Niche adaptation of Frankia do not drastically influence their metabolic profiling

Abstract

ABSTRACT 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.