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

• Published in: Plant, cell and environment cell and environment, 2015-04, Vol.38 (4), p.693-709
• Main Authors: FRAGKOSTEFANAKIS, SOTIRIOS, SIMM, STEFAN, PAUL, PUNEET, BUBLAK, DANIELA, SCHARF, KLAUS‐DIETER, SCHLEIFF, ENRICO
• Format: Article
• Language: English
• Subjects: biological network; cluster analysis; co‐expression analysis; DNA-Binding Proteins - genetics; Droughts; Gene Expression Profiling; Gene Expression Regulation, Plant; Heat Shock Transcription Factors; heat stress; Heat-Shock Proteins - genetics; Heat-Shock Response; Hot Temperature; Hsf; HSP; Lycopersicon esculentum - genetics; Lycopersicon esculentum - physiology; MACE; Oligonucleotide Array Sequence Analysis; orthologue search; Plant Proteins - genetics; protein homeostasis; tomato; Transcription Factors - genetics
• ISSN: 0140-7791; 1365-3040
• DOI: 10.1111/pce.12426

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. Molecular chaperones are involved in maintenance of protein homeostasis, thereby affecting various aspects of plant development and stress response. Transcriptome analysis revealed that 9.6% of genes expressed in tomato leaves are upregulated in response to heat stress, including a subset of Hsps and Hsfs. Meta‐analysis of existing microarray datasets led to the identification of putative Hsf‐chaperone networks with distinct functions in abiotic stress responses and developmental processes. Among them, a cluster including HsfA2 and many stress induced genes as well as a second cluster with constitutively expressed plastidial chaperones and other genes involved in chloroplast protein homeostasis are considered as major networks in abiotic stress responses of tomato.