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Label Free MS quantitation of rice Oryza sativa (control vs drought)

ABSTRACT: Label Free MS quantitation of rice Oryza sativa (control vs drought)

INSTRUMENT(S): maXis

ORGANISM(S): Oryza Sativa (rice)

SUBMITTER: Ibon Iloro

LAB HEAD: Luis C. Romero

PROVIDER: PXD036637 | Pride | 2024-10-17

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	210812_210728B_Luis_1_Control1_1_S2-C10_1_4148.d.zip	Other
	210812_210728B_Luis_1_Control1_1_S2-C10_1_4148_5.3.236.mgf	Mgf
	210812_210728B_Luis_2_Control1_2_S2-C9_1_4147.d.zip	Other
	210812_210728B_Luis_2_Control1_2_S2-C9_1_4147_5.3.236.mgf	Mgf
	210812_210728B_Luis_3_Control1_3_S2-C8_1_4146.d.zip	Other

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Publications

Analysis of sulfide signaling in rice highlights specific drought responses.

Zhang Jing J Aroca Angeles A Hervás Manuel M Navarro José A JA Moreno Inmaculada I Xie Yanjie Y Romero Luis C LC Gotor Cecilia C

Journal of experimental botany 20240801 16

Hydrogen sulfide regulates essential plant processes, including adaptation responses to stress situations, and the best characterized mechanism of action of sulfide consists of the post-translational modification of persulfidation. In this study, we reveal the first persulfidation proteome described in rice including 3443 different persulfidated proteins that participate in a broad range of biological processes and metabolic pathways. In addition, comparative proteomics revealed specific protein ...[more]

PMID: 38808567

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Proteomic responses to drought vary widely among eight diverse genotypes of rice (Oryza sativa)

Project description:Rice is a critically important food source but yields worldwide are vulnerable to periods of drought. We exposed eight genotypes of upland and lowland rice (Oryza sativa L. ssp. japonica and indica) to drought stress at the late vegetative stage and harvested leaves for protein extraction and subsequent label-free shotgun proteomics. Gene ontology analysis revealed some differentially expressed proteins were induced by drought in all eight genotypes; we speculate that these play a universal role in drought tolerance. However, some highly genotype-specific patterns of response to drought suggest that some mechanisms of metabolic reprogramming are not universal. Such proteins had largely uncharacterized functions, making them biomarker candidates for drought tolerance screens.

2020-01-17 | PXD016150 | Pride

Screening Salinity Tolerance and Transcriptome Analysis in Rice (Oryza sativa L.)

Project description:Comparative transcriptome sequencing in leaf and root tissues of Control and Salt-treated Oryza sativa generated 52.2 and 17.29 million high-quality reads.

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Oryza sativa Lysine Acetylation LC-MS/MS

Project description:By the combination of affinity enrichment and high-resolution LC-MS/MS analysis, large-scale lysine acetylome analysis was performed in oryza sativa. Altogether, 1,003 lysine acetylation sites in 692 proteins were identified.

2018-10-24 | PXD002773 | Pride

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5M-bM-^@M-^Y rapid amplification of cDNA ends (RLM 5M-bM-^@M-^Y-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice. The degradome sequence of Young inflorescences from Oryza sativa L. ssp. indica (93-11) was sequenced

2010-01-01 | E-GEOD-19050 | biostudies-arrayexpress

R-loop landscapes in Rice (Oryza sativa) [DRIP-seq]

Project description:The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes and associated with many human diseases. Here, we take the advantage of our recently developed ssDRIP-seq method to profile genome-wide R-loop levels and provided a first-hand R-loop atlas of Rice (Oryza sativa) at different developmental stages.

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Project description:To evaluate the roles of gene regulation in Oryza sativa leaf, dynamic profiles of transcriptome were investigated in Oryza sativa L. spp. indica with different treatments, the aerial tissues of one-month-old plants from four different areas (groups 1–4) were treated with 0, 40 mL of 25% azoxystrobin, 0.01 g of VdAL, or 40 mL of 25% azoxystrobin plus 0.01 g VdAL, respectively.

2018-12-18 | GSE108204 | GEO

Rice (Oryza sativa) lysine-acetylation LC-MS/MS

Project description:Lysine acetylation is a dynamic and reversible post-translational modification that plays an imporant role in the gene transcription regulation. Here, we report high quality proteome-scale data for lysine-acetylation sites and proteins in rice (Oryza sativa). A total of 1337 Kac sites in 716 Kac proteins with diverse biological functions and subcellular localizations were identified in rice seedlings.

2016-02-24 | PXD002291 | Pride

A phosphoproteomic landscape of rice (Oryza sativa L.) tissues

Project description:Here, we first reported the construction of a phosphoproteomic landscape of 6 tissues, including callus, leaves, roots, shoot meristem (SM), young panicles (YP) and mature panicles (MP), from Nipponbare (Oryza sativa ssp. japonica). By employing a non-gel, quantitative phosphoproteomic approach, a total of 4792 phosphopeptides from 2657 phosphoproteins were identified, which were found to be differentially phosphorylated among tissues.

2018-04-11 | PXD005241 | Pride

Introgression of genes and mechanisms conferring tolerance to iron toxicity from wild rice species Oryza meridionalis into domesticated rice Oryza sativa

Project description:Iron toxicity is one of the most common mineral disorders affecting Oryza sativa production in flooded lowland fields. Efforts have been made to develop new rice varieties tolerant to Fe toxicity (+Fe). Oryza meridionalis is an endemic from Northern Australia and grows in regions with Fe rich soils, which may provide Fe tolerance genes and mechanisms that can be used for adaptive breeding. Aiming to understand tolerance mechanisms in rice, we screened a population of interspecific introgression lines (IL) from a cross between O. sativa and O. meridionalis for the identification of QTLs contributing to Fe excess tolerance. Six putative QTLs were identified. A line carrying one introgression from O. meridionalis on chromosome 9 associated with one QTL for leaf bronzing score was identified as tolerant in terms of lipid peroxidation and electrolyte leakage despite presenting very high shoot Fe concentrations. Further physiological, biochemical, ionomic and transcriptomic analyses showed that the IL tolerance could be partly explained by Fe partitioning between the leaf sheath and culm. After the in silico construction of an interspecific hybrid genome to map the sequences from transcriptomic analysis, we identified 47 and 27 genes from O. meridionalis up and down-regulated, respectively, by Fe treatment on the tolerant IL. Among possible genes associated with shoot-based tolerance, we identified metallothionein-like proteins, genes from glutathione S-transferase family and transporters from ABC and Major Facilitator Superfamily. This is the first work to demonstrate that introgressions of O. meridionalis in O. sativa genome confer increased tolerance to +Fe

2021-10-08 | GSE151559 | GEO

Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM 5’-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.

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