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Meta-analysis of heat- and chemically upregulated chaperone genes in plant and human cells

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Cell Stress and Chaperones Aims and scope

Abstract

Molecular chaperones are central to cellular protein homeostasis. In mammals, protein misfolding diseases and aging cause inflammation and progressive tissue loss, in correlation with the accumulation of toxic protein aggregates and the defective expression of chaperone genes. Bacteria and non-diseased, non-aged eukaryotic cells effectively respond to heat shock by inducing the accumulation of heat-shock proteins (HSPs), many of which molecular chaperones involved in protein homeostasis, in reducing stress damages and promoting cellular recovery and thermotolerance. We performed a meta-analysis of published microarray data and compared expression profiles of HSP genes from mammalian and plant cells in response to heat or isothermal treatments with drugs. The differences and overlaps between HSP and chaperone genes were analyzed, and expression patterns were clustered and organized in a network. HSPs and chaperones only partly overlapped. Heat-shock induced a subset of chaperones primarily targeted to the cytoplasm and organelles but not to the endoplasmic reticulum, which organized into a network with a central core of Hsp90s, Hsp70s, and sHSPs. Heat was best mimicked by isothermal treatments with Hsp90 inhibitors, whereas less toxic drugs, some of which non-steroidal anti-inflammatory drugs, weakly expressed different subsets of Hsp chaperones. This type of analysis may uncover new HSP-inducing drugs to improve protein homeostasis in misfolding and aging diseases.

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Acknowledgments

This research was financed in part by grant no. 3100A0-109290 from the Swiss National Science Foundation, the Alzheimer’s Drug Discovery Foundation New York, and the Zwahlen Grant from the Faculty of Biology and Medicine from Lausanne University.

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  1. Department of Plant Molecular Biology, University of Lausanne, 1015, Lausanne, Switzerland

    Andrija Finka, Rayees U. H. Mattoo & Pierre Goloubinoff

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  1. Andrija Finka
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  3. Pierre Goloubinoff
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Correspondence to Pierre Goloubinoff.

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Supplemental Fig. 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 Center for Biotechnology Information (NCBI) Gene Expression Omnibus under the series accession numbers GSE4760 (Hsf2 mutant, 4 days at 23°C to 2 h at 38°C), GSE16222 (5 days at 23°C to 1 h at 37°C), GSE12619 (7 days at 22°C to 1 h at 37°C), GSE4062 (15 days at 22°C to 2 h at 37°C), and GSE11758 (mature leaves at 20°C to 1 h at 37°C) (PDF 956 kb)

Supplemental Fig. 2

Clustering of RNA 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) (b) are indicated with brackets. The presumed subcellular localizations are indicated with different background colors (PDF 1032 kb)

Supplemental Fig. 3

Clustering of RNA 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, and 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 subcellular localizations are indicated with different background colors of the gene names (PDF 442 kb)

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 www.picard.ch (XLS 45 kb)

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 and 300 bp from the translation start site of each chaperone gene (XLS 32 kb)

Table 2

List of identified Arabidopsis thaliana chaperome genes. (1) Small HSPs were obtained by BLAST using α-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) PDIs families have been previously annotated (Houston et al. 2005). (10) Human Hsp90 co-chaperones were identified in yeast and animals according to http://www.picard.ch and used as queries to identify Arabidopsis orthologs in the protein subset of the NCBI database (XLS 162 kb)

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Finka, A., Mattoo, R.U.H. & Goloubinoff, P. Meta-analysis of heat- and chemically upregulated chaperone genes in plant and human cells. Cell Stress and Chaperones 16, 15–31 (2011). https://doi.org/10.1007/s12192-010-0216-8

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