Genome-wide characterization of sulphur metabolism gene families and recombination dynamics in mangrove-derived Bacillus aryabhattai NM1-A2 and Bacillus cereus NR1
Source: PubMed Central Open Access, NCBI / U.S. National Library of Medicine
Graphical Abstract Mangrove-isolatedNM1-A2 andNR1 genome-wide analyses reveal conserved motif, recombination-driven evolution and purifying selection shaping structurally adaptive sulphur metabolism genes driving functional diversification and biogeochemical transformation. graphical Abstract This study presents a comprehensive genome-wide analysis of sulphur metabolism-related gene families instrain NM1-A2 andstrain NR1, isolated from marine mangrove habitats. We investigated phylogenetic relationships, conserved motifs, recombination events and physicochemical properties of sulphur metabolism genes. Phylogenetic analysis identified 4 major clades (35 genes in NM1-A2 and 34 in NR1), highlighting significant evolutionary relationships. Multiple Expectation Maximization for Motif Elicitation analysis revealed ten conserved motifs, including domains associated with cysteine/methionine metabolism and sulfurtransferases, validated by Pfam and CDD databases. Recombination analysis detected 87 and 64 putative recombination events in NM1-A2 and NR1, respectively, with significant PHI test results (<0.00001), suggesting distinct parental contributions. Physicochemical characterization indicated that sulphur metabolism proteins in both strains exhibit an acidic nature, instability and hydrophobicity, with minimal thermostability. Eleven gene pairs in NM1-A2 and nine in NR1 were identified under purifying selection. Recombination breakpoints were detected at site 682 in NM1-A2 and site
Abstract
Graphical Abstract Mangrove-isolatedNM1-A2 andNR1 genome-wide analyses reveal conserved motif, recombination-driven evolution and purifying selection shaping structurally adaptive sulphur metabolism genes driving functional diversification and biogeochemical transformation. graphical Abstract This study presents a comprehensive genome-wide analysis of sulphur metabolism-related gene families instrain NM1-A2 andstrain NR1, isolated from marine mangrove habitats. We investigated phylogenetic relationships, conserved motifs, recombination events and physicochemical properties of sulphur metabolism genes. Phylogenetic analysis identified 4 major clades (35 genes in NM1-A2 and 34 in NR1), highlighting significant evolutionary relationships. Multiple Expectation Maximization for Motif Elicitation analysis revealed ten conserved motifs, including domains associated with cysteine/methionine metabolism and sulfurtransferases, validated by Pfam and CDD databases. Recombination analysis detected 87 and 64 putative recombination events in NM1-A2 and NR1, respectively, with significant PHI test results (<0.00001), suggesting distinct parental contributions. Physicochemical characterization indicated that sulphur metabolism proteins in both strains exhibit an acidic nature, instability and hydrophobicity, with minimal thermostability. Eleven gene pairs in NM1-A2 and nine in NR1 were identified under purifying selection. Recombination breakpoints were detected at site 682 in NM1-A2 and site 2397 in NR1 using Genetic Algorithm Recombination Detection. Secondary structure analysis showed disorder percentages of 0–19% in NM1-A2 and 0–16% in NR1, with alpha-helical and beta-sheet and TM helix composition variations. These findings provide new insights into the evolutionary dynamics, functional diversity and structural adaptations of sulphur metabolism genes in marinestrains, enhancing our understanding of their ecological roles in mangrove ecosystems.