Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Chen, Bin ^a,b   Zhong, Daibin ^b   Monteiro, Antónia ^b  

^a SOUTHWEST UNIVERSITY   (China)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEAT SHOCK PROTEIN 90; THROMBIN RECEPTOR ACTIVATING PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL STRAIN; COMPARATIVE STUDY; CONTROLLED STUDY; ENDOSYMBIONT; EUKARYOTE; EUKARYOTIC CELL; EXON; FLAGELLATE; FUNGAL STRAIN; GENE DUPLICATION; GENE IDENTIFICATION; GENE LOCATION; GENE LOSS; GENE SEQUENCE; GENE STRUCTURE; GENETIC CODE; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOMICS; HIGHER PLANT; MOLECULAR EVOLUTION; MOLECULAR WEIGHT; NOMENCLATURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PARAPHYLY; PHYLOGENY; PROTEIN PROCESSING; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; ANIMALS; ARCHAEAL PROTEINS; BACTERIAL PROTEINS; CHROMOSOME MAPPING; COMPLEMENTARITY DETERMINING REGIONS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOMICS; HSP90 HEAT-SHOCK PROTEINS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; TERMINOLOGY AS TOPIC; VERTEBRATES;

ANIMALIA; DIPLOMONADIDA; EMBRYOPHYTA; EUKARYOTA; FIRMICUTES; FUNGI; PLANTAE; PROTISTA; VERTEBRATA;

EID: 33746660802     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-156     Document Type: Article

References (74)

1. Csermely P, Schnaider T, Soti C, Prohászka Z, Nardai G: The 90-kDa molecular chaperone family: structure, function, and clinical applications. A comprehensive review. Pharmacol Ther 1998, 79:129-168.
2. Ali A, Bharadwaj S, O'Carrol R, Ovsenek N: Hsp90 interacts with and regulates the activity of heat shock factor 1 in Xenopus oocytes. Mol Cell Biol 1998, 18:4949-4960.
3. Chen B, Kayukawa T, Monteiro A, Ishikawa Y: The expression of HSP90 gene in response to diapauses and thermal-stress in the onion maggot, Delia antique. Insect Mol Biol 2005, 14:697-702.
4. Nadeau K, Das A, Walsh CT: Hsp90 chaperonins possess ATPase activity and bind heat-shock transcription factors and peptidylprolyl isomerases. J Biol Chem 1993, 268:1479-1487.
5. Jakob U, Lilie H, Meyer I, Buchner J: Transient interactions of Hsp90 with early unfolding intermediates of citrate synthase. Implications for heat shock in vivo. J Biol Chem 1995, 270:7288-7294.
6. Schatz G, Dobberstein B: Common principles of protein translocation across membranes. Science 1996, 271:1519-1526.
7. Rutherford SL, Lindquist S: Hsp90 as a capacitor for morphological evolution. Nature 1998, 396:336-342.
8. Young JC, Moarefi I, Hartl FU: Hsp90: a specialist but essential protein-folding tool. J Cell Biol 2001, 154:267-273.
9. Garcia-Cardena G, Fan R, Shah V, Sorrentino R, Cirino, G, Papapetropoulos A, Sessa WC: Dynamic activation of endothelial nitric oxide synthase by Hsp90. Nature 1998, 392:821-824.
10. Imai J, Yahara I: Role of HSP90 in salt stress tolerance via stabilization and regulation of calcineurin. Mol Cell Biol 2000, 20:9262-9270.
11. Richter K, Buchner J: Hsp90: chaperoning signal transduction. J Cell Physiol 2001, 188:281-290.
12. Pratt WB, Toft DO: Regulation of signaling protein function and trafficking by the hsp90/hsp70-based chaperone machinery. Exp Biol Med 2003, 228:111-133.
13. Wegele H, Müller L, Buchner J: Hsp70 and Hsp90-a relay team for protein folding. Rev Physiol Biochem Pharmacol 2004, 151:1-44.
14. Queitsch C, Sangster TA, Lindquist S: Hsp90 as a capacitor of phenotypic variation. Nature 2002, 417:618-624.
15. Sreedhar AS, Kalmar E, Csermely P, Shen YF: Hsp90 isoforms: functions, expression and clinical importance. FEBS Letters 2004, 562:11-15.
16. Tanaka N, Nakamoto H: HtpG is essential for the thermal stress management in cyanobacteria. FEBS Lett 1999, 458:117-123.
17. Stechmann A, Cavalier-Smith T: Evolutionary origins of Hsp90 chaperones and a deep paralogy in their bacterial ancestors. J Eukaryot Microbiol 2004, 51:364-373.
18. Felts SJ, Owen BAL, Nguyen P, Trepel J, Donner DB, Toft DO: The hsp90-related protein TRAP1 is a mitochontrial protein with distinct functional properties. J Biol Chem 2000, 275:3305-3312.
19. Krishna P, Gloor G: The Hsp90 family of proteins in Arabidopsis thaliana. Cell Stress Chaperon 2001, 6:238-246.
20. Rebbe NF, Ware J, Bertina RM, Modrich P, Stafford DW: Nucleotide sequence of a cDNA for a member of the human 90-kDa heat-shock protein family. Gene 1987, 53:235-245.
21. Hoffmann T, Hovemann B: Heat-shock proteins, Hsp84 and Hsp86, of mice and men: two related genes encode formerly identified tumour-specific transplantation antigens. Gene 1988, 74:491-501.
22. Krone PH, Sass JB: Hsp90α and Hsp90β genes are present in the zebrafish and are differentially regulated on developing embryos. Biochem Biophys Res Co 1994, 204:746-752.
23. Gupta RS: Phylogenetic analysis of the 90 kD heat shock family of protein sequences and an examination of the relationship among animals, plants, and fungi species. Mol Biol Evol 1995, 12:1063-1073.
24. Emelyanov VV: Phylogenetic relationships of organellar Hsp90 homologs reveal fundamental differences to organellar Hsp70 and Hsp60 evolution. Gene 2002, 299:125-133.
25. Song HY, Dunbar JD, Zhang YX, Guo D, Donner DB: Identification of a protein with homology to hsp90 that binds the type I tumor necrosis factor receptor. J Biol Chem 1995, 270:3574-3581.
26. Chen CF, Chen YM, Dai K, Chen PL, Riley DJ, Lee WH: A new member of the Hsp90 family of molecular chaperones interacts with the retinoblastoma protein during mitosis and after heat shock. Mol Cell Biol 1996, 16:4691-4699.
27. Stechmann A, Cavalier-Smith T: Phylogenetic analysis of eukaryotes using heat-shock protein Hsp90. J Mol Evol 2003, 57:408-419.
28. Chen B, Piel WH, Gui LM, Bruford E, Monteiro A: The HSP90 family of genes in the human genome: insights into their divergence and evolution. Genomics 2005, 86:627-637.
29. HUGO Gene Nomenclature Committee [http://www.gene.ucl.ac.uk/nomenclature]
30. Schroda M: The Chlamydomonas genome reveals its secrets: chaperone genes and the potential roles of their gene products in the chloroplast. Photosyn Res 2004, 82:221-240.
31. White JA, McAlpine PJ, Antonarakis S, Cann H, Eppig JT, Frazer K, Frezal J, Lancet D, Nahmias J, Pearson P, Peters J, Scott A, Scott H, Spurr N, Talbot C, Povey S: Guidelines for human gene nomenclature (1997). Genomics 1997, 45:468-471.
32. Maltais LJ, Blake JA, Eppig JT, Davisson MT: Rules and guidelines for mouse gene nomenclature: a condensed version. Genomics 1997, 45:471-476.
33. Obermann WMJ, Sondermann H, Russo AA, Pavletich NP, Hard FU: In vivo function of Hsp90 is dependent on ATP binding and ATP hydrolysis. J Cell Biol 1998, 143:901-910.
34. Lindquist S: The heat-shock response. Annu Rev Biochem 1986, 55:1151-1191.
35. Gupta RS: Origin of eukaryotic cells: was metabolic symbiosis based on hydrogen driving force? Trends Biochem Sci 1998, 24:423.
36. Cavalier-Smith T: The neomuran origin of archaebacteria, the neigibacteria root of the universal tree and bacterial mega-classification. Int J Sys Evol Microbiol 2002, 52:7-76.
37. Cavalier-Smith T: Only six kingdoms of life. Proc R Soc Lond B 2004, 271:1251-1262.
38. Rossello-Mora R: Updating prokaryotic taxonomy. J Bacteriol 2005, 187:6255-6257.
39. Cechetto ID, Gupta RS: Immunoelectron microscopy provides evidence that tumor necrosis factors receptor-associated protein 1 (TRAP-1) is a mitochondrial protein which also localizes as specific extramitochondrial sites. Exp Cell Res 2000, 260:30-39.
40. Morita T, Amagai A, Maeda Y: Unique behaviors of a Dictyostelium homolog of TRAP-1, coupling with differentiation of D. discoideum cell. Exp Cell Res 2002, 280:45-54.
41. Kurland CG, Andersson SG: Origin and evolution of the mitochondrial proteome. Microbiol Mol Biol Rev 2000, 64:786-820.
42. Emelyanov VV: Evolutionary relationship of rickettsiae and mitochondria. FEBS Lett 2001, 501:11-18.
43. Martin W, Muller M: The hydrogen hypothesis for the first eukaryote. Nature 1998, 392:37-41.
44. Gupta RS, Aitken K, Falah M, Singh B: Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum. Proc Nat Acad Sci USA 1994, 91:2895-2899.
45. Gupta RS: Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes. Microbiol Mol Biol Rev 1998, 62:1435-1491.
46. Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD: Molecular biology of the cell Garland Publishing, Inc., New York; 1994.
47. Craig EA: Chaperones: helpers along the pathways to protein foldings. Science 1993, 260:1902-1903.
48. Nicchitta CV: Biochemical, cell biological and immunological issues surrounding the endoplasmic reticulum chaperone GRP94/gp96. Curr Opin Immunol 1998, 10:103-109.
49. Schmitz G, Schmidt M, Feierabend J: Characterization of a plastid-specific HSP90 homologue: Identification of a cDNA sequence, phylogenetic descendence and analysis of its mRNA and protein expression. Plant Mol Biol 1996, 30:479-492.
50. Cao DS, Froehlich JE, Zhang H, Cheng CL: The chlorate-resistant and photomorphogenesis-defensive mutant cr88 encodes a chloroplast-targeted HSP90. Plant J 2003, 33:107-118.
51. Willmund F, Schroda M: Heat shock protein 90C is a bona fide HSP90 that interacts with plastidic HSP70B in Chlamydomonas reinhardtii. Plant Physiol 2005, 138:2310-2322.
52. Martin W, Stoebe B, Goremykin V, Hansmann S, Hasegawa M, Kowallik KV: Gene transfer to the nucleus and the evolution of chloroplasts. Nature 1998, 393:162-165.
53. Gray MW: Evolution of organellar genomes. Curr Opin Genet Dev 1999, 9:678-687.
54. Moreira D, Le Guyader H, Philippe H: The origin of red algae and the evolution of chloroplasts. Nature 2000, 405:69-72.
55. Lee JJ, Leedale GF, Bradgeny P: An illustrated guide of Protozoa 2nd edition. Society of Protozoologist. Lawrence, Kans; 2000.
56. Cavalier-Smith T: The phagoretophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Sys Evol Microbiol 2002, 52:297-354.
57. Arisue N, Hasegawa M, Hashimoto T: Root of the Eukaryota tree as inferred from combined maximum likelihood analysis of multiple molecular sequence data. Mol Bio Evol 2005, 22:409-420.
58. Sogin ML, Gunderson JH, Elwood HJ, Alonso RA, Peattie DA: Phylogenetic meaning of the kingdom concept - an unusual ribosomal-RNA from Giardia lamblia. Science 1989, 243:75-77.
59. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
60. NCBI [http://www.ncbi.nlm.nih.gov]
61. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 1997, 25:4876-4882.
62. Orengo CA, Jones DT, Thornton JM: Bioinformatics: genes, proteins & computers BIOS Scientific Publisher Ltd, Oxford, UK; 2003.
63. Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999, 41:95-98.
64. Burge CB, Karlin S: Finding the genes in genomic DNA. Curr Opin Struct Biol 1998, 8:346-354.
65. Nielsen H, Engelbrecht J, Brunak S, von Heijne G: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997, 10:1-6.
66. ScanProsite software [http://us.expasy.org/prosite]
67. Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340:783-795.
68. Hulo N, Sigrist CJA, Le Saux V, Langendijk-Genevaux PS, Bordoli L, Gattiker A, De Castro E, Bucher P, Bairoch A: Recent improvements to the PROSITE database. Nucl Acids Res 2004, 32:D134-D137.
69. Zdobnov EM, Apweiler R: InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848.
70. InterPro [http://www.ebi.ac.uk/interpro]
71. Swofford D: PAUP*: Phylogenetic analysis using parsimony (and other methods), version 4.0b8 Sinauer Associates, Inc, Sunderlands, Massachusetts; 2001.
72. Grenert JP, Sullivan WP, Fadden P, Haystead TAJ, Clark J, Mimnaugh E, Krutzsch H, Oche HJ, Schulte TW, Sausville E, Neckers LM, Toft DO: The amino-terminal domain of heat shock protein 90 (hsp90) that binds geldanamycin is an ATP/ADP switch domain that regulates hsp90 conformation. J Biol Chem 1997, 272:23843-23850.
73. Meyer P, Prodromou C, Hu B, Vaughan C, Roe SM, Panaretou B, Piper PW, Pearl LH: Structural and functional analysis of the middle segment of Hsp90: implications for ATP hydrolysis and client protein and cochaperone interactions. Mol Cell 2003, 11:647-658.
74. Lees-Miller SP, Anderson CW: Two human 90-kDa heat shock proteins are phosphorylated in vivo at conserved serines that are hosphorylated in vitro by casein kinase II. J Biol Chem 1989, 264:2431-2437.