In Silico characterization of phosphorylase kinase: Evidence for an alternate intronic polyadenylation site in PHKG1

Molecular Genetics and Metabolism

Volumn 92, Issue 3, 2007, Pages 234-242

  Winchester, Joni S ^a   Rouchka, Eric C ^b   Rowland, Naomi S ^a   Rice, Nancy A ^a  

^a WESTERN KENTUCKY UNIVERSITY   (United States)

^b University of Louisville   (United States)

Author keywords

Alternative splicing; Composite exon; PHKG1; Phosphorylase kinase; Polyadenylation

Indexed keywords

MESSENGER RNA; PHOSPHORYLASE KINASE;

ARTICLE; CATALYSIS; COMPUTER MODEL; EXON; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; HUMAN; IN VIVO STUDY; INTRON; NUCLEOTIDE SEQUENCE; ORGAN DISTRIBUTION; POLYADENYLATION; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; PHOSPHORYLASE KINASE; POLYADENYLATION; RNA, MESSENGER; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; TISSUE DISTRIBUTION;

EID: 34948850295     PISSN: 10967192     EISSN: 10967206     Source Type: Journal    
DOI: 10.1016/j.ymgme.2007.06.015     Document Type: Article

References (46)

1. Pickett-Gies C.R., and Walsh D.A. In: Boyer P.D.a.K., and Krebs E.G. (Eds). The Enzymes. third ed. vol. 17 (1986), Academic Press, Orlando 395-459
2. Brushia R.J., and Walsh D.A. Phosphorylase kinase: the complexity of its regulation is reflected in the complexity of its structure. Front. Biosci. 4 (1999) D618-D641
3. Francke U., et al. Assignment of human genes for phosphorylase kinase subunits alpha (PHKA) to Xq12-q13 and beta (PHKB) to 16q12-q13. Am. J. Hum. Genet. 45 2 (1989) 276-282
4. Davidson J.J., et al. cDNA cloning of a liver isoform of the phosphorylase kinase alpha subunit and mapping of the gene to Xp22.2-p22.1 the region of human X-linked liver glycogenosis. Proc. Natl. Acad. Sci. USA 89 6 (1992) 2096-2100
5. Geng Y., et al. Mapping of a liver phosphorylase kinase alpha-subunit gene on the mouse X chromosome. Genomics 15 1 (1993) 191-193
6. Jones T.A., et al. Localisation of the gene encoding the catalytic gamma subunit of phosphorylase kinase to human chromosome bands 7p12-q21. Biochim. Biophys. Acta 1048 1 (1990) 24-29
7. Burwinkel B., et al. Variability of biochemical and clinical phenotype in X-linked liver glycogenosis with mutations in the phosphorylase kinase PHKA2 gene. Hum. Genet. 102 4 (1998) 423-429
8. 2+dependent modulator protein as the fourth subunit of rabbit skeletal muscle phosphorylase kinase. FEBS Lett. 92 2 (1978) 287-293
9. Berchtold M.W., et al. Localization of the human bona fide calmodulin genes CALM1 CALM2 and CALM3 to chromosomes 14q24-q31, 2p21.1-p21.3, and 19q13.2-q13.3. Genomics 16 2 (1993) 461-465
10. Kobayashi T., et al. Phosphorylation of myelin basic protein by glycogen phosphorylase kinase. FEBS Lett. 169 2 (1984) 224-228
11. Ozawa E. Activation of phosphorylase kinase from brain by small amounts of calcium ion. J. Neurochem. 20 5 (1973) 1487-1488
12. Paudel H.K. The regulatory Ser262 of microtubule-associated protein tau is phosphorylated by phosphorylase kinase. J. Biol. Chem. 272 3 (1997) 1777-1785
13. Paudel H.K., Zwiers H., and Wang J.H. Phosphorylase kinase phosphorylates the calmodulin-binding regulatory regions of neuronal tissue-specific proteins B-50 (GAP-43) and neurogranin. J. Biol. Chem. 268 9 (1993) 6207-6213
14. Psarra A.M., and Sotiroudis T.G. Subcellular distribution of phosphorylase kinase in rat brain. Association of the enzyme with mitochondria and membranes. Int. J. Biochem. Cell Biol. 28 1 (1996) 29-42
15. Liu L., et al. The testis isoform of the phosphorylase kinase catalytic subunit (PhK-gammaT) plays a critical role in regulation of glycogen mobilization in developing lung. J. Biol. Chem. 271 20 (1996) 11761-11766
16. Bakker H.D., et al. Hepatic phosphorylase b kinase deficiency with normal enzyme activity in leukocytes and erythrocytes. J. Inherit. Metab. Dis. 14 2 (1991) 269-270
17. Bashan N., et al. Phosphorylase kinase in leukocytes and erythrocytes of a patient with glycogen storage disease type IX. J. Inherit. Metab. Dis. 10 2 (1987) 119-127
18. Kikuchi M., et al. Enzymatic analysis in lymphocytes and erythrocytes from six patients with different phenotypes of phosphorylase kinase deficiency. J. Inherit. Metab. Dis. 11 3 (1988) 315-318
19. Morishita Y., et al. Hepatic phosphorylase kinase deficiency: a survey of phosphorylase kinase activity in erythrocytes. Kobe J. Med. Sci. 24 4 (1978) 211-222
20. Harmann B., Zander N.F., and Kilimann M.W. Isoform diversity of phosphorylase kinase alpha and beta subunits generated by alternative RNA splicing. J. Biol. Chem. 266 24 (1991) 15631-15637
21. Wullrich A., et al. The multiphosphorylation domain of the phosphorylase kinase alpha M and alpha L subunits is a hotspot of differential mRNA processing and of molecular evolution. J. Biol. Chem. 268 31 (1993) 23208-23214
22. Boguski M.S., Lowe T.M.J., and Tolstoshev C.M. dbEST-database for "expressed sequence tags". Nat. Genet. 4 4 (1993) 332-333
23. Meyer W.L., Fischer E.H., and Krebs E.G. Activation of skeletal muscle phosphorylase B kinase by Ca. Biochemistry 3 (1964) 1033-1039
24. 2+. J. Biol. Chem. 246 7 (1971) 1961-1967
25. Burks C., Cassidy M., Cinkosky M.J., Cumella K.E., Gilna P., Hayden J.E., Keen G.M., Kelley T.A., Kelly M., Kristofferson D., and Ryals J. GenBank. Nucleic Acids Res. 19 Suppl. (1991) 2221-2225
26. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 3 (1990) 403-410
27. Wheeler D.L., Barrett T., Benson D.A., Bryant S.H., Canese K., Chetvernin V., Church D.M., DiCuccio M., Edgar R., Federhen S., Geer L.Y., Kapustin Y., Khovayko O., Landsman D., Lipman D.J., Madden T.L., Maglott D.R., Ostell J., Miller V., Pruitt K.D., Schuler G.D., Sequeira E., Sherry S.T., Sirotkin K., Souvorov A., Starchenko G., Tatusov R.L., Tatusova T.A., Wagner L., and Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 35 (2007) D5-D12
28. Higgins D.G., and Sharp P.M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73 1 (1988) 237-244
29. Florea L., et al. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8 9 (1998) 967-974
30. Pruitt K.D., Tatusova T., and Maglott D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35 suppl_1 (2007) D61-D65
31. Colgan D.F., and Manley J.L. Mechanism and regulation of mRNA polyadenylation. Genes Dev. 11 21 (1997) 2755-2766
32. Gilmartin G.M. Eukaryotic mRNA 3′ processing: a common means to different ends. Genes Dev. 19 21 (2005) 2517-2521
33. Zhang H., Lee J., and Tian B. Biased alternative polyadenylation in human tissues. Genome Biology 6 12 (2005) R100
34. Yan J., and Marr T.G. Computational analysis of 3'-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. Genome Res. 15 3 (2005) 369-375
35. Bairoch A. PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res. 19 Suppl. (1991) 2241-2245
36. Edwalds-Gilbert G., Veraldi K.L., and Milcarek C. Alternative poly(A) site selection in complex transcription units: means to an end?. Nucleic Acids Res. 25 13 (1997) 2547-2561
37. Ayers N. Interactions of the Alpha Subunit of Phosphorylase-b Kinase in Biochemistry (1999), University of Tennessee, Memphis p. 154.
38. Archila S., et al. The cytoskeletal organizing protein Cdc42-interacting protein 4 associates with phosphorylase kinase in skeletal muscle. Biochem. Biophys. Res. Commun. 345 4 (2006) 1592-1599
39. Watson J.D., Myers R.M., Caudy A.A., and Witkowski J.A. Recombinant DNA. third ed. (2007), W.H. Freeman and Company, New York 474
40. Lowe E.D., et al. The crystal structure of a phosphorylase kinase peptide substrate complex: kinase substrate recognition. EMBO J. 16 22 (1997) 6646-6658
41. Owen D.J., et al. Two structures of the catalytic domain of phosphorylase kinase: an active protein kinase complexed with substrate analogue and product. Structure 3 5 (1995) 467-482
42. Taylor S.S., and Radzio-Andzelm E. Three protein kinase structures define a common motif. Structure 2 5 (1994) 345-355
43. Sanchez V.E., and Carlson G.M. Isolation of an autoinhibitory region from the regulatory beta-subunit of phosphorylase kinase. J. Biol. Chem. 268 24 (1993) 17889-17895
44. Nadeau O.W., Sacks D.B., and Carlson G.M. Differential affinity cross-linking of phosphorylase kinase conformers by the geometric isomers of phenylenedimaleimide. J. Biol. Chem. 272 42 (1997) 26196-26201
45. Skuster J.R., Chan K.F., and Graves D.J. Isolation and properties of the catalytically active gamma subunit of phosphorylase b kinase. J. Biol. Chem. 255 5 (1980) 2203-2210
46. Lorenz M., et al. Alternative splicing in intron 13 of the human eNOS gene: a potential mechanism for regulating eNOS activity. FASEB J. (2007) p. fj.06-7434com