Regulatory motifs found in the small heat shock protein (sHSP) gene family in tomato

• Published in: BMC genomics Vol. 19; no. Suppl 8; pp. 860 - 7
• Main Authors: Arce, Debora, Spetale, Flavio, Krsticevic, Flavia, Cacchiarelli, Paolo, Las Rivas, Javier De, Ponce, Sergio, Pratta, Guillermo, Tapia, Elizabeth
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 11-12-2018; BioMed Central; BMC
• Subjects: Architecture; Binding sites; Computation; Computer applications; Deoxyribonucleic acid; DNA; Gene Duplication; Gene expression; Gene Expression Regulation, Plant; Genes; Genetic aspects; Genetic engineering; Genomics; Heat shock factors; Heat shock protein; Heat shock proteins; Heat stress; Heat tolerance; Heat-Shock Proteins, Small - genetics; Heat-Shock Proteins, Small - metabolism; Heat-Shock Response; Homeostasis; Homology; HSE; Hsp70 protein; Hsp90 protein; Lycopersicon esculentum - genetics; Lycopersicon esculentum - growth & development; Lycopersicon esculentum - metabolism; Nucleotide Motifs; Plant Proteins - genetics; Plant Proteins - metabolism; Promoter Regions, Genetic; Protein interaction; Protein Interaction Maps; Proteins; Proteomics; Redundancy; Regulatory motif; Regulatory Sequences, Nucleic Acid; Reproduction (copying); Ripening; sHSP; sHSP protein; Small heat shock proteins; Solanum lycopersicum; Stress response; TFBS; Tomato; Tomatoes; Transcription factors; HSE; Regulatory motif; TFBS; Tomato; Heat shock protein; sHSP
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-018-5190-z

In living organisms, small heat shock proteins (sHSPs) are triggered in response to stress situations. This family of proteins is large in plants and, in the case of tomato (Solanum lycopersicum), 33 genes have been identified, most of them related to heat stress response and to the ripening process. Transcriptomic and proteomic studies have revealed complex patterns of expression for these genes. In this work, we investigate the coregulation of these genes by performing a computational analysis of their promoter architecture to find regulatory motifs known as heat shock elements (HSEs). We leverage the presence of sHSP members that originated from tandem duplication events and analyze the promoter architecture diversity of the whole sHSP family, focusing on the identification of HSEs.
We performed a search for conserved genomic sequences in the promoter regions of the sHSPs of tomato, plus several other proteins (mainly HSPs) that are functionally related to heat stress situations or to ripening. Several computational analyses were performed to build multiple sequence motifs and identify transcription factor binding sites (TFBS) homologous to HSF1AE and HSF21 in Arabidopsis. We also investigated the expression and interaction of these proteins under two heat stress situations in whole tomato plants and in protoplast cells, both in the presence and in the absence of heat shock transcription factor A2 (HsfA2). The results of these analyses indicate that different sHSPs are up-regulated depending on the activation or repression of HsfA2, a key regulator of HSPs. Further, the analysis of protein-protein interaction between the sHSP protein family and other heat shock response proteins (Hsp70, Hsp90 and MBF1c) suggests that several sHSPs are mediating alternative stress response through a regulatory subnetwork that is not dependent on HsfA2.
Overall, this study identifies two regulatory motifs (HSF1AE and HSF21) associated with the sHSP family in tomato which are considered genomic HSEs. The study also suggests that, despite the apparent redundancy of these proteins, which has been linked to gene duplication, tomato sHSPs showed different up-regulation and different interaction patterns when analyzed under different stress situations.