Conserved protein motifs and structural organization of a fish gene homologous to mammalian apolipoprotein E

European Journal of Biochemistry

Volumn 267, Issue 2, 2000, Pages 549-559

  Durliat, Michèle ^a   André, Michèle ^a   Babin, Patrick J ^a  

^a CNRS   (France)

Author keywords

Apolipoprotein; Lipoprotein; Protein motifs; Trout; Zebrafish

Indexed keywords

APOLIPOPROTEIN E; LIPOPROTEIN;

AMINO ACID SEQUENCE; ARTICLE; EXON; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN LIPID INTERACTION; PROTEIN STRUCTURE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TROUT; ZEBRA FISH;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; APOLIPOPROTEINS E; BASE SEQUENCE; CONSERVED SEQUENCE; EXONS; FISHES; GENE EXPRESSION REGULATION; HUMANS; INTRONS; MAMMALS; MOLECULAR SEQUENCE DATA; ONCORHYNCHUS MYKISS; RESTRICTION MAPPING; SEQUENCE HOMOLOGY, AMINO ACID; ZEBRAFISH;

DANIO RERIO; MAMMALIA; SALMONIDAE; TELEOSTEI; VERTEBRATA;

EID: 0033974171     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.2000.01033.x     Document Type: Article

References (58)

1. 1. Mahley, R.W. (1988) Apolipoprotein E: cholesterol transport protein with expanding role in cell biology. Science 240, 622-630.
2. 2. St Clair, R.W. & Beisiegel, U. (1997) What do all the apolipoprotein E receptors do? Curr. Opin. Lipidol. 8, 243-245.
3. 3. Schneider, W.J., Nimpf, J. & Bujo, H. (1997) Novel members of the low density lipoprotein receptor superfamily and their potential roles in lipid metabolism. Curr. Opin. Lipidol. 8, 315-319.
4. 4. Driscoll, D.M. & Getz, G.S. (1984) Extrahepatic synthesis of apolipoprotein E. J. Lipid Res. 25, 1368-1379.
5. 5. Lenich, C., Brecher, P., Makrides, S., Chobanian, A. & Zannis, V.I. (1988) Apolipoprotein gene expression in the rabbit: abundance, size, and distribution of apolipoprotein mRNA species in different tissues. J. Lipid Res. 29, 755-764.
6. 6. Davignon, J., Greeg, R.E. & Sing, C.F. (1988) Apolipoprotein E polymorphism and atherosclerosis. Arteriosclerosis 8, 1-21.
7. 7. Weisgraber, K.H. (1994) Apolipoprotein E: Structure-function relationships. Adv. Protein Chem. 45, 249-302.
8. 8. Strittmatter, W.J. & Roses, A.D. (1996) Apolipoprotein E and Alzheimer's disease. Annu. Rev. Neurosci. 19, 53-77.
9. 9. Weisgraber, K.H. & Mahley, R.W. (1996) Human apolipoprotein E: The Alzheimer's disease connection. FASEB J. 10, 1485-1494.
10. 10. Beffert, U., Danik, M., Krzywkowski, P., Ramassamy, C., Berrada, F. & Poirier, J. (1998) The neurobiology of apolipoproteins and their receptors in the CNS and Alzheimer's disease. Brain Res. Rev. 27, 119-142.
11. 11. Laskowitz, D.T., Horsburgh, K. & Roses, A.D. (1998) Apolipoprotein E and the CNS response to injury. J. Cereb. Blood Flow Metab. 18, 465-471.
12. 12. Li, W.-H., Tanimura, M., Luo, C.-C., Datta, S. & Chan, L. (1988) The apolipoprotein multigene family: Biosynthesis, structure, structure-function relationships, and evolution. J. Lipid Res. 29, 245-271.
13. 13. Barker, W.C. & Dayhoff, M.O. (1977) Evolution of lipoproteins deduced from protein sequence data. Comp. Biochem. Physiol. 57B, 309-315.
14. 14. Boguski, M.S., Birkenmeier, E.H., Elshouebagy, N.A., Taylor, J.M. & Gordon, J.I. (1986) Evolution of apolipoproteins. Structure of the rat apoA-IV gene and its relationship to the human genes for apoA-I, C-III and E. J. Biol. Chem. 261, 6398-6407.
15. 15. Luo, C.-C., Li, W.-H., Moore, M.N. & Chan, L. (1986) Structure and evolution of the apolipoprotein multigene family. J. Mol. Biol. 187, 325-340.
16. 16. Babin, P.J., Thisse, C., Durliat, M., André, M., Akimenko, M.-A. & Thisse, B. (1997) Both apolipoprotein E and A-I genes are present in a nonmammalian vertebrate and are highly expressed during embryonic development. Proc. Natl Acad. Sci. USA 94, 8622-8627.
17. 17. Monnot, M.-J., Babin, P.J., Poleo, G., André, M., Laforest, L., Ballagny, C. & Akimenko, M.-A. (1999) Epidermal expression of apolipoprotein E gene during fin and scale development and fin regeneration in zebrafish. Dev. Dyn. 214, 207-215.
18. 18. Sambrook, J., Fritsch, E.F. & Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
19. 19. Pakdel, F., Le Guellec, C., Vaillant, C., Le Roux, M.G. & Valotaire, Y. (1989) Identification and estrogen induction of two estrogen receptors (ER) messenger ribonucleic acids in the rainbow trout liver: Sequence homology with other ERs. Mol. Endocrinol. 3, 44-51.
20. 20. Davis, R.W., Pierotti, V.R., Lauer, S.J., Hubl, S.T., McLean, J.W., Witztum, J.L. & Young, S.G. (1991) Lipoproteins in pinnipeds: analysis of a high molecular weight form of apolipoprotein E. J. Lipid Res. 32, 1013-1023.
21. 21. Komatsu, Y., Horiuchi, M., Ishiguro, N., Matsui, T. & Shinagawa, M. (1998) Characterization of the sheep apolipoprotein E (Apo E) gene and allelic variations of the apo E gene in scrapie Suffolk sheep. Gene 208, 131-138.
22. 22. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
23. 23. Bork, P. & Koonin, E.V. (1996) Protein sequence motifs. Curr. Opin. Struct. Biol. 6, 366-376.
24. 24. Bailey, T.L. & Gribskov, M. (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14, 48-54.
25. 25. Bailey, T.L. & Gribskov, M. (1998) Methods and statistics for combining motif match scores. J. Comput. Biol. 5, 211-221.
26. 26. Quandt, K., Frech, K., Karas, H., Wingender, E. & Werner, T. (1995) MatInd and MatInspector. New fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 23, 4878-4884.
27. 27. Yang, Y.-W., Chan, L. & Li, W.-H. (1991) Cloning and sequencing of bovine apolipoprotein E complementary DNA and molecular evolution of apolipoproteins E, C-I, and C-II. J. Mol. Evol. 32, 469-475.
28. 28. Nelson, J.S. (1994) Fishes of the World, 3rd edn. John Wiley, New York.
29. 29. Delcuve, G.P., Sun, J.M. & Davie, J.R. (1992) Expression of rainbow trout apolipoprotein A-I genes in liver and hepatocellular carcinoma. J. Lipid Res. 33, 251-262.
30. 30. Poupard, G., André, M., Durliat, M., Ballagny, C., Bœuf, G. & Babin, P.J. (2000) Apolipoprotein E gene expression correlates with endogenous lipid nutrition and yolk syncytial layer lipoprotein synthesis during fish development. Cell Tissue Res. in press.
31. 31. Amores, A., Force, A., Yan, Y.-L., Joly, L., Amemiya, C., Fritz, A., Ho, R.K., Langeland, J., Prince, V., Wang, Y.-L., Westerfield, M., Ekker, M. & Postlethwait, J.H. (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282, 1711-1714.
32. 32. Wittbrodt, J., Meyer, A. & Schartl, M. (1998) More genes in fish? Bioessays 20, 511-515.
33. 33. Das, H.K., McPherson, J., Bruns, G.A.P., Karathanasis, S.K. & Breslow, J.L. (1985) Isolation, characterization, and mapping to chromosome 19 of the human apolipoprotein E gene. J. Biol. Chem. 260, 6240-6247.
34. 34. Paik, Y.-K., Chang, D.J., Reardon, C.A., Davies, G.E., Mahley, R.W. & Taylor, J.M. (1985) Nucleotide sequence and structure of the human apolipoprotein E gene. Proc. Natl Acad. Sci. USA 82, 3445-3449.
35. 35. Fukazawa, C., Matsumoto, A. & Taylor, J.M. (1986) Complete nucleotide sequence of the gene encoding the rat apolipoprotein E. Nucleic Acids Res. 14, 9527-9528.
36. 36. Fung, W.P., Howlett, G.J. & Schreiber, G. (1986) Structure and expression of the rat apolipoprotein E gene. J. Biol. Chem. 261, 13777-13783.
37. 37. Rajavashisth, T.B., Haptein, J.S., Reue, K.L. & Lusis, A.J. (1985) Evolution of apolipoprotein E: mouse sequence and evidence for an 11-nucleotide ancestral unit. Proc. Natl Acad. Sci. USA 82, 8085-8089.
38. 38. Horiuchi, K., Tajima, S., Menju, M. & Yamamoto, A. (1989) Structure and expression of mouse apolipoprotein E gene. J. Biochem. 106, 98-103.
39. 39. Hixson, J.E., Cox, L.A. & Borenstein, S. (1988) The baboon apolipoprotein E gene: Structure, expression, and linkage with the gene for apolipoprotein C-I. Genomics 2, 315-323.
40. 40. Ramsoondar, J.J., Rucker, E.B., Vasquez, J.C., Gallagher, D.S., Grimm, D.R., Lunney, J.K., Schook, L.B. & Piedrahita, J.A. (1998) Isolation and genetic characterization of the porcine apolipoprotein E gene: Isolation, cloning, sequencing, microsatellite polymorphism, and chromosome assignment. Anim. Genet. 29, 43-47.
41. 41. Senapathy, P., Shapiro, M.B. & Harris, N.L. (1990) Splice junctions, branch point sites, and exons: Sequence statistics, identification, and applications to genome project. Methods Enzymol. 183, 252-278.
42. 42. Izsvak, Z., Ivics, Z. & Hackett, P.B. (1997) Repetitive elements and their genetic applications in zebrafish. Biochem. Cell Biol. 75, 507-523.
43. 43. Lauer, S.J., Walker, D., Elshourbagy, N.A., Reardon, C.A., Levy-Wilson, B. & Taylor, J.M. (1988) Two copies of the human apolipoprotein CI gene are linked closely to the apolipoprotein E gene. J. Biol. Chem. 263, 7277-7286.
44. 44. Allan, C.M., Walker, D., Segrest, J.P. & Taylor, J.M. (1995) Identification and characterization of a new human gene (APOC4) in the apolipoprotein E, C-I, and C-II gene locus. Genomics 28, 291-300.
45. 45. Smith, J.D., Melian, A., Leff, T. & Breslow, J.L. (1988) Expression of the human apolipoprotein E gene is regulated by multiple positive and negative elements. J. Biol. Chem. 263, 8300-8308.
46. 46. Paik, Y.-K., Chang, D.L., Reardon, C.A., Walker, M.D., Taxman, E. & Taylor, J.M. (1988) Identification and characterization of transcriptional regulatory regions associated with expression of the human apoliprotein E gene. J. Biol. Chem. 263, 13340-13349.
47. 47. Chang, D.J., Paik, Y.-K., Leren, T.P., Walker, D.W., Howlett, G.J. & Taylor, J.M. (1990) Characterization of a human apolipoprotein E gene enhancer element and its associated protein factors. J. Biol. Chem. 265, 9496-9504.
48. 48. Jo, D.-W., Leren, T.P., Yang, Z.-Y, Chung, Y.-H., Taylor, J.M. & Park, Y.-K. (1995) Characterization of an upstream regulatory element of the human apolipoprotein E gene, and purification of its binding protein from the human placenta. J. Biochem. 117, 915-922.
49. 49. Garcia, M.A., Vasquez, J., Gimenez, C., Valdivieso, F. & Zafra, F. (1996) Transcription factor AP-2 regulates human apolipoprotein E gene expression in astrocytoma cells. J. Neuroscience 16, 7550-7556.
50. 50. Artiga, M.J., Bullido, M.J., Sastre, I., Recuero, M., Garcia, M.A., Aldudo, J., Vasquez, J. & Valdivieso, F. (1998) Allelic polymorphisms in the transcriptional regulatory region of apolipoprotein E gene. FEBS Lett 421, 105-108.
51. 51. Simonet, W.S., Bucay, N., Lauer, S.J., Wirak, D.O., Stevens, M.E., Weisgraber, K.H., Pitas, R.E. & Taylor, J.M. (1990) In the absence of a downstream element, the apolipoprotein E gene is expressed at high levels in kidneys of transgenic mice. J. Biol. Chem. 265, 10809-10812.
52. 52. Simonet, W.S., Bucay, N., Pitas, R., Lauer, S.J. & Taylor, J.M. (1991) Multiple tissue-specific elements control the apolipoprotein E/C-I gene locus in transgenic mice. J. Biol. Chem. 266, 8651-8654.
53. 53. Dang, Q. & Taylor, J.M. (1996) In vivo footprinting analysis of the hepatic control region of the human apolipoprotein E/C-I/C-IV/C-II gene locus. J. Biol. Chem. 271, 28667-28676.
54. 54. Allan, C.M., Taylor, S. & Taylor, J.M. (1997) Two hepatic enhancers, HCR.1 and HCR.2, coordinate the liver expression of the entire human apolipoprotein E/C-I/C-IV/C-II gene cluster. J. Biol. Chem. 272, 29113-29119.
55. 55. De Souza, S.J., Long, M., Schoenbach, L., Roy, S.W. & Gilbert, W. (1996) Intron positions correlate with module boundaries in ancient proteins. Proc. Nad Acad. Sci. USA 93, 14632-14636.
56. 56. Dibb, N.J. & Newman, A.J. (1989) Evidence that introns arose at protospice sites. EMBO J. 8, 2015-2021.
57. 57. Golding, G.B., Tsao, N. & Pearlman, R.E. (1994) Evidence for intron capture: an unusual path for the evolution of proteins. Proc. Nad Acad. Sci. USA 91, 7506-7509.
58. 58. Steinmetz, A., Hermann, M., Nimpf, J., Aebersold, R., Ducret, A., Weinberg, R.B. & Schneider, W.J. (1998) Expression and conservation of apolipoprotein AIV in an avian species. J. Biol. Chem. 273, 10543-10549.