Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of a Potential Ripening Regulator, SlNAC3, from Solanum Lycopersicum.

ABSTRACT: NAC (for NAM, ATAF1-2, and CUC2) proteins are one of the largest transcription factor families in plants. They have various functions and are closely related to developmental processes of fruits. Tomato (Solanum lycopersicum) is a model plant for studies of fruit growth patterns. In this study, the functional characteristics and action mechanisms of a new NAC-type transcription factor, SlNAC3 (SGN-U568609), were examined to determine its role in tomato development and ripening. The SlNAC3 protein was produced by prokaryotic expression and used to immunize New Zealand white rabbits to obtain a specific polyclonal antibody against SlNAC3. By co-immunoprecipitation and MALDI-TOF-MS assays, we showed that there was an interaction between the SlNAC3 protein and Polygalacturonase-2 (PG-2), which is related to the ripening and softening of fruit. Chromatin immunoprecipitation assays revealed the genome of the highly stress-tolerant Solanum pennellii chromosome 10 (sequence ID, HG975449.1), further demonstrating that SlNAC3 is a negative regulator of drought and salinity stress resistance in tomato, consistent with previous reports. These results indicate that SlNAC3 is not only involved in abiotic stress, but also plays a necessary role in mediating tomato ripening.

SUBMITTER: Jing L

PROVIDER: S-EPMC7874718 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Light and ripening-regulated BBX protein-encoding genes in Solanum lycopersicum.

Project description:Light controls several aspects of plant development through a complex signalling cascade. Several B-box domain containing proteins (BBX) were identified as regulators of Arabidopsis thaliana seedling photomorphogenesis. However, the knowledge about the role of this protein family in other physiological processes and species remains scarce. To fill this gap, here BBX protein encoding genes in tomato genome were characterised. The robust phylogeny obtained revealed how the domain diversity in this protein family evolved in Viridiplantae and allowed the precise identification of 31 tomato SlBBX proteins. The mRNA profiling in different organs revealed that SlBBX genes are regulated by light and their transcripts accumulation is directly affected by the chloroplast maturation status in both vegetative and fruit tissues. As tomato fruits develops, three SlBBXs were found to be upregulated in the early stages, controlled by the proper chloroplast differentiation and by the PHYTOCHROME (PHY)-dependent light perception. Upon ripening, other three SlBBXs were transcriptionally induced by RIPENING INHIBITOR master transcriptional factor, as well as by PHY-mediated signalling and proper plastid biogenesis. Altogether, the results obtained revealed a conserved role of SlBBX gene family in the light signalling cascade and identified putative members affecting tomato fruit development and ripening.

| S-EPMC7648751 | biostudies-literature

Characterization of the Tomato (Solanum lycopersicum) Pectin Methylesterases: Evolution, Activity of Isoforms and Expression During Fruit Ripening.

Project description:Pectin methylesterase (PME, EC 3.1.1.11) is a hydrolytic enzyme of pectin that plays multiple roles in different plant development processes and responses to biotic stress. To characterize the molecular evolution and functional divergence of the PME gene family, a genome-wide analysis of the PME gene family in the tomato was performed. In total, 57 non-redundant PME genes were identified, and these PME genes were divided into five groups based on their phylogeneny; their classification was supported by similar gene structures and domain distributions. The PME genes were found to be unevenly distributed among 12 chromosomes of the tomato. In addition, 11 segmental duplication and 11 tandem duplication events occurred in these PME genes, implying that both contributed to the expansion of the tomato PME gene family. Non-synonymous/synonymous mutation ratio analysis revealed that positive selection played a key role in the functional divergence of PME genes. Interspecific collinear analysis indicated a large divergence in the PME gene family after the divergence of monocot and dicot plants in ancient times. Gene expression pattern analysis suggested that PMEs plays roles in the different parts of the tomato plant, including the fruit. Three newly identified candidate genes (Solyc03g083360, Solyc07g071600, and Solyc12g098340) may have functions during fruit ripening. Immunoassays suggested that the tomato isoform PE1 and PE2 may change pectin structure at cell junctions, which could be associated with fruit softening. In addition, our analysis indicate that two undescribed PE isoforms might be active in leaves and fruits. This study increases our understanding of the PME gene family in the tomato and may facilitate further functional analyses to elucidate PME function, especially during fruit ripening.

| S-EPMC7063471 | biostudies-literature

Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants.

Project description:Application of mass spectrometry enables the detection of metabolic differences between groups of related organisms. Differences in the metabolic fingerprints of wild-type Solanum lycopersicum and three monogenic mutants, ripening inhibitor (rin), non-ripening (nor) and Colourless non-ripening (Cnr), of tomato are captured with regard to ripening behaviour. A high-resolution tandem mass spectrometry system coupled to liquid chromatography produced a time series of the ripening behaviour at discrete intervals with a focus on changes post-anthesis. Internal standards and quality controls were used to ensure system stability. The raw data of the samples and reference compounds including study protocols have been deposited in the open metabolomics database MetaboLights via the metadata annotation tool Isatab to enable efficient re-use of the datasets, such as in metabolomics cross-study comparisons or data fusion exercises.

| S-EPMC4322568 | biostudies-literature

HEBE, a novel positive regulator of senescence in Solanum lycopersicum.

Project description:Leaf senescence and plant aging are traits of great interest for breeders. Senescing cells undergo important physiological and biochemical changes, while cellular structures such as chloroplasts are degraded with dramatic metabolic consequences for the whole plant. The possibility of prolonging the photosynthetic ability of leaves could positively impact the plant's life span with benefits for biomass production and metabolite accumulation; plants with these characteristics display a stay-green phenotype. A group of plant transcription factors known as NAC play a pivotal role in controlling senescence: here we describe the involvement of the tomato NAC transcription factor Solyc12g036480, which transcript is present in leaves and floral buds. Since its silencing delays leaf senescence and prevents plants from ageing, we renamed Solyc12g0364 H?B?, for the Greek goddess of youth. In this manuscript we describe how HEB downregulation negatively affects the progression of senescence, resulting in changes in transcription of senescence-promoting genes, as well as the activity of enzymes involved in chlorophyll degradation, thereby explaining the stay-green phenotype.

| S-EPMC7335192 | biostudies-literature

Seaweed Extract Improved Yields, Leaf Photosynthesis, Ripening Time, and Net Returns of Tomato (Solanum lycopersicum Mill.).

Project description:Overuse of chemical fertilizers in the intensive greenhouse tomato cultivation system has limited the increase of plant production. Nowadays, seaweed extract has been gradually applied in agriculture as an effective way to achieve a higher yield of crops, but its effects on tomato cultivation have not been fully explored. In this study, a greenhouse experiment was conducted in Shandong province of China with a novel seaweed extract (SES) originated from Sargassum horneri, to investigate the effects of different doses of SES (0, 30, 60, and 90 kg hm-2) on yields, quality, ripening time, and net returns of tomato. The results indicated that the application of SES significantly increased tomato yield by 4.6-6.9% compared to the control, which is attributed to the improved photosynthetic capacity of tomato leaves. The yields of tomato increased first and then decreased with increasing dosage of SES, and SES applied at the dose of 60 kg hm-2 achieved the highest tomato yield. Compared to the control, SES at 60 and 90 kg hm-2 significantly increased the hardness of tomato by 10.2 and 19.8%, respectively, and this can help to reduce losses during transportation and storage. Moreover, SES shortened the ripening time of tomato, and the coincidence between tomato harvest and sale price peak achieved a high net return.

| S-EPMC7057707 | biostudies-literature

Comprehensive Profiling of Tubby-Like Protein Expression Uncovers Ripening-Related TLP Genes in Tomato (Solanum lycopersicum).

Project description:Tubby-like proteins (TLPs), which were firstly identified in obese mice, play important roles in male gametophyte development, biotic stress response, and abiotic stress responses in plants. To date, the role of TLP genes in fruit ripening is largely unknown. Here, through a bioinformatics analysis, we identified 11 TLPs which can be divided into three subgroups in tomato (Solanum lycopersicum), a model plant for studying fruit development and ripening. It was shown that all SlTLPs except SlTLP11 contain both the Tub domain and F-box domain. An expression profiling analysis in different tomato tissues and developmental stages showed that 7 TLP genes are mainly expressed in vegetative tissues, flower, and early fruit developmental stages. Interestingly, other 4 TLP members (SlTLP1, SlTLP2, SlTLP4, and SlTLP5) were found to be highly expressed after breaker stage, suggesting a potential role of these genes in fruit ripening. Moreover, the induced expression of SlTLP1 and SlTLP2 by exogenous ethylene treatment and the down expression of the two genes in ripening mutants, further support their putative role in the ripening process. Overall, our study provides a basis for further investigation of the function of TLPs in plant development and fruit ripening.

| S-EPMC7037718 | biostudies-literature

Characterization of Oligopeptides in <i>Solanum lycopersicum</i> Xylem Exudates.

Project description:The xylem is the main pathway for the transport of water and molecules from roots to shoots. To date, it has been reported that secreted oligopeptides mediate root-to-shoot signaling, and some long-distance mobile oligopeptides have been detected in xylem exudates. However, the conservation of a number of oligopeptides and the overall features of peptide fragments contained in xylem exudates are poorly understood. Here, we conducted a comprehensive analysis of small proteins and peptides in tomato (Solanum lycopersicum) xylem exudates and characterized the identified peptide fragments. We found that putative secreted proteins were enriched in xylem exudates compared with all proteins in the tomato protein database. We identified seven oligopeptides that showed common features of bioactive oligopeptides, including homologs of CLV3/ESR-related (CLE), C-TERMINALLY ENCODED PEPTIDE (CEP), and CASPARIAN STRIP INTEGRITY FACTOR (CIF) peptides. Furthermore, five of the identified oligopeptides were homologs of the soybean xylem exudate-associated oligopeptides that we previously reported. Our results suggest that oligopeptides in xylem exudates are conserved across plant species and provide insights into not only root-to-shoot signaling but also the maintenance of the xylem conduit.

| S-EPMC9028419 | biostudies-literature

Identification and characterization of histone deacetylases in tomato (Solanum lycopersicum).

Project description:Histone acetylation and deacetylation at the N-terminus of histone tails play crucial roles in the regulation of eukaryotic gene activity. Histone acetylation and deacetylation are catalyzed by histone acetyltransferases and histone deacetylases (HDACs), respectively. A growing number of studies have demonstrated the importance of histone deacetylation/acetylation on genome stability, transcriptional regulation, development and response to stress in Arabidopsis. However, the biological functions of HDACs in tomato have not been investigated previously. Fifteen HDACs identified from tomato (Solanum lycopersicum) can be grouped into RPD3/HDA1, SIR2 and HD2 families based on phylogenetic analysis. Meanwhile, 10 members of the RPD3/HDA1 family can be further subdivided into four groups, namely Class I, Class II, Class III, and Class IV. High similarities of protein sequences and conserved domains were identified among SlHDACs and their homologs in Arabidopsis. Most SlHDACs were expressed in all tissues examined with different transcript abundance. Transient expression in Arabidopsis protoplasts showed that SlHDA8, SlHDA1, SlHDA5, SlSRT1 and members of the HD2 family were localized to the nucleus, whereas SlHDA3 and SlHDA4 were localized in both the cytoplasm and nucleus. The difference in the expression patterns and subcellular localization of SlHDACs suggest that they may play distinct functions in tomato. Furthermore, we found that three members of the RPD3/HDA1 family, SlHDA1, SIHDA3 and SlHDA4, interacted with TAG1 (TOMATO AGAMOUS1) and TM29 (TOMATO MADS BOX29), two MADS-box proteins associated with tomato reproductive development, indicating that these HDACs may be involved in gene regulation in reproductive development.

| S-EPMC4285013 | biostudies-literature

Tomato (Solanum lycopersicum) SlIPT4, encoding an isopentenyltransferase, is involved in leaf senescence and lycopene biosynthesis during fruit ripening.

Project description:BackgroundLycopene is an important carotenoid pigment in red fruits and vegetables, especially in tomato. Although lycopene biosynthesis and catabolism have been found to be regulated by multiple factors including phytohormones, little is known about their regulatory mechanism. Cytokinins are crucial to various aspects of plant growth. Isopentenyltransferases (IPTs) catalyze the initial rate-limiting step of cytokinins biosynthesis, however, their roles in fruit ripening remain unclear.ResultsHere, the functions of SlIPT4, encoding an isopentenyltransferase, were characterized via RNAi-mediated gene silencing in tomato. As we expected, silencing of SlIPT4 expression resulted in accelerated leaf senescence. However, down-expression of SlIPT4 generated never-red orange fruits, corresponding with a dramatic reduction of lycopene. Among lycopene biosynthesis-related genes, the fact of remarkable decrease of ZISO transcript and upregulation of other genes, revealed that SlIPT4 regulates positively lycopene biosynthesis via directly affecting ZISO expression, and also supported the existence of regulatory loops in lycopene biosynthesis pathway. Meanwhile, the accumulation of abscisic acid (ABA) was reduced and the transcripts PSY1 were increased in SlIPT4-RNAi fruits, supporting the feedback regulation between ABA and lycopene biosynthesis.ConclusionThe study revealed the crucial roles of SlIPT4 in leaf senescence and the regulatory network of lycopene biosynthesis in tomato, providing a new light on the lycopene biosynthesis and fruit ripening.

| S-EPMC5987576 | biostudies-literature

Ethylene and Auxin: Hormonal Regulation of Volatile Compound Production During Tomato (<i>Solanum lycopersicum</i> L.) Fruit Ripening.

Project description:As the auxin-ethylene interaction in climacteric fruit ripening has been highlighted, the hormonal regulation of aroma changes in climacteric fruits requires clarification. The influence of both phytohormones on the volatile organic compound (VOC) metabolism was evaluated during tomato (Solanum lycopersicum L.) fruit ripening. Tomato fruits cv. Micro-Tom and Sweet Grape at the mature green stage were randomly grouped according to treatment with ethylene (ETHY), auxin (IAA), or both (ETHY + IAA). At middle ripening, Micro-Tom ETHY + IAA fruits present VOC profiles similar to those of ETHY fruits, while Sweet Grape presents VOC profiles closer to those of IAA fruits. At full ripeness, Micro-Tom and Sweet Grape ETHY + IAA fruits show profiles closer to those of IAA fruits, suggesting that the auxin overlaps the ethylene effects. Aroma compounds positively correlated with consumer preferences (2-isobutylthiazole, 6-methyl-5-hepten-2-one, and others) are identified in both cultivars and have their contents affected by both hormone treatments. The transcription of genes related to the biosynthesis of important tomato VOCs that have fatty-acid and carotenoid precursors evidences their regulation by both plant hormones. Additionally, the results indicate that the observed effects on the VOC metabolism are not restricted to the Micro-Tom cultivar, as these are also observed in the Sweet Grape cultivar. In conclusion, ethylene and auxin directly regulate the metabolic pathways related to VOC formation, impacting tomato aroma formation during ripening since Micro-Tom fruits apparently at the same maturation stage have different aromas.

| S-EPMC8702562 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data