Gupta Nitin, Tanner Stephen, Jaitly Navdeep, Adkins Joshua N, Lipton Mary, Edwards Robert, Romine Margaret, Osterman Andrei, Bafna Vineet, Smith Richard D, Pevzner Pavel A
Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA.
Genome Res. 2007 Sep;17(9):1362-77. doi: 10.1101/gr.6427907. Epub 2007 Aug 9.
While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages, and cleavages of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs, and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.
尽管近年来细菌基因组注释有了显著改善，但细菌蛋白质组注释技术（包括翻译后化学修饰、信号肽、蛋白水解事件等）仍处于起步阶段。与此同时，已测序的细菌基因组数量急剧增加，远远超过了我们验证预测基因的能力，更不用说注释细菌蛋白质组了。在本研究中，我们使用串联质谱（MS/MS）对用于生物修复的重要微生物——嗜水气单胞菌MR-1的蛋白质组进行注释。特别是，我们提供了细菌基因组中翻译后修饰的首张综合图谱，包括大量化学修饰、信号肽切割以及N端甲硫氨酸残基的切割。我们还检测到多个被基因预测程序遗漏或指定了错误起始位置的基因，并提出了改进基因注释的校正建议。这项研究表明，通过MS/MS项目对每个基因组测序项目进行补充，将以合理的成本显著改善基因组和蛋白质组注释。
