Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.
Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.
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DOI：
10.1371/journal.pcbi.0020002
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发表时间：
2006-01
影响因子：
4.3
通讯作者：
Palsson, Bernhard O
中科院分区：
文献类型：
--
作者：
Allen, Timothy E;Price, Nathan D;Joyce, Andrew R;Palsson, Bernhard O
基因组组织可以通过分析序列衍生参数中的染色体位置依赖模式来研究。在原核生物序列和基因组规模的功能数据的这种模式的全面分析尚未进行。我们检测到的空间模式序列衍生的参数发生在135个细菌和16个古细菌生物体的163条染色体，利用小波分析。模式强度被发现与生物体的特定功能，如基因组大小，整体GC含量，并发生已知的运动和染色体结合蛋白。鉴于大肠杆菌的额外的功能数据，我们发现显着的相关性染色体的位置依赖的模式在许多属性，其中一些是一致的，与以前的实验确定的染色体宏域。这些结果表明，大多数测序基因组的大规模组织是显着非随机的，而且，这种组织可能与基因组大小，核苷酸组成和信息传递过程。因此，基因组进化和设计的限制不仅取决于信息内容，而且还取决于染色体复杂的多参数、多长度尺度组织。十多年来，越来越多的微生物生物体的遗传物质已经使用基因组测序技术通过实验确定。这些测序的基因组为研究人员提供了关于每个生物体的组成和能力的丰富信息，因为它们作为“部件列表”，指定每个细胞产生的蛋白质机制。然而，基因组不仅仅是“列表”，而且通常以非随机顺序排列。人们认为，这种顺序可能在某种程度上与每个基因组被包装在细胞的微小范围内的方式有关（通常超过1,000倍包装）。作者使用信号处理方法来识别大多数测序微生物基因组排列中的长距离空间模式，并且他们将每个基因组中的组织程度与相应生物体特有的各种特征联系起来。他们还详细分析了一种模式细菌大肠杆菌（Escherichia coli）的许多不同类型数据中模式之间的重叠程度。他们的研究结果最终证明，基因组组织和基因组内容存在重要的进化约束，并且在从根本上理解微生物细胞如何工作时，组织和功能之间的相互作用不可忽视。
Genome organization can be studied through analysis of chromosome position-dependent patterns in sequence-derived parameters. A comprehensive analysis of such patterns in prokaryotic sequences and genome-scale functional data has yet to be performed. We detected spatial patterns in sequence-derived parameters for 163 chromosomes occurring in 135 bacterial and 16 archaeal organisms using wavelet analysis. Pattern strength was found to correlate with organism-specific features such as genome size, overall GC content, and the occurrence of known motility and chromosomal binding proteins. Given additional functional data for Escherichia coli, we found significant correlations among chromosome position dependent patterns in numerous properties, some of which are consistent with previously experimentally identified chromosome macrodomains. These results demonstrate that the large-scale organization of most sequenced genomes is significantly nonrandom, and, moreover, that this organization is likely linked to genome size, nucleotide composition, and information transfer processes. Constraints on genome evolution and design are thus not solely dependent upon information content, but also upon an intricate multi-parameter, multi-length-scale organization of the chromosome. For more than a decade, the genetic material for a growing number of microbial organisms has been determined experimentally using genome sequencing techniques. These sequenced genomes provide researchers with an abundance of information regarding the composition and capabilities of each organism since they serve as “parts lists” that specify the protein machinery that each cell generates. However, genomes are not merely “lists” but also are typically arranged in nonrandom order. It is thought that this order may be related to some extent to the way in which each genome is packed into the tiny confines of a cell (often more than 1,000-fold packing). The authors have used signal processing methods to identify long-range spatial patterns in the arrangement of most sequenced microbial genomes, and they have related the degree of organization in each genome to various characteristics specific to the corresponding organisms. They have also analyzed in detail the degree of overlap among patterns in numerous different kinds of data for a model bacterial organism, Escherichia coli. Their results conclusively demonstrate that there are significant evolutionary constraints that act upon genome organization as well as genome content, and that the interplay between organization and function cannot be ignored in understanding fundamentally how a microbial cell works.