Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative Analysis Highlights Uniconazole’s Efficacy in Enhancing the Cold Stress Tolerance of Mung Beans by Targeting Photosynthetic Pathways

ABSTRACT: Soybean (Glycine max) and mung bean (Vigna radiata) are key legumes with global importance, but their mechanisms for coping with cold stress—a major challenge in agriculture—have not been thoroughly investigated, especially in a comparative study. This research aimed to fill this gap by examining how these two major legumes respond differently to cold stress and exploring the role of uniconazole, a potential stress mitigator. Our comprehensive approach involved transcriptomic and metabolomic analyses, revealing distinct responses between soybean and mung bean under cold stress conditions. Notably, uniconazole was found to significantly enhance cold tolerance in mung bean by upregulating genes associated with photosynthesis, while its impact on soybean was either negligible or adverse. To further understand the molecular interactions, we utilized advanced machine learning algorithms for protein structure prediction, focusing on photosynthetic pathways. This enabled us to identify LOC106780309 as a direct binding target for uniconazole, confirmed through isothermal titration calorimetry. This research establishes a new comparative approach to explore how soybean and mung bean adapt to cold stress, offers key insights to improve the hardiness of legumes against environmental challenges, and contributes to sustainable agricultural practices and food security.

ORGANISM(S): Vigna radiata

PROVIDER: GSE193328 | GEO | 2024/07/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcript profiling of common bean using the Soybean Genome Array: optimizing analysis by masking biased probes

Project description:Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and specificity in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and specificity. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by about 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR analysis of a total of 20 randomly selected genes and purine-ureides pathway genes demonstrated an increased specificity after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The results from this study suggested that transcript profiling in common bean can be done using the soybean GeneChip. However, a significant decrease in sensitivity and specificity can be expected. Problems associated with CSH GeneChip data can be mitigated by masking probes targeting ISV regions. In addition to transcript profiling CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.

2010-03-01 | GSE18822 | GEO

Transcript profiling of common bean using the Soybean Genome Array: optimizing analysis by masking biased probes

2010-03-07 | E-GEOD-18822 | biostudies-arrayexpress

Changes in gene expression due to alpha-crystallin mutations cryaa-R49C and cryab-R120G in mutant knock-in mouse lenses

Project description:To investigate the relationship between histones, chaperone function, and cataracts, we performed RNA-seq, isothermal titration calorimetry (ITC), size-exclusion chromatography, and gel electrophoresis of histones. The RNA-seq of postnatal lenses from 2-day-old cryaa -R49C mice revealed increased histone gene expression, suggesting that a α-crystallin mutation regulates histones via a transcriptional mechanism .

2017-08-20 | GSE98027 | GEO

Endogenous small-noncoding RNAs and their roles in cold response and stress acclimation in Cassava

Project description:Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs. In order to understand sncRNAsM-bM-^@M-^Y roles in plant cold response and stress acclimation, we studied miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate cold stresses, that underwent further severe cold stress after cold acclimation at moderate stress, and that grew under the normal condition. We also included Castor bean (Ricinus communis) to understand conservation of sncRNAs. In addition to known miRNAs, we identified dozens of novel miRNAs as well as ta-siRNA-yielding and nat-siRNA-yielding loci in Cassava and Castor bean, respectively. Among the expressed sncRNAs, many sncRNAs were differentially expressed under cold stresses. Our study provided the results on gene regulation by sncRNAs in cold acclimation of Euphorbiaceous plants and the role of sncRNA-mediated pathways affected by cold stress and stress acclimation in Cassava. Examination of small RNA populations in Cassava cultivar SC124 under the normal condition (NC), gradual cold acclimation (CA), cold shock (CS) and stress acclimation Cold stress after cold acclimation (CCA).

2014-07-05 | E-GEOD-52177 | biostudies-arrayexpress

Endogenous small-noncoding RNAs and their roles in cold response and stress acclimation in Cassava

Project description:Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs. In order to understand sncRNAs’ roles in plant cold response and stress acclimation, we studied miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate cold stresses, that underwent further severe cold stress after cold acclimation at moderate stress, and that grew under the normal condition. We also included Castor bean (Ricinus communis) to understand conservation of sncRNAs. In addition to known miRNAs, we identified dozens of novel miRNAs as well as ta-siRNA-yielding and nat-siRNA-yielding loci in Cassava and Castor bean, respectively. Among the expressed sncRNAs, many sncRNAs were differentially expressed under cold stresses. Our study provided the results on gene regulation by sncRNAs in cold acclimation of Euphorbiaceous plants and the role of sncRNA-mediated pathways affected by cold stress and stress acclimation in Cassava.

2014-07-05 | GSE52177 | GEO

Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Phaseolus vulgaris L.

Project description:Cold tolerance of crop plants influences survival and productivity under low-temperature conditions. Elucidation of molecular mechanisms underlying low temperature tolerance could be helpful in breeding. In this study, based on transcriptome and metabolomic analysis, we successfully identified a number of candidate genes and metabolites involved in key biological pathways during cold stress response. During cold stress, a total of 22335 differentially expressed genes were detected in each group (093Cvs120C, 093Tvs120T, 093Cvs093T, 120Cvs120T), of which 12978 were up-regulated and 9357 were down-regulated. A total of 18,166 metabolites were detected and 7,670 metabolites were annotated, among which 654 were secondary metabolites with significant differences. Under cold stress, the petC gene in both common bean cultivars was down-regulated, which led to the decrease of photosynthetic efficiency. Transcriptome and metabolome results under cold stress showed that the synthesis pathways of various unsaturated fatty acids including alpha-linolenic acid were significantly up-regulated and their contents were enriched. In addition, leukotriene-A4 hydrolase in the catabolic pathway of 120 arachidonic acid was inhibited under cold stress. Furthermore, the content of arachidonic acid was increased. A variety of amino acids in both 093 and 120 were enriched under cold stress, which was beneficial to the resistance of bean to osmotic stress caused by cold stress. However, in addition to a few amino acids that were enriched together, 093 was mainly positively charged and 120 was negatively charged among the amino acids that were enriched differently. This is an interesting phenomenon that needs to be further studied. In addition, under cold stress, we found that genes in multiple metabolic pathways, including ABA, GA, JA and other hormone metabolism pathways, were differentially expressed in 093 and 120.

2022-01-05 | GSE192891 | GEO

Project description:Cold stress of soybean plants

| PRJNA1171642 | ENA

miRNAs target conserved motifs of diverse genes encoding NB-LRRs to trigger trans-acting siRNAs in legumes.

Project description:Trans-acting siRNAs (tasiRNAs) negatively regulate target transcripts and are characterized by siRNAs spaced in 21-nucleotide 'phased' intervals. TasiRNAs have not been extensively described in many plant species. We identified dozens of new miRNAs in Medicago and soybean and confirmed 119 Medicago targets. A search for phased tasiRNA-like small RNAs ('phasiRNAs') found at least 114 Medicago loci, the majority of which were NB-LRR encoding genes. Notably, conserved domains in NB-LRR-encoding RNAs are targeted by several 22-nt miRNA families to trigger phasiRNA production. DCL2 and SGS3 transcripts were also cleaved by these 22-nt miRNAs, generating phased small RNAs, suggesting synchronization between silencing and pathogen defense pathways. A second example of 'two-hit' phasiRNA processing was identified, utilizing miR156-miR172 sites. Our data illustrate a complex tasiRNA-mediated regulatory circuit that potentially modulates plant-microbe interactions. A few miRNA triggers regulate an extremely large gene family by targeting highly conserved protein motif-encoding sequences, representing a new paradigm for miRNA function. Examination of different tissue types in legumes (Medicago, soybean, common bean, peanut) by high throughput sequencing for small RNA profiling

2011-10-24 | E-GEOD-31061 | biostudies-arrayexpress

Contrasting defence mechanisms against spider mite infestation in Cyanogenic and Non-Cyanogenic legumes

Project description:Understanding the complex interactions between plants and herbivores is essential for improving crop resistance. To deep into the role of cyanogenesis in plant defence, we investigated the response of the cyanogenic Phaseolus lunatus (lima bean) and the non-cyanogenic Phaseolus vulgaris (common bean) to Tetranychus urticae infestation. Despite spider mite infesting both legumes, severity of leaf damage was reduced in lima bean. Comparative transcriptome analysis revealed that both species exhibited substantial metabolic and transcriptional changes upon infestation, yet the response in P. lunatus was significantly more pronounced. Specific differences in amino acid homeostasis and in the expression of key genes of the cyanogenic pathway were observed in P. lunatus. Moreover, the mandelonitrile lyase gene (PlMNL1) was upregulated following T. urticae feeding concomitantly to an enzyme activity increase. Lima bean plants also displayed an induction of β-cyanoalanine synthase (PlCYSC1), a key enzyme for cyanide detoxification, suggesting an internal regulatory mechanism to manage the toxicity of their defence responses. These findings contribute to have a major comprehension of the plant-insect interactions and underscore the potential role of cyanogenesis in the elaboration of unique specific defensive responses, even within the same genus, which may reflect distinctive evolutionary adaptations or varying metabolic capabilities between species.

2024-07-16 | GSE253336 | GEO

Project description:Cold hardiness mechanism in peach tree shoots

| PRJNA587386 | ENA