In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB).

Area of Science:

• Microbiology
• Enzymology
• Bioinformatics

Background:

• Poly(cis-1,4-isoprene) is a natural polymer with limited biodegradation pathways.
• Enzymes capable of cleaving this polymer are of significant biotechnological interest.
• Understanding the evolution and function of such enzymes can reveal novel biodegradation mechanisms.

Purpose of the Study:

• To identify and characterize bacterial enzymes involved in poly(cis-1,4-isoprene) degradation.
• To explore the evolutionary history and functional diversification of these enzymes.
• To investigate the potential emergence of novel rubber oxygenases.

Main Methods:

• In silico identification of putative poly(cis-1,4-isoprene) cleaving enzymes (RoxA, RoxB).
• Comparative genomics and phylogenetic analysis to trace evolutionary pathways.
• Analysis of gene duplication, horizontal gene transfer, recombination, and selective pressures.
• In silico examination of conserved motifs and functionally important residues.

Main Results:

• RoxA and RoxB orthologs are primarily found in Gram-negative Proteobacteria (beta, gamma, delta classes).
• Horizontal gene transfer is a key mechanism in the evolution of RoxA and RoxB within Proteobacteria.
• Differential selective pressures drive diversification of RoxA and conservation of RoxB, with conserved functional sites.
• Phylogenetic analysis revealed a distinct RoxA/RoxB split and the emergence of a putative RoxC variant in Gammaproteobacteria.
• RoxC shows characteristics of both RoxA and RoxB but is more similar to RoxB in key motifs.

Conclusions:

• RoxA and RoxB represent a conserved enzymatic system for poly(cis-1,4-isoprene) cleavage in Proteobacteria.
• Evolutionary dynamics, including HGT and diversifying selection, have shaped the Rox enzyme family.
• The putative RoxC enzyme may represent a novel functional variant with potential biotechnological applications.