Xu Xingye, Liu Tao, Ren Xianwen, Liu Bo, Yang Jian, Chen Lihong, Wei Candong, Zheng Jianhua, Dong Jie, Sun Lilian, Zhu Yafang, Jin Qi
J Proteome Res. 2015 May 1;14(5):2207-18. doi: 10.1021/acs.jproteome.5b00009. Epub 2015 Apr 20.
Infections caused by dermatophytes, Trichophyton rubrum in particular, are among the most common diseases in humans. In this study, we present a proteogenomic analysis of T. rubrum based on whole-genome proteomics and RNA-Seq studies. We confirmed 4291 expressed proteins in T. rubrum and validated their annotated gene structures based on 35 874 supporting peptides. In addition, we identified 323 novel peptides (not present in the current annotated protein database of T. rubrum) that can be used to enhance current T. rubrum annotations. A total of 104 predicted genes supported by novel peptides were identified, and 127 gene models suggested by the novel peptides that conflicted with existing annotations were manually assigned based on transcriptomic evidence. RNA-Seq confirmed the validity of 95% of the total peptides. Our study provides evidence that confirms and improves the genome annotation of T. rubrum and represents the first survey of T. rubrum genome annotations based on experimental evidence. Additionally, our integrated proteomics and multisourced transcriptomics approach provides stronger evidence for annotation refinement than proteomic data alone, which helps to address the dilemma of one-hit wonders (uncertainties supported by only one peptide).
由皮肤癣菌引起的感染，尤其是红色毛癣菌，是人类最常见的疾病之一。在本研究中，我们基于全基因组蛋白质组学和RNA测序研究，对红色毛癣菌进行了蛋白质基因组分析。我们确认了红色毛癣菌中4291种表达的蛋白质，并基于35874条支持肽段验证了它们的注释基因结构。此外，我们鉴定出323条新肽段（在红色毛癣菌当前注释蛋白质数据库中不存在），可用于增强当前对红色毛癣菌的注释。总共鉴定出104个由新肽段支持的预测基因，并且根据转录组学证据手动分配了127个由新肽段提出但与现有注释冲突的基因模型。RNA测序证实了95%的总肽段的有效性。我们的研究提供了证实和改进红色毛癣菌基因组注释的证据，并且代表了基于实验证据对红色毛癣菌基因组注释的首次调查。此外，我们的综合蛋白质组学和多源转录组学方法比单独的蛋白质组学数据为注释优化提供了更强的证据，这有助于解决“一锤定音”（仅由一条肽段支持的不确定性）的困境。
