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A three‐way proteomics strategy allows differential analysis of yeast mitochondrial membrane protein complexes under anaerobic and aerobic conditions
Author(s) -
Helbig Andreas O.,
de Groot Marco J. L.,
van Gestel Renske A.,
Mohammed Shabaz,
de Hulster Erik A. F.,
Luttik Marijke A. H.,
DaranLapujade Pascale,
Pronk Jack T.,
Heck Albert J. R.,
Slijper Monique
Publication year - 2009
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200800951
Subject(s) - anaerobic exercise , biology , respiratory chain , biochemistry , proteome , protein subunit , mitochondrion , mitochondrial respiratory chain , yeast , inner mitochondrial membrane , proteomics , gene , physiology
To investigate the effect of anaerobiosis on the Saccharomyces cerevisiae mitochondrial proteome and the formation of respiratory chain and other protein complexes, we analyzed mitochondrial protein extracts that were enriched from lysates of aerobic and anaerobic steady‐state chemostat cultures. We chose an innovative approach in which native mitochondrial membrane protein complexes were separated by 1‐D blue native PAGE, which was combined with quantitative analysis of each complex subunit using stable isotope labeling. LC‐FT(ICR)‐MS/MS analysis was applied to identify and quantify the mitochondrial proteins. In addition, to establish if changes in mitochondrial complex composition occurred under anaerobiosis, we investigated the 1‐D blue native PAGE protein migration patterns by Pearson correlation analysis. Surprisingly, we discovered that under anaerobic conditions, where the yeast respiratory chain is not active, the respiratory chain supercomplexes, such as complex V dimer, complex (III) 2 (IV) 2 and complex (III) 2 (IV) were still present, although at reduced levels. Pearson correlation analysis showed that the composition of the mitochondrial complexes was unchanged under aerobic or anaerobic conditions, with the exception of complex II. In addition, this latter approach allowed screening for possible novel complex interaction partners, since for example protein Aim38p, with a yet unknown function, was identified as a possible component of respiratory chain complex IV.