How to quickly, efficiently and robustly screen metagenome-derived enzymes
2023-11-08
Over the past few decades, the use of metagenomics to mine genomes from non-cultured microorganisms has been a powerful tool for discovering new proteins and other valuable biomolecules. The vast amount of sequencing data generated by metagenomics gives a glimpse into the biosynthetic potential of uncultured microorganisms. However, the functional identification of biomolecules relies heavily on the successful expression and subsequent biochemical validation of target genes. While functional metagenomics has the potential to produce truly novel enzymes, it has encountered serious challenges in protein expression. It requires long and laborious processes, such as generating a large library of clones from environmental DNA. And a series of subcloning steps of positive clones are also required to confirm the target gene.
The inefficient expression and lengthy process of functional metagenomics has been the greatest limitation to the discovery of new biomolecules. In classical functional metagenomics, environmental DNA is directly cloned in a large insertion vector vector and shuttled into E. coli after phage packaging. Subsequent screening success is based on the host's ability to actively express foreign DNA, fold and secrete proteins. In addition to the low positive hit rate, it is highly biased towards the phylogenetic origin of the host tissue. In industrial screening, a large number of candidate genes need to be pre-screened and cloned, which is very time-consuming. There is an urgent need to develop a rapid, unbiased method for activity screening of metagenomic resources.
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