Primers: Bacterial Genes Encoding Enzymes for Aerobic Hydrocarbon Degradation

Abstract

Alkanes are saturated hydrocarbons that are ubiquitous in the environment. Microbial degradation pathways evolved to activate and catabolise these compounds in order to gain energy and building blocks for cell growth. These pathways involve a number of hydroxylases, which primarily differ according to the nature of the hydrocarbon itself (e.g. aromatic or aliphatic). Given the widespread distribution of alkanes in the environment, a number of variants of such enzymes are present among microbes. Hence, primers designed to detect such environmental variants would require a database with a sufficiently large number of sequences. In the present chapter, we selected the integral-membrane alkane hydroxylases (AlkB) and cytochrome P450 alkane hydroxylases (CYP153) superfamilies for sketching a general proposal of a design pipeline to target bacterial genes involved in aerobic alkane degradation. Further, we introduce HyDeg, a web-based tool that targets multiple subfamilies of enzymes involved in the microbial degradation of aromatic/aliphatic hydrocarbons. The website allows to retrieve amino acid and nucleotide sequences of the target family and proposes an evolutionary relationship for the selected enzyme.