Interplay of metagenomics and in vitro compartmentalization.
In recent years, the application of approaches for harvesting DNA from the environment, the so-called, 'metagenomic approaches' has proven to be highly successful for the identification, isolation and generation of novel enzymes. Functional screening for the desired catalytic activity is one of the key steps in mining metagenomic libraries, as it does not rely on sequence homology. In this mini-review, we survey high-throughput screening tools, originally developed for directed evolution experiments, which can be readily adapted for the screening of large libraries. In particular, we focus on the use of in vitro compartmentalization (IVC) approaches to address potential advantages and problems the merger of culture-independent and IVC techniques might bring on the mining of enzyme activities in microbial communities.
CSIC, Institute of Catalysis, Department of Applied Biocatalysis, Madrid, Spain. mferrer@icp.csic.es
Manuel
M
Ferrer
Ana
A
Beloqui
José María
JM
Vieites
María Eugenia
ME
Guazzaroni
Ilana
I
Berger
Amir
A
Aharoni
D004783:Environmental Microbiology; D015723:Gene Library; D057166:High-Throughput Screening Assays; D056186:Metagenomics / Q000379:methods*
Appl Environ Microbiol. 1999 Feb;65(2):477-82
9925571
Nature. 2006 Aug 17;442(7104):806-9
16915287
PLoS Biol. 2007 Mar;5(3):e16
17355171
Nature. 2004 Mar 4;428(6978):37-43
14961025
FEMS Microbiol Lett. 2008 Jul;284(1):28-34
18462390
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W332-5
18480121
Curr Opin Biotechnol. 2004 Aug;15(4):314-22
15358001
Curr Opin Biotechnol. 2003 Jun;14(3):303-10
12849784
Nucleic Acids Res. 2004 Jul 06;32(12):e95
15247328
Anal Biochem. 2004 Feb 1;325(1):151-7
14715296
Nat Biotechnol. 1998 Jul;16(7):652-6
9661199
Chem Biol. 2005 Dec;12(12):1291-300
16356846
PLoS Biol. 2006 Nov;4(11):e368
17090214
Curr Opin Microbiol. 2008 Jun;11(3):240-8
18554976
Nat Biotechnol. 2004 Jun;22(6):755-9
15156154
Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4552-7
11274352
Curr Opin Microbiol. 2007 Oct;10(5):490-8
17936679
Science. 2004 Apr 2;304(5667):66-74
15001713
Chembiochem. 2006 Jan;7(1):49-53
16329153
Nucleic Acids Res. 2008 Jan;36(Database issue):D475-9
17981842
PLoS Biol. 2007 Mar;5(3):e77
17355176
Methods Enzymol. 2004;388:134-45
15289067
Appl Environ Microbiol. 2007 Nov;73(21):7059-66
17827313
BMC Genomics. 2006 Mar 20;7:57
16549033
J Mol Biol. 2005 Feb 4;345(5):1015-26
15644201
Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10
18316740
Nat Protoc. 2008;3(7):1202-12
18600226
EMBO J. 2003 Jan 2;22(1):24-35
12505981
Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20
16880384
Trends Biotechnol. 2006 Sep;24(9):395-402
16843558
Biotechnol J. 2007 Feb;2(2):201-6
17294408
Trends Biotechnol. 2005 Oct;23(10):497-506
16125262
Mol Biosyst. 2008 May;4(5):363-71
18414733
Curr Opin Microbiol. 2007 Jun;10(3):207-14
17548239
PLoS One. 2008 Jan 23;3(1):e1456
18213365
Environ Microbiol. 2007 Nov;9(11):2707-19
17922755
Chem Biol. 2005 Dec;12(12):1281-9
16356845
Nucleic Acids Res. 2008 Apr;36(7):2230-9
18285365
Nat Methods. 2006 Jul;3(7):561-70
16791215
HFSP J. 2007 May;1(1):67-78
19404461
Curr Opin Chem Biol. 2005 Apr;9(2):210-6
15811807
Nat Biotechnol. 2007 Mar;25(3):338-44
17322872
Chem Commun (Camb). 2006 Oct 28;(40):4201-3
17031431
Appl Environ Microbiol. 2003 Aug;69(8):4927-34
12902288
Environ Microbiol. 2004 Sep;6(9):981-9
15305923
Curr Opin Biotechnol. 2002 Dec;13(6):543-7
12482512