Avian proteomics: Advances, challenges and new technologies

Cytogenetic and Genome Research

Volumn 117, Issue 1-4, 2007, Pages 358-369

  Doherty, M K ^a   McLean, L ^a   Beynon, R J ^a  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY; BONE GROWTH; BRAIN DEVELOPMENT; CELL DEATH; CEREBROSPINAL FLUID; EMBRYO DEVELOPMENT; FOWL; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NECROTIZING ENTERITIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; REVIEW; SKELETAL MUSCLE;

AGING; ANIMALS; AVIAN PROTEINS; BIRD DISEASES; BIRDS; FOOD ANALYSIS; PROTEOME; PROTEOMICS;

AVES;

EID: 34547622842     PISSN: 14248581     EISSN: None     Source Type: Journal    
DOI: 10.1159/000103199     Document Type: Review

References (67)

1. Agudo DF, Gomez-Esquer F, Diaz-Gil G, Martinez-Arribas F, Delcan J, et al: Proteomic analysis of the Gallus gallus embryo at stage-29 of development. Proteomics 5:4946-4957 (2005).
2. Almeida JS, Stanislaus R, Krug E, Arthur JM: Normalization and analysis of residual variation in two-dimensional gel electrophoresis for quantitative differential proteomics. Proteomics 5:1242-1249 (2005).
3. Anderson-MacKenzie JM, Hulmes DJ, Thorp BH: Effects of body mass and genotype on avian degenerative joint disease pathology and articular cartilage proteoglycan distribution. Clin Exp Rheumatol 16:403-408 (1998).
4. Arifuzzaman M, Maeda M, et al: Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 16:686-691 (2006).
5. Bendixen E: The use of proteomics in meat science. Meat Science 71:138-149 (2005).
6. Beynon RJ, Pratt JM: Metabolic labeling of proteins for proteomics. Mol Cell Proteomics 4:857-872 (2005).
7. Beynon RJ, Pratt JM: Strategies for measuring dynamics: the temporal component of proteomics. Methods Biochem Anal 49:15-25 (2006).
8. Beynon RJ, Doherty MK, Pratt JM, Gaskell SJ: Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat Methods 2:587-589 (2005).
9. Borisov OV, Goshe MB, Conrads TP, Rakov VS, Veenstra TD, Smith RD: Low-energy collision-induced dissociation fragmentation analysis of cysteinyl-modified peptides. Anal Chem 74:2284-2292 (2002).
10. Brand J, Haslberger TH, Zolg W, Pestlin G, Palme S:Depletion efficiency and recovery of trace markers from a multiparameter immunodepletion column. Proteomics 6:3236-3242 (2006).
11. Brown WRA, Hubbard SJ, Tickle C, Wilson SA: The chicken as a model for large-scale analysis of vertebrate gene function. Nat Rev Genet 4:87-98 (2003).
12. Burgess SC: Proteomics in the chicken: tools for understanding immune responses to avian diseases. Poult Sci 83:552-573 (2004).
13. Burgess SC, Young JR, Baaten BJ, Hunt L, Ross LN, et al: Marek's disease is a natural model for lymphomas overexpressing Hodgkin's disease antigen (CD30). Proc Natl Acad Sci USA 101:13879-13884 (2004).
14. Burt DW: Chicken genome: current status and future opportunities. Genome Res 15:1692-1698 (2005).
15. Cabiscol E, Piulats E, Echave P, Herrero E, Ros J: Oxidative stress promotes specific protein damage in Saccharomyces cerevisiae. J Biol Chem 275:27393-27398 (2000).
16. Castegna A, Aksenov M, Thongboonkerd V, Klein JB, Pierce WM, et al: Proteomic identification of oxidatively modified proteins in Alzheimer's disease brain. Part II: dihydropyrimidinase-related protein 2, alpha-enolase and heat shock cognate 71. J Neurochem 82:1524-1532 (2002).
17. Corzo A, Kidd MT, Pharr GT, Burgess SC: Initial mapping of the chicken blood plasma proteome. Int J Poult Sci 3:157-162 (2004).
18. Currie RJ: Ascites in poultry: recent investigations. Avian Pathol 28:313-326 (1999).
19. Doherty MK, McLean L, Hayter JR, Pratt JM, Robertson DH, et al: The proteome of chicken skeletal muscle: changes in soluble protein expression during growth in a layer strain. Proteomics 4:2082-2093 (2004).
20. Doherty MK, Whitehead C, McCormack H, Gaskell SJ, Beynon RJ: Proteome dynamics in complex organisms: Using stable isotopes to monitor individual protein turnover rates. Proteomics 5:522-533 (2005).
21. Etches RJ, Petitte JN, Anderson-Langmuir CE: Interrelationships between the hypothalamus, pituitary gland, ovary, adrenal gland, and the open period for LH release in the hen (Gallus domesticus). J Exp Zool 232:501-511 (1984).
22. Etches R, Kelly J, Anderson-Langmuir CE, Olson DM: Prostaglandin production by the largest preovulatory follicles in the domestic hen (Gallus domesticus). Biol Reprod 43:378-384 (1990).
23. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP: Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 100:6940-6945 (2003).
24. Gevaert K, Goethals M, Martens L, Van Damme J, Staes A, et al: Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat Biotechnol 21:566-569 (2003).
25. Gevaert K, Van Damme P, Martens L, Vandekerckhove J: Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics? Anal Biochem 345:18-29 (2005).
26. Gevaert K, Van Damme P, Ghesquiere B, Vandekerckhove J: Protein processing and other modifications analyzed by diagonal peptide chromatography. Biochim Biophys Acta 1764:1801-1810 (2006).
27. Gingras A-C, Aebersold R, Raught B: Advances in protein complex analysis using mass spectrometry. J Physiol (Lond) 563:11-21 (2005).
28. Granger J, Siddiqui J, Copeland S, Remick D: Albumin depletion of human plasma also removes low abundance proteins including the cytokines. Proteomics 5:4713-4718 (2005).
29. Groenen MA, Cheng HH, Bumstead N, Benkel BF, Briles WE, et al: A consensus linkage map of the chicken genome. Genome Res 10:137-147 (2000).
30. Gruhler A, Olsen JV, Shabaz M, Mortensen P, Faergeman NJ, et al: Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics 4:310-327 (2005).
31. Han BK, Kim JN, Shin JH, Kim JK, Jo DH, et al: Proteome analysis of chicken embryonic gonads: identification of major proteins from cultured gonadal primordial germ cells. Mol Reprod Dev 72:521-529 (2005).
32. Hayter JR, Robertson DH, Gaskell SJ, Beynon RJ: Proteome analysis of intact proteins in complex mixtures. Mol Cell Proteomics 2:85-95 (2003).
33. Hayter JR, Doherty MK, Whitehead C, McCormack H, Gaskell SJ, Beynon RJ: The subunit structure and dynamics of the 20S proteasome in chicken skeletal muscle. Mol Cell Proteomics 4:1370-1381 (2005).
34. Hellerstein MK, Neese RA: Mass isotopomer distribution analysis: a technique for measuring biosynthesis and turnover of polymers. Am J Physiol 263:E988-1001 (1992).
35. Hellerstein MK, Neese RA: Mass isotopomer distribution analysis at eight years: theoretical, analytic, and experimental considerations. Am J Physiol 276:E1146-1170 (1999).
36. Hillier LW, Miller W, et al: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716 (2004).
37. Hocking PM, Thorp BH, Bernard R, Dick L: Comparative development of the antitrochanter in three strains of domestic fowl. Res Vet Sci 60:37-43 (1996).
38. Huang SY, Lin JH, Chen YH, Chuang CK, Chiu YF, et al: Analysis of chicken serum proteome and differential protein expression during development in single-comb White Leghorn hens. Proteomics 6:2217-2224(2006).
39. Kirkpatrick DS, Gerber SA, Gygi SP: The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35:265-273 (2005).
40. Kuo YM, Shiue YL, Chen CF, Tang PC, Lee YP: Proteomic analysis of hypothalamic proteins of high and low egg production strains of chickens. Theriogenology 64:1490-1502 (2005).
41. Lam TC, Li KK, Lo SC, Guggenheim JA, To CH: A chick retinal proteome database and differential retinal protein expressions during early ocular development. J Proteome Res 5:771-784 (2006).
42. Levisohn S, Kleven SH: Avian mycoplasmosis (Mycoplasma gallisepticum). Rev Sci Tech 19:425-442 (2000).
43. Liu HC, Soderblom EJ, Goshe MB: A mass spectrometry-based proteomic approach to study Marek's disease virus gene expression. J Virol Methods 135:66-75 (2006).
44. Long JR, Pettit JR, Barnum DA: Necrotic enteritis in broiler chickens. II. Pathology and proposed pathogenesis. Can J Comp Med 38:467-474 (1974).
45. Mangum JE, Farlie PG, Hubbard MJ: Proteomic profiling of facial development in chick embryos. Proteomics 5:2542-2550 (2005).
46. Masabanda JS, Burt DW, O'Brien PC, Vignal A, Fillon V, et al: Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype. Genetics 166:1367-1373 (2004).
47. McCarthy FM, Cooksey AM, Wang N, Bridges SM, Pharr GT, Burgess SC: Modeling a whole organ using proteomics: the avian bursa of Fabricius. Proteomics 6:2759-2771 (2006).
48. McDonald L, Beynon RJ: Positional proteomics: preparation of amino-terminal peptides as a strategy for proteome simplification and characterization. Nat Protocols 1:1790-1798 (2006).
49. McDonald L, Robertson DH, Hurst JL, Beynon RJ: Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides. Nat Methods 2:955-957 (2005).
50. McLean L, Doherty MK, Deeming DC, Beynon RJ: A proteome analysis of the subcutaneous gel in avian hatchlings. Mol Cell Proteomics 3:250-256 (2004).
51. Papageorgopoulos C, Caldwell K, Shackleton C, Schweingrubber H, Hellerstein MK: Measuring protein synthesis by mass isotopomer distribution analysis (MIDA). Anal Biochem 267:1-16 (1999).
52. Papageorgopoulos C, Caldwell K, Schweingrubber H, Neese RA, Shackleton CH, Hellerstein M: Measuring synthesis rates of muscle creatine kinase and myosin with stable isotopes and mass spectrometry. Anal Biochem 309:1-10 (2002).
53. Parada C, Gato A, Bueno D: Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. J Proteome Res 4:2420-2428 (2005).
54. Pedrioli PGA, Raught B, Zhang X-D, Rogers R, Aitchison J, et al: Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. 3:533-539 (2006).
55. Pratt JM, Simpson DM, Doherty MK, Rivers J, Gaskell SJ, Beynon RJ: Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. 1:1029-1043 (2006).
56. Ramirez AS, Naylor CJ, Hammond PP, Bradbury JM: Development and evaluation of a diagnostic PCR for Mycoplasma synoviae using primers located in the intergenic spacer region and the 23S rRNA gene. Vet Microbiol 118:76-82 (2006).
57. Righetti PG, Boschetti E, Lomas L, Citterio A: Protein equalizer technology: the quest for a democratic proteome. Proteomics 6:3980-3992 (2006).
58. Scott TR, Messersmith AR, McCrary WJ, Herlong JL, Burgess SC: Hematopoietic prostaglandin D2 synthase in the chicken Harderian gland. Vet Immunol Immunopathol 108:295-306 (2005).
59. Stagsted J, Bendixen E, Andersen HJ: Identification of specific oxidatively modified proteins in chicken muscles using a combined immunologic and proteomic approach. J Agric Food Chem 52:3967-3974 (2004).
60. Stern CD: The chick: a great model system becomes even greater. Develop Cell 8:9-17 (2005).
61. Tamarit J, Cabiscol E, Ros J: Identification of the major oxidatively damaged proteins in Escherichia coli cells exposed to oxidative stress. J Biol Chem 273:3027-3032 (1998).
62. Tanaka M, Sugisaki K, Nakashima K: Purification, characterization, and distribution of enolase isozymes in chicken. J Biochem (Tokyo) 98:1527-1534 (1985).
63. Tanaka M, Maeda K, Nakashima K: Chicken alphaenolase but not beta-enolase has a Src-dependent tyrosine-phosphorylation site: cDNA cloning and nucleotide sequence analysis. J Biochem (Tokyo) 117:554-559 (1995).
64. Todd D, Mawhinney KA, McNulty MS: Detection and differentiation of chicken anemia virus isolates by using the polymerase chain reaction. J Clin Microbiol 30:1661-1666 (1992).
65. Wilmarth PA, Taube JR, Riviere MA, Duncan MK, David LL: Proteomic and sequence analysis of chicken lens crystallins reveals alternate splicing and translational forms of beta B2 and beta A2 crystallins. Invest Ophthalmol Vis Sci 45:2705-2715 (2004).
66. Wise MG, Siragusa GR: Quantitative detection of Clostridium perfringens in the broiler fowl gastrointestinal tract by real-time PCR. Appl Environ Microbiol 71:3911-3916 (2005).
67. Zhou S, Bailey MJ, Dunn MJ, Preedy VR, Emery PW: A quantitative investigation into the losses of proteins at different stages of a two-dimensional gel electrophoresis procedure. Proteomics 5:2739-2747 (2005).