CBU, University of Bergen, 5020 Bergen, Norway, Department of Informatics, University of Bergen, 5020 Bergen, Norway, Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671 Singapore and Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel.
Nucleic Acids Res. 2014 Mar;42(5):2879-92. doi: 10.1093/nar/gkt1336. Epub 2013 Dec 25.
DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea.
DNA、RNA 和蛋白质是主要的生物大分子，它们作为一个高度相互关联的系统的组成部分共同进化和适应环境。我们在这里探讨这些分子适应机制的序列/结构决定因素、它们之间的联系以及它们相互进化的结果。我们通过对 RNA 分子的折叠模拟补充了对基因组和蛋白质组序列的统计分析，揭示了反映 DNA、RNA 和蛋白质水平分子适应的组成和序列偏倚之间的因果关系。我们发现了许多与环境适应和生活方式相关的组成上的特殊性。具体来说，古菌中与蛋白质编码序列相关的热适应特征是密码子偏向性比细菌更强。第三密码子位置的鸟嘌呤和胞嘧啶负载对于支持需氧生活方式很重要，在细菌中这种现象非常明显。第三密码子位置还提供了精氨酸和赖氨酸之间的权衡，它们分别有利于热适应和需氧性。二核苷酸组成通过在 ApG 二核苷酸中形成强碱基堆积为核酸提供稳定性。关于核酸和蛋白质的共同进化，对氨基酸组成的耐热性相关需求会影响古菌中第二密码子位置的核苷酸含量。
