Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata.
Parmelia sulcata
Parmeliaceae
biosynthetic gene cluster
long-read sequencing
phylogeny
polyketide synthesis
Journal
MicrobiologyOpen
ISSN: 2045-8827
Titre abrégé: Microbiologyopen
Pays: England
ID NLM: 101588314
Informations de publication
Date de publication:
10 2023
10 2023
Historique:
revised:
15
09
2023
received:
03
08
2023
accepted:
26
09
2023
medline:
26
10
2023
pubmed:
25
10
2023
entrez:
25
10
2023
Statut:
ppublish
Résumé
Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus), which together generate a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here, we provide a comparative view of the biosynthetic gene clusters of three lichen mycobionts derived from Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. In addition, we present a high-quality PacBio metagenome of Parmelia sulcata, from which we extracted the mycobiont bin containing 214 biosynthetic gene clusters. Most biosynthetic gene clusters in these genomes were associated with T1PKSs, followed by NRPSs and terpenes. This study focused on biosynthetic gene clusters related to polyketide synthesis. Based on ketosynthase homology, we identified nine highly syntenic clusters present in all three species. Among the four clusters belonging to nonreducing PKSs, two are putatively linked to lichen substances derived from orsellinic acid (orcinol depsides and depsidones, e.g., lecanoric acid, physodic acid, lobaric acid), one to compounds derived from methylated forms of orsellinic acid (beta orcinol depsides, e.g., atranorin), and one to melanins. Five clusters with orthologs in all three species are linked to reducing PKSs. Our study contributes to sorting and dereplicating the vast PKS diversity found in lichenized fungi. High-quality sequences of biosynthetic gene clusters of these three common species provide a foundation for further exploration into biotechnological applications and the molecular evolution of lichen substances.
Identifiants
pubmed: 37877655
doi: 10.1002/mbo3.1386
pmc: PMC10582450
doi:
Substances chimiques
orsellinic acid
11XLA0494B
orcinol
534PMB3438
Polyketide Synthases
79956-01-7
Depsides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1386Informations de copyright
© 2023 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
Références
Nat Prod Rep. 2023 Jan 25;40(1):9-27
pubmed: 35543313
J Fungi (Basel). 2022 Apr 26;8(5):
pubmed: 35628705
J Infect Public Health. 2022 Apr;15(4):491-497
pubmed: 34688575
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Biomolecules. 2020 Jan 05;10(1):
pubmed: 31948092
BMC Genomics. 2021 May 6;22(1):330
pubmed: 33957869
Curr Protoc. 2021 Mar;1(3):e59
pubmed: 33656283
J Fungi (Basel). 2023 Jan 25;9(2):
pubmed: 36836275
mBio. 2021 Jun 29;12(3):e0111121
pubmed: 34154413
Trends Microbiol. 2015 Oct;23(10):642-652
pubmed: 26433696
Nat Prod Res. 2018 Nov;32(22):2735-2739
pubmed: 28901170
Trends Ecol Evol. 2007 Mar;22(3):148-55
pubmed: 17129636
Biol Direct. 2018 Apr 20;13(1):6
pubmed: 29678199
Methods Mol Biol. 2019;1962:65-95
pubmed: 31020555
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15670-5
pubmed: 14676319
BMC Genomics. 2013 Sep 11;14:611
pubmed: 24020438
Front Microbiol. 2016 Feb 18;7:180
pubmed: 26925047
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Mol Ecol. 2022 Apr 10;:
pubmed: 35398946
mSystems. 2022 Dec 20;7(6):e0063222
pubmed: 36445112
Nat Chem Biol. 2015 Sep;11(9):625-31
pubmed: 26284661
J Nat Prod. 2013 Nov 22;76(11):2094-9
pubmed: 24175613
Nat Rev Microbiol. 2005 Dec;3(12):937-47
pubmed: 16322742
Bioinformatics. 2014 May 1;30(9):1236-40
pubmed: 24451626
Nat Chem Biol. 2020 Jan;16(1):60-68
pubmed: 31768033
Nucleic Acids Res. 2023 Jan 6;51(D1):D603-D610
pubmed: 36399496
J Biol Chem. 2010 Jul 23;285(30):22764-73
pubmed: 20479000
Z Naturforsch C J Biosci. 2007 Jul-Aug;62(7-8):619-21
pubmed: 17913083
Pharmaceuticals (Basel). 2022 Oct 11;15(10):
pubmed: 36297361
Mol Biol Evol. 2005 Oct;22(10):2027-39
pubmed: 15958783
Front Microbiol. 2021 Nov 04;12:684565
pubmed: 34803938
Phytopathology. 1997 Sep;87(9):888-91
pubmed: 18945058
J Fungi (Basel). 2023 May 09;9(5):
pubmed: 37233257
Appl Environ Microbiol. 2009 Jun;75(11):3721-32
pubmed: 19346345
New Phytol. 2020 Sep;227(5):1281-1283
pubmed: 32484275
Food Chem Toxicol. 2013 Mar;53:112-8
pubmed: 23220145
Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14558-63
pubmed: 19666480
mBio. 2022 Jun 28;13(3):e0022322
pubmed: 35616333
Mycol Res. 2008 Feb;112(Pt 2):225-30
pubmed: 18280128
mBio. 2021 Aug 31;12(4):e0139921
pubmed: 34281384
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Mikrobiologiia. 2007 Nov-Dec;76(6):817-21
pubmed: 18297873
Front Microbiol. 2021 Sep 28;12:677558
pubmed: 34659136
ACS Chem Biol. 2015 Jun 19;10(6):1443-9
pubmed: 25714897
mBio. 2019 Aug 13;10(4):
pubmed: 31409675
Gigascience. 2015 Aug 25;4:39
pubmed: 26336600
Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296
pubmed: 33885785
Microbiol Spectr. 2022 Aug 31;10(4):e0010922
pubmed: 35867425
Microbiol Spectr. 2017 Jul;5(4):
pubmed: 28820125
Front Genet. 2020 Sep 08;11:516269
pubmed: 33101371
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Metab Eng Commun. 2021 Apr 30;13:e00172
pubmed: 34430202
Chem Biol Interact. 2017 Feb 1;263:36-45
pubmed: 28012710
Genome Biol Evol. 2023 Feb 3;15(2):
pubmed: 36634008
J Food Sci Technol. 2016 Jun;53(6):2804-16
pubmed: 27478237
mBio. 2022 Oct 26;13(5):e0180022
pubmed: 36000736
Environ Microbiol. 2021 Aug;23(8):4260-4275
pubmed: 34097344
PLoS One. 2016 Oct 5;11(10):e0163962
pubmed: 27706213
NAR Genom Bioinform. 2021 Jan 06;3(1):lqaa108
pubmed: 33575650
Nat Rev Microbiol. 2010 Dec;8(12):879-89
pubmed: 21079635
J Biomol Struct Dyn. 2020 Aug;38(12):3544-3562
pubmed: 31524074
mBio. 2016 Feb 09;7(1):e01948-15
pubmed: 26861018
Sci Rep. 2018 Nov 9;8(1):16600
pubmed: 30413766
Science. 2016 Jul 29;353(6298):488-92
pubmed: 27445309
Genome Biol Evol. 2020 Apr 1;12(4):309-324
pubmed: 32163141
Nat Rev Microbiol. 2018 Dec;16(12):731-744
pubmed: 30194403
Molecules. 2019 Jan 08;24(1):
pubmed: 30626017
Life (Basel). 2018 May 22;8(2):
pubmed: 29789469
Nat Rev Microbiol. 2019 Mar;17(3):167-180
pubmed: 30531948
Methods Enzymol. 2012;517:161-82
pubmed: 23084938
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Bioinformatics. 2013 Apr 15;29(8):1072-5
pubmed: 23422339
Nat Biotechnol. 2022 May;40(5):711-719
pubmed: 34980911
Nat Commun. 2022 Jun 8;13(1):3175
pubmed: 35676264
Microb Biotechnol. 2020 Mar;13(2):397-405
pubmed: 32053291
Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14873-7
pubmed: 8962148
Plants (Basel). 2022 Apr 15;11(8):
pubmed: 35448805
Genome Res. 2004 Jul;14(7):1394-403
pubmed: 15231754
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Sci Rep. 2018 Dec 18;8(1):17957
pubmed: 30560908
New Phytol. 2015 Dec;208(4):1217-26
pubmed: 26299211
Nat Prod Res. 2013;27(23):2235-9
pubmed: 23822758
Biomolecules. 2021 Oct 02;11(10):
pubmed: 34680078
Methods Mol Biol. 2019;1910:591-604
pubmed: 31278678
mSystems. 2020 Jun 2;5(3):
pubmed: 32487740
Nucleic Acids Res. 2022 Jul 5;50(W1):W345-W351
pubmed: 35446428
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
Microorganisms. 2019 Jun 24;7(6):
pubmed: 31238501
Bioinformatics. 2016 Mar 1;32(5):767-9
pubmed: 26559507
Nature. 2009 Oct 22;461(7267):1139-43
pubmed: 19847268
Front Bioeng Biotechnol. 2021 Feb 18;9:632230
pubmed: 33681170
Curr Opin Chem Biol. 2011 Feb;15(1):137-43
pubmed: 21111669
Genome Biol Evol. 2020 Oct 1;12(10):1858-1868
pubmed: 33151307
Curr Opin Chem Biol. 2011 Feb;15(1):48-56
pubmed: 21087894
Chem Biol. 2002 Sep;9(9):981-8
pubmed: 12323372
Nat Methods. 2020 Nov;17(11):1103-1110
pubmed: 33020656
Nucleic Acids Res. 2021 Jul 2;49(W1):W29-W35
pubmed: 33978755
Plants (Basel). 2023 Feb 01;12(3):
pubmed: 36771729
Mol Biol Evol. 2013 May;30(5):1188-95
pubmed: 23418397
Bioinformatics. 2011 Apr 1;27(7):1009-10
pubmed: 21278367