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In addition to the transcriptive machinery of the host, the expression of genes in a metagenomic library host also depends on the DNA insert size [56]. The selection of an appropriate vector based on the nature of the host expression is another hurdle in functional metagenomics. Small insert sizes may limit the detection of important biosynthetic pathways required for novel biomolecule synthesis. Fosmid and Cosmid libraries could accommodate insert sizes of ~15–40 kb, which may be limiting for cloning large size DNA fragments. Large insert libraries like BACs are preferred as they permit the cloning of genes for entire biosynthetic pathways of targeted biomolecules [79]. BACs (Bacterial Artificial Chromosome) can accommodate 100–200 kb of DNA fragments, rendering them suitable for metagenomic libraries. However, maintaining large size metagenomic DNA with a high molecular weight is the other challenge in functional screening. Owing to difficulties such as this in screening large clones, newer technologies like fluorescence‐based assay are gaining importance for the rapid detection of an enzymatic activity. Furthermore, use of a robotic assay simplifies the screening process in high‐throughput screening within a short time period [19].