Supplemental figure 1: Correlation of Arabidopsis chaperome transcription in five independent heat shock treatments. Heat shock cognates are indicated by arrows. The microarray data were extracted from the National Centerfor Biotechnology Information (NCBI) Gene Expression Omnibus underthe series accession numbers: GSE4760 (Hsf2 mutant, 4 days at 23°C to 2h at 38°C), GSE16222 (5 days at 23°C to 1h at 37°C), GSE12619 (7 days at 22°C to 1h at 37°C), GSE4062 (15 days at 22°C to 2h at 37°C) and GSE11758 (mature leaves at 20°C to 1h at 37°C).

Supplemental figure 2. Clustering ofRNA expression levels of the Arabidopsis chaperome under seven abiotic and chemical treatments: dithiothreitol (DTT), tunicamycin, salicylic acid, ibuprofen, 2,3,5- triiodobenzoicacid (TIBA), 2,4,6-trihydroxybenzamide(2,4,6-T), and heat treatment as indicated. Gene clusters typical of the of the cellular stress response (CSR) (a) or of the unfolded protein response (UPR) (a) are indicated with brackets. The presumed sub-cellular localizations are indicated with different background colors.

Supplementalfigure 3.Clustering ofRNA expression levels of 168 genes from the human chaperome under 21 treatments: A 2-deoxyglucose; B tunicamycin; C phorbol 12-myristate 13-acetate; D cadmium; E N-acetylcysteine; F paclitaxel; G doxycycline; H echinomycin; I heat shock study; J elesclomol; K smoking; L simvastatin; M etoposide; N VAF347; O sapphyrin PCI-5002; P propiconazole; Q myclobutanil; R rifampicin; S dihydrotestosterone; T estrogen; U apple procyanidin. Gene clusters typical (a) of the cellular stress response (CSR), (b) of the unfolded protein response (UPR) and (c) of a main less specific cell response, are indicated with brackets. The presumed sub-cellular localizations are indicated with different background colors of the gene names.

Supplemental table 1a: List of identified human chaperone genes.

(1) Small HSP, GroEL and CCT-like chaperonins, Hsp70, DNAJ, Hsp100 and Hsp90 families have been previously annotated (Kampinga et al. 2009).(2) The Bag family has been previously annotated (Takayama et al. 1999).(3) FKBP and CYP like peptide-prolyl isomerase families have been previously annotated (Barik 2006).(4) Protein disulfide isomerase family has been previously annotated (Ellgaard and Ruddock 2005).(5)Human Hsp90 co-chaperones have been identified according to

Supplemental table 1b: List of identified heat shock elements (HSEs) in human chaperome. Nucleotide sequences of canonical HSEs in cis and trans orientations were identified between position -3000 bp and +300 bp from the translation start site of each chaperone gene.

Supplemental table 2: List of identified Arabidopsis thaliana chaperome genes.

(1) Small HSPs were obtained by BLAST using -crystalline domain as queries against the Arabidopsis protein subset of the NCBI database. (2) Chaperonins have been previously annotated (Hill and Hemmingsen 2001). (3) DnaJ proteins were re-annotated as compared to the previous J-protein nomenclature (Rajan and D'Silva 2009, as shown in brackets). All isoforms, splice variants, and paralogous protein according to previous annotations have been removed. The gene loci At2g02200, At5g34895, At2g07010 (MWJ3.6), At1g31210, At2g14930, At2g13940 and At2g24660 (corresponding to AtDjC6, AtDjC7, AtDjC50 and AtDjC58-AtDjC61, respectively) contained transposable elements and were removed as such.(4) The Hsp70 and Hsp110 were obtained by BLAST using DnaK from E. coli as query against the Arabidopsis protein subset of the NCBI database. (5) The Hsp100 were obtained by BLAST using ClpB from E. coli as the query against Arabidopsis protein subset of the NCBI database. Only the most ClpB-like proteins were retained, while ClpA/C proteins that are associated to the ClpP protease were excluded.(6) The Bag family has been previously annotated (Yan 2003).(7) The Hsp90 family has been previously annotated (Krishna and Gloor 2001).(8) PPIase families have been previously annotated (Romano et al. 2005). (9) Protein disulfide isomerase (PDIs) families have been previously annotated (Houston et al. 2005). (10) Human Hsp90 co-chaperones were identified in yeast and animals according to and used as queries to identify Arabidopsis orthologs in the protein subset of the NCBI database.

Supplemental references

1.Kampinga, H.H., Hageman, J., Vos, M.J., Kubota, H., Tanguay, R.M., Bruford, E.A., Cheetham, M.E., Chen, B. and Hightower, L.E. (2009) Guidelines for the nomenclature of the human heat shock proteins. Cell Stress Chaperon, 14, 105-111.

2.Takayama, S., Xie, Z.H. and Reed, J.C. (1999) An evolutionarily conserved family of Hsp70/Hsc70 molecular chaperone regulators. J Biol Chem, 274, 781-786.

3.Barik, S. (2006) Immunophilins: for the love of proteins. Cell Mol Life Sci, 63, 2889-2900.

4.Ellgaard, L. and Ruddock, L.W. (2005) The human protein disulphide isomerase family: substrate interactions and functional properties. Embo Rep, 6, 28-32.

5.Hill, J.E. and Hemmingsen, S.M. (2001) Arabidopsis thaliana type I and II chaperonins. Cell Stress Chaperon, 6, 190-200.

6.Rajan, V.B.V. and D'Silva, P. (2009) Arabidopsis thaliana J-class heat shock proteins: cellular stress sensors. FunctIntegr Genomic, 9, 433-446.

7.Yan, J.Q., He, C.X. and Zhang, H. (2003) The BAG-family proteins in Arabidopsis thaliana. Plant Sci, 165, 1-7.

8.Krishna, P. and Gloor, G. (2001) The Hsp90 family of proteins in Arabidopsis thaliana. Cell Stress Chaperon, 6, 238-246.

9.Romano, P., Gray, J., Horton, P. and Luan, S. (2005) Plant immunophilins: functional versatility beyond protein maturation. New Phytol, 166, 753-769.

10.Houston, N.L., Fan, C.Z., Xiang, Q.Y., Schulze, J.M., Jung, R. and Boston, R.S. (2005) Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins. Plant Physiol, 137, 762-778

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