Isolation an Aldehyde Dehydrogenase Gene from Metagenomics Based on Semi-nest Touch-Down PCR

Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water

Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.

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

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 K_m values were found to be 13.77 mM with a V_max of 0.009135 μmol.min^− 1 and 2.832 mM with a V_max 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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12896-021-00677-8.

Engineering of a chromogenic enzyme screening system based on an auxiliary indole-3-carboxylic acid monooxygenase

Here, we present a proof‐of‐principle for a new high‐throughput functional screening of metagenomic libraries for the selection of enzymes with different activities, predetermined by the substrate being used. By this approach, a total of 21 enzyme‐coding genes were selected, including members of xanthine dehydrogenase, aldehyde dehydrogenase (ALDH), and amidohydrolase families. The screening system is based on a pro‐chromogenic substrate, which is transformed by the target enzyme to indole‐3‐carboxylic acid. The later compound is converted to indoxyl by a newly identified indole‐3‐carboxylate monooxygenase (Icm). Due to the spontaneous oxidation of indoxyl to indigo, the target enzyme‐producing colonies turn blue. Two types of pro‐chromogenic substrates have been tested. Indole‐3‐carboxaldehydes and the amides of indole‐3‐carboxylic acid have been applied as substrates for screening of the ALDHs and amidohydrolases, respectively. Both plate assays described here are rapid, convenient, easy to perform, and adaptable for the screening of a large number of samples both in Escherichia coli and Rhodococcus sp. In addition, the fine‐tuning of the pro‐chromogenic substrate allows screening enzymes with the desired substrate specificity.