Identification of plu genes and cis-acting elements of PCNA in the Drosophila genus using conservation of gene order

Gene

Volumn 307, Issue 1-2, 2003, Pages 77-86

  Renault, Andrew D ^a,b   Axton, J Myles ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

DNA replication; RpS18

Indexed keywords

ANKYRIN; CIS ACTING ELEMENT;

ARTICLE; CELL CYCLE; DROSOPHILA; DROSOPHILA MELANOGASTER; GENE AMPLIFICATION; GENE IDENTIFICATION; GENE ORDER; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; INTRON; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE HOMOLOGY;

DROSOPHILA MELANOGASTER; MELANOGASTER;

EID: 0037468879     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(03)00444-X     Document Type: Article

References (39)

1. Altschul S., Madden T.A., Schaffer A., Zhang J., Zhang Z., Miller W., Lipman D. Gapped blast and PSI-blast: a new generation of protein database search programs. Nucleic Acids Res. 25:(17):1997;3389-3402.
2. Axton J.M., Shamanski F., Young L., Henderson D., Boyd J., Orr-Weaver T. The inhibitor of DNA-replication encoded by the Drosophila gene plutonium is a small, ankyrin repeat protein. EMBO J. 13:(2):1994;462-470.
3. Bailey T., Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. ISMB. 2:1994;28-36.
4. Baumgartner R., Fernandez-Catalan C., Winoto A., Huber R., Engh R., Holak T. Structure of human cyclin-dependent kinase inhibitor p19(INK4D): comparison to known ankyrin-repeat-containing structures and implications for the dysfunction of tumor suppressor p16(INK4A). Structure. 6:(10):1998;1279-1290.
5. Brower A., DeSalle R., Vogler A. Gene trees, species trees, and systematics: a cladistic perspective. Annu. Rev. Ecol. Syst. 27:1996;423-450.
6. Caccone A., Moriyama E., Gleason J., Nigro L., Powell J. A molecular phylogeny for the Drosophila melanogaster subgroup and the problem of polymorphism data. Mol. Biol. Evol. 13:(9):1996;1224-1232.
7. Cariou M. Biochemical phylogeny of the eight species in the Drosophila melanogaster subgroup, including D. sechellia and D. orena. Genet. Res. 50:(3):1987;181-185.
8. Cavener D. Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates. Nucleic Acids Res. 15:(4):1987;1353-1361.
9. Elfring L., Axton J.M., Fenger D., Page A., Carminati J., Orr-Weaver T. Drosophila Plutonium protein is a specialized cell cycle regulator required at the onset of embryogenesis. Mol. Biol. Cell. 8:(4):1997;583-593.
10. Fenger D.D., et al. PAN GU: a protein kinase that inhibits S phase and promotes mitosis in early Drosophila development. Development. 127:2000;4763-4774.
11. Fernandes M., Xiao H., Lis J. Fine structure analyses of the Drosophila and Saccharomyces heat shock factor-heat shock element interactions. Nucleic Acids Res. 22:(2):1994;167-173.
12. Freeman M., Glover D. The gnu mutation of Drosophila causes inappropriate DNA-synthesis in unfertilized and fertilized-eggs. Genes Dev. 1:(9):1987;924-930.
13. Freeman M., Nüsslein-Volhard C., Glover D. The dissociation of nuclear and centrosomal division in gnu, a mutation causing giant nuclei in Drosophila. Cell. 46:(3):1986;457-468.
14. Garwood J., Lepesant J. The Drosophila melanogaster homolog of ribosomal protein S18. Gene. 141:(2):1994;231-235.
15. Gorina S., Pavletich N. Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2. Science. 274:(5289):1996;1001-1005.
16. Hardie G., Carling D., Carlson M. The AMP-activated/SNF1 protein kinase subfamily: metabolic sensors of the eukaryotic cell? Annu. Rev. Biochem. 67:1998;821-855.
17. Harr B., Weiss S., David J., Brem G., Schlotterer C. A microsatellite-based multilocus phylogeny of the Drosophila melanogaster species complex. Curr. Biol. 8:(21):1998;1183-1186.
18. Hayashi Y., Hirose F., Nishimoto Y., Shiraki M., Yamagishi M., Matsukage A., Yamaguchi M. Identification of CFDD (common regulatory factor for DNA replication and DREF genes) and role of its binding site in regulation of the proliferating cell nuclear antigen gene promoter. J. Biol. Chem. 272:(36):1997;22848-22858.
19. Hayashi Y., Yamagishi M., Nishimoto Y., Taguchi O., Matsukage A., Yamaguchi M. A binding site for the transcription factor grainyhead/nuclear transcription factor-1 contributes to regulation of the Drosophila proliferating cell nuclear antigen gene promoter. J. Biol. Chem. 274:1999;35080-35088.
20. Hirose F., Yamaguchi M., Handa H., Inomata Y., Matsukage A. Novel-8-base pair sequence (Drosophila DNA replication-related element) and specific binding-factor involved in the expression of Drosophila genes for DNA polymerase-alpha and proliferating cell nuclear antigen. J. Biol. Chem. 268:(3):1993;2092-2099.
21. Jonsson Z., Hubscher U. Proliferating cell nuclear antigen: more than a clamp for DNA polymerases. Bioessays. 19:(11):1997;967-975.
22. Kalantzi-Makri M., Trougakos I., Tafas T., Sourdis J., Margaritis L. Phylogenetic and taxonomical relationships of the eight species in the melanogaster subgroup of the genus Drosophila (sophophora) based on the electrophoretic mobility of the major chorion proteins and the eggshell ultrastructure. J. Zool. 249:(Pt 3):1999;295-306.
23. Lachaise D., David J., Lemeunier F., Tsacas L., Ashburner M. The reproductive relationships of Drosophila sechellia with Drosophila mauritiana, Drosophila simulans, and Drosophila melanogaster from the afro-tropical region. Evolution. 40:(2):1986;262-271.
24. Lachaise D., Cariou M., David J., Lemeunier F., Tsacas L., Ashburner M. Historical biogeography of the Drosophila-melanogaster species subgroup. Evol. Biol. 22:1988;159-225.
25. McGinnis W., Beckendorf S. Association of a Drosophila transposable element of the Roo family with chromosomal deletion breakpoints. Nucleic Acids Res. 11:(3):1983;737-751.
26. Michaely P., Bennett V. The ANK repeat: a ubiquitous motif involved in macromolecular recognition. Trends Cell Biol. 2:1992;127-129.
27. Russo C., Takezaki N., Nei M. Molecular phylogeny and divergence times of Drosophilid species. Mol. Biol. Evol. 12:(3):1995;391-404.
28. Samuels-Lev Y., O'Connor D.J., Bergamaschi D., Trigiante G., Hsieh J.K., Zhong S., Campargue I., Naumovski L., Crook T., Lu X. ASPP proteins specifically stimulate the apoptotic function of p53. Mol. Cell. 8:2001;781-794.
29. Sedgwick S.G., Smerdon S.J. The ankyrin repeat: a diversity of interactions on a common structural framework. Trends Biochem. Sci. 8:1999;311-316.
30. Shamanski F., Orr-Weaver T. The Drosophila plutonium and pan gu genes regulate entry into S-phase at fertilization. Cell. 66:(6):1991;1289-1300.
31. Solignac M., Monnerot M. Race formation, speciation, and introgression within Drosophila simulans, Drosophila mauritiana, and Drosophila sechellia inferred from mitochondrial-DNA analysis. Evolution. 40:(3):1986;531-539.
32. Takahashi Y., Yamaguchi M., Hirose F., Kobayashi J., Miyajima S., Matsukage A. Involvement of the DNA replication-related element (DRE) and DRE-binding factor (DREF) in transcriptional regulation of the Bombyx mori PCNA gene. J. Biochem. 122:(6):1997;1215-1223.
33. Templeton A., Hollocher H., Johnston J. The molecular through ecological genetics of abnormal-abdomen in Drosophila mercatorum. 5. Female phenotypic-expression on natural genetic backgrounds and in natural environments. Genetics. 134:(2):1993;475-485.
34. Thompson J., Higgins D., Gibson T. CLUSTALw - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:(22):1994;4673-4680.
35. Throckmorton L. The phylogeny, ecology and geography of Drosophila. King R. Invertebrates of Genetic Interest - Handbook of Genetics. 3:1975;421-469 Plenum Press, New York and London.
36. Weekes J., Ball K.L., Caudwell F.B., Hardie D.G. Specificity determinants for the AMP-activated protein kinase and its plant homologue analysed using synthetic peptides. FEBS Lett. 334:(3):1993 Nov 22;335-339.
37. Yamaguchi M., Nishida Y., Moriuchi T., Hirose F., Hui C., Suzuki Y., Matsukage A. Drosophila proliferating cell nuclear antigen (cyclin) gene - structure, expression during development, and specific binding of homeodomain proteins to its 5′-flanking region. Mol. Cell. Biol. 10:(3):1990;872-879.
38. Yamaguchi M., Hayashi Y., Matsukage A. Essential role of E2F recognition sites in regulation of the proliferating cell nuclear antigen gene promoter during Drosophila development. J. Biol. Chem. 270:(42):1995;25159-25165.
39. Yamaguchi M., Hirose F., Matsukage A. Roles of multiple promoter elements of the proliferating cell nuclear antigen gene during Drosophila development. Genes Cells. 1:(1):1996;47-58.