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

Abstract

BackgroundIn 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.ResultsWe 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.ConclusionsOverall, 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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5190-z) contains supplementary material, which is available to authorized users.

Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment

“…The NJJS4 gene is a type of HSP20coding gene, which participates in regulating strawberry fruit ripening [61]. In addition, Arce et al [62] report that the sHSP gene family in tomato is related to fruit ripening, as indicated by the sequence-conserved promoter architecture. Moreover, an sHSP influences pectin depolymerization in tomato fruit ripening [63].…”

“…In a proteome-wide study, eight HSP genes were associated with tomato fruit development and ripening [64], demonstrating that HSP genes indeed participate in tomato fruit ripening [65]. Stress is a well-known stimulus that triggers the induction of sHSPs [62]. In particular, sHSPs are also induced during tomato ripening [66], suggesting that the stress induced affected the HSP genes, thereby causing tomato fruit ripening.…”

Elevated Temperatures Impose Transcriptional Constraints and Elicit Intraspecific Differences Between Coffee Genotypes

“…These results indicate a core conservative thermoregulatory mechanism within the coffee genotypes. The homologs of SMALL HEAT SHOCK PROTEINS (Cc11_g16360) are triggered in response to stress and during the ripening process, acting as chaperones presenting a complex expression pattern ( Ohama et al, 2016 ; Arce et al, 2018 ). RUBISCO ACTIVASE (Cc04_g14500), whose homologs enhance RUBISCO activity ( Salvucci and Ogren, 1996 ), is up-regulated by WaT in coffee.…”

Genome-wide identification and classification of theHsfandsHspgene families inPrunus mume, and transcriptional analysis under heat stress

“…For example, 24 Hsfs have been identified in Arabidopsis (Nover et al, 2001), 24 in tomato (Scharf et al, 2012), 27 in poplar (Zhang et al, 2015a), 40 in cotton (Wang et al, 2014), 27 in willow (Zhang et al, 2015a), 25 in rice (Scharf et al, 2012), and 56 in wheat (Xue et al, 2014). Additionally, 19, 33, 37, 94, 23, and 27 sHsps have been identified in Arabidopsis (Scharf, Siddique & Vierling, 2001), tomato (Arce et al, 2018), poplar (Zhang et al, 2015b), cotton (Ma et al, 2016), rice (Sarkar, Kim & Grover, 2009), and wheat (Pandey et al, 2015), respectively. This reveals that the number of different Hsfs and sHsps varies among plant species, which may be the result of gene duplication and whole-genome duplication (WGD).…”