Chromosomal organization of biosynthetic gene clusters, including those of nine novel species, suggests plasticity of myxobacterial specialized metabolism.
Nannocystis
biosynthetic gene clusters
genome mining
myxobacteria
specialized metabolism
Journal
Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977
Informations de publication
Date de publication:
2023
2023
Historique:
received:
22
05
2023
accepted:
11
07
2023
medline:
21
8
2023
pubmed:
21
8
2023
entrez:
21
8
2023
Statut:
epublish
Résumé
Natural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism. In this study, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America. Nine isolates were determined to be novel species of myxobacteria including representatives from the genera Continued discovery and sequencing of novel myxobacteria from the environment provide BGCs for the genome mining pipeline. Utilizing complete or near-complete genome sequences, we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest that the spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.
Identifiants
pubmed: 37601375
doi: 10.3389/fmicb.2023.1227206
pmc: PMC10435759
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1227206Subventions
Organisme : NIGMS NIH HHS
ID : P20 GM130460
Pays : United States
Organisme : NIAID NIH HHS
ID : R15 AI137996
Pays : United States
Informations de copyright
Copyright © 2023 Ahearne, Phillips, Knehans, Hoing, Dowd and Stevens.
Déclaration de conflit d'intérêts
SD was employed by Molecular Research LP (MR DNA). The remaining 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. The reviewer DW is currently organizing a Research Topic with the author DS.
Références
Chemistry. 2022 Feb 21;28(10):e202104484
pubmed: 34990513
Front Microbiol. 2020 Jan 28;11:34
pubmed: 32047489
Microorganisms. 2021 Oct 12;9(10):
pubmed: 34683458
Nat Biotechnol. 2007 Apr;25(4):447-53
pubmed: 17369815
Genome Res. 2017 May;27(5):737-746
pubmed: 28100585
Nat Prod Rep. 2020 Apr 1;37(4):566-599
pubmed: 31822877
BMC Bioinformatics. 2023 May 3;24(1):181
pubmed: 37131131
Microorganisms. 2021 Jun 24;9(7):
pubmed: 34202719
Appl Environ Microbiol. 2020 Jan 7;86(2):
pubmed: 31676482
Nat Prod Rep. 2017 Feb 1;34(2):135-160
pubmed: 27907217
PLoS Comput Biol. 2014 Dec 04;10(12):e1004016
pubmed: 25474254
J Ind Microbiol Biotechnol. 2021 Dec 23;48(9-10):
pubmed: 34279640
Angew Chem Int Ed Engl. 2017 Feb 13;56(8):2192-2197
pubmed: 28098952
Nat Commun. 2019 May 16;10(1):2182
pubmed: 31097708
Int J Syst Evol Microbiol. 2016 Feb;66(2):928-938
pubmed: 26637815
Int J Syst Evol Microbiol. 2016 Feb;66(2):1100-1103
pubmed: 26585518
J Am Chem Soc. 2008 Jun 18;130(24):7554-5
pubmed: 18498160
Front Microbiol. 2022 Nov 10;13:995049
pubmed: 36439860
mBio. 2014 Feb 11;5(1):e00939-13
pubmed: 24520059
Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4601-8
pubmed: 18216259
Int J Syst Evol Microbiol. 2015 Nov;65(11):4032-4042
pubmed: 26286530
Nucleic Acids Res. 2016 Jul 8;44(W1):W41-5
pubmed: 27141960
J Mol Biol. 2007 Nov 16;374(1):24-38
pubmed: 17919655
ACS Chem Biol. 2017 Feb 17;12(2):456-463
pubmed: 27977135
Arch Mikrobiol. 1969;68(3):210-7
pubmed: 4315734
Nucleic Acids Res. 2020 Jan 8;48(D1):D454-D458
pubmed: 31612915
Science. 1979 Apr 13;204(4389):193-5
pubmed: 107586
J Microbiol Biotechnol. 2016 Sep 28;26(9):1636-42
pubmed: 27291672
Angew Chem Int Ed Engl. 2012 Jan 16;51(3):811-6
pubmed: 22162209
Int J Syst Evol Microbiol. 2015 Mar;65(Pt 3):745-753
pubmed: 24591423
Gigascience. 2019 May 1;8(5):
pubmed: 31089679
ISME J. 2021 Sep;15(9):2665-2675
pubmed: 33746204
Int J Syst Evol Microbiol. 2016 Jun;66(6):2389-2395
pubmed: 27046779
Nat Chem Biol. 2020 Jan;16(1):60-68
pubmed: 31768033
Int J Syst Evol Microbiol. 2017 Feb;67(2):472-478
pubmed: 27902273
Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11136-41
pubmed: 11562468
Nat Chem Biol. 2007 Nov;3(11):711-5
pubmed: 17873868
Biotechnol Adv. 2020 Mar - Apr;39:107480
pubmed: 31707075
Microorganisms. 2018 Aug 11;6(3):
pubmed: 30103481
Microbiologyopen. 2017 Aug;6(4):
pubmed: 28401707
Nucleic Acids Res. 2021 Jan 8;49(D1):D639-D643
pubmed: 33152079
Gene. 2005 Jun 20;353(1):53-66
pubmed: 15936160
Angew Chem Int Ed Engl. 2018 Oct 22;57(43):14270-14275
pubmed: 30088846
Microorganisms. 2022 Sep 10;10(9):
pubmed: 36144418
Front Microbiol. 2022 Sep 29;13:1031346
pubmed: 36246230
Nat Biotechnol. 2019 May;37(5):540-546
pubmed: 30936562
ACS Chem Biol. 2019 Jan 18;14(1):88-98
pubmed: 30543288
Chem Biol. 2008 Aug 25;15(8):771-81
pubmed: 18721748
Eur J Biochem. 1995 Oct 1;233(1):238-48
pubmed: 7588751
J Bacteriol. 2011 Sep;193(18):4626-33
pubmed: 21764930
Angew Chem Int Ed Engl. 2022 Dec 23;61(52):e202212946
pubmed: 36208117
J Bacteriol. 1969 Feb;97(2):905-11
pubmed: 5773035
Anal Chem. 2019 Nov 5;91(21):13703-13711
pubmed: 31600444
Syst Appl Microbiol. 2021 Nov;44(6):126274
pubmed: 34763291
J Nat Prod. 2022 Nov 25;85(11):2610-2619
pubmed: 36331369
Chemistry. 2017 Nov 13;23(63):15917-15921
pubmed: 28944573
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W339-46
pubmed: 21672958
Appl Environ Microbiol. 2022 Apr 12;88(7):e0009322
pubmed: 35323022
J Biotechnol. 2014 Dec 10;191:54-63
pubmed: 25102237
Microorganisms. 2022 Sep 30;10(10):
pubmed: 36296235
ISME J. 2022 Jan;16(1):101-111
pubmed: 34253854
Int J Syst Evol Microbiol. 2014 Oct;64(Pt 10):3360-3368
pubmed: 25048208
Chembiochem. 2012 Feb 13;13(3):416-26
pubmed: 22278953
Microb Genom. 2017 Sep 14;3(10):e000132
pubmed: 29177090
Eur J Biochem. 2000 Nov;267(21):6476-85
pubmed: 11029592
Microorganisms. 2022 Jun 21;10(7):
pubmed: 35888982
Antimicrob Agents Chemother. 2012 Apr;56(4):2014-21
pubmed: 22232277
Appl Microbiol Biotechnol. 2011 Sep;91(6):1463-75
pubmed: 21779844
Int J Syst Evol Microbiol. 2018 Oct;68(10):3101-3110
pubmed: 30113300
Nat Commun. 2021 Sep 1;12(1):5221
pubmed: 34471117
J Bacteriol. 2016 Nov 18;198(24):3335-3344
pubmed: 27698086
J Ind Microbiol Biotechnol. 2019 Mar;46(3-4):281-299
pubmed: 30484124
Genome Biol. 2019 Jun 24;20(1):129
pubmed: 31234903
J Ind Microbiol Biotechnol. 2019 Mar;46(3-4):319-334
pubmed: 30506464
J Am Chem Soc. 2004 Sep 22;126(37):11432-3
pubmed: 15366877
Angew Chem Int Ed Engl. 2015 Aug 24;54(35):10149-54
pubmed: 26179970
Genome Biol Evol. 2020 Dec 6;12(12):2289-2302
pubmed: 33022031
Comput Struct Biotechnol J. 2020 Sep 15;18:2547-2555
pubmed: 33033577
Int J Syst Evol Microbiol. 2018 Nov;68(11):3576-3586
pubmed: 30234476
Nat Chem Biol. 2014 Jun;10(6):425-7
pubmed: 24814673
Int J Syst Evol Microbiol. 2018 Mar;68(3):721-729
pubmed: 29458458
Int J Syst Evol Microbiol. 2013 Nov;63(Pt 11):4354-4360
pubmed: 24187023
Int J Syst Evol Microbiol. 2017 May;67(5):1422-1430
pubmed: 28141508
Genome Announc. 2014 Dec 11;2(6):
pubmed: 25502681
Antimicrob Agents Chemother. 1974 Feb;5(2):121-32
pubmed: 4840428
J Ind Microbiol Biotechnol. 2017 May;44(4-5):573-588
pubmed: 27520548
Int J Syst Evol Microbiol. 2013 Apr;63(Pt 4):1360-1369
pubmed: 22821734
Nucleic Acids Res. 2021 Jan 8;49(D1):D490-D497
pubmed: 33010170
Microbiologyopen. 2016 Apr;5(2):268-78
pubmed: 26669488
Int J Syst Evol Microbiol. 2012 May;62(Pt 5):1191-1198
pubmed: 21742821
Gigascience. 2021 Jan 13;10(1):
pubmed: 33438731
Nucleic Acids Res. 2021 Jul 2;49(W1):W29-W35
pubmed: 33978755
Nat Commun. 2018 Feb 23;9(1):803
pubmed: 29476047
Int J Syst Evol Microbiol. 2014 Nov;64(Pt 11):3733-3742
pubmed: 25114157