Insights into the metabolism pathway and functional genes of long-chain aliphatic alkane degradation in haloarchaea

Abstract

The mineralization of alkane is mainly driven by microorganisms, and the detailed mechanisms of long-chain aliphatic alkane degradation are undeciphered in archaea. We used a hexadecane-degrading haloarchaeon, Halorientalis hydrocarbonoclasticus IM1011 (= CGMCC 13754), as a model system to decode this through transcriptomic and biochemical studies. During growth on hexadecane as sole carbon source, the activity of 3-hydroxyacyl-CoA dehydrogenase, a β-oxidation pathway enzyme, was measured. Biochemical and culture growth experiments confirmed the role of the β-oxidation pathway in aliphatic alkane degradation. Subsequently, transcriptomic analysis of H. hydrocarbonoclasticus cultured in acetate vs. acetate and hexadecane revealed that seven up-regulated genes were common in 5- and 24-h samples. Three were annotated as ribonucleoside-diphosphate reductase R2-like (RNRR2-like) genes, which were predicted to involve in the biodegradation of hexadecane. Based on the transcriptomic level, the putative functional genes were inferred from multiple isogenes. Among these genes, an important cluster encodes three enzymes for the β-oxidation pathway as well as long-chain fatty acid-CoA ligase for pre-step. The present research identified the function of the β-oxidation pathway in aliphatic alkane degradation and recognized the functional genes in haloarchaea. The mineralization of aliphatic alkane in extreme environments driven by archaea was further understood through this study.

Keywords: Aliphatic alkane; Archaea; Haloarchaea; Mineralization; Transcriptomic analysis; β-oxidation pathway.