Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales.
Evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in Rhizobiales.
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DOI：
10.1186/1471-2148-5-55
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发表时间：
2005-10-17
影响因子：
3.4
通讯作者：
Mora, J
中科院分区：
文献类型：
--
作者：
Guerrero, G;Peralta, H;Aguilar, A;Díaz, R;Villalobos, MA;Medrano-Soto, A;Mora, J
比较基因组学为了解密切相关的细菌物种的基因序列变异和染色体组织的本质提供了宝贵的见解。然而，关于基因顺序保守或同线性的生物学意义的问题仍然悬而未决。此外，关于根瘤菌基因组的综合研究报道很少。我们分析了四种快速生长的根瘤菌（苜蓿中华根瘤菌、根瘤农杆菌、洛地中生根瘤菌和羊布鲁氏菌）的基因组序列。我们进行了全面的基因分类，以定义染色体直向同源物、与其他复制子（例如质粒）中的同源物的基因以及物种特异性的基因。预计每条染色体上大约有 2000 个基因是直向同源基因，其中大约 80% 是同线性的。在成对的生物体中发现了显着的基因共线性，并且大部分微同线区域和操纵子是相似的。同线产品比非同线产品表现出更高的同一性水平，表明由于功能限制而对序列变异具有抵抗力；此外，同线产品中含有膜片段的比例异常高。同线性基因编码高比例的基本细胞功能，呈现出高水平的功能关系和非常低的水平基因转移率。蛋白质的序列变异性可以被认为是响应特定生态位适应的物种特征。相比之下，对肠杆菌目基因组的分析显示出不同的基因组织，但在同线保守性、同线基因的重要作用以及微同线区域基因之间的更高功能连锁方面给出了相似的结果。同线性细菌基因代表了一个共同进化的群体。它们不仅揭示了最后共同祖先中存在的核心染色体片段并确定了这些微生物共有的代谢特征，而且还表现出对序列变异和重排的抵抗力，这可能是由于它们的基本特征。在根瘤菌目和肠杆菌目中，同线基因编码大部分基本细胞功能，并呈现出高水平的功能关系。
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.
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DOI：
10.1073/pnas.94.22.11911
发表时间：
1997-10-28
影响因子：
11.1
作者：
Gerstein, M;Levitt, M
通讯作者：
Levitt, M
影响因子：
7
作者：
Bankier, AT;Spriggs, HF;Dear, PH
通讯作者：
Dear, PH
影响因子：
3.6
作者：
FERNANDEZHERRERO, LA;BADETDENISOT, MA;BERENGUER, J
通讯作者：
BERENGUER, J
影响因子：
3.2
作者：
HIRSCH, AM;DRAKE, D;LONG, SR
通讯作者：
LONG, SR
影响因子：
1.4
作者：
Jordan, IK;Rogozin, IB;Koonin, EV
通讯作者：
Koonin, EV