A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms.
N-terminal acetylation
N-terminal acetyltransferases
N-terminomics
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2022
2022
Historique:
entrez:
6
5
2022
pubmed:
7
5
2022
medline:
11
5
2022
Statut:
ppublish
Résumé
Especially in eukaryotes, the N-terminal acetylation status of a protein reveals translation initiation sites and substrate specificities and activities of N-terminal acetyltransferases (NATs). Here, we discuss a bottom-up proteomics protocol for the enrichment of N-terminal peptides via strong cation exchange chromatography. This protocol is based on depleting internal tryptic peptides from proteome digests through their retention on strong cation exchangers, leaving N-terminally acetylated/blocked peptides enriched among the nonretained peptides. As such, one can identify novel N-terminal proteoforms and quantify the degree of N-terminal protein acetylation.
Identifiants
pubmed: 35524124
doi: 10.1007/978-1-0716-2257-5_17
doi:
Substances chimiques
Peptides
0
Proteome
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
293-309Informations de copyright
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Calligaris R, Bottardi S, Cogoi S et al (1995) Alternative translation initiation site usage results in two functionally distinct forms of the GATA-1 transcription factor. Proc Natl Acad Sci U S A 92:11598–11602
doi: 10.1073/pnas.92.25.11598
pubmed: 8524811
pmcid: 40449
Claus P, Doring F, Gringel S et al (2003) Differential intranuclear localization of fibroblast growth factor-2 isoforms and specific interaction with the survival of motoneuron protein. J Biol Chem 278:479–485
doi: 10.1074/jbc.M206056200
pubmed: 12397076
Thomas D, Plant LD, Wilkens CM et al (2008) Alternative translation initiation in rat brain yields K2P2.1 potassium channels permeable to sodium. Neuron 58:859–870
doi: 10.1016/j.neuron.2008.04.016
pubmed: 18579077
pmcid: 2529466
Gawron D, Ndah E, Gevaert K et al (2016) Positional proteomics reveals differences in N-terminal proteoform stability. Mol Syst Biol 12:858
doi: 10.15252/msb.20156662
pubmed: 26893308
pmcid: 4770386
Hartmann EM, Armengaud J (2014) N-terminomics and proteogenomics, getting off to a good start. Proteomics 14:2637–2646
doi: 10.1002/pmic.201400157
pubmed: 25116052
Varshavsky A (2019) N-degron and C-degron pathways of protein degradation. Proc Natl Acad Sci U S A 116:358–366
doi: 10.1073/pnas.1816596116
pubmed: 30622213
pmcid: 6329975
Kazak L, Reyes A, Duncan AL et al (2013) Alternative translation initiation augments the human mitochondrial proteome. Nucleic Acids Res 41:2354–2369
doi: 10.1093/nar/gks1347
pubmed: 23275553
Bogaert A, Fernandez E, Gevaert K (2020) N-terminal proteoforms in human disease. Trends Biochem Sci 45(4):308–320
doi: 10.1016/j.tibs.2019.12.009
pubmed: 32001092
Ree R, Varland S, Arnesen T (2018) Spotlight on protein N-terminal acetylation. Exp Mol Med 50:1–13
doi: 10.1038/s12276-018-0116-z
pubmed: 30054468
pmcid: 6063853
Van Damme, P., T. Arnesen and K. Gevaert (2011) Protein alpha-N-acetylation studied by N-terminomics. FEBS J 278(20): 3822–3834
Bogaert A, Gevaert K (2020) Protein amino-termini and how to identify them. Expert Rev Proteomics 17:581–594
doi: 10.1080/14789450.2020.1821657
pubmed: 32896182
Perrar A, Dissmeyer N, Huesgen PF (2019) New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology. J Exp Bot 70:2021–2038
doi: 10.1093/jxb/erz104
pubmed: 30838411
pmcid: 6460961
Arnesen T, van Damme P, Polevoda B et al (2009) Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans. Proc Natl Acad Sci U S A 106:8157–8162
doi: 10.1073/pnas.0901931106
pubmed: 19420222
pmcid: 2688859
Goetze S, Qeli E, Mosimann C et al (2009) Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biol 7:e1000236
doi: 10.1371/journal.pbio.1000236
pubmed: 19885390
pmcid: 2762599
Nevitt C, Tooley JG, Schaner Tooley CE (2018) N-terminal acetylation and methylation differentially affect the function of MYL9. Biochem J 475:3201–3219
doi: 10.1042/BCJ20180638
pubmed: 30242065
Thompson CR, Champion MM, Champion PA (2018) Quantitative N-terminal footprinting of pathogenic mycobacteria reveals differential protein acetylation. J Proteome Res 17:3246–3258
doi: 10.1021/acs.jproteome.8b00373
pubmed: 30080413
pmcid: 6264890
van Damme P, Stove SI, Glomnes N et al (2014) A Saccharomyces cerevisiae model reveals in vivo functional impairment of the Ogden syndrome N-terminal acetyltransferase NAA10 Ser37Pro mutant. Mol Cell Proteomics 13:2031–2041
doi: 10.1074/mcp.M113.035402
pubmed: 24408909
pmcid: 4125735
van Damme P, van Damme J, Demol H et al (2009) A review of COFRADIC techniques targeting protein N-terminal acetylation. BMC Proc 3(Suppl 6):S6
doi: 10.1186/1753-6561-3-S6-S6
pubmed: 19660099
pmcid: 2722099
Bhagwat SR, Hajela K, Bhutada S et al (2020) Identification of unexplored substrates of the serine protease, thrombin, using N-terminomics strategy. Int J Biol Macromol 144:449–459
doi: 10.1016/j.ijbiomac.2019.12.137
pubmed: 31862363
Gevaert K, Goethals M, Martens L et al (2003) Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol 21:566–569
doi: 10.1038/nbt810
pubmed: 12665801
Impens F, Colaert N, Helsens K et al (2010) MS-driven protease substrate degradomics. Proteomics 10:1284–1296
doi: 10.1002/pmic.200900418
pubmed: 20058249
Mahrus S, Trinidad JC, Barkan DT et al (2008) Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 134:866–876
doi: 10.1016/j.cell.2008.08.012
pubmed: 18722006
pmcid: 2566540
Tam LX, Aigner H, Timmerman E et al (2015) Proteomic approaches to identify substrates of the three Deg/HtrA proteases of the cyanobacterium Synechocystis sp. PCC 6803. Biochem J 468:373–384
doi: 10.1042/BJ20150097
pubmed: 25877158
Tsiatsiani L, Timmerman E, de Bock PJ et al (2013) The Arabidopsis metacaspase9 degradome. Plant Cell 25:2831–2847
doi: 10.1105/tpc.113.115287
pubmed: 23964026
pmcid: 3784583
Xu G, Shin SB, Jaffrey SR (2009) Global profiling of protease cleavage sites by chemoselective labeling of protein N-termini. Proc Natl Acad Sci U S A 106:19310–19315
doi: 10.1073/pnas.0908958106
pubmed: 19892738
pmcid: 2780798
van Damme P, Gawron D, van Criekinge W et al (2014) N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men. Mol Cell Proteomics 13:1245–1261
doi: 10.1074/mcp.M113.036442
pubmed: 24623590
pmcid: 4014282
van der Meijden E, Kazem S, Dargel CA et al (2015) Characterization of T antigens, including middle T and alternative T, expressed by the human polyomavirus associated with Trichodysplasia spinulosa. J Virol 89:9427–9439
doi: 10.1128/JVI.00911-15
pubmed: 26136575
pmcid: 4542345
Staes A, van Damme P, Timmerman E et al (2017) Protease substrate profiling by N-terminal COFRADIC. Methods Mol Biol 1574:51–76
doi: 10.1007/978-1-4939-6850-3_5
pubmed: 28315243
Drazic A, Aksnes H, Marie M et al (2018) NAA80 is actin’s N-terminal acetyltransferase and regulates cytoskeleton assembly and cell motility. Proc Natl Acad Sci U S A 115:4399–4404
doi: 10.1073/pnas.1718336115
pubmed: 29581253
pmcid: 5924898
Staes A, Impens F, van Damme P et al (2011) Selecting protein N-terminal peptides by combined fractional diagonal chromatography. Nat Protoc 6:1130–1141
doi: 10.1038/nprot.2011.355
pubmed: 21799483
Meier F, Brunner AD, Koch S et al (2018) Online parallel accumulation-serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer. Mol Cell Proteomics 17:2534–2545
doi: 10.1074/mcp.TIR118.000900
pubmed: 30385480
pmcid: 6283298
Staes A, van Damme P, Helsens K et al (2008) Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics 8:1362–1370
doi: 10.1002/pmic.200700950
pubmed: 18318009
Ning Z, Seebun D, Hawley B et al (2013) From cells to peptides: “one-stop” integrated proteomic processing using amphipols. J Proteome Res 12:1512–1519
doi: 10.1021/pr301064z
pubmed: 23394071
Ning Z, Hawley B, Seebun D et al. (2014) APols-aided protein precipitation: a rapid method for concentrating proteins for proteomic analysis. J Membr Biol 247:941–947
Ning Z, Seebun D, Hawley B et al. (2013) From cells to peptides: “one-stop” integrated proteomic processing using amphipols. J Proteome Res 12:1512–1519
Aksnes H, van Damme P, Goris M et al (2015) An organellar nalpha-acetyltransferase, naa60, acetylates cytosolic N termini of transmembrane proteins and maintains Golgi integrity. Cell Rep 10:1362–1374
doi: 10.1016/j.celrep.2015.01.053
pubmed: 25732826
Dimarchi RD, Tam JP, Kent SB et al (1982) Weak acid-catalyzed pyrrolidone carboxylic acid formation from glutamine during solid phase peptide synthesis. Minimization by rapid coupling. Int J Pept Protein Res 19:88–93
doi: 10.1111/j.1399-3011.1982.tb03027.x
pubmed: 7118385
Rehder DS, Dillon TM, Pipes GD et al (2006) Reversed-phase liquid chromatography/mass spectrometry analysis of reduced monoclonal antibodies in pharmaceutics. J Chromatogr A 1102:164–175
doi: 10.1016/j.chroma.2005.10.053
pubmed: 16297926
Bovine pitu itary pyrrolidonecarboxylyl peptidase. Endocrinology 93:1428–1434
Browne P, O’Cuinn G (1983) An evaluation of the role of a pyroglutamyl peptidase, a post proline cleaving enzyme and a post-proline dipeptidyl amino peptidase, each purified from the soluble fraction of guinea-pig brain, in the degradation of thyroliberin in vitro. Eur J Biochem 137:75–87
Ning Z, Hawley B, Seebun D et al (2014) APols-aided protein precipitation: a rapid method for concentrating proteins for proteomic analysis. J Membr Biol 247:941–947
doi: 10.1007/s00232-014-9668-6
pubmed: 24838764
pmcid: 4196042
van Damme P, Arnesen T, Gevaert K (2011) Protein alpha-N-acetylation studied by N-terminomics. FEBS J 278:3822–3834
doi: 10.1111/j.1742-4658.2011.08230.x
pubmed: 21736701