Recovery and functional validation of hidden soil enzymes in metagenomic libraries.
Environmental microbiology
Functional genomics
Metagenomics
Microbial genomics
Journal
MicrobiologyOpen
ISSN: 2045-8827
Titre abrégé: Microbiologyopen
Pays: England
ID NLM: 101588314
Informations de publication
Date de publication:
04 2019
04 2019
Historique:
received:
12
06
2017
revised:
01
11
2017
accepted:
09
11
2017
pubmed:
10
3
2019
medline:
27
6
2019
entrez:
10
3
2019
Statut:
ppublish
Résumé
The vast microbial diversity on the planet represents an invaluable source for identifying novel activities with potential industrial and therapeutic application. In this regard, metagenomics has emerged as a group of strategies that have significantly facilitated the analysis of DNA from multiple environments and has expanded the limits of known microbial diversity. However, the functional characterization of enzymes, metabolites, and products encoded by diverse microbial genomes is limited by the inefficient heterologous expression of foreign genes. We have implemented a pipeline that combines NGS and Sanger sequencing as a way to identify fosmids within metagenomic libraries. This strategy facilitated the identification of putative proteins, subcloning of targeted genes and preliminary characterization of selected proteins. Overall, the in silico approach followed by the experimental validation allowed us to efficiently recover the activity of previously hidden enzymes derived from agricultural soil samples. Therefore, the methodology workflow described herein can be applied to recover activities encoded by environmental DNA from multiple sources.
Identifiants
pubmed: 30851083
doi: 10.1002/mbo3.572
pmc: PMC6460280
doi:
Substances chimiques
Bacterial Proteins
0
Enzymes
0
Soil
0
Banques de données
GENBANK
['CP001637']
Types de publication
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e00572Informations de copyright
© 2019 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
Références
Appl Microbiol Biotechnol. 2012 Feb;93(3):1005-20
pubmed: 22189864
AMB Express. 2011 Mar 28;1(1):3
pubmed: 21906326
Curr Opin Biotechnol. 2012 Feb;23(1):9-15
pubmed: 22154470
J Biotechnol. 2007 Jan 20;127(4):575-92
pubmed: 16963141
Drug Discov Today. 2010 Sep;15(17-18):792-9
pubmed: 20656054
Nat Rev Microbiol. 2016 Mar;14(3):135-49
pubmed: 26876034
PLoS One. 2014 Jun 09;9(6):e98968
pubmed: 24911009
Microbiologyopen. 2019 Apr;8(4):e00572
pubmed: 30851083
J Mol Biol. 1994 Feb 4;235(5):1501-31
pubmed: 8107089
J Bioinform Comput Biol. 2015 Jun;13(3):1541004
pubmed: 25790784
Environ Microbiol. 2013 Jan;15(1):1-5
pubmed: 22882611
Front Microbiol. 2015 Jun 05;6:563
pubmed: 26097471
J Biosci Bioeng. 2016 Dec;122(6):694-700
pubmed: 27323930
Crit Rev Microbiol. 2011 Aug;37(3):262-76
pubmed: 21599542
Curr Opin Microbiol. 2008 Jun;11(3):240-8
pubmed: 18554976
Microb Biotechnol. 2015 Jan;8(1):52-64
pubmed: 25123225
Sci Rep. 2013;3:1107
pubmed: 23346364
Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3790-5
pubmed: 22357762
Appl Microbiol Biotechnol. 2010 May;86(5):1281-92
pubmed: 20309540
Brief Bioinform. 2012 Nov;13(6):711-27
pubmed: 22772835
Genome Res. 2008 Nov;18(11):1798-805
pubmed: 18701636
Biotechnol Lett. 2007 Mar;29(3):465-72
pubmed: 17203343
Appl Environ Microbiol. 2009 Apr;75(8):2506-16
pubmed: 19218412
Nat Commun. 2015 May 06;6:7045
pubmed: 25944046
Appl Environ Microbiol. 2011 Feb;77(4):1153-61
pubmed: 21169428
J Ind Microbiol Biotechnol. 2011 Sep;38(9):1321-8
pubmed: 21108039
Curr Opin Biotechnol. 2009 Dec;20(6):616-22
pubmed: 19850467
Appl Microbiol Biotechnol. 2014 Mar;98(6):2819-28
pubmed: 24121932
J Bacteriol. 2011 Jun;193(11):2902-3
pubmed: 21460085
Microbiol Mol Biol Rev. 1998 Sep;62(3):597-635
pubmed: 9729602
Genomics Inform. 2013 Sep;11(3):114-20
pubmed: 24124406
Nat Biotechnol. 2012 Jun 07;30(6):513-20
pubmed: 22678395
OMICS. 2013 Feb;17(2):61-70
pubmed: 23308385
Nucleic Acids Res. 2010 Jul;38(12):e132
pubmed: 20403810
J Biotechnol. 2006 May 29;123(3):281-7
pubmed: 16414138
Appl Microbiol Biotechnol. 2011 Aug;91(3):635-44
pubmed: 21494865
Appl Microbiol Biotechnol. 2007 Jul;75(6):1225-32
pubmed: 17404726
Microb Biotechnol. 2016 Jan;9(1):22-34
pubmed: 26275154
Cell. 1998 Jul 24;94(2):161-70
pubmed: 9695945
Enzyme Microb Technol. 2014 Feb 5;55:140-50
pubmed: 24411457
Front Microbiol. 2013 Sep 23;4:282
pubmed: 24069019
Springerplus. 2013 Aug 28;2:410
pubmed: 24024096
Mar Drugs. 2014 Jun 10;12(6):3516-59
pubmed: 24918453
Biotechnol Prog. 2013 Nov-Dec;29(6):1441-7
pubmed: 24124029
Front Genet. 2015 Jul 21;6:234
pubmed: 26257768
Lett Appl Microbiol. 2008 Nov;47(5):361-6
pubmed: 19146522
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712