA参与多种细胞作用，包括环境适应以及对毒力和致病性的调节。预计sRNAs对假伯克霍尔德菌（Burkholderia pseudomallei）可能也具有类似的功能，伯克霍尔德菌可适应多种环境条件，从而引起类弧菌病并且还可以感染多种宿主。结果通过将几种成熟的sRNA预测程序整合到计算管道中，可获得Burkholderia spp。筛选基因组以鉴定sRNA基因候选物。然后通过比较分析鉴定直系同源的sRNA候选物。从总预测中，发现21名候选者具有Rfam同源物。 RT-PCR和未知功能候选sRNA基因的测序揭示了6个推定的sRNA，它们在Burkholderia spp中高度保守。正常培养条件转录组中存在的两个假苹果芽孢杆菌特有的。经过验证的sRNA包括与蛋氨酸代谢调节相关的潜在顺式作用元件以及一种预期与Hfq蛋白质结合的假芽孢杆菌特异性sRNA。结论利用在这项研究中开发的管道以及随后的比较分析，已成功地协助了sRNA基因候选物的发现和筛选。这种综合方法确定了29个假疟原虫sRNA基因-其中21个具有Rfam同源物，而8个是新的。

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