Mitaku Shigeki, Sawada Ryusuke
Emeritus Professor of Nagoya University, Kokubunji, Tokyo 185-0021, Japan.
Division of System Cohort, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan.
Biophys Physicobiol. 2016 Nov 18;13:305-310. doi: 10.2142/biophysico.13.0_305. eCollection 2016.
"Life" is a particular state of matter, and matter is composed of various molecules. The state corresponding to "life" is ultimately determined by the genome sequence, and this sequence determines the conditions necessary for survival of the organism. In order to elucidate one parameter characterizing the state of "life", we analyzed the amino acid sequences encoded in the total genomes of 557 prokaryotes and 40 eukaryotes using a membrane protein prediction online tool called SOSUI. SOSUI uses only the physical parameters of the encoded amino acid sequences to make its predictions. The ratio of membrane proteins in a genome predicted by the SOSUI online tool was around 23% for all genomes, indicating that this parameter is controlled by some mechanism in cells. In order to identify the property of genome DNA sequences that is the possible cause of the constant ratio of membrane proteins, we analyzed the nucleotide compositions at codon positions and observed the existence of systematic biases distinct from those expected based on random distribution. We hypothesize that the constant ratio of membrane proteins is the result of random mutations restricted by the systematic biases inherent to nucleotide codon composition. A new approach to the biological sciences based on the holistic analysis of whole genomes is discussed in order to elucidate the principles underlying "life" at the biological system level.
“生命”是物质的一种特殊状态，而物质由各种分子组成。与“生命”相对应的状态最终由基因组序列决定，并且这个序列决定了生物体生存所需的条件。为了阐明一个表征“生命”状态的参数，我们使用一个名为SOSUI的膜蛋白预测在线工具，分析了557种原核生物和40种真核生物的全基因组中编码的氨基酸序列。SOSUI仅使用编码氨基酸序列的物理参数进行预测。SOSUI在线工具预测的所有基因组中膜蛋白的比例约为23%，这表明该参数受细胞中的某种机制控制。为了确定可能导致膜蛋白比例恒定的基因组DNA序列的特性，我们分析了密码子位置的核苷酸组成，并观察到存在与基于随机分布预期的偏差不同的系统性偏差。我们假设膜蛋白比例恒定是由核苷酸密码子组成固有的系统性偏差所限制的随机突变的结果。讨论了一种基于全基因组整体分析的生物科学新方法，以阐明生物系统水平上“生命”的潜在原理。
