Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil.
Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil.
Mol Phylogenet Evol. 2022 Dec;177:107624. doi: 10.1016/j.ympev.2022.107624. Epub 2022 Sep 7.
Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.
饶河根瘤菌是从小麦中分离出来的固氮细菌，具有多种促进植物生长的能力。除了传统的钼氮酶外，该菌还含有一种替代的铁氮酶，其许多与调节、生理和进化相关的方面仍有待阐明。在这项工作中，研究了该替代系统的起源，探索了氮酶在泛菌科家族中的分布和多样化。我们的分析表明，固氮菌占泛菌科基因组的 17%，其中只有 14.4%（泛菌科基因组的 2.5%）也含有铁或 V-氮酶。还描述了多种 nif 样序列，主要出现在也含有替代系统的基因组中。含有铁氮酶的基因组分析显示，nifEN anfHDGK 簇在三个属中是保守的：戈尔利伯克氏菌、丰棒杆菌和类芽孢杆菌。anfHDGK 的系统发育将铁氮酶分为三个主要组。我们的分析表明，铁氮酶是通过水平基因转移（HGT）从丰棒杆菌、戈尔利伯克氏菌和类芽孢杆菌属的祖先谱系中获得的，而这一替代氮酶在这些属中的进化进一步标志着转移和基因丢失事件的发生。固氮泛菌科的物种系统发育将固氮菌分为五个分支，其中一个分支包含了所有携带类芽孢杆菌属替代氮酶的菌株。该分支的泛基因组是开放的，由超过 96%的辅助基因组成。在灵活的基因组中，丰富了多种功能类别，包括与复制和修复相关的功能。后者涉及与 HGT 相关的多种基因，表明这些事件可能在固氮类芽孢杆菌的进化中起着重要作用。本研究从不同的基因组角度深入了解了泛菌科中替代氮酶基因的组织、分布和进化。
