Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains

Nucleic Acids Research

Volumn 33, Issue 13, 2005, Pages 3994-4006

  Balaji, S ^a   Madan Babu, M ^a   Iyer, Lakshminarayan M ^a   Aravind, L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APETALA2 INTEGRASE DNA BINDING PROTEIN; DNA BINDING PROTEIN; PROTOZOAL DNA; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; HOMEODOMAIN PROTEIN; INTEGRASE; NUCLEAR PROTEIN; VEGETABLE PROTEIN;

ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CRYPTOSPORIDIUM; EUKARYOTE EVOLUTION; GENE EXPRESSION REGULATION; GENE SEQUENCE; HOST PARASITE INTERACTION; LIFE CYCLE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMODIUM; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; STRUCTURE ANALYSIS; THEILERIA; TRANSCRIPTION REGULATION; AMINO ACID SEQUENCE; ANIMAL; APICOMPLEXA; CHEMISTRY; GENE EXPRESSION; GENETICS; GENOMICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR GENETICS; PHYSIOLOGY; PLASMODIUM FALCIPARUM; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

APICOMPLEXA; BOS TAURUS; CRYPTOSPORIDIUM; EUKARYOTA; PLASMODIUM (APICOMPLEXA); PLASMODIUM FALCIPARUM; THEILERIA;

AMINO ACID SEQUENCE; ANIMALS; APICOMPLEXA; CRYPTOSPORIDIUM; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENOMICS; HOMEODOMAIN PROTEINS; INTEGRASES; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PLANT PROTEINS; PLASMODIUM FALCIPARUM; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; THEILERIA; TRANSCRIPTION FACTORS;

EID: 23144448511     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki709     Document Type: Article

References (70)

1. Lodish,H., Berk,A., Zipursky,S.L., Matsudaira,P., Baltimore,D. and Darnell,J.E. (1999) Molecular Cell Biology. W.H. Freeman & Co., NY.
2. Cramer,P. (2002) Common structural features of nucleic acid polymerases. Bioessays, 24, 724-729.
3. Iyer,L.M., Koonin,E.V. and Aravind,L. (2003) Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. BMC Struct. Biol., 3, 1.
4. Borukhov,S. and Nudler,E. (2003) RNA polymerase holoenzyme: Structure, function and biological implications. Curr. Opin. Microbiol., 6, 93-100.
5. Langer,D., Hain,J., Thuriaux,P. and Zillig,W. (1995) Transcription in archaea: Similarity to that in eucarya. Proc. Natl Acad. Sci. USA, 92, 5768-5772.
6. Losick,R. (1998) Summary: Three decades after sigma. Cold Spring Harb. Symp. Quant. Biol., 63, 653-666.
7. Gross,C.A., Chan,C., Dombroski,A., Gruber,T., Sharp,M., Tupy,J. and Young,B. (1998) The functional and regulatory roles of sigma factors in transcription. Cold Spring Harb. Symp. Quant. Biol., 63, 141-155.
8. Fassler,J.S. and Gussin,G.N. (1996) Promoters and basal transcription machinery in eubacteria and eukaryotes: Concepts, definitions, and analogies. Methods Enzymol., 273, 3-29.
9. Bell,S.D. and Jackson,S.P. (1998) Transcription and translation in Archaea: A mosaic of eukaryal and bacterial features. Trends Microbiol., 6, 222-228.
10. Bell,S.D., Jaxel,C., Nadal,M., Kosa,P.F. and Jackson,S.P. (1998) Temperature, template topology, and factor requirements of archaeal transcription. Proc. Natl Acad. Sci. USA, 95, 15218-15222.
11. Aravind,L. and Koonin,E.V. (1999) DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res., 27, 4658-4670.
12. Aravind,L., Anantharaman,V., Balaji,S., Babu,M.M. and Iyer,L.M. (2005) The many faces of the helix-turn-helix domain: Transcription regulation and beyond. FEMS Microbiol. Rev., 29, 231-262.
13. Englbrecht,C.C., Schoof,H. and Bohm,S. (2004) Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics, 5, 39.
14. Grishin,N.V. (2001) Treble clef finger - a functionally diverse zinc-binding structural motif. Nucleic Acids Res., 29, 1703-1714.
15. Riechmann,J.L., Heard,J., Martin,G., Reuber,L., Jiang,C., Keddie,J., Adam,L., Pineda,O., Ratcliffe,O.J., Samaha,R.R. et al. (2000) Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes. Science, 290, 2105-2110.
16. Schjerling,P. and Holmberg,S. (1996) Comparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators. Nucleic Acids Res., 24, 4599-4607.
17. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
18. Chervitz,S.A., Aravind,L., Sherlock,G., Ball,C.A., Koonin,E.V., Dwight,S.S., Harris,M.A., Dolinski,K., Mohr,S., Smith,T. et al. (1998) Comparison of the complete protein sets of worm and yeast: Orthology and divergence. Science, 282, 2022-2028.
19. Lespinet,O., Wolf,Y.I., Koonin,E.V. and Aravind,L. (2002) The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res., 12, 1048-1059.
20. Doerks,T., Copley,R.R., Schultz,J., Ponting,C.P. and Bork,P. (2002) Systematic identification of novel protein domain families associated with nuclear functions. Genome Res., 12, 47-56.
21. Aravind,L. and Subramanian,G. (1999) Origin of multicellular eukaryotes - insights from proteome comparisons. Curr. Opin. Genet Dev., 9, 688-694.
22. Aravind,L., Iyer,L.M., Wellems,T.E. and Miller,L.H. (2003) Plasmodium biology: Genomic gleanings. Cell, 115, 771-785.
23. Templeton,T.J., Iyer,L.M., Anantharaman,V., Enomoto,S., Abrahante,J.E., Subramanian,G.M., Hoffman,S.L., Abrahamsen,M.S. and Aravind,L. (2004) Comparative analysis of apicomplexa and genomic diversity in eukaryotes. Genome Res., 14, 1686-1695.
24. Coulson,R.M., Hall,N. and Ouzounis,C.A. (2004) Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res., 14, 1548-1554.
25. Le Roch,K.G., Zhou,Y., Blair,P.L., Grainger,M., Moch,J.K., Haynes,J.D., De La Vega,P., Holder,A.A., Batalov,S., Carucci,D.J. and Winzeler,E.A. (2003) Discovery of gene function by expression profiling of the malaria parasite life cycle. Science, 301, 1503-1508.
26. Bozdech,Z., Llinas,M., Pulliam,B.L., Wong,E.D., Zhu,J. and DeRisi,J.L. (2003) The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol., 1, E5.
27. Wessler,S.R. (2005) Homing into the origin of the AP2 DNA binding domain. Trends Plant Sci., 10, 54-56.
28. Magnani,E., Sjolander,K. and Hake,S. (2004) From endonucleases to transcription factors: Evolution of the AP2 DNA binding domain in plants. Plant Cell, 16, 2265-2277.
29. Wuitschick,J.D., Lindstrom,P.R., Meyer,A.E. and Karrer,K.M. (2004) Homing endonucleases encoded by germ line-limited genes in Tetrahymena thermophila have APETELA2 DNA binding domains. Eukaryot. Cell, 3, 685-694.
30. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
31. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
32. Schaffer,A.A., Aravind,L., Madden,T.L., Shavirin,S., Spouge,J.L., Wolf,Y.I., Koonin,E.V. and Altschul,S.F. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
33. Wootton,J.C. (1994) Non-globular domains in protein sequences: Automated segmentation using complexity measures. Comput. Chem., 18, 269-285.
34. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
35. Edgar,R.C. (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
36. Cuff,J.A., Clamp,M.E., Siddiqui,A.S., Finlay,M. and Barton,G.J. (1998) JPred: A consensus secondary structure prediction server. Bioinformatics, 14, 892-893.
37. Cuff,J.A. and Barton,G.J. (2000) Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins, 40, 502-511.
38. Guex,N. and Peitsch,M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
39. Delano,W.L. (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA.
40. Holm,L. and Sander,C. (1995) Dali: A network tool for protein structure comparison. Trends Biochem. Sci., 20, 478-480.
41. Holm,L. and Sander,C. (1996) The FSSP database: Fold classification based on structure-structure alignment of proteins. Nucleic Acids Res., 24, 206-209.
42. Krissinel,E. and Henrick,K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta. Crystallogr. D. Biol. Crystallogr., 60, 2256-2268.
43. Kumar,S., Tamma,K. and Nei,M. (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform., 5, 150-163.
44. Troyanskaya,O., Cantor,M., Sherlock,G., Brown,P., Hastie,T., Tibshirani,R., Botstein,D. and Altman,R.B. (2001) Missing value estimation methods for DNA microarrays. Bioinformatics, 17, 520-525.
45. de Hoon,M.J., Imoto,S., Nolan,J. and Miyano,S. (2004) Open source clustering software. Bioinformatics, 20, 1453-1454.
46. Pavlidis,P. and Noble,W.S. (2003) Matrix2png: A utility for visualizing matrix data. Bioinformatics, 19, 295-296.
47. Aravind,L. and Landsman,D. (1998) AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res., 26, 4413-4421.
48. Allen,M.D., Yamasaki,K., Ohme-Takagi,M., Tateno,M. and Suzuki,M. (1998) A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. EMBO J., 17, 5484-5496.
49. Cernac,A. and Benning,C. (2004) WRINKLED1 encodes an AP2/EREB domain protein involved in the control of storage compound biosynthesis in Arabidopsis. Plant J., 40, 575-585.
50. Krizek,B.A. (2003) AINTEGUMENTA utilizes a mode of DNA recognition distinct from that used by proteins containing a single AP2 domain. Nucleic Acids Res., 31, 1859-1868.
51. Moure,C.M., Gimble,F.S. and Quiocho,F.A. (2002) Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence. Nature Struct. Biol., 9, 764-770.
52. Buttner,M. and Singh,K.B. (1997) Arabidopsis thaliana ethylene-responsive element binding protein (AtEBP), an ethylene-inducible, GCC box DNA-binding protein interacts with an ocs element binding protein. Proc. Natl Acad. Sci. USA, 94, 5961-5966.
53. Ohme-Takagi,M. and Shinshi,H. (1995) Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell, 7, 173-182.
54. Jones,D.T., Taylor,W.R. and Thornton,J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-282.
55. Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
56. Leander,B.S., Clopton,R.E. and Keeling,P.J. (2003) Phylogeny of gregarines (Apicomplexa) as inferred from small-subunit rDNA and beta-tubulin. Int. J. Syst. Evol. Microbiol., 53, 345-354.
57. Musacchio,A., Gibson,T., Rice,P., Thompson,J. and Saraste,M. (1993) The PH domain: A common piece in the structural patchwork of signalling proteins. Trends Biochem. Sci., 18, 343-348.
58. Blomberg,N., Baraldi,E., Nilges,M. and Saraste,M. (1999) The PH superfold: A structural scaffold for multiple functions. Trends. Biochem. Sci., 24, 441-445.
59. Gervais,V., Lamour,V., Jawhari,A., Frindel,F., Wasielewski,E., Dubaele,S., Egly,J.-M., Thierry,J.-C., Kieffer,B. and Poterszman,A. (2004) TFIIH contains a PH domain involved in DNA nucleotide excision repair. Nature Struct. Mol. Biol., 11, 616-622.
60. She,M., Decker,C.J., Sundramurthy,K., Liu,Y., Chen,N., Parker,R. and Song,H. (2004) Crystal structure of Dep1p and its functional implications in mRNA decapping. Nature Struct. Mol. Biol., 11, 249-256.
61. Vetter,I.R., Nowak,C., Nishimoto,T., Kuhlmann,J. and Wittinghofer,A. (1999) Structure of a Ran-binding domain complexed with Ran bound to a GTP analogue: Implications for nuclear transport. Nature, 398, 39-46.
62. Yoon,H.S., Hajduk,P.J., Petros,A.M., Olejniczak,E.T., Meadows,R.P. and Fesik,S.W. (1994) Solution structure of a pleckstrin-homology domain. Nature, 369, 672-675.
63. Fulop,V. and Jones,D.T. (1999) Beta propellers: Structural rigidity and functional diversity. Curr. Opin. Struct. Biol., 9, 715-721.
64. Smit,A.F. and Riggs,A.D. (1996) Tiggers and DNA transposon fossils in the human genome. Proc. Natl Acad. Sci. USA, 93, 1443-1448.
65. Izsvak,Z., Khare,D., Behlke,J., Heinemann,U., Plasterk,R.H. and Ivics,Z. (2002) Involvement of a bifunctional, paired-like DNA-binding domain and a transpositional enhancer in Sleeping Beauty transposition. J. Biol. Chem., 277, 34581-34588.
66. Sitbon,E. and Pietrokovski,S. (2003) New types of conserved sequence domains in DNA-binding regions of homing endonucleases. Trends Biochem. Sci., 28, 473-477.
67. Aravind,L. (2000) The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases. Trends Biochem. Sci., 25, 421-423.
68. Yamasaki,K., Kigawa,T., Inoue,M., Tateno,M., Yamasaki,T., Yabuki,T., Aoki,M., Seki,E., Matsuda,T., Tomo,Y. et al. (2004) Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1. Plant Cell, 16, 3448-3459.
69. Foth,B.J. and McFadden,G.I. (2003) The apicoplast: A plastid in Plasmodium falciparum and other Apicomplexan parasites. Int. Rev. Cytol., 224, 57-110.
70. Martin,W., Stoebe,B., Goremykin,V., Hapsmann,S., Hasegawa,M. and Kowallik,K.V. (1998) Gene transfer to the nucleus and the evolution of chloroplasts. Nature, 393, 162-165.