Skip to main content
PMC home page
Protein & Cell logoLink to Protein & Cell
. 2012 Aug 12;3(9):691–700. doi: 10.1007/s13238-012-2039-0

Proteomic characteristics of the liver and skeletal muscle in the Chinese tree shrew (Tupaia belangeri chinensis)

Rongxia Li 1, Wei Xu 1, Zhen Wang 1, Bin Liang 2, Jia-Rui Wu 1, Rong Zeng 1,✉
PMCID: PMC4875369  PMID: 22886497

Abstract

Valid animal models are useful for studying the pathophysiology of specific disorders, such as neural disease, diabetes and cancer. Previous molecular phylogeny studies indicate that the tree shrew is in the same order as (or a close sister to) primates, and thus may be an ideal model in which to study human disease. In this study, the proteome of liver and muscle tissue in tree the shrew was identified by combining peptide fractionation and LC-MS/MS identification. In total, 2146 proteins were detected, including 1759 proteins in liver samples and 885 proteins in skeletal muscle samples from the tree shrew. Further sub-source analysis revealed that nearly half of the identified proteins (846 proteins and 418 proteins) were derived from human database. In this study, we are the first to describe the characteristics of the proteome from the liver and skeletal muscle of the tree shrew. Phylogenetic tree analysis based on these proteomic data showed that the tree shrew is closer to primates (human) than to glires (the mouse and rat).

Keywords: proteome, Chinese tree shrew, phylogenetic tree, liver, muscle

References

  1. Abascal F., Zardoya R., Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 2005;21:2104–2105. doi: 10.1093/bioinformatics/bti263. [DOI] [PubMed] [Google Scholar]
  2. Arnason U., Adegoke J.A., Bodin K., Born E.W., Esa Y.B., Gullberg A., Nilsson M., Short R.V., Xu X., Janke A. Mammalian mitogenomic relationships and the root of the eutherian tree. Proc Natl Acad Sci U S A. 2002;99:8151–8156. doi: 10.1073/pnas.102164299. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cao J., Yang E.B., Su J.J., Li Y., Chow P. The tree shrews: adjuncts and alternatives to primates as models for biomedical research. J Med Primatol. 2003;32:123–130. doi: 10.1034/j.1600-0684.2003.00022.x. [DOI] [PubMed] [Google Scholar]
  4. Deng W.J., Nie S., Dai J., Wu J.R., Zeng R. Proteome, phosphoproteome, and hydroxyproteome of liver mitochondria in diabetic rats at early pathogenic stages. Mol Cell Proteomics. 2010;9:100–116. doi: 10.1074/mcp.M900020-MCP200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Helgen K.M., Wilson D. E., Reeder, DeeAnn M. Mammal Species of the World (3rd ed.) Baltimore: Johns Hopkins University Press; 2005. pp. 104–109. [Google Scholar]
  6. Janecka J.E., Miller W., Pringle T.H., Wiens F., Zitzmann A., Helgen K.M., Springer M.S., Murphy W.J. Molecular and genomic data identify the closest living relative of primates. Science. 2007;318:792–794. doi: 10.1126/science.1147555. [DOI] [PubMed] [Google Scholar]
  7. Kennedy R.T., Jorgenson J.W. Quantitative analysis of individual neurons by open tubular liquid chromatography with voltammetric detection. Anal Chem. 1989;61:436–441. doi: 10.1021/ac00180a012. [DOI] [PubMed] [Google Scholar]
  8. Lescuyer P., Hochstrasser D.F., Sanchez J.C. Comprehensive proteome analysis by chromatographic protein prefractionation. Electrophoresis. 2004;25:1125–1135. doi: 10.1002/elps.200305792. [DOI] [PubMed] [Google Scholar]
  9. Li C., Ruan H.Q., Liu Y.S., Xu M.J., Dai J., Sheng Q.H., Tan Y.X., Yao Z.Z., Wang H.Y., Wu J.R., et al. Quantitative proteomics reveal up-regulated protein expression of the SET complex associated with hepatocellular carcinoma. J Proteome Res. 2011;11:871–885. doi: 10.1021/pr2006999. [DOI] [PubMed] [Google Scholar]
  10. Liu Y., Li C., Xing Z., Yuan X., Wu Y., Xu M., Tu K., Li Q., Wu C., Zhao M., et al. Proteomic mining in the dysplastic liver of WHV/c-myc mice—insights and indicators for early hepatocarcinogenesis. FEBS J. 2010;277:4039–4053. doi: 10.1111/j.1742-4658.2010.07795.x. [DOI] [PubMed] [Google Scholar]
  11. Lu W.D., Li B.Y., Yu F., Cai Q., Zhang Z., Yin M., Gao H.Q. Quantitative proteomics study on the protective mechanism of phlorizin on hepatic damage in diabetic db/db mice. Mol Med Report. 2012;5:1285–1294. doi: 10.3892/mmr.2012.803. [DOI] [PubMed] [Google Scholar]
  12. Murphy W.J., Eizirik E., O’Brien S.J., Madsen O., Scally M., Douady C.J., Teeling E., Ryder O.A., Stanhope M.J., de Jong W.W., et al. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001;294:2348–2351. doi: 10.1126/science.1067179. [DOI] [PubMed] [Google Scholar]
  13. Nielsen P.A., Olsen J.V., Podtelejnikov A.V., Andersen J.R., Mann M., Wisniewski J.R. Proteomic mapping of brain plasma membrane proteins. Mol Cell Proteomics. 2005;4:402–408. doi: 10.1074/mcp.T500002-MCP200. [DOI] [PubMed] [Google Scholar]
  14. Orengo J.P., Cooper T.A. Alternative splicing in disease. Adv Exp Med Biol. 2007;623:212–223. doi: 10.1007/978-0-387-77374-2_13. [DOI] [PubMed] [Google Scholar]
  15. Perkins D.N., Pappin D.J., Creasy D.M., Cottrell J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 1999;20:3551–3567. doi: 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2. [DOI] [PubMed] [Google Scholar]
  16. Rappsilber J., Mann M., Ishihama Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat protoc. 2007;2:1896–1906. doi: 10.1038/nprot.2007.261. [DOI] [PubMed] [Google Scholar]
  17. Schmitz J., Ohme M., Zischler H. The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of scandentia to other eutherian orders. Mol Biol Evol. 2000;17:1334–1343. doi: 10.1093/oxfordjournals.molbev.a026417. [DOI] [PubMed] [Google Scholar]
  18. Shevchenko A., Jensen O.N., Podtelejnikov A.V., Sagliocco F., Wilm M., Vorm O., Mortensen P., Boucherie H., Mann M. Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc Natl Acad Sci U S A. 1996;93:14440–14445. doi: 10.1073/pnas.93.25.14440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Staunton L., Jockusch H., Ohlendieck K. Proteomic analysis of muscle affected by motor neuron degeneration: the wobbler mouse model of amyotrophic lateral sclerosis. Biochem Biophys Res Commun. 2011;406:595–600. doi: 10.1016/j.bbrc.2011.02.099. [DOI] [PubMed] [Google Scholar]
  20. Tieleman A.A., den Broeder A.A., van de Logt A.E., van Engelen B.G. Strong association between myotonic dystrophy type 2 and autoimmune diseases. J Neurol Neurosurg Psychiatry. 2009;80:1293–1295. doi: 10.1136/jnnp.2008.156562. [DOI] [PubMed] [Google Scholar]
  21. van der Worp H.B., Howells D.W., Sena E.S., Porritt M.J., Rewell S., O’Collins V., Macleod M.R. Can animal models of disease reliably inform human studies? PLoS Med. 2010;7:e1000245. doi: 10.1371/journal.pmed.1000245. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Wang J., Zhou Q.X., Tian M., Yang Y.X., Xu L. Tree shrew models: a chronic social defeat model of depression and a one-trial captive conditioning model of learning and memory. Dongwuxue Yanjiu. 2011;32:24–30. doi: 10.3724/SP.J.1141.2011.01024. [DOI] [PubMed] [Google Scholar]
  23. Wilkins M.R., Sanchez J.C., Williams K.L., Hochstrasser D.F. Current challenges and future applications for protein maps and post-translational vector maps in proteome projects. Electrophoresis. 1996;17:830–838. doi: 10.1002/elps.1150170504. [DOI] [PubMed] [Google Scholar]
  24. Wilm M., Mann M. Analytical properties of the nanoenanoelectrospray ion source. Anal Chem. 1996;68:1–8. doi: 10.1021/ac9509519. [DOI] [PubMed] [Google Scholar]
  25. Wisniewski J.R., Zougman A., Nagaraj N., Mann M. Universal sample preparation method for proteome analysis. Nat Methods. 2009;6:359–362. doi: 10.1038/nmeth.1322. [DOI] [PubMed] [Google Scholar]
  26. Wu C.Y., Whye D., Glazewski L., Choe L., Kerr D., Lee K.H., Mason R.W., Wang W. Proteomic assessment of a cell model of spinal muscular atrophy. BMC Neurosci. 2011;12:25. doi: 10.1186/1471-2202-12-25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Xu L., Chen S.Y., Nie W.H., Jiang X.L., Yao Y.G. Evaluating the phylogenetic position of Chinese tree shrew (Tupaia belangeri chinensis) based on complete mitochondrial genome: implication for using tree shrew as an alternative experimental animal to primates in biomedical research. J Genet Genomics. 2012;39:131–137. doi: 10.1016/j.jgg.2012.02.003. [DOI] [PubMed] [Google Scholar]
  28. Zhang H., Stoeckli M., Andren P.E., Caprioli R.M. Combining solid-phase preconcentration, capillary electrophoresis and off-line matrix-assisted laser desorption/ionization mass spectrometry: intracerebral metabolic processing of peptide E in vivo. J Mass Spectrom. 1999;34:377–383. doi: 10.1002/(SICI)1096-9888(199904)34:4<377::AID-JMS778>3.0.CO;2-D. [DOI] [PubMed] [Google Scholar]

Articles from Protein & Cell are provided here courtesy of Oxford University Press

RESOURCES