Identification of proteoforms of short open reading frame-encoded peptides in
gut microbiome
microproteins
proteoforms
sORF-encoded peptides
short open reading frames
small open reading frames
top-down proteomics
Journal
Microbiology spectrum
ISSN: 2165-0497
Titre abrégé: Microbiol Spectr
Pays: United States
ID NLM: 101634614
Informations de publication
Date de publication:
02 Oct 2023
02 Oct 2023
Historique:
medline:
2
10
2023
pubmed:
2
10
2023
entrez:
2
10
2023
Statut:
aheadofprint
Résumé
Short open reading frames (sORF) have the potential to encode small proteins, sORF-encoded peptides (SEP), which are less than or equal to 100 amino acids in length. These SEP have been associated with various physiological processes and are known for their potential roles in modulating immune responses, signaling pathways, and cellular functions. Using bottom-up and top-down proteomics, we identified 45 novel and formerly reported SEP under different growth conditions and stress exposure in single cultures of
Identifiants
pubmed: 37782090
doi: 10.1128/spectrum.02528-23
pmc: PMC10715070
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0252823Références
Genome Res. 2017 Dec;27(12):2083-2095
pubmed: 29141959
Microbiome. 2021 Feb 23;9(1):55
pubmed: 33622394
Nat Biotechnol. 2014 Mar;32(3):223-6
pubmed: 24727771
J Bacteriol. 2022 Jan 18;204(1):e0035321
pubmed: 34748388
Nucleic Acids Res. 2021 Oct 11;49(18):10800
pubmed: 34530444
Nat Methods. 2014 Nov;11(11):1114-25
pubmed: 25357241
Anal Chem. 2022 Mar 1;94(8):3600-3607
pubmed: 35172570
Exp Cell Res. 2020 Jun 1;391(1):111923
pubmed: 32135166
Cell. 2019 Aug 22;178(5):1245-1259.e14
pubmed: 31402174
Mol Cell Proteomics. 2013 Nov;12(11):3420-30
pubmed: 23908556
Curr Opin Microbiol. 2017 Oct;39:81-88
pubmed: 29111488
Gut Microbes. 2020 Jul 3;11(4):1116-1129
pubmed: 31918607
Chembiochem. 2019 Jun 14;20(12):1479-1486
pubmed: 30648812
Nucleic Acids Res. 2020 Jan 8;48(D1):D265-D268
pubmed: 31777944
Mol Biol Evol. 2021 Dec 9;38(12):5825-5829
pubmed: 34597405
Bioinformatics. 2019 Apr 1;35(7):1249-1251
pubmed: 30169737
Annu Rev Genet. 2010;44:71-90
pubmed: 21047256
Annu Rev Biochem. 2014;83:753-77
pubmed: 24606146
Bioinformatics. 2017 Jul 01;33(13):1921-1929
pubmed: 28203715
Biochem Soc Trans. 2023 Jun 28;51(3):1071-1082
pubmed: 37171061
J Bacteriol. 2022 Jan 18;204(1):e0034421
pubmed: 34516282
Front Microbiol. 2021 Jan 28;12:611413
pubmed: 33584614
J Am Soc Mass Spectrom. 2022 Jul 6;33(7):1293-1302
pubmed: 35758524
J Proteome Res. 2014 Jul 3;13(7):3231-40
pubmed: 24922115
Annu Rev Microbiol. 2019 Sep 8;73:111-132
pubmed: 31091420
J Proteomics. 2010 Oct 10;73(11):2124-35
pubmed: 20620248
J Mol Biol. 2004 May 14;338(5):1027-36
pubmed: 15111065
Mol Cell Proteomics. 2016 Oct;15(10):3297-3320
pubmed: 27451424
Nat Rev Genet. 2014 Mar;15(3):193-204
pubmed: 24514441
Anal Chem. 2013 Jun 18;85(12):5989-95
pubmed: 23692435
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Biochimie. 1993;75(12):1061-75
pubmed: 8199241
IEEE Trans Vis Comput Graph. 2014 Dec;20(12):1983-92
pubmed: 26356912
Genome Res. 2019 Mar;29(3):485-493
pubmed: 30610011
FEBS J. 2022 Jan;289(1):53-74
pubmed: 33595896
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W72-6
pubmed: 15980571
J Proteome Res. 2021 May 7;20(5):2895-2903
pubmed: 33760615
Sci Rep. 2023 Feb 14;13(1):2602
pubmed: 36788287
Nat Biotechnol. 2022 Jun;40(6):921-931
pubmed: 35241840
J Proteome Res. 2020 Oct 2;19(10):4004-4018
pubmed: 32812434
Philos Trans R Soc Lond B Biol Sci. 2015 Oct 5;370(1679):
pubmed: 26370932
Nat Chem Biol. 2013 Jan;9(1):59-64
pubmed: 23160002
Microlife. 2023 Mar 10;4:uqad012
pubmed: 37223733
Brief Bioinform. 2019 Jun 03;:
pubmed: 31155657
Proteomics. 2021 Dec;21(23-24):e2100008
pubmed: 34145981
Curr Protoc Chem Biol. 2019 Dec;11(4):e77
pubmed: 31750990
J Proteome Res. 2013 Dec 6;12(12):5830-8
pubmed: 24188097
Trends Biochem Sci. 2020 Apr;45(4):308-320
pubmed: 32001092
Front Microbiol. 2019 Jul 12;10:1604
pubmed: 31354686
Bioinformatics. 2008 Aug 15;24(16):i42-8
pubmed: 18689838
Methods Mol Biol. 2017;1550:61-67
pubmed: 28188523
Biochim Biophys Acta Mol Cell Res. 2017 Nov;1864(11 Pt B):2191-2199
pubmed: 28711385
iScience. 2023 Jan 27;26(2):106069
pubmed: 36818287
Nat Methods. 2009 Nov;6(11):786-7
pubmed: 19876014
Proteomics. 2015 Jul;15(14):2503-18
pubmed: 26017780
Mol Syst Biol. 2019 Feb 22;15(2):e8290
pubmed: 30796087
Bioinformatics. 2018 Aug 15;34(16):2740-2747
pubmed: 29590297
Bioinform Adv. 2021 Dec 10;2(1):vbab041
pubmed: 36699412
Methods Mol Biol. 2017;1550:339-368
pubmed: 28188540
J Proteomics. 2010 Oct 10;73(11):2092-123
pubmed: 20816881
Mol Omics. 2019 Apr 1;15(2):108-116
pubmed: 30810554
J Proteome Res. 2019 Apr 5;18(4):1725-1734
pubmed: 30779583
J Pept Sci. 2014 Jan;20(1):25-9
pubmed: 24254748
J Mol Biol. 1999 Jul 16;290(3):607-14
pubmed: 10395817