Vertebrate 2xRBD hnRNP proteins: A comparative analysis of genome, mRNA and protein sequences

Computational Biology and Chemistry

Volumn 29, Issue 1, 2005, Pages 13-23

  Akindahunsi, Akintunde A ^a   Bandiera, Antonella ^a   Manzini, Giorgio ^a  

^a UNIVERSITY OF TRIESTE   (Italy)

Author keywords

hnRNP exon intron structure; RBD phylogenesis

Indexed keywords

CHROMATOGRAPHY; DATABASE SYSTEMS; DNA SEQUENCES; FUNGI; GENES; HUMAN ENGINEERING; MASS SPECTROMETRY; PLANTS (BOTANY); RNA;

BIOMOLECULAR INFORMATION; HNRNP EXON/INTRON STRUCTURE; INTRONS; RBD PHYLOGENESIS; VERTEBRATES;

PROTEINS;

HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; MESSENGER RNA; RNA BINDING PROTEIN;

AMINO ACID SEQUENCE; AMPHIBIA; ANIMAL; ARTICLE; COMPARATIVE STUDY; FISH; GENETICS; GENOME; HUMAN; MAMMAL; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; AMPHIBIA; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; FISHES; GENOME; HETEROGENEOUS-NUCLEAR RIBONUCLEOPROTEINS; HUMANS; MAMMALS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, MESSENGER; RNA-BINDING PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

ARABIDOPSIS; CAENORHABDITIS; CIONA; DANIO; DANIO RERIO; EUKARYOTA; GALLUS GALLUS; MURINAE; SACCHAROMYCES; SILURANA; TAKIFUGU; TAKIFUGU RUBRIPES; TETRAODONTIDAE; VERTEBRATA; XENOPUS LAEVIS; XENOPUS TROPICALIS;

EID: 12444329819     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2004.11.002     Document Type: Article

References (37)

1. N. Abdul-Manan, and K.R. Williams hnRNP A1 binds promiscuously to oligoribonucleotides: utilization of random and homo-oligonucleotides to discriminate sequence from base-specific binding Nucleic Acids Res. 24 1996 4063 4070
2. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
3. A. Bandiera, G. Tell, E. Marsich, A. Scaloni, G. Pocsfalvi, A.A. Akindahunsi, L. Cesaratto, and G. Manzini Cytosine-block telomeric type DNA-binding activity of hnRNP proteins from human cell lines Arch. Biochem. Biophys. 409 2003 305 314
4. G. Biamonti, M. Buvoli, M.T. Bassi, C. Morandi, F. Cobianchi, and S. Riva Isolation of an active gene encoding human hnRNP protein A1. Evidence for alternative splicing J. Mol. Biol. 207 1989 491 503
5. G. Biamonti, M. Ruggiu, S. Saccone, G. Della Valle, and S. Riva Two homologous genes, originated by duplication, encode the human hnRNP proteins A2 and A1 Nucleic Acids Res. 22 1994 1996 2002
6. E. Birney, S. Kumar, and A.R. Krainer Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors Nucleic Acids Res. 21 1993 5803 5816
7. C.G. Burd, M.S. Swanson, M. Gorlach, and G. Dreyfuss Primary structures of the heterogeneous nuclear ribonucleoprotein A2, B1, and C2 proteins: a diversity of RNA binding proteins is generated by small peptide inserts Proc. Natl. Acad. Sci. U.S.A. 86 1989 9788 9792
8. M.R. Conte, T. Grune, G. Kelly, A. Ladas, S. Matthews, and S. Curry Structure of tandem RNA recognition motifs from polypyrimidine tract binding protein reveals novel features of the RRM fold EMBO J. 19 2000 3132 3141
9. L.A. Dempsey, M.J. Li, A. DePace, P. Bray-Ward, and N. Maizels The human HNRPD locus maps to 4q21 and encodes a highly conserved protein Genomics 49 1998 378 384
10. J. Ding, M.K. Hayashi, Y. Zhang, L. Manche, A.R. Krainer, and R.M. Xu Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA Genes Dev. 13 1999 1102 1115
11. A. Eversole, and N. Maizels In vitro properties of the conserved mammalian protein hnRNP D suggest a role in telomeric maintenance Mol. Cell Biol. 20 2000 5425 5432
12. Felsenstein, J., 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle (http://evolution.genetics.washington.edu/phylip.html).
13. F. Ishikawa, M.J. Matunis, G. Dreyfuss, and T.R. Cech Nuclear proteins that bind the pre-mRNA 3′ splice site sequence r(UUAG/G) and the human telomeric DNA sequence d(TTAGGG)n Mol. Cell Biol. 13 1993 4301 4310
14. T. Kajita, J. Nakayama, M. Aizawa, and F. Ishikawa The UUAG-specific RNA binding protein, heterogeneous nuclear ribonucleoprotein D0. Common modular structure and binding properties of the 2xRBD-Gly family J. Biol. Chem. 270 1995 22167 22175
15. H. Kamma, M. Fujimoto, M. Fujiwara, M. Matsui, H. Horiguchi, M. Hamasaki, and H. Satoh Interaction of hnRNP A2/B1 isoforms with telomeric ssDNA and the in vitro function Biochem. Biophys. Res. Commun. 280 2001 625 630
16. M. Katahira, Y. Miyanoiri, Y. Enokizono, G. Matsuda, T. Nagata, F. Ishikawa, and S. Uesugi Structure of the C-terminal RNA-binding domain of hnRNP D0 (AUF1), its interactions with RNA and DNA, and change in backbone dynamics upon complex formation with DNA J. Mol. Biol. 311 2001 973 988
17. A.M. Krecic, and M.S. Swanson hnRNP complexes: composition, structure, and function Curr. Opin. Cell Biol. 11 1999 363 371
18. H. LaBranche, S. Dupuis, Y. Ben-David, M.R. Bani, R.J. Wellinger, and B. Chabot Telomere elongation by hnRNP A1 and a derivative that interacts with telomeric repeats and telomerase Nat. Genet. 19 1998 199 202
19. L. Lacroix, H. Lienard, E. Labourier, M. Djavaheri-Mergny, J. Lacoste, H. Leffers, J. Tazi, C. Helene, and J.L. Mergny Identification of two human nuclear proteins that recognise the cytosine-rich strand of human telomeres in vitro Nucleic Acids Res. 28 2000 1564 1575
20. P.P. Lau, H.J. Zhu, M. Nakamuta, and L. Chan Cloning of an Apobec-1-binding protein that also interacts with apolipoprotein B mRNA and evidence for its involvement in RNA editing J. Biol. Chem. 272 1997 1452 1455
21. Z.J. Lorkovic, and A. Barta Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana Nucleic Acids Res. 30 2002 623 635
22. A.S. Ma, K. Moran-Jones, J. Shan, T.P. Munro, M.J. Snee, K.S. Hoek, and R. Smith heterogeneous nuclear ribonucleoprotein A3, a novel RNA trafficking response element-binding protein J. Biol. Chem. 277 2002 18010 18020
23. E. Marsich, A. Bandiera, G. Tell, A. Scaloni, and G. Manzini A chicken hnRNP of the A/B family recognizes the single-stranded d(CCCTAA)n telomeric repeated motif Eur. J. Biochem. 268 2001 139 148
24. A. Mayeda, S.H. Munroe, R.M. Xu, and A.R. Krainer Distinct functions of the closely related tandem RNA-recognition motifs of hnRNP A1 RNA 4 1998 1111 1123
25. S.J. McKay, and H. Cooke hnRNP A2/B1 binds specifically to single stranded vertebrate telomeric repeat TTAGGGn Nucleic Acids Res. 20 1992 6461 6464
26. V.E. Myer, and J.A. Steitz Isolation and characterization of a novel, low abundance hnRNP protein: A0 RNA 1 1995 171 182
27. T. Nagata, Y. Kurihara, G. Matsuda, J. Saeki, T. Kohno, Y. Yanagida, F. Ishikawa, S. Uesugi, and M. Katahira Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0 J. Mol. Biol. 287 1999 221 237
28. M. Nakamura, H. Okano, J.A. Blendy, and C. Montell Musashi, a neural RNA-binding protein required for Drosophila adult external sensory organ development Neuron 13 1994 67 81
29. S. Saccone, G. Biamonti, S. Maugeri, M.T. Bassi, G. Bunone, S. Riva, and G. Della Valle Assignment of the human heterogeneous nuclear ribonucleoprotein A1 gene (HNRPA1) to chromosome 12q13.1 by cDNA competitive in situ hybridization Genomics 12 1992 171 174
30. S. Takiguchi, T. Tokino, T. Imai, A. Tanigami, K. Koyama, and Y. Nakamura Identification and characterization of a cDNA, which is highly homologous to the ribonucleoprotein gene, from a locus (D10S102) closely linked to MEN2 (multiple endocrine neoplasia type 2) Cytogenet. Cell Genet. 64 1993 128 130
31. T. Thisted, D.L. Lyakhov, and J. Liebhaber Optimized RNA targets of two closely related triple KH domain proteins, heterogeneous nuclear ribonucleoprotein K and alphaCP-2KL, suggest distinct modes of RNA recognition J. Biol. Chem. 276 2001 17484 17496
32. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
33. N. Tsuchiya, D. Kamei, A. Takano, T. Matsui, and M. Yamada Cloning and characterization of a cDNA encoding a novel heterogeneous nuclear ribonucleoprotein-like protein and its expression in myeloid leukemia cells J. Biochem. (Tokyo) 123 1998 499 507
34. S. Tsui, T. Dai, S. Roettger, W. Schempp, E.C. Salido, and P.H. Yen Identification of two novel proteins that interact with germ-cell-specific RNA-binding proteins DAZ and DAZL1 Genomics 65 2000 266 273
35. J. Tymowska, and M. Fischberg A comparison of the karyotype, constitutive heterochromatin, and nucleolar organizer regions of the new tetraploid species Xenopus epitropicalis Fischberg and Picard with those of Xenopus tropicalis Gray (Anura: Pipidae) Cytogenet. Cell Genet. 34 1982 149 157
36. R.M. Xu, L. Jokhan, X. Cheng, A. Mayeda, and A.R. Krainer Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs Structure 5 1997 559 570
37. W. Zhang, B.J. Wagner, K. Ehrenman, A.W. Schaefer, C.T. DeMaria, D. Crater, K. DeHaven, L. Long, and G. Brewer Purification, characterization, and cDNA cloning of an AU-rich element RNA-binding protein, AUF1 Mol. Cell Biol. 13 1993 7652 7665