Researchers in Freiburg and Bonn provide the first comprehensive mapping of the protein machineries in the mitochondria, the powerhouses of the cell
Mitochondria are membrane-enclosed structures found in all cells of higher organisms, where they produce most of the necessary energy ("powerhouses of the cell"). In addition, these organelles serve important functions in the synthesis and degradation of certain biomolecules as well as in numerous intercellular signaling processes. In close collaboration, a team of researchers led by Nikolaus Pfanner and Bernd Fakler from the University of Freiburg Institutes of Biochemistry and Physiology, respectively, and by Thomas Becker from the Institute of Biochemistry at the University of Bonn have now applied a newly developed analytical method to comprehensively map the structural organization of proteins in mitochondria. The results provide initial insight into the structure and organization of the mitochondrial proteins in protein machineries of varying complexity, thus laying the foundation for future studies of new protein functions and structures. This study was published in the journal Nature.
Comprehensive picture of the composition of protein complexes indispensable
The mitochondria of baker’s yeast (Saccharomyces cerevisiae) contain around 1000 different proteins. It has already been demonstrated that several of these proteins perform their function only in close cooperation with other proteins, in so-called protein complexes. For the majority of the proteins, however, little was known about how they are organized in complexes or more dynamic structures. A comprehensive picture of the composition of these protein complexes is indispensable for understanding the mechanisms and interrelations that enable mitochondria to perform their many biological functions with the high precision and reliability for which they are known.
To conduct their analyses, the researchers applied a method they developed for high-resolution complexome analysis. This method involves first separating protein complexes in intact form according to their size in a gel, which is then deep frozen and cut into 0.3-millimeter-thick slices. The researchers can then identify and quantitatively analyze all proteins contained in the slices by means of mass spectrometry. The protein profiles thus created, collectively termed MitCOM (for mitochondrial complexome) by the researchers, yielded the most comprehensive and accurate dataset to date of the quantitative size distribution of more than 90 percent of the mitochondrial proteins. "The analysis of MitCOM demonstrated that more than 99 percent of all mitochondrial proteins are organized in multiple complexes, in average 7 per protein," says Dr. Uwe Schulte , lead author of the study. "That is a significantly higher degree of complexity than previously assumed." This complexity does not seem to depend on the biochemical properties of the individual proteins but mainly on their function and localization in mitochondrial structures.
In a second step, the researchers took advantage of the enormously large dynamic range of MitCOM to elucidate previously unknown links between several signaling pathways and to explain new mechanisms for the control of protein import in mitochondria. "MitCOM showed us interactions between proteins and the TOM complex that together are responsible for the quality control of protein import," explains Pfanner.
The MitCOM data are therefore a unique resource that will doubtlessly provide impetus for more exciting discoveries in mitochondria research. And yet, mitochondria are only the beginning: "The method of complexome analysis can be transferred directly to other organelles and cell compartments and will presumably give us many more insights into evolutionary creativity," explains Fakler, whose team works primarily on the rapid transmission of signals to cell membranes.
Schulte, U., den Brave, F., Haupt, A., Gupta, A., Song, J., Müller, C.S., Engelke, J., Mishra, S., Mårtensson, C., Ellenrieder, L., Priesnitz, C., Straub, S.P., Doan, K.N., Kulawiak, B., Bildl, W., Rampelt, H., Wiedemann, N., Pfanner, N., Fakler, B., and Becker, T. (2023): Mitochondrial complexome reveals quality control pathways of protein import. In: Nature. https://doi.org/10.1038/s41586’022 -05641-w
Bernd Fakler, Nikolaus Pfanner, and Uwe Schulte are members of the Cluster of Excellence CIBSS - Centre for Integrative Biological Signalling Studies
Profiles of the subunits of individual complexes (top) and overall representation of all around 5200 protein signals in MitCOM. Source: AG Fackler/Pfanner/Becker