The Integration of Genome Mining, Comparative Genomics, and Functional Genetics for Biosynthetic Gene Cluster Identification.
EDGAR 2
Pantoea
agar overlay assay
antiSMASH
biosynthetic gene cluster
comparative genomics
genome mining
secondary metabolites
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2020
2020
Historique:
received:
28
08
2020
accepted:
11
11
2020
entrez:
21
12
2020
pubmed:
22
12
2020
medline:
22
12
2020
Statut:
epublish
Résumé
Antimicrobial resistance is a worldwide health crisis for which new antibiotics are needed. One strategy for antibiotic discovery is identifying unique antibiotic biosynthetic gene clusters that may produce novel compounds. The aim of this study was to demonstrate how an integrated approach that combines genome mining, comparative genomics, and functional genetics can be used to successfully identify novel biosynthetic gene clusters that produce antimicrobial natural products. Secondary metabolite clusters of an antibiotic producer are first predicted using genome mining tools, generating a list of candidates. Comparative genomic approaches are then used to identify gene suites present in the antibiotic producer that are absent in closely related non-producers. Gene sets that are common to the two lists represent leading candidates, which can then be confirmed using functional genetics approaches. To validate this strategy, we identified the genes responsible for antibiotic production in
Identifiants
pubmed: 33343637
doi: 10.3389/fgene.2020.600116
pmc: PMC7744662
doi:
Types de publication
Journal Article
Langues
eng
Pagination
600116Informations de copyright
Copyright © 2020 Williams, Sorout, Cameron and Stavrinides.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Biochim Biophys Acta. 2009 May;1794(5):769-81
pubmed: 19026770
Genome Announc. 2013 Nov 07;1(6):
pubmed: 24201193
DNA Res. 2014 Aug;21(4):447-57
pubmed: 24727546
Appl Environ Microbiol. 2009 Dec;75(24):7710-7
pubmed: 19820144
FEMS Microbiol Rev. 2015 Nov;39(6):968-84
pubmed: 26109597
Drug Discov Today. 2016 Feb;21(2):204-7
pubmed: 25617672
Antimicrob Agents Chemother. 2013 Jul;57(7):3348-57
pubmed: 23650175
Mar Drugs. 2015 Jul 31;13(8):4754-83
pubmed: 26264003
Sci Rep. 2015 Feb 10;5:8365
pubmed: 25666585
Int J Med Microbiol. 2014 Jan;304(1):14-22
pubmed: 24120363
J Am Chem Soc. 2006 Aug 23;128(33):10660-1
pubmed: 16910643
Nat Chem Biol. 2015 Sep;11(9):625-31
pubmed: 26284661
Curr Opin Microbiol. 2009 Oct;12(5):520-7
pubmed: 19695947
Curr Opin Microbiol. 2019 Oct;51:1-8
pubmed: 30776510
Arch Microbiol. 2001 Nov;176(5):386-90
pubmed: 11702082
Appl Environ Microbiol. 2001 Jan;67(1):284-92
pubmed: 11133457
Microbiol Res. 2020 Aug;237:126479
pubmed: 32416447
J Biol Chem. 2004 Jun 18;279(25):26066-73
pubmed: 15066985
Infect Drug Resist. 2018 Oct 10;11:1645-1658
pubmed: 30349322
Nat Prod Rep. 2018 Feb 21;35(2):147-173
pubmed: 29384544
Nucleic Acids Res. 2015 Nov 16;43(20):9645-62
pubmed: 26442528
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W273-9
pubmed: 16845009
Chem Biol. 2010 May 28;17(5):483-94
pubmed: 20534346
Braz J Infect Dis. 2012 Sep-Oct;16(5):466-71
pubmed: 22975171
Curr Opin Microbiol. 2019 Oct;51:72-80
pubmed: 31733401
Gene. 1990 May 31;90(1):21-9
pubmed: 2199328
Int J Syst Evol Microbiol. 2016 Dec;66(12):5575-5599
pubmed: 27620848
Open Forum Infect Dis. 2020 Mar 23;7(4):ofaa104
pubmed: 32352020
Appl Environ Microbiol. 2012 Jun;78(12):4412-9
pubmed: 22504810
Angew Chem Int Ed Engl. 2003 Jun 30;42(25):2898-901
pubmed: 12833353
BMC Bioinformatics. 2009 May 20;10:154
pubmed: 19457249
Mar Drugs. 2010 Dec 13;8(12):2946-60
pubmed: 21339958
Arch Microbiol. 2019 Aug;201(6):713-722
pubmed: 30868174
Nucleic Acids Res. 2017 Jul 3;45(W1):W42-W48
pubmed: 28472505
Front Microbiol. 2015 Jan 14;5:774
pubmed: 25642215
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W339-46
pubmed: 21672958
Curr Opin Microbiol. 2017 Oct;39:113-120
pubmed: 29156309
Nucleic Acids Res. 2010 Jul;38(12):e132
pubmed: 20403810
Plant Dis. 2002 Jun;86(6):639-644
pubmed: 30823238
PLoS One. 2018 Jul 10;13(7):e0200481
pubmed: 29990341
Nat Chem Biol. 2015 Sep;11(9):639-48
pubmed: 26284671
BMC Bioinformatics. 2009 Jun 16;10:185
pubmed: 19531248
Microbiol Res. 2020 Jan 15;234:126412
pubmed: 32062363
World J Microbiol Biotechnol. 2013 Oct;29(10):1773-81
pubmed: 23558460
Mol Genet Genomics. 2018 Dec;293(6):1453-1467
pubmed: 30027301
Curr Top Med Chem. 2016;16(15):1645-94
pubmed: 26456468
Bioinformatics. 2016 Apr 15;32(8):1138-43
pubmed: 26656005
J Nat Prod. 2010 Mar 26;73(3):441-6
pubmed: 20041689
Annu Rev Phytopathol. 1998;36:227-48
pubmed: 15012499
Nucleic Acids Res. 2016 Jul 8;44(W1):W22-8
pubmed: 27098043
J Ind Microbiol Biotechnol. 2016 Mar;43(2-3):155-76
pubmed: 26739136
Genetics. 1988 Nov;120(3):621-3
pubmed: 2852134
Appl Environ Microbiol. 2005 Dec;71(12):8531-6
pubmed: 16332844
Cell. 2014 Jul 17;158(2):412-421
pubmed: 25036635
Nucleic Acids Res. 2018 Jul 2;46(W1):W278-W281
pubmed: 29788290
Front Microbiol. 2017 Mar 15;8:394
pubmed: 28360891
Angew Chem Int Ed Engl. 2003 Jun 30;42(25):2902-5
pubmed: 12833354
Microbiologyopen. 2012 Dec;1(4):438-49
pubmed: 23233458
Biochem Biophys Res Commun. 2002 Apr 19;292(5):1155-66
pubmed: 11969206
Nat Prod Rep. 2016 Aug 27;33(8):988-1005
pubmed: 27272205
Phytopathology. 2002 Nov;92(11):1202-9
pubmed: 18944246
J Bacteriol. 2019 Apr 9;201(9):
pubmed: 30745372
J Antibiot (Tokyo). 1997 Mar;50(3):270-3
pubmed: 9439702
Prim Care. 2018 Sep;45(3):467-484
pubmed: 30115335
Environ Microbiol. 2016 Nov;18(11):3635-3650
pubmed: 26914969
J Bacteriol. 2003 Oct;185(19):5657-64
pubmed: 13129936
Nat Prod Rep. 2019 Oct 16;36(10):1412-1436
pubmed: 30620035
PLoS One. 2014 May 05;9(5):e96208
pubmed: 24796857
Nucleic Acids Res. 2017 Jul 3;45(W1):W49-W54
pubmed: 28460067
Medchemcomm. 2018;9:12-21
pubmed: 29527285
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Curr Opin Microbiol. 2019 Oct;51:9-15
pubmed: 30999085
Bioinformatics. 2011 Apr 1;27(7):1009-10
pubmed: 21278367
Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87
pubmed: 31032519