TY - JOUR

T1 - Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends

AU - Ferrer, Manuel

AU - Martinez, Monica

AU - Bargiela, Rafael

AU - Streit, Wolfgang R.

AU - Golyshina, Olga

AU - Golyshin, Peter

N1 - European Community project MAMBA. Grant Number: FP7-KBBE-2008–226977; MAGIC-PAH. Grant Number: FP7-KBBE-2009–245226; ULIXES. Grant Number: FP7-KBBE-2010–266473; MicroB3. Grant Number: FP7-OCEAN.2011-2-287589; KILL-SPILL. Grant Number: FP7-KBBE-2012–312139; Royal Society UK-Russia Exchange Grant. Grant Number: IE130218; The Royal Society UK. Grant Number: AN130110; Spanish Ministry of Economy and Competitiveness. Grant Numbers: BIO2011-25012, PCIN-2014-107, BIO2014-54494-R; UK Biotechnology and Biological Sciences Research Council (BBSRC); German Federal Ministry of Education and Research (BMBF). Grant Number: ERA-IB-14–030; European Regional Development Fund (ERDF)

PY - 2016/1/1

Y1 - 2016/1/1

N2 - Recent reports have suggested that the establishment of industrially relevant enzyme collections from environmental genomes has become a routine procedure. Across the studies assessed, a mean number of approximately 44 active clones were obtained in an average size of approximately 53 000 clones tested using naïve screening protocols. This number could be significantly increased in shorter times when novel metagenome enzyme sequences obtained by direct sequencing are selected and subjected to high-throughput expression for subsequent production and characterization. The pre-screening of clone libraries by naïve screens followed by the pyrosequencing of the inserts allowed for a 106-fold increase in the success rate of identifying genes encoding enzymes of interest. However, a much longer time, usually on the order of years, is needed from the time of enzyme identification to the establishment of an industrial process. If the hit frequency for the identification of enzymes performing at high turnover rates under real application conditions could be increased while still covering a high natural diversity, the very expensive and time-consuming enzyme optimization phase would likely be significantly shortened. At this point, it is important to review the current knowledge about the success of fine-tuned naïve- and sequence-based screening protocols for enzyme selection and to describe the environments worldwide that have already been subjected to enzyme screen programmes through metagenomic tools. Here, we provide such estimations and suggest the current challenges and future actions needed before environmental enzymes can be successfully introduced into the market.

AB - Recent reports have suggested that the establishment of industrially relevant enzyme collections from environmental genomes has become a routine procedure. Across the studies assessed, a mean number of approximately 44 active clones were obtained in an average size of approximately 53 000 clones tested using naïve screening protocols. This number could be significantly increased in shorter times when novel metagenome enzyme sequences obtained by direct sequencing are selected and subjected to high-throughput expression for subsequent production and characterization. The pre-screening of clone libraries by naïve screens followed by the pyrosequencing of the inserts allowed for a 106-fold increase in the success rate of identifying genes encoding enzymes of interest. However, a much longer time, usually on the order of years, is needed from the time of enzyme identification to the establishment of an industrial process. If the hit frequency for the identification of enzymes performing at high turnover rates under real application conditions could be increased while still covering a high natural diversity, the very expensive and time-consuming enzyme optimization phase would likely be significantly shortened. At this point, it is important to review the current knowledge about the success of fine-tuned naïve- and sequence-based screening protocols for enzyme selection and to describe the environments worldwide that have already been subjected to enzyme screen programmes through metagenomic tools. Here, we provide such estimations and suggest the current challenges and future actions needed before environmental enzymes can be successfully introduced into the market.

U2 - 10.1111/1751-7915.12309

DO - 10.1111/1751-7915.12309

M3 - Article

VL - 9

SP - 22

EP - 34

JO - Microbial Biotechnology

JF - Microbial Biotechnology

SN - 1751-7915

IS - 1

ER -