Proteomic approaches to understanding the role of the cytoskeleton in host-defense mechanisms

Expert Review of Proteomics

Volumn 8, Issue 1, 2011, Pages 117-126

  Radulovic, Marko ^a   Godovac Zimmermann, Jasminka ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

actin; cytoskeleton; host defense; immune cell; immune response; mass spectrometry; microtubule; protein; proteomics; purification strategies

Indexed keywords

ACTIN; CHEMOKINE RECEPTOR CCR6; DNA; PHOSPHOLIPID; PROTEIN; PROTEOME;

CELL DIVISION; CELL MEMBRANE; CELL MIGRATION; CELL ORGANELLE; CYTOSKELETON; HOST RESISTANCE; HUMAN; IMMUNOCOMPETENT CELL; INTRACELLULAR TRANSPORT; MACROPHAGE; MASS SPECTROMETRY; NEUTROPHIL; NONHUMAN; PHAGOCYTOSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW; SIGNAL TRANSDUCTION; T LYMPHOCYTE ACTIVATION;

ACTINS; ANIMALS; APOPTOSIS; CARRIER PROTEINS; CYTOSKELETON; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; IMMUNITY; MACROPHAGES; MICROTUBULES; PHAGOCYTOSIS; PROTEOME; PROTEOMICS; SIGNAL TRANSDUCTION;

EID: 79951923873     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/epr.10.91     Document Type: Review

References (81)

1. Kustermans G, El Mjiyad N, Horion J, Jacobs N, Piette J, Legrand-Poels S. Actin cytoskeleton differentially modulates NF-κB-mediated IL-8 expression in myelomonocytic cells. Biochem. Pharmacol. 76(10), 1214-1228 (2008).
2. Selve N, Wegner A. Rate of treadmilling of actin filaments in vitro. J. Mol. Biol. 187(4), 627-631 (1986).
3. Disanza A, Steffen A, Hertzog M, Frittoli E, Rottner K, Scita G. Actin polymerization machinery: the finish line of signaling networks, the starting point of cellular movement. Cell Mol. Life Sci. 62(9), 955-970 (2005). (Pubitemid 40655613)
4. dos Remedios CG, Chhabra D, Kekic M et al. Actin binding proteins: regulation of cytoskeletal microfilaments. Physiol. Rev. 83(2), 433-473 (2003). (Pubitemid 36378678)
5. Marin-Esteban V, Charron D, Gelin C, Mooney N. Chemotherapeutic agents targeting the tubulin cytoskeleton modify LPS-induced cytokine secretion by dendritic cells and increase antigen presentation. J. Immunother. 33(4), 364-370 (2010).
6. Wickramarachchi DC, Theofilopoulos AN, Kono DH. Immune pathology associated with altered actin cytoskeleton regulation. Autoimmunity 43(1), 64-75 (2010).
7. Liebl D, Griffiths G. Transient assembly of F-actin by phagosomes delays phagosome fusion with lysosomes in cargo-overloaded macrophages. J. Cell Sci. 122(Pt 16), 2935-2945 (2009).
8. Kitano M, Nakaya M, Nakamura T, Nagata S, Matsuda M. Imaging of Rab5 activity identifies essential regulators for phagosome maturation. Nature 453(7192), 241-245 (2008). (Pubitemid 351667973)
9. Song W, Xuan H, Lin Q. Epidermal growth factor induces changes of interaction between epidermal growth factor receptor and actin in intact cells. Acta Biochim. Biophys. Sin. (Shanghai) 40(8), 754-760 (2008).
10. Caplan S, Baniyash M. Normal T cells express two T cell antigen receptor populations, one of which is linked to the cytoskeleton via zeta chain and displays a unique activation-dependent phosphorylation pattern. J. Biol. Chem. 271(34), 20705-20712 (1996). (Pubitemid 26281853)
11. Gimborn K, Lessmann E, Kuppig S, Krystal G, Huber M. SHIP down-regulates FcεR1-induced degranulation at supraoptimal IgE or antigen levels. J. Immunol. 174(1), 507-516 (2005). (Pubitemid 40007441)
12. Onabajo OO, Seeley MK, Kale A et al. Actin-binding protein 1 regulates B cell receptor-mediated antigen processing and presentation in response to B cell receptor activation. J. Immunol. 180(10), 6685-6695 (2008).
13. Stie J, Jesaitis AJ. Reorganization of the human neutrophil plasma membrane is associated with functional priming: implications for neutrophil preparations. J. Leukoc. Biol. 81(3), 672-685 (2007). (Pubitemid 46393545)
14. Thrasher AJ, Burns SO. WASP: a key immunological multitasker. Nat. Rev. Immunol. 10(3), 182-192 (2010).
15. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422(6928), 198-207 (2003). (Pubitemid 36362757)
16. Tyers M, Mann M. From genomics to proteomics. Nature 422(6928), 193-197 (2003). (Pubitemid 36362756)
17. Cravatt BF, Simon GM, Yates JR 3rd. The biological impact of mass-spectrometry-based proteomics. Nature 450(7172), 991-1000 (2007). (Pubitemid 350273629)
18. Mathivanan S, Ahmed M, Ahn NG et al. Human Proteinpedia enables sharing of human protein data. Nat.Biotechnol. 26(2), 164-167 (2008). (Pubitemid 351225942)
19. Foster LJ, de Hoog CL, Zhang Y, Xie X, Mootha VK, Mann M. A mammalian organelle map by protein correlation profiling. Cell 125(1), 187-199 (2006).
20. Godovac-Zimmermann J, Kleiner O, Brown LR, Drukier AK. Perspectives in spicing up proteomics with splicing. Proteomics 5(3), 699-709 (2005). (Pubitemid 40316054)
21. Razzaq TM, Ozegbe P, Jury EC, Sembi P, Blackwell NM, Kabouridis PS. Regulation of T-cell receptor signalling by membrane microdomains. Immunology 113(4), 413-426 (2004). (Pubitemid 39593360)
22. Foster LJ. Lessons learned from lipid raft proteomics. Expert Rev. Proteomics 5(4), 541-543 (2008).
23. Nebl T, Pestonjamasp KN, Leszyk JD, Crowley JL, Oh SW, Luna EJ. Proteomic analysis of a detergent-resistant membrane skeleton from neutrophil plasma membranes. J. Biol. Chem. 277(45), 43399-43409 (2002). (Pubitemid 35285728)
24. Viola A, Gupta N. Tether and trap: regulation of membrane-raft dynamics by actin-binding proteins. Nat. Rev. Immunol. 7(11), 889-896 (2007). (Pubitemid 350006240)
25. Jones GE. Cellular signaling in macrophage migration and chemotaxis. J. Leukoc. Biol. 68(5), 593-602 (2000).
26. Han X, Smith NL, Sil D, Holowka DA, McLafferty FW, Baird BA. IgE receptor-mediated alteration of membrane-cytoskeleton interactions revealed by mass spectrometric analysis of detergent-resistant membranes. Biochemistry 48(27), 6540-6550 (2009).
27. Lin SL, Chien CW, Han CL et al. Temporal proteomics profiling of lipid rafts in CCR6-activated T cells reveals the integration of actin cytoskeleton dynamics. J. Proteome Res. 9(1), 283-297 (2010).
28. Kobayashi M, Katagiri T, Kosako H, Iida N, Hattori S. Global analysis of dynamic changes in lipid raft proteins during T-cell activation. Electrophoresis 28(12), 2035-2043 (2007). (Pubitemid 47040409)
29. Xu P, Crawford M, Way M, Godovac- Zimmermann J, Segal AW, Radulovic M. Subproteome analysis of the neutrophil cytoskeleton. Proteomics 9(7), 2037-2049 (2009).
30. Kolli S, Zito CI, Mossink MH, Wiemer EA, Bennett AM. The major vault protein is a novel substrate for the tyrosine phosphatase SHP-2 and scaffold protein in epidermal growth factor signaling. J. Biol. Chem. 279(28), 29374-29385 (2004). (Pubitemid 38915816)
31. Patel PC, Fisher KH, Yang EC, Deane CM, Harrison RE. Proteomic analysis of microtubule-associated proteins during macrophage activation. Mol. Cell Proteomics 8(11), 2500-2514 (2009).
32. Clegg J, Kell D, Knull H, Welch GR, Wilson J. Macromolecular interactions: tracing the roots. Trends Biochem. Sci. 26(2), 91 (2001).
33. Knull HR, Walsh JL. Association of glycolytic enzymes with the cytoskeleton. Curr. Top. Cell Regul. 33, 15-30 (1992).
34. Hudder A, Nathanson L, Deutscher MP. Organization of mammalian cytoplasm. Mol. Cell Biol. 23(24), 9318-9326 (2003). (Pubitemid 37499818)
35. Nacife VP, Soeiro Mde N, Gomes RN, DAvila H, Castro-Faria Neto HC, Meirelles Mde N. Morphological and biochemical characterization of macrophages activated by carrageenan and lipopolysaccharide in vivo. Cell Struct. Funct. 29(2), 27-34 (2004).
36. Hermann P, Rubio M, Nakajima T, Delespesse G, Sarfati M. IFN-α priming of human monocytes differentially regulates Gram-positive and Gram-negative bacteria-induced IL-10 release and selectively enhances IL-12p70, CD80, and MHC class I expression. J. Immunol. 161(4), 2011-2018 (1998). (Pubitemid 28387627)
37. Meng X, Wilkins JA. Compositional characterization of the cytoskeleton of NK-like cells. J. Proteome Res. 4(6), 2081-2087 (2005). (Pubitemid 41814274)
38. Pederson T. As functional nuclear actin comes into view, is it globular, filamentous, or both? J. Cell Biol. 180(6), 1061-1064 (2008). (Pubitemid 351468464)
39. Sheng WY, Wang TC. Proteomic analysis of the differential protein expression reveals nuclear GAPDH in activated T lymphocytes. PLoS One 4(7), e6322 (2009).
40. Shakib K, Norman JT, Fine LG, Brown LR, Godovac-Zimmermann J. Proteomics profiling of nuclear proteins for kidney fibroblasts suggests hypoxia, meiosis, and cancer may meet in the nucleus. Proteomics 5(11), 2819-2838 (2005). (Pubitemid 41059760)
41. Qattan AT, Mulvey C, Crawford M, Natale DA, Godovac-Zimmermann J. Quantitative organelle proteomics of MCF-7 breast cancer cells reveals multiple subcellular locations for proteins in cellular functional processes. J. Proteome Res. 9(1), 495-508 (2010).
42. Chuong SD, Good AG, Taylor GJ, Freeman MC, Moorhead GB, Muench DG. Large-scale identification of tubulin-binding proteins provides insight on subcellular trafficking, metabolic channeling, and signaling in plant cells. Mol. Cell Proteomics 3(10), 970-983 (2004). (Pubitemid 40361232)
43. Vallee RB. A taxol-dependent procedure for the isolation of microtubules and microtubule-associated proteins (MAPs). J. Cell Biol. 92(2), 435-442 (1982). (Pubitemid 12157416)
44. Kjeken R, Egeberg M, Habermann A et al. Fusion between phagosomes, early and late endosomes: a role for actin in fusion between late, but not early endocytic organelles. Mol. Biol. Cell 15(1), 345-358 (2004). (Pubitemid 38044968)
45. Li N, Mak A, Richards DP et al. Monocyte lipid rafts contain proteins implicated in vesicular trafficking and phagosome formation. Proteomics 3(4), 536-548 (2003). (Pubitemid 36428305)
46. Wiederhold E, Veenhoff LM, Poolman B, Slotboom DJ. Proteomics of Saccharomyces cerevisiae organelles. Mol. Cell Proteomics 9(3), 431-445 (2010).
47. Yan W, Aebersold R, Raines EW. Evolution of organelle-associated protein profiling. J. Proteomics 72(1), 4-11 (2009).
48. Michelsen U, von Hagen J. Isolation of subcellular organelles and structures. Methods Enzymol. 463, 305-328 (2009).
49. Newberg J, Hua J, Murphy RF. Location proteomics: systematic determination of protein subcellular location. Methods Mol. Biol. 500, 313-332 (2009).
50. Ploscher M, Granvogl B, Reisinger V, Masanek A, Eichacker LA. Organelle proteomics. Methods Mol. Biol. 519, 65-82 (2009).
51. Gauthier DJ, Lazure C. Complementary methods to assist subcellular fractionation in organellar proteomics. Expert Rev. Proteomics 5(4), 603-617 (2008).
52. Lu B, Motoyama A, Ruse C, Venable J, Yates JR 3rd. Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data. Anal. Chem. 80(6), 2018-2025 (2008). (Pubitemid 351458047)
53. Chuong SD, Mullen RT, Muench DG. Identification of a rice RNA- and microtubule-binding protein as the multifunctional protein, a peroxisomal enzyme involved in the β-oxidation of fatty acids. J. Biol. Chem. 277(4), 2419-2429 (2002). (Pubitemid 34953263)
54. Radulovic M, Crane E, Crawford M, Godovac-Zimmermann J, Yu VP. CKS proteins protect mitochondrial genome integrity by interacting with mitochondrial single-stranded DNA-binding protein. Mol. Cell Proteomics 9(1), 145-152 (2010).
55. Sohn J, Parks JM, Buhrman G et al. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry 44(50), 16563-16573 (2005). (Pubitemid 41832038)
56. Danuser G, Waterman-Storer CM. Quantitative fluorescent speckle microscopy of cytoskeleton dynamics. Annu. Rev. Biophys. Biomol. Struct. 35, 361-387 (2006). (Pubitemid 43877383)
57. Olsen JV, Schwartz JC, Griep-Raming J et al. A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol. Cell Proteomics 8(12), 2759-2769 (2009).
58. Pan S, Aebersold R, Chen R et al. Mass spectrometry based targeted protein quantification: methods and applications. J. Proteome Res. 8(2), 787-797 (2009).
59. Godovac-Zimmermann J. Cancer-omics failure: warehouses, magic bullets, space/ time and The Life of Brian in cancer cells. Expert Rev. Proteomics 7(3), 303-306 (2010).
60. Mann K, Poustka AJ, Mann M. Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin. Proteome Sci. 8(1), 6 (2010).
61. Chi A, Huttenhower C, Geer LY et al. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc. Natl Acad. Sci. USA 104(7), 2193-2198 (2007). (Pubitemid 46391374)
62. Nguyen V, Cao L, Lin JT et al. A new approach for quantitative phosphoproteomic dissection of signaling pathways applied to T cell receptor activation. Mol. Cell Proteomics 8(11), 2418-2431 (2009).
63. Mayya V, Lundgren DH, Hwang SI et al. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci. Signal. 2(84), ra46 (2009).
64. Grant MM, Scheel-Toellner D, Griffiths HR. Contributions to our understanding of T cell physiology through unveiling the T cell proteome. Clin. Exp. Immunol. 149(1), 9-15 (2007). (Pubitemid 46897105)
65. Rosas-Acosta G, Russell WK, Deyrieux A, Russell DH, Wilson VG. A universal strategy for proteomic studies of SUMO and other ubiquitin-like modifiers. Mol. Cell Proteomics 4(1), 56-72 (2005). (Pubitemid 40309325)
66. Hofmann WA, Arduini A, Nicol SM et al. SUMOylation of nuclear actin. J. Cell Biol. 186(2), 193-200 (2009).
67. Jockusch BM, Schoenenberger CA, Stetefeld J, Aebi U. Tracking down the different forms of nuclear actin. Trends Cell Biol. 16(8), 391-396 (2006). (Pubitemid 44118783)
68. Ong SE, Blagoev B, Kratchmarova I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 1(5), 376-386 (2002).
69. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17(10), 994-999 (1999). (Pubitemid 29474856)
70. Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74(20), 5383-5392 (2002). (Pubitemid 35215372)
71. Hubner NC, Ren S, Mann M. Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics 8(23-24), 4862-4872 (2008).
72. Mulvey C, Thur B, Crawford M, Godovac-Zimmermann J. How many proteins are missed in quatitative proteomics experiments based on current MS/MS sequencing methods? Proteomics 3, 61-63 (2010).
73. Livesay EA, Tang K, Taylor BK et al. Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses. Anal. Chem. 80(1), 294-302 (2008). (Pubitemid 351448434)
74. Motoyama A, Xu T, Ruse CI, Wohlschlegel JA, Yates JR 3rd. Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides. Anal. Chem. 79(10), 3623-3634 (2007). (Pubitemid 46799057)
75. Fessler MB, Malcolm KC, Duncan MW, Worthen GS. A genomic and proteomic analysis of activation of the human neutrophil by lipopolysaccharide and its mediation by p38 mitogen-activated protein kinase. J. Biol. Chem. 277(35), 31291-31302 (2002). (Pubitemid 34968927)
76. Wang D, Bodovitz S. Single cell analysis: the new frontier in omics. Trends Biotechnol 28(6), 281-290 (2010).
77. Louzoun Y. The evolution of mathematical immunology. Immunol. Rev. 216, 9-20 (2007). (Pubitemid 46426515)
78. Bellomo N, Forni G. Complex multicellular systems and immune competition: new paradigms looking for a mathematical theory. Curr. Top. Dev. Biol. 81, 485-502 (2008).
79. Bieling P, Laan L, Schek H et al. Reconstitution of a microtubule plus-end tracking system in vitro. Nature 450(7172), 1100-1105 (2007). (Pubitemid 350273611)
80. Liu Y, Sanoff HK, Cho H et al. INK4/ARF transcript expression is associated with chromosome 9p21 variants linked to atherosclerosis. PLoS One 4(4), e5027 (2009).
81. Proteomics encyclopeida www.humanproteinpedia.org