Cell Stress and Chaperones

, Volume 14, Issue 1, pp 1–21 | Cite as

Computational analysis of the human HSPH/HSPA/DNAJ family and cloning of a human HSPH/HSPA/DNAJ expression library

Perspective and Reflection Article

Abstract

In this manuscript, we describe the generation of a gene library for the expression of HSP110/HSPH, HSP70/HSPA and HSP40/DNAJ members. First, the heat shock protein (HSP) genes were collected from the gene databases and the gene families were analyzed for expression patterns, heat inducibility, subcellular localization, and protein homology using several bioinformatics approaches. These results can be used as a working draft model until data are confirmed by experimental approaches. In addition, we describe the generation of a HSPA/DNAJ overexpression library and tested the effect of different fusion tags on HSPA and DNAJ members using different techniques for measuring chaperone activity. These results show that we have cloned a high-quality heat shock protein expression library containing most members from the HSPH, HSPA, DNAJA and DNAJB families which will be useful for the chaperone community to unravel the function of the highly diverse family of human molecular chaperones.

Keywords

HspH HspA DnaJ Hsp110 Hsp70 Hsp40 Human chaperones Bio-informatics 

Notes

Acknowledgements

We would like to thank Maria A.W.H. van Waarde for expert assistance on biochemical analysis. We thank Eefje Pelster, Alette H. Faber, and Reinier Bron for assistance on gene cloning. Lenja Bystrykh (Department of Cell Biology, Stem Cell Biology Section, University Medical Center Groningen, The Netherlands) is kindly acknowledged for help on the Unigene EST collection and Ron Dirks (section Biochemistry, Radbout University, Nijmegen, The Netherlands) for help on the Affimetrix gene array data. Russell S. Thomas (CIIT Centers for Health Research, NC, USA) is acknowledged for providing the array data sets. This work was supported by Innovatiegerichte Onderzoeksprogramma Genomics Grant IGE03018.

References

  1. Albanese V, Yam AY, Baughman J, Parnot C, Frydman J (2006) Systems analyses reveal two chaperone networks with distinct functions in eukaryotic cells. Cell 124:75–88 doi:10.1016/j.cell.2005.11.039 PubMedCrossRefGoogle Scholar
  2. Brocchieri L, Conway de ME, Macario AJ (2007) Chaperonomics, a new tool to study ageing and associated diseases. Mech Ageing Dev 128:125–136 doi:10.1016/j.mad.2006.11.019 PubMedCrossRefGoogle Scholar
  3. Brocchieri L, Conway de ME, Macario AJ (2008) HSP70 genes in the human genome: conservation and differentiation patterns predict a wide array of overlapping and specialized functions. BMC Evol Biol 8:19 doi:10.1186/1471-2148-8-19 PubMedCrossRefGoogle Scholar
  4. Carra S, Sivilotti M, Chavez Zobel AT, Lambert H, Landry J (2005) HSPB8, a small heat shock protein mutated in human neuromuscular disorders, has in vivo chaperone activity in cultured cells. Hum Mol Genet 14:1659–1669 doi:10.1093/hmg/ddi174 PubMedCrossRefGoogle Scholar
  5. Chapple JP, Cheetham ME (2003) The chaperone environment at the cytoplasmic face of the endoplasmic reticulum can modulate rhodopsin processing and inclusion formation. J Biol Chem 278:19087–19094 doi:10.1074/jbc.M212349200 PubMedCrossRefGoogle Scholar
  6. Garcia-Otin AL, Guillou F (2006) Mammalian genome targeting using site-specific recombinases. Front Biosci 11:1108–1136 doi:10.2741/1867 PubMedCrossRefGoogle Scholar
  7. Gascuel O, Steel M (2006) Neighbor-joining revealed. Mol Biol Evol 23:1997–2000 doi:10.1093/molbev/msl072 PubMedCrossRefGoogle Scholar
  8. Graham FL, Smiley J, Russell WC, Nairn R (1977) Characteristics of a human cell line transformed by DNA from human adenovirus type 5. J Gen Virol 36:59–74 doi:10.1099/0022-1317-36-1-59 PubMedCrossRefGoogle Scholar
  9. Gribaldo S, Lumia V, Creti R, de Macario EC, Sanangelantoni A, Cammarano P (1999) Discontinuous occurrence of the HSP70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein. J Bacteriol 181:434–443PubMedGoogle Scholar
  10. Guda C (2006) pTARGET: a web server for predicting protein subcellular localization. Nucleic Acids Res 34:W210–W213 doi:10.1093/nar/gkl093 PubMedCrossRefGoogle Scholar
  11. Hageman J, Eggen BJ, Rozema T, Damman K, Kampinga HH, Coppes RP (2005) Radiation and transforming growth factor-beta cooperate in transcriptional activation of the profibrotic plasminogen activator inhibitor-1 gene. Clin Cancer Res 11:5956–5964 doi:10.1158/1078-0432.CCR-05-0427 PubMedCrossRefGoogle Scholar
  12. Held T, Paprotta I, Khulan J et al (2006) HSPA4l-deficient mice display increased incidence of male infertility and hydronephrosis development. Mol Cell Biol 26:8099–8108 doi:10.1128/MCB.01332-06 PubMedCrossRefGoogle Scholar
  13. Hennessy F, Nicoll WS, Zimmermann R, Cheetham ME, Blatch GL (2005) Not all J domains are created equal: implications for the specificity of HSP40–HSP70 interactions. Protein Sci 14:1697–1709 doi:10.1110/ps.051406805 PubMedCrossRefGoogle Scholar
  14. Hoglund A, Donnes P, Blum T, Adolph HW, Kohlbacher O (2006) MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinformatics 22:1158–1165 doi:10.1093/bioinformatics/btl002 PubMedCrossRefGoogle Scholar
  15. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35:W585–W587 doi:10.1093/nar/gkm259 PubMedCrossRefGoogle Scholar
  16. Ito Y, Ando A, Ando H, Ando J, Saijoh Y, Inoko H, Fujimoto H (1998) Genomic structure of the spermatid-specific HSP70 homolog gene located in the class III region of the major histocompatibility complex of mouse and man. J Biochem 124:347–353PubMedGoogle Scholar
  17. Kampinga HH (2006) Chaperones in preventing protein denaturation in living cells and protecting against cellular stress. Handb Exp Pharmacol 172:1–42PubMedCrossRefGoogle Scholar
  18. Knopf CW, Zavidij O, Rezuchova I, Rajcani J (2008) Evaluation of the T-REx transcription switch for conditional expression and regulation of HSV-1 vectors. Virus Genes 36:55–66 doi:10.1007/s11262-007-0178-9 PubMedCrossRefGoogle Scholar
  19. Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948 doi:10.1093/bioinformatics/btm404 PubMedCrossRefGoogle Scholar
  20. Maglott D, Ostell J, Pruitt KD, Tatusova T (2007) Entrez gene: gene-centered information at NCBI. Nucleic Acids Res 35:D26–D31 doi:10.1093/nar/gkl993 PubMedCrossRefGoogle Scholar
  21. Maurer-Stroh S, Koranda M, Benetka W, Schneider G, Sirota FL, Eisenhaber F (2007) Towards complete sets of farnesylated and geranylgeranylated proteins. PLoS Comput Biol 3:e66 doi:10.1371/journal.pcbi.0030066 PubMedCrossRefGoogle Scholar
  22. Michels AA, Nguyen VT, Konings AW, Kampinga HH, Bensaude O (1995) Thermostability of a nuclear-targeted luciferase expressed in mammalian cells. Destabilizing influence of the intranuclear microenvironment. Eur J Biochem 234:382–389 doi:10.1111/j.1432-1033.1995.382_b.x PubMedCrossRefGoogle Scholar
  23. Michels AA, Kanon B, Konings AW, Ohtsuka K, Bensaude O, Kampinga HH (1997) HSP70 and HSP40 chaperone activities in the cytoplasm and the nucleus of mammalian cells. J Biol Chem 272:33283–33289 doi:10.1074/jbc.272.52.33283 PubMedCrossRefGoogle Scholar
  24. Michels AA, Kanon B, Bensaude O, Kampinga HH (1999) Heat shock protein (HSP) 40 mutants inhibit HSP70 in mammalian cells. J Biol Chem 274:36757–36763 doi:10.1074/jbc.274.51.36757 PubMedCrossRefGoogle Scholar
  25. Mishra GR, Suresh M, Kumaran K et al (2006) Human protein reference database – 2006 update. Nucleic Acids Res 34:D411–D414 doi:10.1093/nar/gkj141 PubMedCrossRefGoogle Scholar
  26. Muller-Taubenberger A (2006) Application of fluorescent protein tags as reporters in live-cell imaging studies. Methods Mol Biol 346:229–246PubMedGoogle Scholar
  27. Nollen EA, Brunsting JF, Song J, Kampinga HH, Morimoto RI (2000) Bag1 functions in vivo as a negative regulator of HSP70 chaperone activity. Mol Cell Biol 20:1083–1088 doi:10.1128/MCB.20.3.1083-1088.2000 PubMedCrossRefGoogle Scholar
  28. Noonan EJ, Place RF, Giardina C, Hightower LE (2007) HSP70B’ regulation and function. Cell Stress Chaperones 12:219–229 doi:10.1379/CSC-278.1 PubMedCrossRefGoogle Scholar
  29. Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358PubMedGoogle Scholar
  30. Page TJ, Sikder D, Yang L, Pluta L, Wolfinger RD, Kodadek T, Thomas RS (2006) Genome-wide analysis of human HSF1 signaling reveals a transcriptional program linked to cellular adaptation and survival. Mol Biosyst 2:627–639 doi:10.1039/b606129j PubMedCrossRefGoogle Scholar
  31. Rudiger S, Germeroth L, Schneider-Mergener J, Bukau B (1997) Substrate specificity of the DnaK chaperone determined by screening cellulose-bound peptide libraries. EMBO J 16:1501–1507 doi:10.1093/emboj/16.7.1501 PubMedCrossRefGoogle Scholar
  32. Rudiger S, Schneider-Mergener J, Bukau B (2001) Its substrate specificity characterizes the DNAJ co-chaperone as a scanning factor for the DnaK chaperone. EMBO J 20:1042–1050 doi:10.1093/emboj/20.5.1042 PubMedCrossRefGoogle Scholar
  33. Rujano MA, Kampinga HH, Salomons FA (2007) Modulation of polyglutamine inclusion formation by the HSP70 chaperone machine. Exp Cell Res 313:3568–3578 doi:10.1016/j.yexcr.2007.07.034 PubMedCrossRefGoogle Scholar
  34. Sahi C, Craig EA (2007) Network of general and specialty J protein chaperones of the yeast cytosol. Proc Natl Acad Sci U S A 104:7163–7168 doi:10.1073/pnas.0702357104 PubMedCrossRefGoogle Scholar
  35. Schuler GD (1997) Pieces of the puzzle: expressed sequence tags and the catalog of human genes. J Mol Med 75:694–698 doi:10.1007/s001090050155 PubMedCrossRefGoogle Scholar
  36. Sprenger J, Fink JL, Teasdale RD (2006) Evaluation and comparison of mammalian subcellular localization prediction methods. BMC Bioinformatics 7(Suppl 5):S3 doi:10.1186/1471-2105-7-S5-S3 PubMedCrossRefGoogle Scholar
  37. Szafron D, Lu P, Greiner R et al (2004) Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Res 32:W365–W371 doi:10.1093/nar/gkh485 PubMedCrossRefGoogle Scholar
  38. Terada K, Mori M (2000) Human DNAJ homologs dj2 and dj3, and bag-1 are positive cochaperones of hsc70. J Biol Chem 275:24728–24734 doi:10.1074/jbc.M002021200 PubMedCrossRefGoogle Scholar
  39. Wheeler DL, Barrett T, Benson DA et al (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 35:D5–D12 doi:10.1093/nar/gkl1031 PubMedCrossRefGoogle Scholar
  40. Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins 64:643–651 doi:10.1002/prot.21018 PubMedCrossRefGoogle Scholar

Copyright information

© Cell Stress Society International 2008

Authors and Affiliations

  1. 1.Section of Radiation and Stress Cell Biology, Department of Cell BiologyUniversity Medical Center Groningen, University of GroningenGroningenThe Netherlands
  2. 2.GroningenThe Netherlands

Personalised recommendations