还原性脱卤酶的生物信息学分析

Bioinformatics analysis of reductive dehalogenases

摘要:

【背景】有机卤呼吸细菌介导的还原性脱卤过程对于卤素循环与有机卤污染场地的修复至关重要。还原性脱卤酶(reductive dehalogenases, RDases)作为有机卤呼吸的末端电子受体还原酶，在脱卤过程中起着关键作用。【目的】系统地了解还原性脱卤酶的序列与结构特征，为阐明还原性脱卤酶及有机卤呼吸细菌作用机制及生物学功能奠定基础。【方法】应用多种生物信息学分析工具对44个还原性脱卤酶蛋白的基本理化性质、跨膜结构、信号肽、磷酸化位点、系统发育关系、多序列比对的同源性矩阵、保守基序、保守结构域、二级结构、三级结构及无序区域进行预测分析。【结果】不同还原性脱卤酶蛋白的理化性质存在差异，但呈现出一定的保守性。不同还原性脱卤酶蛋白的磷酸化位点、保守结构域分布、保守基序分布，以及二级结构的保守性较高。底物类别相似或相同的还原性脱卤酶在蛋白序列和三级结构上更为相似。大多数还原性脱卤酶蛋白的亲缘关系较近。还原性脱卤酶蛋白主要为分泌型蛋白、非膜定位蛋白和固有无序蛋白。【结论】不同还原性脱卤酶蛋白具有一定的保守性，因此能够发挥相似的生物学功能。研究结果对进一步研究还原性脱卤酶具有一定的参考价值，尤其是为基于还原性脱卤酶的有机卤呼吸细菌应用于实际场地修复提供科学依据与理论参考。

关键词:还原性脱卤酶;生物信息学;有机卤呼吸细菌

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.

Key words:reductive dehalogenase;bioinformatics;organohalide-respiring bacteria