Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
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DOI：
10.1128/mbio.01990-15
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发表时间：
2016-02-09
期刊：
影响因子：
6.4
通讯作者：
Shaw LN
中科院分区：
文献类型：
--
作者：
Carroll RK;Weiss A;Broach WH;Wiemels RE;Mogen AB;Rice KC;Shaw LN
在金黄色葡萄球菌中，已鉴定出数百个小的调节性或小RNA(SRNAs)，但这类分子仍然知之甚少，研究严重不足。SRNA基因通常不在基因组注释文件中，因此，它们的存在经常被忽视，特别是在全球转录学研究中。为了更好地检测和分析金黄色葡萄球菌中的sRNA，我们为三种常用的金黄色葡萄球菌菌株(MRSA252、NCTC 8325和USA300)生成了更新的GenBank文件，其中我们添加了对>；260以前识别的sRNA的注释。这些文件是第一个包括金黄色葡萄球菌中sRNA的全基因组注释的文件，然后被用作识别社区相关的甲氧西林耐药菌株USA300中新的sRNA的基础。这一分析导致发现了39个以前未识别的sRNA。研究新发现的sRNA的基因组位置发现，金黄色葡萄球菌基因组注释的不一致程度令人惊讶，这可能阻碍了对这些元件的分析和功能探索。最后，以我们新创建的注释文件为参考，我们对金黄色葡萄球菌中sRNA基因的表达进行了全局分析，并证明了新发现的tsr25是人血清中表达最高的sRNA。这项研究以我们新生成的注释文件的形式向金黄色葡萄球菌研究界提供了一个宝贵的资源，同时也提出了第一次检查在病理生理相关条件下的差异sRNA表达。尽管有大量研究确定了金黄色葡萄球菌中的调节性或小RNA(SRNA)基因，但它们的注释明显缺乏可用的基因组文件。除此之外，在确定这些要素的大量研究中，缺乏相互参照，往往导致同一个SNA被多次确定，并带有多个名称。在这项工作中，我们从文献中整合和整理了已知的sRNA基因，并将它们映射到它们在金黄色葡萄球菌基因组上的位置，创建了新的基因组注释文件。这些文件现在可以被科学界广泛用于实验，以搜索以前未发现的sRNA基因，并通过转录组测序(RNA-seq)监测sRNA基因的表达。我们展示了这一应用，识别了39个新的sRNA，并研究了它们在金黄色葡萄球菌在人血清中生长过程中的表达。
In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome annotation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. Despite a large number of studies identifying regulatory or small RNA (sRNA) genes in Staphylococcus aureus, their annotation is notably lacking in available genome files. In addition to this, there has been a considerable lack of cross-referencing in the wealth of studies identifying these elements, often leading to the same sRNA being identified multiple times and bearing multiple names. In this work, we have consolidated and curated known sRNA genes from the literature and mapped them to their position on the S. aureus genome, creating new genome annotation files. These files can now be used by the scientific community at large in experiments to search for previously undiscovered sRNA genes and to monitor sRNA gene expression by transcriptome sequencing (RNA-seq). We demonstrate this application, identifying 39 new sRNAs and studying their expression during S. aureus growth in human serum.