Discovery of eight novel divergent homologs expressed in cattle placenta

Physiological Genomics

Volumn 25, Issue 3, 2006, Pages 405-413

  Larson, Joshua H ^a   Kumar, Charu G ^a   Everts, Robin E ^a   Green, Cheryl A ^a   Everts van Der Wind, Annelie ^a   Band, Mark R ^a   Lewin, Harris A ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b Department of Animal Sciences   (United States)

Author keywords

Bovine genome; Comparative genomics; Molecular evolution

Indexed keywords

CATTLE CEREBRUM AND SKELETAL MUSCLE SPECIFIC TRANSCRIPT FACTOR 1; CATTLE INTESTINE SPECIFIC TRANSCRIPT FACTOR 1; HEPATITIS A VIRUS CELLULAR RECEPTOR 1 AMINO TERMINAL DOMAIN CONTAINING PROTEIN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MEMBRANE PROTEIN; PLACENTA PROTEIN; PROLACTIN RELATED PROTEINS 11; PROLACTIN RELATED PROTEINS 8; PROLACTIN RELATED PROTEINS 9; SECRETED AND TRANSMEMBRANE PROTEIN 1A; SECRETED AND TRANSMEMBRANE PROTEIN 1B; TRANSCRIPTION FACTOR; TROPHOBLAST KUNITZ DOMAIN PROTEIN 1; TROPHOBLAST KUNITZ DOMAIN PROTEIN 4; TROPHOBLAST PROTEIN 1; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; CATTLE; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; FEMALE; GENE EXPRESSION; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GENOME; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLACENTA; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; ANIMALS; CATTLE; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; MICE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PAN TROGLODYTES; PLACENTA; PREGNANCY PROTEINS; RADIATION HYBRID MAPPING; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

BOS TAURUS; HEPATITIS A VIRUS;

EID: 33646789780     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00307.2005     Document Type: Article

References (77)

1. Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ. Basic local alignment search tool. J Mol Biol 215: 403-410, 1990.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402, 1997.
3. Anisimova M, Bielawski JP, and Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18: 1585-1592, 2001.
4. Aruffo A and Seed B. Molecular cloning of two CD7 (T-cell leukemia antigen) cDNAs by a COS cell expression system. EMBO J 6: 3313-3316, 1987.
5. Band MR, Olmstead C, Everts RE, Liu ZL, and Lewin HA. A 3800 gene microarray for cattle functional genomics: comparison of gene expression in spleen, placenta, and brain. Anim Biotechnol 13: 163-172, 2002.
6. Byatt JC, Shimomura K, Duello TM, and Bremel RD. Isolation and characterization of multiple forms of bovine placental lactogen from secretory granules of the fetal cotyledon. Endocrinology 119: 1343-1350, 1986.
7. + T cells. Eur J Immunol 21: 1195-1200, 1991.
8. Crespi B and Semeniuk C. Parent-offspring conflict in the evolution of vertebrate reproductive mode. Am Nat 163: 635-653, 2004.
9. Dietz AB, Georges M, Threadgill DW, Womack JE, and Schuler LA. Somatic cell mapping, polymorphism, and linkage analysis of bovine prolactin-related proteins and placental lactogen. Genomics 14: 137-143, 1992.
10. Eisenhaber B, Bork P, and Eisenhaber F. Prediction of potential GPI-modification sites in proprotein sequences. J Mol Biol 292: 741-758, 1999.
11. Elkins PA, Christinger HW, Sandowski Y, Sakal E, Gertler A, de Vos AM, and Kossiakoff AA. Ternary complex between placental lactogen and the extracellular domain of the prolactin receptor. Nat Struct Biol 7: 808-815, 2000.
12. Endo T, Ikeo K, and Gojobori T. Large-scale search for genes on which positive selection may operate. Mol Biol Evol 13: 685-690, 1996.
13. Everts RE, Band MR, Liu ZL, Kumar CG, Liu L, Loor JJ, Oliveira R, and Lewin HA. A 7872 cDNA microarray and its use in bovine functional genomics. Vet Immunol Immunopathol 105: 235-245, 2005.
14. Everts-van der Wind A, Larkin DM, Green CA, Elliott JS, Olmstead CA, Chiu R, Schein JE, Marra MA, Womack JE, and Lewin HA. A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proc Natl Acad Sci USA 102: 18526-18531, 2005.
15. Ewing B, Hillier L, Wendl MC, and Green P. Base-calling of automated sequencer traces using PHRED. I. Accuracy assessment. Genome Res 8: 175-185, 1998.
16. Feigelstock D, Thompson P, Mattoo P, Zhang Y, and Kaplan GG. The human homolog of HAVcr-1 codes for a hepatitis A virus cellular receptor. J Virol 72: 6621-6628, 1998.
17. Guex N and Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18: 2714-2723, 1997.
18. Hart GW. Glycophospholipid anchors. In: Essentials of Glycobiology, edited by Varki A, Cummings R, Esko J, Freeze H, Hart G, and Marth J. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 1999, p. 131-144.
19. Hashizume K, Ishiwata H, Kizaki K, Yamada O, Takahashi T, Imai K, Patel OV, Akagi S, Shimizu M, Takahashi S, Katsuma S, Shiojima S, Hirasawa A, Tsujimoto G, Todoroki J, and Izaike Y. Implantation and placental development in somatic cell clone recipient cows. Cloning Stem Cells 4: 197-209, 2002.
20. Hedge P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, and Quackenbush J. A concise guide to cDNA microarray analysis. Biotechniques 29: 548-562, 2000.
21. Hein WR and Mackay CR. Prominence of γδ T cells in the ruminant immune system. Immunol Today 12: 30-34, 1991.
22. Heyborne K, Fu YX, Nelson A, Farr A, O'Brien R, and Born W. Recognition of trophoblasts by γδ T cells. J Immunol 153: 2918-2926, 1994.
23. Hofmann K and Stoffel W. Tmbase - a database of membrane spanning protein segments (Abstract). Biol Chem Hoppe-Seyler 374: 166, 1993.
24. Huang X and Madan A. CAP3: A DNA sequence assembly program. Genome Res 9: 868-877, 1999.
25. Ichimura T, Bonventre JV, Bailly V, Wei H, Hession CA, Cate RL, and Sanicola M. Kidney injury molecule-1 (KIM-1), a putative epithelial cell adhesion molecule containing a novel immunoglobulin domain, is up-regulated in renal cells after injury. J Biol Chem 273: 4135-4142, 1998.
26. Ishiwata H, Katsuma S, Kizaki K, Patel OV, Nakano H, Takahashi T, Imai K, Hirasawa A, Shiojima S, Ikawa H, Suzuki Y, Tsujimoto G, Iziake Y, Todoroki J, and Hashizume K. Characterization of gene expression profiles in early bovine pregnancy using a custom cDNA microarray. Mol Reprod Dev 65: 9-18, 2003.
27. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, and Gibson TJ. Multiple sequence alignment with Clustal X. Trends Biochem Sci 23: 403-405, 1998.
28. Kan CC, Solomon E, Belt KT, Chain AC, Hiorns LR, and Fey G. Nucleotide sequence of cDNA encoding human 2-macroglobulin and assignment of the chromosomal locus. Proc Natl Acad Sci USA 82: 2282-2286, 1985.
29. Kaplan G, Totsuka A, Thompson P, Akatsuka T, Moritsugu Y, and Feinstone SM. Identification of a surface glycoprotein on African green monkey kidney cells as a receptor for hepatitis A virus. EMBO J 15: 4282-4296, 1996.
30. Keeler C, Dannies PS, and Hodsdon ME. The tertiary structure and backbone dynamics of human prolactin. J Mol Biol 328: 1105-1121, 2003.
31. Kent WJ. The human genome browser at UCSC. Genome Res 12: 996-1006, 2002.
32. Kessler MA, Duello TM, and Schuler LA. Expression of prolactin-related hormones in the early bovine conceptus, and potential for paracrine effect on the endometrium. Endocrinology 129: 1885-1895, 1991.
33. Kessler MA, Milosavljevic M, Zieler CG, and Schuler LA. A subfamily of bovine prolactin-related transcripts distinct from placental lactogen in the fetal placenta. Biochemistry 28: 5154-5161, 1989.
34. Kessler MA and Schuler LA. Purification and properties of placental prolactin-related protein-I. Placenta 18: 29-36, 1997.
35. Knowles NJ and Samuel AR. Molecular epidemiology of foot-and-mouth disease virus. Virus Res 91: 65-80, 2003.
36. Koonin EV. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39: 309-338, 2005.
37. Kramer KK, Duffy JY, Klemann SW, Bixby JA, Low BG, Pope WF, and Roberts RM. Selective cloning of cDNA for secretory proteins of early embryos. Identification of a transiently expressed Kunitz domain protein from preimplantation sheep trophoblast. J Biol Chem 269: 7255-7261, 1994.
38. Larson JH, Rebeiz MJ, Stiening CM, Windish RL, Beever JE, and Lewin HA. MHC class I-like genes in cattle, MHCLA, with similarity to genes encoding NK cell stimulatory ligands. Immunogenetics 55: 16-22, 2003.
39. + intraepithelial lymphocytes induced by the local presence of the sheep conceptus. Am J Reprod Immunol 37: 199-205, 1997.
40. Lyman SD, Escobar S, Rousseau AM, Armstrong A, and Fanslow WC. Identification of CD7 as a cognate of the human K12 (SECTM1) protein. J Biol Chem 275: 3431-3437, 2000.
41. Mackay CR and Hein WR. A large proportion of bovine T cells express the γδ T cell receptor and show a distinct tissue distribution and surface phenotype. Int Immunol 1: 540-545, 1989.
42. MacLean JA 2nd, Chakrabarty A, Xie S, Bixby JA, Roberts RM, and Green JA. Family of Kunitz proteins from trophoblast: expression of the trophoblast Kunitz domain proteins (TKDP) in cattle and sheep. Mol Reprod Dev 65: 30-40, 2003.
43. MacLean JA 2nd, Roberts RM, and Green JA. Atypical Kunitz-type serine proteinase inhibitors produced by the ruminant placenta. Biol Reprod 71: 455-463, 2004.
44. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, and Bryant SH. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 30: 281-283, 2002.
45. Medawar PD. Some immunological and endocrinological problems raised by the evolution of viviparity in vertebrates. Symp Soc Exp Biol 7: 320-338, 1953.
46. Milosavljevic M, Duello TM, and Schuler LA. In situ localization of two prolactin-related messenger ribonucleic acids to binucleate cells of bovine placentomes. Endocrinology 125: 883-889, 1989.
47. Mossman HW. Vertebrate Fetal Membranes: Comparative Ontogeny and Morphology, Evolution, Phylogenetic Significance, Basic Functions, Research Opportunities. New Brunswick, NJ: Rutgers Univ. Press, 1987.
48. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562, 2002.
49. Nakai K and Kanehisa M. A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14: 897-911, 1992.
50. Nei M and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426, 1986.
51. Ohno S. Evolution by Gene Duplication. New York: Springer-Verlag, 1970.
52. Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428: 493-521, 2004.
53. Richardson RT, Sivashanmugam P, Hall SH, Hamil KG, Moore PA, Ruben SM, French FS, and O'Rand M. Cloning and sequencing of human Eppin: a novel family of protease inhibitors expressed in the epididymis and testis. Gene 270: 93-102, 2001.
54. Roberts RM, Ealy AD, Alexenko AP, Han CS, and Ezashi T. Trophoblast interferons. Placenta 20: 259-264, 1999.
55. Roberts RM, Xie S, and Mathialagan N. Maternal recognition of pregnancy. Biol Reprod 54: 294-302, 1996.
56. Rost B and Liu J. The PredictProtein server. Nucleic Acids Res 31: 3300-3304, 2003.
57. Schuler LA and Hurley WL. Molecular cloning of a prolactin-related mRNA expressed in bovine placenta. Proc Natl Acad Sci USA 84: 5650-5654, 1987.
58. Schuler LA, Kessler MA, Tanaka M, and Nakashima K. Nomenclature clarification for the bovine placental prolactin-related hormones. Endocrinology 129: 2057, 1991.
59. Silberstein E, Dveksler G, and Kaplan GG. Neutralization of hepatitis A virus (HAV) by an immunoadhesin containing the cysteine-rich region of HAV cellular receptor-1. J Virol 75: 717-725, 2001.
60. Silberstein E, Xing L, van de Beek W, Lu J, Cheng H, and Kaplan GG. Alteration of hepatitis A virus (HAV) particles by a soluble form of HAV cellular receptor 1 containing the immunoglobin- and mucin-like regions. J Virol 77: 8765-8774, 2003.
61. Slentz-Kesler KA, Hale LP, and Kaufman RE. Identification and characterization of K12 (SECTM1), a novel human gene that encodes a Golgi-associated protein with transmembrane and secreted isoforms. Genomics 47: 327-340, 1998.
62. Springer MS, Murphy WJ, Eizirik E, and O'Brien SJ. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc Natl Acad Sci USA 100: 1056-1061, 2003.
63. Tanaka M, Minoura H, Ushiro H, and Nakashima K. A novel cDNA clone encoding a prolactin-like protein that lacks the two C-terminal cysteine residues isolated from bovine placenta. Biochim Biophys Acta 1088: 385-389, 1991.
64. Tanaka M, Yamakawa M, Watahiki M, Yamamoto M, and Nakashima K. Isolation of a novel prolactin-like cDNA clone from bovine placenta: occurrence of new family members. Biochim Biophys Acta 1008: 193-197, 1989.
65. Thompson P, Lu J, and Kaplan GG. The Cys-rich region of hepatitis A virus cellular receptor 1 is required for binding of hepatitis A virus and protective monoclonal antibody 190/4. J Virol 72: 3751-3761, 1998.
66. Trivers RL. Parent-offspring conflict. Am Zool 14: 249-264, 1974.
67. Ushizawa K, Kaneyama K, Takahashi T, Tokunaga T, Tsunoda Y, and Hashizume K. Cloning and expression of a new member of prolactin-related protein in bovine placenta: bovine prolactin-related protein-VII. Biochem Biophys Res Commun 326: 435-441, 2005.
68. Wang HY, Malek RL, Kwitek AE, Greene AS, Luu TV, Behbahani B, Frank B, Quackenbush J, and Lee NH. Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biol 4: R5.1-R5.13, 2003.
69. Womack JE, Johnson JS, Owens EK, Rexroad CE 3rd, Schlapfer J, and Yang YP. A whole-genome radiation hybrid panel for bovine gene mapping. Mamm Genome 8: 854-856, 1997.
70. Wooding FB and Wathes DC. Binucleate cell migration in the bovine placentome. J Reprod Fertil 59: 425-430, 1980.
71. Xie S, Green J, Bixby JB, Szafranska B, DeMartini JC, Hecht S, and Roberts RM. The diversity and evolutionary relationships of the pregnancy-associated glycoproteins, an aspartic proteinase subfamily consisting of many trophoblast-expressed genes. Proc Natl Acad Sci USA 94: 12809-12816, 1997.
72. Yamada O, Todoroki J, Kizaki K, Takahashi T, Imai K, Patel OV, Schuler LA, and Hashizume K. Expression of prolactin-related protein I at the fetomaternal interface during the implantation period in cows. Reproduction 124: 427-437, 2002.
73. Yamakawa M, Tanaka M, Koyama M, Kagesato Y, Watahiki M, Yamamoto M, and Nakashima K. Expression of new members of the prolactin growth hormone gene family in bovine placenta. Isolation and characterization of two prolactin-like cDNA clones. J Biol Chem 265: 8915-8920, 1990.
74. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556, 1997.
75. Yang Z and Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17: 32-43, 2000.
76. Yang Z, Nielsen R, Goldman N, and Pedersen AM. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449, 2000.
77. Zieler CG, Kessler MA, and Schuler LA. Characterization of a novel prolactin-related protein from bovine fetal placenta. Endocrinology 126: 2377-2382, 1990.