PXD067255

PXD067255 is an original dataset announced via ProteomeXchange.

Title	The impact of 24h of anoxia and re-aeration on rice proteome using 2-DIGE
Description	In this study, we analyzed the impact of anoxia and re-aeration on tolerant rice at a proteomic level using two-dimensional gel electrophoresis followed by mass spectrometry. Mass spectrometry revealed 82 spots corresponding to 13 and 8 unique proteins in shoots and roots, respectively. Spot-wise clusterization showed the re-aeration proteome to resemble anoxic but not control conditions. We found 4 groups of proteins displaying distinct patterns of intensities of the spots. The most notable group contained proteins whose content continually decreased during stress, such as RuBisCO and fructose-bisphosphate aldolase. The second group included proteins whose synthesis started in anoxia and reached a peak during re-aeration. It involved OEE1 (oxygen-evolving enhancer protein 1), heat shock proteins, and pathogenesis-related (PR) proteins, implying defense from oxidative damage and pathogens to which plants become vulnerable during re-aeration. Promotor regions of genes encoding these proteins were enriched with transcription factors binding sites of stress-related TFs, both well-studied (ERF, WRKY, MYB) and not as frequently discussed in such contexts (TCP, TBP, SBP). By comparing our observations with proteomic and transcriptomic research, we revealed that plant reactions to anoxia and reoxygenation are starkly similar. The results suggest that rice shoots and roots become pre-adapted to post-stress during anoxia. The experimental setup was as follows. Plants were exposed to 24 h of pure anoxia followed by 24 h of re-aeration. 2-DIGE gel figures were scanned with Typhoon, and the intensities of spots were calculated using the PDQuest software. After excision, spots were analyzed with MALDI-TOF MS/MS. Proteins were identified using MASCOT and MGSFplus utilities. Significantly different spots were identified with the limma package. Individual spots and the whole proteomes were then clustered with k-means and hierarchical clustering methods. Functional annotation of protein sequences was performed using the eggNOG standalone tool v2.0.1b-2-g816e190 (Huerta-Cepas et al., 2017a) and the topGO v.2.34.0 (Alexa and Rahnenfuhrer, 2007) package. The upstream regions of genes encoding identified proteins and the respective orthologs from A. thaliana were obtained from the EnsemblPlants (Bolser et al., 2016) database. Finally, transcription factor binding sites within the promoter regions were predicted using the PlantPAN v.3.0 (Chow et al., 2019) and AthaMap (Hehl et al., 2016) tools. Ten-day-old rice seedlings (Oryza sativa L., cv. Flagman, Federal Scientific Center of Rice, Krasnodar, Russia) were studied. Seeds were sterilized using 5% NaClO for 15 min and washed with warm distilled water. Seeds were then soaked for 1 h in hot water (50-55 °С) to induce germination in dark conditions for 3 days at 28°С. Germinated seedlings were planted on perforated plastic plates on containers filled with continuously aerated Knop nutrient solution (0.2 strength) and grown at an irradiance of 100 W/m2 with a photoperiod of 12 h at 23-25°C as described earlier (Emel’yanov et al., 2003; Yemelyanov et al., 2020). Plants were divided into control and experimental groups. For each condition (control, anoxia, and re-aeration), 3 glass beakers containing 20 mL of Knop nutrient solution (0.2 N strength) with 20 seedlings in each were used. To replicate anaerobic conditions, beakers with seedlings were placed into 1.5-liter jars (exicators). The gaseous nitrogen with less than 0.01% of oxygen oxygen was pumped to the exicators for 45 min until reaching complete anoxia. The purity of anaerobic conditions was confirmed via the Anaerotest® anaerobic indicator (Merck, Germany). Once anaerobic conditions were reached, exicators were tightly closed and put in the dark for 24 h to prevent oxygen production during photosynthesis. Control plants were exposed to the dark in aerobic conditions for 24 h. No less than three biological replicates were done for each condition. After 24 h of anoxia, the jars were opened, followed by collecting plant shoots and roots for further protein extraction in the case of anoxic proteomes and control settings. The post-anoxic beakers were exposed to 24 h of dark conditions and were then separately treated for protein extraction as well.
HostingRepository	PRIDE
AnnounceDate	2025-09-29
AnnouncementXML	Submission_2025-09-29_09:45:51.656.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD067255
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Anton Shikov
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	No PTMs are included in the dataset
Instrument	ultraflex

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-12 03:58:37	ID requested
⏵ 1	2025-09-29 09:45:52	announced

10.6019/PXD067255;

10.3389/FPLS.2025.1647411;

submitter keyword: anoxia, roots, shoots, post-anoxia, re-aeration, plants,Rice

Yemelyanov V.V.
contact affiliation	Faculty of Biology, St. Petersburg State University (SPbSU), 199034, Universitetskaya em., 7/9, St. Petersburg, Russia
contact email	bootika@mail.ru
lab head
Anton Shikov
contact affiliation	All‐Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, Podbelsky chausse 3, Pushkin 8, St. Petersburg
contact email	antonshikov96@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD067255
     1. Label: PRIDE project
     2. Name: The impact of 24h of anoxia and re-aeration on rice proteome using 2-DIGE