1. Biochemistry and Chemical Biology
  2. Cell Biology
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Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals

  1. Inge Kühl  Is a corresponding author
  2. Maria Miranda
  3. Ilian Atanassov
  4. Irina Kuznetsova
  5. Yvonne Hinze
  6. Arnaud Mourier
  7. Aleksandra Filipovska
  8. Nils-Göran Larsson  Is a corresponding author
  1. Max Planck Institute for Biology of Ageing, Germany
  2. Institute of Integrative Biology of the Cell (I2BC) UMR9198, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, France
  3. The University of Western Australia, Australia
  4. Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, France
  5. Karolinska Institutet, Sweden
Tools and Resources
Cite this article as: eLife 2017;6:e30952 doi: 10.7554/eLife.30952
8 figures, 2 tables and 10 additional files

Figures

Figure 1 with 4 supplements
Label-free quantification and comparison of mitoproteomes of mouse hearts with mitochondrial dysfunction.

(A) Schematic representation of the tissue-specific knockout strains (L/L, cre) used, with impaired mtDNA gene expression leading to mitochondrial dysfunction and corresponding controls (L/L). Nuclear-encoded mitochondrial proteins are illustrated in yellow and mtDNA-encoded mitochondrial proteins in blue. (B) Experimental workflow of the analysis of the transcriptomes and mitoproteomes from mouse heart generating three distinct datasets (1-3). Files are provided in Supplementary file 15, 8 and 9.

https://doi.org/10.7554/eLife.30952.002
Figure 1—figure supplement 1
Activity of citrate synthase in heart from different L/L, cre and L/L mice.

Error bars ± SEM; *p<0.05, ***p<0.001; two-tailed unpaired Student’s t-test.

https://doi.org/10.7554/eLife.30952.003
Figure 1—figure supplement 1—source data 1

Determination of citrate synthase activity.

https://doi.org/10.7554/eLife.30952.007
Figure 1—figure supplement 2
High reproducibility of the transcriptomic and mitoproteomic data.

(A) Reproducibility of the RNA-Seq (left) and label-free mass spectrometry (right) data is illustrated in heatmaps representing the Pearson’s correlation coefficient of all samples of the five different conditional knockouts (L/L, cre) and their corresponding controls (L/L) with the same scale; as an example of reproducibility a scatter plot of the label-free protein intensity values in two Polrmt L/L, cre samples and their correlation coefficient is shown. The number of biological replicates is indicated in parenthesis. (B) Number of identified (851 to 1348 proteins), quantified (673 to 1039 proteins) and mitochondrial proteins (586 to 704 proteins) across all L/L, cre hearts compared to corresponding L/L; error bars: ±SEM.

https://doi.org/10.7554/eLife.30952.004
Figure 1—figure supplement 3
Analysis of systematic bias in the detection of mitochondrial proteins.

Cumulative distribution plots for mitochondrial proteins based on (A) GRAVY score as a measurement of hydrophobicity removing either only the first methionine of the amino acid sequence (left) of the first methionine and the mitochondrial targeting peptide (right). (B) Isoelectric point as a measure of charge hydrophobicity removing either only the first methionine of the amino acid sequence (left) of the first methionine and the mitochondrial targeting peptide (right). (C) mean RNA counts of L/L samples across all mouse strains as a measure of protein abundance. Met, methionine; mTP, mitochondrial targeting peptide; black, detected in at least one knockout mouse strain; red, not detected.

https://doi.org/10.7554/eLife.30952.005
Figure 1—figure supplement 4
Distribution of label-free quantification (LFQ) intensities and fold changes of quantified proteins.

(A) Distribution of LFQ intensities of quantified proteins on L/L, cre and L/L mitoproteomes per knockout mouse strain. (B) Distribution of fold changes in L/L, cre and L/L mitoproteomes per knockout mouse strain. (C) MA-plots showing the distribution of fold changes in the mitoproteome mice compared to the average LFQ intensity of the proteins in L/L (top), L/L, cre (middle), or both genotypes (bottom) per knockout mouse strain. Black, p<0.05; gray p>0.05.

https://doi.org/10.7554/eLife.30952.006
Figure 2 with 1 supplement
Mitochondrial transcriptome and proteome during post-natal development of mouse heart.

(A–B) Venn diagram of significantly changed (A) mitochondrial proteins and (B) genes encoding for transcripts of mitochondrial proteins of L/L mice (3–20 weeks). (C) Hierarchical clustering analysis of mitoproteomes of L/L mice (3–20 weeks). Left to right: pie chart illustrating percentages of significantly changed mitochondrial proteins in each cluster (1-4), in white: not classified (8%); protein changes over ages for each cluster, fold change relative to 3 week old mice were scaled and presented as Z-score; top three enriched categories of each cluster. Dotted line: Benjamini-Hochberg adjusted p=0.05. Parentheses indicate the number of proteins changed in that category per total number of proteins classified in that category. m.a. = mature adulthood. (D) Mitochondrial transcriptomic and proteomic 2D enrichment analysis showing enriched functional categories of L/L mice at different ages compared to weeks 3–4 based on the fold change. (E) Correlation plots of the L/L, cre versus L/L fold changes between mitoribosomal transcripts and proteins in L/L mice at different ages. Black line indicates the trend.

https://doi.org/10.7554/eLife.30952.009
Figure 2—figure supplement 1
Rapid post-natal increase of mtDNA levels and factors required to maintain and express mtDNA in young wild-type mouse heart.

(A) mtDNA levels in total DNA from wild-type (+/+) mouse heart at different ages. 18S rDNA was used to normalize nuclear input. (B) Immunoblot quantification of some mitochondrial protein levels in heart extracts from wild-type mice at different ages. α-Tubulin was used for normalization. (C) Clustering analysis of significantly changing mitochondrial proteins in control mice (L/L) at different ages. m.a. = mature adulthood.

https://doi.org/10.7554/eLife.30952.010
Figure 2—figure supplement 1—source data 1

qPCR determination of mtDNA levels in wild type mice.

https://doi.org/10.7554/eLife.30952.011
Figure 2—figure supplement 1—source data 2

Densitometry analyses of western blots on total proteins.

https://doi.org/10.7554/eLife.30952.012
Figure 3 with 1 supplement
Enrichment of signalling and metabolic pathways in mouse hearts with severe mitochondrial dysfunction.

(A) Canonical pathway analysis of significantly changed genes in all knockouts with representation of the 12 most significant pathways. Grayscale heatmap: p value of each pathway based on Fisher’s exact test. Rectangles in horizontal heatmaps: average expression level in the five knockouts of each gene detected per pathway; Parenthesis: fraction of genes detected per pathway. (B) Transcript levels of genes encoding transcription factors involved in mitochondrial biogenesis in L/L, cre and L/L hearts. Normalization: B2M (beta-2-microglobulin). Twnk, Tfam, Polrmt, Lrpprc, and Mterf4 were used as controls for the corresponding knockout strains. (C–D) Expression levels of differentially expressed MYC and ATF4 target genes encoding mitochondrial proteins. Graphs average expression level in the five knockouts of each gene ± SD.

https://doi.org/10.7554/eLife.30952.013
Figure 3—source data 1

qRT-PCR of genes encoding mitochondrial biogenesis factors in the five knockout mouse strains.

https://doi.org/10.7554/eLife.30952.015
Figure 3—figure supplement 1
Several targets of MYC and ATF4 transcription factors are differentially regulated upon mitochondrial dysfunction.

Heatmaps illustrate the fold-change transcript levels in L/L, cre and L/L mouse hearts in an alphabetical order. Adjusted p<0.05 in all knockout mouse strains. (A) MYC target genes. (B) ATF4 target genes.

https://doi.org/10.7554/eLife.30952.014
Figure 4 with 3 supplements
Remodeling of the mitochondrial transcriptome and proteome upon severe mitochondrial dysfunction.

Files are provided in Supplementary files 1 and 4. (A) Number of significantly changed transcripts (left) and mitochondrial proteins (right) quantified from L/L, cre compared to L/L; red: increased, blue: decreased. (B) Venn diagram of number of mitochondrial transcripts and proteins quantified and significant in ≥1 knockout strain. (C) Correlations of the L/L, cre versus L/L fold changes of significantly regulated mitochondrial transcripts and proteins. (D) Mitochondrial transcriptomic and proteomic 2D enrichment analysis showing the trend and degree of regulation of 15 functional categories in all different knockouts. (E) Scatterplots plots of the L/L, cre versus L/L fold changes of mitochondrial transcripts and proteins in different knockouts in a selection of categories. Black line indicates the trend. Same color code applied as in Figure 4D except for the OXPHOS category where the mitochondrial-encoded genes are colored in blue and the nuclear-encoded genes are colored in yellow.

https://doi.org/10.7554/eLife.30952.016
Figure 4—source data 1

Pearson correlation coefficient matrixes of fold changes of L/L, cre versus L/L of significantly regulated mitochondrial transcripts and proteins.

https://doi.org/10.7554/eLife.30952.020
Figure 4—figure supplement 1
Most of the identified transcripts of nuclear genes encoding mitochondrial proteins are decreased, whereas most of the quantified mitochondrial proteins were increased in abundance.

(A) Volcano plots of transcripts of genes encoding mitochondrial proteins for each knockout mouse strain. (B) Volcano plots of mitoproteomes for each knockout mouse strain. Black: p<0.05, grey: p>0.05. Top 1% of significantly changed mitochondrial transcripts and top 5% of significantly changed mitochondrial proteins are shown and listed in the dotted line boxes; red: increased, blue: decreased; p values were adjusted using Benjamini-Hochberg method. (C) Scatterplots showing the correlation between the mitochondrial transcriptomics and proteomics data for each knockout mouse strain (L/L, cre compared to L/L). Each point corresponds to one quantified gene. Correlation coefficient and p values were calculated with Pearson correlation test.

https://doi.org/10.7554/eLife.30952.017
Figure 4—figure supplement 2
Correlations of the L/L, cre versus L/L fold changes of significantly regulated mitochondrial transcripts and proteins.
https://doi.org/10.7554/eLife.30952.018
Figure 4—figure supplement 3
Distribution of MYC and ATF4 target genes in scatterplots plots of the L/L, cre versus L/L fold changes of mitochondrial transcripts and proteins in different knockouts in a selection of categories.
https://doi.org/10.7554/eLife.30952.019
Figure 5 with 2 supplements
Effects of impaired mtDNA gene expression on mitochondrial protein levels in heart.

Heatmaps illustrating the fold-change transcript (left) and mitochondrial protein (right) levels in L/L, cre and L/L mouse hearts in alphabetical order; blank boxes: not detected or not quantified. Adjusted p<0.05 in≥1 knockout strain. (A) OXPHOS complexes (complex II is only nuclear encoded). (B) OXPHOS assembly. (C) Mitochondrial ribosomal proteins; n/a = not applicable. (D) Degradation and stress response. (E) Apoptosis. For a selection of mitochondrial proteins the steady state levels were verified by immunoblotting shown in Figure 5—figure supplement 2.

https://doi.org/10.7554/eLife.30952.021
Figure 5—figure supplement 1
Proteins regulating mitochondrial morphology, iron sulphur cluster and heme biogenesis are increased.

Heatmaps illustrating the fold-change transcript (left) and mitochondrial protein (right) levels in L/L, cre and L/L mouse hearts in alphabetical order; blank boxes in heatmap: not identified or not quantified. Adjusted p<0.05 in at least one of the knockout mouse strains for the genes encoding mitochondrial transcript or protein levels. (A) Mitochondrial morphology. (B) Mitochondrial import and chaperones. (C) Iron sulphur cluster and heme biogenesis. (D) Mitochondrial DNA replication and maintenance. (E) Mitochondrial transcription and mt-RNA metabolism. (F) Other mitochondrial protein synthesis factors.

https://doi.org/10.7554/eLife.30952.022
Figure 5—figure supplement 2
Immunoblot of several mitochondrial proteins in extracts from L/L, cre and L/L hearts; Loading of 6 different membranes: SDHA, SDHB or VDAC1.
https://doi.org/10.7554/eLife.30952.023
Figure 6 with 1 supplement
Up-regulation of the enzymes of the mitochondrial 1C pathway happens before deficient OXPHOS is detectable in mouse heart.

(A) Scheme of 1C pathway. Colored boxes: protein levels; red: increased, grey: not detected or not quantified. (B) Heatmaps showing the fold-change in transcript (left) and protein (right) levels in alphabetical order of L/L, cre and L/L mouse hearts of the 1C pathway; p<0.0001 in≥1 knockout strain. (C) Immunoblot of enzymes of the 1C pathway in total protein extracts from L/L, cre and L/L; Loading: tubulin. (D) Quantification of 1C donor metabolite levels in L/L, cre and L/L. Graphs represent mean ± SEM (*p<0.05, **p<0.01, ***p<0.001). (E) Time point analysis of protein levels of enzymes of the 1C pathway (top), and LRPPRC and VDAC (bottom) in Lrpprc knockout hearts compared to controls. Yellow line: average value of nuclear and mitochondrial encoded OXPHOS complex IV subunits. Adjusted p<0.05, except for VDAC. LRPPRC and VDAC protein levels at the different time points were verified by immunoblotting presented in Figure 6—figure supplement 1.

https://doi.org/10.7554/eLife.30952.024
Figure 6—source data 1

Determination of 1C pathway donor metabolites.

https://doi.org/10.7554/eLife.30952.025
Figure 6—figure supplement 1
Steady-state LRPPRC protein levels at different time points in mitochondrial extracts from Lrpprc L/L, cre and L/L hearts; Loading: VDAC1.
https://doi.org/10.7554/eLife.30952.026
Up-regulated glutamate to proline conversion in mitochondrial OXPHOS deficient heart.

(A) Scheme of the glutamate to proline conversion pathway. Colored boxes: protein levels; red: increased, blue: decreased. (B) Heatmaps illustrating the fold-change transcript (left) and protein (right) levels. Adjusted p<0.05 in≥1 knockout strain for genes encoding mitochondrial transcript or protein levels. (C) Time point analysis of protein levels of enzymes of the glutamate to proline conversion pathway in Lrpprc knockout hearts compared to controls. Yellow line: average value of nuclear and mitochondrial encoded OXPHOS complex IV subunits. Adjusted p<0.05. (D) Quantification of proline and glutamate in different L/L, cre and L/L mouse hearts. Error bars:± SEM; **p<0.01; two-tailed unpaired Student’s t-test.

https://doi.org/10.7554/eLife.30952.027
Figure 7—source data 1

Determination of proline and glutamate metabolites.

https://doi.org/10.7554/eLife.30952.028
Figure 8 with 1 supplement
OXPHOS dysfunction leads to decreased cellular Q levels, but the enzymes of the mevalonate pathway are normal.

(A) Scheme of the mevalonate and Q biosynthesis pathways, and OXPHOS complexes (Nuclear-encoded OXPHOS proteins are shown in yellow and mtDNA-encoded OXPHOS proteins in blue). Colored boxes: protein levels; red: increased, blue: decreased, grey: not detected or not quantified. (B) Heatmaps illustrating the fold-change protein levels of the Q biosynthesis pathway in alphabetical order of L/L, cre and L/L mouse hearts; blank boxes: not detected or not quantified proteins; p<0.05 in≥1 knockout strain. (C) Immunoblot of enzymes of the mevalonate pathway on total protein extracts from different L/L, cre and L/L hearts. Loading: tubulin. (D) Transcript levels of genes encoding enzymes of the mevalonate and coenzyme Q synthesis pathway in L/L, cre and L/L hearts. Normalization: B2M (beta-2-microglobulin). (E) Protein levels of OXPHOS complexes I-V and the downregulated Q biosynthesis enzymes at different time points in Lrpprc knockout mouse hearts compared to controls. The graph represents a mean log2 fold-change of all the proteins in that category. (F) Time point analysis of protein levels of enzymes of the Q biosynthesis pathway in Lrpprc knockout mouse hearts compared to controls. Adjusted p across time <0.05. (G) Quinone quantification (Q9 and Q10) in different L/L, cre and L/L mouse hearts. Error bars:± SEM; *p<0.05, **p<0.01, ***p<0.001; two-tailed unpaired Student’s t-test.

https://doi.org/10.7554/eLife.30952.029
Figure 8—source data 1

qRT-PCR of genes encoding ubiquinone and mevalonate pathway enzymes in the five knockout mouse strains.

https://doi.org/10.7554/eLife.30952.031
Figure 8—source data 2

Determination of coenzyme Q9 and 10.

https://doi.org/10.7554/eLife.30952.032
Figure 8—figure supplement 1
Transcript levels of genes encoding for enzymes of the mevalonate and the Q synthesis pathways.

(A) Heatmaps showing the fold-change transcript levels in alphabetical order of L/L, cre and L/L mouse hearts of the mevalonate and the Q biosynthesis pathways by RNA-Seq.; blank boxes: not detected or not quantified transcript; adjusted p<0.05 in≥1 knockout mouse line. (B) qRT-PCR of transcript levels of genes encoding enzymes of coenzyme Q synthesis pathway in different L/L, cre and L/L hearts, normalized to B2M (beta-2-microglobulin). All graphs represent mean ± SEM; *p<0.05, **p<0.01, ***p<0.001.

https://doi.org/10.7554/eLife.30952.030

Tables

Table 1
Summary of Major Characteristics of the Five Different Tissue-Specific Knockout Mouse Strains.

Arrows: increase or decrease; tilde: stable. Conditional knockouts: TwnkloxP/loxP, +/Ckmm-cre (Milenkovic et al., 2013), TfamloxP/loxP, +/Ckmm-cre (Larsson et al., 1998), PolrmtloxP/loxP, +/Ckmm-cre (Kühl et al., 2014; Kühl et al., 2016), LrpprcloxP/loxP, +/Ckmm-cre (Ruzzenente et al., 2012), Mterf4loxP/loxP, +/Ckmm-cre (Cámara et al., 2011).

https://doi.org/10.7554/eLife.30952.008
Conditional knockout
(L/L, cre)
TwnkTfamPolrmtLrpprcMterf4
Gene productMitochondrial DNA helicase TWINKLEMitochondrial transcription factor AMitochondrial RNA polymeraseLeucine-rich pentatricopeptide repeat containing proteinMitochondrial transcription termination factor 4
Lifespan (weeks)< 19< 10< 6< 16< 21
Mitochondrial cardiomyopathy+++++
Mitochondrial DNA
Mitochondrial DNA transcripts*
OXPHOS
  1. * except 12S mt-rRNA, 16S mt-rRNA, mt-Nd6 and most mt-tRNAs

Key resources table
Reagent type (species)
or resource
DesignationSource or referenceIdentifiersAdditional
information
Organism, C57BL/6N (Mus musculus)TwnkLoxP/LoxP;
Twnk L/L
Milenkovic et al., 2013RRID: MGI:5496889
Organism, C57BL/6N (Mus musculus)TwnkLoxP/LoxP, +/Ckmm-cre;
Twnk L/L, cre
Milenkovic et al., 2013RRID: MGI:5496891
Organism, C57BL/6N (Mus musculus)TfamLoxP/LoxP;
Tfam L/L
Larsson et al., 1998RRID: MGI:2177633
Organism, C57BL/6N (Mus musculus)TfamLoxP/LoxP, +/Ckmm-cre;
Tfam L/L, cre
Larsson et al., 1998RRID: MGI:2177634
Organism, C57BL/6N (Mus musculus)PolrmtLoxP/LoxP; Polrmt L/LKühl et al., 2014, 2016MGI:5704129
Organism, C57BL/6N (Mus musculus)PolrmtLoxP/LoxP, +/Ckmm-cre; Polrmt L/L, creKühl et al., 2014, 2016RRID: MGI:5704131
Organism, C57BL/6N (Mus musculus)LrpprcLoxP/LoxP; Lrpprc L/LRuzzenente et al., 2012RRID: MGI:5438915
Organism, C57BL/6N (Mus musculus)LrpprcLoxP/LoxP, +/Ckmm-cre;Lrpprc L/L, creRuzzenente et al., 2012RRID: MGI:5438914
Organism, C57BL/6N (Mus musculus)Mterf4LoxP/LoxP; Mterf4 L/LCámara et al., 2011RRID: MGI:5288508
Organism, C57BL/6N (Mus musculus)Mterf4LoxP/LoxP, +/Ckmm-cre;Mterf4 L/L, creCámara et al., 2011RRID: MGI:5292478
AntibodyALDH18A1Thermofisher ScientificCat#PA5-19392
RRID: AB_10985670
(1:200)
AntibodyCLPPSigma-AldrichCat#WH0008192M1
RRID: AB_1840782
(1:300)
AntibodyCOX4Cell SignalingCat#4850
RRID: AB_2085424
(1:500)
AntibodyCSAbcamCat#ab129095
RRID: AB_11143209
(1:200)
AntibodyFDPSAbcamCat#ab189874
RRID: AB_2716301
(1:500)
AntibodyGLSAbcamCat#ab93434
RRID: AB_10561964
(1:200)
AntibodyHMGCS1AbcamCat#ab194971
RRID: AB_2716299
(1:500)
AntibodyHSPA9/mtHSP70/Grp75AbcamCat#ab82591
RRID: AB_1860633
(1:200)
AntibodyLONP1AbcamCat#ab103809
RRID: AB_10858161
(1:500)
AntibodyLRPPRC mouseN.-G. Larsson; Ruzzenente et al., 2012RRID: AB_2716302(1:1000)
AntibodyMRPL37Sigma-AldrichCat#HPA025826
RRID: AB_1854106
(1:500)
AntibodyMRLP44ProteintechCat#16394–1-AP
RRID: AB_2146062
(1:300)
AntibodyMRPS35ProteintechCat#16457–1-AP
RRID: AB_2146521
(1:500)
AntibodyMTHFD1AbcamCat#ab103698
RRID: AB_10862775
(1:500)
AntibodyMTHFD2AbcamCat#ab37840
RRID: AB_776544
(1:500)
AntibodyNDUFA9AbcamCat#ab14713
RRID: AB_301431
(1:500)
AntibodyPOLRMT mouseN.-G. Larsson;Kühl et al., 2014RRID: AB_2716297
AntibodyPYCR1ProteintechCat#13108–1-AP
RRID: AB_2174878
(1:200)
AntibodySDHAThermofisher ScientificCat#459200
RRID: AB_2532231
(1:100)
AntibodySHMT2Sigma-AldrichCat#HPA020543
RRID: AB_1856833
(1:500)
AntibodyTFAMAbcamCat#ab131607
RRID: AB_11154693
(1:500)
AntibodyTotal OXPHOS Rodent WB Antibody CocktailAbcamCat#ab110413
RRID: AB_2629281
(1:1000)
AntibodyTubulinCell SignalingCat#2125
RRID: AB_2619646
(1:1000)
AntibodyTWINKLE mouseN.-G. Larsson,Milenkovic et al., 2013RRID: AB_2716298
AntibodyUQCRFS1AbcamCat#ab131152
RRID:AB_2716303
(1:200)
AntibodyVDAC1MilliporeCat#MABN504
RRID:AB_2716304
(1:1000)
Sequence-based reagentTaqman Assay - Mouse Adck3Life technologiesMm00469737_m1
Sequence-based reagentTaqman Assay - Mouse Adck4Life technologiesMm00505363_m1
Sequence-based reagentTaqman Assay - Mouse Atf4Life technologiesMm00515325_m1
Sequence-based reagentTaqman Assay - Mouse MycLife technologiesMm00487804_m1
Sequence-based reagentTaqman Assay - Mouse Coq2Life technologiesMm01203260_g1
Sequence-based reagentTaqman Assay - Mouse Coq4Life technologiesMm00618552_m1
Sequence-based reagentTaqman Assay - Mouse Coq5Life technologiesMm00518239_m1
Sequence-based reagentTaqman Assay - Mouse Coq7Life technologiesMm00501587_m1
Sequence-based reagentTaqman Assay - Mouse FdpsLife technologiesMm00836315_g1
Sequence-based reagentTaqman Assay - Mouse GabpaLife technologiesMm00484598_m1
Sequence-based reagentTaqman Assay - Mouse Hmgcs1Life technologiesMm01304569_m1
Sequence-based reagentTaqman Assay - Mouse HmgcrLife technologiesMm01282499_m1
Sequence-based reagentTaqman Assay - Mouse Mterf4Life technologiesMm00508298_m1
Sequence-based reagentTaqman Assay -Mouse Nrf1Life technologiesMm00447996_m1
Sequence-based reagentTaqman Assay - Mouse Pdss1Life technologiesMm00450958_m1
Sequence-based reagentTaqman Assay - Mouse Pdss2Life technologiesMm01190168_m1
Sequence-based reagentTaqman Assay - Mouse Ppargc1Life technologiesMm00447183_m1
Sequence-based reagentTaqman Assay - Mouse PolrmtLife technologiesMm00553272_m1
Sequence-based reagentTaqman Assay - Mouse TfamLife technologiesMm00627275_m1
Sequence-based reagentTaqman Assay - Mouse Peo1/TwnkLife technologiesMm00467928_m1
Commercial assay or kitmiRNeasy Mini kitQiagenCat#217004
Commercial assay or kitRibo-Zero rRNA removal kitIlluminaMRZH11124
Commercial assay or kitTru-Seq Sample preparationIlluminaRS-122–2002
Commercial assay or kitHigh Capacity cDNA revese transcription kitApplied BiosystemsCat#4368814
Commercial assay or kitTaqMan Universal PCR Master Mix, No Amperase UNGApplied BiosystemsCat#4324020
Commercial assay or kitCitrate Synthase Assay KitSigma-AldrichCat#CS0720
Chemical compound, drugEDTA-free complete protease inhibitor cocktailRocheCat#05056489001
Chemical compound, drugPhosSTOP tabletsRocheCat#04906837001
Chemical compound, drugPercollGE HeathcareCat#17-0891-02
Chemical compound, drugTrypsin goldPromegaCat#V5280
Chemical compound, drugStandard Coenzyme Q9Sigma-AldrichCat#27597
Chemical compound, drugStandard Coenzyme Q10Sigma-AldrichCat#C9538
Chemical compound, drugStandard Glutamate (Glutamic acid)Sigma-AldrichCat#G1251
Chemical compound, drugStandard GlycineSigma-AldrichCat#G7126
Chemical compound, drugStandard ProlineSigma-AldrichCat#P0380
Chemical compound, drugStandard SarcosineSigma-AldrichCat#S7672
Chemical compound, drugStandard SerineSigma-AldrichCat#S4500
Software, algorithmCytoscape v. 3.5.0Shannon et al., 2003http://www.cytoscape.org
RRID:SCR_003032
Software, algorithmDESeq2 package R v. 3.3.2OtherLove et al. (2014)
Software, algorithmIngenuity Pathway Analysis - Ingenuity SystemsQiagenwww.ingenuity.com
RRID:SCR_008653
Software, algorithmiRegulon v. 1.3Janky et al., 2014http://iregulon.aertslab.org/download.html
Software, algorithmMaxQuant v. 1.5.2.8Cox and Mann, 2008http://www.coxdocs.org/doku.php id=maxquant:start
RRID:SCR_014485
Software, algorithmR - The R project for Statistical Computinghttps://www.r-project.org
RRID:SCR_001905
Software, algorithmPerseusCox and Mann, 2012http://www.coxdocs.org/doku.php?id=perseus:start
Software, algorithmTargetP v. 1.1Emanuelsson et al., 2000; Nielsen et al., 1997


http://www.cbs.dtu.dk/services/TargetP/
Other1.9 mm ReproSil-Pur 120 C18-AQ mediaDr. MaischCat#r119.aq
Other25 cm, (75 mm internal diameter) PicoFrit analytical columnNew ObjectiveCat#PF7508250

Additional files

Supplementary file 1

Comparative analysis of mitoproteomic data from heart of Tfam, Twnk, Polrmt, Lrpprc and Mterf4 knockout mice and corresponding controls.

https://doi.org/10.7554/eLife.30952.033
Supplementary file 2

Analysis of mitoproteomic data from heart at different ages of Lrpprc knockout mice and controls.

https://doi.org/10.7554/eLife.30952.034
Supplementary file 3

Analysis of mitoproteomic data from heart at different ages of control mouse strains.

https://doi.org/10.7554/eLife.30952.035
Supplementary file 4

Analysis of total cellular transcriptome from heart of Tfam, Twnk, Polrmt, Lrpprc and Mterf4 knockout and control mouse strains at different ages.

https://doi.org/10.7554/eLife.30952.036
Supplementary file 5

Number of biological replicates and p values of qRT-PCR, metabolomic analyses and enzyme activity measurements.

https://doi.org/10.7554/eLife.30952.037
Supplementary file 6

iRegulon analysis of RNA-Seq data of total RNA from hearts of end-stage conditional knockout mice.

https://doi.org/10.7554/eLife.30952.038
Supplementary file 7

Analysis of proteomic bias in mitoproteomics data from heart of Tfam, Twnk, Polrmt, Lrpprc and Mterf4 knockout mice and corresponding controls.

https://doi.org/10.7554/eLife.30952.039
Supplementary file 8

Complete set of differential expression proteomic analysis in heart of the five knockout mouse strains and according controls; boxplots of the intensity detected by mass spectrometry per protein.

https://doi.org/10.7554/eLife.30952.040
Supplementary file 9

Complete set of sequential mitoproteomic changes at different time points of progressive mitocondrial dysfunction in heart of one knockout mouse strain.

Time curves of differential expression analysis of each protein on the Lrpprc knockout analysis at different ages.

https://doi.org/10.7554/eLife.30952.041
Transparent reporting form
https://doi.org/10.7554/eLife.30952.042

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