Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
复制标题
DOI：
10.1038/nature05624
复制
发表时间：
2007-03-29
期刊：
影响因子：
64.8
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
--
作者：
Lo, Ian;Denef, Vincent J.;Banfield, Jillian F.
微生物构成了现存有机体的大多数，但关于微生物多样化的本质和驱动力仍有许多需要了解。我们对微生物如何适应和进化的理解可以通过对基因交换模式的全基因组记录来推进，特别是如果分析针对的是自然群落中共存的成员。在这里，我们使用群落基因组数据集来鉴定具有菌株特异性的表达蛋白质，这些蛋白质来自基因组未描述的、天然的、嗜酸性生物膜的主要成员。蛋白质组学结果揭示了一种通过重组而形成的基因组，该基因组涉及数十到数百个碱基的染色体区域，这些区域来自两个密切相关的细菌种群。通过对分离株和未培植的自然群体进行多位点序列分析，证实了种群间的遗传交换。这些发现表明，大块基因变异的交换对于适应非常酸性、富含金属的环境中的特定生态位至关重要。基于质谱学对表达的蛋白质产品的区分，差异小至单一氨基酸，使我们能够区分密切相关的共存生物体的行为。这一点很重要，因为作为单一物种组合在一起的微生物在自然系统中可能扮演着截然不同的角色(1-3)，它们的相互作用可能是生态系统优化的关键。由于蛋白质组数据同时传达有关基因组类型和活性的信息，菌株解析的群落蛋白质组学是对自然环境中微生物的独立培养基因组(元基因组)分析的重要补充(4-6)。
Microbes comprise the majority of extant organisms, yet much remains to be learned about the nature and driving forces of microbial diversification. Our understanding of how microorganisms adapt and evolve can be advanced by genome-wide documentation of the patterns of genetic exchange, particularly if analyses target coexisting members of natural communities. Here we use community genomic data sets to identify, with strain specificity, expressed proteins from the dominant member of a genomically uncharacterized, natural, acidophilic biofilm. Proteomics results reveal a genome shaped by recombination involving chromosomal regions of tens to hundreds of kilobases long that are derived from two closely related bacterial populations. Inter-population genetic exchange was confirmed by multilocus sequence typing of isolates and of uncultivated natural consortia. The findings suggest that exchange of large blocks of gene variants is crucial for the adaptation to specific ecological niches within the very acidic, metal-rich environment. Mass-spectrometry-based discrimination of expressed protein products that differ by as little as a single amino acid enables us to distinguish the behaviour of closely related coexisting organisms. This is important, given that microorganisms grouped together as a single species may have quite distinct roles in natural systems(1-3) and their interactions might be key to ecosystem optimization. Because proteomic data simultaneously convey information about genome type and activity, strain-resolved community proteomics is an important complement to cultivation-independent genomic ( metagenomic) analysis(4-6) of microorganisms in the natural environment.