Crossref journal-article
Oxford University Press (OUP)
Genome Biology and Evolution (286)
Bibliography

Kominek, J., Marszalek, J., Neuvéglise, C., Craig, E. A., & Williams, B. L. (2013). The Complex Evolutionary Dynamics of Hsp70s: A Genomic and Functional Perspective. Genome Biology and Evolution, 5(12), 2460–2477.

Authors 5
  1. Jacek Kominek (first)
  2. Jaroslaw Marszalek (additional)
  3. Cécile Neuvéglise (additional)
  4. Elizabeth A. Craig (additional)
  5. Barry L. Williams (additional)
References 96 Referenced 45
  1. 10.1016/S0022-2836(05)80360-2 / J Mol Biol. / Basic local alignment search tool by Altschul (1990)
  2. 10.1093/sysbio/syr100 / Syst Biol. / BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics by Ayres (2012)
  3. 10.1016/S0014-5793(00)02364-4 / FEBS Lett. / Ecm10, a novel hsp70 homolog in the mitochondrial matrix of the yeast Saccharomyces cerevisiae by Baumann (2000)
  4. 10.1093/oxfordjournals.molbev.a003912 / Mol Biol Evol. / Hsp70 duplication in the Drosophila melanogaster species group: how and when did two become five? by Bettencourt (2001)
  5. 10.1007/s00239-001-0044-7 / J Mol Evol. / Rapid concerted evolution via gene conversion at the Drosophila hsp70 genes by Bettencourt (2002)
  6. 10.1007/BF00175490 / J Mol Evol. / Molecular evolution of the HSP70 multigene family by Boorstein (1994)
  7. 10.1038/nature11510 / Nature / Epistasis as the primary factor in molecular evolution by Breen (2012)
  8. 10.1016/j.febslet.2009.04.029 / FEBS Lett. / The role of molecular chaperones in human misfolding diseases by Broadley (2009)
  9. 10.1186/1471-2148-8-19 / BMC Evol Biol. / hsp70 genes in the human genome: conservation and differentiation patterns predict a wide array of overlapping and specialized functions by Brocchieri (2008)
  10. 10.1083/jcb.150.1.65 / J Cell Biol. / The heat shock protein Ssa2p is required for import of fructose-1, 6-bisphosphatase into Vid vesicles by Brown (2000)
  11. 10.1093/nar/gkj041 / Nucleic Acids Res. / Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser by Byrne (2006)
  12. 10.1074/jbc.275.19.14494 / J Biol Chem. / The phosphorylation state and expression of soybean BiP isoforms are differentially regulated following abiotic stresses by Cascardo (2000)
  13. 10.1093/oxfordjournals.molbev.a026334 / Mol Biol Evol. / Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis by Castresana (2000)
  14. 10.1007/s12192-008-0014-8 / Cell Stress Chaperones / Antarctic marine molluscs do have an HSP70 heat shock response by Clark (2008)
  15. 10.1093/bioinformatics/btp163 / Bioinformatics / Biopython: freely available Python tools for computational molecular biology and bioinformatics by Cock (2009)
  16. {'key': 'key\n\t\t\t\t20170627103610_evt192-B16', 'volume-title': 'Hsp70 chaperones. Encyclopedia of life sciences (ELS)', 'author': 'Craig', 'year': '2011'} / Hsp70 chaperones. Encyclopedia of life sciences (ELS) by Craig (2011)
  17. 10.1093/bioinformatics/btr088 / Bioinformatics / ProtTest 3: fast selection of best-fit models of protein evolution by Darriba (2011)
  18. 10.1016/j.febslet.2007.05.039 / FEBS Lett. / The heat shock protein 70 family: highly homologous proteins with overlapping and distinct functions by Daugaard (2007)
  19. 10.1105/tpc.3.9.1025 / Plant Cell / The tobacco luminal binding-protein is encoded by a multigene family by Denecke (1991)
  20. 10.1038/332800a0 / Nature / A subfamily of stress proteins facilitates translocation of secretory and mitochondrial precursor polypeptides by Deshaies (1988)
  21. 10.1038/299111a0 / Nature / Molecular drive: a cohesive mode of species evolution by Dover (1982)
  22. 10.1073/pnas.0504070102 / Proc Natl Acad Sci U S A. / Why highly expressed proteins evolve slowly by Drummond (2005)
  23. 10.1038/nrg2811 / Nat Rev Genet. / Yeast evolutionary genomics by Dujon (2010)
  24. 10.1093/nar/gkh340 / Nucleic Acids Res. / MUSCLE: multiple sequence alignment with high accuracy and high throughput by Edgar (2004)
  25. 10.1038/nprot.2007.131 / Nat Protoc. / Locating proteins in the cell using TargetP, SignalP and related tools by Emanuelsson (2007)
  26. 10.1186/1471-2148-6-99 / BMC Evol Biol. / A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis by Fitzpatrick (2006)
  27. 10.1186/1471-2164-11-290 / BMC Genomics / Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser by Fitzpatrick (2010)
  28. 10.1038/nrg3456 / Nat Rev Genet. / Functional and evolutionary implications of gene orthology by Gabaldon (2013)
  29. 10.1016/j.gene.2006.07.033 / Gene / Comparative expression analysis of members of the Hsp70 family in the chytridiomycete Blastocladiella emersonii by Georg Rde (2007)
  30. 10.1111/j.1550-7408.1999.tb04594.x / J Eukaryot Microbiol. / Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family by Germot (1999)
  31. 10.1371/journal.pgen.1000485 / PLoS Genet. / Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome by Gordon (2009)
  32. 10.1093/oxfordjournals.molbev.a026080 / Mol Biol Evol. / Statistical methods for testing functional divergence after gene duplication by Gu (1999)
  33. 10.1093/oxfordjournals.molbev.a003824 / Mol Biol Evol. / Maximum-likelihood approach for gene family evolution under functional divergence by Gu (2001)
  34. 10.1080/10635150390235520 / Syst Biol. / A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood by Guindon (2003)
  35. 10.1128/jb.179.2.345-357.1997 / J Bacteriol. / Sequencing of heat shock protein 70 (DnaK) homologs from Deinococcus proteolyticus and Thermomicrobium roseum and their integration in a protein-based phylogeny of prokaryotes by Gupta (1997)
  36. 10.1016/S0960-9822(00)00249-9 / Curr Biol. / Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus by Gupta (1994)
  37. 10.1038/nrg3540 / Nat Rev Genet. / Evolutionary biochemistry: revealing the historical and physical causes of protein properties by Harms (2013)
  38. 10.1371/journal.pone.0065269 / PLoS One / Identification of a testis-enriched heat shock protein and fourteen members of hsp70 family in the swamp eel by He (2013)
  39. 10.1073/pnas.0404319101 / Proc Nati Acad Sci U S A. / Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts by Hittinger (2004)
  40. 10.1038/nsmb942 / Nat Struct Mol Biol. / The Hsp70 Ssz1 modulates the function of the ribosome-associated J-protein Zuo1 by Huang (2005)
  41. {'key': 'key\n\t\t\t\t20170627103610_evt192-B41', 'first-page': '243', 'article-title': 'Nonlinear relationships among evolutionary rates identify regions of functional divergence in heat-shock protein 70 genes', 'volume': '10', 'author': 'Hughes', 'year': '1993', 'journal-title': 'Mol Biol Evol.'} / Mol Biol Evol. / Nonlinear relationships among evolutionary rates identify regions of functional divergence in heat-shock protein 70 genes by Hughes (1993)
  42. 10.1007/s10142-013-0331-6 / Funct Integr Genomics. / Genome-wide expression analysis of HSP70 family genes in rice and identification of a cytosolic HSP70 gene highly induced under heat stress by Jung (2013)
  43. 10.2174/138920208785133280 / Curr Genomics. / Multiple hsp70 isoforms in the eukaryotic cytosol: mere redundancy or functional specificity? by Kabani (2008)
  44. 10.1038/nrm2941 / Nat Rev Mol Cell Biol. / The HSP70 chaperone machinery: J proteins as drivers of functional specificity by Kampinga (2010)
  45. 10.1093/molbev/mst010 / Mol Biol Evol. / MAFFT multiple sequence alignment software version 7: improvements in performance and usability by Katoh (2013)
  46. 10.1093/molbev/msj115 / Mol Biol Evol. / Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae by Kim (2006)
  47. 10.1146/annurev-biochem-060208-092442 / Annu Rev Biochem. / Molecular chaperone functions in protein folding and proteostasis by Kim (2013)
  48. 10.1093/molbev/msh146 / Mol Biol Evol. / Gene conversion and GC-content evolution in mammalian Hsp70 by Kudla (2004)
  49. 10.1093/molbev/msn067 / Mol Biol Evol. / An improved general amino acid replacement matrix by Le (2008)
  50. 10.1379/1466-1268(2001)006<0201:GAOTHS>2.0.CO;2 / Cell Stress Chaperones / Genomic analysis of the Hsp70 superfamily in Arabidopsis thaliana by Lin (2001)
  51. 10.1016/j.cell.2007.08.039 / Cell / Insights into Hsp70 chaperone activity from a crystal structure of the yeast Hsp110 Sse1 by Liu (2007)
  52. 10.1016/j.parint.2010.08.008 / Parasitol Int. / The Hsp70 chaperones of the Tritryps are characterized by unusual features and novel members by Louw (2010)
  53. 10.1007/s11033-007-9178-z / Mol Biol Rep. / Cloning and expression of glucose regulated protein 78 (GRP78) in Fenneropenaeus chinensis by Luan (2009)
  54. 10.1186/1471-2105-7-113 / BMC Bioinformatics / An improved map of conserved regulatory sites for Saccharomyces cerevisiae by MacIsaac (2006)
  55. 10.1093/molbev/mst042 / Mol Biol Evol. / Comparative genome analysis and gene finding in Candida species using CGOB by Maguire (2013)
  56. 10.1105/tpc.3.5.507 / Plant Cell / Three high-lysine mutations control the level of ATP-binding HSP70-like proteins in the maize endosperm by Marocco (1991)
  57. 10.1074/jbc.M113.479253 / J Biol Chem. / Hsp110 is a bona fide chaperone using ATP to unfold stable misfolded polypeptides and reciprocally collaborate with hsp70 to solubilize protein aggregates by Mattoo (2013)
  58. 10.1007/s00018-004-4464-6 / Cell Mol Life Sci. / Hsp70 chaperones: cellular functions and molecular mechanism by Mayer (2005)
  59. 10.1091/mbc.9.12.3533 / Mol Biol Cell. / Specific molecular chaperone interactions and an ATP-dependent conformational change are required during posttranslational protein translocation into the yeast ER by McClellan (1998)
  60. 10.1016/S0305-0491(96)00219-2 / Comp Biochem Physiol B Biochem Mol Biol. / Isolation and characterization of a cDNA encoding a Xenopus immunoglobulin binding protein, BiP (grp78) by Miskovic (1997)
  61. 10.1146/annurev.genet.39.073003.112240 / Annu Rev Genet. / Concerted and birth-and-death evolution of multigene families by Nei (2005)
  62. 10.1093/molbev/msh041 / Mol Biol Evol. / Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes by Nikolaidis (2004)
  63. 10.1074/jbc.M110.197434 / J Biol Chem. / Primary sequence that determines the functional overlap between mitochondrial heat shock protein 70 Ssc1 and Ssc3 of Saccharomyces cerevisiae by Pareek (2011)
  64. {'key': 'key\n\t\t\t\t20170627103610_evt192-B64', 'volume-title': 'Analysis of codon usage', 'author': 'Peden', 'year': '1999'} / Analysis of codon usage by Peden (1999)
  65. 10.1093/emboj/17.14.3981 / EMBO J. / The molecular chaperone Ssb from Saccharomyces cerevisiae is a component of the ribosome-nascent chain complex by Pfund (1998)
  66. {'key': 'key\n\t\t\t\t20170627103610_evt192-B96', 'volume-title': 'R: a language and environment for statistical computing [Internet] R version 3.0.1', 'author': 'R Development Core Team', 'year': '2013'} / R: a language and environment for statistical computing [Internet] R version 3.0.1 by R Development Core Team (2013)
  67. 10.1038/emboj.2012.264 / EMBO J. / Metazoan Hsp70 machines use Hsp110 to power protein disaggregation by Rampelt (2012)
  68. 10.1016/j.febslet.2005.11.069 / FEBS Lett. / Human and yeast Hsp110 chaperones exhibit functional differences by Raviol (2006)
  69. 10.1126/science.1203357 / Science / Comparative functional genomics of the fission yeasts by Rhind (2011)
  70. 10.1093/sysbio/sys029 / Syst Biol. / MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space by Ronquist (2012)
  71. 10.1016/S0006-291X(03)01548-1 / Biochem Biophys Res Commun. / Ecm10p localizes in yeast mitochondrial nucleoids and its overexpression induces extensive mitochondrial DNA aggregations by Sakasegawa (2003)
  72. 10.1534/g3.111.000273 / G3 (Bethesda) / The awesome power of yeast evolutionary genetics: new genome sequences and strain resources for the Saccharomyces sensu stricto genus by Scannell (2011)
  73. 10.1016/j.cub.2006.06.069 / Curr Biol. / Evolution of mitochondrial chaperones utilized in Fe-S cluster biogenesis by Schilke (2006)
  74. 10.1016/j.molcel.2008.05.006 / Mol Cell. / Structure of the Hsp110:Hsc70 nucleotide exchange machine by Schuermann (2008)
  75. 10.1379/CSC-245R.1 / Cell Stress Chaperones / All in the family: atypical Hsp70 chaperones are conserved modulators of Hsp70 activity by Shaner (2007)
  76. 10.1371/journal.pone.0006644 / PLoS One / Function of SSA subfamily of Hsp70 within and across species varies widely in complementing Saccharomyces cerevisiae cell growth and prion propagation by Sharma (2009)
  77. 10.1073/pnas.1107421108 / Proc Nat Acad Sci U S A. / Single methyl group determines prion propagation and protein degradation activities of yeast heat shock protein (Hsp)-70 chaperones Ssa1p and Ssa2p by Sharma (2011)
  78. 10.1002/yea.320070702 / Yeast / Synonymous codon usage in Saccharomyces cerevisiae by Sharp (1991)
  79. 10.1038/msb.2010.65 / Mol Syst Biol. / An interdomain sector mediating allostery in Hsp70 molecular chaperones by Smock (2010)
  80. 10.1093/bioinformatics/btl446 / Bioinformatics / RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models by Stamatakis (2006)
  81. 10.1126/science.1092287 / Science / Coordinated activation of Hsp70 chaperones by Steel (2004)
  82. 10.1016/j.tig.2006.09.014 / Trends Genet. / Selection for more of the same product as a force to enhance concerted evolution of duplicated genes by Sugino (2006)
  83. 10.1093/molbev/msp211 / Mol Biol Evol. / Selection to maintain paralogous amino acid differences under the pressure of gene conversion in the heat-shock protein genes in yeast by Takuno (2009)
  84. 10.1080/15572536.2006.11832614 / Mycologia / Dating divergences in the fungal tree of life: review and new analyses by Taylor (2006)
  85. 10.1093/nar/gkn304 / Nucleic Acids Res. / RSAT: regulatory sequence analysis tools by Thomas-Chollier (2008)
  86. 10.1379/CSC-137R.1 / Cell Stress Chaperones / A genomewide analysis of genes for the heat shock protein 70 chaperone system in the ascidian Ciona intestinalis by Wada (2006)
  87. 10.1074/mcp.O111.014704 / Mol Cell Proteomics / PaxDb, a database of protein abundance averages across all three domains of life by Wang (2012)
  88. 10.1128/jb.171.5.2680-2688.1989 / J Bacteriol. / Yeast Hsp70 RNA levels vary in response to the physiological status of the cell by Werner-Washburne (1989)
  89. 10.1128/MCB.7.7.2568 / Mol Cell Biol. / Complex interactions among members of an essential subfamily of hsp70 genes in Saccharomyces cerevisiae by Werner-Washburne (1987)
  90. 10.1038/42711 / Nature / Molecular evidence for an ancient duplication of the entire yeast genome by Wolfe (1997)
  91. 10.1016/0378-1119(90)90491-9 / Gene / The ‘effective number of codons’ used in a gene by Wright (1990)
  92. 10.2478/s11756-013-0182-6 / Biologia / Molecular cloning and expression analysis of glucose-regulated protein 78 (GRP78) gene in silkworm Bombyx mori by Xi (2013)
  93. 10.1074/jbc.M111.275057 / J Biol Chem. / Unique peptide substrate binding properties of 110-kDa heat-shock protein (Hsp110) determine its distinct chaperone activity by Xu (2012)
  94. 10.1007/s12192-012-0323-9 / Cell Stress Chaperones / Molecular characterization and mRNA expression of grp78 and hsp90A in the estuarine copepod Eurytemora affinis by Xuereb (2012)
  95. 10.1093/molbev/msm088 / Mol Biol Evol. / PAML 4: phylogenetic analysis by maximum likelihood by Yang (2007)
  96. 10.1126/science.272.5268.1606 / Science / Structural analysis of substrate binding by the molecular chaperone DnaK by Zhu (1996)
Dates
Type When
Created 11 years, 9 months ago (Nov. 25, 2013, 9:47 p.m.)
Deposited 8 years ago (Aug. 23, 2017, 12:32 a.m.)
Indexed 1 week, 1 day ago (Aug. 23, 2025, 9:56 p.m.)
Issued 11 years, 9 months ago (Nov. 24, 2013)
Published 11 years, 9 months ago (Nov. 24, 2013)
Published Online 11 years, 9 months ago (Nov. 24, 2013)
Published Print 11 years, 9 months ago (Dec. 1, 2013)
Funders 0

None

@article{Kominek_2013, title={The Complex Evolutionary Dynamics of Hsp70s: A Genomic and Functional Perspective}, volume={5}, ISSN={1759-6653}, url={http://dx.doi.org/10.1093/gbe/evt192}, DOI={10.1093/gbe/evt192}, number={12}, journal={Genome Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Kominek, Jacek and Marszalek, Jaroslaw and Neuvéglise, Cécile and Craig, Elizabeth A. and Williams, Barry L.}, year={2013}, month=nov, pages={2460–2477} }