Chaperone network composition in Solanum lycopersicum explored by transcriptome profiling and microarray meta-analysis

Plant Cell Environ. 2015 Apr;38(4):693-709. doi: 10.1111/pce.12426. Epub 2014 Oct 1.


Heat shock proteins (Hsps) are molecular chaperones primarily involved in maintenance of protein homeostasis. Their function has been best characterized in heat stress (HS) response during which Hsps are transcriptionally controlled by HS transcription factors (Hsfs). The role of Hsfs and Hsps in HS response in tomato was initially examined by transcriptome analysis using the massive analysis of cDNA ends (MACE) method. Approximately 9.6% of all genes expressed in leaves are enhanced in response to HS, including a subset of Hsfs and Hsps. The underlying Hsp-Hsf networks with potential functions in stress responses or developmental processes were further explored by meta-analysis of existing microarray datasets. We identified clusters with differential transcript profiles with respect to abiotic stresses, plant organs and developmental stages. The composition of two clusters points towards two major chaperone networks. One cluster consisted of constitutively expressed plastidial chaperones and other genes involved in chloroplast protein homeostasis. The second cluster represents genes strongly induced by heat, drought and salinity stress, including HsfA2 and many stress-inducible chaperones, but also potential targets of HsfA2 not related to protein homeostasis. This observation attributes a central regulatory role to HsfA2 in controlling different aspects of abiotic stress response and tolerance in tomato.

Keywords: HSP; Hsf; MACE; biological network; cluster analysis; co-expression analysis; heat stress; orthologue search; protein homeostasis; tomato.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA-Binding Proteins / genetics*
  • Droughts
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant*
  • Heat Shock Transcription Factors
  • Heat-Shock Proteins / genetics*
  • Heat-Shock Response*
  • Hot Temperature
  • Oligonucleotide Array Sequence Analysis
  • Plant Proteins / genetics*
  • Solanum lycopersicum / genetics*
  • Solanum lycopersicum / physiology
  • Transcription Factors / genetics*


  • DNA-Binding Proteins
  • Heat Shock Transcription Factors
  • Heat-Shock Proteins
  • Plant Proteins
  • Transcription Factors