Wang H C, Badger J, Kearney P, Li M
Department of Computer Science, University of Waterloo, Waterloo, Ontario, Canada.
Mol Biol Evol. 2001 May;18(5):792-800. doi: 10.1093/oxfordjournals.molbev.a003861.
Codon usage varies both between organisms and between different genes in the same organism. This observation has been used as a basis for earlier work in identifying highly expressed and horizontally transferred genes in Escherichia coli. In this work, we applied Kohonen's self-organizing map to analysis of the codon usage pattern of the Escherichia coli, Aquifex aeolicus, Archaeoglobus fulgidus, Haemophilus influenzae RD:, Methanococcus jannaschii, Methanobacterium thermoautotrophicum, and Pyrococcus horikoshii genomes for evidence of highly expressed genes and horizontally transferred genes. All of the analyzed genomes had a clear category of horizontally transferred genes, and their apparent percentages ranged from 7.7% to 21.4%. The apparent percentage of highly expressed genes ranges from 0% to 11.8%. A clustering of average codon usage of main gene categories of the seven genomes showed an interesting mixing of gene classes in four thermophilic/hyperthermophilic organisms, A. aeolicus, A. fulgidus, M. thermoautotrophicum, and P. horikoshii, which suggests possible origins of their horizontally transferred genes as well as the need for adaptation to a specific environment. Further classification of the three gene categories in E. coli and H. influenzae according to gene function revealed that genes involved in communication (such as regulation and cell process) and structure (cell structure and structural proteins) are more likely to be horizontally transferred than are genes involved in information (transcription, translation, and related processes) and in some groups of energy (such as energy metabolism and carbon compound catabolism).
密码子使用情况在不同生物体之间以及同一生物体的不同基因之间都存在差异。这一观察结果已被用作早期研究的基础，用于在大肠杆菌中识别高表达基因和水平转移基因。在这项研究中，我们应用Kohonen自组织映射来分析大肠杆菌、嗜热栖热菌、古生球菌、流感嗜血杆菌RD、詹氏甲烷球菌、嗜热自养甲烷杆菌和堀越热球菌基因组的密码子使用模式，以寻找高表达基因和水平转移基因的证据。所有分析的基因组都有一个明确的水平转移基因类别，其明显比例在7.7%至21.4%之间。高表达基因的明显比例在0%至11.8%之间。对这七个基因组主要基因类别的平均密码子使用情况进行聚类分析，结果显示在嗜热栖热菌、古生球菌、嗜热自养甲烷杆菌和堀越热球菌这四种嗜热/超嗜热生物体中，基因类别出现了有趣的混合，这表明了它们水平转移基因的可能来源以及适应特定环境的必要性。根据基因功能对大肠杆菌和流感嗜血杆菌中的三类基因进行进一步分类，结果显示，与信息传递（如调控和细胞过程）及结构（细胞结构和结构蛋白）相关的基因比与信息（转录、翻译及相关过程）和某些能量组（如能量代谢和碳化合物分解代谢）相关的基因更有可能发生水平转移。
