Guerrero Gabriela, Peralta Humberto, Aguilar Alejandro, Díaz Rafael, Villalobos Miguel Angel, Medrano-Soto Arturo, Mora Jaime
Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, PO Box 565-A, Cuernavaca, Morelos, 62210, Mexico.
BMC Evol Biol. 2005 Oct 17;5:55. doi: 10.1186/1471-2148-5-55.
Comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. However, questions about the biological significance of gene order conservation, or synteny, remain open. Moreover, few comprehensive studies have been reported for rhizobial genomes.
We analyzed the genomic sequences of four fast growing Rhizobiales (Sinorhizobium meliloti, Agrobacterium tumefaciens, Mesorhizobium loti and Brucella melitensis). We made a comprehensive gene classification to define chromosomal orthologs, genes with homologs in other replicons such as plasmids, and those which were species-specific. About two thousand genes were predicted to be orthologs in each chromosome and about 80% of these were syntenic. A striking gene colinearity was found in pairs of organisms and a large fraction of the microsyntenic regions and operons were similar. Syntenic products showed higher identity levels than non-syntenic ones, suggesting a resistance to sequence variation due to functional constraints; also, an unusually high fraction of syntenic products contained membranal segments. Syntenic genes encode a high proportion of essential cell functions, presented a high level of functional relationships and a very low horizontal gene transfer rate. The sequence variability of the proteins can be considered the species signature in response to specific niche adaptation. Comparatively, an analysis with genomes of Enterobacteriales showed a different gene organization but gave similar results in the synteny conservation, essential role of syntenic genes and higher functional linkage among the genes of the microsyntenic regions.
Syntenic bacterial genes represent a commonly evolved group. They not only reveal the core chromosomal segments present in the last common ancestor and determine the metabolic characteristics shared by these microorganisms, but also show resistance to sequence variation and rearrangement, possibly due to their essential character. In Rhizobiales and Enterobacteriales, syntenic genes encode a high proportion of essential cell functions and presented a high level of functional relationships.
比较基因组学为深入了解密切相关细菌物种的基因序列变异性质和染色体组织提供了有价值的见解。然而，关于基因顺序保守性（即共线性）的生物学意义问题仍未解决。此外，针对根瘤菌基因组的全面研究报道较少。
我们分析了四种快速生长的根瘤菌目细菌（苜蓿中华根瘤菌、根癌土壤杆菌、百脉根中慢生根瘤菌和羊种布鲁氏菌）的基因组序列。我们进行了全面的基因分类，以定义染色体直系同源基因、在其他复制子（如质粒）中有同源物的基因以及物种特异性基因。预计每条染色体上约有两千个基因是直系同源基因，其中约80%是共线的。在成对的生物体中发现了显著的基因共线性，并且大部分微共线区域和操纵子是相似的。共线产物比非共线产物显示出更高的同一性水平，这表明由于功能限制而对序列变异具有抗性；此外，共线产物中异常高比例包含膜片段。共线基因编码了很大比例的基本细胞功能，呈现出高水平的功能关系，并且水平基因转移率非常低。蛋白质的序列变异性可被视为物种对特定生态位适应的特征。相比之下，对肠杆菌目的基因组分析显示出不同的基因组织，但在共线性保守、共线基因的重要作用以及微共线区域基因之间更高的功能联系方面给出了相似的结果。
共线细菌基因代表了一个共同进化的群体。它们不仅揭示了存在于最后共同祖先中的核心染色体片段，决定了这些微生物共有的代谢特征，而且还显示出对序列变异和重排的抗性，这可能归因于它们的基本特性。在根瘤菌目和肠杆菌目中，共线基因编码了很大比例的基本细胞功能，并呈现出高水平的功能关系。
