Niche adaptation of Frankia do not drastically influence their metabolic profiling

Metabolic-profiling (metabolomics/metabonomics) is a measurement strategy among biological systems for low-molecular-weight metabolites and their corresponding intermediates acting as dynamic physiological, pathophysiological and developmental stimuli. Information regarding the metabolomics of Frankia is elusive. In this study, we analyzed 48 Frankia whole-genome sequences. Kyoto Encyclopedia of Genes and Genomes (KEGG) database and KEGG Automatic Annotation Server (KAAS) were used for the prediction and functional annotation of genes associated with diverse metabolic pathways. Comprehensive codon and amino-acid usage analyses along with tRNA adaptation index and dN/dS-based evolutionary inquest were performed. We have used the Database-of-Essential-Genes (DEG) server to predict the essentiality of the metabolic pathway-related-genes. We found a strong effect of compositional constraints on the metabolic pathway genes of Frankia. The evolutionary analysis revealed the conserved nature of the studied genes. Since the metabolic pathway-related genes were found to be housekeeping genes, they are conserved and less evolved. This was further validated with a dN/dS value of less than 1. Moreover, the number of synonymous changes was more than non-synonymous changes so that the amino acid sequence remains identical. The cluster of orthologs (COG) analysis revealed “metabolism” as the main functional category of the studied gene set. The core metabolic pathway-related genes among considered Frankia strains accumulated 115 genes. This study for the first time reveals the genomic characteristics of the metabolic pathway-related genes among Frankia. From all the analysis, we could hypothesize that in spite of their host specificity and differential taxonomical distribution, Frankia maintain a core metabolic proficiency among them.代谢谱分析（metabolomics/metabonomics）是针对生物系统内低分子量代谢物及其对应中间产物的检测策略，此类物质可作为动态的生理、病理生理及发育刺激因子。目前关于弗兰克氏菌（Frankia）的代谢组学相关信息仍较为匮乏。本研究共分析了48株弗兰克氏菌的全基因组序列，采用京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）数据库及KEGG自动注释服务器（KEGG Automatic Annotation Server，KAAS）对参与多种代谢通路的基因进行预测与功能注释。本研究开展了全面的密码子与氨基酸使用偏好分析，并结合tRNA适应指数及基于dN/dS的进化分析展开探究，同时借助必需基因数据库（Database-of-Essential-Genes，DEG）服务器对代谢通路相关基因的必需性进行了预测。研究发现，碱基组成约束对弗兰克氏菌的代谢通路基因具有显著影响。进化分析结果显示，本次研究涉及的基因具有保守性。由于代谢通路相关基因属于持家基因（housekeeping genes），因此它们具备保守性且进化速率较慢，这一结论通过dN/dS值小于1的结果得到了进一步验证。此外，同义替换的数量多于非同义替换，使得氨基酸序列得以保持稳定。直系同源簇（cluster of orthologs，COG）分析结果显示，“代谢”为本次研究基因集的主要功能类别。所分析的弗兰克氏菌菌株中，核心代谢通路相关基因共计115个。本研究首次揭示了弗兰克氏菌代谢通路相关基因的基因组学特征。综合所有分析结果，本研究可提出如下假说：尽管弗兰克氏菌具有宿主特异性及分类分布差异，但其种群内部仍维持着核心代谢能力。