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Volumn 14, Issue 9, 2004, Pages 1686-1695

Comparative analysis of apicomplexa and genomic diversity in eukaryotes

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

EID: 4644353894     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2615304     Document Type: Article
Times cited : (173)

References (51)
  • 3
    • 18844468317 scopus 로고    scopus 로고
    • The SWIRM domain: A conserved module found in chromosomal proteins points to novel chromatin-modifying activities
    • RESEARCH0039
    • Aravind, L. and Iyer, L.M. 2002. The SWIRM domain: A conserved module found in chromosomal proteins points to novel chromatin-modifying activities. Genome Biol. 3: RESEARCH0039.
    • (2002) Genome Biol. , vol.3
    • Aravind, L.1    Iyer, L.M.2
  • 4
    • 0032804892 scopus 로고    scopus 로고
    • Origin of multicellular eukaryotes - Insights from proteome comparisons
    • Aravind, L. and Subramanian, G. 1999. Origin of multicellular eukaryotes - Insights from proteome comparisons. Curr. Opin. Genet. Dev. 9: 688-694.
    • (1999) Curr. Opin. Genet. Dev. , vol.9 , pp. 688-694
    • Aravind, L.1    Subramanian, G.2
  • 5
    • 0034633626 scopus 로고    scopus 로고
    • Lineage-specific loss and divergence of functionally linked genes in eukaryotes
    • Aravind, L., Watanabe, H., Lipman, D.J., and Koonin, E.V. 2000. Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc. Natl. Acad. Sci. 97: 11319-11324.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 11319-11324
    • Aravind, L.1    Watanabe, H.2    Lipman, D.J.3    Koonin, E.V.4
  • 6
    • 0347985825 scopus 로고    scopus 로고
    • Plasmodium biology: Genomic gleanings
    • Aravind, L., Iyer, L.M., Wellems, T.E., and Miller, L.H. 2003. Plasmodium biology: Genomic gleanings. Cell 115: 771-785.
    • (2003) Cell , vol.115 , pp. 771-785
    • Aravind, L.1    Iyer, L.M.2    Wellems, T.E.3    Miller, L.H.4
  • 7
    • 0029045587 scopus 로고
    • Sexual-stage-specific RNA expression of a new Plasmodium falciparum gene detected by in situ hybridization
    • Baker, D.A., Thompson, J., Daramola, O.O., Carlton, J.M., and Targett, G.A. 1995. Sexual-stage-specific RNA expression of a new Plasmodium falciparum gene detected by in situ hybridization. Mol. Biochem. Parasitol. 72: 193-201.
    • (1995) Mol. Biochem. Parasitol. , vol.72 , pp. 193-201
    • Baker, D.A.1    Thompson, J.2    Daramola, O.O.3    Carlton, J.M.4    Targett, G.A.5
  • 8
    • 0034602344 scopus 로고    scopus 로고
    • A kingdom-level phylogeny of eukaryotes based on combined protein data
    • Baldauf, S.L., Roger, A.J., Wenk-Siefert, I., and Doolittle, W.F. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290: 972-977.
    • (2000) Science , vol.290 , pp. 972-977
    • Baldauf, S.L.1    Roger, A.J.2    Wenk-Siefert, I.3    Doolittle, W.F.4
  • 9
    • 0029052741 scopus 로고
    • Cloning the P. falciparum gene encoding PfEMP1, a malarial antigen and adherence receptor on the surface of parasitized human erythrocytes
    • Baruch, D.I., Pasloske, B.L., Singh, H.B., Bi, X., Ma, X.C., Feldman, M., Taraschi, T.F., and Howard, R.J. 1995. Cloning the P. falciparum gene encoding PfEMP1, a malarial antigen and adherence receptor on the surface of parasitized human erythrocytes. Cell 82: 77-87.
    • (1995) Cell , vol.82 , pp. 77-87
    • Baruch, D.I.1    Pasloske, B.L.2    Singh, H.B.3    Bi, X.4    Ma, X.C.5    Feldman, M.6    Taraschi, T.F.7    Howard, R.J.8
  • 11
    • 4243071596 scopus 로고    scopus 로고
    • The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
    • 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.
    • (2003) PLoS Biol. , vol.1
    • Bozdech, Z.1    Llinas, M.2    Pulliam, B.L.3    Wong, E.D.4    Zhu, J.5    DeRisi, J.L.6
  • 12
    • 0033984609 scopus 로고    scopus 로고
    • Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction
    • Bruno, W.J., Socci, N.D., and Halpern, A.L. 2000. Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction. Mol. Biol. Evol. 17: 189-197.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 189-197
    • Bruno, W.J.1    Socci, N.D.2    Halpern, A.L.3
  • 13
    • 0032882626 scopus 로고    scopus 로고
    • Cryptosporidium is more closely related to the gregarines than to coccidia as shown by phylogenetic analysis of Apicomplexan parasites inferred using small- subunit ribosomal RNA gene sequences
    • Carreno, R.A., Martin, D.S., and Barta, J.R. 1999. Cryptosporidium is more closely related to the gregarines than to coccidia as shown by phylogenetic analysis of Apicomplexan parasites inferred using small- subunit ribosomal RNA gene sequences. Parasitol. Res. 85: 899-904.
    • (1999) Parasitol. Res. , vol.85 , pp. 899-904
    • Carreno, R.A.1    Martin, D.S.2    Barta, J.R.3
  • 14
    • 0032583111 scopus 로고    scopus 로고
    • Stevor and rif are Plasmodium falciparum multicopy gene families which potentially encode variant antigens
    • Cheng, Q., Cloonan, N., Fischer, K., Thompson, J., Waine, G., Lanzer, M., and Saul, A. 1998. stevor and rif are Plasmodium falciparum multicopy gene families which potentially encode variant antigens. Mol. Biochem. Parasitol. 97: 161-176.
    • (1998) Mol. Biochem. Parasitol. , vol.97 , pp. 161-176
    • Cheng, Q.1    Cloonan, N.2    Fischer, K.3    Thompson, J.4    Waine, G.5    Lanzer, M.6    Saul, A.7
  • 16
    • 0028568176 scopus 로고
    • TopPred II: An improved software for membrane protein structure predictions
    • Claros, M.G. and von Heijne, G. 1994. TopPred II: An improved software for membrane protein structure predictions. Comput. Appl. Biosci. 10: 685-686.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 685-686
    • Claros, M.G.1    von Heijne, G.2
  • 17
    • 0035253752 scopus 로고    scopus 로고
    • Transformation of malaria parasites by the spontaneous uptake and expression of DNA from human erythrocytes
    • Deitsch, K., Driskill, C., and Wellems, T. 2001. Transformation of malaria parasites by the spontaneous uptake and expression of DNA from human erythrocytes. Nucleic Acids Res. 29: 850-853.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 850-853
    • Deitsch, K.1    Driskill, C.2    Wellems, T.3
  • 18
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 19
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny inference package
    • (Version 3.2)
    • Felsenstein, J. 1989. PHYLIP - Phylogeny inference package (Version 3.2). Cladistics 5: 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 20
    • 0029901637 scopus 로고    scopus 로고
    • Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
    • Felsenstein, J. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol. 266: 418-427.
    • (1996) Methods Enzymol. , vol.266 , pp. 418-427
    • Felsenstein, J.1
  • 23
    • 0342813091 scopus 로고    scopus 로고
    • Crystal structure of a Hedgehog autoprocessing domain: Homology between Hedgehog and self-splicing proteins
    • Hall, T.M., Porter, J.A., Young, K.E., Koonin, E.V., Beachy, P.A., and Leahy, D.J. 1997. Crystal structure of a Hedgehog autoprocessing domain: Homology between Hedgehog and self-splicing proteins. Cell 91: 85-97.
    • (1997) Cell , vol.91 , pp. 85-97
    • Hall, T.M.1    Porter, J.A.2    Young, K.E.3    Koonin, E.V.4    Beachy, P.A.5    Leahy, D.J.6
  • 24
    • 0025873443 scopus 로고
    • On the maximum likelihood method in molecular phylogenetics
    • Hasegawa, M., Kishino, H., and Saitou, N. 1991. On the maximum likelihood method in molecular phylogenetics. J. Mol. Evol. 32: 443-445.
    • (1991) J. Mol. Evol. , vol.32 , pp. 443-445
    • Hasegawa, M.1    Kishino, H.2    Saitou, N.3
  • 25
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. 2001. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305: 567-580.
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 26
    • 0036139211 scopus 로고    scopus 로고
    • MEGA2: Molecular evolutionary genetics analysis software
    • Kumar, S., Tamura, K., Jakobsen, I.B., and Nei, M. 2001. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17: 1244-1245.
    • (2001) Bioinformatics , vol.17 , pp. 1244-1245
    • Kumar, S.1    Tamura, K.2    Jakobsen, I.B.3    Nei, M.4
  • 30
    • 0036066765 scopus 로고    scopus 로고
    • The role of lineage-specific gene family expansion in the evolution of eukaryotes
    • 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.
    • (2002) Genome Res. , vol.12 , pp. 1048-1059
    • Lespinet, O.1    Wolf, Y.I.2    Koonin, E.V.3    Aravind, L.4
  • 31
    • 0035400296 scopus 로고    scopus 로고
    • Characterization of the subpellicular network, a filamentous membrane skeletal component in the parasite Toxoplasma gondii
    • Mann, T. and Beckers, C. 2001. Characterization of the subpellicular network, a filamentous membrane skeletal component in the parasite Toxoplasma gondii. Mol. Biochem. Parasitol. 115: 257-268.
    • (2001) Mol. Biochem. Parasitol. , vol.115 , pp. 257-268
    • Mann, T.1    Beckers, C.2
  • 32
    • 0031791395 scopus 로고    scopus 로고
    • Cloning, sequencing, and expression of the gene encoding cyclic 2,3-diphosphoglycerate synthetase, the key enzyme of cyclic 2,3-diphosphoglycerate metabolism in Methanothermus fervidus
    • Matussek, K., Moritz, P., Brunner, N., Eckerskorn, C., and Hensel, R. 1998. Cloning, sequencing, and expression of the gene encoding cyclic 2,3-diphosphoglycerate synthetase, the key enzyme of cyclic 2,3-diphosphoglycerate metabolism in Methanothermus fervidus. J. Bacteriol. 180: 5997-6004.
    • (1998) J. Bacteriol. , vol.180 , pp. 5997-6004
    • Matussek, K.1    Moritz, P.2    Brunner, N.3    Eckerskorn, C.4    Hensel, R.5
  • 33
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10: 1-6.
    • (1997) Protein Eng. , vol.10 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    von Heijne, G.4
  • 34
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C., Higgins, D.G., and Heringa, J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Bio. 302: 205-217.
    • (2000) J. Mol. Bio. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 36
    • 0029091208 scopus 로고
    • Isolation of multiple sequences from the Plasmodium falciparum genome that encode conserved domains homologous to those in erythrocyte-binding proteins
    • Peterson, D.S., Miller, L.H., and Wellems, T.E. 1995. Isolation of multiple sequences from the Plasmodium falciparum genome that encode conserved domains homologous to those in erythrocyte-binding proteins. Proc. Natl. Acad. Sci. 92: 7100-7104.
    • (1995) Proc. Natl. Acad. Sci. , vol.92 , pp. 7100-7104
    • Peterson, D.S.1    Miller, L.H.2    Wellems, T.E.3
  • 37
    • 0026164394 scopus 로고
    • Plasmodium falciparum: Evidence for a DNA methylation pattern
    • Pollack, Y., Kogan, N., and Golenser, J. 1991. Plasmodium falciparum: Evidence for a DNA methylation pattern. Exp. Parasitol. 72: 339-344.
    • (1991) Exp. Parasitol. , vol.72 , pp. 339-344
    • Pollack, Y.1    Kogan, N.2    Golenser, J.3
  • 38
    • 0033057517 scopus 로고    scopus 로고
    • Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer
    • Ponting, C.P., Aravind, L., Schultz, J., Bork, P., and Koonin, E.V. 1999. Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J. Mol. Biol. 289: 729-745.
    • (1999) J. Mol. Biol. , vol.289 , pp. 729-745
    • Ponting, C.P.1    Aravind, L.2    Schultz, J.3    Bork, P.4    Koonin, E.V.5
  • 39
    • 2942672722 scopus 로고    scopus 로고
    • A multidomain adhesion protein family expressed in Plasmodium falciparum is essential for transmission to the mosquito
    • Pradel, G., Hayton, K., Aravind, L., Iyer, L.M., Abrahamsen, M.S., Bonawitz, A., Mejia, C., and Templeton, T.J. 2004. A multidomain adhesion protein family expressed in Plasmodium falciparum is essential for transmission to the mosquito. J. Exp. Med. 199: 1533-1544.
    • (2004) J. Exp. Med. , vol.199 , pp. 1533-1544
    • Pradel, G.1    Hayton, K.2    Aravind, L.3    Iyer, L.M.4    Abrahamsen, M.S.5    Bonawitz, A.6    Mejia, C.7    Templeton, T.J.8
  • 42
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist, F. and Huelsenbeck, J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 43
    • 0030038634 scopus 로고    scopus 로고
    • Topology prediction for helical transmembrane proteins at 86% accuracy
    • Rost, B., Fariselli, P., and Casadio, R. 1996. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 5: 1704-1718.
    • (1996) Protein Sci. , vol.5 , pp. 1704-1718
    • Rost, B.1    Fariselli, P.2    Casadio, R.3
  • 44
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt, H.A., Strimmer, K., Vingron, M., and von Haeseler, A. 2002. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    von Haeseler, A.4
  • 45
    • 0028982168 scopus 로고
    • Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes
    • Smith, J.D., Chitnis, C.E., Craig, A.G., Roberts, D.J., Hudson-Taylor, D.E., Peterson, D.S., Pinches, R., Newbold, C.I., and Miller, L.H. 1995. Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes. Cell 82: 101-110.
    • (1995) Cell , vol.82 , pp. 101-110
    • Smith, J.D.1    Chitnis, C.E.2    Craig, A.G.3    Roberts, D.J.4    Hudson-Taylor, D.E.5    Peterson, D.S.6    Pinches, R.7    Newbold, C.I.8    Miller, L.H.9
  • 46
    • 0029070914 scopus 로고
    • The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes
    • Su, X.Z., Heatwole, V.M., Wertheimer, S.P., Guinet, F., Herrfeldt, J.A., Peterson, D.S., Ravetch, J.A., and Wellems, T.E. 1995. The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes. Cell 82: 89-100.
    • (1995) Cell , vol.82 , pp. 89-100
    • Su, X.Z.1    Heatwole, V.M.2    Wertheimer, S.P.3    Guinet, F.4    Herrfeldt, J.A.5    Peterson, D.S.6    Ravetch, J.A.7    Wellems, T.E.8
  • 47
    • 0033955942 scopus 로고    scopus 로고
    • Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum
    • Subramanian, G., Koonin, E.V., and Aravind, L. 2000. Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum. Infect. Immun. 68: 1633-1648.
    • (2000) Infect. Immun. , vol.68 , pp. 1633-1648
    • Subramanian, G.1    Koonin, E.V.2    Aravind, L.3
  • 48
    • 0141706713 scopus 로고    scopus 로고
    • The eukaryotic DNMT2 genes encode a new class of cytosine-5 DNA methyltransferases
    • Tang, L.Y., Reddy, M.N., Rasheva, V., Lee, T.L., Lin, M.J., Hung, M.S., and Shen, C.K. 2003. The eukaryotic DNMT2 genes encode a new class of cytosine-5 DNA methyltransferases. J. Biol. Chem. 278: 33613-33616.
    • (2003) J. Biol. Chem. , vol.278 , pp. 33613-33616
    • Tang, L.Y.1    Reddy, M.N.2    Rasheva, V.3    Lee, T.L.4    Lin, M.J.5    Hung, M.S.6    Shen, C.K.7


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