Mining of two novel aldehyde dehydrogenases (DHY-SC-VUT5 and DHY-G-VUT7) from metagenome of hydrocarbon contaminated soils

Cindy Baburam,Naser Aliye Feto

doi:10.1186/s12896-021-00677-8

Abstract

BackgroundAldehyde dehydrogenases are vital for aerobic hydrocarbon degradation and is involved in the last step of catalysing the oxidation of aldehydes to carboxylic acids. With the global increase in hydrocarbon pollution of different environments, these enzymes have the potential to be used in enzymatic bioremediation applications.ResultsFifteen fosmid clones with hydrocarbon degrading potential were functionally screened to identify dehydrogenase enzymes. Accordingly, the fosmid insert of the positive clones were sequenced using PacBio next generation sequencing platform and de novo assembled using CLC Genomic Work Bench. The 1233 bp long open reading frame (ORF) for DHY-SC-VUT5 was found to share a protein sequence similarity of 97.7% to short-chain dehydrogenase from E. coli. The 1470 bp long ORF for DHY-G-VUT7 was found to share a protein sequence similarity of 23.9% to glycine dehydrogenase (decarboxylating) (EC 1.4.4.2) from Caulobacter vibrioides (strain NA1000 / CB15N) (Caulobacter crescentus). The in silico analyses and blast against UNIPROT protein database with the stated similarity show that the two dehydrogenases are novel. Biochemical characterization revealed, that the highest relative activity was observed at substrate concentrations of 150 mM and 50 mM for DHY-SC-VUT5 and DHY-G-VUT7, respectively. The Km values were found to be 13.77 mM with a Vmax of 0.009135 μmol.min− 1 and 2.832 mM with a Vmax of 0.005886 μmol.min− 1 for DHY-SC-VUT5 and DHY-G-VUT7, respectively. Thus, a potent and efficient enzyme for alkyl aldehyde conversion to carboxylic acid.ConclusionThe microorganisms overexpressing the novel aldehyde dehydrogenases could be used to make up microbial cocktails for biodegradation of alkanes. Moreover, since the discovered enzymes are novel it would be interesting to solve their structures by crystallography and explore the downstream applications.

Highlights

Aldehyde dehydrogenases are vital for aerobic hydrocarbon degradation and is involved in the last step of catalysing the oxidation of aldehydes to carboxylic acids
The longest assembled contigs for each clone obtained from this software program was used to obtain open reading frames and find regions of local similarity between known sequences to identify aldehyde dehydrogenase genes involved in the third step of aerobic hydrocarbon degradation Uniprot-Swiss prot database
An open reading frame (ORF) of 1233 bp in length encoding a polypeptide of 406 amino acids with 50.6 kDa predicted molecular mass was compared to UniProt protein database using BlastP and found to share a protein sequence similarity of 97.7% to short-chain dehydrogenase from E. coli

Summary

Introduction

Aldehyde dehydrogenases are vital for aerobic hydrocarbon degradation and is involved in the last step of catalysing the oxidation of aldehydes to carboxylic acids. With the global increase in hydrocarbon pollution of different environments, these enzymes have the potential to be used in enzymatic bioremediation applications. Anthropogenic disturbances such as hydrocarbon contamination in soil environments can affect the microbial community structure and diversity since it is toxic to microbial cells [1, 2]. Some microorganisms have the ability to use hydrocarbons as a sole carbon source such soils represent a complex environment teeming with microbial diversity, which is preferred for gene mining and natural product discovery [3]. Hydrocarbon-polluted soil sites can be targeted with confidence in identifying novel aldehyde dehydrogenases (ALDHs) involved in aerobic pathways for petroleum hydrocarbon breakdown [4]. Enzymes are sought-after biomolecules for their potential in industrial processes and environmental bioremediation [11]

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Conclusion