Dataset Information

Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics

ABSTRACT: Aiming at defining the protein content and composition of a single mitochondrion of Arabidopsis thaliana, shotgun analyses were performed on purified mitochondria from cultured heterotrophic Arabidopsis cells. Based on microscopic observations on the size of mitochondria, as well as biochemical properties, such as protein concentration, average molecular mass of proteins, and the average length of the signal peptide, intensity-based absolute quantification (iBAQ) values were applied to calculate the copy number of each identified protein species within a single mitochondrion. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40,000 for Voltage-Dependent Anion Channel 1 (VDAC1) to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat (PPR) proteins that modify mitochondrial transcripts. Aiming at defining the protein content and composition of a single mitochondrion of Arabidopsis thaliana, shotgun analyses were performed on purified mitochondria from cultured heterotrophic Arabidopsis cells. Based on microscopic observations on the size of mitochondria, as well as biochemical properties, such as protein concentration, average molecular mass of proteins, and the average length of the signal peptide, intensity-based absolute quantification (iBAQ) values were applied to calculate the copy number of each identified protein species within a single mitochondrion. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40,000 for Voltage-Dependent Anion Channel 1 (VDAC1) to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat (PPR) proteins that modify mitochondrial transcripts. Aiming at defining the protein content and composition of a single mitochondrion of Arabidopsis thaliana, shotgun analyses were performed on purified mitochondria from cultured heterotrophic Arabidopsis cells. Based on microscopic observations on the size of mitochondria, as well as biochemical properties, such as protein concentration, average molecular mass of proteins, and the average length of the signal peptide, intensity-based absolute quantification (iBAQ) values were applied to calculate the copy number of each identified protein species within a single mitochondrion. Copy numbers of the individual proteins span five orders of magnitude, ranging from >40,000 for Voltage-Dependent Anion Channel 1 (VDAC1) to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat (PPR) proteins that modify mitochondrial transcripts.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Cell Culture

SUBMITTER: Holger Eubel

LAB HEAD: Hans-Peter Braun

PROVIDER: PXD014292 | Pride | 2019-09-11

REPOSITORIES: pride

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Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics.

Fuchs Philippe P Rugen Nils N Carrie Chris C Elsässer Marlene M Finkemeier Iris I Giese Jonas J Hildebrandt Tatjana M TM Kühn Kristina K Maurino Veronica G VG Ruberti Cristina C Schallenberg-Rüdinger Mareike M Steinbeck Janina J Braun Hans-Peter HP Eubel Holger H Meyer Etienne H EH Müller-Schüssele Stefanie J SJ Schwarzländer Markus M

The Plant journal : for cell and molecular biology 20191103 2

Mitochondria host vital cellular functions, including oxidative phosphorylation and co-factor biosynthesis, which are reflected in their proteome. At the cellular level plant mitochondria are organized into hundreds of discrete functional entities, which undergo dynamic fission and fusion. It is the individual organelle that operates in the living cell, yet biochemical and physiological assessments have exclusively focused on the characteristics of large populations of mitochondria. Here, we exp ...[more]

PMID: 31520498

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Project description:Mitochondria are subcellular organelles that are more than just the powerhouse of cells, they also dictate if a cell dies or survives. The mitochondrial outer-membrane voltage-dependent anion channel 1 (VDAC1) has been shown to play a crucial role in metabolism and apoptosis, however its involvement in ischemic pathologies and cancer is not clear. Transcriptome analysis of Vdac1-/- mouse embryonic fibroblasts (MEF) highlighted cancer and inflammation as top diesases but also activation of the HIF-1 signaling pathway in normoxia. HIF-1α protein was stable due to ROS accumulation that decreased respiration and glycolysis and maintained basal apoptosis. However, in hypoxia increased activation of ERK in combination with maintenance of respiration and increased glycolysis counterbalanced the deleterious effects of ROS, thereby allowing Vdac1-/- MEF to proliferate better than wild-type MEF. Xenografts of RAS-transformed Vdac1-/- MEF in mice showed stabilization of both HIF-1α and HIF-2α which led to blood vessel destabilization and a strong inflammatory response. Moreover, expression of Cdkn2a, a HIF-1-target and tumor suppressor gene, was strongly decreased. Consequently RAS-transformed Vdac1-/- MEF tumors grew faster than wild-type MEF tumors. These findings provide new perspectives into the understanding of VDAC1 in the function of mitochondria not only in cancer but also in inflammatory diseases. Profiling of VDAC1-/- and wild-type (Wt) Mouse Embryonic Fibroblasts (MEFs) was performed using whole genome mouse microarrays. in normoxic or hypoxic conditions. MEF (Wt and Vdac1-/-) were incubated in normoxia (Nx, ie: 20% O2) or hypoxia (Hx, ie: 1% O2) for 72h and then lysed prior to RNA isolation, labelling and hybridization on microarrays. One color experiment with 2 biological replicates (marked 1 or 2) of the 4 experimental conditions. One condition (MEF WT Nx2) has been removed from the statistical analysis after microarray quality check due to high background. Total of 7 samples.

			Action	DRS
	MaxQuant_1.6.0.1.zip	Other
	MaxQuant_Analysis.zip	Other
	Mito_2.raw	Raw
	Mito_4.raw	Raw
	Mito_6.raw	Raw