Metagenomic Mining of Enzyme Diversity
Enzymes are remarkable biocatalysts, accelerating the rates of a wide range of biochemical reactions and providing “green” solutions for a variety of biotech applications. Because their impact, numerous efforts are being undertaken worldwide, with an ulti
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K. N. Timmis (ed.), Handbook of Hydrocarbon and Lipid Microbiology, DOI 10.1007/978-3-540-77587-4_216, # Springer-Verlag Berlin Heidelberg, 2010
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Metagenomic Mining of Enzyme Diversity
Abstract: Enzymes are remarkable biocatalysts, accelerating the rates of a wide range of biochemical reactions and providing ‘‘green’’ solutions for a variety of biotech applications. Because their impact, numerous efforts are being undertaken worldwide, with an ultimate goal to deliver new, usable substances of enzymatic origin to the marketplace. However, the suboptimal performance of natural enzymes in specific biotechnological settings is also a major bottleneck in catalytic applications (enzymes generally work in a natural cell context, which differs from industrial specifications). The use of metagenomics, a culture-independent technique, to isolate new enzymes coupled with their catalytic understanding would thus maximize our chances of obtaining the ideal biocatalysts, namely biocatalysts that can meet process requirements for a variety of biotech applications while expanding our understanding of the structure, function, and evolution of protein catalysis.
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Introduction
Enzymes are remarkable biocatalysts, accelerating the rates of a wide range of biochemical reactions. In recent years, the potential of enzymes has been harnessed for industrial applications, exploiting their high catalytic efficiency, specificity, and activity under benign conditions. As enzymes do not involve polluting reagents that are hallmark characteristics of chemical synthesis, enzyme-catalyzed reactions provide ‘‘green’’ solutions for manufacturing a variety of compounds (Alcalde et al., 2006). Moreover, enzymes can also offer an efficient solution for the biodegradation of polluting chemicals, thereby playing important roles in the field of bioremediation (Phale et al., 2007). The exploitation of natural microbial diversity for the identification and isolation of novel enzymes is currently an extremely active field in microbiology (Beloqui et al., 2008a; Gabor et al., 2007) that allows genomic analysis of microbial communities in a culture-independent manner. It is estimated that in some environments, more than 99% of the organisms cannot be cultivated, yet can be studied using metagenomic tools (Ward et al., 2008). Indeed, the diversity that can be accessed by metagenomic analysis is overwhelming: it was shown that a pristine soil sample contains more than 104 different microbial species and over thousand million open reading frames (ORFs), many of which encode putative enzymes (Raes et al., 2007). Through the generation of metagenomic libraries from a variety of different habitants, followed by library enrichment and functional screening for different enzymatic activities, a variety of novel enzymes have already been identified (for extensive reviews see Beloqui et al., 2008a; Ferrer et al., 2007). Further, the powers of metagenomics approaches can be combined with directed evolution methodologies for the generation of a biotechnolog
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