Nichio Bruno Thiago de Lima, Chaves Roxana Beatriz Ribeiro, Pedrosa Fábio de Oliveira, Raittz Roberto Tadeu
Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technical Education Sector - SEPT, UFPR, Curitiba, Paraná, Brazil.
Department of Biochemistry, Biological Sciences Sector, Federal University of Paraná (UFPR), Curitiba, Paraná, Brazil.
BMC Genomics. 2025 Jan 27;26(1):81. doi: 10.1186/s12864-024-10994-9.
Diazotrophs carry out biological nitrogen fixation (BNF) using the nitrogenase enzyme complex (NEC), which relies on nitrogenase encoded by nif genes. Horizontal gene transfer (HGT) and gene duplications have created significant diversity among these genes, making it challenging to identify potential diazotrophs. Previous studies have established a minimal set of Nif proteins, known as the Nif core, which includes NifH, NifD, NifK, NifE, NifN, and NifB. This study aimed to identify potential diazotroph groups based on the Nif core and to analyze the inheritance patterns of accessory Nif proteins related to Mo-nitrogenase, along with their impact on N2 fixation maintenance.
In a systematic study, 118 diazotrophs were identified, resulting in a database of 2,156 Nif protein sequences obtained with RAFTS³G. Using this Nif database and a data mining strategy, we extended our analysis to 711 species and found that 544 contain the Nif core. A partial Nif core set was observed in eight species in this study. Finally, we cataloged 662 species with Nif core, of which 52 were novel. Our analysis generated 10,076 Nif proteins from these species and revealed some Nif core duplications. Additionally, we determined the optimal cluster value (k = 10) for analyzing diazotrophic diversity. Combining synteny and phylogenetic analyses revealed distinct syntenies in the nif gene composition across ten groups.
This study advances our understanding of the distribution of nif genes, aiding in the prediction and classification of N₂-fixing organisms. Furthermore, we present a comprehensive overview of the diversity, distribution, and evolutionary relationships among diazotrophic organisms associated with the Nif core. The analysis revealed the phylogenetic and functional organization of different groups, identifying synteny patterns and new nif gene arrangements across various bacterial and archaeal species.The identified groups serve as a valuable framework for further exploration of the molecular mechanisms underlying biological nitrogen fixation and its evolutionary significance across different bacterial lineages.
固氮微生物利用固氮酶复合物（NEC）进行生物固氮（BNF），该复合物依赖于由nif基因编码的固氮酶。水平基因转移（HGT）和基因复制在这些基因之间产生了显著的多样性，使得识别潜在的固氮微生物具有挑战性。先前的研究已经确定了一组最小的Nif蛋白，称为Nif核心，其中包括NifH、NifD、NifK、NifE、NifN和NifB。本研究旨在基于Nif核心识别潜在的固氮微生物群体，并分析与钼固氮酶相关的辅助Nif蛋白的遗传模式，以及它们对固氮维持的影响。
在一项系统研究中，鉴定出118种固氮微生物，通过RAFTS³G获得了一个包含2156个Nif蛋白序列的数据库。利用这个Nif数据库和数据挖掘策略，我们将分析扩展到711个物种，发现其中544个含有Nif核心。在本研究的8个物种中观察到部分Nif核心集。最后，我们编目了662个含有Nif核心的物种，其中52个是新物种。我们的分析从这些物种中生成了10076个Nif蛋白，并揭示了一些Nif核心的重复。此外，我们确定了用于分析固氮微生物多样性的最佳聚类值（k = 10）。结合共线性和系统发育分析揭示了十个组中nif基因组成的不同共线性。
本研究推进了我们对nif基因分布的理解，有助于对固氮生物的预测和分类。此外，我们全面概述了与Nif核心相关的固氮生物之间的多样性、分布和进化关系。分析揭示了不同组的系统发育和功能组织，确定了各种细菌和古菌物种中的共线性模式和新的nif基因排列。所鉴定的组为进一步探索生物固氮的分子机制及其在不同细菌谱系中的进化意义提供了有价值的框架。
