The NfeD protein family and its conserved gene neighbours throughout prokaryotes: Functional implications for stomatin-like proteins

Journal of Molecular Evolution

Volumn 69, Issue 6, 2009, Pages 657-667

  Green, Jasper B ^a   Lower, Ryan P J ^a   Young, J Peter W ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Eoslipin; Flotillin; NfeD; Paraslipin; Phylogeny; SLP 2; SPFH; Stomatin; YqeZ; YqfA

Indexed keywords

BACTERIAL PROTEIN; EOSLIPIN; FLOTILIN; NFED PROTEIN; NFED1A PROTEIN; NFED1B PROTEIN; PARASLIPIN; STOMATIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; DEINOCOCCI; EUKARYOTE; FIRMICUTES; GENE; GENE CLUSTER; GENETIC CONSERVATION; GENOME; MEMBRANE; NONHUMAN; PROKARYOTE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; MEMBRANE PROTEINS; MULTIGENE FAMILY; PHYLOGENY; PROKARYOTIC CELLS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

DEINOCOCCI; EUKARYOTA; FIRMICUTES; PROKARYOTA;

EID: 72449165351     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-009-9304-8     Document Type: Article

References (40)

1. F Abascal R Zardoya D Posada 2005 ProtTest: selection of best-fit models of protein evolution Bioinformatics 21 2104 2105 10.1093/bioinformatics/bti263 1:CAS:528:DC%2BD2MXjsl2ns7Y%3D 15647292 (Pubitemid 40668057)
2. J Adachi PJ Waddell W Martin M Hasegawa 2000 Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA J Mol Evol 50 348 358 1:CAS:528:DC%2BD3cXivFyjur8%3D 10795826
3. D Borthakur X Gao 1996 A 150-megadalton plasmid in Rhizobium etli strain TAL182 contains genes for nodulation competitiveness on Phaseolus vulgaris L Can J Microbiol 42 903 910 10.1139/m96-116 1:CAS:528:DyaK28XmtFCgtLk%3D 8864213
4. N Boute O Gribouval S Roselli F Benessy H Lee A Fuchshuber K Dahan MC Gubler P Niaudet C Antignac 2000 NPHS2, encoding the glomerular protein podocin, is mutated in autosomal recessive steroid-resistant nephrotic syndrome Nat Genet 24 349 354 10.1038/74166 1:CAS:528:DC%2BD3cXisVCjsb4%3D 10742096 (Pubitemid 30187431)
5. DT Browman MB Hoegg SM Robbins 2007 The SPFH domain-containing proteins: more than lipid raft markers Trends Cell Biol 17 394 402 10.1016/j.tcb.2007.06. 005 1:CAS:528:DC%2BD2sXhtVCisLrO 17766116 (Pubitemid 47375100)
6. BG Butcher JD Helmann 2006 Identification of Bacillus subtilis sigma-dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli Mol Microbiol 60 765 782 10.1111/j.1365-2958.2006. 05131.x 1:CAS:528:DC%2BD28XkslClsbk%3D 16629676
7. J Castresana 2000 Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol Biol Evol 17 540 552 1:CAS:528:DC%2BD3cXisVSgt7g%3D 10742046
8. S Chiba K Ito Y Akiyama 2006 The Escherichia coli plasma membrane contains two PHB (prohibitin homology) domain protein complexes of opposite orientations Mol Microbiol 60 448 457 10.1111/j.1365-2958.2006.05104.x 1:CAS:528:DC%2BD28XksV2is7k%3D 16573693
9. Z Cui L Zhang Z Hua W Cao W Feng Z Liu 2007 Stomatin-like protein 2 is overexpressed and related to cell growth in human endometrial adenocarcinoma Oncol Rep 17 829 833 1:CAS:528:DC%2BD2sXkt1WntbY%3D 17342323
10. MW Dimmic JS Rest DP Mindell RA Goldstein 2002 rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny J Mol Evol 55 65 73 10.1007/s00239-001-2304-y 1:CAS:528: DC%2BD38XlvVCqsbY%3D 12165843 (Pubitemid 34634360)
11. C Donovan M Bramkamp 2009 Characterization and subcellular localization of a bacterial flotillin homologue Microbiology 155 1786 1799 10.1099/mic.0.025312-0 1:CAS:528:DC%2BD1MXnvFGmtL8%3D 19383680
12. RC Edgar 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 32 1792 1797 10.1093/nar/gkh340 1:CAS:528:DC%2BD2cXisF2ks7w%3D 15034147 (Pubitemid 38832724)
13. J Felsenstein 1978 Cases in which parsimony or compatibility methods will be positively misleading Syst Zool 27 401 410 10.2307/2412923
14. N Galtier M Gouy C Gautier 1996 SEAVIEW and PHYLO-WIN: two graphic tools for sequence alignment and molecular phylogeny Bioinformatics 12 543 548 10.1093/bioinformatics/12.6.543 1:CAS:528:DyaK2sXhtlWktLw%3D
15. FM García-Rodríguez N Toro 2000 Sinorhizobium meliloti nfe (nodulation formation efficiency) genes exhibit temporal and spatial expression patterns similar to those of genes involved in symbiotic nitrogen fixation Mol Plant Microbe Interact 13 583 591 10.1094/MPMI.2000.13.6.583 10830257
16. JP Gogarten H Kibak P Dittrich L Taiz EJ Bowman BJ Bowman MF Manolson RJ Poole T Date T Oshima 1989 Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes Proc Natl Acad Sci USA 86 6661 6665 10.1073/pnas.86.17.6661 1:CAS:528:DyaL1MXlslSjtrc%3D 2528146
17. JB Green JP Young 2008 Slipins: ancient origin, duplication and diversification of the stomatin protein family BMC Evol Biol 8 44 10.1186/1471-2148-8-44 18267007 (Pubitemid 351322920)
18. JB Green B Fricke MC Chetty M von Düring GF Preston GW Stewart 2004 Eukaryotic and prokaryotic stomatins: the proteolytic link Blood Cells Mol Dis 32 411 422 10.1016/j.bcmd.2004.01.016 1:CAS:528:DC%2BD2cXjs1Cjtrk%3D 15121101 (Pubitemid 38581863)
19. S Guindon O Gascuel 2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 52 696 704 10.1080/10635150390235520 14530136 (Pubitemid 37365050)
20. M Hinderhofer CA Walker A Friemel CA Sturmer HM Moller A Reuter 2009 Evolution of prokaryotic SPFH proteins BMC Evol Biol 9 10 10.1186/1471-2148-9-10 19138386
21. N Iwabe K Kuma M Hasegawa S Osawa T Miyata 1989 Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes Proc Natl Acad Sci USA 86 9355 9359 10.1073/pnas.86.23.9355 1:CAS:528:DyaK3cXkvF2rtg%3D%3D 2531898 (Pubitemid 20010424)
22. B Johannes 2005 A review of long-branch attraction Cladistics 21 163 193 10.1111/j.1096-0031.2005.00059.x (Pubitemid 40817232)
23. L Käll A Krogh EL Sonnhammer 2005 An HMM posterior decoder for sequence feature prediction that includes homology information Bioinformatics 21 Suppl 1 i251 i257 10.1093/bioinformatics/bti1014 15961464 (Pubitemid 41794496)
24. K Katoh K Misawa K Kuma T Miyata 2002 MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Res 30 3059 3066 10.1093/nar/gkf436 1:CAS:528:DC%2BD38XlslOqu7s%3D 12136088
25. Y Kuwahara A Ohno T Morii HY Yokoyama I Matsui H Tochio M Shirakawa H Hiroaki 2008 The solution structure of the C-terminal domain of NfeD reveals a novel membrane-anchored OB-fold Protein Sci 17 1915 1924 10.1110/ps.034736.108 1:CAS:528:DC%2BD1cXhtlGlsb%2FP 18687870
26. SQ Le O Gascuel 2008 An improved general amino acid replacement matrix Mol Biol Evol 25 1307 1320 10.1093/molbev/msn067 1:CAS:528:DC%2BD1cXotlKgsbg%3D 18367465 (Pubitemid 351882003)
27. L Li CJ Stoeckert DS Roos 2003 OrthoMCL: identification of ortholog groups for eukaryotic genomes Genome Res 13 2178 2189 10.1101/gr.1224503 1:CAS:528:DC%2BD3sXnslKhtLk%3D 12952885 (Pubitemid 37161775)
28. T Müller M Vingron 2000 Modeling amino acid replacement J Comput Biol 7 761 776 10.1089/10665270050514918 11382360
29. Rambaut A (2007) FigTree, a graphical viewer of phylogenetic trees. http://tree.bio.ed.ac.uk/software/figtree/
30. E Rivera-Milla CA Stuermer E Málaga-Trillo 2006 Ancient origin of reggie (flotillin), reggie-like, and other lipid-raft proteins: convergent evolution of the SPFH domain Cell Mol Life Sci 63 343 357 10.1007/s00018-005- 5434-3 1:CAS:528:DC%2BD28XhvFKmt78%3D 16389450 (Pubitemid 43202315)
31. F Ronquist JP Huelsenbeck 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models Bioinformatics 19 1572 1574 10.1093/bioinformatics/btg180 1:CAS:528:DC%2BD3sXntlKms7k%3D 12912839 (Pubitemid 37038874)
32. MJ Soto A Zorzano FM García-Rodríguez J Mercado-Blanco IM López-Lara J Olivares N Toro 1994 Identification of a novel Rhizobium meliloti nodulation efficiency nfe gene homolog of Agrobacterium ornithine cyclodeaminase Mol Plant Microbe Interact 7 703 707 1:CAS:528:DyaK2MXivFOgtLY%3D 7873778
33. GW Stewart BE Hepworth-Jones JN Keen BC Dash AC Argent CM Casimir 1992 Isolation of cDNA coding for an ubiquitous membrane protein deficient in high Na+, low K+ stomatocytic erythrocytes Blood 79 1593 1601 1:CAS:528: DyaK3sXhvVKjsbk%3D 1547348
34. N Tavernarakis M Driscoll NC Kyrpides 1999 The SPFH domain: implicated in regulating targeted protein turnover in stomatins and other membrane-associated proteins Trends Biochem Sci 24 425 427 10.1016/S0968-0004(99)01467-X 1:CAS:528:DC%2BD3cXkvVKnug%3D%3D 10542406 (Pubitemid 29528200)
35. CA Walker M Hinderhofer DJ Witte W Boos HM Möller 2008 Solution structure of the soluble domain of the NfeD protein YuaF from Bacillus subtilis J Biomol NMR 42 69 76 10.1007/s10858-008-9261-3 1:CAS:528:DC%2BD1cXhtV2js73L 18696230
36. Y Wang JS Morrow 2000 Identification and characterization of human SLP-2, a novel homologue of stomatin (band 7.2b) present in erythrocytes and other tissues J Biol Chem 275 8062 8071 10.1074/jbc.275.11.8062 1:CAS:528: DC%2BD3cXitVyltLg%3D 10713127 (Pubitemid 30159719)
37. S Whelan N Goldman 2001 A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach Mol Biol Evol 18 691 699 1:CAS:528:DC%2BD3MXjtFyktr4%3D 11319253
38. H Yokoyama I Matsui 2004 A novel thermostable membrane protease forming an operon with a stomatin homolog from the hyperthermophilic archaebacterium Pyrococcus horikoshii J Biol Chem 280 6588 6594 10.1074/jbc.M411748200 15611110
39. H Yokoyama E Matsui T Akiba K Harata I Matsui 2006 Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii J Mol Biol 358 1152 1164 10.1016/j.jmb.2006.02.052 1:CAS:528:DC%2BD28XjvVamu74%3D 16574150
40. HM Zhang Z Li M Tsudome S Ito H Takami K Horikoshi 2005 An alkali-inducible flotillin-like protein from Bacillus halodurans C-125 Protein J 24 125 131 10.1007/s10930-004-1519-3 1:CAS:528:DC%2BD2MXksVaisLo%3D 16003954 (Pubitemid 40875252)