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Quantitative analysis of the mitochondrial proteome and
phosphoproteome in the yeast Saccharomyces cerevisiae
Claire LEMAIRE
CNRS-UMR8221, CEA-IBITECS, Université Paris-Sud, I2BC, F-91191 Gif-sur-Yvette, FRANCE.
July 14th 2015 International Summit on Current Trends in Mass Spectrometry 2015
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Mitochondrial respiratory chain complexes
2
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3
Mitochondrion: an essential organelle
http://conceptcours.fr/www/term_s/spe/energie
External membrane Cristae
Internal membrane Matrix
Essential function: energy production
Mitochondrion
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4
OXPHOS
The mitochondrial respiratory chain complexes (OXPHOS)
http://conceptcours.fr/www/term_s/spe/energie
External membrane Cristae
Internal membrane (IM) Matrix
Variations among the metabolism of the cell
I II III IV V
IM
Matrix
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5
The mitochondrial respiratory chain complexes (OXPHOS)
Dysregulation
Pathologies
I II III IV V
Metabolic demand/various stresses, adjustement of the activity
IM
Matrix
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Levels of regulation
6
Change in the expression level of proteins
Reversible interaction with effectors
Post-translational modifications
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Post-TranslationalModifications
7
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Post-TranslationalModifications
Glycosylation Ubiquitination
Phosphorylation
S-Nitrosylation
Methylation
N-Acetylation
Lipidation
SUMOylation
8
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Importance of protein regulation by phosphorylation
9
Phosphorylation
Functionalproperties
Cellular localization
Interaction with partners
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10
Phosphorylation
Pathologies
Link between phosphorylation and pathologies
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11
Phosphorylation
Pathologies
Link between phosphorylation and pathologies
Abnormal phosphorylation events
Cancers and neurodegenerative diseases (Alzheimer’s, Parkinson’s or Huntington’s disease)
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12
Pathologies
Mitochondria
In human, dysregulation of mitochondrial functions, particularly of the respiratory chain are associated with different pathologies (neurodegenerative, neuromuscular, cardiovascular diseases for example)
Link between mitochondria and pathologies
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13
Phosphorylation
Pathologies
Mitochondria
?- Few data
(cellular extracts) - Qualitative
Link between mitochondria and phosphorylation?
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14Data on phosphorylation in mitochondria: Reproducible Quantitative Obtained in different physiological conditions variations
Phosphorylation
Pathologies
Mitochondria
?
Link between mitochondria and phosphorylation?
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15
I – General strategy
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16
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
m/z
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
m/z
Identification and quantification of proteins accumulation and
phosphorylation level in well-defined physiological states
Mass spectrometrySTRATEGY
I1
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17
Ser, Thr , Tyr
STRATEGY
I
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
m/z
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
m/z
Identification and quantification of proteins accumulation and
phosphorylation level in well-defined physiological states
Mass spectrometry
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18
Ser, Thr , Tyr Glu, Asp
Site-directed mutagenesis
Permanent phosphorylated state
STRATEGY
I
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
m/z
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
m/z
Identification and quantification of proteins accumulation and
phosphorylation level in well-defined physiological states
Mass spectrometry
2
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19
Ser , Thr Ala Tyr Phe
Permanent dephosphorylated state
STRATEGY
I
Ser, Thr , Tyr Glu, Asp
Site-directed mutagenesis
Permanent phosphorylated state-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
m/z
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
m/z
Identification and quantification of proteins accumulation and
phosphorylation level in well-defined physiological states
Mass spectrometry
2
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20Structural and functional analysis of the respiratory complexes
Ser , Thr Ala Tyr Phe
Permanent dephosphorylated state
Ser, Thr , Tyr Glu, Asp
Site-directed mutagenesis
Permanent phosphorylated state-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
m/z
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:-
400 450 500 550 600 650 700 750 800 850 900 950 1000m/z0
100
%
1:580.24
779.27
773.34
729.33
556.91
417.93
523.73
511.25418.19
474.74
463.18
418.44461.21
495.21
556.57
528.22
557.23
580.75
694.26
674.30
612.74581.24
597.74654.27
640.27639.94
629.23
694.77
703.81
704.34
728.77
756.29
779.81
959.40916.91780.30
916.33801.38 837.37
836.89
820.32
872.42 902.43872.93
948.48917.36
947.42
923.32
959.95
960.39
967.34
968.36
989.39
m/z
Identification and quantification of proteins accumulation and
phosphorylation level in well-defined physiological states
Mass spectrometrySTRATEGY
I
3
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II – Biological study model : the yeast Saccharomyces cerevisiae
21
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22
Facultative aerobe study of various physiological states, dependent on culture conditions
WT Respiratory mutant
Fermentescible medium(glucose, galactose)
Respiratory medium(Lactate)
Molecular genetics techniques
Complete sequenced genome
Numerous homologies with the human respiratory chain
STUDY
MODEL
IISaccharomyces cerevisiae
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III – First aim
23
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Quantitative variations of the mitochondrial proteome and
phosphoproteome during fermentative and respiratory
growth in Saccharomyces cerevisiae
Renvoisé et al. , J Proteomics (2014) 106, 140-150 24
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IV -Methodology
25
METHODOLOGY
IV
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26
A B C
Growth in three conditions
Mitochondria purification
Protein quantification by LC-MS/MS
Respiration(Lactate)
Fermentation(Glucose)
Fermentation(Galactose)
A B C
Metabolism
(Substrate)
4 independant biological replicates for each of the 3 growth conditions
Trypsin digestion
1
2
3
METHODOLOGY
IV
software developed by the PAPPSO Platform/ Gif-sur-Yvette/ France
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27
Mix the 3 samples in 1:1:1ratio
CH2O CD2O 13CD2O
Multiplex stable isotope dimethyl labeling (Boersema et al., Nat Protoc., 2009)
Strong Cation Exchange Chromatography (SCX)
Affinity Chromatography (IMAC)
Phosphopeptides quantification by LC-MS/MS
Enrichment in
Phosphopeptides
Labeling Efficiency:93-97,7%
4
5
Trypsic peptides
6
7
METHODOLOGY
IV
Primary amines Formaldehyde Cyanoborohydride
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V – Results
28
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V-1- Proteomic results
29
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Variations of mitochondrial protein abundances
30
176(32%)
368(68%)
significative variationno variation
544 mitochondrial proteins quantified(only peptides quantified in at least 3 replicates/condition were keptOnly proteins quantified with at least two peptides were kept)
PROTEOMICS
V-1
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Significant changes of protein abundances according to the substrate
31
Cluster168 proteins
Cluster233 proteins
Cluster349 proteins
Cluster426 proteins
1 2 3
3: Lactate
1: Glucose
2: Galactose
PROTEOMICS
V-1
1st groupClassification:2 major groups
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Cluster168 proteins
Cluster233 proteins
Cluster349 proteins
Cluster426 proteins
1 2 3
1 2 3
1 2 3
Significant changes of protein abundances according to the substrate
3: Lactate
1: Glucose
2: Galactose
PROTEOMICS
V-1
2nd group
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33
Cluster168 proteins
Cluster233 proteins
Cluster349 proteins
Cluster426 proteins
1 2 3
1 2 3
1 2 3
Significant changes of protein abundances according to the substrate
3: Lactate
1: Glucose
2: Galactose
PROTEOMICS
V-1
1 2 3
Differences glucose vs galactose
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Conclusions
34
This study allows ,for the first time, an overall comparison of mitochondrial protein abundances in fermentation and respiration
Differences between the two fermentative substrates (glucose and galactose) are highlighted
Galactose could be considered as a substrate displaying an intermediate metabolism between fermentation and respiration
respiro-fermentative substrate
PROTEOMICS
V-1
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V-2 Phosphoproteomic results
35
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670 phosphosites
Phosphosites selection
LC-MS/MS identification
PHOSPHOROTEOMICS
V-2
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670 phosphosites
650 (97%)
Phosphosites selection LC-MS/MS
identification
LC-MS/MS quantification
PHOSPHOROTEOMICS
V-2
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670 phosphosites
650
330 (49%)
LC-MS/MS identification
LC-MS/MS quantification
Present in at least3 replicates
Phosphosites selection
PHOSPHOROTEOMICS
V-2
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LC-MS/MS identification670
phosphosites
650
330
289(43%)
LC-MS/MS quantification
Normalization according to protein abundance
Phosphosites selection
PHOSPHOROTEOMICS
V-2
Present in at least3 replicates
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Variations of mitochondrial protein phosphorylation
40
289 mitochondrial phosphosites quantified, of which 214 were new
90(31%)
199(69%)
significative variationno variation
PHOSPHOROTEOMICS
V-2
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Variations of mitochondrial protein phosphorylation
41
90 mitochondrial phosphosites quantified with significative variation
1 condition
2 conditions
3 conditions9
42
39
PHOSPHOROTEOMICS
V-2
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Significant changes of phosphorylation according to the substrate
42
Cluster P316 sites
Cluster P28 sites
Cluster P45 sites
Cluster P17 sites
Cluster P5
3 sites
1 2 3
39 varying phosphosites quantified in the 3 conditions
PHOSPHOROTEOMICS
V-2
1 2 3
1 2 3
1 2 3
Clusters P1 to P4 : same pattern as clusters 1 to 4
Classification
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Significant changes of phosphorylation according to the substrate
43
Cluster P316 sites
Cluster P28 sites
Cluster P45 sites
Cluster P17 sites
Cluster P5
3 sites
PHOSPHOROTEOMICS
V-2
Additional cluster P5: specific regulation in galactose
1 2 3
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300 mitochondrial proteins were identified as phosphorylated ≈ 30% mitochondrial proteins
289 phosphorylation sites were quantified of which 214 were new significant enlargement of the yeast mitochondrial phosphosites map
1/3 of the phosphorylation sites varies from the 3 culture conditions tested (glucose, galactose, lactate)
Specific regulation seems to occur in galactose (respiro-fermentative medium)
Conclusions PHOSPHOROTEOMICS
V-2
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Variations of mitochondrial protein abundances and protein phosphorylation
according to their metabolic pathways
Proteins associated with metabolic pathways according to the MIPS functional classification ( http:// mips.helmholtz-muenchen.de)
Conclusion: The most regulated metabolic pathway at both proteomic and phosphoproteomic levels is energy metabolism
UnknownTransport
TranscriptionProtein synthesis
Protein fateNucleotide metabolism
Mitochondria biogenesisMetabolism of vitamins, cofactors and prosthetic groups
Lipid metabolismEnergy
Cell rescue, defense and virulenceCell cycle and DNA processing
C-compound and carbohydrate metabolismAmino acid metabolism
0 10 20 30 40 50 60 70
Proteins
Phosphosites
Number
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OXPHOS proteins
46
OXPHOS
31 OXPHOS proteins were reproducibly quantified in the 3 growth conditions and showed different abundances according to the condition
19 of these proteins were phosphorylated, displaying 37 phosphosites
important role of phosphorylation in the regulation of the respiratory chain
For most of them, proteins were more abundant and more phosphorylated in lactate medium (respiratory condition) except for 2 proteins
C II (CIII)
2
(CIV)2 CV
matrix
Intermembranary space
NDI1
NDE1Innermembrane
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In progress
47
Ser, Thr , Tyr Glu, Asp
Site-directed mutagenesis
Permanent phosphorylated state
2
Ser , Thr Ala Tyr Phe
Structural and functional analysis of the respiratory complexes
Permanent dephosphorylated state
3
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Acknowledgements
48
The team « Regulation of mitochondrial energy-transducing complexes »
Francis Erwan
Elodie
Mehdi Qian
Deborah
Margaux Claire
Tiona
Francis ErwannBoscoLaurélie
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Acknowledgements
49
SBIGEM, Saclay
Gwenaëlle Le RouxChristophe Carles
Financial support and encouragements: Bruno Robert, head of department B3S
Thank you for your attention
Michel ZivyLudovic BonhommeMarlène Davanture
Benoit ValotThierry Bailleau
I.B.G.C. ,Bordeaux
Marie-France GiraudDaniel Brèthes
Isabelle Larrieu
Anne DevinMichel Rigoulet
Ohio State UniversityColumbus, U.S.A.
Patrice Hamel
Collaborations
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75%
11%
8%2%
4%
mitochondriapolysomescytoplasmenucleusothers
Cellular localization of the 724 proteins identified
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Median
Maximum
Minimum
1:50%
2:50%
1Q
2Q
3Q
4Q
Q : quartile
.
.
Middle of 1
Middle of 2
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Q : quartile
Median
Maximum
Minimum
1:50%
2:50%
1Q
2Q
3Q
4Q ..
Middle of 1
Middle of 2
outlier
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Variations of mitochondrial protein abundances and protein phosphorylation
according to their metabolic pathways
55
Proteins associated with metabolic pathways according to the MIPS functional classification ( http:// mips.helmholtz-muenchen.de)
Conclusion: The most regulated metabolic pathway at both proteomic and phosphoproteomice levels is energy metabolism
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Localization of phosphorylation sites on yeast OXPHOS proteins
56
C II (CIII)2 (CIV)2 CV
matrix
Intermembranary space
NDI1
SDH2 RIP1
NDE1Innermembrane
SDH1
COR1
ATP2
INH1
OXPHOS
Globally, the level of phosphorylation varied in the same direction as protein amounts, except for 2 proteins (Rip1 and Atp2)
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Stable Isotope Dimethyl labeling of trypsic peptides
RegularFormaldehyde/ cyanoborohydride
DeuteredFormaldehyde/cyanoborohydride
Deutered and C13-labeledFormaldehyde/ cyanoborodeuteride
Reaction of peptide primary amines with formaldehyde - base Schiff, reduced by addition of cyanoborohydride
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- SILAC: stable isotope labeling by amino acids in cell culture cells are grown in culture media lacking essential (auxotrophic) amino acid(s). These amino acids are then supplied in either their natural form or in a stable isotope form to cause in vivo incorporation of the labeled amino acid(s). The differentially labeled samples are mixed and digested with a protease (most often trypsin) to obtain samples that can be readily analyzed by the mass spectrometer.
- iTRAQ : isobaric tagging for relative and absolute quantification
The ITRAQ method is based on the covalent labeling of the N-terminus and side chain amines of peptides from protein digestions with tags of varying mass. There are currently two mainly used reagents: 4-plex and 8-plex,
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- Labeled peptides were dried by vacuum centrifugation and re-suspended in ACN/H2O:30/70, 0.5% formic acid, pH2- Sample fractionation by strong cation exchange chromatography(Bonhomme et al. , Mol Cell Proteomics, 2012, 11,957-972) using a Zorbax BioSCX-Series II column on a Ultimate LC system combined with a Famos autosampler and a Switchos II microcolumn switch system (LC packings)- Samples automatically collected to form 12 fractions- Each fraction was dried by vacuum centrifugation and re-suspended in ACN/H2O:30/70, 250mM acetic acid- Incubation with Phos-select affinity gel during 1H- Washed in SigmaPrep spin column 2 fold with ACN/H2O:30/70, 250mM acetic acid- Elution of phosphopeptides in SigmaPrep spin column with ACN/H2O:30/70, 0.4M ammonium hydroxideEnrichment very effective :24% phosphorylated peptides (non-enriched samples: 4 phosphopeptides)88% of unphosphorylated peptides contained one ASP or GLU - limit of IMAC methodology (strong affinity for acidic peptides)
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Phosphoproteomic analysis
62
The phosphopeptides were identified in 299 proteins of which :
- 150 displayed 1 site of phosphorylation- 72 displayed 2 sites of phosphorylation- 27 displayed 3 sites of phosphorylation- 50 displayed 4 sites of phosphorylation or more
- 71% serine- 16% threonine- 0.6% tyrosine- 12.6% not precisely localized in the peptide sequence