Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.
Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.
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DOI：
10.1186/1471-2164-15-851
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发表时间：
2014-10-03
期刊：
影响因子：
4.4
通讯作者：
Yuan ZC
中科院分区：
文献类型：
--
作者：
Eastman AW;Heinrichs DE;Yuan ZC
拟青霉属植物根际细菌是重要的植物生长促生菌，可以作为生物反应器。多粘类芽孢杆菌能促进多种重要经济作物的生长。我们实验室最近完成了多粘类芽孢杆菌CR1的基因组测序。截至2014年1月，4个多粘菌基因组已完成测序，但尚未有比较基因组分析的报道。在这里，我们报告了四个测序的多粘菌基因组的比较和遗传分析，揭示了一个非常保守的核心基因组。复杂的代谢途径和调控网络是高度保守的，并允许多粘菌对动态环境线索做出快速反应。与植物激素合成、磷酸盐溶解、铁的获取、转录调控、σ因子、胁迫响应、转运蛋白和生物量降解有关的基因被很好地保守，表明与植物寄主和根际生态位密切相关。此外，每个菌株的核心和副基因组中都存在与抗菌素耐药性和非核糖体肽/聚酮合成有关的基因。比较分析还揭示了副基因组的变异，包括菌株M1和SC2中存在的大质粒。此外，相当数量的菌株特有基因和基因组岛不规则地分布在每个基因组中。尽管所有菌株都编码了各种植物生长促进特性，但只有多粘菌CR1编码了在其他芽孢杆菌中发现的独特的固氮簇。我们的研究表明，与寄主相互作用和生态适合度相关的基因组座位在所分析的多粘虫基因组中高度保守，尽管辅助基因组存在变异。这项工作表明，多粘菌对植物生长的促进作用主要是通过植物激素的产生、养分利用率的增加和生物控制机制来实现的。这项研究提供了对该物种基因组结构的深入了解，从而促进了未来的基因工程和在农业、工业和医学中的应用。此外，这项研究突出了我们目前对革兰氏阳性细菌中复杂的植物生物量代谢的了解的差距。本文的在线版本(DOI：10.1186/1471-2164-15-851)包含补充材料，可供授权用户使用。
Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported. Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp. Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria. The online version of this article (doi:10.1186/1471-2164-15-851) contains supplementary material, which is available to authorized users.
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影响因子：
14.9
作者：
Blin K;Medema MH;Kazempour D;Fischbach MA;Breitling R;Takano E;Weber T
通讯作者：
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影响因子：
4.9
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通讯作者：
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