SILAC-based complexome profiling dissects the structural organization of the human respiratory supercomplexes in SCAFIKO cells

Complexome Profiling: Assembly and Remodeling of Protein Complexes

“…The aim of each complexome profiling experiment is to gain information of native protein complexes and to compare the appearance and abundance of assemblies under different conditions or in disease states. Biological samples for CP range from bacteria [39,40], yeast [41] or cell culture [4,[17][18][19]21,36,[42][43][44][45][46][47][48][49][50][51], tissue or organ specimens from patients and animals [17,19,37,38,52,53] to plants [54][55][56][57][58][59][60][61][62]. Biochemical preparations of subcellular fractions (e.g., mitochondria, microsomes) reduce sample complexity for a more in depth complexome analysis [17,51].…”

“…Assembly of protein complexes [70] or even further association of several protein complexes require a coordinated process with the help of chaperons also called assembly factors. In recent years, classical CP became a very popular tool to study the significance of individual subunits and assembly factors of the OXPHOS complexes in bacteria [39,40,61] and mitochondria from mammals [17,21,22,27,28,36,[41][42][43][44][45][46][47][48][49][50]53,[64][65][66] and plants [54][55][56][57]60,62].…”

“…As all fragments from each gel lane or density gradients have to be measured in single MS runs, such approaches need extensive machine time and the data from several separation gradients have to be merged. The introduction of metabolic labels in SILAC-based CP allows direct comparison of protein migration and the abundance of two or three different samples in one native gel lane [21,65]. Although this duplex approach introduces more complexity in data analysis, the advantage is a precise annotation of the differences in the complexes between two different conditions.…”

“…This review provides a concise survey on the complexome profiling method and applications to elucidate composition and dynamics of macromolecular complexes. Additional combinations with stable isotope labeling of amino acids in cell culture (SILAC) [21] and tandem mass tag labeling (TMT) [22] recently expanded the spectrum of applications. As comprehensive CP data sets contain more information than addressed in the initial publication, complexome profiles are rich in untapped accessible data uploaded to repositories for additional investigations by the scientific community.…”

Looking Back to the Future of Mitochondrial Research

“…An important question is the role of the supercomplex assembly factor SCAF1, which has been shown to promote supercomplex formation between CIII and IV (III 2 IV) and contribute to "branching" of the respiratory chain (Calvo et al, 2020). This topic is generating a very lively discussion that is likely to continue in the future (Mourier et al, 2014;Enríquez, 2016;Milenkovic et al, 2017;Lobo-Jarne et al, 2018;García-Poyatos et al, 2020;Protasoni et al, 2020;Fernández-Vizarra et al, 2021).…”