Proteomic profiling of a fast neutron induced soybean mutant unveiled regulators of increased seed protein content
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ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion mass spectrometer Lumos
ORGANISM(S): Glycine Max (ncbitaxon:3847)
SUBMITTER: 
Savithiry Natarajan (Savi)
PROVIDER: MSV000084228 | MassIVE | Fri Aug 23 08:20:00 BST 2019
REPOSITORIES: MassIVE
Similar Datasets
Project description:Global analyses of protein profiling during seed development in soybean is paramount to understand the metabolic processes that correspond to the differential protein accumulation and hence seed quality in soybean. Using high throughput tandem mass tag (TMT) based tagging techniques, we identified 4,172 proteins in three stages namely early, mid, and late seed filling. We mapped the identified metabolic pathways associated with seed filling. An elevated level of several kinases was observed from the early to mid-stages of seed filling, indicating that protein phosphorylation was a major event that occurred during this period. The early to late stages of seed filling was characterized by an increased level of proteins associated with the cell wall, oil, and vacuolar-related processes. Twenty-five seed storage protein genes located on 12 different chromosomes were identified. Among the seed storage proteins, 7S (B-subunit) and 11S (Gy3, Gy4, Gy5) exhibited steadily increased abundance from early to late-stage seed development, whereas, 2S albumin exhibited decreased abundance during the same period. An increased abundance of proteases, senescence-associated proteins and, oil synthesis proteins was observed from the mid to late stages of seed filling. The mid to late stages of seed filling were also characterized by a lower abundance of transferases, transporters, Kunitz family trypsin, and protease inhibitors. Two enzymes associated with methionine synthesis exhibited lower abundance from early to late stages. This study unveiled the expression of several key enzymes/proteins associated with amino acid and protein syntheses and their accumulation during seed development which will assist scientists and breeders to develop new value-added soybeans with improved protein quality.
2021-06-06 | MSV000087577 | MassIVE
Project description:Plant vacuoles serve as the primary intracellular compartments for inorganic phosphate (Pi) storage. Passage of Pi across vacuolar membranes plays a critical role in buffering the cytoplasmic Pi level against fluctuations of external Pi and metabolic activities. To gain new insights into the proteins and processes vacuolar Pi level regulated by Vacuolar phosphate transporter1 (VPT1) in Arabidopsis, we carried out TMT labeling proteome and phosphoproteome profiling of Arabidopsis wild-type (WT) and vpt1 loss-of-function mutant plants. The vpt1 mutant had a reduced vacuolar Pi level, but an increased cytosol Pi level. The mutant was stunted as reflected in the reduction of the fresh weight compared with WT plants, and bolting earlier under normal growth conditions in soil. Over 5566 proteins and 7965 phosphopeptides were quantified. About 146 and 83 proteins were significantly changed at protein abundance or site-specific phosphorylation levels, but only 6 proteins were shared between them. Functional enrichment analysis revealed that Pi starvation signal in Arabidopsis vacuole is associated with photosynthesis, translation, RNA splicing, and defense response, consistent with similar studies in Arabidopsis. Except for PAP26, EIN2, and KIN10, which are reported to be associated with phosphate starvation signal, we also found many differential proteins involved in abscisic acid (ABA) signaling, such as CARK1, SnRK1, and AREB3, were changed in response to vacuolar Pi starvation. Our study illuminates several new aspects of the phosphate starvation response and identifies important targets for further investigation and potential crop improvement.
2023-03-08 | PXD040698 |
Project description:An altered response to methylamine (MA) has been used to identify genes involved in nitrogen metabolism in many microbes and as an uncoupler of proton motive force in both prokaryotes and eukaryotes. The aim of this study was to attempt the use of MA to identify critical genes for response to exogenous nitrogen sources in Arabidopsis thaliana (thale cress). EMS mutagenesis and selection on MA were used to identify a series of mutants that showed increased sensitivity to MA but failed to identify any MA resistant mutants. The eight sensitive mutants were allelic as judged by segregation and map location so one mutant, gsr1-1, was selected for intensive analysis. Co-segregation of gsr1 with DNA markers showed the gene was on chromosome 5 between markers CA72 and nga151, an interval of about 0.42 Mbp. The co-segregating mutant phenotypes associated with gsr1 included; yellow color caused by a reduction in chloroplast number; reduced chlorophyll content; decreased nitrate reductase (EC 1.7.1.3) activity in the root; and increased glutamate dehydrogenase (EC 1.4.1.2) activity in root and shoot. Decreased transcripts included those encoding several nitrogen metabolism enzymes. In contrast, the mutation increased only 4 and 7 transcript abundances by more than two fold. RT-PCR showed that in the dark, regulation of transcript abundance by exogenously applied glutamine and to a lesser extent sucrose were altered. Gene action of the gsr1 mutant was recessive for chloroplast number but co-dominant for transcript abundances and co-dominant for enzyme activities. Supplementary data from the analysis of preliminary microarray data from AFGC used 10,560 targets and two reverse labeled slides to show that more than 351 ESTs were increased in transcript abundance by more than 2 fold in the green plants. In yellow plants only seventy-three ESTs were up-regulated in transcript abundance by more than 2 fold. Therefore, the gsr1 locus may regulate responses to endogenous and exogenous glutamine in an organ-specific fashion that could coordinately regulate the activity of genes enzymes and metabolic pathways that determine cellular nitrogen, carbon and bioenergetic (redox) status. A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. replicate_design
2012-04-12 | E-GEOD-37220 | biostudies-arrayexpress
Project description:An altered response to methylamine (MA) has been used to identify genes involved in nitrogen metabolism in many microbes and as an uncoupler of proton motive force in both prokaryotes and eukaryotes. The aim of this study was to attempt the use of MA to identify critical genes for response to exogenous nitrogen sources in Arabidopsis thaliana (thale cress). EMS mutagenesis and selection on MA were used to identify a series of mutants that showed increased sensitivity to MA but failed to identify any MA resistant mutants. The eight sensitive mutants were allelic as judged by segregation and map location so one mutant, gsr1-1, was selected for intensive analysis. Co-segregation of gsr1 with DNA markers showed the gene was on chromosome 5 between markers CA72 and nga151, an interval of about 0.42 Mbp. The co-segregating mutant phenotypes associated with gsr1 included; yellow color caused by a reduction in chloroplast number; reduced chlorophyll content; decreased nitrate reductase (EC 1.7.1.3) activity in the root; and increased glutamate dehydrogenase (EC 1.4.1.2) activity in root and shoot. Decreased transcripts included those encoding several nitrogen metabolism enzymes. In contrast, the mutation increased only 4 and 7 transcript abundances by more than two fold. RT-PCR showed that in the dark, regulation of transcript abundance by exogenously applied glutamine and to a lesser extent sucrose were altered. Gene action of the gsr1 mutant was recessive for chloroplast number but co-dominant for transcript abundances and co-dominant for enzyme activities. Supplementary data from the analysis of preliminary microarray data from AFGC used 10,560 targets and two reverse labeled slides to show that more than 351 ESTs were increased in transcript abundance by more than 2 fold in the green plants. In yellow plants only seventy-three ESTs were up-regulated in transcript abundance by more than 2 fold. Therefore, the gsr1 locus may regulate responses to endogenous and exogenous glutamine in an organ-specific fashion that could coordinately regulate the activity of genes enzymes and metabolic pathways that determine cellular nitrogen, carbon and bioenergetic (redox) status. A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
2012-04-13 | GSE37220 | GEO
Project description:The disruption of vacuolar protein sorting related genes vps13 and vps21 in filamentou fungi Trichoderma reesei resulted in a dramtic increase in cellulase transcription especially in the late Avicel induction phase, relieving the RESS (REpression under Secretion Stress) effect. Great interest arisen concered about the reason and underlying mechanism of vps13 and vps21 disruption for increased cellulase transcription. Thus, transcriptome analysis through RNA-Seq could give a deep insight of the potential pathways involved in enhanced cellulase transcription in late Avicel induction.
2021-11-10 | GSE187573 | GEO
Project description:The present work provides a multi-omics systems-wide view on S. rimosus. Using genomics, transcriptomics, proteomics, and metabolomics, we compared the wild type with an OTC-overproducing derivative, previously obtained by classical mutagenesis. The integration of the data provided a deep insight into the underlying metabolic and regulatory networks that mediate high-level OTC formation. Strikingly, the overproducer revealed a synergistically activated supply of acetyl-CoA and malonyl CoA and increased abundance of various CoA thioesters.
2023-05-16 | GSE232318 | GEO
Project description:Plant vacuoles serve as the primary intracellular compartments for inorganic phosphate (Pi) storage. Passage of Pi across vacuolar membranes plays a critical role in buffering the cytoplasmic Pi level against fluctuations of external Pi and metabolic activities. Here we demonstrate that the SPX-MFS proteins, designated as Phosphate Transporter 5 family (PHT5), also named Vacuolar Phosphate Transporter (VPT), function as vacuolar Pi transporters. Based on 31P-magnetic resonance spectroscopy analysis, Arabidopsis pht5;1 loss-of-function mutants accumulate less Pi and exhibit a lower vacuolar-to-cytoplasmic Pi ratio than controls. Conversely, overexpression of PHT5 leads to massive Pi sequestration into vacuoles and altered regulation of Pi starvation-responsive genes. Furthermore, we show that heterologous expression of OsSPX-MFS1, the rice PHT5 homolog, mediates Pi influx to yeast vacuoles. Our findings uncover a group of Pi transporters in vacuolar membranes that regulate the cytoplasmic Pi homeostasis required for the fitness of plant growth. 10-day seedlings grown on Pi-sufficient medium or followed by 1-day or 3-day Pi starvation, shoot RNA and root RNA were extracted separately
2016-03-28 | E-GEOD-74856 | biostudies-arrayexpress
Project description:The screen for genes involved in the spontaneous loss of heterozygosity mutagenesis (SLM) in diploid cells was done on the collections of deletion strains of Saccharomyces cerevisiae created by the Saccharomyces Genome Deletion Project (http://www-sequence.stanford.edu/group/yeast_deletion_project/). Screens were performed on the pools of clones. Barcode microarrays were used to detect the increased SLM frequency leading to relative increase in abundance of deletion clone in a pool. Collections used were: Homozygous Diploid (HD) and Essential (E) mixed to create single HDE pool. Three mutagenesis markers were used: (1) naturally existing mating type locus, and two newly introduced markers, (2) CAN1/can1delta, (3) URA3/ura3delta. <br>1. To detect the increased SLM frequency at the mating type locus HDE pool was crossed to MATa or MATalpha strain. Deletion clones that gained mating competence due to loss of heterozygosity (LOH) at the mating type locus gave rise to clones with the ability to grow on minimal medium. The relative abundance of these clones was compared to the abundance in the original HDE pool.<br>2. To detect the increased SLM frequency at the CAN1/can1delta locus the derivative HDE pool was created. Every cell of this pool had one of two copies of CAN1 gene deleted. The increased SLM frequency led to increased relative abundance of respective deletion clone under canavanine selection and could be estimated by comparing it to the abundance when pool was grown without selection.<br>3. To detect the increased SLM frequency at the URA3/ura3delta locus the derivative HDE pool was created. Every cell of this pool had one of two copies of URA3 gene deleted. The increased SLM frequency led to increased relative abundance of respective deletion clone under 5M-^R-fluoroorotic acid selection and could be estimated by comparing it to the abundance when pool was grown without selection.<br>4. For screens of SLM at CAN1 and URA3 markers the resistance control experiments were performed to detect genes whose deletion is sufficient to enable yeast cells with functional CAN1 or URA3 to grow in the presence of canavanine or 5M-^R- fluoroorotic acid respectively.<br>5. To include in the analysis slow-growing deletion clones control hybridizations were performed to detect genes whose deletion extends the doubling time of yeast cells.<br>
2011-06-28 | E-MEXP-2685 | biostudies-arrayexpress
Project description:Type 2C protein phosphatases are encoded in Saccharomyces cerevisiae by several related genes (PTC1-5 and PTC7). To gain insight into the functions attributable to specific members of this gene family, we have investigated the transcriptional profiles of ptc1-5 mutants. Two main patterns were obtained as follows: the one generated by the ptc1 mutation and the one resulting from the lack of Ptc2-5. ptc4 and ptc5 profiles were quite similar, whereas that of ptc2 was less related to this group. Mutation of PTC1 resulted in increased expression of numerous genes that are also induced by cell wall damage, such as YKL161c, SED1, or CRH1, as well as in higher amounts of active Slt2 mitogen-activated protein kinase, indicating that lack of the phosphatase activates the cell wall integrity pathway. ptc1 cells were even more sensitive than slt2 mutants to a number of cell wall-damaging agents, and both mutations had additive effects. The sensitivity of ptc1 cells was not dependent on Hog1. Besides these phenotypes, we observed that calcineurin was hyperactivated in ptc1 cells, which were also highly sensitive to calcium ions, heavy metals, and alkaline pH, and exhibited a random haploid budding pattern. Remarkably, many of these traits are found in certain mutants with impaired vacuolar function. As ptc1 cells also display fragmented vacuoles, we hypothesized that lack of Ptc1 would primarily cause vacuolar malfunction, from which other phenotypes would derive. In agreement with this scenario, overexpression of VPS73, a gene of unknown function involved in vacuolar protein sorting, largely rescues not only vacuolar fragmentation but also sensitivity to cell wall damage, high calcium, alkaline pH, as well as other ptc1-specific phenotypes. Keywords: yeast, type 2C protein phosphatases, mutant strains, transcriptional profiles
2007-01-24 | GSE6801 | GEO
Project description:In this project, we studied a mouse model of human Down Syndrome (DS) megakaryocytic leukemia involving mutations in the GATA1 transcription factor (called GATA1s mutation). The model was generated through retroviral insertional mutagenesis in Gata1s mutant fetal liver progenitors. In this study, we analyzed the dependency of these leukemic cells on the Gata1s mutant protein. Here we report Gata1s mutant leukemic cells were dependent on this mutant protein. Introduction of the full-length Gata1 protein to these cells led to their reduced proliferation and increased differentiation along the megakaryocytic lineage.
2010-08-01 | GSE16676 | GEO