Integrative analysis of the mitochondrial proteome in yeast.
In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans.
Prokisch
Holger
H
Institute of Human Genetics, GSF National Research Center for Environment and Health, Neuherberg, Germany.
Scharfe
Curt
C
Camp
David G
DG
Xiao
Wenzhong
W
David
Lior
L
Andreoli
Christophe
C
Monroe
Matthew E
ME
Moore
Ronald J
RJ
Gritsenko
Marina A
MA
Kozany
Christian
C
Hixson
Kim K
KK
Mottaz
Heather M
HM
Zischka
Hans
H
Ueffing
Marius
M
Herman
Zelek S
ZS
Davis
Ronald W
RW
Meitinger
Thomas
T
Oefner
Peter J
PJ
Smith
Richard D
RD
Steinmetz
Lars M
LM
D005591:Chemical Fractionation; D002853:Chromatography, Liquid / Q000379:methods; D020869:Gene Expression Profiling; D016678:Genome; D013058:Mass Spectrometry / Q000379:methods; D008928:Mitochondria / Q000502:physiology*; D024101:Mitochondrial Proteins / Q000737:chemistry / Q000378:metabolism* / Q000502:physiology; D010641:Phenotype; D040901:Proteomics / Q000379:methods*; D012680:Sensitivity and Specificity; D015003:Yeasts
D024101:Mitochondrial Proteins