PXD008920

PXD008920 is an original dataset announced via ProteomeXchange.

Title	Imperfect Redundancy in the Family of Thylakoid Lumen Deg Proteases in Arabidopsis Helps Identifying Their Potential Substrates
Description	Deg proteases are involved in protein quality control and response to stress in prokaryotic organisms. Out of the 16 Deg-encoding genes of Arabidopsis, the products of three, Deg1, Deg5 and Deg8, are located in the thylakoid lumen. Deg1 forms homo-hexamers, degrading photosynthetic proteins, especially during photoinhibition. Deg5 and Deg8 form hetero-complexes, performing apparently similar functions, raising the question whether the two complexes are redundant. To answer this, single, double and triple knockout mutants were generated and their phenotypes were compared. Under optimal growth conditions deg5 and deg8 mutants looked like WT, whereas all combinations of deg1 mutants were smaller and more sensitive to photoinhibition. Under harsher conditions, deg5 and deg8 mutants were also affected, although less than deg1 mutants. Overexpression of Deg5-Deg8 could partially compensate for the loss of Deg1, but only in optimal conditions. Comparative proteomic analysis of deg1 mutants vs. WT revealed moderate up-regulation of thylakoid proteins involved in photoprotection, assembly, repair and house-keeping functions, and down-regulation of all photosynthetic complexes, consistent with the reduced growth of the deg1 mutants. Testing the steady-state level of Deg proteases in WT plants demonstrated that Deg1 was approximately two-fold more abundant than the Deg5-Deg8 complex. Moreover, recombinant Deg1 had higher in vitro proteolytic activity compared with Deg5 and Deg8. Affinity enrichment assays on transgenic plants expressing epitope-tagged Deg proteases revealed that Deg1 was pulled-down almost exclusively, whereas Deg5 and Deg8 were associated with a plethora of thylakoid membrane and lumen proteins, suggesting that they are capable of binding potential substrates, but are unable to degrade them efficiently. Two of the co-precipitated proteins, TL29 and Psb27-H1, were found slightly up-regulated in the triple mutant, suggesting that they are substrates of lumenal Deg proteases. Other pulled-down proteins were the D1 protein, LHCB proteins and subunits of the OEC of PSII, and components of the Cyt b6-f and NADH dehydrogenase complexes, suggesting that these might also be substrates of lumenal Deg proteases. Altogether, the results of this study suggest that differences in abundance and proteolytic activity are the source of the differential importance of the two Deg protease complexes observed in vivo.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:49:27.381.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008920
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Meital Kupervaser
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	Deamidated; Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-09 08:52:05	ID requested
⏵ 1	2023-11-14 08:49:27	announced

10.6019/PXD008920;

curator keyword: Biological

submitter keyword: Deg proteins, Thylakoids,Arabidopsis

Zach Adam
contact affiliation	The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rehovot 76100, Israel
contact email	zach.adam@mail.huji.ac.il
lab head
Meital Kupervaser
contact affiliation	Weizmann Institute of Science
contact email	meital.kupervaser@weizmann.ac.il
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/2022/01/PXD008920

PRIDE project URI

• PRIDE
  1. PXD008920
     1. Label: PRIDE project
     2. Name: Imperfect Redundancy in the Family of Thylakoid Lumen Deg Proteases in Arabidopsis Helps Identifying Their Potential Substrates