Protein amino-terminal modifications and proteomic approaches for N-terminal profiling

Current Opinion in Chemical Biology

Volumn 24, Issue , 2015, Pages 71-79

  Lai, Zon W ^a   Petrera, Agnese ^a   Schilling, Oliver ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOPEPTIDASE; AMYLOID BETA PROTEIN; ARGININE; CATHEPSIN B; CELL PROTEIN; DIHYDROLIPOAMIDE DEHYDROGENASE; EXOPEPTIDASE; GONADORELIN; GUANINE NUCLEOTIDE BINDING PROTEIN; HEMIN; METALLOPROTEINASE; MONOCYTE CHEMOTACTIC PROTEIN 1; MONOCYTE CHEMOTACTIC PROTEIN 2; PEPTIDE ALPHA N ACETYLTRANSFERASE; PRION PROTEIN; PROTEIN; PYROGLUTAMIC ACID; STROMELYSIN 2; UBIQUITIN PROTEIN LIGASE E3; PROTEOME;

AFFINITY CHROMATOGRAPHY; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; APOPTOSIS; BIOTINYLATION; CHEMICAL MODIFICATION; COMPLEX FORMATION; ENZYME ACTIVE SITE; ENZYME INHIBITION; ESCHERICHIA COLI; GENE MUTATION; HALF LIFE TIME; HYDROPHOBICITY; ION EXCHANGE CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NEISSERIA MENINGITIDIS; NONHUMAN; PLASMODIUM CHABAUDI; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ACETYLATION; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEIN INDUCTION; PROTEIN METABOLISM; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEIN STABILITY; PROTEOMICS; RENIN ANGIOTENSIN ALDOSTERONE SYSTEM; REVIEW; ROSEOBACTER; SACCHAROMYCES CEREVISIAE; UBIQUITINATION; ANIMAL; CHEMISTRY; HUMAN; MOLECULAR GENETICS; PROCEDURES;

AMINO ACID SEQUENCE; ANIMALS; HUMANS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOME; PROTEOMICS;

EID: 84909619767     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2014.10.026     Document Type: Review

References (60)

1. Lai Z.W., Nice E.C., Schilling O. Glycocapture-based proteomics for secretome analysis. Proteomics 2013, 13:512-525.
2. Jornvall H. Acetylation of protein n-terminal amino-groups structural observations on alpha-amino acetylated proteins. J Theor Biol 1975, 55:1-12.
3. Hershko A., Heller H., Eytan E., Kaklij G., Rose I.A. Role of the a-amino group of protein in ubiquitin-mediated protein breakdown. Proc Natl Acad Sci U S A 1984, 81:7021-7025.
4. Persson B., Flinta C., Vonheijne G., Jornvall H. Structures of n-terminally acetylated proteins. Eur J Biochem 1985, 152:523-527.
5. Forte G.M., Pool M.R., Stirling C.J. N-terminal acetylation inhibits protein targeting to the endoplasmic reticulum. PLoS Biol 2011, 9:e1001073.
6. Hofmann I., Munro S. An n-terminally acetylated arf-like gtpase is localised to lysosomes and affects their motility. J Cell Sci 2006, 119:1494-1503.
7. Dikiy I., Eliezer D. N-terminal acetylation stabilizes n-terminal helicity in lipid- and micelle-bound alpha-synuclein and increases its affinity for physiological membranes. J Biol Chem 2014, 289:3652-3665.
8. Scott D.C., Monda J.K., Bennett E.J., Harper J.W., Schulman B.A. N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex. Science 2011, 334:674-678.
9. Shemorry A., Hwang C.S., Varshavsky A. Control of protein quality and stoichiometries by n-terminal acetylation and the n-end rule pathway. Mol Cell 2013, 50:540-551.
10. Hwang C.S., Shemorry A., Varshavsky A. N-terminal acetylation of cellular proteins creates specific degradation signals. Science 2010, 327:973-977.
11. Holmes W.M., Mannakee B.K., Gutenkunst R.N., Serio T.R. Loss of amino-terminal acetylation suppresses a prion phenotype by modulating global protein folding. Nat Commun 2014, 5:4383.
12. Foyn H., Van Damme P., Stove S.I., Glomnes N., Evjenth R., Gevaert K., Arnesen T. Protein n-terminal acetyltransferases act as n-terminal propionyltransferases in vitro and in vivo. Mol Cell Proteomics 2013, 12:42-54.
13. Rope A.F., Wang K., Evjenth R., Xing J.C., Johnston J.J., Swensen J.J., Johnson W.E., Moore B., Huff C.D., Bird L.M., Carey J.C., et al. Using vaast to identify an x-linked disorder resulting in lethality in male infants due to n-terminal acetyltransferase deficiency. Am J Hum Genet 2011, 89:28-43.
14. Hollebeke J., Van Damme P., Gevaert K. N-terminal acetylation and other functions of nalpha-acetyltransferases. Biol Chem 2012, 393:291-298.
15. Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., et al. N-terminal acetylome analyses and functional insights of the n-terminal acetyltransferase natb. Proc Natl Acad Sci U S A 2012, 109:12449-12454.
16. Van Damme P., Arnesen T., Ruttens B., Gevaert K. In-gel n-acetylation for the quantification of the degree of protein in vivo n-terminal acetylation. Methods Mol Biol 2013, 981:115-126.
17. Kumar A., Bachhawat A.K. Pyroglutamic acid: throwing light on a lightly studied metabolite. Curr Sci India 2012, 102:288-297.
18. Van Coillie E., Proost P., Van Aelst I., Struyf S., Polfliet M., De Meester I., Harvey D.J., Van Damme J., Opdenakker G. Functional comparison of two human monocyte chemotactic protein-2 isoforms, role of the amino-terminal pyroglutamic acid and processing by cd26/dipeptidyl peptidase iv. Biochemistry 1998, 37:12672-12680.
19. Shih Y.P., Chou C.C., Chen Y.L., Huang K.F., Wang A.H. Linked production of pyroglutamate-modified proteins via self-cleavage of fusion tags with tev protease and autonomous n-terminal cyclization with glutaminyl cyclase in vivo. PLoS One 2014, 9:e94812.
20. Wirths O., Bethge T., Marcello A., Harmeier A., Jawhar S., Lucassen P.J., Multhaup G., Brody D.L., Esparza T., Ingelsson M., Kalimo H., et al. Pyroglutamate abeta pathology in app/ps1ki mice, sporadic and familial alzheimer's disease cases. J Neural Transm 2010, 117:85-96.
21. Cynis H., Kehlen A., Haegele M., Hoffmann T., Heiser U., Fujii M., Shibazaki Y., Yoneyama H., Schilling S., Demuth H.U. Inhibition of glutaminyl cyclases alleviates ccl2-mediated inflammation of non-alcoholic fatty liver disease in mice. Int J Exp Pathol 2013, 94:217-225.
22. Kehlen A., Haegele M., Menge K., Gans K., Immel U.D., Hoang-Vu C., Klonisch T., Demuth H.U. Role of glutaminyl cyclases in thyroid carcinomas. Endocr Relat Cancer 2013, 20:79-90.
23. Staes A., Impens F., Van Damme P., Ruttens B., Goethals M., Demol H., Timmerman E., Vandekerckhove J., Gevaert K. Selecting protein n-terminal peptides by combined fractional diagonal chromatography. Nat Protoc 2011, 6:1130-1141.
24. Mommen G.P., van de Waterbeemd B., Meiring H.D., Kersten G., Heck A.J., de Jong A.P. Unbiased selective isolation of protein n-terminal peptides from complex proteome samples using phospho tagging (ptag) and tio(2)-based depletion. Mol Cell Proteomics 2012, 11:832-842.
25. Bachmair A., Finley D., Varshavsky A. In vivo half-life of a protein is a function of its amino-terminal residue. Science 1986, 234:179-186.
26. Tasaki T., Sriram S.M., Park K.S., Kwon Y.T. The n-end rule pathway. Annu Rev Biochem 2012, 81:261-289.
27. Kim H.K., Kim R.R., Oh J.H., Cho H., Varshavsky A., Hwang C.S. The n-terminal methionine of cellular proteins as a degradation signal. Cell 2013, 156:158-169.
28. Piatkov K.I., Brower C.S., Varshavsky A. The n-end rule pathway counteracts cell death by destroying proapoptotic protein fragments. Proc Natl Acad Sci U S A 2012, 109:E1839-E1847.
29. Humbard M.A., Surkov S., De Donatis G.M., Jenkins L.M., Maurizi M.R. The n-degradome of escherichia coli: Limited proteolysis in vivo generates a large pool of proteins bearing n-degrons. J Biol Chem 2013, 288:28913-28924.
30. Perez-Vazquez V., Guzman-Flores J.M., Mares-Alvarez D., Hernandez-Ortiz M., Macias-Cervantes M.H., Ramirez-Emiliano J., Encarnacion-Guevara S. Differential proteomic analysis of the pancreas of diabetic db/db mice reveals the proteins involved in the development of complications of diabetes mellitus. Int J Mol Sci 2014, 15:9579-9593.
31. Nazarian A., Lawlor K., Yi S.S., Philip J., Ghosh M., Yaneva M., Villanueva J., Saghatelian A., Assel M., Vickers A.J., Eastham J.A., et al. Inhibition of circulating dipeptidyl peptidase 4 activity in patients with metastatic prostate cancer. Mol Cell Proteomics 2014, m114.038836.
32. Carneiro L.G., Nouh H., Salih E. Quantitative gingival crevicular fluid proteome in health and periodontal disease using stable isotope chemistries and mass spectrometry. J Clin Periodontol 2014, 41:733-747.
33. Hildebrand D., Merkel P., Eggers L.F., Schluter H. Proteolytic processing of angiotensin-i in human blood plasma. Plos One 2013, 8:e64027.
34. Mahrus S., Trinidad J.C., Barkan D.T., Sali A., Burlingame A.L., Wells J.A. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein n termini. Cell 2008, 134:866-876.
35. Agard N.J., Wells J.A. Methods for the proteomic identification of protease substrates. Curr Opin Chem Biol 2009, 13:503-509.
36. Huesgen P.F., Overall C.M. N- and c-terminal degradomics: new approaches to reveal biological roles for plant proteases from substrate identification. Physiol Plantarum 2012, 145:5-17.
37. Xu G.Q., Shin S.B.Y., Jaffrey S.R. Global profiling of protease cleavage sites by chemoselective labeling of protein n-termini. Proc Natl Acad Sci U S A 2009, 106:19310-19315.
38. Timmer J.C., Enoksson M., Wildfang E., Zhu W., Igarashi Y., Denault J.B., Ma Y., Dummitt B., Chang Y.H., Mast A.E., Eroshkin A., et al. Profiling constitutive proteolytic events in vivo. Biochem J 2007, 407:41-48.
39. Timmer J.C., Zhu W.H., Pop C., Regan T., Snipas S.J., Eroshkin A.M., Riedl S.J., Salvesen G.S. Structural and kinetic determinants of protease substrates. Nat Struct Mol Biol 2009, 16:U1101-U1128.
40. Impens F. Ms-driven protease substrate degradomics (vol 10, pg 1284, 2010). Proteomics 2010, 10:2560.
41. Tholen S., Koczorowska M.M., Lai Z.W., Dengjel J., Schilling O. Limited and degradative proteolysis in the context of posttranslational regulatory networks: current technical and conceptional advances. Proteases: Structure and Function 2013, 175-216. Springer-Verlag. K. Brix, W. Stoecker (Eds.).
42. Shen P.T., Hsu J.L., Chen S.H. Dimethyl isotope-coded affinity selection for the analysis of free and blocked n-termini of proteins using lc-ms/ms. Anal Chem 2007, 79:9520-9530.
43. Kleifeld O., Doucet A., Keller U.A.D., Prudova A., Schilling O., Kainthan R.K., Starr A.E., Foster L.J., Kizhakkedathu J.N., Overall C.M. Isotopic labeling of terminal amines in complex samples identifies protein n-termini and protease cleavage products. Nat Biotechnol 2010, 28. 281-U144.
44. Mommen G.P.M., van de Waterbeemd B., Meiring H.D., Kersten G., Heck A.J.R., de Jong A.P.J.M. Unbiased selective isolation of protein n-terminal peptides from complex proteome samples using phospho tagging (ptag) and tio2-based depletion. Mol Cell Proteomics 2012, 11:832-842.
45. Venne A.S., Vogtle F.N., Meisinger C., Sickmann A., Zahedi R.P. Novel highly sensitive, specific, and straightforward strategy for comprehensive n-terminal proteomics reveals unknown substrates of the mitochondrial peptidase icp55. J Proteome Res 2013, 12:3823-3830.
46. Van Damme P., Stove S.I., Glomnes N., Gevaert K., Arnesen T. A saccharomyces cerevisiae model reveals in vivo functional impairment of the ogden syndrome n-terminal acetyltransferase naa10 ser37pro mutant. Mol Cell Proteomics 2014, 13:2031-2041.
47. Bland C., Hartmann E.M., Christie-Oleza J.A., Fernandez B., Armengaud J. N-terminal-oriented proteogenomics of the marine bacterium roseobacter denitrificans och114 using n-succinimidyloxycarbonylmethyl) tris(2,4,6trimethoxyphenyl) phosphonium bromide (tmpp) labeling and diagonal chromatography. Mol Cell Proteomics 2014, 13:1369-1381.
48. Kaiserman D., Stewart S.E., Plasman K., Gevaert K., Van Damme P., Bird P.I. Identification of serpinb6b as a species-specific mouse granzyme a inhibitor suggests functional divergence between human and mouse granzyme a. J Biol Chem 2014, 289:9408-9417.
49. Impens F., Van Damme P., Demol H., Van Damme J., Vandekerckhove J., Gevaert K. Mechanistic insight into taxol-induced cell death. Oncogene 2008, 27:4580-4591.
50. Vande Walle L., Van Damme P., Lamkanfi M., Saelens X., Vandekerckhove J., Gevaert K., Vandenabeele P. Proteome-wide identification of htra2/omi substrates. J Proteome Res 2007, 6:1006-1015.
51. Tholen S., Biniossek M.L., Gansz M., Ahrens T.D., Schlimpert M., Kizhakkedathu J.N., Reinheckel T., Schilling O. Double deficiency of cathepsins b and l results in massive secretome alterations and suggests a degradative cathepsin-mmp axis. Cell Mol Life Sci 2014, 71:899-916.
52. Shahinian H., Loessner D., Biniossek M.L., Kizhakkedathu J.N., Clements J.A., Magdolen V., Schilling O. Secretome and degradome profiling shows that kallikrein-related peptidases 4, 5, 6, and 7 induce tgfbeta-1 signaling in ovarian cancer cells. Mol Oncol 2014, 8:68-82.
53. Prudova A., auf dem Keller U., Butler G.S., Overall C.M. Multiplex n-terminome analysis of mmp-2 and mmp-9 substrate degradomes by itraq-tails quantitative proteomics. Mol Cell Proteomics 2010, 9:894-911.
54. Schlage P., Egli F.E., Nanni P., Wang L.W., Kizhakkedathu J.N., Apte S.S., Keller U.A.D. Time-resolved analysis of the matrix metalloproteinase 10 substrate degradome. Mol Cell Proteomics 2014, 13:580-593.
55. Hartmann E.M., Armengaud J. N-terminomics and proteogenomics, getting off to a good start. Proteomics 2014, 10.1002/pmic.201400157.
56. Min H., Han D., Kim Y., Cho J.Y., Jin J., Kim Y. Label-free quantitative proteomics and n-terminal analysis of human metastatic lung cancer cells. Mol Cells 2014, 37:457-466.
57. Nika H., Hawke D.H., Angeletti R.H. N-terminal protein characterization by mass spectrometry after cyanogen bromide cleavage using combined microscale liquid- and solid-phase derivatization. J Biomol Tech 2014, 25:19-30.
58. Taylor J.M., Yaneva M., Velasco K., Philip J., Erdjument-Bromage H., Ostrovnaya I., Lilja H.G., Bochner B.H., Tempst P. Aminopeptidase activities as prospective urinary biomarkers for bladder cancer. Proteomics Clin Appl 2014, 8:317-326.
59. Villanueva J., Shaffer D.R., Philip J., Chaparro C.A., Erdjument-Bromage H., Olshen A.B., Fleisher M., Lilja H., Brogi E., Boyd J., Sanchez-Carbayo M., et al. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest 2006, 116:271-284.
60. Meinnel T., Giglione C. Tools for analyzing and predicting n-terminal protein modifications. Proteomics 2008, 8:626-649.