Transcriptional regulation of tomato fruit ripening.

An intrinsic and genetically determined ripening program of tomato fruits often depends upon the appropriate activation of tissue- and stage-specific transcription factors in space and time. The past two decades have yielded considerable progress in detailing these complex transcriptional as well as hormonal regulatory circuits paramount to fleshy fruit ripening. This non-linear ripening process is strongly controlled by the MADS-box and NOR family of proteins, triggering a transcriptional response associated with the progression of fruit ripening. Deepening insights into the connection between MADS-RIN and plant hormones related transcription factors, such as ERFs and ARFs, further conjugates the idea that several signaling units work in parallel to define an output fruit ripening transcriptome. Besides these TFs, the role of other families of transcription factors such as MYB, GLK, WRKY, GRAS and bHLH have also emerged as important ripening regulators. Other regulators such as EIN and EIL proteins also determine the transcriptional landscape of ripening fruits. Despite the abundant knowledge of the complex spectrum of ripening networks in the scientific domain, identifying more ripening effectors would pave the way for a better understanding of fleshy fruit ripening at the molecular level. This review provides an update on the transcriptional regulators of tomato fruit ripening.

Elevated methylglyoxal levels inhibit tomato fruit ripening by preventing ethylene biosynthesis.

Methylglyoxal (MG), a toxic compound produced as a by-product of several cellular processes, such as respiration and photosynthesis, is well known for its deleterious effects, mainly through glycation of proteins during plant stress responses. However, very little is known about its impact on fruit ripening. Here, we found that MG levels are maintained at high levels in green tomato (Solanum lycopersicum L.) fruits and decline during fruit ripening despite a respiratory burst during this transition. We demonstrate that this decline is mainly mediated through a glutathione-dependent MG detoxification pathway and primarily catalyzed by a Glyoxalase I enzyme encoded by the SlGLYI4 gene. SlGLYI4 is a direct target of the MADS-box transcription factor RIPENING INHIBITOR (RIN), and its expression is induced during fruit ripening. Silencing of SlGLYI4 leads to drastic MG overaccumulation at ripening stages of transgenic fruits and interferes with the ripening process. MG most likely glycates and inhibits key enzymes such as methionine synthase and S-adenosyl methionine synthase in the ethylene biosynthesis pathway, thereby indirectly affecting fruit pigmentation and cell wall metabolism. MG overaccumulation in fruits of several nonripening or ripening-inhibited tomato mutants suggests that the tightly regulated MG detoxification process is crucial for normal ripening progression. Our results underpin a SlGLYI4-mediated regulatory mechanism by which MG detoxification controls fruit ripening in tomato.

A glutathione-independent DJ-1/PfpI domain-containing tomato glyoxalaseIII2, SlGLYIII2, confers enhanced tolerance under salt and osmotic stresses.

In plants, glyoxalase enzymes are activated under stress conditions to mitigate the toxic effects of hyperaccumulated methylglyoxal (MG), a highly reactive carbonyl compound. Until recently, a glutathione-dependent bi-enzymatic pathway involving glyoxalase I (GLYI) and glyoxalase II (GLYII) was considered the primary MG-detoxification system. Recently, a new glutathione-independent glyoxalase III (GLYIII) mediated direct route was also reported in plants. However, the physiological significance of this new pathway remains to be elucidated across plant species. This study identified the full complement of 22 glyoxalases in tomato. Based on their strong induction under multiple abiotic stresses, SlGLYI4, SlGLYII2 and SlGLYIII2 were selected candidates for further functional characterisation. Stress-inducible overexpression of both glutathione-dependent (SlGLYI4 + SlGLYII2) and independent (SlGLYIII2) pathways led to enhanced tolerance in both sets of transgenic plants under abiotic stresses. However, SlGLYIII2 overexpression (OE) plants outperformed the SlGLYI4 + SlGLYII2 OE counterparts for their stress tolerance under abiotic stresses. Further, knockdown of SlGLYIII2 resulted in plants with exacerbated stress responses than those silenced for both SlGLYI4 and SlGLYII2. The superior performance of SlGLYIII2 OE tomato plants for better growth and yield under salt and osmotic treatments could be attributed to better GSH/GSSG ratio, lower reactive oxygen species levels, and enhanced antioxidant potential, indicating a prominent role of GLYIII MG-detoxification pathway in abiotic stress mitigation in this species.

Ethylene response factor ERF.D7 activates auxin response factor 2 paralogs to regulate tomato fruit ripening.

Despite the obligatory role of ethylene in climacteric fruit ripening and the identification of 77 ethylene response factors (ERFs) in the tomato (Solanum lycopersicum) genome, the role of few ERFs has been validated in the ripening process. Here, using a comprehensive morpho-physiological, molecular, and biochemical approach, we demonstrate the regulatory role of ERF D7 (SlERF.D7) in tomato fruit ripening. SlERF.D7 expression positively responded to exogenous ethylene and auxin treatments, most likely in a ripening inhibitor-independent manner. SlERF.D7 overexpression (OE) promoted ripening, and its silencing had the opposite effect. Alterations in its expression modulated ethylene production, pigment accumulation, and fruit firmness. Consistently, genes involved in ethylene biosynthesis and signaling, lycopene biosynthesis, and cell wall loosening were upregulated in the OE lines and downregulated in RNAi lines. These transgenic lines also accumulated altered levels of indole-3-acetic acid at late-breaker stages. A positive association between auxin response factor 2 (ARF2) paralog's transcripts and SlERF.D7 mRNA levels and that SlARF2A and SlARF2B are direct targets of SlERF.D7 underpinned the perturbed auxin-ethylene crosstalk for the altered ripening program observed in the transgenic fruits. Overall, this study uncovers that SlERF.D7 positively regulates SlARF2A/B abundance to amalgamate auxin and ethylene signaling pathways for controlling tomato fruit ripening.

Genome-wide analysis of genes encoding MBD domain-containing proteins from tomato suggest their role in fruit development and abiotic stress responses.

In tomato, DNA methylation has an inhibitory effect on fruit ripening. The inhibition of DNA methyltransferase by 5-azacytidine results in premature fruit ripening. Methyl CpG binding domain (MBD) proteins are the readers of DNA methylation marks and help in the recruitment of chromatin-modifying enzymes which affect gene expression. Therefore, we investigate their contribution during fruit development. In this study, we identified and analyzed 18 putative genes of Solanum lycopersicum and Solanum pimpinellifolium encoding MBD proteins. We also identified tomato MBD syntelogs in Capsicum annum and Solanum tuberosum. Sixty-three MBD genes identified from four different species of solanaceae were classified into three groups. An analysis of the conserved domains in these proteins identified additional domains along with MBD motif. The transcript profiling of tomato MBDs in wild-type and two non-ripening mutants, rin and Nr, indicated constructive information regarding their involvement during fruit development. When we performed a stage-specific expression analysis during fruit ripening, a gradual decrease in transcript accumulation in the wild-type fruit was detected. However, a very low expression was observed in the ripening mutants. Furthermore, many ethylene-responsive cis-elements were found in SlMBD gene promoters, and some of them were induced in the presence of exogenous ethylene. Further, we detected the possible role of these MBDs in abiotic stresses. We found that few genes were differentially expressed under various abiotic stress conditions. Our results provide an evidence of the involvement of the tomato MBDs in fruit ripening and abiotic stress responses, which would be helpful in further studies on these genes in tomato fruit ripening.

Identification of miRNA-mediated drought responsive multi-tiered regulatory network in drought tolerant rice, Nagina 22.

Comparative characterization of microRNA-mediated stress regulatory networks in contrasting rice cultivars is critical to decipher plant stress response. Consequently, a multi-level comparative analysis, using sRNA sequencing, degradome analysis, enzymatic and metabolite assays and metal ion analysis, in drought tolerant and sensitive rice cultivars was conducted. The study identified a group of miRNAs "Cultivar-specific drought responsive" (CSDR)-miRNAs (osa-miR159f, osa-miR1871, osa-miR398b, osa-miR408-3p, osa-miR2878-5p, osa-miR528-5p and osa-miR397a) that were up-regulated in the flag-leaves of tolerant cultivar, Nagina 22 (N22) and Vandana, but down-regulated in the sensitive cultivar, Pusa Basmati 1 (PB1) and IR64, during drought. Interestingly, CSDR-miRNAs target several copper-protein coding transcripts like plantacyanins, laccases and Copper/Zinc superoxide dismutases (Cu/Zn SODs) and are themselves found to be similarly induced under simulated copper-starvation in both N22 and PB1. Transcription factor OsSPL9, implicated in Cu-homeostasis also interacted with osa-miR408-3p and osa-miR528-5p promoters. Further, N22 flag leaves showed lower SOD activity, accumulated ROS and had a higher stomata closure. Interestingly, compared to PB1, internal Cu levels significantly decreased in the N22 flag-leaves, during drought. Thus, the study identifies the unique drought mediated dynamism and interplay of Cu and ROS homeostasis, in the flag leaves of drought tolerant rice, wherein CSDR-miRNAs play a pivotal role.