Evolutionary tuning of a cellular ’power plant’

Protein profiles generated by mass spectrometry, referred to as MitCOM. Source: Protein profiles generated by mass spectrometry, referred to as MitCOM. Source: AG Fackler/Pfanner/Becker

Researchers from Freiburg and Bonn succeed in the first comprehensive description of the protein machines in the mitochondria, the power plants of the cell.

Mitochondria are membrane-enveloped structures found in all cells of higher organisms, where they produce most of the necessary energy ("power plants of the cell"). In addition, these organelles have important functions in the synthesis and degradation of certain biomolecules and in a variety of intracellular signaling processes. In close collaboration, researchers from the Institutes of Biochemistry led by Nikolaus Pfanner and Physiology led by Bernd Fakler at the University of Freiburg and the Institute of Biochemistry at the University of Bonn led by Thomas Becker have now applied a newly developed analytical method to comprehensively map the structural organization of proteins in mitochondria. The results provide the first comprehensive insight into the structure and organization of mitochondrial proteins in protein machines of varying complexity, providing the basis for future studies of new protein functions and structures. This study is currently published in Nature.

Comprehensive picture of the composition of protein assemblies essential

The mitochondria of baker’s yeast (Saccharomyces cerevisiae) contain around 1,000 different proteins. For some proteins, it has already been shown that they fulfill their function only in solid association with other proteins, so-called protein complexes. For the majority of proteins, however, little was known about how they are organized in complexes or more dynamic associations. A comprehensive picture of the composition of these protein assemblies or protein machineries is essential to understand the molecular mechanisms and interactions that enable mitochondria to perform their diverse biological functions with known high precision and reliability.

For their analyses, the researchers used a method they developed for high-resolution complexome analysis. Protein complexes are first separated in intact form according to their size in a gel, which is then cut into slices 0.3 millimeters thick after deep freezing. Mass spectrometry is then used to identify and quantitatively analyze all the proteins contained in the slices. The protein profiles generated in this way, collectively referred to by the researchers as MitCOM (for mitochondrial complexome), yielded the most comprehensive and precise data set to date of the quantitative size distribution of more than 90 percent of mitochondrial proteins. "The analysis of MitCOM showed that more than 99 percent of all mitochondrial protein are organized in complexes with an average of seven partner proteins," said Uwe Schulte , first author of the paper. "This is a significantly higher level of complexity than previously thought. The complexity does not seem to depend on the biochemical properties of the individual proteins, but mainly on their function and localization in mitochondrial substructures.

In a second step, the researchers exploited the enormous dynamic range of MitCOM to elucidate previously unknown connections between several signaling pathways and to decipher new mechanisms for controlling protein import into mitochondria. "MitCOM has shown us interactions of proteins with the TOM complex, which together are responsible for the quality control of protein import," explains Pfanner.

The MitCOM data thus represent a unique resource that will certainly provide impetus for further exciting discoveries in mitochondrial research. Mitochondria are just the beginning. The method of complexome analysis can be directly transferred to other organelles and cell compartments and will probably give us many more insights into evolutionary creativity," explains Fakler, who is working with his colleagues primarily on rapid signal transmission at cell membranes.

Fact Sheet:

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.

Protein profiles generated by mass spectrometry, referred to as MitCOM. Source: AG Fackler/Pfanner/Becker