A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
09 08 2021
09 08 2021
Historique:
received:
22
02
2021
accepted:
22
07
2021
entrez:
10
8
2021
pubmed:
11
8
2021
medline:
24
8
2021
Statut:
epublish
Résumé
Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of multiple biological networks into a single model for cell analysis and engineering. One of the most accurate models of biological systems include Expression and Thermodynamics FLux (ETFL), which efficiently integrates RNA and protein synthesis with traditional genome-scale metabolic models. However, ETFL is so far only applicable for E. coli. To adapt this model for Saccharomyces cerevisiae, we developed yETFL, in which we augmented the original formulation with additional considerations for biomass composition, the compartmentalized cellular expression system, and the energetic costs of biological processes. We demonstrated the ability of yETFL to predict maximum growth rate, essential genes, and the phenotype of overflow metabolism. We envision that the presented formulation can be extended to a wide range of eukaryotic organisms to the benefit of academic and industrial research.
Identifiants
pubmed: 34373465
doi: 10.1038/s41467-021-25158-6
pii: 10.1038/s41467-021-25158-6
pmc: PMC8352978
doi:
Substances chimiques
Glucose
IY9XDZ35W2
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4790Informations de copyright
© 2021. The Author(s).
Références
Genome Biol. 2019 Jun 13;20(1):121
pubmed: 31196170
Biotechnol J. 2014 May;9(5):609-20
pubmed: 24677744
Proc Natl Acad Sci U S A. 2019 Aug 27;116(35):17592-17597
pubmed: 31405984
Nucleic Acids Res. 2015 Jan;43(Database issue):D479-84
pubmed: 25313161
Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12663-8
pubmed: 17652176
Appl Microbiol Biotechnol. 2012 Feb;93(3):917-30
pubmed: 22159888
Curr Opin Biotechnol. 2014 Aug;28:111-5
pubmed: 24556244
Nat Rev Microbiol. 2020 Dec;18(12):731-743
pubmed: 32958892
PLoS One. 2017 Jan 13;12(1):e0169437
pubmed: 28085902
Yeast. 1998 Mar 30;14(5):471-7
pubmed: 9559554
Biotechnol Bioeng. 2020 May;117(5):1562-1574
pubmed: 32022245
Nat Commun. 2012 Jul 03;3:929
pubmed: 22760628
Nat Protoc. 2011 Aug 04;6(9):1290-307
pubmed: 21886097
Nat Protoc. 2010 Jan;5(1):93-121
pubmed: 20057383
Nat Commun. 2020 Jan 13;11(1):30
pubmed: 31937763
Bioinformatics. 2019 Jan 1;35(1):167-169
pubmed: 30561545
Database (Oxford). 2013 Aug 09;2013:bat059
pubmed: 23935056
Trends Microbiol. 2015 Feb;23(2):99-109
pubmed: 25475882
J Bacteriol. 2001 Feb;183(4):1441-51
pubmed: 11157958
ScientificWorldJournal. 2014 Mar 13;2014:476207
pubmed: 24715814
BMC Syst Biol. 2012 Jun 04;6:55
pubmed: 22663945
Bioinformatics. 2017 Nov 15;33(22):3603-3609
pubmed: 29036557
Science. 2009 May 22;324(5930):1029-33
pubmed: 19460998
Nat Commun. 2021 Aug 9;12(1):4790
pubmed: 34373465
Mol Syst Biol. 2017 Aug 3;13(8):935
pubmed: 28779005
Nat Commun. 2019 Aug 8;10(1):3586
pubmed: 31395883
Genome Res. 2003 Feb;13(2):244-53
pubmed: 12566402
Arch Biochem Biophys. 1998 May 1;353(1):116-30
pubmed: 9578607
Mol Syst Biol. 2010 Jul;6:390
pubmed: 20664636
BMC Biol. 2006 Sep 05;4:30
pubmed: 16953894
Antonie Van Leeuwenhoek. 2007 Jul;92(1):109-28
pubmed: 17268890
Nucleic Acids Res. 2008 Jan;36(Database issue):D623-31
pubmed: 17965431
Biotechnol Bioeng. 1990 Dec 5;36(10):1070-82
pubmed: 18595046
Appl Environ Microbiol. 2009 Sep;75(17):5607-14
pubmed: 19592533
Appl Environ Microbiol. 1998 Nov;64(11):4226-33
pubmed: 9797269
Biophys J. 2007 Mar 1;92(5):1792-805
pubmed: 17172310
Ind Biotechnol (New Rochelle N Y). 2013 Aug;9(4):215-228
pubmed: 24678285
Enzyme Microb Technol. 2000 Jun 1;26(9-10):724-736
pubmed: 10862878
Biotechnol Bioeng. 2001 Nov 5;75(3):334-44
pubmed: 11590606
Nat Biotechnol. 2010 Mar;28(3):245-8
pubmed: 20212490
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
Biochem J. 1998 Feb 1;329 ( Pt 3):433-48
pubmed: 9445368
Metabolites. 2015 Sep 29;5(4):536-70
pubmed: 26426067
Mol Syst Biol. 2013 Oct 01;9:693
pubmed: 24084808
Biotechnol Prog. 1999 Jan-Feb;15(1):81-90
pubmed: 9933517
Proc Natl Acad Sci U S A. 2021 Feb 23;118(8):
pubmed: 33602812
Mol Cell Proteomics. 2012 Aug;11(8):492-500
pubmed: 22535208
Curr Opin Biotechnol. 2015 Dec;35:7-15
pubmed: 25544013
PLoS Comput Biol. 2018 Jul 5;14(7):e1006302
pubmed: 29975681
BMC Syst Biol. 2013 Aug 08;7:74
pubmed: 23927696