Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa.
Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa.
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DOI：
10.1186/1471-2164-15-783
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发表时间：
2014-09-11
期刊：
影响因子：
4.4
通讯作者：
Molin S
中科院分区：
文献类型：
--
作者：
Gómez-Lozano M;Marvig RL;Tulstrup MV;Molin S
RNA测序技术揭示细菌表达RNA分子而不是mRNA、rRNA或tRNA。在过去的几年中，全基因组细菌转录组已被证明包括基因间RNA，反义RNA和非翻译区，所有能够执行不同的调节功能。在这项研究中，我们使用RNA-seq在13种不同条件下生长的机会致病菌铜绿假单胞菌中鉴定了232种反义RNA（asRNA）。研究的条件包括指数和静止生长以及渗透，氧化和抗生素应激。我们发现了一个显着的过度表达的asRNA转录相反的基因参与细胞分裂和细胞壁，脂多糖（LPS），和胶囊的生物合成，最有可能反映在这项研究中使用的条件。大量asRNA在渗透、氧化和抗生素胁迫下显著改变了它们的表达，表明asRNA在这些条件下可能起调节作用。我们还将本研究中在铜绿假单胞菌PAO 1中检测到的asRNA与之前两项研究中在铜绿假单胞菌PA 14中检测到的asRNA进行了比较，发现研究之间的重叠程度非常有限。RNA-seq实验揭示了所有研究的细菌基因组中数百种新的转录本。使用RNA-seq检测铜绿假单胞菌中新型asRNA的独立研究之间的比较表明，报告结果之间的重叠非常窄。有必要解决如何报告这类研究的重现性，以避免在比较不同方法产生的数据时得出误导性结论。本文的在线版本（doi：10.1186/1471-2164-15-783）包含补充材料，可供授权用户使用。
RNA sequencing technologies reveal that bacteria express RNA molecules other than mRNA, rRNA or tRNA. During the last years genome-wide bacterial transcriptomes have been shown to comprise intergenic RNA, antisense RNA, and untranslated regions, all capable of performing diverse regulatory functions. In this study we used RNA-seq to identify 232 antisense RNAs (asRNAs) in the opportunistic pathogen Pseudomonas aeruginosa grown under 13 different conditions. The conditions studied include exponential and stationary growth as well as osmotic, oxidative and antibiotic stress. We found a significant overrepresentation of asRNAs that are transcribed opposite to genes involved in cell division and in cell wall, lipopolysaccharide (LPS), and capsule biosynthesis, most likely reflecting the conditions used in this study. A substantial number of asRNAs significantly changed their expression under osmotic, oxidative and antibiotic stress, suggesting that asRNAs may play regulatory roles during these conditions. We also made a comparison between the asRNAs detected in this study in P. aeruginosa PAO1 with the asRNAs detected in two previous studies in P. aeruginosa PA14, and found that the extent of overlap between the studies is very limited. RNA-seq experiments are revealing hundreds of novel transcripts in all bacterial genomes investigated. The comparison between independent studies that used RNA-seq to detect novel asRNAs in P. aeruginosa shows that the overlap between the results reported is very narrow. It is necessary to address how reproducibility of these kind of studies should be reported in order to avoid misleading conclusions when comparing data generated by non-identical methods. The online version of this article (doi:10.1186/1471-2164-15-783) contains supplementary material, which is available to authorized users.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
DOI：
10.1007/978-1-4939-0473-0_34
发表时间：
2014-01-01
期刊：
PSEUDOMONAS: METHODS AND PROTOCOLS
影响因子：
--
作者：
Gomez-Lozano, Maria;Marvig, Rasmus Lykke;Long, Katherine S.
通讯作者：
Long, Katherine S.
影响因子：
2.9
作者：
Larkin, Angelyn;Imperali, Barbara
通讯作者：
Imperali, Barbara
影响因子：
10
作者：
Hull, J;Vervaart, P;Phelan, P
通讯作者：
Phelan, P
影响因子：
56.9
作者：
Gueell, Marc;van Noort, Vera;Serrano, Luis
通讯作者：
Serrano, Luis