PXD000869

PXD000869 is an original dataset announced via ProteomeXchange.

Title	CLPC1 maintains chloroplast proteome and RNA homeostasis
Description	In chloroplasts, homeostasis of the proteome maintained by protein synthesis, importation, and degradation is critical to the development of chloroplasts. The caseinolytic protease complex component CLPC1, a member of the HSP100 family of chaperones, not only facilitates the translocation of pre-proteins into chloroplasts, but also mediates protein degradation via its associated caseinolytic protease complex (CLPPs). Although CLPC1 has been shown to affect the abundance of some chloroplast proteins, its overall functions and coordination with other protease systems in maintaining proteome homeostasis have not been fully elucidated. Its possible roles in gene expression are also unclear. Here we used the iTRAQ technique to profile the chloroplast proteomes of the clpc1 mutant and its various complementation lines. Whereas proteins involved in photosynthesis were found to be dramatically decreased in the clcp1 mutant, many involved in chloroplast transcription and translation were increased. Expression of the full-length CLPC1 protein, but not of the N-terminal truncated form (ΔN), in clpc1 restored the level of most of these proteins to that of the wild type. Interestingly, the ΔN complementation line could also restore certain proteins to the wild type level. We found that nearly half of previously suggested candidate substrates of the CLPS1, another CLPP component, were mis-regulated in clpc1, indicating that CLPC1 greatly affects CLPS1 targets. We provide the first experimental evidence to show that CLPC1 profoundly affects gene transcription in chloroplasts. Sense transcripts of many chloroplast genes are up-regulated whereas antisense transcripts down-regulated in the clpc1 mutant. We propose that this altered transcript landscape is a result of the transcription and degradation dynamics conditioned by the changed proteomic profile in the mutant. Our study reveals that CLPC1 and likely the CLPP proteasome complex have a greater than previously recognized role in coordinating and maintaining the proteome and transcriptome homeostasis in chloroplasts.
HostingRepository	PRIDE
AnnounceDate	2018-10-19
AnnouncementXML	Submission_2018-10-19_00:27:19.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000869
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	shoudong zhang
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	iTRAQ4plex; Oxidation; Carbamidomethyl
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2014-04-02 00:33:29	ID requested
⏵ 1	2018-10-19 00:27:20	announced

Zhang S, Zhang H, Xia Y, Xiong L, The caseinolytic protease complex component CLPC1 in Arabidopsis maintains proteome and RNA homeostasis in chloroplasts. BMC Plant Biol, 18(1):192(2018) [pubmed]

submitter keyword: CLPC1, chloroplast, proteome, RNA, homeostasis

Liming Xiong
contact affiliation	Division of Chemical and Life Sciences & Engineering 4700 King Abdullah University of Science and Technology (KAUST)
contact email	liming.xiong@kaust.edu.sa
lab head
shoudong zhang
contact affiliation	KAUST
contact email	shoudong.zhang@kaust.edu.sa
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000869
     1. Label: PRIDE project
     2. Name: CLPC1 maintains chloroplast proteome and RNA homeostasis