Analysis of septins across kingdoms reveals orthology and new motifs

BMC Evolutionary Biology

Volumn 7, Issue , 2007, Pages

  Pan, Fangfang ^a   Malmberg, Russell L ^a   Momany, Michelle ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CDC10 PROTEIN; CDC11 PROTEIN; CDC12 PROTEIN; CDC3 PROTEIN; FUNGAL PROTEIN; GUANOSINE TRIPHOSPHATASE; SEPT7 PROTEIN; SEPT9 PROTEIN; SEPTIN; UNCLASSIFIED DRUG; CAENORHABDITIS ELEGANS PROTEIN; CDC3 PROTEIN, S CEREVISIAE; CELL CYCLE PROTEIN; CYTOSKELETON PROTEIN; DROSOPHILA PROTEIN; INSECT PROTEIN; ISOPROTEIN; PROFILIN; PROTOZOAL PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; ZEBRAFISH PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; ASPERGILLUS NIDULANS; COMPARATIVE STUDY; EVOLUTION; FUNGUS; HISTORY; MICROSPORIDA; NOMENCLATURE; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN MOTIF; REGNUM; SACCHAROMYCES CEREVISIAE; ANIMAL; CHEMISTRY; CLASSIFICATION; CONSENSUS SEQUENCE; ENZYMOLOGY; GENE DUPLICATION; GENETICS; HUMAN; MOLECULAR EVOLUTION; MOUSE; MULTIGENE FAMILY; PROTEIN TERTIARY STRUCTURE; RAT; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

ANIMALIA; EMERICELLA NIDULANS; FUNGI; MICROSPORIDIA; SACCHAROMYCES CEREVISIAE;

AMINO ACID MOTIFS; ANIMALS; CAENORHABDITIS ELEGANS PROTEINS; CELL CYCLE PROTEINS; CONSENSUS SEQUENCE; CONSERVED SEQUENCE; CYTOSKELETAL PROTEINS; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; FUNGAL PROTEINS; FUNGI; GENE DUPLICATION; GTP PHOSPHOHYDROLASES; HUMANS; INSECT PROTEINS; MICE; MICROSPORIDIA; MULTIGENE FAMILY; PHYLOGENY; PROFILINS; PROTEIN ISOFORMS; PROTEIN STRUCTURE, TERTIARY; PROTOZOAN PROTEINS; RATS; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY; TERMINOLOGY; ZEBRAFISH PROTEINS;

EID: 34547121710     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-103     Document Type: Article

References (53)

1. The septins: roles in cytokinesis and other processes. MS Longtine DJ DeMarini ML Valencik OS Al-Awar H Fares C De Virgilio JR Pringle, Curr Opin Cell Biol 1996 8 1 106 119 10.1016/S0955-0674(96)80054-8 8791410
2. Identification of a developmentally regulated septin and involvement of the septins in spore formation in Saccharomyces cerevisiae. H Fares L Goetsch JR Pringle, J Cell Biol 1996 132 3 399 411 10.1083/jcb.132.3.399 8636217
3. SPR28, a sixth member of the septin gene family in Saccharomyces cerevisiae that is expressed specifically in sporulating cells. C De Virgilio DJ DeMarini JR Pringle, Microbiology 1996 142 ( Pt 10) 2897 2905 8885406
4. Regulation of septin organization and function in yeast. MS Longtine E Bi, Trends Cell Biol 2003 13 8 403 409 10.1016/S0962-8924(03)00151-X 12888292
5. Septin Function in Yeast Model Systems and Pathogenic Fungi. LM Douglas FJ Alvarez C McCreary JB Konopka, Eukaryotic Cell 2005 4 9 1503 1512 16151244 10.1128/EC.4.9.1503-1512.2005
6. Mammalian septin function in hemostasis and beyond. C Martinez J Ware, Exp Biol Med (Maywood) 2004 229 11 1111 1119 15564437
7. The pathobiology of the septin gene family. PA Hall SE Russell, J Pathol 2004 204 4 489 505 10.1002/path.1654 15495264
8. A mitotic septin scaffold required for Mammalian chromosome congression and segregation. ET Spiliotis M Kinoshita WJ Nelson, Science 2005 307 5716 1781 1785 10.1126/science.1106823 15774761
9. Diversity of septin scaffolds. M Kinoshita, Curr Opin Cell Biol 2006 18 1 54 60 10.1016/j.ceb.2005.12.005 16356703
10. Classification and evolution of P-loop GTPases and related ATPases. DD Leipe YI Wolf EV Koonin L Aravind, J Mol Biol 2002 317 1 41 72 10.1006/jmbi.2001.5378 11916378
11. The GTPase superfamily: conserved structure and molecular mechanism. HR Bourne DA Sanders F McCormick, Nature 1991 349 6305 117 127 10.1038/349117a0 1898771
12. The P-loop - a common motif in ATP- and GTP-binding proteins. M Saraste PR Sibbald A Wittinghofer, Trends Biochem Sci 1990 15 11 430 434 10.1016/0968-0004(90)90281-F 2126155
13. Nucleoside triphosphate-binding proteins: different scaffolds to achieve phosphoryl transfer. IR Vetter A Wittinghofer, Q Rev Biophys 1999 32 1 1 56 10.1017/S0033583599003480 10800520
14. GTP-binding domain: three consensus sequence elements with distinct spacing. TE Dever MJ Glynias WC Merrick, Proceedings of the National Academy of Sciences of the United States of America 1987 84 7 1814 1818 3104905 10.1073/pnas.84.7.1814
15. Septins: cytoskeletal polymers or signalling GTPases? CM Field D Kellogg, Trends Cell Biol 1999 9 10 387 394 10.1016/S0962-8924(99)01632-3 10481176
16. A purified Drosophila septin complex forms filaments and exhibits GTPase activity. CM Field O al-Awar J Rosenblatt ML Wong B Alberts TJ Mitchison, J Cell Biol 1996 133 3 605 616 10.1083/jcb.133.3.605 8636235
17. GTP binding induces filament assembly of a recombinant septin. M Mendoza AA Hyman M Glotzer, Curr Biol 2002 12 21 1858 1863 10.1016/S0960-9822(02)01258-7 12419187
18. The majority of the Saccharomyces cerevisiae septin complexes do not exchange guanine nucleotides. AM Vrabioiu SA Gerber SP Gygi CM Field TJ Mitchison, J Biol Chem 2004 279 4 3111 3118 10.1074/jbc.M310941200 14597621
19. Molecular dissection of a yeast septin: distinct domains are required for septin interaction, localization, and function. A Casamayor M Snyder, Mol Cell Biol 2003 23 8 2762 2777 12665577 10.1128/MCB.23.8.2762-2777.2003
20. Phosphatidylinositol polyphosphate binding to the mammalian septin H5 is modulated by GTP. J Zhang C Kong H Xie PS McPherson S Grinstein WS Trimble, Curr Biol 1999 9 24 1458 1467 10.1016/S0960-9822(00)80115-3 10607590
21. Protein-protein interactions governing septin heteropentamer assembly and septin filament organization in Saccharomyces cerevisiae. M Versele B Gullbrand MJ Shulewitz VJ Cid S Bahmanyar RE Chen P Barth T Alber J Thorner, Mol Biol Cell 2004 15 10 4568 4583 15282341 10.1091/mbc.E04-04-0330
22. Requirements of fission yeast septins for complex formation, localization, and function. H An JL Morrell JL Jennings AJ Link KL Gould, Mol Biol Cell 2004 15 12 5551 5564 15385632 10.1091/mbc.E04-07-0640
23. Some assembly required: yeast septins provide the instruction manual. M Versele J Thorner, Trends in Cell Biology 2005 15 8 414 424 16009555 10.1016/j.tcb.2005.06.007
24. Characterization of the Aspergillus nidulans septin (asp) gene family. M Momany J Zhao R Lindsey PJ Westfall, Genetics 2001 157 3 969 977 11238387
25. The septins. M Kinoshita, Genome Biol 2003 4 11 236 14611653 10.1186/gb-2003-4-11-236
26. SMART, a simple modular architecture research tool: identification of signaling domains. J Schultz F Milpetz P Bork CP Ponting, Proceedings of the National Academy of Sciences of the United States of America 1998 95 11 5857 5864 9600884 10.1073/pnas.95.11.5857
27. An Ustilago maydis septin is required for filamentous growth in culture and for full symptom development on maize. KJ Boyce H Chang CA D'Souza JW Kronstad, Eukaryot Cell 2005 4 12 2044 2056 16339722 10.1128/EC.4.12.2044-2056. 2005
28. Expression profiling the human septin gene family. PA Hall K Jung KJ Hillan SE Russell, J Pathol 2005 206 3 269 278 10.1002/path.1789 15915442
29. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 12 1572 1574 10.1093/bioinformatics/ btg180 12912839
30. Novel roles for mammalian septins: from vesicle trafficking to oncogenesis. B Kartmann D Roth, J Cell Sci 2001 114 Pt 5 839 844 11181167
31. Assembly of mammalian septins. M Kinoshita, J Biochem (Tokyo) 2003 134 4 491 496 14607974
32. Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae). MJ Sanderson MF Wojciechowski, Syst Biol 2000 49 4 671 685 10.1080/106351500750049761 12116433
33. Applying the Bootstrap in Phylogeny Reconstruction. PS Soltis DE Soltis, Statistical Science Institute of Mathematical Statistics 2003 18 2 256 267 10.1214/ss/1063994980
34. WebLogo: a sequence logo generator. GE Crooks G Hon JM Chandonia SE Brenner, Genome Res 2004 14 6 1188 1190 15173120 10.1101/gr.849004
35. Sequence logos: a new way to display consensus sequences. TD Schneider RM Stephens, Nucleic Acids Res 1990 18 20 6097 6100 2172928 10.1093/nar/18.20.6097
36. Coiled coil domains: stability, specificity, and biological implications. JM Mason KM Arndt, Chembiochem 2004 5 2 170 176 10.1002/cbic.200300781 14760737
37. Coiled coils: new structures and new functions. A Lupas, Trends Biochem Sci 1996 21 10 375 382 10.1016/0968-0004(96)10052-9 8918191
38. A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae. JR Newman E Wolf PS Kim, Proceedings of the National Academy of Sciences of the United States of America 2000 97 24 13203 13208 11087867 10.1073/pnas.97.24.13203
39. Predicting coiled coils from protein sequences. A Lupas M Van Dyke J Stock, Science 1991 252 5010 1162 1164 10.1126/science.252.5009.1162 2031185
40. MultiCoil: a program for predicting two- and three-stranded coiled coils. E Wolf PS Kim B Berger, Protein Sci 1997 6 6 1179 1189 9194178
41. Genomic organization, complex splicing pattern and expression of a human septin gene on chromosome 17q25.3. MA McIlhatton JF Burrows PG Donaghy S Chanduloy PG Johnston SE Russell, Oncogene 2001 20 41 5930 5939 10.1038/sj.onc.1204752 11593400
42. Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes. F Thomarat CP Vivares M Gouy, J Mol Evol 2004 59 6 780 791 10.1007/s00239-004-2673-0 15599510
43. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 9254694 10.1093/nar/25.17.3389
44. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins, Nucleic Acids Res 1997 25 24 4876 4882 9396791 10.1093/nar/25.24.4876
45. BioEdit Sequence Alignment Editor for Windows 95/98/NT/XP. http://www.mbio.ncsu.edu/BioEdit/bioedit.html
46. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 5 696 704 10.1080/10635150390235520 14530136
47. SMART 4.0: towards genomic data integration. I Letunic RR Copley S Schmidt FD Ciccarelli T Doerks J Schultz CP Ponting P Bork, Nucleic Acids Res 2004 32 Database issue D142 4 14681379 10.1093/nar/gkh088
48. CD-Search: protein domain annotations on the fly. A Marchler-Bauer SH Bryant, Nucleic Acids Res 2004 32 Web Server issue W327 31 15215404 10.1093/nar/gkh454
49. The PSIPRED protein structure prediction server. LJ McGuffin K Bryson DT Jones, Bioinformatics 2000 16 4 404 405 10.1093/bioinformatics/16.4.404 10869041
50. The new animal phylogeny: reliability and implications. A Adoutte G Balavoine N Lartillot O Lespinet B Prud'homme R de Rosa, Proceedings of the National Academy of Sciences of the United States of America 2000 97 9 4453 4456 10781043 10.1073/pnas.97.9.4453
51. A five-gene phylogeny of Pezizomycotina. JW Spatafora GH Sung D Johnson C Hesse B O'Rourke M Serdani R Spotts F Lutzoni V Hofstetter J Miadlikowska V Reeb C Gueidan E Fraker T Lumbsch R Lucking I Schmitt K Hosaka A Aptroot C Roux AN Miller DM Geiser J Hafellner G Hestmark AE Arnold B Budel A Rauhut D Hewitt WA Untereiner MS Cole C Scheidegger M Schultz H Sipman CL Schoch, Mycologia 2006 98 6 1018 1028 17486977
52. Where Do Rodents Fit? Evidence from the Complete Mitochondrial Genome of Sciurus vulgaris. A Reyes C Gissi G Pesole FM Catzeflis C Saccone, Mol Biol Evol 2000 17 6 979 983 10833205
53. Phylogenetic utility of protein (RPB2, beta-tubulin) and ribosomal (LSU, SSU) gene sequences in the systematics of Sordariomycetes (Ascomycota, Fungi). AM Tang R Jeewon KD Hyde, Antonie van Leeuwenhoek 2007 91 4 327 349 10.1007/s10482-006-9120-8 17072532