Dataset Information

Protein exchange rates within mitochondrial protein complexes of differentiated myotubes using pulsed SILAC complexome profiling

ABSTRACT: We studied dynamics within stable mitochondrial complexes in differentiated mouse myotubes by pulsed SILAC complexome profiling.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Ilka Wittig

LAB HEAD: Aleksandra Trifunovic

PROVIDER: PXD017465 | Pride | 2020-03-05

REPOSITORIES: Pride

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			Action	DRS
	6_an_7Hours.jpg	Other
	P18_039_ComplexRemodeling_Z01_6h_02.raw	Raw
	P18_039_ComplexRemodeling_Z01_6h_02_180731141331.raw	Raw
	P18_039_ComplexRemodeling_Z01_6h_03.raw	Raw
	P18_039_ComplexRemodeling_Z01_6h_04.raw	Raw

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Publications

A salvage pathway maintains highly functional respiratory complex I.

Szczepanowska Karolina K Senft Katharina K Heidler Juliana J Herholz Marija M Kukat Alexandra A Höhne Michaela Nicole MN Hofsetz Eduard E Becker Christina C Kaspar Sophie S Giese Heiko H Zwicker Klaus K Guerrero-Castillo Sergio S Baumann Linda L Kauppila Johanna J Rumyantseva Anastasia A Müller Stefan S Frese Christian K CK Brandt Ulrich U Riemer Jan J Wittig Ilka I Trifunovic Aleksandra A

Nature communications 20200402 1

Regulation of the turnover of complex I (CI), the largest mitochondrial respiratory chain complex, remains enigmatic despite huge advancement in understanding its structure and the assembly. Here, we report that the NADH-oxidizing N-module of CI is turned over at a higher rate and largely independently of the rest of the complex by mitochondrial matrix protease ClpXP, which selectively removes and degrades damaged subunits. The observed mechanism seems to be a safeguard against the accumulation ...[more]

PMID: 32242014

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Project description:Steady-state RNA levels are a result of RNA synthesis and degradation. The importance of transcription-factor mediated induction or repression of mRNA synthesis is well established, but the role and mechanisms of RNA degradation are less well understood. We globally evaluated the RNA decay rates in proliferating and differentiated mouse myoblasts on whole-genome Affymetrix exon arrays, allowing for the assessment of directionality of RNA degradation and the detection of splice variant-specific differences in RNA decay rates. We found large differences in decay rates. mRNAs coding for proteins involved in signal transduction and transcriptional regulation have shortest half lives, whereas mRNAs coding for DNA replication enzymes and muscle contraction proteins are among the most stable. Many genes differentially expressed between proliferating and differentiated myoblasts demonstrate major differences in RNA decay rates. Quantitative PCR experiments confirmed the higher stability of transcripts with increased expression levels. RNA degradation has no apparent preferential directionality. RNA degradation appears to affect the ratio of different splice variants. For example, Itga7 isoforms with higher abundance in differentiated than in proliferating cells are more stable in differentiated cells, despite the sharing of a common 3’ untranslated region. Thus, where it was previously thought that the abundance of different splice isoforms was mainly controlled by tissue-specific splicing factors, we now demonstrate that isoforms may be produced at comparable levels but degraded with different efficiencies, depending on the differentiation status of the cells. Our results indicate that control of RNA degradation rates contributes significantly to the differentiation stage-dependent differences in abundance of transcripts and splice variants. Keywords: total RNA expression profiling; cultured cells We analyzed proliferating C2C12 cells and C2C12 cells differentiated into myotubes by serum starvation (8 days after induction of differentiation). We analyzed 7 time points after addition of actionmycin D (0, 10, 20, 30, 60, 150, 480 minutes). There were two biological replicates per condition.