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Series GSE141942 Query DataSets for GSE141942
Status Public on Dec 13, 2019
Title Coordination and assembly of protein complexes encoded across mitochondrial and nuclear genomes is assisted by mtCLPXP in Arabidopsis thaliana
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Protein homeostasis in eukaryotic organelles and their progenitor prokaryotes is regulated by a series of ATP-dependent proteases including the caseinolytic protease complex (ClpXP). In chloroplasts, ClpXP has essential roles in organelle biogenesis and maintenance , but the significance of the plant mitochondrial ClpXP remains unknown and factors that aid coordination of nuclear and mitochondrial encoded subunits for complex assembly in mitochondria await discovery. In this study, we generated knock-out lines of the single copy mitochondrial Clp protease subunit, CLPP2, in Arabidopsis thaliana. They have higher abundance of transcripts from mitochondrial genes encoding OXPHOS protein complexes, while transcripts for nuclear genes encoding other subunits of the same complexes showed no change in transcript abundance. In contrast, the protein abundance of specific nuclear-encoded subunits in OXPHOS complexes I and V increased in knockouts, without accumulation of mitochondrial-encoded counterparts in the same complex. Protein complexes mainly or wholly encoded in the nucleus were unaffected. Analysis of protein import, assembly and function of Complex I revealed that while function was retained, protein homeostasis was disrupted through slower assembly, leading to accumulation of soluble subcomplexes of nuclear-encoded subunits after import. It is proposed that CLPP contributes to the mitochondrial protein degradation network through supporting coordination and assembly of protein complexes encoded across mitochondrial and nuclear genomes.  
Overall design Overall we analysed 9 samples of Arabidopsis thaliana total RNA extracts by high throughput RNA sequencing. The samples were 3 replicates of WT (Wild type - Arabidopsis ecotype Columbio-0, used at control), clpp2-1 (knock-out mutant 1 of the mitochondrial CLPP2 protease (AT5G23140)) and clpp2-2 (knock-out 2 of the mitochondrial CLPP2 potease). Both mutations were produced from Arabidopsis ecotype Columbia-0. Replicates are indicated by the numbering after the underscore.
Contributor(s) Petereit J, Huang S
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Submission date Dec 12, 2019
Last update date Dec 15, 2019
Contact name Jakob Petereit
Phone 0434533807
Organization name ARC Centre of Excellence in Plant Energy Biology
Street address 35 Stirling Highway
City Crawley
State/province WA
ZIP/Postal code 6009
Country Australia
Platforms (1)
GPL24025 BGISEQ-500 (Arabidopsis thaliana)
Samples (9)
GSM4216730 wt_1
GSM4216731 wt_2
GSM4216732 wt_3
BioProject PRJNA595358
SRA SRP237356

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GSE141942_deseq2_assay_clpp2_rnaseq.tsv.gz 401.6 Kb (ftp)(http) TSV
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