Exploring the sound-modulated delay in tomato ripening through expression analysis of RNA.
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ABSTRACT:
PROVIDER: PRJNA416331 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6234980_1.fastq.gz | Fastqsanger.gz | |||
| SRR6234980_2.fastq.gz | Fastqsanger.gz | |||
| SRR6234981_1.fastq.gz | Fastqsanger.gz | |||
| SRR6234981_2.fastq.gz | Fastqsanger.gz | |||
| SRR6234982_1.fastq.gz | Fastqsanger.gz |
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Project description:We evaluated the molecular mechanism underlying this delaying fruit ripening by performing RNA-sequencing analysis of tomato fruits at 6 h, 2 days (d), 5 d and 7 d after 1 kHz sound vibration treatment. Differentially expressed genes revealed that some of these genes are involved in plant hormone and cell wall modification processes. Ethylene and cytokinin biosynthesis and signalling genes were downregulated by sound vibration treatment, whereas genes involved in flavonoid, phenylpropanoid and glucan biosynthesis were upregulated. Our results indicate that sound vibration helps delay fruit ripening through the sophisticated regulation of RNAs and transcription factor genes.
2018-11-01 | GSE106337 | GEO
Project description:Background and aimsSound is omnipresent in nature. Recent evidence supports the notion that naturally occurring and artificially generated sound waves induce inter- and intracellular changes in plants. These changes, in turn, lead to diverse physiological changes, such as enhanced biotic and abiotic stress responses, in both crops and model plants.MethodsWe previously observed delayed ripening in tomato fruits exposed to 1 kHz sound vibrations for 6 h. Here, we evaluated the molecular mechanism underlying this delaying fruit ripening by performing RNA-sequencing analysis of tomato fruits at 6 h, 2 d, 5 d and 7 d after 1 kHz sound vibration treatment.Key resultsBioinformatic analysis of differentially expressed genes and non-coding small RNAs revealed that some of these genes are involved in plant hormone and cell wall modification processes. Ethylene and cytokinin biosynthesis and signalling-related genes were downregulated by sound vibration treatment, whereas genes involved in flavonoid, phenylpropanoid and glucan biosynthesis were upregulated. Furthermore, we identified two sound-specific microRNAs and validated the expression of the pre-microRNAs and the mRNAs of their target genes.ConclusionsOur results indicate that sound vibration helps to delay fruit ripening through the sophisticated regulation of coding and non-coding RNAs and transcription factor genes.
| S-EPMC6324751 | biostudies-literature
Project description:Here, we found that the tomato jmjC domain-containing gene SlJMJ6 encodes a histone lysine demethylase that specifically demethylates H3K27 methylation. Overexpression of SlJMJ6 accelerated fruit ripening in tomato, which is associated with the up-regulated expression of a large number of ripening-related genes. Integrated analysis of RNA-seq and ChIP-seq data identified 55 genes that are targeted directly by SlJMJ6 and transcriptionally up-regulated with decreased H3K27m3 in SlJMJ6 overexpressing (SlJMJ6-OE) fruits. A large number of the SlJMJ6-regulated genes are involved in transcription regulation, ethylene biosynthesis, cell wall degradation, pigment biosynthesis, and hormone signaling. Fourteen ripening-related genes including RIN, ACS4, ACO1, PL, TBG4 were confirmed to be directly regulated by SlJMJ6 through removing H3K27me3. Taken together, these results indicated that SlJMJ6 is a ripening prompting H3K27me3 demethylase that activates the expression of the ripening-related genes by modulating H3K27me3, thereby facilitating fruit ripening in tomato. To our knowledge, this is the first report of the involvement of a histone lysine demethylase in the regulation of fruit ripening.
2020-04-13 | GSE142713 | GEO
Project description:Here, we found that the tomato jmjC domain-containing gene SlJMJ6 encodes a histone lysine demethylase that specifically demethylates H3K27 methylation. Overexpression of SlJMJ6 accelerated fruit ripening in tomato, which is associated with the up-regulated expression of a large number of ripening-related genes. Integrated analysis of RNA-seq and ChIP-seq data identified 55 genes that are targeted directly by SlJMJ6 and transcriptionally up-regulated with decreased H3K27m3 in SlJMJ6 overexpressing (SlJMJ6-OE) fruits. A large number of the SlJMJ6-regulated genes are involved in transcription regulation, ethylene biosynthesis, cell wall degradation, pigment biosynthesis, and hormone signaling. Fourteen ripening-related genes including RIN, ACS4, ACO1, PL, TBG4 were confirmed to be directly regulated by SlJMJ6 through removing H3K27me3. Taken together, these results indicated that SlJMJ6 is a ripening prompting H3K27me3 demethylase that activates the expression of the ripening-related genes by modulating H3K27me3, thereby facilitating fruit ripening in tomato. To our knowledge, this is the first report of the involvement of a histone lysine demethylase in the regulation of fruit ripening.
2020-04-13 | GSE142712 | GEO
Project description:Transcription factors (TFs) are important regulators of plant growth and development and responses to stresses. TFs themselves are also susceptible to multiple post-translational modifications (PTMs). Relatively, redox-mediated PTM of TFs in plants is not well elucidated. Here, we found that NON-RIPENING (NOR), a master TF regulating tomato fruit ripening, is a target of SlMsrE4 or SlMsrB2, the methionine sulfoxide reductase A and B in tomato, respectively. Methionine oxidation in NOR, i.e. sulfoxidation, or mimicking sulfoxidation by mutating Met138 to glutamine, leads to the decreased DNA-binding capacity and transcriptional regulatory activity in vitro. On the other hand, SlMsrE4 and SlMsrB2 can partially repair oxidized-NOR and restore its DNA-binding capacity. Genetic transformation of the nor mutant with NOR genomic DNA almost completely rescues the ripening phenotype. However, transformation of nor with NOR-M138Q, the mimicked methionine sulfoxidation, inhibits the restore of fruit ripening phenotype, and this is associated with the decreased DNA-binding and transcriptional activation of numerous ripening-related genes. Taken together, these findings uncover a novel mechanism by which Msr-mediated redox modification of NOR regulates the expression of ripening-related genes, thereby influencing tomato fruit ripening. To our knowledge, this is the first report that redox modification of TF regulates fruit ripening. nor is a NOR mutant, the phenotype is obstructed by maturity; NOR-12 is a rotational NOR in NOR mutant, the phenotype is a mature inhibition phenotype that basically restores nor mutant; Nor-18 is a rotation of NOR-M138Q in nor mutant, phenotype with the effect of restoring maturity, but the recovery efficiency is lower than the swing NOR.
2020-05-22 | GSE140853 | GEO
Project description:DNA methylation is a conserved epigenetic mark important for genome integrity, development and environmental responses in plants and mammals. Active DNA demethylation in plants is initiated by a family of 5mC DNA glycosylases/lyases (i.e. DNA demethylases). The role of DNA demethylases in transposon regulation, pathogen responses, and gene imprinting and other developmental processes have been studied extensively in the model plant Arabidopsis thaliana. Recent studies suggested a role of active DNA demethylation in fruit ripening in tomato. In this study, we generated loss-of-function mutant alleles of a tomato gene, SlROS1/SlDML1/2, which is a close homolog of the Arabidopsis DNA demethylase gene ROS1. In the fruits of the tomato mutants, increased DNA methylation was found in thousands of genes. These genes include not only hundreds of ripening induced genes but also many ripening repressed genes. Our results show that SlROS1 is critical for tomato fruit ripening, and suggest that active DNA demethylation is required for both the activation of ripening induced genes and inhibition of ripening repressed genes.
2017-05-02 | GSE94903 | GEO
Project description:Postharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes in order to facilitate infections and promote disease. Assessments of ripening progression revealed that B. cinerea accelerated external coloration, ethylene production, and softening in unripe fruit, while mRNA sequencing of inoculated unripe fruit confirmed the corresponding upregulation of host genes involved in ripening processes, such as ethylene biosynthesis and cell wall degradation. Furthermore, ELISA-based glycomics profiling of fruit cell wall polysaccharides revealed remarkable similarities in the cell wall polysaccharide changes caused by both infections of unripe fruit and ripening of healthy fruit, particularly in the increased accessibility of pectin polysaccharides. Virulence and additional ripening assessment experiments with B. cinerea knockout mutants showed that induction of ripening is dependent on the ability to infect the host and break down pectin. The B. cinerea double knockout Δbcpg1Δbcpg2 lacking two critical pectin degrading enzymes was found to be incapable of emerging from quiescence even long after the fruit had ripened at its own pace, suggesting that the failure to accelerate ripening severely inhibits fungal survival on unripe fruit. These findings demonstrate that active induction of ripening in unripe tomato fruit is an important infection strategy for B. cinerea.
2022-01-01 | GSE183836 | GEO
Project description:Combinational analyses of genome-wide transcription, binding sites and histone H3K4 trimethylation profiles revealed that SlJMJ7 directly binds and represses the expression of a series of key ripening-associated factors, including ethylene biosynthesis genes ACS2/4/8 and ACO2, DNA demethylase DML2, as well as the ripening-related transcription factors RIN and NOR by removal the mark of H3K4-trimethylation. Moreover, SlJMJ7 directly and indirectly modulates the transcription of genes related to diverse physiological traits of fruit ripening.
2021-06-22 | GSE153080 | GEO
Project description:Gene expression in three stages of ripening tomato fruit (variety Ailsa Craig) was determined with the EUTOM3 Affymetrix array in order to compare with degradrome sequencing data from study GSE42661, treated as RNAseq.
2013-04-05 | GSE42783 | GEO
Project description:The study of climacteric fruit ripening in tomato has been facilitated by the spontaneous ripening mutants Colorless non-ripening (Cnr), non-ripening (nor), and ripening inhibitor (rin). These mutants effect the genes encoding ripening transcription factors (TFs) SPL-CNR, NAC-NOR, and MADS-RIN causing pleiotropic defects to the ripening program. Here, we demonstrate that some ripening processes occur in the mutant fruit but at later stages of development compared to the wild type. The rin and nor mutant fruit exhibit similar quality traits to wildtype at later stages of ripening and senescence and delayed expression of ripening-associated genes. In addition, we propose that the Cnr mutant has a broader range of effects to fruit development than just fruit ripening. Cnr fruit show distinct differences from wild type in ripening phenotypic traits and gene expression profiles prior to the initiation of ripening. We provide new evidence that some mutants can produce more ethylene than basal levels and demonstrate ABA accumulation is also affected by the mutations. Studies have examined the relationship between the CNR, RIN, and NOR TFs based on protein-protein interactions and transcriptional regulation during fruit ripening. We describe the genetic interactions affecting specific fruit traits by using homozygous double mutants. Cnr predominantly influences the phenotype of the Cnr/nor and Cnr/rin double mutants but additional defects beyond either single mutation is evident in the transcriptome of the Cnr/nor double mutant. Our reevaluation of the Cnr, nor, and rin mutants provides new insights the utilization of the mutants in breeding and studying fruit development.
2020-12-24 | GSE163745 | GEO