Fleshy fruit metabolism is intricately influenced by environmental changes, yet the hormonal regulations underlying these responses remain poorly elucidated. ABA and ethylene, pivotal in stress responses across plant vegetative tissues, play crucial roles in triggering fleshy fruit ripening. Their actions are intricately governed by complex mechanisms, influencing key aspects such as nutraceutical compound accumulation, sugar content, and softening parameters. Both hormones are essential orchestrators of significant alterations in fruit development in response to stressors like drought, salt, and temperature fluctuations. These alterations encompass colour development, sugar accumulation, injury mitigation, and changes in cell-wall degradation and ripening progression. This review provides a comprehensive overview of recent research progress on the roles of ABA and ethylene in responding to drought, salt, and temperature stress, as well as the molecular mechanisms controlling ripening in environmental cues. Additionally, we propose further studies aimed at genetic manipulation of ABA and ethylene signalling, offering potential strategies to enhance fleshy fruit resilience in the face of future climate change scenarios.

Transcription factors (TFs) are crucial for regulating fruit ripening in tomato (Solanum lycopersicum). The GRAS (GAI, RGA, and SCR) TFs are involved in various physiological processes, but their role in fruit ripening has seldom been reported. We have previously identified a gene encoding GRAS protein named SlFSR (Fruit Shelf-life Regulator), which is implicated in fruit ripening by regulating cell wall metabolism; however, the underlying mechanism remains unclear. Here, we demonstrate that SlFSR proteins are localized to the nucleus, where they could bind to specific DNA sequences. SlFSR acts downstream of the master ripening regulator RIN and could collaborate with RIN to control the ripening process by regulating expression of ethylene biosynthesis genes. In SlFSR-CR (CRISPR/Cas9) mutants, the initiation of fruit ripening was not affected but the reduced ethylene production and a delayed coloring process occurred. RNA-sequencing (RNA-seq) and promoter analysis reveal that SlFSR directly binds to the promoters of two key ethylene biosynthesis genes (SlACO1 and SlACO3) and activates their expression. However, SlFSR-CR fruits displayed a significant down-regulation of key rate-limiting genes (SlDXS1 and SlGGPPS2) in the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, which may account for the impaired lycopene synthesis. Altogether, we propose that SlFSR positively regulates ethylene biosynthesis and lycopene accumulation, providing valuable insights into the molecular mechanisms underlying fruit ripening.

Long non-coding RNAs (lncRNAs) play crucial roles in various biological processes in plants. However, the functional mechanism of lncRNAs in fruit ripening, particularly the transition from unripe to ripe stages, remains elusive. One such lncRNA1840, reported by our group, was found to have important role in tomato fruit ripening. In the present study, we gain insight into its functional role in fruit ripening. CRISPR-Cas9 mediated lncRNA1840 mutants caused the delayed tomato fruit ripening. Notably, loss function of lncRNA1840 did not directly impact ethylene signaling but rather delay ethylene synthesis. Transcriptomic analysis revealed differences in the expression of ripening related genes in lncRNA1840 mutants, suggesting that it is involved in gene regulation of fruit ripening. We used Chromatin Isolation by RNA Purification (ChIRP)-Seq to identify lncRNA1840 binding sites on chromatin. ChIRP-seq suggested that lncRNA1840 had occupancy on 40 genes, but none of them is differentially expressed genes in transcriptomic analysis, which indicated lncRNA1840 might indirectly modulate the gene expression. ChIRP-mass spectrometry analysis identified potential protein interactors of lncRNA1840, Pre-mRNA processing splicing factor 8, highlighting its involvement in post-transcriptional regulatory pathways. In summary, lncRNA1840 is key player in tomato plant growth and fruit ripening, with multifaceted roles in gene expression and regulatory networks.

Many studies showed NAC transcription factors play an important role in fruit ripening. Moreover, sucrose and starch metabolism is also closely related to fruit ripening. However, there are a few studies focus on whether NAC regulates sucrose and starch metabolism to influence fruit ripening. In this study, virus-induced gene silencing (VIGS) of SlNAP1 suppressed fruit ripening and delayed color transformation. The chlorophyll (including Chla, Chlb, and Chla + b) degradation and carotenoid synthesis in SlNAP1-silenced fruits were dramatically suppressed. Silencing SlNAP1 decreased soluble sugar and reducing sugar accumulation in fruits, and increased starch content. The activity of starch degrading enzymes, including α amylase (AMY) and β amylase (BAM) was significantly lower in SlNAP1-silenced fruits than in the control fruits, whereas denosine diphosphoglucose pyrophosphorylase (AGP) activity was significantly higher. In addition, the expression of starch degradation-related genes (SlAMY1, SlAMY2, SlBAM1, SlBAM7, SlGWD, SlPWD) in SlNAP1-silenced fruits was significantly suppressed, while starch synthesis-related genes (SlAGPase1, SlAGPase2) was significantly increased. Compared with the control fruits, SlNAP1-silenced fruits showed significantly lower sucrose and glucose content. The expression level of sucrose and glucose metabolism-related genes such as Slsus1, Slsus3, SlSPS, SlHxk1, SlHxk2, SlPK1, and SlPK2 was significantly lower in SlNAP1-silenced fruits than in the control fruits. Overall, this study revealed that SlNAP1 gene might positively regulate fruit ripening by influencing carbohydrate metabolism.

Fruit ripening is a highly intricate process, where the dynamic interplay of soluble sugar and organic acid metabolism is crucial for developing the characteristic flavor qualities. Pyruvate orthophosphate dikinase (PPDK) plays a pivotal role in modulating the process of gluconeogenesis during plant development. However, the specific physiological role of PPDK in fruit development has yet to be elucidated. In this study, we investigated the expression pattern, subcellular localization and functional significance of SlPPDK in tomato fruits. Our results reveal that SlPPDK is highly expressed in fruits and flowers, with its expression progressively increasing as the fruit ripens. Subcellular localization analyses demonstrate that SlPPDK is distributed in the cell membrane, cytoplasm, and nucleus. Using CRISPR/Cas9 technology, we generated SlPPDK knockout mutants, which exhibited a marked reduction in enzyme activity, leading to significant alterations in sugar and organic acid metabolism. These findings highlight the critical role of SlPPDK in maintaining the sugar-acid balance essential for tomato flavor quality and provide a foundation for future breeding strategies aimed at enhancing tomato fruit flavor.

The ripening process of Chinese bayberries (Myrica rubra) is intricate, involving a multitude of molecular interactions. Here, we integrated transcriptomic and metabolomic analysis across three developmental stages of the Myrica rubra (M. rubra) to elucidate these processes. A differential gene expression analysis categorized the genes into four distinct groups based on their expression patterns. Gene ontology and pathway analyses highlighted processes such as cellular and metabolic processes, including protein and sucrose metabolism. A metabolomic analysis revealed significant variations in metabolite profiles, underscoring the dynamic interplay between genes and metabolites during ripening. Flavonoid biosynthesis and starch and sucrose metabolism were identified as key pathways, with specific genes and metabolites playing crucial roles. Our findings provide insights into the molecular mechanisms governing fruit ripening in M. rubra and offer potential targets for breeding strategies aimed at enhancing fruit quality.

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The B-box (BBX) family, which is a class of zinc finger transcription factors, exhibits special roles in plant growth and development as well as in plants\' ability to cope with various stresses. Even though Rubus chingii is an important traditional medicinally edible plant in east Asia, there are no comprehensive studies of BBX members in R. chingii. In this study, 32 RcBBX members were identified, and these were divided into five groups. A collinearity analysis showed that gene duplication events were common, and when combined with a motif analysis of the RcBBX genes, it was concluded that group V genes might have undergone deletion of gene fragments or mutations. Analysis of cis-acting elements revealed that each RcBBX gene contained hormone-, light-, and stress-related elements. Expression patterns of the 32 RcBBX genes during fruit ripening revealed that highest expression occurred at the small green fruit stage. Of note, the expression of several RcBBX genes increased rapidly as fruit developed. These findings, combined with the expression profiles of anthocyanin biosynthetic genes during fruit ripening, allowed us to identify the nuclear-targeted RcBBX26, which positively promoted anthocyanin production in R. chingii. The collective findings of this study shed light on the function of RcBBX genes in different tissues, developmental stages, and in response to two abiotic stresses.

CONCLUSIONS: Auxin (AUX) promotion of apple fruit ripening is ethylene-dependent, and AUX-MdARF17-MdERF003 plays a role in AUX-promoted ethylene synthesis in apple. Phytohormones play important roles in plant growth and fleshy fruit ripening, and the phytohormone auxin (AUX) can either promote or inhibit the ripening of fleshy fruits. Although AUX can influence ethylene (ETH) synthesis in apple (Malus domestica) fruits by affecting ETH system II, this mechanism remains to be explored. Here, we identified an ETH response factor (ERF) family transcription factor, MdERF003, whose expression could be activated by naphthalene acetic acid. The transient silencing of MdERF003 inhibited ETH synthesis in fruits, and MdERF003 could bind to the MdACS1 promoter. To explore the upstream target genes of MdERF003, we screened the MdARF family members by yeast one-hybrid assays of the MdERF003 promoter, and found that the transcription factor MdARF17, which showed AUX-promoted expression, could bind to the MdERF003 promoter and promote its expression. Finally, we silenced MdERF003 in apple fruits overexpressing MdARF17 and found that MdERF003 plays a role in MdARF17-promoted ETH synthesis in apple. Thus, AUX-MdARF17-MdERF003 promotes ETH synthesis in apple fruits.

BACKGROUND: The fruit ripening period is an important target trait in fruit tree crop breeding programs. Thus, citrus tree breeders seek to develop extreme early ripening cultivars that allow optimization of citrus maturation periods. In this study, we explored the regulatory network involved in fruit ripening in Citrus sinensis using the \'Newhall\' navel orange variety and its early-ripening mutant, \'Gannanzao\'. This research will provide a basis for further research on important signaling pathways, gene functions and variety breeding of Citrus sinensis related to fruit ripening period.
RESULTS: Physiological analyses suggested that early fruit ripening in \'Gannanzao\' is regulated by early accumulation of abscisic acid (ABA), persistently high levels of jasmonic acid (JA), and higher sucrose content in the pericarp. Pericarp samples from \'Gannanzao\' and \'Newhall\' navel oranges were sampled for RNA sequencing analysis at 180, 200, and 220 days after flowering; 1430 differentially expressed genes (DEGs) were identified. Functional enrichment analysis indicated that these DEGs were mainly enriched in the plant hormone signal transduction and sugar metabolism pathways, as well as other pathways related to fruit ripening. Important DEGs associated with fruit ripening in \'Gannanzao\' included genes involved in ABA and JA metabolism and signal transduction, as well as sugar metabolism. Weighted gene co-expression network analysis showed that the deep pink module had the strongest correlations with ABA content, JA content, and early ripening. Based on gene functionality and gene expression analyses of 37 genes in this module, two candidate hub genes and two ethylene response factor 13 (ERF13) genes (Cs_ont_5g000690 and Cs_ont_5g000700) were identified as key genes regulated by ABA and JA signaling. These findings will help to clarify the mechanisms that underlie early citrus fruit ripening and will lead to the development of excellent genetic resources for further breeding of extreme early-ripening varieties.
CONCLUSIONS: Through analyses of the \'Newhall\' navel orange cultivar and its early-ripening mutant \'Gannanzao\', we identified genes involved in ABA and JA metabolism, signal transduction, and sugar metabolism that were related to fruit ripening. Among these, two ERF13 genes were inferred to be key genes in the regulation of fruit ripening. These findings provide insights into the genetic architecture related to early fruit ripening in C. sinensis.