Interactome Mapping: Using Protein Microarray Technology to Reconstruct Diverse Protein Networks

Genomics, Proteomics and Bioinformatics

Volumn 11, Issue 1, 2013, Pages 18-28

  Uzoma, Ijeoma ^a   Zhu, Heng ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Biomarker; Interactome; Protein microarray; Protein network; Serum profiling; Systems biology

Indexed keywords

ACYLTRANSFERASE; ARABIDOPSIS PROTEIN; AUTOANTIGEN; CELL EXTRACT; CELL PROTEIN; GLYCAN; LATENCY ASSOCIATED NUCLEAR ANTIGEN; LECTIN; MITOGEN ACTIVATED PROTEIN KINASE; UBIQUITIN PROTEIN LIGASE E3;

ANTIGEN ANTIBODY REACTION; AUTOIMMUNE HEPATITIS; CELL COMPONENT; CROHN DISEASE; HERPES VIRUS; HISTONE ACETYLATION; HOST PATHOGEN INTERACTION; HUMAN; NONHUMAN; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN GLYCOSYLATION; PROTEIN INTERACTION; PROTEIN METABOLISM; PROTEIN MICROARRAY; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEOMICS; REVIEW; SARS CORONAVIRUS; SIGNAL TRANSDUCTION; SUMOYLATION; SYSTEMS BIOLOGY; UBIQUITINATION; ULCERATIVE COLITIS;

ANIMALS; BIOLOGICAL MARKERS; DNA; HOST-PATHOGEN INTERACTIONS; HUMANS; LECTINS; POLYSACCHARIDES; PROTEIN ARRAY ANALYSIS; PROTEIN INTERACTION MAPPING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOME; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 84875381367     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2012.12.005     Document Type: Review

References (73)

1. Kenyon G.L., DeMarini D.M., Fuchs E., Galas D.J., Kirsch J.F., Leyh T.S., et al. Defining the mandate of proteomics in the post-genomics era: workshop report. Mol Cell Proteomics 2002, 1:763-780.
2. Neet K.E., Lee J.C. Biophysical characterization of proteins in the post-genomic era of proteomics. Mol Cell Proteomics 2002, 1:415-420.
3. Aebersold R., Mann M. Mass spectrometry-based proteomics. Nature 2003, 422:198-207.
4. Desiere F., Deutsch E.W., Nesvizhskii A.I., Mallick P., King N.L., Eng J.K., et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol 2005, 6:R9.
5. Yang L., Guo S., Li Y., Zhou S., Tao S. Protein microarrays for systems biology. Acta Biochim Biophys Sin (Shanghai) 2011, 43:161-171.
6. Smith M.G., Jona G., Ptacek J., Devgan G., Zhu H., Zhu X., et al. Global analysis of protein function using protein microarrays. Mech Ageing Dev 2005, 126:171-175.
7. Zhu H., Qian J. Applications of functional protein microarrays in basic and clinical research. Adv Genet 2012, 79:123-155.
8. Chen C.S., Sullivan S., Anderson T., Tan A.C., Alex P.J., Brant S.R., et al. Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip. Mol Cell Proteomics 2009, 8:1765-1776.
9. Tao S.C., Li Y., Zhou J., Qian J., Schnaar R.L., Zhang Y., et al. Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers. Glycobiology 2008, 18:761-769.
10. Kumble K.D. Protein microarrays: new tools for pharmaceutical development. Anal Bioanal Chem 2003, 377:812-819.
11. Hu S., Xie Z., Qian J., Blackshaw S., Zhu H. Functional protein microarray technology. Wiley Interdiscip Rev Syst Biol Med 2011, 3:255-268.
12. Zhu H., Bilgin M., Bangham R., Hall D., Casamayor A., Bertone P., et al. Global analysis of protein activities using proteome chips. Science 2001, 293:2101-2105.
13. Zhu H., Hu S., Jona G., Zhu X., Kreiswirth N., Willey B.M., et al. Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray. Proc Natl Acad Sci U S A 2006, 103:4011-4016.
14. Li R., Wang L., Liao G., Guzzo C.M., Matunis M.J., Zhu H., et al. SUMO binding by the Epstein-Barr virus protein kinase BGLF4 is crucial for BGLF4 function. J Virol 2012, 86:5412-5421.
15. Popescu S.C., Popescu G.V., Bachan S., Zhang Z., Gerstein M., Snyder M., et al. MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev 2009, 23:80-92.
16. Jeong J.S., Jiang L., Albino E., Marrero J., Rho H.S., Hu J., et al. Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics 2012, 11:1-10.
17. Huang J., Zhu H., Haggarty S.J., Spring D.R., Hwang H., Jin F., et al. Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc Natl Acad Sci U S A 2004, 101:16594-16599.
18. Hu S., Xie Z., Onishi A., Yu X., Jiang L., Lin J., et al. Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell 2009, 139:610-622.
19. Zhu J., Gopinath K., Murali A., Yi G., Hayward S.D., Zhu H., et al. RNA-binding proteins that inhibit RNA virus infection. Proc Natl Acad Sci U S A 2007, 104:3129-3134.
20. Ptacek J., Devgan G., Michaud G., Zhu H., Zhu X., Fasolo J., et al. Global analysis of protein phosphorylation in yeast. Nature 2005, 438:679-684.
21. Merbl Y., Kirschner M.W. Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays. Proc Natl Acad Sci U S A 2009, 106:2543-2548.
22. Lu J.Y., Lin Y.Y., Qian J., Tao S.C., Zhu J., Pickart C., et al. Functional dissection of a HECT ubiquitin E3 ligase. Mol Cell Proteomics 2008, 7:35-45.
23. Lin Y.Y., Lu J.Y., Zhang J., Walter W., Dang W., Wan J., et al. Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 2009, 136:1073-1084.
24. Foster M.W., Forrester M.T., Stamler J.S. A protein microarray-based analysis of S-nitrosylation. Proc Natl Acad Sci U S A 2009, 106:18948-18953.
25. Song Q., Liu G., Hu S., Zhang Y., Tao Y., Han Y., et al. Novel autoimmune hepatitis-specific autoantigens identified using protein microarray technology. J Proteome Res 2010, 9:30-39.
26. Asai T., Tena G., Plotnikova J., Willmann M.R., Chiu W.L., Gomez-Gomez L., et al. MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 2002, 415:977-983.
27. Ichimura K., Mizoguchi T., Yoshida R., Yuasa T., Shinozaki K. Various abiotic stresses rapidly activate Arabidopsis MAP kinases ATMPK4 and ATMPK6. Plant J 2000, 24:655-665.
28. VanDemark A.P., Hill C.P. Structural basis of ubiquitylation. Curr Opin Struct Biol 2002, 12:822-830.
29. Close P., Creppe C., Gillard M., Ladang A., Chapelle J.P., Nguyen L., et al. The emerging role of lysine acetylation of non-nuclear proteins. Cell Mol Life Sci 2010, 67:1255-1264.
30. Allard S., Utley R.T., Savard J., Clarke A., Grant P., Brandl C.J., et al. NuA4, an essential transcription adaptor/histone H4 acetyltransferase complex containing Esa1p and the ATM-related cofactor Tra1p. EMBO J 1999, 18:5108-5119.
31. Lu J.Y., Lin Y.Y., Sheu J.C., Wu J.T., Lee F.J., Chen Y., et al. Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell 2011, 146:969-979.
32. Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 2009, 325:834-840.
33. Chen Y., Zhao W., Yang J.S., Cheng Z., Luo H., Lu Z., et al. Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways. Mol Cell Proteomics 2012, 11:1048-1062.
34. Zhang T., Wang S., Lin Y., Xu W., Ye D., Xiong Y., et al. Acetylation negatively regulates glycogen phosphorylase by recruiting protein phosphatase 1. Cell Metab 2012, 15:75-87.
35. Li R., Zhu J., Xie Z., Liao G., Liu J., Chen M.R., et al. Conserved herpesvirus kinases target the DNA damage response pathway and TIP60 histone acetyltransferase to promote virus replication. Cell Host Microbe 2011, 10:390-400.
36. Shamay M., Liu J., Li R., Liao G., Shen L., Greenway M., et al. A protein array screen for Kaposi's sarcoma-associated herpesvirus LANA interactors links LANA to TIP60, PP2A activity and telomere shortening. J Virol 2012, 86:5179-5191.
37. Human herpesviruses: biology, therapy and immunoprophylaxis 2007, Cambridge University Press, Cambridge. A. Arvin, G. Campadelli-Fiume, E. Mocarski, P.S. Moore, B. Roizman, R. Whitley (Eds.).
38. Gershburg E., Pagano J.S. Conserved herpesvirus protein kinases. Biochim Biophys Acta 2008, 1784:203-212.
39. Romaker D., Schregel V., Maurer K., Auerochs S., Marzi A., Sticht H., et al. Analysis of the structure-activity relationship of four herpesviral UL97 subfamily protein kinases reveals partial but not full functional conservation. J Med Chem 2006, 49:7044-7053.
40. Meng Q., Hagemeier S.R., Fingeroth J.D., Gershburg E., Pagano J.S., Kenney S.C. The Epstein-Barr virus (EBV)-encoded protein kinase, EBV-PK, but not the thymidine kinase (EBV-TK), is required for ganciclovir and acyclovir inhibition of lytic viral production. J Virol 2010, 84:4534-4542.
41. Gershburg E., Raffa S., Torrisi M.R., Pagano J.S. Epstein-Barr virus-encoded protein kinase (BGLF4) is involved in production of infectious virus. J Virol 2007, 81:5407-5412.
42. Gershburg E., Pagano J.S. Phosphorylation of the Epstein-Barr virus (EBV) DNA polymerase processivity factor EA-D by the EBV-encoded protein kinase and effects of the l-riboside benzimidazole 1263W94. J Virol 2002, 76:998-1003.
43. Gareau J.R., Lima C.D. The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat Rev Mol Cell Biol 2010, 11:861-871.
44. Johnson E.S. Protein modification by SUMO. Annu Rev Biochem 2004, 73:355-382.
45. Ye F., Lei X., Gao S.J. Mechanisms of Kaposi's sarcoma-associated herpesvirus latency and reactivation. Adv Virol 2011, 2011:193860.
46. Grundhoff A., Ganem D. The latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus permits replication of terminal repeat-containing plasmids. J Virol 2003, 77:2779-2783.
47. Hu J., Garber A.C., Renne R. The latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus supports latent DNA replication in dividing cells. J Virol 2002, 76:11677-11687.
48. Fakhari F.D., Jeong J.H., Kanan Y., Dittmer D.P. The latency-associated nuclear antigen of Kaposi sarcoma-associated herpesvirus induces B cell hyperplasia and lymphoma. J Clin Invest 2006, 116:735-742.
49. An J., Sun Y., Rettig M.B. Transcriptional coactivation of c-Jun by the KSHV-encoded LANA. Blood 2004, 103:222-228.
50. Cai Q., Lan K., Verma S.C., Si H., Lin D., Robertson E.S. Kaposi's sarcoma-associated herpesvirus latent protein LANA interacts with HIF-1 alpha to upregulate RTA expression during hypoxia: latency control under low oxygen conditions. J Virol 2006, 80:7965-7975.
51. Kusano S., Eizuru Y. Human I-mfa domain proteins specifically interact with KSHV LANA and affect its regulation of Wnt signaling-dependent transcription. Biochem Biophys Res Commun 2010, 396:608-613.
52. Krithivas A., Fujimuro M., Weidner M., Young D.B., Hayward S.D. Protein interactions targeting the latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus to cell chromosomes. J Virol 2002, 76:11596-11604.
53. Barbera A.J., Chodaparambil J.V., Kelley-Clarke B., Joukov V., Walter J.C., Luger K., et al. The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA. Science 2006, 311:856-861.
54. Chen W., Dittmer D.P. Ribosomal protein S6 interacts with the latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus. J Virol 2011, 85:9495-9505.
55. Zhu H., Cox E., Qian J. Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics. Proteomics Clin Appl 2012, 6:548-562.
56. Mattoon D., Michaud G., Merkel J., Schweitzer B. Biomarker discovery using protein microarray technology platforms: antibody-antigen complex profiling. Expert Rev Proteomics 2005, 2:879-889.
57. Manns M.P., Vogel A. Autoimmune hepatitis, from mechanisms to therapy. Hepatology 2006, 43:S132-S144.
58. Satija N., Lal S.K. The molecular biology of SARS coronavirus. Ann N Y Acad Sci 2007, 1102:26-38.
59. Thoreson R., Cullen J.J. Pathophysiology of inflammatory bowel disease: an overview. Surg Clin North Am 2007, 87:575-585.
60. Bossuyt X. Serologic markers in inflammatory bowel disease. Clin Chem 2006, 52:171-181.
61. Hakomori S. Aberrant glycosylation in cancer cell membranes as focused on glycolipids: overview and perspectives. Cancer Res 1985, 45:2405-2414.
62. Hakomori S. Glycosylation defining cancer malignancy: new wine in an old bottle. Proc Natl Acad Sci U S A 2002, 99:10231-10233.
63. Dennis J.W., Granovsky M., Warren C.E. Glycoprotein glycosylation and cancer progression. Biochim Biophys Acta 1999, 1473:21-34.
64. Dwek M.V., Ross H.A., Leathem A.J. Proteome and glycosylation mapping identifies post-translational modifications associated with aggressive breast cancer. Proteomics 2001, 1:756-762.
65. Kung L.A., Tao S.C., Qian J., Smith M.G., Snyder M., Zhu H. Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes. Mol Syst Biol 2009, 5:308.
66. Hirabayashi J. Lectin-based structural glycomics: glycoproteomics and glycan profiling. Glycoconj J 2004, 21:35-40.
67. Ebe Y., Kuno A., Uchiyama N., Koseki-Kuno S., Yamada M., Sato T., et al. Application of lectin microarray to crude samples: differential glycan profiling of LEC mutants. J Biochem 2006, 139:323-327.
68. Kuno A., Uchiyama N., Koseki-Kuno S., Ebe Y., Takashima S., Yamada M., et al. Evanescent-field fluorescence-assisted lectin microarray: a new strategy for glycan profiling. Nat Methods 2005, 2:851-856.
69. Tan M., Luo H., Lee S., Jin F., Yang J.S., Montellier E., et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 2011, 146:1016-1028.
70. Chen F., Lv H., Chen Z., Zhao T., Yang G. Optical real-time monitoring of the laser molecular-beam epitaxial growth of perovskite oxide thin films by an oblique-incidence reflectance-difference technique. J Opt Soc Am B 2000, 18:1031-1035.
71. Landry J.P., Zhu X.D., Gregg J.P. Label-free detection of microarrays of biomolecules by oblique-incidence reflectivity difference microscopy. Opt Lett 2004, 29:581-583.
72. Lu H., Wen J., Wang X., Yuan K., Li W., Lv H., et al. Detection of the specific binding on protein microarrays by oblique-incidence reflectivity difference method. J Opt 2010, 12:1-5.
73. Wang X., Lu H., Wen J., Yuan K., Lv H., Jin K., et al. Label-free and high-throughput detection of protein microarrays by oblique-incidence reflectivity difference method. Chinese Phys Lett 2010, 27:1-4.