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ABSTRACT:
PROVIDER: PRJNA1315184 | ENA |
REPOSITORIES: ENA
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Project description:Paper mulberry as a valuable woody species has a well chilling tolerance. In this study, phosphoproteomic analysis in combination with physiological measurement and mRNA quantification were employed to explore the molecular mechanism of chilling (4 °C) tolerance in paper mulberry. After chilling for 6 hours, there were 427 significant changed phosphoproteins detected in paper mulberry seedlings without obvious physiological injury. When obvious physiological injury occurred after chilling for 48 hours, a total of 611 phosphoproteins were found significantly change at phosphorylation level. According to 9 phosphorylation motifs extracted by Motif-X analysis, MAPKs, CDPKs, CDKs and CKs were considered as the primary upstream protein kinases. Results of GO analysis showed that phosphoproteins were mainly responsible for signal transduction, protein modification and translation during chilling. Additionally, transport and cellular component organization were respectively enriched after chilling for 6 and 48 hours. Based on the analysis of protein-protein interaction network, a protein kinases and phosphatases hub protein was thought as the key of phosphorylation regulation, which probably modulates cross-talk between Ca2+, BR, ABA and ethylene mediated signaling pathways. Together with results, we concluded a schematic chilling tolerance mechanism at phosphorylation level.
2018-04-20 | PXD005516 | Pride
Project description:Chilling stress is a major abiotic stress that affects rice growth and development. Rice seedlings are quite sensitive to chilling stress and this harms global rice production. Comprehensive studies of the molecular mechanisms for response to low temperature are of fundamental importance to chilling tolerance improvement. The number of identified cold regulated genes (CORs) in rice is still very small. Circadian clock is an endogenous timer that enables plants to cope with forever changing surroundings including light–dark cycles imposed by the rotation of the planet. Previous studies have demonstrated that the circadian clock regulates stress tolerances in plants show circadian clock regulation of plant stress tolerances. However, little is known about coordination of the circadian clock in rice chilling tolerance. In this study, we investigated rice responses to chilling stress under conditions with natural light-dark cycles. We demonstrated that chilling stress occurring at nighttime significantly decreased chlorophyll content and photosynthesis efficiency in comparison with that occurring at daytime. Transcriptome analysis characterized novel CORs in indica rice, and suggested that circadian clock obviously interferes with cold effects on key genes in chlorophyll (Chl) biosynthesis pathway and photosynthesis-antenna proteins. Expression profiling revealed that chilling stress during different Zeitberger times (ZTs) at nighttime repressed the expression of those genes involved Chl biosynthesis and photosynthesis, whereas stress during ZTs at daytime increases their expression dramatically. Moreover, marker genes OsDREBs for chilling tolerance were regulated differentially by the chilling stress occurring at different ZTs. The phase and amplitude of oscillation curves of core clock component genes such as OsLHY and OsPRR1 are regulated by chilling stress, suggesting the role of chilling stress as an input signal to the rice circadian clock. Our work revealed impacts of circadian clock on chilling responses in rice, and proved that the effects on the fitness costs are varying with the time in a day when the chilling stress occurs.
2022-03-01 | GSE146174 | GEO
Project description:Nedd4-2 E3 ligase regulates Na+ homeostasis by ubiquitinating various channels and membrane transporters, including the epithelial sodium channel ENaC. In turn, Nedd4-2 dysregulation leads to various conditions, including electrolytic imbalance, respiratory distress, hypertension, and kidney diseases. However, Nedd4-2 regulation remains mostly unclear. The present study aims at elucidating Nedd4-2 regulation by structurally characterizing Nedd4-2 and its complexes using several biophysical techniques. Our cryo-EM reconstruction showed that the C2 domain blocks the E2-binding surface of the HECT domain. This blockage, ubiquitin-binding exosite masking by the WW1 domain, catalytic C922 blockage and HECT domain stabilization provide the structural basis for Nedd4-2 autoinhibition. Furthermore, Ca2+-dependent C2 membrane binding disrupts C2/HECT interactions, but not Ca2+ alone, whereas 14-3-3 protein binds to a flexible region of Nedd4-2 containing the WW2 and WW3 domains, thereby inhibiting its catalytic activity and membrane binding. Overall, our data provide key mechanistic insights into Nedd4-2 regulation toward fostering the development of strategies targeting Nedd4-2 function.
2025-05-12 | PXD058899 | Pride
Project description:Plants respond to low temperature through an intricately coordinated transcriptional network controlled by specific groups of transcription factors. Major regulatory pathways in plants that evolved to withstand freezing by cold acclimation have been elucidated in Arabidopsis. A prominent pathway is the CBF/DREB regulon, which was also shown to be evolutionarily conserved between temperate and warm-season plants. This study exploited the wide contrast in chilling tolerance between indica and japonica rice as model to dissect the hierarchical organization of early response regulatory networks by integrative analysis of promoter architecture and gene expression profiles. Analysis of the transcriptome of japonica rice identified a group of genes that were upregulated during the initial 24 hours at 10oC. Included among the 120 ‘early response’ genes were two transcription factors (ROS-bZIP1, OsMyb4) and another larger sub-group with a common denominator of having the as1/ocs element in their promoters. ROS-bZIP1, OsMyb4 and the as1/ocs element-containing genes were also induced by exogenous H2O2 at ambient temperature, thus are likely components of a regulatory module (ROS-bZIP1-as1/ocs regulatory module) that is activated by elevated intracellular ROS induced by cold stress. Comparative analysis of the expression of ROS-bZIP1-as1/ocs regulatory module between tolerant (CT6748-8-CA-17) and intolerant (INIAP12) rice cultivars showed positive correlation of the activity of the regulon with genotypic differences in chilling tolerance. A hypothetical model of an ROS-mediate gene regulon was developed. Based on this model, it was hypothesized that the putative ROSbZIP1-as1/ocs regulatory module has a prominent role in configuring early or rapid responses to chilling in rice seedlings and that such pathway is independent of the CBF/DREB-mediated and ABA-mediated regulons. Background Keywords: Response to temperature at different time points
2007-05-31 | GSE7071 | GEO
Project description:Improvement of chilling tolerance is a key strategy to face potential menace from abnormal temperature in rice production, which depends on the signaling network triggered by receptors. However, little is known about the QTL genes encoding membrane complexes for sensing cold. Here, Chilling-tolerance in Gengdao/japonica rice 1 (COG1) was isolated from a chromosome segment substitution line containing a QTL (qCS11-jap) for chilling sensitivity. The major gene COG1 was found to confer chilling tolerance in japonica rice. In natural rice populations, only the haplogroup1 encoded a functional COG1. Evolutionary analysis showed that COG1 originated from Chinese O. Rufipogon and was fixed in japonica rice during domestication. COG1, a membrane-localized LRR-RLP, targeted and activated the kinase OsSERL2 in a cold-induced manner, promoting chilling tolerance. Furthermore, the cold signal transmitted by COG1-OsSERL2 activates OsMAPK3 in the cytoplasm. Our findings reveal a cold-sensing complex, which mediates signaling network for the chilling defense in rice.
2023-06-18 | PXD042294 | Pride
Project description:The physiological indicators, transcriptome, and metabolome of two melon varieties with contrasting chilling tolerance (‘162’, chilling-tolerant; ‘13-5A’ ,chilling-sensitive) were analyzed under chilling stress.
2023-02-25 | GSE225921 | GEO
Project description:To understand how CTS-12 the ABA-dependent multi-levels of regulation, the integration of transcriptomic and metabolomic profiling using the two-way orthogonal projections to latent structures (O2PLS) and OPLS discriminant analysis (OPLS-DA) modeling was performed to investigate the mechanisms underlying chilling tolerance. Our results revealed that metabolic flux shifts, including the activation of stachyose biosynthesis, amino acid metabolism pathways, phenylpropanoid/flavonoid biosynthesis, and ABA biosynthesis, and inhibition of glycolysis, occurred under chilling treatment, and in the recovery period, the differentially expressed genes/metabolites (DEGs/DEMs) that mapped to glutamate-related pathways, β-alanine biosynthesis and degradation, and serotonin biosynthesis pathways were differentiated between 9311 and DC90. Particularly, the differential alterations of the DEMs/DEGs, including galactinol, β-alanine, glutamate, naringenin, serotonin, abscisic acid (ABA), and LOC_Os03g44380 (OsNCED3), might be involved in the chilling stress phenotype variation of 9311 and DC90. The involvement of ABA pathway was validated by CRISPR/Cas9-edited of discriminatory DEGs OsNCED3 which impaired chilling tolerance of japonica rice. In addition, chilling tolerance of rice was associated with the balance of water uptake and loss that was modulated by stomatal movement under chilling stress. Therefore, we speculated that the CTS-12-mediated ABA signaling pathway leads to transcriptional regulation of chilling-responsive genes and, in turn, triggers metabolic shifts to coordinately regulate the stomatal movement of guard cells. The results of this study improve our understanding of the multilevel regulation of wild rice in response to chilling stress.
2020-10-21 | GSE143878 | GEO
Project description:To understand the molecular mechanisms underlying chilling tolerance in rice, transcriptomic deep sequencing was performed to reveal the differentially expressed genes between chilling tolerance chromosome substitution line (CSL), DC90 and its chilling-sensitive recurrent parent 9311 under early chilling stress events. Our results revealed a set of DEGs with higher basal expression in DC90 by comparison with 9311. They were functionally enriched in GO terms, such as, response to stress, response to stimulus, and response to abiotic stimulus, suggesting their positive role in intrinsic chilling tolerance. Common up-regulated and down-regulated DEGs were enriched in 26 and 34 GO terms, including response to stimulus, response to stress, and response to abiotic stimulus, respectively. Furthermore, comparative transcriptomic analysis between DC90 and 9311 in response to early chilling stress revealed 502 DEGs specifically identified in DC90. Most of gene loci were located beyond introgressed regions, implying that the introgression led to reprogramming of transcriptome in response to early chilling stress. CARMO platform analysis of these DEGs presented a complex regulatory network, including phytohormone signaling, photosynthesis pathway, that coordinately involved in chilling tolerance response of DC90. Here, the unveiled molecular regulatory network shed light on deep understanding the mechanisms of rice chilling tolerance. As well, chilling tolerant-QTLs and co-localized DEGs in introgressed fragments, will be focused for further functional investigation of the molecular mechanisms of early chilling stress response in rice.
2017-06-25 | GSE76415 | GEO