Differential expression of the 1-aminocyclopropane-1-carboxylate oxidase gene family of tomato

The MYB transcription factor SmMYB113 directly regulates ethylene-dependent flower abscission in eggplant

Flower abscission is an important developmental process that can significantly reduce the yield of horticultural plants. We previously reported that SmMYB113 is a key transcription factor promoting anthocyanin biosynthesis and improve fruit quality. However, the overexpression of SmMYB113 in eggplant increased flower drop rate and reduced fruit yield. Here, we elucidate the regulatory mechanisms of SmMYB113 on flower abscission in eggplant. RNA-seq analysis indicated that the regulation of flower abscission by SmMYB113 was associated with altered expression of genes related to ethylene biosynthesis and signal transduction, including ethylene biosynthetic genes SmACS1, SmACS8 and SmACO4. Then, the ethylene content in flowers and the function of ethephon (ETH, which promotes fruit ripening) and 1-Methylcyclopropene (1-MCP, which acts as an ethylene perception inhibitor) were analyzed, which revealed that SmMYB113 directly regulates ethylene-dependent flower abscission. Yeast one-hybrid and dual-luciferase assays revealed that SmMYB113 could directly bind to the promoters of SmACS1, SmACS8, and SmACO4 to activate their expression. Through construction of a yeast two-hybrid (Y2H) screening library, the protein SmERF38 was found to interact with SmMYB113, and verified by Y2H, bimolecular fluorescence complementation (BiFC), and luciferase complementation assay. Furthermore, dual-luciferase assays showed that SmERF38 enhanced the role of SmMYB113 on the promoters of SmACS1. Our results provided new insight into the molecular mechanism of flower abscission in eggplant.

Quantitative proteomic analysis of tomato fruit ripening behavior in response to exogenous abscisic acid

BACKGROUND

To determine how abscisic acid (ABA) affects tomato fruit ripening at the protein level, mature green cherry tomato fruit were treated with ABA, nordihydroguaiaretic acid (NDGA) or sterile water (control, CK). The proteomes of treated fruit were analyzed and quantified using tandem mass tags (TMTs) at 7 days after treatment, and the gene transcription abundances of differently expressed proteins (DEPs) were validated with quantitative real-time polymerase chain reaction.

RESULTS

Postharvest tomato fruit underwent faster color transformation and ripening than the CK when treated with ABA. In total, 6310 proteins were identified among the CK and treatment groups, of which 5359 were quantified. Using a change threshold of 1.2 or 0.83 times, 1081 DEPs were identified. Among them, 127 were upregulated and 127 were downregulated in the ABA versus CK comparison group. According to KEGG and protein-protein interaction network analyses, the ABA-regulated DEPs were primarily concentrated in the photosynthesis system and sugar metabolism pathways, and 102 DEPs associated with phytohormones biosynthesis and signal transduction, pigment synthesis and metabolism, cell wall metabolism, photosynthesis, redox reactions, allergens and defense responses were identified in the ABA versus CK and NDGA versus CK comparison groups.

CONCLUSION

ABA affects tomato fruit ripening at the protein level to some extent. The results of this study provided comprehensive insights and data for further research on the regulatory mechanism of ABA in tomato fruit ripening. © 2023 Society of Chemical Industry.

Trihelix transcription factor SlGT31 regulates fruit ripening mediated by ethylene in tomato

Trihelix proteins are plant-specific transcription factors that are classified as GT factors due to their binding specificity for GT elements, and they play crucial roles in development and stress responses. However, their involvement in fruit ripening and transcriptional regulatory mechanisms remains largely unclear. In this study, we cloned SlGT31, encoding a trihelix protein in tomato (Solanum lycopersicum), and determined that its relative expression was significantly induced by the application of exogenous ethylene whereas it was repressed by the ethylene-inhibitor 1-methylcyclopropene. Suppression of SlGT31 expression resulted in delayed fruit ripening, decreased accumulation of total carotenoids, and reduced ethylene content, together with inhibition of expression of genes related to ethylene and fruit ripening. Conversely, SlGT31-overexpression lines showed opposite results. Yeast one-hybrid and dual-luciferase assays indicated that SlGT31 can bind to the promoters of two key ethylene-biosynthesis genes, ACO1 and ACS4. Taken together, our results indicate that SlGT31 might act as a positive modulator during fruit ripening.

Ethylene, ACC, and the Plant Growth-Promoting Enzyme ACC Deaminase

Here, a brief summary of the biosynthesis of 1-aminocyclopropane-1-carboxylate (ACC) and ethylene in plants, as well as overviews of how ACC and ethylene act as signaling molecules in plants, is presented. Next, how the bacterial enzyme ACC deaminase cleaves plant-produced ACC and thereby decreases or prevents the ethylene or ACC modulation of plant gene expression is considered. A detailed model of ACC deaminase functioning, including the role of indoleacetic acid (IAA), is presented. Given that ACC is a signaling molecule under some circumstances, this suggests that ACC, which appears to have evolved prior to ethylene, may have been a major signaling molecule in primitive plants prior to the evolution of ethylene and ethylene signaling. Due to their involvement in stimulating ethylene production, the role of D-amino acids in plants is then considered. The enzyme D-cysteine desulfhydrase, which is structurally very similar to ACC deaminase, is briefly discussed and the possibility that ACC deaminase arose as a variant of D-cysteine desulfhydrase is suggested.

Plant Promoters: Their Identification, Characterization, and Role in Gene Regulation

One of the strategies to overcome diseases or abiotic stress in crops is the use of improved varieties. Genetic improvement could be accomplished through different methods, including conventional breeding, induced mutation, genetic transformation, or gene editing. The gene function and regulated expression through promoters are necessary for transgenic crops to improve specific traits. The variety of promoter sequences has increased in the generation of genetically modified crops because they could lead to the expression of the gene responsible for the improved trait in a specific manner. Therefore, the characterization of the promoter activity is necessary for the generation of biotechnological crops. That is why several analyses have focused on identifying and isolating promoters using techniques such as reverse transcriptase-polymerase chain reaction (RT-PCR), genetic libraries, cloning, and sequencing. Promoter analysis involves the plant genetic transformation method, a potent tool for determining the promoter activity and function of genes in plants, contributing to understanding gene regulation and plant development. Furthermore, the study of promoters that play a fundamental role in gene regulation is highly relevant. The study of regulation and development in transgenic organisms has made it possible to understand the benefits of directing gene expression in a temporal, spatial, and even controlled manner, confirming the great diversity of promoters discovered and developed. Therefore, promoters are a crucial tool in biotechnological processes to ensure the correct expression of a gene. This review highlights various types of promoters and their functionality in the generation of genetically modified crops.

Subsurface aeration mitigates organic material mulching-induced anaerobic stress via regulating hormone signaling in Phyllostachys praecox roots

Organic material mulching has been used extensively to allow Phyllostachys praecox to promote growth and development of shoots. However, the bamboo forest always showed a significant degradation, probably due to anaerobic damage caused by the mulching after several years. Therefore, we have innovatively proposed an improvement measure to aerate the underground pipes for the first time. We investigated the role of subsurface pipe aeration in regulating root hypoxia to reduce the stress and to identify the degradation mechanism. Results showed that aeration increased oxygen concentration, shoot yield and root growth compared with mulching, and the aeration enhanced the concentration of indole-3-acetic acid (IAA) and the expression of Aux/IAAs (Aux1, Aux2, Aux3, and Aux4). Aeration reduced gibberellin (GA), ethylene (ETH), and abscisic acid (ABA) contents as well as anaerobic enzyme activities (alanine transaminase, AlaAT; alcohol dehydrogenase, ADH; pyruvate decarboxylase, PDC; and lactate dehydrogenase, LDH), which alleviated root damage in anoxic conditions. Furthermore, correlation showed that the activities of ADH, LDH, PDC, and AlaAT showed significant linear correlations with soil oxygen levels. RDA analyses showed that ABA, IAA, and ETH were found as the key driving hormones of Aux/IAAs in the root of the forest mulched with organic material. Here we show that subsurface aeration increases soil oxygen concentration, shoot yield, root growth and regulates phytohormone concentrations and Aux/IAAs expression, which reduces anaerobic enzyme activities. Consequently, subsurface pipe aeration is an effective measure to mitigate the degradation of bamboo forests caused by soil hypoxia that results from organic material mulching.

Integrated Metabolites and Transcriptomics at Different Growth Stages Reveal Polysaccharide and Flavonoid Biosynthesis in Cynomorium songaricum

Cynomorium songaricum is a perennial parasitic herb, and its stem is widely used as a traditional Chinese medicine, which largely relies on bioactive compounds (e.g., polysaccharides, flavonoids, and triterpenes). To date, although the optimum harvest time of stems has been demonstrated at the unearthed stage (namely the early flowering stage, EFS), the accumulation mechanism of polysaccharides and flavonoids during growth stages is still limited. In this study, the physiological characteristics (stem fresh weight, contents of soluble sugar and flavonoids, and antioxidant capacity) at four different growth stages (germination stage (GS), vegetative growth stage (VGS), EFS, and flowering stage (FS)) were determined, transcriptomics were analyzed by illumina sequencing, and expression levels of key genes were validated by qRT-PCR at the GS, VGS, and EFS. The results show that the stem biomass, soluble sugar and total flavonoids contents, and antioxidant capacity peaked at EFS compared with GS, VGS, and FS. A total of 6098 and 13,023 differentially expressed genes (DEGs) were observed at VGS and EFS vs. GS, respectively, with 367 genes co-expressed. Based on their biological functions, 109 genes were directly involved in polysaccharide and flavonoid biosynthesis as well as growth and development. The expression levels of key genes involved in polysaccharides (e.g., GLCs, XTHs and PMEs), flavonoids (e.g., 4CLLs, CYPs and UGTs), growth and development (e.g., AC58, TCPs and AP1), hormones biosynthesis and signaling (e.g., YUC8, AIPT and ACO1), and transcription factors (e.g., MYBs, bHLHs and WRKYs) were in accordance with changes of physiological characteristics. The combinational analysis of metabolites with transcriptomics provides insight into the mechanism of polysaccharide and flavonoid biosynthesis in C. songaricum during growth stages.

Strawberry Proteome Responses to Controlled Hot and Cold Stress Partly Mimic Post-harvest Storage Temperature Effects on Fruit Quality

To determine the effect of different temperature on strawberry after harvest, physiological indicator analysis and proteomics analysis were conducted on ripened strawberry (“Sweet Charlie”) fruit stored at 4, 23, and 37°C for 10 or 20 days. Results showed that 4°C maintained a better visual quality of strawberry, and the weight loss and firmness remained stable within 3 days. Low temperature negatively affected anthocyanin but positively affected soluble sugars. Though anthocyanin content was higher with increasing temperature, anthocyanin synthesis related proteins were downregulated. Higher indole-acetic acid (IAA) content in seeds and lower abscisic acid (ABA) content were found in berry at 4°C. Antioxidant related proteins were upregulated during storage, showing a significant up-regulation of peroxidase (POD) at 4°C, and ascorbate-glutathione (AsA-GSH) cycle related proteins and heat shock proteins (HSPs) at 37°C. In addition, overexpressed sugar phosphate/phosphate translocator, 1-aminocyclopropane-1-carboxylate oxidase, and aquaporin PIP2-2 had a positive effect in response to low temperature stress for containing higher protopectin content and POD activity.

The Ethylene Biosynthesis Gene CpACO1A: A New Player in the Regulation of Sex Determination and Female Flower Development in Cucurbita pepo

A methanesulfonate-generated mutant has been identified in Cucurbita pepo that alters sex determination. The mutation converts female into hermaphrodite flowers and disrupts the growth rate and maturation of petals and carpels, delaying female flower opening, and promoting the growth rate of ovaries and the parthenocarpic development of the fruit. Whole-genome resequencing allowed identification of the causal mutation of the phenotypes as a missense mutation in the coding region of CpACO1A, which encodes for a type I ACO enzyme that shares a high identity with Cucumis sativus CsACO3 and Cucumis melo CmACO1. The so-called aco1a reduced ACO1 activity and ethylene production in the different organs where the gene is expressed, and reduced ethylene sensitivity in flowers. Other sex-determining genes, such as CpACO2B, CpACS11A, and CpACS27A, were differentially expressed in the mutant, indicating that ethylene provided by CpACO1A but also the transcriptional regulation of CpACO1A, CpACO2B, CpACS11A, and CpACS27A are responsible for determining the fate of the floral meristem toward a female flower, promoting the development of carpels and arresting the development of stamens. The positive regulation of ethylene on petal maturation and flower opening can be mediated by inducing the biosynthesis of JA, while its negative control on ovary growth and fruit set could be mediated by its repressive effect on IAA biosynthesis.

Both Two CtACO3 Transcripts Promoting the Accumulation of the Flavonoid Profiles in Overexpressed Transgenic Safflower

The unique flavonoids, quinochalcones, such as hydroxysafflor yellow A (HSYA) and carthamin, in the floret of safflower showed an excellent pharmacological effect in treating cardiocerebral vascular disease, yet the regulating mechanisms governing the flavonoid biosynthesis are largely unknown. In this study, CtACO3, the key enzyme genes required for the ethylene signaling pathway, were found positively related to the flavonoid biosynthesis at different floret development periods in safflower and has two CtACO3 transcripts, CtACO3-1 and CtACO3-2, and the latter was a splice variant of CtACO3 that lacked 5' coding sequences. The functions and underlying probable mechanisms of the two transcripts have been explored. The quantitative PCR data showed that CtACO3-1 and CtACO3-2 were predominantly expressed in the floret and increased with floret development. Subcellular localization results indicated that CtACO3-1 was localized in the cytoplasm, whereas CtACO3-2 was localized in the cytoplasm and nucleus. Furthermore, the overexpression of CtACO3-1 or CtACO3-2 in transgenic safflower lines significantly increased the accumulation of quinochalcones and flavonols. The expression of the flavonoid pathway genes showed an upward trend, with CtCHS1, CtF3H1, CtFLS1, and CtDFR1 was considerably induced in the overexpression of CtACO3-1 or CtACO3-2 lines. An interesting phenomenon for CtACO3-2 protein suppressing the transcription of CtACO3-1 might be related to the nucleus location of CtACO3-2. Yeast two-hybrid (Y2H), glutathione S-transferase (GST) pull-down, and BiFC experiments revealed that CtACO3-2 interacted with CtCSN5a. In addition, the interactions between CtCSN5a and CtCOI1, CtCOI1 and CtJAZ1, CtJAZ1 and CtbHLH3 were observed by Y2H and GST pull-down methods, respectively. The above results suggested that the CtACO3-2 promoting flavonoid accumulation might be attributed to the transcriptional activation of flavonoid biosynthesis genes by CtbHLH3, whereas the CtbHLH3 might be regulated through CtCSN5-CtCOI1-CtJAZ1 signal molecules. Our study provided a novel insight of CtACO3 affected the flavonoid biosynthesis in safflower.

Distinct Functions of Ethylene and ACC in the Basal Land Plant Marchantia polymorpha

Ethylene is a gaseous phytohormone involved in various physiological processes, including fruit ripening, senescence, root hair development and stress responses. Recent genomics studies have suggested that most homologous genes of ethylene biosynthesis and signaling are conserved from algae to angiosperms, whereas the function and biosynthesis of ethylene remain unknown in basal plants. Here, we examined the physiological effects of ethylene, an ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC) and an inhibitor of ethylene perception, silver thiosulfate (STS), in a basal land plant, Marchantia polymorpha. M. polymorpha plants biosynthesized ethylene, and treatment with high concentrations of ACC slightly promoted ethylene production. ACC remarkably suppressed the growth of thalli (vegetative organs) and rhizoids (root-hair-like cells), whereas exogenous ethylene slightly promoted thallus growth. STS suppressed thallus growth and induced ectopic rhizoid formation on the dorsal surface of thalli. Thus, ACC and ethylene have different effects on the vegetative growth of M. polymorpha. We generated single and double mutants of ACC synthase-like (ACSL) genes, MpACSL1 and MpACSL2. The mutants did not show obvious defects in thallus growth, ACC content and ethylene production, indicating that MpACSL genes are not essential for the vegetative growth and biosynthesis of ACC and ethylene. Gene expression analysis suggested the involvement of MpACSL1 and MpACSL2 in stress responses. Collectively, our results imply ethylene-independent function of ACC and the absence of ACC-mediated ethylene biosynthesis in M. polymorpha.

Genome-Wide Identification and Functional Investigation of 1-Aminocyclopropane-1-carboxylic Acid Oxidase (ACO) Genes in Cotton

ACO is one of the rate-limiting enzymes in the biosynthesis of ethylene, and it plays a critical role in the regulation of plant growth and development. However, the function of ACO genes in cotton is not well studied. In this study, a total of 332 GhACOs, 187 GaACOs, and 181 GrACOs were identified in G. hirsutum, G. arboretum, and G. raimondii, respectively. Gene duplication analysis showed that whole-genome duplication (WGD) and tandem duplication were the major forces driving the generation of cotton ACO genes. In the promoters of GhACOs, there were cis-acting elements responding to stress, phytohormones, light, and circadian factors, indicating the possible involvement of GhACOs in these processes. Expression and co-expression analyses illustrated that most GhACOs were not only widely expressed in various tissues but also coexpressed with other genes in response to salt and drought stress. GhACO106_At overexpression in Arabidopsis promoted flowering and increased salt tolerance. These results provide a comprehensive overview of the ACO genes of cotton and lay the foundation for subsequent functional studies of these genes.

Mutations in tomato 1-aminocyclopropane carboxylic acid synthase2 uncover its role in development beside fruit ripening

The role of ethylene in plant development is mostly inferred from its exogenous application. The usage of mutants affecting ethylene biosynthesis proffers a better alternative to decipher its role. In tomato (Solanum lycopersicum), 1-aminocyclopropane carboxylic acid synthase2 (ACS2) is a key enzyme regulating ripening-specific ethylene biosynthesis. We characterised two contrasting acs2 mutants; acs2-1 overproduces ethylene, has higher ACS activity, and has increased protein levels, while acs2-2 is an ethylene underproducer, displays lower ACS activity, and has lower protein levels than wild type. Consistent with high/low ethylene emission, the mutants show opposite phenotypes, physiological responses, and metabolomic profiles compared with the wild type. The acs2-1 mutant shows early seed germination, faster leaf senescence, and accelerated fruit ripening. Conversely, acs2-2 has delayed seed germination, slower leaf senescence, and prolonged fruit ripening. The phytohormone profiles of mutants were mostly opposite in the leaves and fruits. The faster/slower senescence of acs2-1/acs2-2 leaves correlated with the endogenous ethylene/zeatin ratio. The genetic analysis showed that the metabolite profiles of respective mutants co-segregated with the homozygous mutant progeny. Our results uncover that besides ripening, ACS2 participates in the vegetative and reproductive development of tomato. The distinct influence of ethylene on phytohormone profiles indicates the intertwining of ethylene action with other phytohormones in regulating plant development.

Mutations in tomato 1-aminocyclopropane carboxylic acid synthase2 uncover its role in development beside fruit ripening

The role of ethylene in plant development is mostly inferred from its exogenous application. The usage of mutants affecting ethylene biosynthesis proffers a better alternative to decipher its role. In tomato (Solanum lycopersicum), 1-aminocyclopropane carboxylic acid synthase2 (ACS2) is a key enzyme regulating ripening-specific ethylene biosynthesis. We characterised two contrasting acs2 mutants; acs2-1 overproduces ethylene, has higher ACS activity, and has increased protein levels, while acs2-2 is an ethylene underproducer, displays lower ACS activity, and has lower protein levels than wild type. Consistent with high/low ethylene emission, the mutants show opposite phenotypes, physiological responses, and metabolomic profiles compared with the wild type. The acs2-1 mutant shows early seed germination, faster leaf senescence, and accelerated fruit ripening. Conversely, acs2-2 has delayed seed germination, slower leaf senescence, and prolonged fruit ripening. The phytohormone profiles of mutants were mostly opposite in the leaves and fruits. The faster/slower senescence of acs2-1/acs2-2 leaves correlated with the endogenous ethylene/zeatin ratio. The genetic analysis showed that the metabolite profiles of respective mutants co-segregated with the homozygous mutant progeny. Our results uncover that besides ripening, ACS2 participates in the vegetative and reproductive development of tomato. The distinct influence of ethylene on phytohormone profiles indicates the intertwining of ethylene action with other phytohormones in regulating plant development.

Proteomics and Metabolomics Reveal the Regulatory Pathways of Ripening and Quality in Post-Harvest Kiwifruits

Understanding the metabolic modulation of major quality traits during ripening is critical for fruit quality improvement in kiwifruits. Here, integrated proteomic and metabolomic profiling was undertaken to comprehensively examine the dynamics of kiwifruit ripening. This data set presents a global view of the critical pathways involved in fruit ripening, and the contributions of key events to the regulation of kiwifruit ripening and softening, amino acid metabolism, balance in sugar accumulation and organic acid metabolism, glycolysis, and tricarboxylic acid (TCA) pathways were discussed. We suggested key enzymes for starch synthesis and degradation, including AGPase, SS, and SBE, especially for BMY, which was considered a key enzyme for starch degradation. In addition, our analysis implicated the key enzymes ACO4 and ACS9 in ethylene synthesis and the aspartate aminotransferase ASP3 in the conversion of amino acids. These results provide new insights into the modulation of fruit ripening, metabolism, and quality in post-harvest kiwifruits.

Integrative Proteomic and Phosphoproteomic Analyses of Pattern- and Effector-Triggered Immunity in Tomato

Plants have evolved a two-layered immune system consisting of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI and ETI are functionally linked, but also have distinct characteristics. Unraveling how these immune systems coordinate plant responses against pathogens is crucial for understanding the regulatory mechanisms underlying plant defense. Here we report integrative proteomic and phosphoproteomic analyses of the tomato-Pseudomonas syringae (Pst) pathosystem with different Pst mutants that allow the dissection of PTI and ETI. A total of 225 proteins and 79 phosphopeptides differentially accumulated in tomato leaves during Pst infection. The abundances of many proteins and phosphoproteins changed during PTI or ETI, and some responses were triggered by both PTI and ETI. For most proteins, the ETI response was more robust than the PTI response. The patterns of protein abundance and phosphorylation changes revealed key regulators involved in Ca²⁺ signaling, mitogen-activated protein kinase cascades, reversible protein phosphorylation, reactive oxygen species (ROS) and redox homeostasis, transcription and protein turnover, transport and trafficking, cell wall remodeling, hormone biosynthesis and signaling, suggesting their common or specific roles in PTI and/or ETI. A NAC (NAM, ATAF, and CUC family) domain protein and lipid particle serine esterase, two PTI-specific genes identified from previous transcriptomic work, were not detected as differentially regulated at the protein level and were not induced by PTI. Based on integrative transcriptomics and proteomics data, as well as qRT-PCR analysis, several potential PTI and ETI-specific markers are proposed. These results provide insights into the regulatory mechanisms underlying PTI and ETI in the tomato-Pst pathosystem, and will promote future validation and application of the disease biomarkers in plant defense.

A nuclear-localized cysteine desulfhydrase plays a role in fruit ripening in tomato

Hydrogen sulfide (H₂S) is a gaseous signaling molecule that plays multiple roles in plant development. However, whether endogenous H₂S plays a role in fruit ripening in tomato is still unknown. In this study, we show that the H₂S-producing enzyme L-cysteine desulfhydrase SlLCD1 localizes to the nucleus. By constructing mutated forms of SlLCD1, we show that the amino acid residue K24 of SlLCD1 is the key amino acid that determines nuclear localization. Silencing of SlLCD1 by TRV-SlLCD1 accelerated fruit ripening and reduced H₂S production compared with the control. A SlLCD1 gene-edited mutant obtained through CRISPR/Cas9 modification displayed a slightly dwarfed phenotype and accelerated fruit ripening. This mutant also showed increased cysteine content and produced less H₂S, suggesting a role of SlLCD1 in H₂S generation. Chlorophyll degradation and carotenoid accumulation were enhanced in the SlLCD1 mutant. Other ripening-related genes that play roles in chlorophyll degradation, carotenoid biosynthesis, cell wall degradation, ethylene biosynthesis, and the ethylene signaling pathway were enhanced at the transcriptional level in the lcd1 mutant. Total RNA was sequenced from unripe tomato fruit treated with exogenous H₂S, and transcriptome analysis showed that ripening-related gene expression was suppressed. Based on the results for a SlLCD1 gene-edited mutant and exogenous H₂S application, we propose that the nuclear-localized cysteine desulfhydrase SlLCD1 is required for endogenous H₂S generation and participates in the regulation of tomato fruit ripening.

Molecular role of ethylene in fruit r​ipening of Ziziphus jujube Mill

The fruit of Chinese jujube (Ziziphus jujube) is widely consumed by human beings due to its high proteins, vitamins, and mineral nutrients. The harvest time of Chinese jujube fruit determines its quality, while ethylene plays a pivotal role in fruit ripening. Nevertheless, the relationship between ethylene biosynthesis/signal transduction and fruit ripening of Chinese jujube is still elusive. Here, the Chinese jujube fruit ripening with its fruit peel color change from cyan to dark red at seven different ripening stages (stage I-VII) and expression levels of genes related to ethylene synthesis and signal transduction were determined. Results showed that expression levels of ZjACO1-3, ZjETR2, ZjERF1, and ZjERF4 were increasingly upregulated, whereas the expression levels of ZjERS1, ZjETI, ZjERF2, and ZjERF3 were downregulated from green to red fruit ripening stages. Among them, ZjACO1-3 promoters contain ethylene response element. Taken together, Chinese jujube fruit ripening might be affected by the ethylene signaling which was mainly regulated by ZjACO, a gene involved in ethylene biosynthesis. This research supports theories and techniques for the storage, preservation and molecular breeding of Z. jujube.

Tomato transcriptional repressor MYB70 directly regulates ethylene-dependent fruit ripening

Ethylene is a key plant hormone controlling the ripening of climacteric fruits, and several transcription factors acting as important regulators of fruit ripening have been identified in tomato (Solanum lycopersicum), a model for climacteric fruits. The vast majority of these transcription factors are transcriptional activators, however, and the associated transcriptional regulatory mechanisms of most regulators are unclear. Here, we report on a tomato transcriptional repressor (termed SlMYB70) that negatively regulates fruit ripening by directly modulating ethylene biosynthesis. As an EAR motif-containing MYB transcription factor-encoding gene, SlMYB70 displayed a ripening-associated expression pattern and was responsive to ethylene. RNA interference (RNAi)-mediated repression of SlMYB70 accelerated fruit ripening, but overexpression of SlMYB70 delayed fruit ripening. Ethylene production was noticeably increased and decreased in SlMYB70-RNAi and SlMYB70-overexpressing lines, respectively, compared with wild-type tomatoes. SlMYB70 was proven to be a transcriptional repressor, dependent on the EAR repression motif, and to repress the transcription of two ethylene biosynthesis genes in fruit ripening, namely SlACS2 and SlACO3. The promoters of SlACS2 and SlACO3 are directly bound by SlMYB70, which was verified using a combination of yeast one-hybrid chromatin immunoprecipitation quantitative polymerase chain reaction and electrophoretic mobility shift assays. These results suggest that SlMYB70 negatively regulates fruit ripening via the direct transcriptional repression of ethylene biosynthesis genes, which provides insights into the ethylene-mediated key regulatory hierarchy in climacteric fruit ripening, and also highlights different types of transcriptional regulation of fruit ripening.

Volatiles from the fungal phytopathogen Penicillium aurantiogriseum modulate root metabolism and architecture through proteome resetting

Volatile compounds (VCs) emitted by the fungal phytopathogen Penicillium aurantiogriseum promote root growth and developmental changes in Arabidopsis. Here we characterised the metabolic and molecular responses of roots to fungal volatiles. Proteomic analyses revealed that these compounds reduce the levels of aquaporins, the iron carrier IRT1 and apoplastic peroxidases. Fungal VCs also increased the levels of enzymes involved in the production of mevalonate (MVA)-derived isoprenoids, nitrogen assimilation and conversion of methionine to ethylene and cyanide. Consistently, fungal VC-treated roots accumulated high levels of hydrogen peroxide (H₂ O₂ ), MVA-derived cytokinins, ethylene, cyanide and long-distance nitrogen transport amino acids. qRT-PCR analyses showed that many proteins differentially expressed by fungal VCs are encoded by VC non-responsive genes. Expression patterns of hormone reporters and developmental characterisation of mutants provided evidence for the involvement of cyanide scavenging and enhanced auxin, ethylene, cytokinin and H₂ O₂ signalling in the root architecture changes promoted by fungal VCs. Our findings show that VCs from P. aurantiogriseum modify root metabolism and architecture, and improve nutrient and water use efficiencies through transcriptionally and non-transcriptionally regulated proteome resetting mechanisms. Some of these mechanisms are subject to long-distance regulation by photosynthesis and differ from those triggered by VCs emitted by beneficial microorganisms.

Menadione Sodium Bisulfite-Protected Tomato Leaves against Grey Mould via Antifungal Activity and Enhanced Plant Immunity

Tomato grey mould has been one of the destructive fungal diseases during tomato production. Ten mM of menadione sodium bisulfite (MSB) was applied to tomato plants for eco-friendly control of the grey mould. MSB-reduced tomato grey mould in the 3rd true leaves was prolonged at least 7 days prior to the fungal inoculation of two inoculum densities (2 × 10⁴ and 2 × 10⁵ conidia/ml) of Botrytis cinerea. Protection efficacy was significantly higher in the leaves inoculated with the lower disease pressure of conidial suspension compared to the higher one. MSB-pretreatment was not effective to arrest oxalic acid-triggered necrosis on tomato leaves. Plant cell death and hydrogen peroxide accumulation were restricted in necrotic lesions of the B. cinereainoculated leaves by the MSB-pretreatment. Decreased conidia number and germ-tube elongation of B. cinerea were found at 10 h, and mycelial growth was also impeded at 24 h on the MSB-pretreated leaves. MSBmediated disease suppressions were found in cotyledons and different positions (1st to 5th) of true leaves inoculated with the lower conidial suspension, but only 1st to 3rd true leaves showed decreases in lesion sizes by the higher inoculum density. Increasing MSB-pretreatment times more efficiently decreased the lesion size by the higher disease pressure. MSB led to inducible expressions of defence-related genes SlPR1a, SlPR1b, SlPIN2, SlACO1, SlChi3, and SlChi9 in tomato leaves prior to B. cinerea infection. These results suggest that MSB pretreatment can be a promising alternative to chemical fungicides for environment-friendly management of tomato grey mould.

Manipulation of β-carotene levels in tomato fruits results in increased ABA content and extended shelf life

Tomato fruit ripening is controlled by the hormone ethylene and by a group of transcription factors, acting upstream of ethylene. During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) resulted in increased β-carotene (provitamin A) content. Unexpectedly, LCYb-overexpressing fruits also exhibited a diverse array of ripening phenotypes, including delayed softening and extended shelf life. These phenotypes were accompanied, at the biochemical level, by an increase in abscisic acid (ABA) content, decreased ethylene production, increased density of cell wall material containing linear pectins with a low degree of methylation, and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoid compounds were also altered in the transgenic fruits, which could be attributed to delayed fruit ripening and/or to ABA. Network correlation analysis and pharmacological experiments with the ABA biosynthesis inhibitor, abamine, indicated that altered ABA levels were a direct effect of the increased β-carotene content and were in turn responsible for the extended shelf life phenotype. Thus, manipulation of β-carotene levels results in an improvement not only of the nutritional value of tomato fruits, but also of their shelf life.

Identification of EIL and ERF Genes Related to Fruit Ripening in Peach

Peach (Prunus persica) is a climacteric fruit with a relatively short shelf life due to its fast ripening or softening process. Here, we report the association of gene families encoding ethylene insensitive-3 like (EIL) and ethylene response factor (ERF) with fruit ripening in peach. In total, 3 PpEILs and 12 PpERFs were highly expressed in fruit, with the majority showing a peak of expression at different stages. All three EILs could activate ethylene biosynthesis genes PpACS1 and PpACO1. One out of the 12 PpERFs, termed PpERF.E2, is a homolog of ripening-associated ERFs in tomato, with a consistently high expression throughout fruit development and an ability to activate PpACS1 and PpACO1. Additionally, four subgroup F PpERFs harboring the EAR repressive motif were able to repress the PpACO1 promoter but could also activate the PpACS1 promoter. Promoter deletion assay revealed that PpEILs and PpERFs could participate in transcriptional regulation of PpACS1 through either direct or indirect interaction with various cis-elements. Taken together, these results suggested that all three PpEILs and PpERF.E2 are candidates involved in ethylene biosynthesis, and EAR motif-containing PpERFs may function as activator or repressor of ethylene biosynthesis genes in peach. Our study provides an insight into the roles of EILs and ERFs in the fruit ripening process.

Silencing of the phytoene desaturase (PDS) gene affects the expression of fruit-ripening genes in tomatoes

BACKGROUND

Past research has shown that virus-induced phytoene desaturase (PDS) gene silencing via agroinjection in the attached and detached fruit of tomato plants results in a pale-yellow fruit phenotype. Although the PDS gene is often used as a marker for gene silencing in tomatoes, little is known about the role of PDS in fruit ripening. In this study, we investigated whether the pepper PDS gene silenced endogenous PDS genes in the fruit of two tomato cultivars, Dotaerang Plus and Legend Summer.

RESULTS

We found that the pepper PDS gene successfully silenced endogenous PDS in tomato fruit at a silencing frequency of 100% for both cultivars. A pale-yellow silenced area was observed over virtually the entire surface of individual fruit due to the transcriptional reduction in phytoene desaturase (PDS), zeta-carotene (ZDS), prolycopene isomerase (CrtlSO), and beta-carotene hydroxylase (CrtR-b2), which are the carotenoid biosynthesis genes responsible for the red coloration in tomatoes. PDS silencing also affected the expression levels of the fruit-ripening genes Tomato AGAMOUS-LIKE1 (TAGL1), RIPENING INHIBITOR (RIN), pectin esterase gene (PE), lipoxygenase (LOX), FRUITFULL1/FRUITFUL2 (FUL1/FUL2), and the ethylene biosynthesis and response genes 1-aminocyclopropane-1-carboxylate oxidase 1 and 3 (ACO1 and ACO3) and ethylene-responsive genes (E4 and E8).

CONCLUSION

These results suggest that PDS is a positive regulator of ripening in tomato fruit, which must be considered when using it as a marker for virus-induced gene silencing (VIGS) experiments in order to avoid fruit-ripening side effects.

Overexpression of a basic helix-loop-helix transcription factor gene, SlbHLH22, promotes early flowering and accelerates fruit ripening in tomato (Solanum lycopersicum L.)

The overexpression of SlbHLH22 functioned in controlling flowering time, accelerated fruit ripening, and produced more ethylene-producing phenotypes in tomato. Flowering and fruit ripening are two complex transition processes regulated by various internal and external factors that ultimately lead to fruit maturation and final seed dispersal. The basic helix-loop-helix (bHLH) transcription factor is the largest TF gene family in plants that controls various biological and developmental aspects, but the actual roles of these genes have not been fully studied. Here, we performed a functional characterization of the bHLH gene SlbHLH22 in tomato. SlbHLH22 was fully expressed in tomato flowers, while a moderate expression level was also observed in fruits at different developmental stages. Overexpression of the SlbHLH22 gene revealed that it is highly involved in controlling flowering time, through the activation of the SlSFT or SlLFY genes, and promoting fruit ripening and improved carotenoid accumulation. The expression patterns of carotenoid-related genes (SlPYS1) were also upregulated in transgenic tomato fruits. In transgenic tomato fruit, we observed clear changes in colour from green to orange with enhanced expression of the SlbHLH22 gene. SlbHLH22 was upregulated under exogenous ACC, IAA, ABA, and ethephon. Overexpression of SlbHLH22 also promotes ethylene production. Moreover, ethylene biosynthesis and perception genes (SlACO3, SlACS1, SlACS2, SlACS4, SlACS1a, SlEIN1, SlEIN2, SlEIN3, SlEIN4, SlETR2, SlETR3, SlSAM3, and SlSAMS) were upregulated. Ripening-related genes (SlAP2a, SlCNR, SlNOR, SlMYB, and SlTAG) were consistent in their expression pattern in transgenic plants. Finally, our study provides evidence that tomato bHLH genes play an important role in flowering, fruit ripening, and development.

1-Aminocyclopropane-1-Carboxylic Acid Oxidase (ACO): The Enzyme That Makes the Plant Hormone Ethylene

The volatile plant hormone ethylene regulates many plant developmental processes and stress responses. It is therefore crucial that plants can precisely control their ethylene production levels in space and time. The ethylene biosynthesis pathway consists of two dedicated steps. In a first reaction, S-adenosyl-L-methionine (SAM) is converted into 1-aminocyclopropane-1-carboxylic acid (ACC) by ACC-synthase (ACS). In a second reaction, ACC is converted into ethylene by ACC-oxidase (ACO). Initially, it was postulated that ACS is the rate-limiting enzyme of this pathway, directing many studies to unravel the regulation of ACS protein activity, and stability. However, an increasing amount of evidence has been gathered over the years, which shows that ACO is the rate-limiting step in ethylene production during certain dedicated processes. This implies that also the ACO protein family is subjected to a stringent regulation. In this review, we give an overview about the state-of-the-art regarding ACO evolution, functionality and regulation, with an emphasis on the transcriptional, post-transcriptional, and post-translational control. We also highlight the importance of ACO being a prime target for genetic engineering and precision breeding, in order to control plant ethylene production levels.

Ethylene biosynthesis controlled by NON-RIPENING: A regulatory conflict between wounding and ripening

The phytohormone ethylene is involved in multiple aspects of morphological and physiological processes in plants. Tomato rapidly and transiently increases ethylene production during fruit ripening and in plant defense responses. The transcription factor non-ripening (NOR) has significant effects on fruit ripening via regulation of ethylene biosynthesis-related genes. The nor loss-of-function allele produces a basal level of ethylene during ripening, in contrast to the induced ethylene evolution observed upon Agrobacterium tumefaciens infection. The use of ACC deaminase represses ethylene production and significantly improves the efficiency of Agrobacterium-mediated T-DNA transfer in nor plants. Analyses of the transcription levels of the ethylene biosynthesis genes ACC synthase (ACS) and ACC oxidase (ACO) in nor plants revealed that the induced ethylene production was largely due to transcriptional accumulation of ACS2 and ACO1. Accumulation of ACS2 and ACO1 mRNA opposes NOR-mediated regulation in tomato fruit during ripening, and the feedback regulation of NOR is rendered ineffective by defense responses, thereby precluding the control of its own expression. The ethylene synthesis mechanisms respond properly to NOR-mediated transcriptional regulation that is differed through the wound-induced and ripening-induced signaling pathway.

Arabidopsis ACC Oxidase 1 Coordinated by Multiple Signals Mediates Ethylene Biosynthesis and Is Involved in Root Development

Ethylene regulates numerous aspects of plant growth and development. Multiple external and internal factors coordinate ethylene production in plant tissues. Transcriptional and post-translational regulations of ACC synthases (ACSs), which are key enzymes mediating a rate-limiting step in ethylene biosynthesis have been well characterized. However, the regulation and physiological roles of ACC oxidases (ACOs) that catalyze the final step of ethylene biosynthesis are largely unknown in Arabidopsis. Here, we show that Arabidopsis ACO1 exhibits a tissue-specific expression pattern that is regulated by multiple signals, and plays roles in the lateral root development in Arabidopsis. Histochemical analysis of the ACO1 promoter indicated that ACO1 expression was largely modulated by light and plant hormones in a tissue-specific manner. We demonstrated that point mutations in two E-box motifs on the ACO1 promoter reduce the light-regulated expression patterns of ACO1. The aco1-1 mutant showed reduced ethylene production in root tips compared to wild-type. In addition, aco1-1 displayed altered lateral root formation. Our results suggest that Arabidopsis ACO1 integrates various signals into the ethylene biosynthesis that is required for ACO1's intrinsic roles in root physiology.

The mode of action of remorin1 in regulating fruit ripening at transcriptional and post-transcriptional levels

Remorins are plant-specific and plasma membrane-associated proteins that display a variety of functions in plant growth, development, biotic and abiotic stresses, and signal transduction. However, little information is available for understanding their role in fruit ripening. Here, remorin 1 (SlREM1) is cloned from tomato and its localization is examined by co-localization analysis and immunoblotting. Functions of SlREM1 in fruit ripening are characterized based on gene expression, co-immunoprecipitation coupled with mass spectroscopy and split luciferase complementation imaging assays in SlREM1 overexpression and RNA interference (RNAi) lines. The results indicate that SlREM1 is localized at the plasma membrane. Overexpression of SlREM1 in tomato stimulates fruit ripening with an increase in ethylene production and lycopene accumulation as compared to the wild-type. Consistently, these genes involved in ethylene and lycopene biosynthesis and ripening regulators also are upregulated in SlREM1 overexpression lines. SlREM1 can interact with ethylene biosynthesis proteins SAM1, ACO1 and ACS2 and is degraded by ubiquitin-mediated proteolysis. Our findings reveal that SlREM1 serves as a positive regulator of fruit ripening and provide novel cues for understanding of the molecular regulation network of fruit ripening.

Regulation of Ethylene Biosynthesis by Phytohormones in Etiolated Rice (Oryza sativa L.) Seedlings

The gaseous hormone ethylene influences many aspects of plant growth, development, and responses to a variety of stresses. The biosynthesis of ethylene is tightly regulated by various internal and external stimuli, and the primary target of the regulation is the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS), which catalyzes the rate-limiting step of ethylene biosynthesis. We have previously demonstrated that the regulation of ethylene biosynthesis is a common feature of most of the phytohormones in etiolated Arabidopsis seedlings via the modulation of the protein stability of ACS. Here, we show that various phytohormones also regulate ethylene biosynthesis from etiolated rice seedlings in a similar manner to those in Arabidopsis. Cytokinin, brassinosteroids, and gibberellic acid increase ethylene biosynthesis without changing the transcript levels of neither OsACS nor ACC oxidases (OsACO), a family of enzymes catalyzing the final step of the ethylene biosynthetic pathway. Likewise, salicylic acid and abscisic acid do not alter the gene expression of OsACS, but both hormones downregulate the transcript levels of a subset of ACO genes, resulting in a decrease in ethylene biosynthesis. In addition, we show that the treatment of the phytohormones results in distinct etiolated seedling phenotypes, some of which resemble ethylene-responsive phenotypes, while others display ethylene-independent morphologies, indicating a complicated hormone crosstalk in rice. Together, our study brings a new insight into crosstalk between ethylene biosynthesis and other phytohormones, and provides evidence that rice ethylene biosynthesis could be regulated by the post-transcriptional regulation of ACS proteins.

Quinclorac resistance induced by the suppression of the expression of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase and ACC oxidase genes in Echinochloa crus-galli var. zelayensis

We previously reported that the mechanism of quinclorac resistance in Echinochloa crus-galli var. zelayensis may be closely related to ethylene biosynthesis and the detoxification of cyanide. Differences in EcCAS gene sequences and expression levels may result in higher capacity to detoxify cyanide in resistant biotypes, which may avoid cyanide accumulation and avoid more ethylene and cyanide production and then avoid damage. In the present study, we focused on the mechanism of resistance related to ethylene biosynthesis in E. crus-galli var. zelayensis. The fresh weight of susceptible and moderately resistant biotypes were significantly reduced after treatment with quinclorac. However, AOA, an ethylene biosynthesis inhibitor, reduced the impact of quinclorac. On pretreatment with AOA, ethylene production was significantly reduced in the three biotypes. The highly resistant biotype produced less ethylene compared to the other two biotypes. Three ACS and seven ACO genes, which are the key genes in ethylene biosynthesis, were obtained. The expression levels of EcACS-like, EcACS7, and EcACO1 varied in the three biotypes upon treatment with quinclorac, which could be manipulated by AOA. In summary, it is inferred that the expression of EcACS-like, EcACS7, and EcACO1 can be stimulated to varying extent after quinclorac treatment in three E. crus-galli var. zelayensis biotypes, which consequently results in varying levels of ethylene production. Lower expression of these three genes results in more resistance to quinclorac, which may also be related to quinclorac resistance in E. crus-galli var. zelayensis.

Effects of the inoculations using bacteria producing ACC deaminase on ethylene metabolism and growth of wheat grown under different soil water contents

Crop growth and productivity are often impacted by the increased ethylene content induced by adverse environmental conditions such drought. Inoculations with bacteria producing ACC deaminase is considered as a potential biological approach to improve the growth and tolerance of stressed plants by lowering endogenous ethylene level. In this study, germinated wheat seeds were inoculated using three species of the rhizobacteria, which were isolated from the rhizosphere of wheat growing in dryland, and sown in pots. After three weeks, wheat seedlings were exposed to non-limiting water condition, medium drought and severe drought, respectively, for six weeks. The results showed that, irrespective of rhizobacterial inoculations, decreased soil water contents stimulated wheat ethylene metabolism, which was reflected by the significantly increased activity of ACC synthetase and ACC oxidase, besides an increased content of ACC both in the roots and leaves, and an enhanced capacity of leaves to release ethylene, concomitant with a significant decline in shoot and roots biomass. The inoculations of all three rhizobacterial species under each water condition reduced ACC content in wheat leaves, but effects of the inoculations on ACC synthase and ACC oxidase activity in the leaves and roots, ACC content in the roots, the capacity of leaves to release ethylene, and wheat growth varied with water conditions and bacterial species. Hence, both soil water conditions and rhizobacterial inoculations acted on all the processes of ethylene metabolism, with the former being dominant. The inoculations under non-limiting water condition and medium drought promoted shoot and root growth of wheat plants.

Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences

The plant hormone ethylene is one of the central regulators of plant development and stress resistance. Optimal ethylene signaling is essential for plant fitness and is under strong selection pressure. Plants upregulate ethylene production in response to stress, and this hormone triggers defense mechanisms. Due to the pleiotropic effects of ethylene, adjusting stress responses to maximize resistance, while minimizing costs, is a central determinant of plant fitness. Ethylene signaling is influenced by the plant-associated microbiome. We therefore argue that the regulation, physiology, and evolution of the ethylene signaling can best be viewed as the interactive result of plant genotype and associated microbiota. In this article, we summarize the current knowledge on ethylene signaling and recapitulate the multiple ways microorganisms interfere with it. We present ethylene signaling as a model system for holobiont-level evolution of plant phenotype: this cascade is tractable, extremely well studied from both a plant and a microbial perspective, and regulates fundamental components of plant life history. We finally discuss the potential impacts of ethylene modulation microorganisms on plant ecology and evolution. We assert that ethylene signaling cannot be fully appreciated without considering microbiota as integral regulatory actors, and we more generally suggest that plant ecophysiology and evolution can only be fully understood in the light of plant-microbiome interactions.

A tomato MADS-box protein, SlCMB1, regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening

The MADS-box transcription factors play essential roles in many physiological and biochemical processes of plants, especially in fruit ripening. Here, a tomato MADS-box gene, SlCMB1, was isolated. SlCMB1 expression declined with the fruit ripening from immature green to B + 7 (7 days after Breaker) fruits in the wild type (WT) and was lower in Nr and rin mutants fruits. Tomato plants with reduced SlCMB1 mRNA displayed delayed fruit ripening, reduced ethylene production and carotenoid accumulation. The ethylene production in SlCMB1-RNAi fruits decreased by approximately 50% as compared to WT. The transcripts of ethylene biosynthesis genes (ACS2, ACS4, ACO1 and ACO3), ethylene-responsive genes (E4, E8 and ERF1) and fruit ripening-related genes (RIN, TAGL1, FUL1, FUL2, LoxC and PE) were inhibited in SlCMB1-RNAi fruits. The carotenoid accumulation was decreased and two carotenoid synthesis-related genes (PSY1 and PDS) were down-regulated while three lycopene cyclase genes (CYCB, LCYB and LCYE) were up-regulated in transgenic fruits. Furthermore, yeast two-hybrid assay showed that SlCMB1 could interact with SlMADS-RIN, SlMADS1, SlAP2a and TAGL1, respectively. Collectively, these results indicate that SlCMB1 is a new component to the current model of regulatory network that regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening.

Silencing of histone deacetylase SlHDT3 delays fruit ripening and suppresses carotenoid accumulation in tomato

The acetylation levels of histones on lysine residues are regulated by histone acetyltransferases and histone deacetylases, which play an important but understudied role in the control of gene expression in plants. There is an increasing research focus on histone deacetylation in crops, but to date, there is little information regarding tomato. With the aim of characterizing the tomato HD2 family of histone deacetylases, an RNA interference (RNAi) expression vector of SlHDT3 was constructed and transformed into tomato plants. The time of fruit ripening was delayed and the shelf life of the fruit was prolonged in SlHDT3 RNAi lines. The accumulation of carotenoid was decreased by altering of the carotenoid pathway flux. Ethylene content was also reduced and expression of ethylene biosynthetic genes (ACS2, ACS4 and ACO1, ACO3) and ripening-associated genes (RIN, E4, E8, PG, Pti4 and LOXB) was significantly down-regulated in SlHDT3 RNAi lines. The expression of genes involved in fruit cell wall metabolism (HEX, MAN, TBG4, XTH5 and XYL) was inhibited compared with wild type. These results indicate that SlHDT3 functions as a positive regulator of fruit ripening by affecting ethylene synthesis and carotenoid accumulation and that SlHDT3 lies upstream of SlMADS-RIN in the fruit ripening regulatory network.

Elucidating the Mechanisms of the Tomato ovate Mutation in Regulating Fruit Quality Using Proteomics Analysis

The ovate mutation has frequently been used to study changes in fruit shape but not fruit quality. A deterioration in fruit quality associated with the ovate mutation was discovered in this study. To elucidate how ovate influences the quality of fruit, we performed a proteomics analysis of the fruits of the ovate mutant (LA3543) and wild-type ("Ailsa Craig", LA2838A) using tandem mass tag analysis. The results indicated that the ovate mutation significantly influences fruit quality in a number of ways, including by reducing the expression of 1-aminocyclopropane-1-carboxylic acid oxidase 3 (ACO3) in ethylene biosynthesis, improving firmness by reducing the amount of pectinesterase and polygalacturonase, reducing sugar accumulation by downregulating the abundance of mannan endo-1,4-β-mannosidase 4, β-galactosidase, and β-amylase, and reducing the malic acid content by downregulating the accumulation of malic enzymes and malate synthase. These findings could inform future improvements in fruit quality.

Penicillium expansum (compatible) and Penicillium digitatum (non-host) pathogen infection differentially alter ethylene biosynthesis in apple fruit

The role of ethylene on inducing plant resistance or susceptibility to certain fungal pathogens clearly depends on the plant pathogen interaction with little or no-information available focused on the apple-Penicillium interaction. Taken advantage that Penicillium expansum is the compatible pathogen and P. digitatum is the non-host of apples, the present study aimed at deciphering how each Penicillium spp. could interfere in the fruit ethylene biosynthesis at the biochemical and molecular level. The infection capacity and different aspects related to the ethylene biosynthesis were conducted at different times post-inoculation. The results show that the fruit ethylene biosynthesis was differently altered during the P. expansum infection than in response to other biotic (non-host pathogen P. digitatum) or abiotic stresses (wounding). The first symptoms of the disease due to P. expansum were visible before the initiation of the fruit ethylene climacteric burst. Indeed, the ethylene climacteric burst was reduced in response to P. expansum concomitant to an important induction of MdACO3 gene expression and an inhibition (ca. 3-fold) and overexpression (ca. 2-fold) of ACO (1-Aminocyclopropane-1-carboxylic acid oxidase) and ACS (1-Aminocyclopropane-1-carboxylic acid synthase) enzyme activities, indicating a putative role of MdACO3 in the P. expansum-apple interaction which may, in turn, be related to System-1 ethylene biosynthesis. System-1 is auto-inhibited by ethylene and is characteristic of non-climateric or pre-climacteric fruit. Accordingly, we hypothesise that P. expansum may 'manipulate' the endogenous ethylene biosynthesis in apples, leading to the circumvention or suppression of effective defences hence facilitating its colonization.

Suppression of the MADS-box gene SlMBP8 accelerates fruit ripening of tomato (Solanum lycopersicum)

MADS-box genes encode important transcription factors that are involved in many biological processes of plants, including fruit ripening. In our research, a MADS-box gene, SlMBP8, was identified, and its tissue-specific expression profiles were analysed. SlMBP8 was highly expressed in fruits of the B+4 stage, in senescent leaves and in sepals. To further characterize its function, an RNA interference (RNAi) expression vector of SlMBP8 was constructed and transferred into tomato. In the transgenic plants, the ripening of fruits was shortened by 2-4 days compared to that of wild type. At the same time, carotenoids accumulated to higher levels and the expression of phytone synthase 1 (PSY1), phytoene desaturase (PDS) and ς-carotene desaturase (ZDS) was enhanced in RNAi fruits. The transgenic fruits and seedlings showed more ethylene production compared with that of the wild type. Furthermore, SlMBP8-silenced seedlings displayed shorter hypocotyls due to higher endogenous ethylene levels, suggesting that SlMBP8 may modulates the ethylene triple response negatively. A yeast two-hybrid assay indicated that SlMBP8 could interact with SlMADS-RIN. Besides, the expression of ethylene-related genes, including ACO1, ACO3, ACS2, ERF1, E4 and E8, was simultaneously up-regulated in transgenic plants. In addition, SlMBP8-silenced fruits showed higher ethylene production, suggesting that suppressed expression of SlMBP8 promotes carotenoid and ethylene biosynthesis. In addition, the fruits of transgenic plants displayed more rapid water loss and decreased storability compared to wild type, which was due to the significantly induced expressions of cell wall metabolism genes such as PG, EXP, HEX, TBG4, XTH5 and XYL. These results suggest that SlMBP8 plays an important role in fruit ripening and softening.

Transcriptome Analysis of Cell Wall and NAC Domain Transcription Factor Genes during Elaeis guineensis Fruit Ripening: Evidence for Widespread Conservation within Monocot and Eudicot Lineages

The oil palm (Elaeis guineensis), a monocotyledonous species in the family Arecaceae, has an extraordinarily oil rich fleshy mesocarp, and presents an original model to examine the ripening processes and regulation in this particular monocot fruit. Histochemical analysis and cell parameter measurements revealed cell wall and middle lamella expansion and degradation during ripening and in response to ethylene. Cell wall related transcript profiles suggest a transition from synthesis to degradation is under transcriptional control during ripening, in particular a switch from cellulose, hemicellulose, and pectin synthesis to hydrolysis and degradation. The data provide evidence for the transcriptional activation of expansin, polygalacturonase, mannosidase, beta-galactosidase, and xyloglucan endotransglucosylase/hydrolase proteins in the ripening oil palm mesocarp, suggesting widespread conservation of these activities during ripening for monocotyledonous and eudicotyledonous fruit types. Profiling of the most abundant oil palm polygalacturonase (EgPG4) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) transcripts during development and in response to ethylene demonstrated both are sensitive markers of ethylene production and inducible gene expression during mesocarp ripening, and provide evidence for a conserved regulatory module between ethylene and cell wall pectin degradation. A comprehensive analysis of NAC transcription factors confirmed at least 10 transcripts from diverse NAC domain clades are expressed in the mesocarp during ripening, four of which are induced by ethylene treatment, with the two most inducible (EgNAC6 and EgNAC7) phylogenetically similar to the tomato NAC-NOR master-ripening regulator. Overall, the results provide evidence that despite the phylogenetic distance of the oil palm within the family Arecaceae from the most extensively studied monocot banana fruit, it appears ripening of divergent monocot and eudicot fruit lineages are regulated by evolutionarily conserved molecular physiological processes.

Label-free deep shotgun proteomics reveals protein dynamics during tomato fruit tissues development

Current innovations in mass-spectrometry-based technologies allow deep coverage of protein expression. Despite its immense value and in contrast to transcriptomics, only a handful of studies in crop plants engaged with global proteome assays. Here, we present large-scale shotgun proteomics profiling of tomato fruit across two key tissues and five developmental stages. A total of 7738 individual protein groups were identified and reliably measured at least in one of the analyzed tissues or stages. The depth of our assay enabled identification of 61 differentially expressed transcription factors, including renowned ripening-related regulators and elements of ethylene signaling. Significantly, we measured proteins involved in 83% of all predicted enzymatic reactions in the tomato metabolic network. Hence, proteins representing almost the complete set of reactions in major metabolic pathways were identified, including the cytosolic and plastidic isoprenoid and the phenylpropanoid pathways. Furthermore, the data allowed us to discern between protein isoforms according to expression patterns, which is most significant in light of the weak transcript-protein expression correspondence. Finally, visualization of changes in protein abundance associated with a particular process provided us with a unique view of skin and flesh tissues in developing fruit. This study adds a new dimension to the existing genomic, transcriptomic and metabolomic resources. It is therefore likely to promote translational and post-translational research in tomato and additional species, which is presently focused on transcription.

Unraveling the target genes of RIN transcription factor during tomato fruit ripening and softening

BACKGROUND

The RIN transcription factor is one of the MADS box family members and predominantly controls fruit ripening. In this study, effort was made to demonstrate the regulation network of RIN transcription factor during tomato fruit ripening and softening. Novel RIN target genes were identified by proteomics, electrophoresis mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) analysis.

RESULTS

Over 700 protein spots were achieved by two-dimensional gel electrophoresis, and 42 proteins were successfully identified. Among them, 1-aminocyclopropane-1-carboxylate oxidase (LeACO4, ethylene synthesis, spot 3) and α-galactosidase-like isoform 2 (α-Gal, cell wall metabolism, spot 26) exhibited varied expression levels in different tomato fruits. Particularly high expression levels of LeACO4 and α-Gal were observed in wild type but not in the rin mutant. Additionally, CArG box, a RIN-binding site, was discovered in the promoter regions of both LeACO4 and α-Gal genes, suggesting that RIN possibly directly regulates their transcriptions, and this assumption was further confirmed by EMSA and ChIP assay.

CONCLUSION

Functional annotations of RIN target genes demonstrated the specific role of RIN in the process of fruit ripening and softening, especially in cell wall degradation and ethylene biosynthesis. This study will further illuminate the mechanism of tomato ripening and softening. © 2016 Society of Chemical Industry.

Different Preclimacteric Events in Apple Cultivars with Modified Ripening Physiology

"Anna" is an early season apple cultivar exhibiting a fast softening and juiciness loss during storage, in comparison to two mid-late season cultivars "Galaxy" and "GD." The poor storage capacity of "Anna" was correlated with high lipid oxidation-related autoluminescence, high respiration and ethylene production rates, associated with high expression of MdACO1, 2, 4, 7, and MdACS1. All cultivars at harvest responded to exogenous ethylene by enhancing ethylene production, typical of system-II. The contribution of pre-climacteric events to the poor storage capacity of "Anna" was examined by comparing respiration and ethylene production rates, response to exogenous ethylene, expression of genes responsible for ethylene biosynthesis and response, and developmental regulators in the three cultivars throughout fruit development. In contrast to the "Galaxy" and "GD," "Anna" showed higher ethylene production and respiration rates during fruit development, and exhibited auto-stimulatory (system II-like) effect in response to exogenous ethylene. The higher ethylene production rate in "Anna" was correlated with higher expression of ethylene biosynthesis genes, MdACS3a MdACO2, 4, and 7 during early fruit development. The expression of negative regulators of ripening (AP2/ERF) and ethylene response pathway, (MdETR1,2 and MdCTR1) was lower in "Anna" in comparison to the other two cultivars throughout development and ripening. Similar pattern of gene expression was found for SQUAMOSA promoter binding protein (SBP)-box genes, including MdCNR and for MdFUL. Taken together, this study provides new understanding on pre-climacteric events in "Anna" that might affect its ripening behavior and physiology following storage.

Accumulation and Transport of 1-Aminocyclopropane-1-Carboxylic Acid (ACC) in Plants: Current Status, Considerations for Future Research and Agronomic Applications

1-aminocyclopropane-1-carboxylic acid (ACC) is a non-protein amino acid acting as the direct precursor of ethylene, a plant hormone regulating a wide variety of vegetative and developmental processes. ACC is the central molecule of ethylene biosynthesis. The rate of ACC formation differs in response to developmental, hormonal and environmental cues. ACC can be conjugated to three derivatives, metabolized in planta or by rhizobacteria using ACC deaminase, and is transported throughout the plant over short and long distances, remotely leading to ethylene responses. This review highlights some recent advances related to ACC. These include the regulation of ACC synthesis, conjugation and deamination, evidence for a role of ACC as an ethylene-independent signal, short and long range ACC transport, and the identification of a first ACC transporter. Although unraveling the complex mechanism of ACC transport is in its infancy, new questions emerge together with the identification of a first transporter. In the light of the future quest for additional ACC transporters, this review presents perspectives of the novel findings and includes considerations for future research toward applications in agronomy.

Functional Characterization of SlSAHH2 in Tomato Fruit Ripening

S-adenosylhomocysteine hydrolase (SAHH) functions as an enzyme catalyzing the reversible hydrolysis of S-adenosylhomocysteine to homocysteine and adenosine. In the present work we have investigated its role in the ripening process of tomato fruit. Among the three SlSAHH genes we demonstrated that SlSAHH2 was highly accumulated during fruit ripening and strongly responded to ethylene treatment. Over-expression of SlSAHH2 enhanced SAHH enzymatic activity in tomato fruit development and ripening stages and resulted in a major phenotypic change of reduced ripening time from anthesis to breaker. Consistent with this, the content of lycopene was higher in SlSAHH2 over-expression lines than in wild-type at the same developmental stage. The expression of two ethylene inducible genes (E4 and E8) and three ethylene biosynthesis genes (SlACO1, SlACO3 and SlACS2) increased to a higher level in SlSAHH2 over-expression lines at breaker stage, and one transgenic line even produced much more ethylene than wild-type. Although inconsistency in gene expression and ethylene production existed between the two transgenic lines, the transcriptional changes of several important ripening regulators such as RIN, AP2a, TAGL1, CNR and NOR showed a consistent pattern. It was speculated that the influence of SlSAHH2 on ethylene production was downstream of the regulation of SlSAHH2 on these ripening regulator genes. The over-expressing lines displayed higher sensitivity to ethylene in both fruit and non-fruit tissues. Ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) treatment accelerated ripening faster in SlSAHH2 over-expressing fruit than in wild-type. Additionally, seedlings of transgenic lines displayed shorter hypocotyls and roots in ethylene triple response assay. In conclusion, SlSAHH2 played an important role in tomato fruit ripening.

Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation

Commercial tomatoes are widely perceived by consumers as lacking flavor. A major part of that problem is a postharvest handling system that chills fruit. Low-temperature storage is widely used to slow ripening and reduce decay. However, chilling results in loss of flavor. Flavor-associated volatiles are sensitive to temperatures below 12 °C, and their loss greatly reduces flavor quality. Here, we provide a comprehensive view of the effects of chilling on flavor and volatiles associated with consumer liking. Reduced levels of specific volatiles are associated with significant reductions in transcripts encoding key volatile synthesis enzymes. Although expression of some genes critical to volatile synthesis recovers after a return to 20 °C, some genes do not. RNAs encoding transcription factors essential for ripening, including RIPENING INHIBITOR (RIN), NONRIPENING, and COLORLESS NONRIPENING are reduced in response to chilling and may be responsible for reduced transcript levels in many downstream genes during chilling. Those reductions are accompanied by major changes in the methylation status of promoters, including RIN Methylation changes are transient and may contribute to the fidelity of gene expression required to provide maximal beneficial environmental response with minimal tangential influence on broader fruit developmental biology.

Comprehensive RNA-Seq Analysis on the Regulation of Tomato Ripening by Exogenous Auxin

Auxin has been shown to modulate the fruit ripening process. However, the molecular mechanisms underlying auxin regulation of fruit ripening are still not clear. Illumina RNA sequencing was performed on mature green cherry tomato fruit 1 and 7 days after auxin treatment, with untreated fruit as a control. The results showed that exogenous auxin maintained system 1 ethylene synthesis and delayed the onset of system 2 ethylene synthesis and the ripening process. At the molecular level, genes associated with stress resistance were significantly up-regulated, but genes related to carotenoid metabolism, cell degradation and energy metabolism were strongly down-regulated by exogenous auxin. Furthermore, genes encoding DNA demethylases were inhibited by auxin, whereas genes encoding cytosine-5 DNA methyltransferases were induced, which contributed to the maintenance of high methylation levels in the nucleus and thus inhibited the ripening process. Additionally, exogenous auxin altered the expression patterns of ethylene and auxin signaling-related genes that were induced or repressed in the normal ripening process, suggesting significant crosstalk between these two hormones during tomato ripening. The present work is the first comprehensive transcriptome analysis of auxin-treated tomato fruit during ripening. Our results provide comprehensive insights into the effects of auxin on the tomato ripening process and the mechanism of crosstalk between auxin and ethylene.

Comprehensive Analysis of ABA Effects on Ethylene Biosynthesis and Signaling during Tomato Fruit Ripening

ABA has been widely acknowledged to regulate ethylene biosynthesis and signaling during fruit ripening, but the molecular mechanism underlying the interaction between these two hormones are largely unexplored. In the present study, exogenous ABA treatment obviously promoted fruit ripening as well as ethylene emission, whereas NDGA (Nordihydroguaiaretic acid, an inhibitor of ABA biosynthesis) application showed the opposite biological effects. Combined RNA-seq with time-course RT-PCR analysis, our study not only helped to illustrate how ABA regulated itself at the transcription level, but also revealed that ABA can facilitate ethylene production and response probably by regulating some crucial genes such as LeACS4, LeACO1, GR and LeETR6. In addition, investigation on the fruits treated with 1-MCP immediately after ABA exposure revealed that ethylene might be essential for the induction of ABA biosynthesis and signaling at the onset of fruit ripening. Furthermore, some specific transcription factors (TFs) known as regulators of ethylene synthesis and sensibility (e.g. MADS-RIN, TAGL1, CNR and NOR) were also observed to be ABA responsive, which implied that ABA influenced ethylene action possibly through the regulation of these TFs expression. Our comprehensive physiological and molecular-level analysis shed light on the mechanism of cross-talk between ABA and ethylene during the process of tomato fruit ripening.