Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
08 2023
08 2023
Historique:
medline:
28
8
2023
pubmed:
24
8
2023
entrez:
24
8
2023
Statut:
epublish
Résumé
In microorganisms, different from primary metabolism for cellular growth, secondary metabolism is for ecological interactions and stress responses and an important source of natural products widely used in various areas such as pharmaceutics and food additives. With advancements of sequencing technologies and bioinformatics tools, a large number of biosynthetic gene clusters of secondary metabolites have been discovered from microbial genomes. However, due to challenges from the difficulty of genome-scale pathway reconstruction and the limitation of conventional flux balance analysis (FBA) on secondary metabolism, the quantitative modeling of secondary metabolism is poorly established, in contrast to that of primary metabolism. This review first discusses current efforts on the reconstruction of secondary metabolic pathways in genome-scale metabolic models (GSMMs), as well as related FBA-based modeling techniques. Additionally, potential extensions of FBA are suggested to improve the prediction accuracy of secondary metabolite production. As this review posits, biosynthetic pathway reconstruction for various secondary metabolites will become automated and a modeling framework capturing secondary metabolism onset will enhance the predictive power. Expectedly, an improved FBA-based modeling workflow will facilitate quantitative study of secondary metabolism and in silico design of engineering strategies for natural product production.
Identifiants
pubmed: 37619239
doi: 10.1371/journal.pcbi.1011391
pii: PCOMPBIOL-D-23-00257
pmc: PMC10449171
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1011391Informations de copyright
Copyright: © 2023 Qiu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors declare that there is no conflict of interests.
Références
BMC Bioinformatics. 2013 Mar 27;14:112
pubmed: 23530693
J Biotechnol. 2016 Feb 10;219:126-41
pubmed: 26724578
Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8
pubmed: 18838391
Biochem Soc Trans. 2018 Aug 20;46(4):931-936
pubmed: 30065105
BMC Syst Biol. 2012 Jan 30;6:8
pubmed: 22289213
Biotechnol Bioeng. 2021 Feb;118(2):745-758
pubmed: 33073364
Front Microbiol. 2019 Jun 20;10:1404
pubmed: 31281299
Microorganisms. 2021 Nov 14;9(11):
pubmed: 34835477
BMC Genomics. 2010 Mar 26;11:202
pubmed: 20338070
J Cheminform. 2019 Jan 3;11(1):1
pubmed: 30604073
Curr Opin Microbiol. 2018 Oct;45:109-116
pubmed: 29656009
BMC Bioinformatics. 2018 Dec 4;19(1):467
pubmed: 30514205
Nucleic Acids Res. 2020 Jan 8;48(D1):D402-D406
pubmed: 31696234
Nucleic Acids Res. 2020 Jan 8;48(D1):D445-D453
pubmed: 31586394
Metab Eng. 2018 Jan;45:158-170
pubmed: 29233745
Microb Biotechnol. 2011 Mar;4(2):165-74
pubmed: 21342462
Appl Environ Microbiol. 1998 Mar;64(3):843-9
pubmed: 9501424
PLoS Comput Biol. 2008 May 16;4(5):e1000082
pubmed: 18483554
Biotechnol Bioeng. 2016 Mar;113(3):651-60
pubmed: 26369755
Bioinformatics. 2020 Feb 1;36(3):942-944
pubmed: 31504190
BMC Bioinformatics. 2021 Feb 23;22(1):81
pubmed: 33622234
BMC Syst Biol. 2019 Jan 10;13(1):3
pubmed: 30630470
Proc Biol Sci. 2018 Jun 13;285(1880):
pubmed: 29899074
Biotechnol Prog. 2014 Sep-Oct;30(5):985-91
pubmed: 25044958
BMC Bioinformatics. 2021 Sep 28;22(1):467
pubmed: 34583645
J Ind Microbiol Biotechnol. 2019 Mar;46(3-4):301-311
pubmed: 30684124
BMC Genomics. 2010 Jan 06;11:10
pubmed: 20053288
Nat Protoc. 2007;2(3):727-38
pubmed: 17406635
Bioinformatics. 2010 Dec 15;26(24):3140-2
pubmed: 21081510
Curr Opin Biotechnol. 2022 Oct;77:102762
pubmed: 35908316
Biotechnol Bioeng. 2021 Jan;118(1):223-237
pubmed: 32926401
Brief Bioinform. 2019 Jul 19;20(4):1103-1113
pubmed: 29112695
Plant Physiol. 2005 May;138(1):27-37
pubmed: 15888675
Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1586-91
pubmed: 24425772
Biotechnol Bioeng. 2014 Jun;111(6):1191-9
pubmed: 24374726
Nat Chem Biol. 2011 May 22;7(7):445-52
pubmed: 21602812
Bioinformatics. 2009 Oct 15;25(20):2755-7
pubmed: 19578041
Cell Syst. 2017 Dec 27;5(6):538-541
pubmed: 29284126
Nucleic Acids Res. 2018 Jan 4;46(D1):D633-D639
pubmed: 29059334
Nucleic Acids Res. 2021 Dec 2;49(21):e126
pubmed: 34614189
AIMS Microbiol. 2020 Nov 17;6(4):451-469
pubmed: 33364538
ACS Synth Biol. 2013 Jul 19;2(7):373-8
pubmed: 23659212
Mol Syst Biol. 2015 Feb 12;11(1):784
pubmed: 25678603
Nucleic Acids Res. 2022 Jun 24;50(11):6052-6066
pubmed: 35694833
Bioinformatics. 2012 Jul 1;28(13):1752-8
pubmed: 22563070
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W273-9
pubmed: 16845009
Brief Bioinform. 2018 Sep 28;19(5):1022-1034
pubmed: 28398567
FEBS Lett. 2012 Jul 16;586(15):2177-83
pubmed: 22710183
Gene. 2015 Jan 10;554(2):140-7
pubmed: 25452194
Biotechnol Bioeng. 2018 Oct;115(10):2604-2612
pubmed: 29873086
BMC Syst Biol. 2008 Feb 26;2:20
pubmed: 18302748
PLoS Comput Biol. 2016 Jun 29;12(6):e1004913
pubmed: 27355325
Nucleic Acids Res. 2017 Jan 4;45(D1):D353-D361
pubmed: 27899662
Metabolites. 2021 May 11;11(5):
pubmed: 34064751
PLoS Comput Biol. 2009 Aug;5(8):e1000489
pubmed: 19714220
Genome Res. 2006 May;16(5):627-35
pubmed: 16606697
J Appl Microbiol. 2001 Nov;91(5):846-52
pubmed: 11722662
Mol Syst Biol. 2017 Aug 3;13(8):935
pubmed: 28779005
Comput Struct Biotechnol J. 2014 Sep 03;11(18):59-65
pubmed: 25379144
Biotechnol Bioeng. 2023 Aug;120(8):2186-2198
pubmed: 37428554
J Ind Microbiol Biotechnol. 2014 Feb;41(2):415-24
pubmed: 24326978
Bioprocess Biosyst Eng. 2018 May;41(5):657-669
pubmed: 29404683
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W339-46
pubmed: 21672958
iScience. 2020 Nov 18;23(12):101818
pubmed: 33354660
Curr Opin Biotechnol. 2011 Aug;22(4):552-8
pubmed: 21498065
BMC Genomics. 2018 Jul 4;19(1):519
pubmed: 29973148
Nat Chem Biol. 2015 Sep;11(9):639-48
pubmed: 26284671
Mol Biosyst. 2013 Jul;9(7):1576-83
pubmed: 23525368
Water Res. 2023 Jan 1;228(Pt A):119365
pubmed: 36413834
J Theor Biol. 2020 Sep 21;501:110317
pubmed: 32446743
Biotechnol J. 2019 Jan;14(1):e1800377
pubmed: 30117679
J Nat Prod. 2019 Jul 26;82(7):2038-2053
pubmed: 31287310
Bioinformatics. 2017 Jul 15;33(14):i311-i318
pubmed: 28881985
ACS Synth Biol. 2016 Oct 21;5(10):1155-1166
pubmed: 27404214
PLoS Comput Biol. 2018 May 23;14(5):e1006146
pubmed: 29791443
PLoS Comput Biol. 2018 Oct 18;14(10):e1006541
pubmed: 30335785
Nat Prod Rep. 2016 Aug 27;33(8):988-1005
pubmed: 27272205
Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17845-50
pubmed: 20876091
J Mol Evol. 2015 Jun;80(5-6):251-7
pubmed: 25987355
Curr Opin Biotechnol. 2021 Feb;67:35-41
pubmed: 33360621
Curr Opin Microbiol. 2018 Oct;45:8-15
pubmed: 29367175
Biotechnol Adv. 2013 Nov;31(6):818-26
pubmed: 23680193
Metab Eng. 2011 Jan;13(1):38-48
pubmed: 21129495
Synth Syst Biotechnol. 2016 Feb 05;1(2):69-79
pubmed: 29062930
Synth Syst Biotechnol. 2017 Nov 15;2(4):243-252
pubmed: 29552648
iScience. 2020 Jan 24;23(1):100795
pubmed: 31926431
Crit Rev Food Sci Nutr. 2020;60(9):1475-1495
pubmed: 30740985
Nat Biotechnol. 2010 Mar;28(3):245-8
pubmed: 20212490
Carbohydr Polym. 2019 Feb 1;205:565-570
pubmed: 30446142
Nature. 2015 Dec 3;528(7580):99-104
pubmed: 26632588
G3 (Bethesda). 2016 Dec 7;6(12):4023-4033
pubmed: 27694115
Science. 2010 Nov 19;330(6007):1099-102
pubmed: 21097934
Nucleic Acids Res. 2017 Jul 3;45(W1):W49-W54
pubmed: 28460067
Methods Mol Biol. 2022;2349:259-289
pubmed: 34718999
Nucleic Acids Res. 2018 Sep 6;46(15):7542-7553
pubmed: 30192979
Nat Biotechnol. 2014 May;32(5):447-52
pubmed: 24811519
Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2607-11
pubmed: 19196991
Nat Rev Microbiol. 2013 Jan;11(1):21-32
pubmed: 23178386
Nucleic Acids Res. 2021 Jan 8;49(D1):D575-D588
pubmed: 32986834
Biotechnol Bioeng. 2003 Dec 20;84(6):647-57
pubmed: 14595777
iScience. 2020 Sep 03;23(9):101525
pubmed: 32942174
Brief Bioinform. 2021 Jan 18;22(1):109-126
pubmed: 31813964
Environ Microbiol. 2001 Sep;3(9):545-50
pubmed: 11683864
Nature. 2004 May 6;429(6987):92-6
pubmed: 15129285