Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
Biol Direct. 2009 Nov 23;4:46. doi: 10.1186/1745-6150-4-46.
Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities.
Equivalent enzyme families with metabolic functions were selected from the genomes of four experimentally characterized bacteria belonging to separate genera. Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. Protein family memberships reflected known metabolic characteristics of the organisms. Differences in divergence of functionally characterized enzyme family members accounted for characteristics of taxa known to differ in those biochemical properties and capabilities. While some members of the gene families will have been acquired by lateral exchange and other former family members will have been lost over time, duplication and divergence of genes and functions appear to have been a significant contributor to the functional diversity of today's microbes.
Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. Thus divergence of the duplicate enzymes has been a major process in the generation of different kinds of bacteria.
基因和蛋白质的序列相关家族在细菌基因组中很常见。在大肠杆菌中，它们构成了基因组的一半以上。蛋白质家族和超家族的存在表明，在进化过程中存在基因复制和分化的历史。基因组编码的蛋白质家族及其大小和功能组成反映了它们所在生物体的代谢潜力。比较不同生物体的蛋白质家族可以深入了解功能上的差异和相似之处。
从属于四个不同属的四个经过实验表征的细菌的基因组中选择了具有代谢功能的等效酶家族。在蛋白质家族成员中检测到了相似性和差异性，而在更相关的生物体中检测到了更多的相似性。蛋白质家族成员反映了生物体已知的代谢特征。功能特征酶家族成员的分化差异解释了在这些生化特性和能力上已知存在差异的分类群的特征。虽然基因家族的一些成员可能是通过水平基因转移获得的，而其他以前的家族成员随着时间的推移已经丢失，但基因和功能的复制和分化似乎是当今微生物功能多样性的一个重要贡献因素。
蛋白质家族似乎是在进化过程中通过基因复制和分化产生的，保留下来的基因拷贝是导致不同细菌生理和分类群的变异。因此，重复酶的分化是产生不同种类细菌的主要过程。
