PXD035623

PXD035623 is an original dataset announced via ProteomeXchange.

Title	Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis
Description	Arabidopsis contains hundreds of ribosomal DNA copies organised within the nucleolar organising regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1-4, based on the polymorphisms of 3' external transcribed sequences and these are variably expressed during plant development. We created a mutant by the CRISPR-Cas9-mediated excision of ~25 nt from only the copies of NOR4 ribosomal DNA, obtaining mosaic mutational events on ~5% of all rDNA copies. The excised region consist of P-loop and Helix-82 region of 25S rRNA. The mutation led to allelic, dosage-dependent defects marked by lateral root inhibition, reduced size, and pointy leaves typical of defective ribosomal function. The mutation in NOR4 led to dosage compensation from the NOR2 copies, marked by its associated single-nucleotide polymorphisms and, thus, resulted in an altered rRNA sub-population. Furthermore, it caused rRNA maturation defects specifically in the minor pathway characterised by 32S pre-rRNA accumulation. The mutated rRNAs were not incorporated into the translating ribosomes and, thus, the accompanying elevated autophagic flux was likely to be related to ribophagy.
HostingRepository	PRIDE
AnnounceDate	2024-01-26
AnnouncementXML	Submission_2024-01-26_06:34:15.045.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Palak Chaturvedi
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-29 07:11:06	ID requested
⏵ 1	2024-01-26 06:34:16	announced

10.1080/15476286.2023.2298532;

Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E, Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. RNA Biol, 21(1):1-15(2024) [pubmed]

submitter keyword: Autophagy / CRISPR / development / plants / rRNA

Palak Chaturvedi
contact affiliation	University of Vienna
contact email	palak.chaturvedi@univie.ac.at
lab head
Palak Chaturvedi
contact affiliation	University of Vienna
contact email	palak.chaturvedi@univie.ac.at
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/01/PXD035623

PRIDE project URI

• PRIDE
  1. PXD035623
     1. Label: PRIDE project
     2. Name: Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis