Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis
Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis
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DOI：
10.1021/pr0700347
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发表时间：
2007-01-01
影响因子：
4.4
通讯作者：
Oesterhelt, Dieter
中科院分区：
文献类型：
--
作者：
Aivaliotis, Michalis;Gevaert, Kris;Oesterhelt, Dieter
蛋白质N-末端肽的表征支持来自基因组序列的数据的质量评估（例如，起始密码子的正确分配），并提示体内N-末端修饰，如N-末端乙酰化和起始甲硫氨酸的去除。目前的工作代表了第一次大规模的鉴定N-末端肽的原核生物，两个嗜盐euryarchaeota盐杆菌和natronomonaspharaonis。使用了两种方法，专门允许蛋白质N-末端肽的表征：组合的分级对角色谱法（COFRADIC）和强阳离子交换色谱法（SCX），这两种方法都已知富集N-末端封闭肽。除了这些特定的方法，N-末端肽鉴定提取我们以前的全基因组蛋白质组数据。结合所有数据，606个N末端肽来自Hbt。salinarum和Nmn.法老是可靠的鉴定。这些结果构成了最大的可用数据集，该数据集包含原核生物（古细菌和细菌）的经鉴定和表征的蛋白质N-末端。它们允许验证/改进起始密码子分配，因为自动基因查找器倾向于错误分配富含GC的基因组的起始密码子。此外，该数据集允许解开古细菌中的N-末端蛋白质成熟，表明60%的蛋白质经历甲硫氨酸切割，并且与目前的知识相反，N-α-乙酰化在古细菌生命结构域中是常见的，其中13-18%的蛋白质被N α-乙酰化。本文中描述的蛋白质组可通过FTP获得，并可用作测试新基因发现器性能的参考组。
Characterization of protein N-terminal peptides supports the quality assessment of data derived from genomic sequences ( e.g., the correct assignment of start codons) and hints to in vivo N-terminal modifications such as N-terminal acetylation and removal of the initiator methionine. The current work represents the first large-scale identification of N-terminal peptides from prokaryotes, of the two halophilic euryarchaeota Halobacterium salinarum and Natronomonas pharaonis. Two methods were used that specifically allow the characterization of protein N-terminal peptides: combined fractional diagonal chromatography ( COFRADIC) and strong cation exchange chromatography (SCX), both known to enrich for N-terminally blocked peptides. In addition to these specific methods, N-terminal peptide identifications were extracted from our previous genome-wide proteomic data. Combining all data, 606 N-terminal peptides from Hbt. salinarum and 328 from Nmn. pharaonis were reliably identified. These results constitute the largest available dataset holding identified and characterized protein N-termini for prokaryotes (archaea and bacteria). They allowed the validation/improvement of start codon assignments as automatic gene finders tend to misassign start codons for GC-rich genomes. In addition, the dataset allowed unravelling N-terminal protein maturation in archaea, showing that 60% of the proteins undergo methionine cleavage and that-in contrast to current knowledges-N-alpha-acetylation is common in the archaeal domain of life with 13-18% of the proteins being N alpha-acetylated. The protein sets described in this paper are available by FTP and might be used as reference sets to test the performance of new gene finders.