Profiling of urinary proteins in Karan Fries cows reveals more than 1550 proteins

Journal of Proteomics

Volumn 127, Issue , 2015, Pages 193-201

  Bathla, Shveta ^a   Rawat, Preeti ^a   Baithalu, Rubina ^a   Yadav, Munna Lal ^a   Naru, Jasmine ^b   Tiwari, Anurag ^a   Kumar, Sudarshan ^a   Balhara, Ashok K ^c   Singh, Surender ^a   Chaudhary, Suman ^a   Kumar, Rajesh ^c   Lotfan, Masoud ^a   Behare, Pradip ^a   Phulia, Sushil K ^c   Mohanty, Tushar K ^a   Kaushik, Jai K ^a   Nallapeta, Shivramaiah ^e   Singh, Inderjeet ^c   Ambatipudi, Srinivas K ^d   Mohanty, Ashok K ^a  

^a NATIONAL DAIRY RESEARCH INSTITUTE   (India)

^b POSTGRADUATE INSTITUTE OF MEDICAL EDUCATION AND RESEARCH   (India)

^c CENTRAL INSTITUTE FOR RESEARCH ON BUFFALOES   (India)

^d INDIAN INSTITUTE OF TECHNOLOGY ROORKEE   (India)

^e BRUKER DALTONIK GMBH   (Germany)

Author keywords

Bovine; In gel; In solution; Profiling; Proteome; Shotgun proteomics; Urine

Indexed keywords

ACETONE; AMMONIUM SULFATE; BIOLOGICAL MARKER; METHANOL; PROTEINASE INHIBITOR; PROTEOME; PROTEIN;

ARTICLE; CATALYSIS; CONTROLLED STUDY; COW; CYTOPLASM; DIAFILTRATION; EXTRACTION; GENE ONTOLOGY; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PRECIPITATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEIN METABOLISM; PROTEIN URINE LEVEL; PROTEOMICS; REFERENCE DATABASE; TWO DIMENSIONAL GEL ELECTROPHORESIS; WOUND HEALING; ANIMAL; BOVINE; CATTLE DISEASE; METABOLISM; PROTEINURIA; URINE; VETERINARY;

ANIMALS; CATTLE; CATTLE DISEASES; HUMANS; PROTEINS; PROTEINURIA; PROTEOMICS;

EID: 84943200867     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2015.05.026     Document Type: Article

References (53)

1. Thongboonkerd V., McLeish K.R., Arthur J.M., Klein J.B. Proteomic analysis of normal human urinary proteins isolated by acetone precipitation or ultracentrifugation. Kidney Int. 2002, 62:1461-1469.
2. Lubon H. Transgenic animal bioreactors in biotechnology and production of blood proteins. Biotechnol. Annu. Rev. 1998, 4:1-54.
3. Clark A.J. The mammary gland as a bioreactor: expression, processing, and production of recombinant proteins. J. Mammary Gland Biol. Neoplasia 1998, 3:337-350.
4. Rudolph N.S. Biopharmaceutical production in transgenic livestock. Trends Biotechnol. 1999, 17:367-374.
5. Kerr D.E., Liang F., Bondioli K.R., Zhao H., Kreibich G., Wall R.J., Sun T.T. The bladder as a bioreactor: urothelium production and secretion of growth hormone into urine. Nat. Biotechnol. 1998, 16:75-79.
6. Kumar S., Muchmore A. Tamm-Horsfall protein-uromodulin (1950-1990). Kidney Int. 1990, 37:1395-1401.
7. Adachi J., Kumar C., Zhang Y., Olsen V.J., Mann M. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol. 2006, 7(9):R80.
8. Noiri E., Doi K., Negishi K., Tanaka T., Hamasaki Y., Fujita T., Portilla D., Sugaya T. Urinary fatty acid-binding protein 1: an early predictive biomarker of kidney injury. Am. J. Physiol. Ren. Physiol. 2009, 296(4):F669-F679.
9. Shaked G.M., Shaked Y., Kariv-Inbal Z., Halimi M., Avraham I., Gabizon R. A protease-resistant prion protein isoform is present in urine of animals and humans affected with prion diseases. J. Biol. Chem. 2001, 276:31479-31482.
10. Pyo J., Hwang S.I., Oh J., Lee S.J., Kang S.C., Kim J.S., Lim J. Characterization of a bovine pregnancy-associated protein using two-dimensional gel electrophoresis, N-terminal sequencing and mass spectrometry. Proteomics 2003, 3(12):2420-2427.
11. Simon S.L., Lamoureux L., Plews M., Stobart M., LeMaistre J., Ziegler U., Graham C., Czub S., Groschup M., Knox J.D. The identification of disease-induced biomarkers in the urine of BSE infected cattle. Proteome Sci. 2008, 6:23.
12. Pieper R., Gatlin C.L., McGrath A.M., Makusky A.J., Mondal M., Seonarain M., Field E., Schatz C.R., Estock M.A., Ahmed N., Anderson N.G., Steiner S. Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots. Proteomics 2004, 4(4):1159-1174.
13. Sun W., Li F., Wu S., Wang X., Zheng D., Wang J., Gao Y. Human urine proteome analysis by three separation approaches. Proteomics 2005, 5(18):4994-5001.
14. Gurnani M., Joshi B.K., Nagarcenkar R. Development of Karan Fries cattle at NDRI, Karnal. Dairy Inf. Bull. 1986, III(9):1-2.
15. Singh K., Gurnani M. Performance evaluation of Karan Fries and Karan Swiss under closed breeding system. Asian Aust. J. Anim. Sci. 2004, 17(1):1-6.
16. Marimuthu A., O'Meally R.N., Chaerkady R., Subbannayya Y., Nanjappa V., Kumar P., Kelkar D.S., Pinto S.M., Sharma R., Renuse S., Goel R., Christopher R., Delanghe B., Cole R.N., Harsha H.C., Pandey A. Comprehensive map of the human urinary proteome. J. Proteome Res. 2011, 10(6):2734-2743.
17. Afkarian M., Bhasin M., Dillon S. Optimizing a proteomics platform for urine biomarker discovery. Mol. Cell. Proteomics 2010, 9(10):2195-2204.
18. Sudha M.R., Kalyani P., Ashok V. Isolation of normal buffalo urinary proteins. Int. J. Pharm. Biosci. 2012, 3(3):49-57.
19. Janjanam J., Jamwal M., Singh S., Kumar S., Panigrahi A.K., Hariprasad G., Jena M.K., Anand V., Kumar S., Kaushik J.K., Dang A.K., Mukesh M., Mishra B.P., Srinivasan A., Reddy V.S., Mohanty A.K. Proteome analysis of functionally differentiated bovine (Bos indicus) mammary epithelial cells isolated from milk. Proteomics 2013, 13:3189-3204.
20. Shevchenko A., Tomas H., Havlis J., Olsen J.V., Mann M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 2006, 1(6):2856-2860.
21. Tetsuya F., Makiko M., Maiko M., Takechi S., Kakinoki K.K., Akikazu N. Improved recovery of human urinary protein for electrophoresis. J. Health Sci. 2006, 52:718-723.
22. Varaprasad K., Paul J., Suzette M., Sevgi T., Olav L., Mahesh C., Sinuhe H. Quantitative proteomics analysis of maternal plasma in down syndrome pregnancies. J. Biomed. Biotechnol. 2010, (Article ID 952047). 10.1155/2010/952047.
23. Kumar C., Matthias M. Bioinformatics analysis of mass spectrometry-based proteomics data setsrticle history. FEBS Lett. 2009, 583(11):1703-1712.
24. Vizcaíno A.J., Deutsch W.E., Wang R., Csordas A., Reisinger F., Ríos D., Farrah T., Xenarios I., et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotechnol. 2014, 32:223-226.
25. Choksawangkarn W., Edwards N., Wang Y., Gutierrez P., Fenselau C. Comparative study of workflows optimized for in-gel, in-solution, and on-filter proteolysis in the analysis of plasma membrane proteins. J. Proteome Res. 2012, 11(5):3030-3034.
26. Li Q.R., Fan K.X., Li R.X., Dai J., Wu C.C., Zhao S.L., Wu J.R., Shieh C.H., Zeng R.A. Comprehensive and non-prefractionation on the protein level approach for the human urinary proteome: touching phosphorylation in urine. Rapid Commun. Mass Spectrom. 2010, 24(6):823-832.
27. Zheng J., Liu L., Wang J., Jin Q. Urinary proteomic and non-prefractionation quantitative phosphoproteomic analysis during pregnancy and non-pregnancy. BMC Genomics 2013, 14:777.
28. Janice J., Mark M., Lyn H., Elizabeth D. Proteomic analysis of early lactation milk of the tammar wallaby (Macropus eugenii). Comp. Biochem. Physiol. D 2007, 2:150-164.
29. Norris L.A. Blood coagulation. Best Pract. Res. Clin. Obstet. Gynaecol. Jun 2003, 17(3):369-383.
30. Pugia J., Lott A. Pathophysiology and diagnostic value of urinary trypsin inhibitors. Clin. Chem. Lab. Med. 2005, 43:1-16.
31. Lewis B. A gene complex controlling segmentation in Drosophila. Nature 1978, 276:565-570.
32. Struhl G. A gene product required for correct initiation of segmental determination in Drosophila. Nature 1981, 293:36-41.
33. Jaenisch R., Young R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 2008, 132(4):567-582.
34. Beck D.B., Bonasio R., Kaneko S., Li G., Li G., Margueron R., Oda H., Sarma K., Sims R.J., Son J., Trojer P., Reinberg D. Cold Spring Harb. Symp. Quant. Biol. 2010, 75:11-22.
35. Tamura M., Shigekazu T., Fujii T., Aoki A., Komiyama H., Ezawa K., Sumiyama K., Sagai T., Shiroishi T. Members of a novel gene family, Gsdm, are expressed exclusively in the epithelium of the skin and gastrointestinal tract in a highly tissue-specific manner. Genomics 2007, 89(5):618-662.
36. Kolker E., Higdon H., Welch D., Broomall W., Doron L., Stanberry L., Kolker N. MOPED: Model Organism Protein Expression Database. Nucleic Acids Res. 2012, 40:1093-1099. (Database issue D).
37. Wang M., Weiss M., Simonovic M., Haertinger G., Schrimpf S.P., Hengartner M.O., Mering C.V. PaxDb, a database of protein abundance averages across all three domains of life. Mol. Cell. Proteomics 2012, 11(8):492-500.
38. Schaab C., Geiger T., Mann M. Analysis of high accuracy, quantitative proteomics data in the MaxQB database. Mol. Cell. Proteomics 2012, 11(3). (M111.014068).
39. Virtanen T. Lipocalin allergens. Allergy 2001, 56(Suppl. 67):48-51.
40. Vincent F., Spinelli S., Ramoni R., Grolli S., Pelosi P., et al. Complexes of porcine odorant binding protein with odorant molecules belonging to different chemical classes. J. Mol. Biol. 2000, 300:127-139.
41. Mitchell G.B., Clark M.E., Lu R., Caswell J.L. Localization and functional characterization of pulmonary bovine odorant-binding protein. Vet. Pathol. 2011, 48(6):1054-1060.
42. Pierce G., Parsons F. Glycoprotein hormones: structure and function. Annu. Rev. Biochem. 1981, 5:465-495.
43. Apaja P.M., Tuusa J.T., Pietila E.M., Rajaniemi H.J., Petarjar-Repo U.E. Luteinizing hormone receptor ectodomain splice variant misroutes the full-length receptor into a sub compartment of the endoplasmic reticulum. Mol. Biol. Cell 2006, 17:2243-2255.
44. Elsik G., Tellan L., Worley C. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009, 324:522-528. The bovine genome sequencing and analysis consortium.
45. Chanson A., Sayd T., Rock E., Chambon C., Santé-Lhoutellier V., Potier de Courcy G., Brachet P. Proteomic analysis reveals changes in the liver protein pattern of rats exposed to dietary folate deficiency. J. Nutr. 2005, 135(11):2524-2529.
46. Daniels M., Webb E., McGilliard L., Meyer J., Van Amburgh E., Akers M. Effects of body weight and nutrition on mammary protein expression profiles in Holstein heifers. J. Dairy Sci. 2006, 89:4276-4288.
47. Kuhla B., Albrecht D., Kuhla S., Metges C. Proteome analysis of fatty liver in feed-deprived dairy cows reveals interaction of fuel sensing, calcium, fatty acid, and glycogen metabolism. Physiol. Genomics 2009, 3:88-98.
48. Rawson P., Stockum C., Peng L., Manivannan B., Lehnert K., Ward H.E., Berry S.D., Davis S.R., Snell R.G., McLauchlan D., Jordan T.W. Metabolic proteomics of the liver and mammary gland during lactation. J. Proteome 2012, 75:4429-4435.
49. Pan B.T., Johnstone R.M. Fate of the transferring receptor during maturation of sheep reticulocytes in vitro: selective externalization of the receptor. Cell 1983, 33:967-978.
50. Pan B.T., Teng K., Wu C., Adam M., Johnstone R.M. Electron microscopic evidence for externalization of the transferring receptor in vesicular form in sheep reticulocytes. J. Cell Biol. 1985, 101:942-948.
51. Gonzales P.A., Pisitkun T., Hoffert J.D., Tchapyjnikov D., Star R.A., Kleta R., Wang N.S., Knepper M.A. Large-scale proteomics and phosphoproteomics of human urinary exosomes. J. Am. Soc. Nephrol. 2009, 20(2):363-379.
52. Pisitkun T., Shen R.F., Knepper M.A. Identification and proteomic profiling of exosomes in human urine. Proc. Natl. Acad. Sci. 2004, 101(36):13368-13373.
53. Simpson R.J., Jensen S.S., Lim J.W. Proteomic profiling of exosomes: current perspectives. Proteomics 2008, 8:4083-4099.