Ozawa Y, Saito R, Washio T, Tomita M
Institute for Advanced Bioscience, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-8520, Japan.
J Mol Evol. 2003 Jun;56(6):665-72. doi: 10.1007/s00239-002-2435-9.
Translation termination is catalyzed by release factors that recognize stop codons. However, previous works have shown that in some bacteria, the termination process also involves bases around stop codons. Recently, Ito et al. analyzed release factors and identified the amino acids therein that recognize stop codons. However, the amino acids that recognize bases around stop codons remain unclear. To identify the candidate amino acids that recognize the bases around stop codons, we aligned the protein sequences of the release factors of various bacteria and searched for amino acids that were conserved specifically in the sequence of bacteria that seemed to regulate translation termination by bases around stop codons. As a result, species having several highly conserved residues in RF1 and RF2 showed positive correlations between their codon usage bias and conservation of the bases around the stop codons. In addition, some of the residues were located very close to the SPF motif, which deciphers stop codons. These results suggest that these conserved amino acids enable the release factors to recognize the bases around the stop codons.
翻译终止由识别终止密码子的释放因子催化。然而，先前的研究表明，在一些细菌中，终止过程还涉及终止密码子周围的碱基。最近，伊藤等人分析了释放因子，并确定了其中识别终止密码子的氨基酸。然而，识别终止密码子周围碱基的氨基酸仍不清楚。为了鉴定识别终止密码子周围碱基的候选氨基酸，我们比对了各种细菌释放因子的蛋白质序列，并寻找在似乎通过终止密码子周围碱基调节翻译终止的细菌序列中特异性保守的氨基酸。结果，在RF1和RF2中具有几个高度保守残基的物种，其密码子使用偏好与终止密码子周围碱基的保守性之间呈现正相关。此外，一些残基位于非常接近解读终止密码子的SPF基序的位置。这些结果表明，这些保守氨基酸使释放因子能够识别终止密码子周围的碱基。
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