Data Sheet 1_The amino acid composition of mammalian mitochondrial proteins correlates with generation time.pdf

Previous studies observed a correlation between the GC contents of the 12 mitochondrial protein-coding genes encoded on the H-strand and the generation times of mammals. However, how variation in GC content influences the amino acid composition of the proteins of these genes remains unclear. To examine this, we analyzed these mitochondrial proteins from 1,208 mammalian species. We first estimated the expected amino acid frequencies based on base frequencies at each codon position and then calculated the observed amino acid frequencies. The expected and observed proportions of almost half of the amino acids (8-9) showed a positive correlation with mammalian generation times, whereas the remaining amino acids (11-12) had a negative relationship. Accordingly, we categorized these amino acids as Group I and Group II, respectively. While the proportion of Group I amino acids showed a significant positive relationship with generation time, the magnitude of correlation was five times greater for highly variable amino acids than that observed for conserved amino acids. As expected, the opposite pattern was observed for the Group II amino acids. These findings are important because amino acid composition influences the structure and function of mitochondrial proteins. Our results suggest that for Group I amino acids, the magnitude of this influence is likely to be greater for mammals with long generation times (e.g., primates) than in those with short generation times (e.g., rodents).

既往研究发现，H链（H-strand）编码的12个线粒体蛋白编码基因的GC含量（GC content）与哺乳动物的世代时间存在相关性。然而，GC含量的变异如何影响这些基因编码蛋白的氨基酸组成，目前仍不明确。为探究这一问题，本研究对1208种哺乳动物的上述线粒体蛋白展开分析。我们首先基于每个密码子（codon）位点的碱基频率估算出预期氨基酸频率，随后计算观测到的氨基酸频率。近半数氨基酸（8~9种）的预期与观测占比均与哺乳动物世代时间呈正相关，其余氨基酸（11~12种）则呈负相关。据此，我们将这些氨基酸分别划分为第I组与第II组。尽管第I组氨基酸占比与世代时间呈显著正相关，但高变异氨基酸的相关强度是保守氨基酸的5倍。如预期一致，第II组氨基酸则呈现出相反的模式。上述发现具有重要意义，因为氨基酸组成会影响线粒体蛋白的结构与功能。本研究结果表明，就第I组氨基酸而言，世代时间较长的哺乳动物（如灵长类）的该类影响强度，大概率高于世代时间较短的类群（如啮齿类）。