Home LiteratureArticle Details
PMID: 15367696 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Determination and augmentation of RNA sequence specificity of the Nova K-homology domains.

Nucleic acids research ·Vol. 32 ·No. 16 ·2004-00-00 ·Pages 4852-61

Musunuru K, Darnell RB

Abstract

The Nova onconeural antigens are implicated in the pathogenesis of paraneoplastic opsoclonus-myoclonus-ataxia (POMA). The Nova antigens are neuron-specific RNA-binding proteins harboring three repeats of the K-homology (KH) motif; they have been implicated in the regulation of alternative splicing of a host of genes involved in inhibitory synaptic transmission. Although the third Nova KH domain (KH3) has been extensively characterized using biochemical and crystallographic techniques, the roles of the KH1 and KH2 domains remain unclear. Furthermore, the specificity determinants that distinguish the Nova KH domains from those of the closely related hnRNP E and hnRNP K proteins are undefined. We demonstrate through the use of RNA selection and biochemical analysis that the sequence specificity of the Nova KH1/2 domains is similar to that of Nova KH3. We also show that the mutagenesis of a Nova KH domain to render it similar to the KH domains of the heterogeneous nuclear ribonucleoprotein E (hnRNP E) and hnRNP K allow it to recognize longer RNA sequences. These data yield important insights into KH domain function and suggest a strategy by which to engineer KH domains with novel sequence preferences.

MeSH Terms
Antigens, Neoplasm/chemistry,genetics,metabolism Arginine/physiology Base Sequence Heterogeneous-Nuclear Ribonucleoproteins/chemistry,metabolism Molecular Sequence Data Mutation Nerve Tissue Proteins/chemistry,genetics,metabolism Neuro-Oncological Ventral Antigen Protein Binding Protein Structure, Tertiary RNA/chemistry,metabolism RNA-Binding Proteins/chemistry,genetics,metabolism Sequence Alignment
Chemicals
Antigens, Neoplasm Heterogeneous-Nuclear Ribonucleoproteins Nerve Tissue Proteins Neuro-Oncological Ventral Antigen RNA-Binding Proteins RNA Arginine
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Musunuru Kiran
Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
Darnell Robert B
References (43)
43 references, click to expand
  1. Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome.
    Cell. 2000 Feb 4;100(3):323-32 PMID: 10676814
  2. Nova regulates GABA(A) receptor gamma2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer.
    Mol Cell Biol. 2003 Jul;23(13):4687-700 PMID: 12808107
  3. DDP1, a heterochromatin-associated multi-KH-domain protein of Drosophila melanogaster, interacts specifically with centromeric satellite DNA sequences.
    Mol Cell Biol. 2000 Jun;20(11):3860-9 PMID: 10805729
  4. The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain.
    Proc Natl Acad Sci U S A. 2000 May 23;97(11):5740-5 PMID: 10811881
  5. Nuclear targeting determinants of the far upstream element binding protein, a c-myc transcription factor.
    Nucleic Acids Res. 2000 Nov 15;28(22):4558-65 PMID: 11071946
  6. Paraneoplastic neurologic disease antigens: RNA-binding proteins and signaling proteins in neuronal degeneration.
    Annu Rev Neurosci. 2001;24:239-62 PMID: 11283311
  7. 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. 2001 May 18;276(20):17484-96 PMID: 11278705
  8. Neurotrophin-induced transport of a beta-actin mRNP complex increases beta-actin levels and stimulates growth cone motility.
    Neuron. 2001 Aug 2;31(2):261-75 PMID: 11502257
  9. An in vitro-selected RNA-binding site for the KH domain protein PSI acts as a splicing inhibitor element.
    RNA. 2001 Sep;7(9):1239-53 PMID: 11565747
  10. Structural basis for recognition of the intron branch site RNA by splicing factor 1.
    Science. 2001 Nov 2;294(5544):1098-102 PMID: 11691992
  11. The Fragile X mental retardation protein.
    Brain Res Bull. 2001 Oct-Nov 1;56(3-4):375-82 PMID: 11719275
  12. Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function.
    Cell. 2001 Nov 16;107(4):489-99 PMID: 11719189
  13. Suppression of 15-lipoxygenase synthesis by hnRNP E1 is dependent on repetitive nature of LOX mRNA 3'-UTR control element DICE.
    J Mol Biol. 2002 Feb 1;315(5):965-74 PMID: 11827469
  14. Structure and dynamics of KH domains from FBP bound to single-stranded DNA.
    Nature. 2002 Feb 28;415(6875):1051-6 PMID: 11875576
  15. Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA.
    EMBO J. 2002 Jul 1;21(13):3476-85 PMID: 12093748
  16. CLIP identifies Nova-regulated RNA networks in the brain.
    Science. 2003 Nov 14;302(5648):1212-5 PMID: 14615540
  17. Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site.
    Biochemistry. 1983 May 24;22(11):2601-10 PMID: 6347247
  18. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
    Science. 1990 Aug 3;249(4968):505-10 PMID: 2200121
  19. Absence of expression of the FMR-1 gene in fragile X syndrome.
    Cell. 1991 Aug 23;66(4):817-22 PMID: 1878973
  20. SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis.
    J Mol Biol. 1991 Dec 5;222(3):739-61 PMID: 1721092
  21. Characterization and primary structure of the poly(C)-binding heterogeneous nuclear ribonucleoprotein complex K protein.
    Mol Cell Biol. 1992 Jan;12(1):164-71 PMID: 1729596
  22. The pre-mRNA binding K protein contains a novel evolutionarily conserved motif.
    Nucleic Acids Res. 1993 Mar 11;21(5):1193-8 PMID: 8464704
  23. The protein product of the fragile X gene, FMR1, has characteristics of an RNA-binding protein.
    Cell. 1993 Jul 30;74(2):291-8 PMID: 7688265
  24. Nova, the paraneoplastic Ri antigen, is homologous to an RNA-binding protein and is specifically expressed in the developing motor system.
    Neuron. 1993 Oct;11(4):657-72 PMID: 8398153
  25. FMR1 protein: conserved RNP family domains and selective RNA binding.
    Science. 1993 Oct 22;262(5133):563-6 PMID: 7692601
  26. Tissue specific expression and cDNA structure of a human transcript encoding a nucleic acid binding [oligo(dC)] protein related to the pre-mRNA binding protein K.
    Nucleic Acids Res. 1994 Mar 25;22(6):959-64 PMID: 8152927
  27. Identity of the RNA-binding protein K of hnRNP particles with protein H16, a sequence-specific single strand DNA-binding protein.
    Nucleic Acids Res. 1994 Oct 11;22(20):4183-6 PMID: 7524036
  28. Characterisation of two major cellular poly(rC)-binding human proteins, each containing three K-homologous (KH) domains.
    Eur J Biochem. 1995 Jun 1;230(2):447-53 PMID: 7607214
  29. Identification of two KH domain proteins in the alpha-globin mRNP stability complex.
    EMBO J. 1995 Sep 1;14(17):4357-64 PMID: 7556077
  30. The onconeural antigen Nova-1 is a neuron-specific RNA-binding protein, the activity of which is inhibited by paraneoplastic antibodies.
    J Neurosci. 1996 Feb 1;16(3):1114-22 PMID: 8558240
  31. Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome.
    Cell. 1996 Apr 19;85(2):237-45 PMID: 8612276
  32. Characterization of a beta-actin mRNA zipcode-binding protein.
    Mol Cell Biol. 1997 Apr;17(4):2158-65 PMID: 9121465
  33. The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo.
    Mol Cell Biol. 1997 Jun;17(6):3194-201 PMID: 9154818
  34. mRNA silencing in erythroid differentiation: hnRNP K and hnRNP E1 regulate 15-lipoxygenase translation from the 3' end.
    Cell. 1997 May 16;89(4):597-606 PMID: 9160751
  35. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.
    Cell. 1997 May 30;89(5):781-7 PMID: 9182766
  36. Two functional complexes formed by KH domain containing proteins with the 5' noncoding region of poliovirus RNA.
    RNA. 1997 Aug;3(8):882-92 PMID: 9257647
  37. Specificity and determinants of Sam68 RNA binding. Implications for the biological function of K homology domains.
    J Biol Chem. 1997 Oct 24;272(43):27274-80 PMID: 9341174
  38. In vitro genetic analysis of the RNA binding site of vigilin, a multi-KH-domain protein.
    Mol Cell Biol. 1998 Jul;18(7):3991-4003 PMID: 9632784
  39. The neuronal RNA-binding protein Nova-2 is implicated as the autoantigen targeted in POMA patients with dementia.
    Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):13254-9 PMID: 9789075
  40. Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains.
    Structure. 1999 Feb 15;7(2):191-203 PMID: 10368286
  41. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
    J Mol Biol. 1999 May 21;288(5):911-40 PMID: 10329189
  42. Two ZBP1 KH domains facilitate beta-actin mRNA localization, granule formation, and cytoskeletal attachment.
    J Cell Biol. 2003 Jan 6;160(1):77-87 PMID: 12507992
  43. Nova-1 regulates neuron-specific alternative splicing and is essential for neuronal viability.
    Neuron. 2000 Feb;25(2):359-71 PMID: 10719891
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkh799
Published
2004-00-00
Epub
2004-00-14
Pages
4852-61
Language
English
Region
England
NLM ID
0411011
PMCID
PMC519101
Subset
IM
Grants
NIGMS NIH HHS · GM07739 · United States
NINDS NIH HHS · R01 NS040955 · United States
NINDS NIH HHS · R01 NS034389 · United States
NINDS NIH HHS · R56 NS034389 · United States
NINDS NIH HHS · NS34389 · United States
NIGMS NIH HHS · T32 GM007739 · United States
External Links
PubMed source DOI: 10.1093/nar/gkh799 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2