A New Phylogenetic Approach to Classification of AlkB Family Alkane Monooxygenases from Rhodococcus (Sensu Lato) Group Reveals Huge Diversity and Allows to Propose Generalized AlkB Types

The elimination of hydrocarbon pollution is a critical environmental challenge, often addressed using biotechnological approaches. The study of alkane oxidizing bacteria is an important task, as it will allow developing new approaches to oil pollution treatment and improving existing ones. Representatives of the genus Rhodococcus are well-known hydrocarbon-oxidizing bacteria with high biotechnological potential. A distinctive feature of some Rhodococcus species is the presence of multiple homologous alkB genes within their genomes. However, the reasons behind this redundancy and the functional diversity of the alkane monooxygenases encoded by these genes remain unclear. Furthermore, despite the significant diversity of alkB genes even within this single genus, a comprehensive classification system has yet to be established. In this study, we conducted a phylogenetic analysis of all AlkB family alkane monooxygenases identified in Rhodococcus genomes and examined the genomic context of their corresponding genes. Our findings reveal a remarkable diversity of AlkB enzymes, refine the classification of previously described AlkB types, and propose three novel types.For the AlkB0 type, we identified deviations from previously reported signature amino acid motifs. Our results highlight the key role of colocalization of alkane monooxygenase alkB genes with rubredoxin rubB genes in the further functional classification of alkane monooxygenases.