Genome-wide identification of bacterial plant colonization genes.
Genome-wide identification of bacterial plant colonization genes.
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DOI：
10.1371/journal.pbio.2002860
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发表时间：
2017-09
期刊：
影响因子：
9.8
通讯作者：
Visel A
中科院分区：
文献类型：
--
作者：
Cole BJ;Feltcher ME;Waters RJ;Wetmore KM;Mucyn TS;Ryan EM;Wang G;Ul-Hasan S;McDonald M;Yoshikuni Y;Malmstrom RR;Deutschbauer AM;Dangl JL;Visel A
不同的土壤细菌可以促进植物的生长和健康，但使它们能够有效地在植物宿主上定居的分子机制仍然知之甚少。我们使用随机条形码转座子突变测序(RB-TnSeq)在拟南芥根部定植的模式细菌-西米氏假单胞菌中建立了一个定殖所需的细菌基因的全基因组图谱。我们鉴定了115个基因(占西洋参基因总数的2%)，它们的功能是最大限度地竞争定植根系所必需的。在我们鉴定的基因中，有一些在运动和碳代谢中具有明显的定植相关作用，还有44个基因没有或没有或没有明确的功能预测。对单个基因的独立验证分析证实了22例中的20例(91%)具有定植功能。为了进一步确定我们筛选的基因的特征，我们用RB-TnSeq方法比较了在90个不同的体外条件下西米松基因对生长的功能贡献，突出了与根定植基因相关的特定代谢功能。我们通过序列驱动的饱和突变对细菌基因的分析揭示了植物根定植的遗传决定因素的全基因组图谱，并为有针对性地提高植物有益微生物的定殖能力提供了一个起点。植物固定碳以产生大量的糖和氨基酸，从而为居住在土壤中的微生物提供诱人的环境。一旦这些微生物在根环境中定居，它们就会极大地影响植物的生长和发育。我们开始使用全基因组转座子突变方法(随机条形码转座子测序[RB-TnSeq])来鉴定一组控制或影响根定植的微生物基因。通过使用这种方法，我们识别了数百个基因，这些基因在突变时会影响西米亚细菌竞争性地在模式植物A.thaliana的根系中定植的能力。这些基因包括许多据称与碳水化合物代谢、细胞壁生物合成和运动性有关的基因，强调了糖代谢、防御和运动性都是根部定植微生物的关键特征。我们还鉴定了几个氨基酸运输和代谢基因，这些基因的突变赋予了根部定植的适合性优势。最后，我们鉴定了几个功能未知的基因，它们在突变时会显著改变根的定植能力。这些发现提出了新的工程策略来改进生物制品的开发，并将促进对根部定植过程的机械性探索。
Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system. Among the genes we identified were some with obvious colonization-related roles in motility and carbon metabolism, as well as 44 other genes that had no or vague functional predictions. Independent validation assays of individual genes confirmed colonization functions for 20 of 22 (91%) cases tested. To further characterize genes identified by our screen, we compared the functional contributions of P. simiae genes to growth in 90 distinct in vitro conditions by RB-TnSeq, highlighting specific metabolic functions associated with root colonization genes. Our analysis of bacterial genes by sequence-driven saturation mutagenesis revealed a genome-wide map of the genetic determinants of plant root colonization and offers a starting point for targeted improvement of the colonization capabilities of plant-beneficial microbes. Plants fix carbon to create an abundance of sugars and amino acids, thus providing an enticing environment for microorganisms that reside in soil. Once these microorganisms have colonized the root environment, they can dramatically influence plant growth and development. We set out to identify a comprehensive set of microbial genes that control or influence root colonization, using a genome-wide transposon mutagenesis approach (randomly barcoded transposon sequencing [RB-TnSeq]). By using this method, we identified several hundred genes that, when mutated, affect the ability of the bacterium P. simiae to competitively colonize the root system of the model plant A. thaliana. These included many genes purported to be involved in carbohydrate metabolism, cell wall biosynthesis, and motility, underscoring the notion that sugar metabolism, defense, and motility are all key features of a root-colonizing microbe. We also identified several amino acid transport and metabolism genes with mutations that confer a fitness advantage in root colonization. Lastly, we identified several genes with no known function that significantly alter root colonization ability when mutated. These findings suggest novel engineering strategies to improve biological product development, and will facilitate the mechanistic exploration of the root colonization process.
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