PXD028866

PXD028866 is an original dataset announced via ProteomeXchange.

Title	Identification of PNPase and RhlB binding proteins in Deinococcus radiodurans
Description	8-oxo-7,8-dihydroguanine (8-oxoG) is a common RNA oxidation that has been implicated in carcinogenesis, neurodegeneration, and aging. Some? Many? RNA-binding proteins have shown binding preference for 8-oxoG modified RNA; such binding? can protect cells from oxidative stress. To date, the presence of specific 8-oxoG-recognizing proteins is only known in model organisms, but, how these proteins cooperate is still unclear. Here, we use RNA affinity chromatography and mass spectrometry to search for proteins that specifically bind 8-oxoG-modified RNA in Deinococcus radiodurans, an extremophilic bacterium with extraordinary resistance to oxidative stresses. We identified four proteins that selectively bind to oxidized RNA: polynucleotide phosphorylase (DR_2063/PNPase), ATP-dependent DEAD-box RNA helicase (DR_0335/RhlB), ribosomal protein S1 (DR_1983/RpsA), and transcriptional termination factor (DR_1338/Rho). The knockout of PNPase and RhlB in D. radiodurans caused increased sensitivity to hydrogen peroxide and a significant accumulation of 8-oxoG modified RNA. Importantly, PNPase directly interacts with RhlB in D. radiodurans; however, no additional phenotypic effect was observed for the double deletion of pnp and rhlB compared to the individual single deletions. Overall, our findings suggest a role of the PNPase-RhlB complex in targeting 8-oxoG-modified RNAs for rapid degradation and thereby constitutes an important component of D. radiodurans resistance to oxidative stress.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:53:26.258.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	RUNHUA HAN
SpeciesList	scientific name: Deinococcus radiodurans ATCC 13939; NCBI TaxID: 1408434;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-09-29 15:01:35	ID requested
1	2022-07-09 09:55:54	announced
⏵ 2	2023-11-14 08:53:26	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: 8-oxo-7,8-dihydroguanine

RNA oxidation

RNA binding proteins

PNPase

RhlB

oxidative stress

Deinococcus radiodurans

RNA degradation

Lydia M. Contreras
contact affiliation	McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
contact email	lcontrer@che.utexas.edu
lab head
RUNHUA HAN
contact affiliation	Univesity of Texas at Austin
contact email	runhuahan@utexas.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD028866
     1. Label: PRIDE project
     2. Name: Identification of PNPase and RhlB binding proteins in Deinococcus radiodurans