Molecular networking in infectious disease models.
Global Natural Product Social Molecular Networking (GNPS)
Infectious diseases
MS2
Mass spectrometry
Metabolomics
Molecular networking
Journal
Methods in enzymology
ISSN: 1557-7988
Titre abrégé: Methods Enzymol
Pays: United States
ID NLM: 0212271
Informations de publication
Date de publication:
2022
2022
Historique:
entrez:
16
2
2022
pubmed:
17
2
2022
medline:
18
3
2022
Statut:
ppublish
Résumé
Small molecule metabolites are the product of many enzymatic reactions. Metabolomics thus opens a window into enzyme activity and function, integrating effects at the post-translational, proteome, transcriptome and genome level. In addition, small molecules can themselves regulate enzyme activity, expression and function both via substrate availability mechanisms and through allosteric regulation. Metabolites are therefore at the nexus of infectious diseases, regulating nutrient availability to the pathogen, immune responses, tropism, and host disease tolerance and resilience. Analysis of metabolomics data is however complex, particularly in terms of metabolite annotation. An emerging valuable approach to extend metabolite annotations beyond existing compound libraries and to identify infection-induced chemical changes is molecular networking. In this chapter, we discuss the applications of molecular networking in the context of infectious diseases specifically, with a focus on considerations relevant to these biological systems.
Identifiants
pubmed: 35168796
pii: S0076-6879(21)00394-3
doi: 10.1016/bs.mie.2021.09.018
pmc: PMC10040239
mid: NIHMS1884355
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
341-375Subventions
Organisme : NIAID NIH HHS
ID : R21 AI148886
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI156669
Pays : United States
Informations de copyright
Copyright © 2022 Elsevier Inc. All rights reserved.
Références
mSystems. 2019 Sep 24;4(5):
pubmed: 31551401
Cell Metab. 2007 Nov;6(5):348-51
pubmed: 17983580
Nat Ecol Evol. 2021 Apr;5(4):495-503
pubmed: 33558733
J Nat Prod. 2017 Mar 24;80(3):598-608
pubmed: 28335605
Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):13738-13743
pubmed: 27856765
Sci Adv. 2020 Jul 22;6(30):eaaz2015
pubmed: 32766448
Anal Chem. 2017 Oct 3;89(19):10414-10421
pubmed: 28892370
Anal Chem. 2014 Oct 7;86(19):9583-9
pubmed: 25160088
Nat Biotechnol. 2020 Jan;38(1):23-26
pubmed: 31894142
Nat Biotechnol. 2021 Feb;39(2):169-173
pubmed: 33169034
Nat Methods. 2015 Jun;12(6):523-6
pubmed: 25938372
Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):12580-5
pubmed: 26392543
Nat Protoc. 2018 Apr;13(4):633-651
pubmed: 29494574
Front Immunol. 2021 Mar 16;12:654574
pubmed: 33796117
PLoS Comput Biol. 2021 Feb 16;17(2):e1008724
pubmed: 33591968
Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):11685-11690
pubmed: 29078340
Metabolomics. 2007 Sep;3(3):211-221
pubmed: 24039616
Metabolites. 2019 Dec 17;9(12):
pubmed: 31861212
BMC Bioinformatics. 2008 Nov 28;9:504
pubmed: 19040729
Nat Protoc. 2013 Jan;8(1):17-32
pubmed: 23222455
PLoS Pathog. 2018 Apr 5;14(4):e1006926
pubmed: 29621358
Anal Chem. 2006 Feb 1;78(3):779-87
pubmed: 16448051
Comput Struct Biotechnol J. 2021 May 21;19:3051-3057
pubmed: 34136103
Nat Methods. 2020 Sep;17(9):901-904
pubmed: 32807955
Nat Commun. 2018 Jun 7;9(1):2208
pubmed: 29880868
Nat Protoc. 2011 Jun 30;6(7):1060-83
pubmed: 21720319
Nat Protoc. 2020 Jun;15(6):1954-1991
pubmed: 32405051
BMC Bioinformatics. 2008 Mar 26;9:163
pubmed: 18366760
Metabolites. 2019 Jul 16;9(7):
pubmed: 31315242
J Am Chem Soc. 2020 May 20;142(20):9097-9105
pubmed: 32275430
Nat Chem Biol. 2017 Jan;13(1):30-37
pubmed: 27820803
Am J Phys Anthropol. 2020 Feb;171(2):177-181
pubmed: 31643083
Nature. 2017 Sep 7;549(7670):48-53
pubmed: 28854168
Nat Methods. 2019 Apr;16(4):299-302
pubmed: 30886413
Nat Methods. 2016 Aug 30;13(9):741-8
pubmed: 27575624
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
J Nat Prod. 2018 Apr 27;81(4):758-767
pubmed: 29498278
ACS Infect Dis. 2021 Jun 11;7(6):1638-1649
pubmed: 33843195
Nat Commun. 2021 Jun 22;12(1):3832
pubmed: 34158495
Cell. 2020 Sep 3;182(5):1311-1327.e14
pubmed: 32888495
Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2490-2495
pubmed: 29463727
Pathogens. 2021 May 13;10(5):
pubmed: 34068119
Nat Biotechnol. 2016 Aug 9;34(8):828-837
pubmed: 27504778
Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):12549-50
pubmed: 26430243
Bioinformatics. 2009 Jan 15;25(2):218-24
pubmed: 19015140
Nat Methods. 2020 Sep;17(9):905-908
pubmed: 32839597
Nat Methods. 2022 Feb;19(2):134-136
pubmed: 34862502
Nature. 2020 Mar;579(7797):123-129
pubmed: 32103176
Nat Protoc. 2018 Jan;13(1):134-154
pubmed: 29266099
FEMS Microbiol Rev. 2021 Aug 17;45(4):
pubmed: 33512504
PLoS Negl Trop Dis. 2021 Oct 4;15(10):e0009819
pubmed: 34606502
Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1743-52
pubmed: 22586093
Nat Methods. 2018 Jan;15(1):53-56
pubmed: 29176591
Cell Host Microbe. 2017 Nov 8;22(5):705-716.e4
pubmed: 29056429
PLoS Negl Trop Dis. 2018 Mar 12;12(3):e0006344
pubmed: 29529084
Nat Methods. 2010 May;7(5):335-6
pubmed: 20383131
Methods Mol Biol. 2020;2104:227-243
pubmed: 31953821
PLoS Comput Biol. 2018 Apr 18;14(4):e1006089
pubmed: 29668671
BMC Bioinformatics. 2010 Jul 23;11:395
pubmed: 20650010
Nat Biotechnol. 2019 Aug;37(8):852-857
pubmed: 31341288
Front Endocrinol (Lausanne). 2020 Dec 21;11:602771
pubmed: 33408694