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Search for proteins with similarity to the CFTR R domain using an optimized RDBMS solution, mBioSQL

  • Research Article
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Central European Journal of Biology

Abstract

The cystic fibrosis transmembrane conductance regulator (CFTR) comprises ATP binding and transmembrane domains, and a unique regulatory (R) domain not found in other ATP binding cassette proteins. Phosphorylation of the R domain at different sites by PKA and PKC is obligatory for the chloride channel function of CFTR. Sequence similarity searches on the R domain were uninformative. Furthermore, R domains from different species show low sequence similarity. Since these R domains resemble each other only in the location of the phosphorylation sites, we generated different R domain patterns masking amino acids between these sites. Because of the high number of the generated patterns we expected a large number of matches from the UniProt database. Therefore, a relational database management system (RDBMS) was set up to handle the results. During the software development our system grew into a general package which we term Modular BioSQL (mBioSQL). It has higher performance than other solutions and presents a generalized method for the storage of biological result-sets in RDBMS allowing convenient further analysis. Application of this approach revealed that the R domain phosphorylation pattern is most similar to those in nuclear proteins, including transcription and splicing factors.

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References

  1. J.R. Riordan et al.: “Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA”, Science, Vol. 245, (1989), pp. 1066–1073.

    PubMed  CAS  Google Scholar 

  2. Y.H. Ko and P.L. Pedersen: “Cystic fibrosis: a brief look at some highlights of a decade of research focused on elucidating and correcting the molecular basis of the disease”, J. Bioenerg. Biomembr., Vol. 33, (2001), pp. 513–521.

    Article  PubMed  CAS  Google Scholar 

  3. S.H. Cheng et al.: “Phosphorylation of the R domain by cAMP-dependent protein kinase regulates the CFTR chloride channel”, Cell, Vol. 66, (1991), pp. 1027–1036.

    Article  PubMed  CAS  Google Scholar 

  4. F.S. Seibert et al.: “Influence of phosphorylation by protein kinase A on CFTR at the cell surface and endoplasmic reticulum”, Biochim. Biophys. Acta, Vol. 1461, (1999), pp. 275–283.

    Article  PubMed  CAS  Google Scholar 

  5. L. Csanady et al.: “Preferential phosphorylation of R-domain Serine 768 dampens activation of CFTR channels by PKA”, J. Gen. Physiol., Vol. 125, (2005), pp. 171–186.

    Article  PubMed  CAS  Google Scholar 

  6. D.C. Gadsby and A.C. Nairn: “Control of CFTR channel gating by phosphorylation and nucleotide hydrolysis”, Physiol. Rev., Vol. 79, (1999), pp. S77–S107.

    PubMed  CAS  Google Scholar 

  7. C. Li et al.: “ATPase activity of the cystic fibrosis transmembrane conductance regulator”, J. Biol. Chem., Vol. 271, (1996), pp. 28463–28468.

    Article  PubMed  CAS  Google Scholar 

  8. J.R. Riordan: “Assembly of functional CFTR chloride channels”, Annu. Rev. Physiol., Vol. 67, (2005), pp. 701–718.

    Article  PubMed  CAS  Google Scholar 

  9. D.P. Rich et al.: “Regulation of the cystic fibrosis transmembrane conductance regulator Cl-channel by negative charge in the R domain”, J. Biol. Chem., Vol. 268, (1993), pp. 20259–20267.

    PubMed  CAS  Google Scholar 

  10. V. Chappe et al.: “Phosphorylation of CFTR by PKA promotes binding of the regulatory domain”, Embo. J., Vol. 24, (2005), pp. 2730–2740.

    Article  PubMed  CAS  Google Scholar 

  11. A.M. Dulhanty and J.R. Riordan: “A two-domain model for the R domain of the cystic fibrosis transmembrane conductance regulator based on sequence similarities”, FEBS Lett., Vol. 343, (1994), pp. 109–114.

    Article  PubMed  CAS  Google Scholar 

  12. A.M. Dulhanty and J.R. Riordan: “Phosphorylation by cAMP-dependent protein kinase causes a conformational change in the R domain of the cystic fibrosis transmembrane conductance regulator”, Biochemistry Vol. 33, (1994), pp. 4072–4079.

    Article  PubMed  CAS  Google Scholar 

  13. L.S. Ostedgaard et al.: “A functional R domain from cystic fibrosis transmembrane conductance regulator is predominantly unstructured in solution”, Proc. Natl. Acad. Sci. USA Vol. 97, (2000), pp. 5657–5662.

    Article  PubMed  CAS  Google Scholar 

  14. J.E. Stajich et al.: “The Bioperl toolkit: Perl modules for the life sciences”, Genome. Res., Vol. 12, (2002), pp. 1611–1618.

    Article  PubMed  CAS  Google Scholar 

  15. A. Bairoch et al.: “The Universal Protein Resource (UniProt)”, Nucleic Acids Res., Vol. 33, (2005), pp. D154–D159.

    Article  PubMed  CAS  Google Scholar 

  16. C. del Val et al.: “High-throughput protein analysis integrating bioinformatics and experimental assays”, Nucleic Acids Res. Vol. 32, (2004), pp. 742–748.

    Article  PubMed  CAS  Google Scholar 

  17. E.L. Grogan et al.: “Volatility: a new vital sign identified using a novel bedside monitoring strategy”, J. Trauma., Vol. 58, (2005), pp. 7–12; discussion 12-14.

    Article  PubMed  Google Scholar 

  18. L.S. Ostedgaard, O. Baldursson and M.J. Welsh: “Regulation of the cystic fibrosis transmembrane conductance regulator Cl-channel by its R domain”, J. Biol. Chem., Vol. 276, (2001), pp. 7689–7692.

    Article  PubMed  CAS  Google Scholar 

  19. V. Chappe et al.: “Stimulatory and inhibitory protein kinase C consensus sequences regulate the cystic fibrosis transmembrane conductance regulator”, Proc. Natl. Acad. Sci. USA, Vol. 101, (2004), pp. 390–395.

    Article  PubMed  CAS  Google Scholar 

  20. L. Csanady et al.: “Functional roles of nonconserved structural segments in CFTR’s NH2-terminal nucleotide binding domain”, J. Gen. Physiol., Vol. 125, (2005), pp. 43–55.

    Article  PubMed  CAS  Google Scholar 

  21. L. Wei et al.: “The C-terminal part of the R-domain, but not the PDZ binding motif, of CFTR is involved in interaction with Ca(2+)-activated Cl-channels”, Pflugers Arch. Vol. 442, (2001), pp. 280–285.

    Article  PubMed  CAS  Google Scholar 

  22. S.B. Ko et al.: “Gating of CFTR by the STAS domain of SLC26 transporters”, Nat. Cell. Biol. Vol. 6, (2004), pp. 343–350.

    Article  PubMed  CAS  Google Scholar 

  23. D.B. Mount and M.F. Romero: “The SLC26 gene family of multifunctional anion exchangers”, Pflugers Arch., Vol. 447, (2004), pp. 710–721.

    Article  PubMed  CAS  Google Scholar 

  24. M.J. Hug, T. Tamada and R.J. Bridges: “CFTR and bicarbonate secretion by [correction of to] epithelial cells”, News Physiol. Sci. Vol. 18, (2003), pp. 38–42.

    PubMed  CAS  Google Scholar 

  25. A. Hemminki et al.: “Intestinal cancer in patients with a germline mutation in the down-regulated in adenoma (DRA) gene”, Oncogene, Vol. 16, (1998), pp. 681–684.

    Article  PubMed  CAS  Google Scholar 

  26. J.M. Chapman et al.: “The colon anion transporter, down-regulated in adenoma, induces growth suppression that is abrogated by E1A”, Cancer Res. Vol. 62, (2002), pp. 5083–5088.

    PubMed  CAS  Google Scholar 

  27. E.M. Schwiebert et al.: “CFTR is a conductance regulator as well as a chloride channel”, Physiol. Rev. Vol. 79, (1999), pp. S145–S166.

    PubMed  CAS  Google Scholar 

  28. K. Kunzelmann: “CFTR: interacting with everything?”, News Physiol. Sci. Vol. 16, (2001), pp. 167–170.

    PubMed  CAS  Google Scholar 

  29. A.P. Naren et al.: “A macromolecular complex of beta 2 adrenergic receptor, CFTR, and ezrin/radixin/moesin-binding phosphoprotein 50 is regulated by PKA”, Proc. Natl. Acad. Sci. USA, Vol. 100, (2003), pp. 342–346.

    Article  PubMed  CAS  Google Scholar 

  30. A.R. Cantrell et al.: “Molecular mechanism of convergent regulation of brain Na(+) channels by protein kinase C and protein kinase A anchored to AKAP-15”, Mol. Cell. Neurosci. Vol. 21, (2002), pp. 63–80.

    Article  PubMed  CAS  Google Scholar 

  31. W.B. Thornhill and S.R. Levinson: “Biosynthesis of ion channels in cell-free and metabolically labeled cell systems”, Methods Enzymol Vol. 207, (1992), pp. 659–670.

    Article  PubMed  CAS  Google Scholar 

  32. S. Pind„ J.R. Riordan and D.B. Williams: “Participation of the endoplasmic reticulum chaperone calnexin (p88, IP90) in the biogenesis of the cystic fibrosis transmembrane conductance regulator”, J. Biol. Chem., Vol. 269, (1994), pp. 12784–12788.

    PubMed  CAS  Google Scholar 

  33. S.P. Shah et al.: “Atlas — a data warehouse for integrative bioinformatics”, BMC Bioinformatics, Vol. 6, (2005), pp. 34.

    Article  PubMed  CAS  Google Scholar 

  34. G. Xie et al.: “Storing biological sequence databases in relational form”, Bioinformatics, Vol. 16, (2000), pp. 288–289.

    Article  PubMed  CAS  Google Scholar 

  35. J. Kohler, S. Philippi and M. Lange: “SEMEDA: ontology based semantic integration of biological databases”, Bioinformatics, Vol. 19, (2003), pp. 2420–2427.

    Article  PubMed  CAS  Google Scholar 

  36. S. Philippi: “Light-weight integration of molecular biological databases”, Bioinformatics, Vol. 20, (2004), pp. 51–57.

    Article  PubMed  CAS  Google Scholar 

  37. S. Stephens: “Data Integration and Knowledge Aggregation in Life Sciences Discovery”, Scientific Comput. Instrum. Vol. 21, (2005).

  38. G. Finak et al.: “BIAS: Bioinformatics Integrated Application Software”, Bioinformatics, Vol. 21, (2005), pp. 1745–1746.

    Article  PubMed  CAS  Google Scholar 

  39. S.A. Kirov et al.: “GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments”, BMC Bioinformatics, Vol. 6, (2005), pp. 72.

    Article  PubMed  CAS  Google Scholar 

  40. S.P. Shah et al.: “Pegasys: software for executing and integrating analyses of biological sequences”, BMC Bioinformatics Vol. 5, (2004), pp. 40.

    Article  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Biochemistry & Biophysics and Cystic Fibrosis T&R Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA

    Tamás Hegedűs & John R. Riordan

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  1. Tamás Hegedűs
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  2. John R. Riordan
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Correspondence to Tamás Hegedűs.

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Hegedűs, T., Riordan, J.R. Search for proteins with similarity to the CFTR R domain using an optimized RDBMS solution, mBioSQL. cent.eur.j.biol. 1, 29–42 (2006). https://doi.org/10.2478/s11535-006-0003-9

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  • DOI: https://doi.org/10.2478/s11535-006-0003-9

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