Genomic Organization of Evolutionarily Correlated Genes in Bacteria: Limits and Strategies
Genomic Organization of Evolutionarily Correlated Genes in Bacteria: Limits and Strategies
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DOI：
10.1016/j.jmb.2012.03.009
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发表时间：
2012-06-22
影响因子：
5.6
通讯作者：
Kepes, Francois
中科院分区：
文献类型：
--
作者：
Junier, Ivan;Herisson, Joan;Kepes, Francois
对细胞内有效的分子在时间和空间上相互作用的需要施加了强烈的限制，如果染色体上的相对基因位置合适，这种限制可以部分放松。比较基因组学研究表明，细菌染色体上的基因邻近性具有短期保守性。此外，进化相关基因在大肠杆菌中的长期周期性定位最近也得到了重视。为了进一步了解这些不同的遗传组织，我们通过评估基准数据集中进化相关的基因组，检验了所有可用真细菌基因组的染色体接近度和周期性之间的妥协。在肠杆菌中，严格的染色体接近度仅限于20个基因以下的组，而周期性在所有超过50个基因的组中都显著。大肠杆菌K12基因组含有511个周期基因(占基因组的12%)，其同源基因在所有真细菌门中都被发现是周期性的。这些周期基因在细胞成分的大分子合成和空间组织中起主要作用。它们富含必需基因和看家基因，往往是结构性表达的。在此基础上，有人认为染色体邻近和周期性是普遍存在的互补基因组策略，有利于协同功能分子局部浓度的建立。特别是，周期性布局可以促进染色体折叠，从而在空间上组织主要细胞成分的构建。20个基因的转变让人想起最长操纵子和拓扑微域的大小。因此，DNA邻域优化生化相互作用的范围可能由DNA拓扑学定义。(C)2012爱思唯尔有限公司。保留所有权利。
The need for efficient molecular interplay in time and space within a cell imposes strong constraints that could be partially relaxed if relative gene positions along chromosomes were appropriate. Comparative genomics studies have demonstrated the short-scale conservation of gene proximity along bacterial chromosomes. Additionally, the long-range periodic positioning of evolutionarily correlated genes within Escherichia coli has recently been highlighted. To gain further insight into these different genetic organizations, we examined the compromise between chromosomal proximity and periodicity for all available eubacterial genomes by evaluating groups of evolutionarily correlated genes from a benchmark data set.In enterobacteria, strict chromosomal proximity is found to be limited to groups under 20 genes, whereas periodicity is significant in all groups over 50. The E. coli K12 genome bears 511 periodic genes (12% of the genome), whose orthologs are found to be periodic in all eubacterial phyla. These periodic genes predominantly function in macromolecular synthesis and spatial organization of cellular components. They are enriched in essential and housekeeping genes and tend to often be constitutively expressed.On this basis, it is argued that chromosomal proximity and periodicity are ubiquitous complementary genomic strategies that favor the build-up of local concentrations of co-functional molecules. In particular, the periodic layout may facilitate chromosome folding to spatially organize the construction of major cell components. The transition at 20 genes is reminiscent of the size of the longest operons and of topological microdomains. The range for which DNA neighborhood optimizes biochemical interactions might therefore be defined by DNA topology. (C) 2012 Elsevier Ltd. All rights reserved.