Evolution of prokaryotic SPFH proteins

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Hinderhofer, Markus ^a   Walker, Christina A ^a   Friemel, Anke ^a   Stuermer, Claudia Ao ^a   Möller, Heiko M ^a   Reuter, Alexander ^a  

^a UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; CHEMISTRY; GENETICS; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CONSERVED SEQUENCE; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; OPERON; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 60649087207     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-10     Document Type: Article

References (39)

1. The SPFH domain: implicated in regulating targeted protein turnover in Stomatins and other membrane-associated proteins. N Tavernarakis M Driscoll NC Kyrpides, Trends Biochem Sci 1999 24 425 427 10.1016/S0968-0004(99)01467-X 10542406
2. The SPFH domain-containing proteins: more than lipid raft markers. DT Browman MB Hoegg SM Robbins, Trends Cell Biol 2007 17 394 402 10.1016/j.tcb.2007.06.005 17766116
3. Flotillins and the PHB domain protein family: rafts, worms and anaesthetics. IC Morrow RG Parton, Traffic 2005 6 725 740 10.1111/j.1600-0854. 2005.00318.x 16101677
4. Ancient origin of reggie (Flotillin), reggie-like, and other lipid-raftproeins: convergent evolution of SPFH domain. E Rivera-Milla CAO Stuermer E Malaga-Trillo, Cell Mol Life Sci 2006 63 343 357 10.1007/s00018-005- 5434-3 16389450
5. Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria. G Xie CA Bonner T Brettin R Gottardo NO Keyhani RA Jensen, Genome Biology 2003 4 R14 12620124 10.1186/gb-2003-4-2-r14
6. Horizontal gene transfer in Glycosyl Hydrolases Inferred from Codon Usage in Escherichia coli and Bacillus subtilis. S Garcia-Vallve J Palau A Romeu, Genome res 2000 10 1719 25 11076857 10.1101/gr.130000
7. Effects opf Nucleotide Composition Bias on the Success of the Parsimony Criterion in Phylogenetic Interference. GC Conant Po Lewis, Mol Biol Evol 2001 18 1024 1033 11371591
8. A review of long-branch attraction. J Bergsten, Cladistics 2005 21 163 193 10.1111/j.1096-0031.2005.00059.x
9. Scaffolding microdomains and beyond: the function of reggie/Flotillin proteins. MF Langhorst A Reuter CA Stuermer, Cell Mol Life Sci 2005 62 2228 2240 10.1007/s00018-005-5166-4 16091845
10. Crystal structure of a core domain of Stomatin from Pyrococcus horikoshii Illustrates a novel trimeric and coiled-coil fold. H Yokoyama S Fujii I Matsui, J Mol Biol 2008 376 868 878 10.1016/j.jmb.2007.12.024 18182167
11. The Escherichia coli plasma membrane contains two PHB (Prohibitin homology) domain protein complexes of opposite orientations. S Chiba K Ito Y Akiyama, Mol Microbiol 2006 60 448 457 10.1111/j.1365-2958.2006.05104.x 16573693
12. Deciphering a complex genetic regulatory network: the Bacillus subtilis sigmaW protein and intrinsic resistance to antimicrobial compounds. JD Helmann, Sci Prog 2006 89 243 266 10.3184/003685006783238290 17338440
13. Identification of Bacillus subtilis sigma-dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli. BG Butcher JD Helmann, Mol Microbiol 2006 60 765 782 10.1111/j.1365-2958.2006.05131.x 16629676
14. Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1. W Gao Y Liu CS Giometti SL Tollaksen T Khare L Wu DM Klingemann MW Fields J Zhou, BMC Genomics 2006 7 76 16600046 10.1186/1471-2164-7-76
15. CDART: protein homology by domain architecture. LY Geer M Domrachew DJ Linman SH Bryant, Genome Res 2000 12 1619 1623 10.1101/gr.278202
16. SMART: a web-based tool for the study of genetically mobile domains. J Schulz RR Copley T Doerks CP Ponting P Bork, Nucleic Acids Res 2000 28 231 234 10592234 10.1093/nar/28.1.231
17. Pfam: clans, web tools and services. RD Finn J Mistry B Schuster-Böckler S Griffiths-Jones V Hollich T Lassmann S Moxon M Marshall A Khanna R Durbin SR Eddy EL Sonnhammer A Bateman, Nucleic Acids Res 2006 34 D247 51 16381856 10.1093/nar/gkj149
18. EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database. V Lombard EB Camon HE Parkinson P Hingamp G Stoesser N Redaschi,. Bioinformatics 2002 18 763 764 10.1093/bioinformatics/18.5.763 12050074
19. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738
20. ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. P Gouet X Robert E Courcelle, Nucleic Acids Res 2003 31 3320 3323 12824317 10.1093/nar/gkg556
21. WinPep 2.11: novel software for PC-based analyses of amino acid sequences. L Hennig, Prep Biochem Biotechnol 2001 31 201 207 11426706
22. Predicting coiled coils from protein sequences. A Lupas M Van Dyke J Stock, Science 1991 252 1162 1164 10.1126/science.252.5009.1162
23. X Xia, Data analysis in molecular biology and evolution Boston: Kluwer Academic Publishers 2000
24. The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes. RS Gupta, FEMS Microbiology Reviews 2000 24 367 402 10.1111/j.1574-6976.2000.tb00547.x 10978543
25. Oligomeric nature of the integral membrane protein Stomatin. L Snyers E Umlauf R Prohaska, J Biol Chem 1998 273 17221 17226 10.1074/jbc.273.27.17221 9642292
26. A protease complex in the Escherichia coli plasma membrane: HflKC (HflA) forms a complex with FtsH (HflB), regulating its proteolytic activity against SecY. A Kihara Y Akiyama K Ito, EMBO J 1996 15 6122 6131 8947034
27. Prohibitins regulate membrane protein degradation by the m-AAA protease in mitochondria. G Steglich W Neupert T Langer, Mol Cell Biol 1999 19 3435 3442 10207067
28. Prohibitins act as a membrane-bound chaperone for the stabilization of mitochondrial proteins. LG Nijtmans L de Jong M Artal Sanz PJ Coates JA Berden JW Back AO Muijsers H van der Spek LA Grivell, EMBO J 2000 19 2444 2451 10835343 10.1093/emboj/19.11.2444
29. The Prohibitins: emerging roles in diverse functions. S Mishra LC Murphy LJ Murphy, J Cell Mol Med 2006 10 353 363 10.1111/j.1582-4934.2006.tb00404.x 16796804
30. NMR structure note: Solution Structure of the Soluble Domain of the NfeD Protein YuaF from Bacillus subtilis. CA Walker M Hinderhofer DJ Witte W Boos HM Möller, J Biomol NMR 2008 42 69 76 10.1007/s10858-008-9261-3 18696230
31. The solution structure of the C-terminal domain of NfeD reveals a novel membrane-anchored OB-fold. Y Kuwahara A Ohno T Morii HY Yokoyama I Matsui H Tochio M Shirakawa H Hiroaki, Protein Sci 2008 18687870
32. The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. DS Wishart BD Sykes, J Biomol NMR 1994 4 171 80 10.1007/BF00175245 8019132
33. Multiple sigma subunits and the partitioning of bacterial transcription space. TM Gruber CA Gross, Annu Rev Microbiol 2003 57 441 466 10.1146/annurev.micro.57.030502.090913 14527287
34. Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. GS Vernikos J Parkhill, Bioinformatics 2006 22 2196 2203 10.1093/bioinformatics/btl369 16837528
35. Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli. J Becq MC Gutierrez V Rosas-Magallanes J Rauzier B Gicquel O Neyrolles P Deschavanne, Mol Biol Evol 2007 24 1861 1871 10.1093/molbev/msm111 17545187
36. Global extent of horizontal gene transfer. IG Choi SH Kim, Proc Natl Acad Sci USA 2007 104 4489 4494 17360551 10.1073/pnas.0611557104
37. Molecular modeling of Prohibitin domains. a Winter O Kämä räinen A Hofmann, Proteins 2007 68 353 362 10.1002/prot.21355 17427253
38. The sorbin homology domain: a motif for the targeting of proteins to lipid rafts. A Kimura CA Baumann SH Chiang AR Saltiel, Proc Natl Acad Sci 2001 98 9098 9103 11481476 10.1073/pnas.151252898
39. Linking membrane microdomains to the cytoskeleton: regulation of the lateral mobility of reggie-1/Flotillin-2 by interaction with actin. MF Langhorst GP Solis S Hannbeck H Plattner CA Stuermer, FEBS Lett 2007 581 4697 703 10.1016/j.febslet.2007.08.074 17854803