Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti.
Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti.
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DOI：
10.1371/journal.pgen.1007357
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发表时间：
2018-04
期刊：
影响因子：
4.5
通讯作者：
Griffitts JS
中科院分区：
文献类型：
--
作者：
diCenzo GC;Benedict AB;Fondi M;Walker GC;Finan TM;Mengoni A;Griffitts JS
细菌基因组进化的特点是功能性遗传片段的获得、丢失和重新排列。大规模基因组改变影响基因型-表型关系的程度尚未以高通量方式进行研究。在共生土壤细菌苜蓿中华根瘤菌中，基因组由一条染色体和两个大型染色体外复制子（pSymA和pSymB，它们共同构成基因组的45%）组成。采用大规模并行转座子插入测序（Tn-seq）来评估染色体基因在存在和不存在这些染色体外复制子的情况下对生长适应性的贡献。来自不同功能类别的 10% 染色体基因显示与 pSymA 和 pSymB 存在遗传相互作用。这些结果证明了染色体外复制子提供的普遍稳健性，基于约束的代谢模型进一步支持了这一点。通过 Tn-seq 引导的计算机模拟代谢网络重建，生成了苜蓿核心代谢的全面图景，产生了包含 726 个基因的核心网络。这种综合方法促进了先前未表征基因的功能分配，同时还揭示了仅 Tn-seq 就错过了超过四分之一的野生型代谢。这项工作强调了细菌复制子之间和整个基因组中可能出现的许多功能依赖性和上位关系，同时还展示了如何将 Tn-seq 和代谢模型结合使用，以产生单独使用任何一种方法都无法获得的见解。苜蓿中华根瘤菌传统上促进了对共生通讯的突破性见解，它也正在成为研究细菌染色体和古代获得的辅助复制子之间功能关系进化的优秀模型。目前测序的细菌基因组中约有 10% 存在多复制子基因组结构。苜蓿基因组由三个环状复制子组成，其中两个复制子是可有可无的，尽管它们包含了该生物体中近一半的蛋白质编码基因。缺乏这些复制子的菌株的构建使得能够对染色体和非必需复制子之间的相互作用进行直接的全基因组分析，揭示这些基因组成分之间广泛的功能合作。该分析使苜蓿根瘤菌的代谢网络模型得到了实质性的改进。大规模并行基因型-表型筛选与计算机代谢重建的整合增强了我们对代谢网络结构的理解，因为它与苜蓿基因组进化相关，并举例说明了一种可以有效应用于其他类群的方法。这里采用的实验和计算相结合的方法进一步为大型细菌基因组中可能存在的普遍遗传相互作用提供了独特的见解。
Bacterial genome evolution is characterized by gains, losses, and rearrangements of functional genetic segments. The extent to which large-scale genomic alterations influence genotype-phenotype relationships has not been investigated in a high-throughput manner. In the symbiotic soil bacterium Sinorhizobium meliloti, the genome is composed of a chromosome and two large extrachromosomal replicons (pSymA and pSymB, which together constitute 45% of the genome). Massively parallel transposon insertion sequencing (Tn-seq) was employed to evaluate the contributions of chromosomal genes to growth fitness in both the presence and absence of these extrachromosomal replicons. Ten percent of chromosomal genes from diverse functional categories are shown to genetically interact with pSymA and pSymB. These results demonstrate the pervasive robustness provided by the extrachromosomal replicons, which is further supported by constraint-based metabolic modeling. A comprehensive picture of core S. meliloti metabolism was generated through a Tn-seq-guided in silico metabolic network reconstruction, producing a core network encompassing 726 genes. This integrated approach facilitated functional assignments for previously uncharacterized genes, while also revealing that Tn-seq alone missed over a quarter of wild-type metabolism. This work highlights the many functional dependencies and epistatic relationships that may arise between bacterial replicons and across a genome, while also demonstrating how Tn-seq and metabolic modeling can be used together to yield insights not obtainable by either method alone. S. meliloti, which has traditionally facilitated ground-breaking insights into symbiotic communication, is also emerging as an excellent model for studying the evolution of functional relationships between bacterial chromosomes and anciently acquired accessory replicons. Multi-replicon genome architecture is present in ~ 10% of presently sequenced bacterial genomes. The S. meliloti genome is composed of three circular replicons, two of which are dispensable even though they encompass nearly half of the protein-coding genes in this organism. The construction of strains lacking these replicons has enabled a straightforward, genome-wide analysis of interactions between the chromosome and the non-essential replicons, revealing extensive functional cooperation between these genomic components. This analysis enabled a substantial refinement of a metabolic network model for S. meliloti. The integration of massively parallel genotype-phenotype screening with in silico metabolic reconstruction has enhanced our understanding of metabolic network structure as it relates to genome evolution in S. meliloti, and exemplifies an approach that may be productively applied to other taxa. The combined experimental and computational approach employed here further provides unique insights into the pervasive genetic interactions that may exist within large bacterial genomes.
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影响因子：
4.4
作者：
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作者：
diCenzo, George C.;Zamani, Maryam;Finan, Turlough M.
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