Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach.
Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach.
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未知氨基酸的采矿核基因组：一种基于停止折叠的方法。
DOI：
10.1186/1471-2105-8-225
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发表时间：
2007-06-28
影响因子：
3
通讯作者：
Kanehisa, Minoru
中科院分区：
文献类型：
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作者：
Fujita, Masashi;Mihara, Hisaaki;Goto, Susumu;Esaki, Nobuyoshi;Kanehisa, Minoru
硒半胱氨酸和吡咯赖氨酸是第21和第22个氨基酸，由终止密码子遗传编码。由于到目前为止，许多微生物基因组已经完全测序，人们不禁要问，这些基因组中是否有第23个氨基酸未被发现。最近，一项计算研究解决了这个问题，并报道在现有的基因组序列中没有发现未知氨基酸的tRNA基因。然而，tRNA预测程序对一个可能具有非典型序列和结构的未知tRNA家族的性能尚不清楚，从而使他们的结果不确定。蛋白质水平的研究将提供对这种新氨基酸的独立见解。假设第23个氨基酸也由终止密码子编码，我们从191个原核基因组中系统地预测了含有终止密码子编码氨基酸的蛋白质。由于我们的预测方法仅依赖于初级序列的保守模式，因此它也为寻找新的硒蛋白和其他通读蛋白提供了机会。它成功地回收了许多目前已知的硒蛋白和吡咯赖氨酸蛋白。然而，没有发现有希望的第23位氨基酸的候选者，只预测了一个新的硒蛋白。我们的结果表明，由终止密码子编码的未知氨基酸不存在，或其系统发育分布相当有限，这与先前对tRNA的研究一致。这里描述的方法可以用于未来的研究，从快速增长的完整基因组中探索新的通读事件。
Selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons. Since a number of microbial genomes have been completely sequenced to date, it is tempting to ask whether the 23rd amino acid is left undiscovered in these genomes. Recently, a computational study addressed this question and reported that no tRNA gene for unknown amino acid was found in genome sequences available. However, performance of the tRNA prediction program on an unknown tRNA family, which may have atypical sequence and structure, is unclear, thereby rendering their result inconclusive. A protein-level study will provide independent insight into the novel amino acid. Assuming that the 23rd amino acid is also encoded by a stop codon, we systematically predicted proteins that contain stop-codon-encoded amino acids from 191 prokaryotic genomes. Since our prediction method relies only on the conservation patterns of primary sequences, it also provides an opportunity to search novel selenoproteins and other readthrough proteins. It successfully recovered many of currently known selenoproteins and pyrrolysine proteins. However, no promising candidate for the 23rd amino acid was detected, and only one novel selenoprotein was predicted. Our result suggests that the unknown amino acid encoded by stop codons does not exist, or its phylogenetic distribution is rather limited, which is in agreement with the previous study on tRNA. The method described here can be used in future studies to explore novel readthrough events from complete genomes, which are rapidly growing.