Analysis of the reticulon gene family demonstrates the absence of the neurite growth inhibitor Nogo-A in fish

Molecular Biology and Evolution

Volumn 22, Issue 8, 2005, Pages 1635-1648

  Diekmann, Heike ^a   Klinger, Michael ^a   Oertle, Thomas ^b,c   Heinz, Dietmar ^a   Pogoda, Hans Martin ^d   Schwab, Martin E ^b,c   Stuermer, Claudia A O ^a  

^a UNIVERSITY OF KONSTANZ   (Germany)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c ETH ZURICH   (Switzerland)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Conserved synteny; Danio rerio; Gene duplication; Nogo; Reticulon; RTN4

Indexed keywords

AMINO ACID; MYELIN; PROTEIN; PROTEIN NOGO A; RETICULON; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CENTRAL NERVOUS SYSTEM; CORRELATION ANALYSIS; FISH; GENE DUPLICATION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENOME; MULTIGENE FAMILY; NERVE FIBER GROWTH; NERVE FIBER REGENERATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN FUNCTION; ZEBRA FISH;

ANIMALS; EVOLUTION, MOLECULAR; GOLDFISH; HUMANS; MYELIN PROTEINS; NERVE REGENERATION; NEURITES; SEQUENCE HOMOLOGY, AMINO ACID; ZEBRAFISH;

DANIO RERIO; MAMMALIA; TETRAODONTIDAE; VERTEBRATA;

EID: 25444450572     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msi158     Document Type: Article

References (58)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Amores, A., et al. (13 co-authors). 1998. Zebrafish hox clusters and vertebrate genome evolution. Science 282:1711-1714.
3. Baka, I. D., N. N. Ninkina, L. G. Pinon, J. Adu, A. M. Davies, G. P. Georgiev, and V. L. Buchman. 1996. Intracellular compartmentalization of two differentially spliced s-rex/NSP mRNAs in neurons. Mol. Cell. Neurosci. 7:289-303.
4. Barbazuk, W. B., I. Korf, C. Kadavi, J. Heyen, S. Tate, E. Wun, J. A. Bedell, J. D. McPherson, and S. L. Johnson. 2000. The syntenic relationship of the zebrafish and human genomes. Genome Res. 10:1351-1358.
5. Bastmeyer, M., M. Beckmann, M. E. Schwab, and C. A. Stuermer. 1991. Growth of regenerating goldfish axons is inhibited by rat oligodendrocytes and CNS myelin but not by goldfish optic nerve tract oligodendrocyte-like cells and fish CNS myelin. J. Neurosci. 11:626-40.
6. Bonner, D. S., J. E. Wiley, and M. A. Farwell. 1998. Assignment1 of the mitochondrial translational initiation factor 2 gene (MTIF2) to human chromosome 2 bands p16→p14 by in situ hybridization and with somatic cell hybrids. Cytogenet. Cell Genet. 83:80-81.
7. Brittis, P. A., and J. G. Flanagan. 2001. Nogo domains and a Nogo receptor: implications for axon regeneration. Neuron 30:11-14.
8. Brunelli, J. P., B. D. Robison, and G. H. Thorgaard. 2001. Ancient and recent duplications of the rainbow trout Wilms' tumor gene. Genome 44:455-462.
9. Chen, M. S., A. B. Huber, M. E. van der Haar, M. Frank, L. Schnell, A. A. Spillmann, F. Christ, and M. E. Schwab. 2000. Nogo-A is a myelin-associated neurite outgrowth inhibitor and an antigen for monoclonal antibody IN-1. Nature 403:434-439.
10. Farber, S. A., R. A. De Rose, E. S. Olson, and M. E. Halpern. 2003. The zebrafish annexin gene family. Genome Res. 13:1082-1096.
11. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
12. Filbin, M. T. 2003. Myelin-associated inhibitors of axonal regeneration in the adult mammalian CNS. Nat. Rev. Neurosci. 4:703-713.
13. Fournier, A. E., T. GrandPré, and S. M. Strittmatter. 2001. Identification of a receptor mediating Nogo-66 inhibition of axonal regeneration. Nature 409:341-346.
14. Gaze, R. M. 1970. The formation of nerve connections. Academic Press Inc., New York.
15. Geisler, J. G., L. J. Stubbs, W. W. Wasserman, and M. L. Mucenski. 1998. Molecular cloning of a novel mouse gene with predominant muscle and neural expression. Mamm. Genome 9:274-282.
16. GrandPré, T., S. Li, and S. M. Strittmatter. 2002. Nogo-66 receptor antagonist peptide promotes axonal regeneration. Nature 417:547-551.
17. GrandPré, T., F. Nakamura, T. Vartanian, and S. M. Strittmatter. 2000. Identification of the Nogo inhibitor of axon regeneration as a reticulon protein. Nature 403:439-444.
18. Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
19. Hamada, N., J. Iwahashi, K. Suzuki, H. Ogi, T. Kashiwagi, K. Hara, M. Toyoda, T. Yamada, and T. Toyoda. 2002. Molecular cloning and characterization of the mouse reticulon 3 cDNA. Cell. Mol. Biol. (Noisy-le-grand) 48:163-172.
20. Hukriede, N. A., et al. (17 co-authors). 1999. Radiation hybrid mapping of the zebrafish genome. Proc. Natl. Acad. Sci. USA 96:9745-9750.
21. Klinger, M., H. Diekmann, D. Heinz, C. Hirsch, S. Hannbeck von Hanwehr, B. Petrausch, T. Oertle, M. E. Schwab, and C. A. O. Stuermer. 2004a. Identification of two nogo/rtn4 genes and analysis of Nogo-A expression in Xenopus laevis. Mol. Cell. Neurosci. 25:205-216.
22. Klinger, M., J. S. Taylor, T. Oertle, M. E. Schwab, C. A. Stuermer, and H. Diekmann. 2004b. Identification of Nogo-66 receptor (NgR) and homologous genes in fish. Mol. Biol. Evol. 21:76-85.
23. Kools, P. F., A. J. Roebroek, H. J. Van de Velde, P. Marynen, J. Bullerdiek, and W. J. Van de Ven. 1994. Regional mapping of the human NSP gene to chromosome region 14q21 →> q22 by fluorescence in situ hybridization analysis. Cytogenet. Cell Genet. 66:48-50.
24. Kozak, M. 1996. Interpreting cDNA sequences: some insights from studies on translation. Mamm. Genome 7:563-574.
25. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
26. Lehmann, F., H. Gathje, S. Kelm, and F. Dietz. 2004. Evolution of sialic acid-binding proteins: molecular cloning and expression of fish siglec-4. Glycobiology 14:959-968.
27. Mayor, C., M. Brudno, J. R. Schwartz, A. Poliakov, E. M. Rubin, K. A. Frazer, L. S. Pachter, and I. Dubchak. 2000. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16:1046-1047.
28. Meyer, A., and M. Schartl. 1999. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr. Opin. Cell Biol. 11:699-704.
29. Moreira, E. F., C. J. Jaworski, and I. R. Rodriguez. 1999. Cloning of a novel member of the reticulon gene family (RTN3): gene structure and chromosomal localization to 11q13. Genomics 58:73-81.
30. Morris, N. J., S. A. Ross, J. M. Neveu, W. S. Lane, and G. E. Lienhard. 1999. Cloning and characterization of a 22 kDa protein from rat adipocytes: a new member of the reticulon family. Biochim. Biophys. Acta 1450:68-76.
31. Nagase, T., K. Ishikawa, N. Miyajima, A. Tanaka, H. Kotani, N. Nomura, and O. Ohara. 1998. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. DNA Res. 5:31-39.
32. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
33. Ninkina, N. N., I. D. Baka, and V. L. Buchman. 1997. Rat and chicken s-rex/NSP mRNA: nucleotide sequence of main transcripts and expression of splice variants in rat tissues. Gene 184:205-210.
34. Oertle, T., C. Huber, H. van der Putten, and M. E. Schwab. 2003a. Genomic structure and functional characterisation of the promoters of human and mouse nogo/rtn4. J. Mol. Biol. 325:299-323.
35. Oertle, T., M. Klinger, C. A. Stuermer, and M. E. Schwab. 2003b. A reticular rhapsody: phylogenic evolution and nomenclature of the RTN/Nogo gene family. FASEB J. 17:1238-1247.
36. Oertle, T., D. Merkler, and M. E. Schwab. 2003. Do cancer cells die because of Nogo-B? Oncogene 22:1390-1399.
37. Oertle, T., and M. E. Schwab. 2003. Nogo and its paRTNers. Trends Cell Biol. 13:187-194.
38. Oertle, T., et al. (13 co-authors). 2003c. Nogo-A inhibits neurite outgrowth and cell spreading with three discrete regions. J. Neurosci. 23:5393-5406.
39. Prinjha, R., S. E. Moore, M. Vinson, S. Blake, R. Morrow, G. Christie, D. Michalovich, D. L. Simmons, and F. S. Walsh. 2000. Inhibitor of neurite outgrowth in humans. Nature 403:383-384.
40. Rise, M. L., et al. (29 co-authors). 2004. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res. 14:478-490.
41. Roebroek, A. J., T. A. Ayoubi, H. J. Van de Velde, E. F. Schoenmakers, I. G. Pauli, and W. J. Van de Ven. 1996. Genomic organization of the human NSP gene, prototype of a novel gene family encoding reticulons. Genomics 32:191-199.
42. Roebroek, A. J., B. Contreras, I. G. Pauli, and W. J. Van de Ven. 1998. cDNA cloning, genomic organization, and expression of the human RTN2 gene, a member of a gene family encoding reticulons. Genomics 51:98-106.
43. Roebroek, A. J., H. J. van de Velde, A. Van Bokhoven, J. L. Broers, F. C. Ramaekers, and W. J. Van de Ven. 1993. Cloning and expression of alternative transcripts of a novel neuroendocrine-specific gene and identification of its 135-kDa translational product. J. Biol. Chem. 268:13439-13447.
44. Schwab, M. E. 2004. Nogo and axon regeneration. Curr. Opin. Neurobiol. 14:118-124.
45. Schwartz, S., Z. Zhang, K. A. Frazer, A. Smit, C. Riemer, J. Bouck, R. Gibbs, R. Hardison, and W. Miller. 2000. PipMaker - a web server for aligning two genomic DNA sequences. Genome Res. 10:577-586.
46. Stubbs, L., et al. (12 co-authors). 1996. Detailed comparative map of human chromosome 19q and related regions of the mouse genome. Genomics 35:499-508.
47. Stuermer, C. A., M. Bastmeyer, M. Bahr, G. Strobel, and K. Paschke. 1992. Trying to understand axonal regeneration in the CNS of fish. J. Neurobiol. 23:537-550.
48. Stuermer, C. A. O. 1988a. Trajectories of regenerating retinal axons in the goldfish tectum: I. A comparison of normal and regenerated axons at late regeneration stages. J. Comp. Neurol. 267:55-68.
49. _. 1988b. Trajectories of regenerating retinal axons in the goldfish tectum: II. Exploratory branches and growth cones on axons at early regeneration stages. J. Comp. Neurol. 267:69-91.
50. Taylor, J. S., I. Braasch, T. Frickey, A. Meyer, and Y. Van De Peer. 2003. Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res. 13:382-390.
51. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
52. van de Velde, H. J., A. J. Roebroek, N. H. Senden, F. C. Ramaekers, and W. J. Van de Ven. 1994. NSP-encoded reticulons, neuroendocrine proteins of a novel gene family associated with membranes of the endoplasmic reticulum. J. Cell Sci. 107:2403-2416.
53. Vielmetter, J., and C. A. Stuermer. 1989. Goldfish retinal axons respond to position-specific properties of tectal cell membranes in vitro. Neuron 2:1331-1339.
54. Wanner, M., D. M. Lang, C. E. Bandtlow, M. E. Schwab, M. Bastmeyer, and C. A. Stuermer. 1995. Reevaluation of the growth-permissive substrate properties of goldfish optic nerve myelin and myelin proteins. J. Neurosci. 15:7500-7508.
55. Woods, I. G., P. D. Kelly, F. Chu, P. Ngo-Hazelett, Y. L. Yan, H. Huang, J. H. Postlethwait, and W. S. Talbot. 2000. A comparative map of the zebrafish genome. Genome Res. 10:1903-1914.
56. Yang, J., L. Yu, A. D. Bi, and S. Y. Zhao. 2000. Assignment of the human reticulon 4 gene (RTN4) to chromosome 2p14→2p13 by radiation hybrid mapping. Cytogenet. Cell Genet. 88:101-102.
57. Yoder, J. A., and G. W. Litman. 2000. The zebrafish fth1, slc3a2, men1, pc, fgf3 and cycd1 genes define two regions of conserved synteny between linkage group 7 and human chromosome 11q13. Gene 261:235-242.
58. Zhang, Z., P. Harrison, and M. Gerstein. 2002. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res. 12:1466-1482.