Technische Universität München, Department of Genome-Oriented Bioinformatics, 85354, Freising, Germany.
Environ Microbiol. 2013 Apr;15(4):983-90. doi: 10.1111/1462-2920.12105.
Over the last 5 years proteogenomics (using mass spectroscopy to identify proteins predicted from genomic sequences) has emerged as a promising approach to the high-throughput identification of protein N-termini, which remains a problem in genome annotation. Comparison of the experimentally determined N-termini with those predicted by sequence analysis tools allows identification of the signal peptides and therefore conclusions on the cytoplasmic or extracytoplasmic (periplasmic or extracellular) localization of the respective proteins. We present here the results of a proteogenomic study of the signal peptides in Escherichia coli K-12 and compare its results with the available experimental data and predictions by such software tools as SignalP and Phobius. A single proteogenomics experiment recovered more than a third of all signal peptides that had been experimentally determined during the past three decades and confirmed at least 31 additional signal peptides, mostly in the known exported proteins, which had been previously predicted but not validated. The filtering of putative signal peptides for the peptide length and the presence of an eight-residue hydrophobic patch and a typical signal peptidase cleavage site proved sufficient to eliminate the false-positive hits. Surprisingly, the results of this proteogenomics study, as well as a re-analysis of the E. coli genome with the latest version of SignalP program, show that the fraction of proteins containing signal peptides is only about 10%, or half of previous estimates.
在过去的 5 年中，蛋白质基因组学（使用质谱法鉴定从基因组序列预测的蛋白质）已成为高通量鉴定蛋白质 N 末端的一种很有前途的方法，而蛋白质 N 末端的鉴定仍然是基因组注释中的一个问题。将实验确定的 N 末端与序列分析工具预测的 N 末端进行比较，可以鉴定信号肽，从而可以得出相应蛋白质是位于细胞质内还是细胞外（周质或细胞外）的结论。本文介绍了对大肠杆菌 K-12 中信号肽的蛋白质基因组学研究结果，并将其与现有的实验数据和 SignalP 和 Phobius 等软件工具的预测结果进行了比较。单次蛋白质基因组学实验就鉴定出了过去三十年来实验确定的超过三分之一的信号肽，并至少确认了 31 个额外的信号肽，这些信号肽主要存在于已知的分泌蛋白中，之前已经被预测但没有被验证。对肽长度和存在 8 个残基疏水性补丁和典型信号肽酶切割位点的假定信号肽进行过滤，足以消除假阳性结果。令人惊讶的是，这项蛋白质基因组学研究的结果，以及对最新版本的 SignalP 程序的大肠杆菌基因组的重新分析，表明含有信号肽的蛋白质的比例仅约为 10%，比之前的估计少一半。
