Bioinformatics analysis of reductive dehalogenases

Abstract:

[Background] The reductive dehalogenation process mediated by organohalide- respiring bacteria is crucial for halogen cycling and the remediation of organohalide- contaminated sites. Reductive dehalogenases (RDases), as terminal electron acceptor reductases in organohalide respiration, play a critical role in dehalogenation. [Objective] To systematically understand the sequence and structural characteristics of RDase proteins and lay a foundation for elucidating the mechanisms and biological functions of RDases and organohalide-respiring bacteria. [Methods] Multiple bioinformatics tools were used to predict the basic physicochemical properties, transmembrane structures, signal peptides, phosphorylation sites, phylogenetic relationship, homology matrix of multiple sequence alignments, conserved motifs, conserved domains, secondary structures, tertiary structures, and disordered regions of 44 RDase proteins. [Results] The physicochemical properties varied among different RDase proteins, but they were conserved to some extent. The phosphorylation sites, distribution of conserved domains, distribution of conserved motifs, and secondary structures were highly conserved among different RDases proteins. The RDases with similar or identical substrate categories tended to have greater similarity in their protein sequences and tertiary structures. The phylogenetic relationships were relatively close among most RDase proteins. RDase proteins were primarily secretory proteins, non-membrane proteins, and intrinsically disordered proteins. [Conclusion] Different RDase proteins are conserved to some extent and thus have similar biological functions. The findings provide a valuable reference for further studies on RDases, particularly offering scientific evidence and theoretical support for the application of organohalide-respiring bacteria based on RDases in site remediation.