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

Abstract

Background 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. Results Fifteen 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. Conclusion The 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.

Use of Shotgun Metagenomics to Assess the Microbial Diversity and Hydrocarbons Degrading Functions of Auto-Mechanic Workshops Soils Polluted with Gasoline and Diesel Fuel

“…Indeed, alkane monooxygenases oxidize n -alkanes to their corresponding primary alcohols. The formed alcohols are in turn oxidized by alcohol dehydrogenases that produce the corresponding alkyl aldehydes and further, carboxylic acids that enter general metabolism through the action of aldehyde dehydrogenase [ 39 , 40 , 41 ]. The alkane−1-monooxygenase enzyme, as found in this study and commonly referred to as AlkB, is encoded by the alkB gene widely spread in bacterial communities and is considered a biomarker for community remediation potential [ 35 , 42 ].…”

Stairway to Stereoisomers: Engineering Short‐ and Medium‐Chain Ketoreductases To Produce Chiral Alcohols

“…Studies also report upregulation in SDRs in dye and pharmaceutical degrading microbes. [5,6] Further, they are used for making catalytic cocktails to degrade oil spills, long-chain alkanes, etc.. [7] Therefore, organisms that grow on decaying wood, rotten fruit, wastewater, or toxic landfills have been good sources for exploring members from both superfamilies.…”

Investigation of Global Trends of Pollutants in Marine Ecosystems around Barrang Caddi Island, Spermonde Archipelago Cluster: An Ecological Approach

“…However, they certainly cannot balance the speed of increase in the volume of pollutants entering the environment, when operating at a limited rate, and especially in the most vulnerable marine ecosystems [51]. This level of pollution could become a severe threat to the Earth's population, especially in marine areas and ecosystems, which could act as giant containers for almost all types of waste that are left over from human activities and dynamic natural processes [52,53].…”