Tomato MED25 regulates fruit ripening by interacting with EIN3-like transcription factors

Key transcription factors regulate fruit ripening and metabolite accumulation in tomato

Fruit ripening is a complex process involving dynamic changes to metabolites and is controlled by multiple factors, including transcription factors (TFs). Several TFs are reportedly essential regulators of tomato (Solanum lycopersicum) fruit ripening. To evaluate the effects of specific TFs on metabolite accumulation during fruit ripening, we combined CRISPR/Cas9-mediated mutagenesis with metabolome and transcriptome analyses to explore regulatory mechanisms. Specifically, we generated various genetically engineered tomato lines that differed regarding metabolite contents and fruit colors. The metabolite and transcript profiles indicated that the selected TFs have distinct functions that control fruit metabolite contents, especially carotenoids and sugars. Moreover, a mutation to ELONGATED HYPOCOTYL5 (HY5) increased tomato fruit fructose and glucose contents by approximately 20% (relative to the wild-type levels). Our in vitro assay showed that HY5 can bind directly to the G-box cis-element in the Sugars Will Eventually be Exported Transporter (SWEET12c) promoter to activate expression, thereby modulating sugar transport. Our findings provide insights into the mechanisms regulating tomato fruit ripening and metabolic networks, providing the theoretical basis for breeding horticultural crops that produce fruit with diverse flavors and colors.

Integrative analysis of the methylome and transcriptome of tomato fruit (Solanum lycopersicum L.) induced by postharvest handling

Tomato fruit ripening is triggered by the demethylation of key genes, which alters their transcriptional levels thereby initiating and propagating a cascade of physiological events. What is unknown is how these processes are altered when fruit are ripened using postharvest practices to extend shelf-life, as these practices often reduce fruit quality. To address this, postharvest handling-induced changes in the fruit DNA methylome and transcriptome, and how they correlate with ripening speed, and ripening indicators such as ethylene, abscisic acid, and carotenoids, were assessed. This study comprehensively connected changes in physiological events with dynamic molecular changes. Ripening fruit that reached 'Turning' (T) after dark storage at 20°C, 12.5°C, or 5°C chilling (followed by 20°C rewarming) were compared to fresh-harvest fruit 'FHT'. Fruit stored at 12.5°C had the biggest epigenetic marks and alterations in gene expression, exceeding changes induced by postharvest chilling. Fruit physiological and chronological age were uncoupled at 12.5°C, as the time-to-ripening was the longest. Fruit ripening to Turning at 12.5°C was not climacteric; there was no respiratory or ethylene burst, rather, fruit were high in abscisic acid. Clear differentiation between postharvest-ripened and 'FHT' was evident in the methylome and transcriptome. Higher expression of photosynthetic genes and chlorophyll levels in 'FHT' fruit pointed to light as influencing the molecular changes in fruit ripening. Finally, correlative analyses of the -omics data putatively identified genes regulated by DNA methylation. Collectively, these data improve our interpretation of how tomato fruit ripening patterns are altered by postharvest practices, and long-term are expected to help improve fruit quality.

The role of Rab GTPase in Plant development and stress

Small GTPase is a type of crucial regulator in eukaryotes. It acts as a molecular switch by binding with GTP and GDP in cytoplasm, affecting various cellular processes. Small GTPase were divided into five subfamilies based on sequence, structure and function: Ras, Rho, Rab, Arf/Sar and Ran, with Rab being the largest subfamily. Members of the Rab subfamily play an important role in regulating complex vesicle transport and microtubule system activity. Plant cells are composed of various membrane-bound organelles, and vesicle trafficking is fundamental to the existence of plants. At present, the function of some Rab members, such as RabA1a, RabD2b/c and RabF2, has been well characterized in plants. This review summarizes the role of Rab GTPase in regulating plant tip growth, morphogenesis, fruit ripening and stress response, and briefly describes the regulatory mechanisms involved. It provides a reference for further alleviating environmental stress, improving plant resistance and even improving fruit quality.

Mediator kinase subunit CDK8 phosphorylates transcription factor TCP15 during tomato pollen development

Pollen development in flowering plants has strong implications for reproductive success. Pollen DNA can be targeted to improve plant traits for yield and stress tolerance. In this study, we demonstrated that the Mediator subunit CYCLIN-DEPENDENT KINASE 8 (CDK8) is a key modulator of pollen development in tomato (Solanum lycopersicum). SlCDK8 knockout led to significant decreases in pollen viability, fruit yield, and fruit seed number. We also found that SlCDK8 directly interacts with transcription factor TEOSINTE BRANCHED1-CYCLOIDEA-PCF15 (SlTCP15) using yeast two-hybrid screens. We subsequently showed that SlCDK8 phosphorylates Ser 187 of SlTCP15 to promote SlTCP15 stability. Phosphorylated TCP15 directly bound to the TGGGCY sequence in the promoters of DYSFUNCTIONAL TAPETUM 1 (SlDYT1) and MYB DOMAIN PROTEIN 103 (SlMYB103), which are responsible for pollen development. Consistently, disruption of SlTCP15 resembled slcdk8 tomato mutants. In sum, our work identified a new substrate of Mediator CDK8 and revealed an important regulatory role of SlCDK8 in pollen development via cooperation with SlTCP15.

Tomato CYP94C1 inactivates bioactive JA-Ile to attenuate jasmonate-mediated defense during fruit ripening

As the master regulators of the ET signaling pathway, EIL transcription factors directly activate the expression of CYP94C1 to inactivate bioactive JA-Ile, thereby attenuating JA-mediated defense during fruit ripening. Knockout of CYP94C1 improves tomato fruit resistance to necrotrophs without compromising fruit quality.

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.

The apple lipoxygenase MdLOX3 positively regulates zinc tolerance

Various abiotic stresses, especially heavy metals near factories around the world, limit plant growth and productivity worldwide. Zinc is a light gray transition metal, and excessive zinc will inactivate enzymes in the soil, weaken the biological function of microorganisms, and enter the food chain through enrichment, thus affecting human health. Lipoxygenase (LOX) can catalyze the production of fatty acid derivatives from phenolic triglycerides in plants and is an important pathway of fatty acid oxidation in plants, which usually begins under unfavorable conditions, especially under biotic and abiotic stresses. Lipoxygenase can be divided into 9-LOX and 13-LOX. MdLOX3 is a homolog of AtLOX3 and has been identified in apples (housefly apples). MdLOX3 has a typical conserved lipoxygenase domain, and promoter analysis shows that it contains multiple stress response elements. In addition, different abiotic stresses and hormonal treatments induced the MdLOX3 response. In order to explore the inherent anti-heavy metal mechanism of MdLOX3, this study verified the properties of MdLOX3 based on genetic analysis and overexpression experiments, including plant taproots length, plant fresh weight, chlorophyll, anthocyanins, MDA, relative electrical conductivity, hydrogen peroxide and superoxide anion, NBT\DAB staining, etc. In the experiment, overexpression of MdLOX3 in apple callus and Arabidopsis effectively enhanced the tolerance to zinc stress by improving the ability to clear ROS. Meanwhile, tomato materials with overexpression of ectopia grew better under excessive zinc ion stress. These results indicated that MdLOX3 had a good tolerance to heavy metal zinc. Homologous mutants are more sensitive to zinc, which proves that MdLOX3 plays an important positive role in zinc stressed apples, which broadens the range of action of LOX3 in different plants.

High temperature elevates carotenoid accumulation of banana fruit via upregulation of MaEIL9 module

Banana is a good source of carotenoids, which are bioactive metabolites with health beneficial properties for human. However, the molecular mechanism of carotenoid accumulation in banana fruit is largely unclear. In this study, we found that high temperature elevated carotenoid production in banana pulp, which is presumably due to upregulation of a subset of carotenogenic genes as well as a carotenoid biosynthesis regulator MaSPL16. Moreover, an ethylene signaling component MaEIL9 was identified, whose transcript and protein contents were also induced by high temperature. In addition, MaEIL9 positively regulates transcription of MaDXR1, MaPDS1, MaZDS1 and MaSPL16 through directly targeting their promoters. Overexpression of MaEIL9 in tomato fruit substantially increased the expression of carotenoid formation genes and elevated carotenoid content. Importantly, transiently silencing MaEIL9 in banana fruit weakened carotenoid production caused by high temperature. Taken together, these results indicate that high temperature induces carotenoid production in banana fruit, at least in part, through MaEIL9-mediated activation of MaDXR1, MaPDS1, MaZDS1 and MaSPL16 expression.

Reducing crop losses by gene-editing control of organ developmental physiology

Some physiological processes in reproductive organs, if not controlled, can lead to crop loss even in the absence of environmental stress. These processes may occur pre- or post- harvest, and in diverse species and include abscission processes in cereal grain, e.g., shattering and in immature fruit, e.g., preharvest drop, preharvest sprouting of cereals, and postharvest senescence in fruit. Some of the molecular mechanisms and genetic determinants underlying these processes are now better detailed, making it possible to refine them by gene editing. Here, we discuss using advanced genomics to identify genetic determinants underlying crop physiological traits. Examples of improved phenotypes developed for preharvest problems are provided, and suggestions for reducing postharvest fruit losses by gene and promoter editing were made.

Salicylic acid delays pear fruit senescence by playing an antagonistic role toward ethylene, auxin, and glucose in regulating the expression of PpEIN3a

Salicylic acid (SA) and ethylene (ET) are crucial fruit senescence hormones. SA inhibited ET biosynthesis. However, the mechanism of SA delaying fruit senescence is less known. ETHYLENE INSENSITIVE 3 (EIN3), a key positive switch in ET perception, functions as a transcriptional activator and binds to the primary ET response element that is present in the promoter of the ETHYLENE RESPONSE FACTOR1 gene. In this study, a gene encoding putative EIN3 protein was cloned from sand pear and designated as PpEIN3a. The deduced PpEIN3a contains a conserved EIN3 domain. The evolutionary analysis results indicated that PpEIN3a belonged to the EIN3 superfamily. Real-time quantitative PCR analysis revealed that the accumulation of PpEIN3a transcripts were detected in all tissues of this pear. Moreover, PpEIN3a expression was regulated during fruit development. Interestingly, the expression of PpEIN3a was downregulated by SA but upregulated by ET, auxin, and glucose. Additionally, the contents of free and conjugated SA were higher than those of the control after SA treatment. While the content of ET and auxin (indole-3-acetic acid, IAA) dramatically decreased after SA treatment compared with control during fruit senescence. The content of glucose increased when fruit were treated by SA for 12 h and then there were no differences between SA treatment and control fruit during the shelf life. SA also delayed the decrease in sand pear (Pyrus pyrifolia Nakai. 'Whangkeumbae') fruit firmness. The soluble solid content remained relatively stable between the SA treated and control fruits. This study showed that SA plays an antagonistic role toward ET, auxin, and glucose in regulating the expression of PpEIN3a to delay fruit senescence.