Murine colon proteome and characterization of the protein pathways
Most of the current proteomic researches focus on proteome alteration due to pathological disorders (i.e.: colorectal cancer) rather than normal healthy state when mentioning colon. As a result, there are lacks of information regarding normal whole tissue- colon proteome.
We report here a detailed murine (mouse) whole tissue- colon protein reference dataset composed of 1237 confident protein (FDR < 2) with comprehensive insight on its peptide properties, cellular and subcellular localization, functional network GO annotation analysis, and its relative abundances. The presented dataset includes wide spectra of pI and Mw ranged from 3–12 and 4–600 KDa, respectively. Gravy index scoring predicted 19.5% membranous and 80.5% globularly located proteins. GO hierarchies and functional network analysis illustrated proteins function together with their relevance and implication of several candidates in malignancy such as Mitogen- activated protein kinase (Mapk8, 9) in colorectal cancer, Fibroblast growth factor receptor (Fgfr 2), Glutathione S-transferase (Gstp1) in prostate cancer, and Cell division control protein (Cdc42), Ras-related protein (Rac1,2) in pancreatic cancer. Protein abundances calculated with 3 different algorithms (NSAF, PAF and emPAI) provide a relative quantification under normal condition as guidance.
This highly confidence colon proteome catalogue will not only serve as a useful reference for further experiments characterizing differentially expressed proteins induced from diseased conditions, but also will aid in better understanding the ontology and functional absorptive mechanism of the colon as well.
- Rose, RC (1980) Water-soluble vitamin absorption in intestine. Annu Rev Physiol 42: pp. 157-171 CrossRef
- Weiser, MM, Bloor, JH, Dasmahapatra, A (1982) Intestinal calcium absorption and vitamin D metabolism. J Clin Gastroenterol 4: pp. 75-86 CrossRef
- Donini, LM, Savina, C, Cannella, C (2009) Nutrition in the elderly: role of fiber. Arch Gerontol Geriatr 49: pp. 61-69 CrossRef
- Davis, CD, Milner, JA (2009) Gastrointestinal microflora, food components and colon cancer prevention. J Nutr Biochem 20: pp. 743-752 CrossRef
- Gourley, GR, Yang, L, Higgins, L, Riviere, MA, David, LL (2010) Proteomic analysis of biopsied human colonic mucosa. J Pediatr Gastroenterol Nutr 51: pp. 46-54 CrossRef
- Patel, BB, Li, XM, Dixon, MP, Blagoi, EL, Seeholzer, SH, Chen, Y, Miller, CG, He, YA, Tetruashvily, M, Chaudhry, AH (2007) Searchable high-resolution 2D gel proteome of the human colon crypt. J Proteome Res 6: pp. 2232-2238 CrossRef
- Lenaerts, K, Bouwman, FG, Lamers, WH, Renes, J, Mariman, EC (2007) Comparative proteomic analysis of cell lines and scrapings of the human intestinal epithelium. BMC genomics 8: pp. 91 CrossRef
- Yi, H, Li, XH, Yi, B, Zheng, J, Zhu, G, Li, C, Li, MY, Zhang, PF, Li, JL, Chen, ZC, Xiao, ZQ (2010) Identification of Rack1, EF-Tu and Rhodanese as aging-related proteins in human colonic epithelium by proteomic analysis. J Proteome Res 9: pp. 1416-1423 CrossRef
- Mazzanti, R, Solazzo, M, Fantappie, O, Elfering, S, Pantaleo, P, Bechi, P, Cianchi, F, Ettl, A, Giulivi, C (2006) Differential expression proteomics of human colon cancer. Am J Physiol 290: pp. G1329-G1338
- Rho, JH, Qin, S, Wang, JY, Roehrl, MH (2008) Proteomic expression analysis of surgical human colorectal cancer tissues: up-regulation of PSB7, PRDX1, and SRP9 and hypoxic adaptation in cancer. J Proteome Res 7: pp. 2959-2972 CrossRef
- Zhao, L, Liu, L, Wang, S, Zhang, YF, Yu, L, Ding, YQ (2007) Differential proteomic analysis of human colorectal carcinoma cell lines metastasis-associated proteins. J Cancer Res Clin Oncol : pp.
- Ramagli, LS, Rodriguez, LV (1985) Quantitation of microgram amounts of protein in two-dimensional polyacrylamide gel electrophoresis sample buffer. Electrophoresis 6: pp. 559-563 CrossRef
- Magdeldin, S, Li, H, Yoshida, Y, Satokata, I, Maeda, Y, Yokoyama, M, Enany, S, Zhang, Y, Xu, B, Fujinaka, H (2010) Differential proteomic shotgun analysis elucidates involvement of water channel aquaporin 8 in presence of alpha-amylase in the colon. J Proteome Res 9: pp. 6635-6646 CrossRef
- Shevchenko, A, Wilm, M, Vorm, O, Mann, M (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68: pp. 850-858 CrossRef
- Perkins, DN, Pappin, DJ, Creasy, DM, Cottrell, JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20: pp. 3551-3567 CrossRef
- Pappin, DJ, Hojrup, P, Bleasby, AJ (1993) Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 3: pp. 327-332 CrossRef
- Liu, H, Sadygov, R, Yates, J (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76: pp. 4193-4201 CrossRef
- Powell, DW, Weaver, CM, Jennings, JL, McAfee, KJ, He, Y, Weil, PA, Link, AJ (2004) Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol Cell Biol 24: pp. 7249-7259 CrossRef
- Ishihama, Y, Oda, Y, Tabata, T, Sato, T, Nagasu, T, Rappsilber, J, Mann, M (2005) Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 4: pp. 1265-1272 CrossRef
- Maere, S, Heymans, K, Kuiper, M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics (Oxford, England) 21: pp. 3448-3449 CrossRef
- Bindea, G, Mlecnik, B, Hackl, H, Charoentong, P, Tosolini, M, Kirilovsky, A, Fridman, WH, Pages, F, Trajanoski, Z, Galon, J (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics (Oxford, England) 25: pp. 1091-1093 CrossRef
- Shannon, P, Markiel, A, Ozier, O, Baliga, NS, Wang, JT, Ramage, D, Amin, N, Schwikowski, B, Ideker, T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: pp. 2498-2504 CrossRef
- Hochberg, Y, Benjamini, Y (1990) More powerful procedures for multiple significance testing. Stat Med 9: pp. 811-818 CrossRef
- Ashburner, M, Ball, CA, Blake, JA, Botstein, D, Butler, H, Cherry, JM, Davis, AP, Dolinski, K, Dwight, SS, Eppig, JT (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: pp. 25-29 CrossRef
- Aoki, KF, Kanehisa, M (2005) Using the KEGG database resource. Curr Protoc Bioinformatics.
- Kyte, J, Doolittle, RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: pp. 105-132 CrossRef
- Murine colon proteome and characterization of the protein pathways
- Open Access
- Available under Open Access This content is freely available online to anyone, anywhere at any time.
- Online Date
- August 2012
- Online ISSN
- BioMed Central
- Additional Links
- Mass spectrometry
- Author Affiliations
- 1. Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- 2. Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Suez Canal, Egypt
- 3. Department of Intensive Care Unit, West-China Hospital, Sichuan University, Sichuan, China
- 4. Animal resource branch, Center of Bio-based researches, Brain research Institute, Niigata University, Niigata, Japan
- 5. Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Suez Canal, Egypt
- 6. Department of Nephrology, Tokyo Medical and Dental University, Tokyo, Japan