Asian-Australasian Journal of Animal Sciences

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
권호 표지
DOI QR코드

DOI QR Code

In silico Discovery of Genes Expressed in Liver, Kidney, Spleen and Small Intestine of Pigs

  • Pan, Zengxiang (College of Animal Science and Technology, Nanjing Agricultural University) ;
  • Liu, Honglin (College of Animal Science and Technology, Nanjing Agricultural University) ;
  • Chen, Jie (College of Animal Science and Technology, Nanjing Agricultural University) ;
  • Xu, Dan (College of Animal Science and Technology, Nanjing Agricultural University) ;
  • Jiang, Zhihua (Department of Animal Sciences, Washington State University) ;
  • Xie, Zhuang (College of Animal Science and Technology, Nanjing Agricultural University)
  • Received : 2004.04.09
  • Accepted : 2004.08.23
  • Published : 2005.02.01
Download PDF
⟨ Previous Next ⟩

Abstract

An in silico approach was developed to survey the genes expressed in four internal organs of pig: liver, kidney, spleen and small intestine. The major procedures of the approach included: (1) BLAST searching against GenBank "est_others" database using human cDNA sequences as queries to screen the porcine orthologous expressed sequence tags (ESTs), (2) classifying the porcine ESTs records by resources according to certain criteria and (3) analyzing data for ESTs specifically expressed in each organ. In order to do so, four Java programs were developed. Based on the ESTs available in the GenBank database, it was found that there were at least 2,100 genes expressed in these four organs, including 128 in the liver, 81 in the kidney, 780 in the spleen, and 1,423 in the small intestine respectively (a few genes co-expressed in these tissues). Gene expression patterns, such as co-expressed genes, preferentially expressed genes and basic active genes were also compared and characterized among these organs. This study provides a comprehensive model on how to use the bioinformatics approach and Genbank databases to facilitate the discovery of new genes in livestock species.

Keywords

References

  1. Adams, M. D., J. M. Kelley, J. D. Gocayne, M. Dubnick, M. H. Polymeropoulos, H. Xiao, C. R. Merril, A. Wu, B. Olde and R. F. Moreno. 1991. Complementary DNA sequencing: expressed sequence tags and human genome project. Sci. 252:1651-1656
  2. Attwood, T. K. and C. J. Miller. 2002. Progress in bioinformatics and the importance of being earnest. Biotechnol. Annu. Rev. 8:1-54
  3. Austen, B., O. el-Agnaf, S. Nagala, B. Patel, N. Gunasekera, M. Lee and V. Lelyveld. 2002. Properties of neurotoxic peptides related to the BRI gene. Biochem. Soc. Trans. 30:557-559 https://doi.org/10.1042/BST0300557
  4. Balas, A., S. Santos, M. J. Aviles, F. Garcia-Sanchez, R. Lillo and J. L. Vicario. 2000. Identification by sequencing based typing and complete coding region analysis of three new HLA class II alleles: DRB3${\times}$0210, DRB3×0211 and DQB1${\times}$0310. Tissue Antigens. 56:380-384 https://doi.org/10.1034/j.1399-0039.2000.560412.x
  5. Barnes, M. R. 2002. Psychiatric genetics in silico: databases and tools for psychiatric geneticists. Psychiatric Genetics 12:67-73
  6. Bedford, M. T., R. Reed and P. Leder. 1998. WW domainmediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif. Proc. Natl. Acad. Sci. USA 95:10602-10607
  7. Birney, E., M. Clamp and T. Hubbard. 2002. Databases and tools for browsing genomes. Annu. Rev. Genomics Hum. Genet. 3:293-310 https://doi.org/10.1146/annurev.genom.3.030502.101529
  8. Buddhikot, M., E. Falkenstein, M. Wehling and S. Meizel. 1999. Recognition of a human sperm surface protein involved in the progesterone-initiated acrosome reaction by antisera against an endomembrane progesterone binding protein from porcine liver. Molecular and Cellular Endocrinology 158:187-193
  9. Campeau, E., L. R. Desviat, D. Leclerc, X. Wu, B. Perez, M. Ugarte and R. A. Gravel. 2001. Structure of the PCCA gene and distribution of mutations causing propionic academia. Mol. Genet. Metab. 74:238-247 https://doi.org/10.1006/mgme.2001.3210
  10. Chalasani, N., J. C. Gorski, M. S. Asghar, R. A. Asgha, B. Foresman, S. D. Hall and D. W. Crabb. 2003. Hepatic cytochrome P450 2E1 activity in nondiabetic patients with nonalcoholic steatohepatitis. Hepatology 37:544-550
  11. Dearden, P. and M. Akam. 2000. Computational biology: Segmentation in silico. Nature 406:131-132
  12. Dumont, P., J. I. Leu, A. C. Della Pietra 3rd, D. L. George and M. Murphy. 2003. The codon 72 polymorphic variants of p53 have markedly different apoptotic potential. Nat. Genet. 33:357-365 https://doi.org/10.1038/ng1093
  13. Esposito, G., L. Vitagliano, R. Santamaria, A. Viola, A. Zagari and F. Salvatore. 2002. Structural and functional analysis of aldolase B mutants related to hereditary fructose intolerance. FEBS Lett. 531:152-156 https://doi.org/10.1016/S0014-5793(02)03451-8
  14. Farber, C. R. and J. F. Medrano. 2003. Putative in silico mapping of DNA sequences to livestock genome maps using SSLP flanking sequences. Animal Genetics 34:11-18
  15. Gerdes, D., M. Wehling, B. Leube and E. Falkenstein. 1998. Cloning and tissue expression of two putative steroid membrane receptors. Biol. Chem. 379:907-911 https://doi.org/10.1515/bchm.1998.379.7.907
  16. Gill, R. W. and P. Sanseau. 2000. Rapid in silico cloning of genes using expressed sequence tags (ESTs). Biotechnol. Ann. Rev. 5:25-44
  17. Gorinstein, S., A. Caspi, A. Rosen, I. Goshev, M. Zemser, M. Weisz, M. C. Anon, I. Libman, H. T. Lerner and S. Trakhtenberg. 2002. Structure characterization of human serum proteins in solution and dry state. J. Pept. Res. 59:71-78
  18. Guimaraes, D. P. and P. Hainaut. 2002. TP53: a key gene in human cancer. Biochimie. 84:83-93
  19. Heaton, J. H., W. M. Dlakic, M. Dlakic and T. D. Gelehrter. 2001. Identification and cDNA cloning of a novel RNA-binding protein that interacts with the cyclic nucleotide-responsive sequence in the Type-1 plasminogen activator inhibitor mRNA. J. Biol. Chem. 276:3341-3347
  20. Ishii, J., H. Adachi, J. Aoki, H. Koizumi, S. Tomita, T. Suzuki, M. Tsujimoto, K. Inoue and H. Arai. 2002. SREC-II, a new member of the scavenger receptor type F family, trans-interacts with SREC-I through its extracellular domain. J. Biol. Chem. 277:39696-39702
  21. Jiang, Z., M. Zhang, V. D. Wasem, J. J. Michal, H. Zhang and R. W. Wright, Jr. 2003. Census of Genes Expressed in Porcine Embryos and Reproductive Tissues by Mining EST Database Based on the Human Genes. Biol. Reprod. 69:1177-1182
  22. Lee, J. H., C. Moran1 and C. S. Park. 2003. Current Status of Comparative Mapping in Livestock. Asian-Aust. J. Anim. Sci. 16:1411-1420
  23. Lejus, C., A. Fautrel, Y. Malledant and A. Guillouzo. 2002. Inhibition of the cytochrome P450 2E1 by propofol in human and porcine liver microsomes. Biochemical pharmacology. 64:1151-1156
  24. Lynn, D. J., A. T. Lloyd and C. O'Farrelly. 2003. Bioinformatics: implications for medical research and clinical practice. Clin. Invest. Med. 26:70-74
  25. Martin, K. J. and A. B. Pardee. 2000. Identifying expressed genes. PNAS. 97:3789-3791
  26. Meijssen, S., H. van Dijk, C. Verseyden, D. W. Erkelens and M. C. Cabezas. 2002. Delayed and exaggerated postprandial complement component 3 response in familial combined hyperlipidemia. Arterioscler. Thromb. Vasc. Biol. 22:811-816 https://doi.org/10.1161/01.ATV.0000014079.98335.72
  27. Moriyama, K. and I. Yahara. 2002. Human CAP1 is a key factor in the recycling of cofilin and actin for rapid actin turnover. J. Cell. Sci. 115:1591-1601
  28. Mostert, V. 2000. Selenoprotein P: properties, functions, and regulation. Arch. Biochem. Biophys. 376:433-438 https://doi.org/10.1006/abbi.2000.1735
  29. Narayanan, B. A., N. K. Narayanan, G. G. Re and D. W. Nixon. 2003. Differential expression of genes induced by resveratrol in LNCaP cells: P53-mediated molecular targets. Int. J. Cancer. 104:204-212 https://doi.org/10.1002/ijc.10932
  30. Nieto, N., S. L. Friedman and A. I. Cederbaum. 2002. Cytochrome P450 2E1-derived reactive oxygen species mediate paracrine stimulation of collagen I protein synthesis by hepatic stellate cells. J. Biol. Chem. 277:9853-9864
  31. Pandey, A. and F. Lewitter. 1999. Nucleotide sequence databases: a gold mine for biologists. Trends Biochem. Sci. 24:276-280 https://doi.org/10.1016/S0968-0004(99)01400-0
  32. Pertea, G., X. Huang, F. Liang, V. Antonescu, R. Sultana, S. Karamycheva, Y. Lee, J. White, F. Cheung, B. Parvizi, J. Tsai and J. Quackenbush. 2003. Bioinformatics 19:651-652
  33. Pittois, K., W. Deleersnijder and J. Merregaert. 1998. cDNA sequence analysis, chromosomal assignment and expression pattern of the gene coding for integral membrane protein 2B. Gene. 217:141-149 https://doi.org/10.1016/S0378-1119(98)00354-0
  34. Pruess, M., W. Fleischmann, A. Kanapin, Y. Karavidopoulou, P. Kersey, E. Kriventseva, V. Mittard, N. Mulder, I. Phan, F. Servant and R. Apweiler. 2003. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 31:414-417 https://doi.org/10.1093/nar/gkg105
  35. Rasmussen, T. N., P. Schmidt, S. S. Poulsen and J. J. Holst. 2001a. Localisation and neural control of the release of calcitonin gene-related peptide (CGRP) from the isolated perfused porcine ileum. Regulatory Peptides. 98:137-143
  36. Rasmussen, T. N., P. Schmidt, S. S. Poulsen and J. J. Holst. 2001b. Effect of calcitonin gene-related peptide (CGRP) on motility and on the release of substance P, neurokinin A, somatostatin and gastrin in the isolated perfused porcine antrum. Neurogastroenterol. Mot. 13:353-359
  37. Rodriguez-Pombo, P., C. Perez-Cerda, L. R. Desviat, B. Perez and M. Ugarte. 2002. Transfection Screening for Defects in the PCCA and PCCB Genes Encoding Propionyl-CoA Carboxylase Subunits. Mol. Genet. Metab. 75:276-279 https://doi.org/10.1006/mgme.2001.3296
  38. Rohrer, G. A., S. C. Fahrenkrug, D. Nonneman, N. Tao and W. C. Warren. 2002. Mapping microsatellite markers identified in porcine EST sequences. Animal Genetics 33:372-376
  39. Saito, Y. and K. Takahashi. 2002. Characterization of selenoprotein P as a selenium supply protein. Eur. J. Biochem. 269:5746-5751
  40. Scarr, R. B. 2002. PDCD2 is a negative regulator of HCF1 (C1). Oncogene. 21:5245-5254 https://doi.org/10.1038/sj.onc.1205647
  41. Shito, M., N. H. Kim, H. Baskaran, A. W. Tilles, R. G. Tompkins, M. L. Yarmush and M. Toner. 2001. In vitro and in vivo evaluation of the Albumin synthesis rate of porcine hepatocytes in a flat-plate bioreactor. Artificial Organs. 25:571-578 https://doi.org/10.1046/j.1525-1594.2001.025007571.x
  42. Skrabanek, L. and F. Campagne. 2001. Tissueinfo: highthroughput identification of tissues expression profiles and specificity. Nucleic Acids Res. 29:21-102
  43. Strausberg, R. L., E. A. Feingold, R. D. Klausner and F. S. Collins. 1999. The Mammalian Gene Collection. Science 286:455-457
  44. Tolan, D. R. and E. E. Penhoet. 1986. Characterization of the human aldolase B gene. Mol. Biol. Med. 3:245-264
  45. Wimmers, K., S. Mekchay, S. Ponsuksili, T. Hardge, M. Yerle and K. Schellander. 2001. Polymorphic sites in exon 15 and 30 of the porcine C3 gene. Animal Genetics 32:40-53
  46. Yamada, Y., T. Doi, T. Hamakubo and T. Kodama. 1998. Scavenger receptor family proteins: roles for atherosclerosis, host defence and disorders of the central nervous system. Cell Mol. Life Sci. 54:628-640 https://doi.org/10.1007/s000180050191