Gómez-Lozano María, Marvig Rasmus L, Tulstrup Monica V L, Molin Søren
Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
BMC Genomics. 2014 Sep 11;15(1):783. doi: 10.1186/1471-2164-15-783.
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.
RNA测序技术表明，细菌表达的RNA分子除了mRNA、rRNA或tRNA之外还有其他种类。在过去几年中，全基因组细菌转录组已被证明包含基因间RNA、反义RNA和非翻译区，所有这些都能够执行多种调节功能。
在本研究中，我们使用RNA测序技术在13种不同条件下生长的机会致病菌铜绿假单胞菌中鉴定出232个反义RNA（asRNA）。所研究的条件包括指数生长期和稳定期生长以及渗透、氧化和抗生素应激。我们发现，与参与细胞分裂以及细胞壁、脂多糖（LPS）和荚膜生物合成的基因反向转录的asRNA显著富集，这很可能反映了本研究中使用的条件。大量asRNA在渗透、氧化和抗生素应激下其表达发生了显著变化，这表明asRNA可能在这些条件下起调节作用。我们还将本研究在铜绿假单胞菌PAO1中检测到的asRNA与之前两项在铜绿假单胞菌PA14中的研究中检测到的asRNA进行了比较，发现研究之间的重叠程度非常有限。
RNA测序实验揭示了所有被研究细菌基因组中的数百种新转录本。使用RNA测序在铜绿假单胞菌中检测新asRNA的独立研究之间的比较表明，所报告结果之间的重叠非常狭窄。有必要探讨如何报告这类研究的可重复性，以避免在比较由不同方法产生的数据时得出误导性结论。
