How many signal peptides are there in bacteria?
How many signal peptides are there in bacteria?
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DOI：
10.1111/1462-2920.12105
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发表时间：
2013-04
影响因子：
5.1
通讯作者：
Frishman D
中科院分区：
文献类型：
--
作者：
Ivankov DN;Payne SH;Galperin MY;Bonissone S;Pevzner PA;Frishman D
在过去的五年中，蛋白质基因组学（使用质谱来识别从基因组序列预测的蛋白质）已经成为一种有前途的方法来高通量地识别蛋白质N-末端，这仍然是基因组注释中的一个问题。将实验测定的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，从而得出相应蛋白质的细胞质或细胞质外（周质或细胞外）定位的结论。在这里，我们提出了在大肠杆菌K-12中的信号肽的蛋白基因组学研究的结果，并将其结果与现有的实验数据和预测的软件工具，如SignalP和Phobius。一个单一的蛋白质组学实验回收了超过三分之一的信号肽，这些信号肽是在过去的三十年中通过实验确定的，并证实了至少31个额外的信号肽，大部分在已知的输出蛋白质中，这些信号肽以前曾被预测但未被验证。推定的信号肽的肽长度和存在的8个残基的疏水补丁和一个典型的信号肽酶裂解位点的过滤证明足以消除假阳性命中。令人惊讶的是，这项蛋白质组学研究的结果，以及对E。用最新版本的SignalP程序对大肠杆菌基因组进行了分析，结果表明，含有信号肽的蛋白质的比例只有10%左右，是以前估计的一半。
Over the last five 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 31additional signal peptides, mostlyin 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.
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影响因子：
3
作者：
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通讯作者：
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影响因子：
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通讯作者：
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