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Mondher Bouzayen - One of the best experts on this subject based on the ideXlab platform.
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The Molecular Regulation of Ethylene in Fruit Ripening
Small Methods, 2020Co-Authors: Yudong Liu, Jing Chen, Mingfeng Tang, Mingchun Liu, Yushuo Gao, Mondher BouzayenAbstract:Fleshy Fruits are major sources of necessary nutrients in many diets worldwide. Most Fruit quality attributes emerge during Ripening making the Fruit more attractive to consumers. Understanding the molecular regulatory network underpinning fleshy Fruit Ripening is important not only for Fruit quality improvement but also for postharvest shelf life. The phytohormone ethylene plays an essential role in climacteric Fruit Ripening and a number of studies have demonstrated that ethylene signaling components and related transcription factors are involved in the regulation of Fruit Ripening. However, the transcriptional network by which ethylene interacts with other signaling pathways to regulate the Ripening process is not fully understood. In this review, focusing on the tomato as a reference species, the key points regarding the role of ethylene in coordinating the Ripening process at the molecular and physiological levels are described. The interplay between ethylene and Ripening‐related regulators and its crosstalk with other phytohormones and present recent data on Ripening‐related epigenetic modifications are also discussed. Overall, the paper summarizes the most advanced research progress in this area to help facilitate its future development.
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ethylene control of Fruit Ripening revisiting the complex network of transcriptional regulation
Plant Physiology, 2015Co-Authors: Julien Pirrello, Christian Chervin, Jeanpaul Roustan, Mondher BouzayenAbstract:The plant hormone ethylene plays a key role in climacteric Fruit Ripening. Studies on components of ethylene signaling have revealed a linear transduction pathway leading to the activation of ethylene response factors. However, the means by which ethylene selects the Ripening-related genes and interacts with other signaling pathways to regulate the Ripening process are still to be elucidated. Using tomato (Solanum lycopersicum) as a reference species, the present review aims to revisit the mechanisms by which ethylene regulates Fruit Ripening by taking advantage of new tools available to perform in silico studies at the genome-wide scale, leading to a global view on the expression pattern of ethylene biosynthesis and response genes throughout Ripening. Overall, it provides new insights on the transcriptional network by which this hormone coordinates the Ripening process and emphasizes the interplay between ethylene and Ripening-associated developmental factors and the link between epigenetic regulation and ethylene during Fruit Ripening.
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Chap.11: Ethylene and Fruit Ripening
2012Co-Authors: J. C. Pech, Mondher Bouzayen, Eduardo Purgatto, Alain LatcheAbstract:The Ripening of fleshy Fruit is a developmentally regulated process unique to plants during which the majority of the sensory quality attributes are elaborated including aroma, flavour, texture and nutritional compounds. In climacteric Fruit, the plant hormone ethylene is the key regulator of the Ripening process as exemplified by the dramatic inhibition of Fruit Ripening that results from the down-expression of ACC (1-amino-cyclopropane-1-carboxylic acid) synthase and ACC oxidase genes involved in ethylene biosynthesis. By contrast, the Ripening of non-climacteric Fruit is not dependent on ethylene but rather on cues of unknown nature though ethylene may contribute at least partly to the control of some aspects of the Ripening process. The expression of the Ripening-associated genes is regulated by a network of signalling pathways among which ethylene perception and transduction play a primary role. Building on the knowledge gained on the Arabidopsis thaliana model system, the importance of ethylene signalling in Fruit Ripening has been extensively studied. This chapter summarizes the present knowledge on the role of ethylene in Fruit Ripening and addresses the molecular mechanisms involved in ethylene perception and responses. It also highlights recent advances and prospects on the means by which the ethylene transduction pathway leads to diversified physiological responses and how ethylene signalling interacts with other hormones to activate the expression of Ripening-related genes. While this review mostly refers to the tomato as major model for Fruit research, it also gives insight on the Ripening process in other Fruit species, including nonclimacteric types.
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Ethylene and Fruit Ripening
The Plant Hormone Ethylene, 2012Co-Authors: J. C. Pech, Mondher Bouzayen, Eduardo Purgatto, Alain LatcheAbstract:The latest advances in our understanding of the relationship between ethylene and Fruit Ripening are reviewed. Considerable progress has been made in the characterisation of genes encoding the key ethylene biosynthetic enzymes, ACC synthase (ACS) and ACC oxidase (ACO) and in the isolation of genes involved in the ethylene signal transduction pathway, particularly those encoding ethylene receptors (ETR). These have allowed the generation of transgenic Fruit with reduced ethylene production and the identification of the Nr tomato Ripening mutant as an ethylene receptor mutant. Through these tools, a clearer picture of the role of ethylene in Fruit Ripening is now emerging. In climacteric Fruit, the transition to autocatalytic ethylene production appears to result from a series of events where developmentally regulated ACO and ACS gene expression initiates a rise in ethylene production, setting in motion the activation of autocatalytic ethylene production. Differential expression of ACS and ACO gene family members is probably involved in such a transition. Finally, we discuss evidence suggesting that the NR ethylene perception and transduction pathway is specific to a defined set of genes expressed in Ripening climacteric Fruit and that a distinct ETR pathway regulates other ethylene-regulated genes in both immature and Ripening climacteric Fruit as well as in non-climacteric Fruit. The emerging picture is one where both ethylene-dependent and -independent pathways coexist in both climacteric and non-climacteric Fruits. Further work is needed in order to dissect the molecular events involved in individual Ripening processes and to understand the regulation of the expression of both ethylene-dependent and -independent genes.
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Ethylene and Fruit Ripening
2012Co-Authors: J. C. Pech, Mondher Bouzayen, Eduardo Purgatto, Alain LatcheAbstract:The Ripening of fleshy Fruit is a developmentally regulated process unique to plants during which the majority of the sensory quality attributes are elaborated including aroma, flavour, texture and nutritional compounds. In climacteric Fruit, the plant hormone ethylene is the key regulator of the Ripening process as exemplified by the dramatic inhibition of Fruit Ripening that results from the down-expression of ACC (1-amino-cyclopropane-1-carboxylic acid) synthase and ACC oxidase genes involved in ethylene biosynthesis. By contrast, the Ripening of non-climacteric Fruit is not dependent on ethylene but rather on cues of unknown nature though ethylene may contribute at least partly to the control of some aspects of the Ripening process. The expression of the Ripening-associated genes is regulated by a network of signalling pathways among which ethylene perception and transduction play a primary role. Building on the knowledge gained on the Arabidopsis thaliana model system, the importance of ethylene signalling in Fruit Ripening has been extensively studied. This chapter summarizes the present knowledge on the role of ethylene in Fruit Ripening and addresses the molecular mechanisms involved in ethylene perception and responses. It also highlights recent advances and prospects on the means by which the ethylene transduction pathway leads to diversified physiological responses and how ethylene signalling interacts with other hormones to activate the expression of Ripening-related genes. While this review mostly refers to the tomato as major model for Fruit research, it also gives insight on the Ripening process in other Fruit species, including nonclimacteric types.
Bernd Muellerroeber - One of the best experts on this subject based on the ideXlab platform.
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tomato Fruit Ripening factor nor controls leaf senescence
Journal of Experimental Botany, 2019Co-Authors: Salma Balazadeh, Bernd MuellerroeberAbstract:NAC transcription factors (TFs) are important regulators of expressional reprogramming during plant development, stress responses, and leaf senescence. NAC TFs also play important roles in Fruit Ripening. In tomato (Solanum lycopersicum), one of the best characterized NACs involved in Fruit Ripening is NON-Ripening (NOR), and the non-Ripening (nor) mutation has been widely used to extend Fruit shelf life in elite varieties. Here, we show that NOR additionally controls leaf senescence. Expression of NOR increases with leaf age, and developmental as well as dark-induced senescence are delayed in the nor mutant, while overexpression of NOR promotes leaf senescence. Genes associated with chlorophyll degradation as well as senescence-associated genes (SAGs) show reduced and elevated expression, respectively, in nor mutants and NOR overexpressors. Overexpression of NOR also stimulates leaf senescence in Arabidopsis thaliana. In tomato, NOR supports senescence by directly and positively regulating the expression of several senescence-associated genes including, besides others, SlSAG15 and SlSAG113, SlSGR1, and SlYLS4. Finally, we find that another senescence control NAC TF, namely SlNAP2, acts upstream of NOR to regulate its expression. Our data support a model whereby NAC TFs have often been recruited by higher plants for both the control of leaf senescence and Fruit Ripening.
Alain Latche - One of the best experts on this subject based on the ideXlab platform.
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Current challenges in postharvest biology of Fruit Ripening
Current Agricultural Science and Technology, 2013Co-Authors: J. C. Pech, Eduardo Purgatto, César Luis Girardi, Cesar Valmor Rombaldi, Alain LatcheAbstract:This paper reviews the recent advances in the understanding of the Fruit Ripening process and describes future challenges. Fruit Ripening is a complex developmental process which is orchestrated by the expression of Ripening-related genes under the control of a network of signaling pathways. In climacteric Fruit components responsible for the production of climacteric ethylene have been identified. Less progress has been made on non-climacteric Fruit. Great advances have been made in the characterization of transcription factors (ERFs, RIN, etc…) that induce gene expression through the binding to their promoters. Genetic resources, genome sequencing and “omics” tools have been developed bringing a huge amount of data that will help to draw an integrative network of regulatory and signaling pathways responsible for triggering and coordinating the Ripening process. The discovery that some Ripening events are controlled at the epigenetic level and not in relation with the DNA sequences opens novel perspectives.
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Current challenges in postharvest biology of Fruit Ripening
Current Agricultural Science and Technology, 2013Co-Authors: J. C. Pech, Eduardo Purgatto, César Luis Girardi, Cesar Valmor Rombaldi, Alain LatcheAbstract:This paper reviews the recent advances in the understanding of the Fruit Ripening process and describes future challenges. Fruit Ripening is a complex developmental process which is orchestrated by the expression of Ripening-related genes under the control of a network of signaling pathways. In climacteric Fruit components responsible for the production of climacteric ethylene have been identified. Less progress has been made on non-climacteric Fruit. Great advances have been made in the characterization of transcription factors (ERFs, RIN, etc...) that induce gene expression through the binding to their promoters. Genetic resources, genome sequencing and "omics" tools have been developed bringing a huge amount of data that will help to draw together an integrative network of regulatory and signaling pathways responsible for triggering and coordinating the Ripening process. The discovery that some Ripening events are controlled at the epigenetic level and, not in relation with the DNA sequences, opens novel perspectives.
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Chap.11: Ethylene and Fruit Ripening
2012Co-Authors: J. C. Pech, Mondher Bouzayen, Eduardo Purgatto, Alain LatcheAbstract:The Ripening of fleshy Fruit is a developmentally regulated process unique to plants during which the majority of the sensory quality attributes are elaborated including aroma, flavour, texture and nutritional compounds. In climacteric Fruit, the plant hormone ethylene is the key regulator of the Ripening process as exemplified by the dramatic inhibition of Fruit Ripening that results from the down-expression of ACC (1-amino-cyclopropane-1-carboxylic acid) synthase and ACC oxidase genes involved in ethylene biosynthesis. By contrast, the Ripening of non-climacteric Fruit is not dependent on ethylene but rather on cues of unknown nature though ethylene may contribute at least partly to the control of some aspects of the Ripening process. The expression of the Ripening-associated genes is regulated by a network of signalling pathways among which ethylene perception and transduction play a primary role. Building on the knowledge gained on the Arabidopsis thaliana model system, the importance of ethylene signalling in Fruit Ripening has been extensively studied. This chapter summarizes the present knowledge on the role of ethylene in Fruit Ripening and addresses the molecular mechanisms involved in ethylene perception and responses. It also highlights recent advances and prospects on the means by which the ethylene transduction pathway leads to diversified physiological responses and how ethylene signalling interacts with other hormones to activate the expression of Ripening-related genes. While this review mostly refers to the tomato as major model for Fruit research, it also gives insight on the Ripening process in other Fruit species, including nonclimacteric types.
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Ethylene and Fruit Ripening
The Plant Hormone Ethylene, 2012Co-Authors: J. C. Pech, Mondher Bouzayen, Eduardo Purgatto, Alain LatcheAbstract:The latest advances in our understanding of the relationship between ethylene and Fruit Ripening are reviewed. Considerable progress has been made in the characterisation of genes encoding the key ethylene biosynthetic enzymes, ACC synthase (ACS) and ACC oxidase (ACO) and in the isolation of genes involved in the ethylene signal transduction pathway, particularly those encoding ethylene receptors (ETR). These have allowed the generation of transgenic Fruit with reduced ethylene production and the identification of the Nr tomato Ripening mutant as an ethylene receptor mutant. Through these tools, a clearer picture of the role of ethylene in Fruit Ripening is now emerging. In climacteric Fruit, the transition to autocatalytic ethylene production appears to result from a series of events where developmentally regulated ACO and ACS gene expression initiates a rise in ethylene production, setting in motion the activation of autocatalytic ethylene production. Differential expression of ACS and ACO gene family members is probably involved in such a transition. Finally, we discuss evidence suggesting that the NR ethylene perception and transduction pathway is specific to a defined set of genes expressed in Ripening climacteric Fruit and that a distinct ETR pathway regulates other ethylene-regulated genes in both immature and Ripening climacteric Fruit as well as in non-climacteric Fruit. The emerging picture is one where both ethylene-dependent and -independent pathways coexist in both climacteric and non-climacteric Fruits. Further work is needed in order to dissect the molecular events involved in individual Ripening processes and to understand the regulation of the expression of both ethylene-dependent and -independent genes.
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Ethylene and Fruit Ripening
2012Co-Authors: J. C. Pech, Mondher Bouzayen, Eduardo Purgatto, Alain LatcheAbstract:The Ripening of fleshy Fruit is a developmentally regulated process unique to plants during which the majority of the sensory quality attributes are elaborated including aroma, flavour, texture and nutritional compounds. In climacteric Fruit, the plant hormone ethylene is the key regulator of the Ripening process as exemplified by the dramatic inhibition of Fruit Ripening that results from the down-expression of ACC (1-amino-cyclopropane-1-carboxylic acid) synthase and ACC oxidase genes involved in ethylene biosynthesis. By contrast, the Ripening of non-climacteric Fruit is not dependent on ethylene but rather on cues of unknown nature though ethylene may contribute at least partly to the control of some aspects of the Ripening process. The expression of the Ripening-associated genes is regulated by a network of signalling pathways among which ethylene perception and transduction play a primary role. Building on the knowledge gained on the Arabidopsis thaliana model system, the importance of ethylene signalling in Fruit Ripening has been extensively studied. This chapter summarizes the present knowledge on the role of ethylene in Fruit Ripening and addresses the molecular mechanisms involved in ethylene perception and responses. It also highlights recent advances and prospects on the means by which the ethylene transduction pathway leads to diversified physiological responses and how ethylene signalling interacts with other hormones to activate the expression of Ripening-related genes. While this review mostly refers to the tomato as major model for Fruit research, it also gives insight on the Ripening process in other Fruit species, including nonclimacteric types.
Yuan-yue Shen - One of the best experts on this subject based on the ideXlab platform.
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Sigma factor FaSigE positively regulates strawberry Fruit Ripening by ABA
Plant Growth Regulation, 2017Co-Authors: Shaohui Zhang, Lu Chai, Bingzhu Hou, Aizhen Yang, Yuan-yue ShenAbstract:Bacterial sigma factor E (SigE) is a positive regulator of sugar catabolism via its interaction with the H subunit of Mg-chelatase (CHLH), which serves as both putative abscisic acid (ABA) receptor (ABAR) in Arabidopsis thaliana and positive regulator of strawberry Fruit Ripening. However, whether SigE influences strawberry Fruit Ripening has not been determined. We used RNA sequencing and a qPCR to confirm that the expression of the strawberry SigE gene (FaSigE) is rapidly upregulated in Fruits turning red, suggesting FaSigE might mediate strawberry Fruit Ripening. Silencing FaSigE by intron-spliced hairpin RNA-mediated RNA interference significantly inhibited Fruit Ripening. This observation was confirmed by analyses of Fruit firmness, soluble sugar, ABA, and anthocyanin contents, as well as transcript levels of genes related to Fruit Ripening and ABA signaling. Interestingly, a firefly luciferase complementation assay revealed that FaSigE can interact with FaABAR, while an in vitro Fruit disc incubation test indicated ABA induces FaSigE expression. Moreover, a surface plasmon resonance assay proved that FaABAR produced in yeast cells can bind to ABA, with a binding dissociation constant of 50 µM. In conclusion, FaSigE can interact with FaABAR and positively regulates strawberry Fruit Ripening via ABA.
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FaABI4 is involved in strawberry Fruit Ripening
Scientia Horticulturae, 2016Co-Authors: Lu Chai, Yuan-yue ShenAbstract:Abstract Abscisic acid (ABA) is regarded as an important regulator in non-climacteric Fruit Ripening, especially in strawberry Fruit. FaABI4, as a critical downstream component of ABA signaling in plants, whether it is involved in strawberry Ripening remains unclear. The octoploid strawberry (Fragaria ananassa, ‘Beinongxiang’) Fruits were used here to explore this question. Our results showed that FaABI4 expressed higher in leaves, followed in flowers and Fruits, but less in roots and stems, and that coupled with the Fruit Ripening, its transcripts increased gradually, suggesting that FaABI4 might play a role in the Ripening. Using tobacco rattle virus-induced gene silencing (VIGS), downregulation of FaABI4 transcripts significantly delayed Fruit Ripening in consistent with changes of firmness, sugar and ABA contents, as well as transcripts of several Ripening-related genes, including CA4H, CHI, DFR, CHS, GAL6, PE5, and XYL2. Interestingly, ABA, sucrose and glucose all induced FaABI4 expression through Fruit-disc incubation in vitro. In conclusion, our results demonstrate that FaABI4 plays an important role in the regulation of strawberry Fruit Ripening, and its expression is induced by ABA, sucrose and glucose.
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New evidence for the role of ethylene in strawberry Fruit Ripening.
Journal of Plant Growth Regulation, 2013Co-Authors: Jing-hua Sun, Yu Xing, Lin Tian, Jing-jing Luo, Yuan-yue ShenAbstract:It has been suggested that the phytohormone ethylene plays a role in strawberry Fruit Ripening, and new genetic evidence for the role of this hormone in strawberry Ripening is provided in this study. The combined analysis of ethylene production and transcripts of the ethylene biosynthesis-related gene FaSAMS1 and the signaling gene FaCTR1 in ‘Camarosa’ strawberry (Fragariaananassa) Fruit showed that an increase in ethylene production was concomitant with a rise in transcripts of the two genes during Fruit red-coloring, suggesting that FaSAMS1 and FaCTR1 might play a role in Fruit Ripening. Downregulation of the FaSAMS1 or FaCTR1 transcript via a recently reported tobacco rattle virus-induced gene-silencing technique not only inhibited Fruit red-coloring and firmness, but it also promoted ethylene biosynthesis. Furthermore, the latter also affected a series of ethylene-signaling components. Importantly, applied ethephon could promote natural strawberry Fruit red-coloring and softening and partially rescue anthocyanin biosynthesis in the two-type RNAi Fruit, but could not markedly affect RNAi Fruit firmness. These data provide new evidence that FaCTR1 positively regulates strawberry Fruit Ripening and that ethylene is required for strawberry Fruit Ripening.
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Brassinosteroid is involved in strawberry Fruit Ripening
Plant Growth Regulation, 2012Co-Authors: Ye-mao Chai, Qing Zhang, Lin Tian, Yu Xing, Ling Qin, Yuan-yue ShenAbstract:Although brassinosteroid (BR) has been suggested to play a role in strawberry Fruit Ripening, the defined function of this hormone remains unclear in the Fruit. Here, BR content and BR receptor gene FaBRI1 expression were analysed during ‘Akihime’ strawberry Fruit development. We found that BR levels increased during the later developmental stages, and the mRNA expression levels of FaBRI1 increased rapidly from white to initial red stages, suggesting that BR is associated with Fruit Ripening. This was further confirmed by exogenous application of BR and its inhibitor brassinazole (BZ) to big-green Fruit, which significantly promoted and inhibited strawberry Fruit Ripening, respectively. More importantly, down-regulation of FaBRI1 expression in de-greening Fruit markedly retarded strawberry red-colouring. In conclusion, we have provided physiological and molecular evidence to demonstrate that BR plays a role in strawberry Fruit Ripening. In addition, both BR content and FaBRI1 expression reached their peak levels in small-green Fruit, suggesting that BR might also be involved in early strawberry Fruit development. Further experiments are required to validate the role of BR in strawberry Fruit cell division.
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FaPYR1 is involved in strawberry Fruit Ripening
Journal of Experimental Botany, 2011Co-Authors: Ye-mao Chai, Hai-feng Jia, Qing-hua Dong, Yuan-yue ShenAbstract:Although the plant hormone abscisic acid (ABA) has been suggested to play a role in the Ripening of non-climatic Fruit, direct genetic/molecular evidence is lacking. In the present study, a strawberry gene homologous to the Arabidopsis ABA receptor gene PYR1, named FaPYR1, was isolated and characterized. The 627 bp cDNA includes an intact open reading frame that encodes a deduced protein of 208 amino acids, in which putative conserved domains were detected by homology analysis. Using tobacco rattle virus-induced gene silencing (VIGS), the FaPYR1 gene was silenced in strawberry Fruit. Down-regulation of the FaPYR1 gene not only significantly delayed Fruit Ripening, but also markedly altered ABA content, ABA sensitivity, and a set of ABA-responsive gene transcripts, including ABI1 and SnRK2. Furthermore, the loss of red colouring in FaPYR1 RNAi (RNA interference) Fruits could not be rescued by exogenously applied ABA, which could promote the Ripening of wild-type Fruits. Collectively, these results demonstrate that the putative ABA receptor FaPYR1 acts as a positive regulator in strawberry Fruit Ripening. It was also revealed that the application of the VIGS technique in strawberry Fruit could be used as a novel tool for studying strawberry Fruit development.
Yunbo Luo - One of the best experts on this subject based on the ideXlab platform.
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Noncoding RNAs: functional regulatory factors in tomato Fruit Ripening.
Theoretical and Applied Genetics, 2020Co-Authors: Donald Grierson, Yunxiang Wang, Lipu Gao, Xiaoyan Zhao, Benzhong Zhu, Yunbo Luo, Kai Shi, Qing WangAbstract:Tomato has emerged as the model system for investigations into the regulation of fleshy-Fruit Ripening and senescence, and the Ripening process involving the coordinated regulation at the gene/chromatin/epigenetic, transcriptional, post-transcriptional and protein levels. Noncoding RNAs play important roles in Fruit Ripening as important transcriptional and post-transcriptional regulatory factors. In this review, we systematically summarize the recent advances in the regulation of tomato Fruit Ripening involved in ethylene biosynthesis and signal transduction, Fruit pigment accumulation, Fruit flavor and aroma, Fruit texture by noncoding RNAs and their coordinate regulatory network model were set up and also suggest future directions for the functional regulations of noncoding RNAs on tomato Fruit Ripening.
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SRNAome and transcriptome analysis provide insight into strawberry Fruit Ripening.
Genomics, 2020Co-Authors: Wang Yunxiang, Yunbo Luo, Jinhua Zuo, Li Wensheng, Chang Hong, Zhou Jiahua, Zhang Kaichun, Wang BaogangAbstract:Strawberry Fruit Ripening is a complex process affected by multiple factors at different regulation levels. To elucidate the regulation mechanisms, the combined analysis of sRNAome and transcriptome were used. A total of 124 known and 190 novel miRNAs were found, 62 of them were significantly differentially expressed (DE). The targets of the DE miRNAs were parsed and several TFs, such as SPL, ARF, WRKY, and TCP, were found to be involved in Ripening. Elevated CO2 can significantly postpone Ripening and miR156, miR166f, miR171a, and miR171d were the DE miRNAs. Transcriptome analysis found 313 DE genes related to Fruit Ripening, including cell wall metabolism-related genes, color-related genes, ethylene-related genes, and genes encoding TFs such as MYB, SPL, NAC, TCP, and ARF. Based on above, a combined regulatory model involved in Fruit Ripening was created. These results provide valuable information for understanding the complicated coordinated regulatory network of strawberry Fruit Ripening.
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Network analysis of noncoding RNAs in pepper provides insights into Fruit Ripening control.
Scientific Reports, 2019Co-Authors: Jinhua Zuo, Yunxiang Wang, Benzhong Zhu, Yunbo Luo, Qing Wang, Lipu GaoAbstract:Pepper is an important vegetable worldwide and is a model plant for nonclimacteric fleshy Fruit Ripening. Drastic visual changes and internal biochemical alterations are involved in Fruit coloration, flavor, texture, aroma, and palatability to animals during the pepper Fruit Ripening process. To explore the regulation of bell pepper Fruit Ripening by noncoding RNAs (ncRNAs), we examined their expression profiles; 43 microRNAs (miRNAs), 125 circular RNAs (circRNAs), 366 long noncoding RNAs (lncRNAs), and 3266 messenger RNAs (mRNAs) were differentially expressed (DE) in mature green and red ripe Fruit. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the targets of the DE ncRNAs and DE mRNAs included several kinds of transcription factors (TFs) (ERF, bHLH, WRKY, MYB, NAC, bZIP, and ARF), enzymes involved in cell wall metabolism (beta-galactosidase, beta-glucosidase, beta-amylase, chitinase, pectate lyase (PL), pectinesterase (PE) and polygalacturonase (PG)), enzymes involved in Fruit color accumulation (bifunctional 15-cis-phytoene synthase, 9-cis-epoxycarotenoid dioxygenase, beta-carotene hydroxylase and carotene epsilon-monooxygenase), enzymes associated with Fruit flavor and aroma (glutamate-1-semialdehyde 2,1-aminomutase, anthocyanin 5-aromatic acyltransferase, and eugenol synthase 1) and enzymes involved in the production of ethylene (ET) (ACO1/ACO4) as well as other plant hormones such as abscisic acid (ABA), auxin (IAA), and gibberellic acid (GA). Based on accumulation profiles, a network of ncRNAs and mRNAs associated with bell pepper Fruit Ripening was developed that provides a foundation for further developing a more refined understanding of the molecular biology of Fruit Ripening.
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The RNA Editing Factor SlORRM4 Is Required for Normal Fruit Ripening in Tomato
Plant Physiology, 2017Co-Authors: Yongfang Yang, Benzhong Zhu, Yunbo Luo, Huiqin Tian, Guoning Zhu, Shijie Yan, Hongliang ZhuAbstract:RNA editing plays a key posttranscriptional role in gene expression. Existing studies on cytidine-to-uridine RNA editing in plants have focused on maize (Zea mays), rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana). However, the importance and regulation of RNA editing in several critical agronomic processes are not well understood, a notable example of which is Fruit Ripening. Here, we analyzed the expression profile of 33 RNA editing factors and identified 11 putative tomato (Solanum lycopersicum) Fruit Ripening-related factors. A rapid virus-induced gene silencing assay indicated that the organelle RNA recognition motif-containing protein SlORRM4 affected tomato Fruit Ripening. Knocking out SlORRM4 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy delayed tomato Fruit Ripening by lowering respiratory rate and ethylene production. Additionally, the expression of numerous genes associated with Fruit Ripening and mitochondrial functions changed significantly when SlORRM4 was knocked out. Moreover, the loss of SlORRM4 function significantly reduced RNA editing of many mitochondrial transcripts, leading to low-level expression of some core subunits that are critical for mitochondrial complex assembly (i.e. Nad3, Cytc1, and COX II). Taken together, these results indicate that SlORRM4 is involved in RNA editing of transcripts in Ripening Fruit that influence mitochondrial function and key aspects of Fruit Ripening.
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RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato Fruit Ripening
Journal of Experimental Botany, 2015Co-Authors: Benzhong Zhu, Yunbo Luo, Yongfang Yang, Liwei Wen, Hongliang ZhuAbstract:Recently, long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in model plants, such as Arabidopsis, rice, and maize. However, the presence of lncRNAs and how they function in fleshy Fruit Ripening are still largely unknown because fleshy Fruit Ripening is not present in the above model plants. Tomato is the model system for Fruit Ripening studies due to its dramatic Ripening process. To investigate further the role of lncRNAs in Fruit Ripening, it is necessary and urgent to discover and identify novel lncRNAs and understand the function of lncRNAs in tomato Fruit Ripening. Here it is reported that 3679 lncRNAs were discovered from wild-type tomato and Ripening mutant Fruit. The lncRNAs are transcribed from all tomato chromosomes, 85.1% of which came from intergenic regions. Tomato lncRNAs are shorter and have fewer exons than protein-coding genes, a situation reminiscent of lncRNAs from other model plants. It was also observed that 490 lncRNAs were significantly up-regulated in Ripening mutant Fruits, and 187 lncRNAs were down-regulated, indicating that lncRNAs could be involved in the regulation of Fruit Ripening. In line with this, silencing of two novel tomato intergenic lncRNAs, lncRNA1459 and lncRNA1840, resulted in an obvious delay of Ripening of wild-type Fruit. Overall, the results indicated that lncRNAs might be essential regulators of tomato Fruit Ripening, which sheds new light on the regulation of Fruit Ripening.
