QKI-NTRK2, quaking with a kinase

The QKI-NTRK2 fusion was mentioned in a report of somatic mutations in pilocytic astrocytoma, the most common childhood brain tumor (Jones 2013). The protein quaking encoded by the QKI gene is an RNA-binding protein. The many splice variations of quaking are making  news in PubMed as miRNA binding/processing proteins.  For now we will concern ourselves with how quaking dimerizes and can activate the kinase domain of TrkB.

Diseases caused by variations in the QKI gene (UniProt unless otherwise noted)

  • 6Q Terminal Deletion Syndrome.
  • schizophrenia.
  • As an aside, QKI got its name from the severe dysmyelination “quaking” mouse phenotype.  The splice variant distribution has been studied in the mouse (Hardy 1996).

Function of protein quaking the QKI gene product (UniProt and genecards.org unless otherwise noted)

  • 3′-UTR-mediated mRNA destabilization.
  • long-chain fatty acid biosynthetic process.
  • mRNA processing.
  • mRNA transport.
  • Muscle cell differentiation.
  • Myelination in the mouse the quaking protein binds to a hexameric sequence of the mylelin basic protein mRNA controlling when and where it is translated into protein (Carmel 2010).
  • Positive regulation of gene expression.
  • RNA splicing.
  • Spermatid development.
  • Vasculogenesis.
    Protein quaking and trkb protein expression levels in various tissues

    Tissue specific expression of protein quaking and TrkB.

    Even though protein quaking is most recognized for its role in myelination, its expression is pretty ubiquitous.

    QKI and NTRK2, the genes

    Note that the QKI gene is located in the same region as fragile site FRA6B: 6q25.1 or 6q26 (Cunliffe 1987)

    Ensembl chromossome diagram showing location of QKI and NTRK2 gene on chromosome 6 and 9 resepectivelyqk1-ntrk2chromosomes.

    Chromosome location of QKI and NTRK2.

    The QKI gene is located after fragile site, FRA6E (Lee 2011).  These authors discuss how loss of the terminal 6q region can explain mental disabilities and other neurological proteins.

    Protein Quaking and TrkB the fusion protein

    The location of the splice sites were obtained by translating the nucleotide sequences of the fusion (Jones 2013). In the case of “protein quaking”, the amino acid number refers to the entire protein coding region as if splicing did not occur.

  • The N-terminal of protein quaking (QKI gene product) has been crystallized bound to its RNA binding partner (Teplova 2015).
  • The UniPort.org entry has not accounted for a  large region of protein quaking.
  • An entry from NCBI/GenBank is added to the UniProt table.
  • Carmel and coworkers (2015) proposed one site symmetrical hexameric binding and asymmetrical binding in which each monomer binds either a high or a lower affinity secondary site.
  • Unique C-terminal sequences of protein quaking splice variants are also shown.

 

  • Cartoon showing domains of protein quaking and TrkB. Inset diagram also show interaction between structural components of TrkB with Qua2 and Qua1.

    Protein domains of protein quaking and TrkB.

    The pink highlighted amino acids in the six protein quaking C-termini were obtained from Jones 2013.  The amino acid numbers are based on individual splice variant/isoform sequences.

    • Isoforms 3 and 4 would be missing only a small portion of the C-terminus in the fusion protein.
    • Isoforms 5 and 6 would lose much more of the C-terminus  in the fusion protein with TrkB.

    Aside from the loss of the C-terminal nuclear localization signal in the TrkB fusion in some isoforms of protein quaking, the possibility exists that the presence of TrkB could interfere with mRNA binding to the protein quaking fusion partner.

    Diagram showing structure of QKI and TrkB.

    A closer look at domains of protein quaking and the kinase domain of TrkB.

     

    A. From Teplova 2015, The structure of the splice variant of protein quaking  and RNA used for crystallography
    B. Ribbon diagrams of QKI and the kinase domain of TrkB from RCSB.org.  Protein quaking, left panel, is red.  The mRNA is blue.  Right panel is the kinase domain of TrkB.  C. Space fill diagrams of the same to show approximate sizes.

    What we do not know

  • The splicing of the protein quaking transcript when it is fused to the TrkB kinase domain transcript
  • The affinity and selectivity of protein quaking for target mRNA untranslated regions when it is part of a fusion protein.
  • If the presence of protein quaking influences the localization of TrkB kinase domain and its interaction with substrates such as phospholipase Cγ.

Ongoing Clinical Trials

  • There is an open TRK fusion clinical trial that is actively enrolling any solid tumor patient with NTRK fusions (STARTRK-2).   For more information go to the NTRK trial website.

 

References:

Carmel AB, Wu J, Lehmann-Blount KA, Williamson JR. (2010) High-affinity consensus binding of target RNAs by the STAR/GSG proteins GLD-1, STAR-2 and Quaking. BMC Mol Biol. 2010 Jun 23;11:48. PubMed

Cunliffe V, Trowsdale J. (1987) The molecular genetics of human chromosome 6. J Med Genet. 24(11):649-58.  PubMed

Hardy RJ, Loushin CL, Friedrich VL Jr, Chen Q, Ebersole TA, Lazzarini RA, Artzt K. (1996) Neural cell type-specific expression of QKI proteins is altered in quaking viable mutant mice. J Neurosci. 16(24):7941-9. PubMed

Jones DT, Hutter B, Jäger N, Korshunov A, Kool M, Warnatz HJ, Zichner T, Lambert SR, Ryzhova M, Quang DA, Fontebasso AM, Stütz AM, Hutter S, Zuckermann M, Sturm D, Gronych J, Lasitschka B, Schmidt S, Seker-Cin H, Witt H, Sultan M, Ralser M, Northcott PA, Hovestadt V, Bender S, Pfaff E, Stark S, Faury D, Schwartzentruber J, Majewski J, Weber UD, Zapatka M, Raeder B, Schlesner M, Worth CL, Bartholomae CC, von Kalle C, Imbusch CD, Radomski S, Lawerenz C, van Sluis P, Koster J, Volckmann R, Versteeg R, Lehrach H, Monoranu C, Winkler B, Unterberg A, Herold-Mende C, Milde T, Kulozik AE, Ebinger M, Schuhmann MU, Cho YJ, Pomeroy SL, von Deimling A, Witt O, Taylor MD, Wolf S, Karajannis MA, Eberhart CG, Scheurlen W, Hasselblatt M, Ligon KL, Kieran MW, Korbel JO, Yaspo ML, Brors B, Felsberg J, Reifenberger G, Collins VP, Jabado N, Eils R, Lichter P(2013) Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat Genet. 45(8):927-3. PubMed

Lee JY, Cho YH, Hallford G. (2011) Delineation of subtelomeric deletion of the long arm of chromosome 6. Ann Hum Genet. 75(6):755-64. PubMed

Teplova M, Hafner M, Teplov D, Essig K, Tuschl T, Patel DJ.(2013)Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites. Genes Dev. 27(8):928-40. PubMed

Further Reading

The role of protein quaking  splice variants in the transition from proliferative to myelinating phenotypes has not been addressed. Wildtype protein quaking seems to function as a tumor suppressor according to some literature reports.  It is possible the presence of a fusion partner interferes with this function.

Bockbrader K, Feng Y. (2008) Essential function, sophisticated regulation and pathological impact of the selective RNA-binding protein QKI in CNS myelin development. Future Neurol. 3(6):655-668.  PubMed

The following review is focused on the oligodendrocyte and protein quaking in their differentiation.  Some of the mRNA targets involved in the myelination process are also introduced.

Yang G, Fu H, Zhang J, Lu X, Yu F, Jin L, Bai L, Huang B, Shen L, Feng Y, Yao L, Lu Z. (2010) RNA-binding protein quaking, a critical regulator of colon epithelial differentiation and a suppressor of colon cancer. Gastroenterology. 138(1):231-40.e1-5.  PubMed

Another review discusses the potential role of splice variants of protein quaking.  (1) The expression of the cytoskeletal protein β-catenin is influenced by protein quaking splice variants 5 and 6. (2) Protein quaking  regulates  cyclin dependent protein kinase inhibitor (p27). (3) The promoter of the QKI gene is regulated by methylation.

Zhao Y, Zhang G, Wei M, Lu X, Fu H, Feng F, Wang S, Lu W, Wu N, Lu Z, Yuan J. (2014) The tumor suppressing effects of QKI-5 in prostate cancer: a novel diagnostic and prognostic protein. Cancer Biol Ther. 15(1):108-18.  PubMed

 

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