bioRxiv preprint doi: https://doi.org/10.1101/860080; this version posted November 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Mass-spectrometry based proteomics reveals mitochondrial supercomplexome 2 plasticity 3 4 Alba Gonzalez-Franquesa1, Ben Stocks1, Sabina Chubanava1, Helle Baltzer Hattel2, Roger 5 Moreno-Justicia1, Jonas T. Treebak1, Juleen R. Zierath1,3, Atul S. Deshmukh1,2,4* 6 1Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 7 Copenhagen 2200, Denmark. 2Novo Nordisk Foundation Center for Protein Research, 8 University of Copenhagen, Copenhagen 2200, Denmark. 3Integrative Physiology, 9 Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 77, 10 Sweden. 4Lead Contact *Correspondence: [email protected] 11 12 Summary: 13 Mitochondrial respiratory complex subunits assemble in supercomplexes. Studies of 14 supercomplexes have typically relied upon antibody-based protein quantification, often 15 limited to the analysis of a single subunit per respiratory complex. To provide a deeper 16 insight into mitochondrial and supercomplex plasticity, we combined Blue Native 17 Polyacrylamide Gel Electrophoresis (BN-PAGE) and mass spectrometry to determine the 18 supercomplexome of skeletal muscle from sedentary and exercise-trained mice. We 19 quantified 422 mitochondrial proteins within ten supercomplex bands, in which we showed 20 the debated presence of complex II and V. Upon exercise-induced mitochondrial biogenesis, 21 non-stoichiometric changes in subunits and incorporation into supercomplexes was 22 apparent. We uncovered the dynamics of supercomplex-related assembly proteins and 23 mtDNA-encoded subunits within supercomplexes, as well as the complexes of ubiquinone 24 biosynthesis enzymes and Lactb, a mitochondrial-localized protein implicated in obesity. 25 Our approach can be applied to broad biological systems. In this instance, comprehensively 26 analyzing respiratory supercomplexes illuminates previously undetectable complexity in 27 mitochondrial plasticity. 28 29 Highlights: 30 • Comprehensive quantification of respiratory subunits within supercomplexes 31 • Complex II and V assemble within supercomplexes 32 • Mitochondrial-encoded subunits display elevated upregulation upon exercise training bioRxiv preprint doi: https://doi.org/10.1101/860080; this version posted November 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 33 • Exercise increases ubiquinone biosynthesis enzyme complexes 34 35 Keywords: mitochondrial respiratory complexes, mitochondrial supercomplexes, oxidative 36 phosphorylation, protein complexes, complexome, exercise 37 2 bioRxiv preprint doi: https://doi.org/10.1101/860080; this version posted November 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 38 Introduction 39 Energy production through oxidative phosphorylation is the primary function of mitochondria. 40 Oxidative phosphorylation is the process by which adenosine triphosphate (ATP) is formed 41 via the transfer of electrons through the electron transport system. The electron transport 42 system is composed of four respiratory complexes (CI to CIV) coupled with ATP-synthase 43 complex (CV). Electrons from the electron carriers NADH and FADH2, which are reduced 44 during glycolysis, tricarboxylic acid cycle and beta-oxidation, enter the electron transport 45 system via CI and CII, respectively. Electrons flow through coenzyme Q/ubiquinone, CIII, 46 cytochrome c, and CIV, resulting in pumping of protons into the intermembrane space. The 47 resultant chemiosmotic proton-motive force is used by CV to generate ATP from ADP. Thus, 48 mitochondria play an essential role in cellular metabolism. 49 50 The organization of the electron transport system has long been debated, with several 51 models proposed. The random-collision model or fluid model stated that individual 52 respiratory complexes are free to diffuse within the inner mitochondrial membrane 53 (Hackenbrock et al., 1986). Later, the solid model, in which complexes were rigidly 54 superassembled into supercomplexes, was proposed (Schagger and Pfeiffer, 2000). 55 Presently accepted is the plasticity model, which takes into account the co-existence of both 56 organisations. In this model, respiratory complexes can dynamically exist in isolation and as 57 supercomplexes depending upon the metabolic requirements of the cell (Acin-Perez et al., 58 2008). Furthermore, functional respiration in CI-III-IV-containing respirasomes has been 59 confirmed (Acin-Perez et al., 2008; Schagger and Pfeiffer, 2000). Supercomplexes are 60 highly conserved and have been identified in several kingdoms of living organisms (i.e., 61 plants, algae, fungi, protozoa and animals) (reviewed in (Chaban et al., 2014)). The 62 organization of supercomplexes is crucial for individual subunit-complex stability (Acin- 63 Perez et al., 2008), but is also important to reduce ROS production by facilitating electron 64 transport across the complexes (Genova and Lenaz, 2014). Clinically, individuals with 65 genetic mutations in mitochondrial respiratory CI (Ugalde et al., 2004) and CIII (Acin-Perez 66 et al., 2004) present disturbances in supercomplex assembly and stability. Moreover, 67 decreased CI-, CIII- and CIV-containing supercomplexes and mitochondrial respiration have 68 been observed in people with type 2 diabetes (Antoun et al., 2015) and rodent models of 69 aging (Lombardi et al., 2009). CIII and CIV assembly into supercomplexes has also been 3 bioRxiv preprint doi: https://doi.org/10.1101/860080; this version posted November 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 70 correlated to substrate utilization and maximal oxygen uptake in humans (Greggio et al., 71 2017). Hence, respiratory supercomplex formation/dynamics is a physiologically and 72 clinically relevant process. 73 74 The formation and plasticity of supercomplexes remain unclear, primarily due to limitations 75 in methodological approaches. Techniques to study respiratory supercomplex formation 76 have typically relied upon Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) 77 coupled to antibody-based detection techniques (i.e., oxidative phosphorylation cocktail 78 antibody), often covering only a single subunit per complex. However, this approach 79 provides limited information, relying upon a single subunit to provide representative 80 information regarding complex incorporation into supercomplexes. In the absence of 81 additional targeted analyses, these conventional approaches may also disregard the 82 influence of additional proteins present within supercomplexes, including assembling factors 83 and soluble electron carriers. To date, different studies have combined one- or two- 84 dimensional BN-PAGE with mass spectrometry to study individual mitochondrial respiratory 85 complexes using MALDI-TOF (Farhoud et al., 2005; Sun et al., 2003) or tandem LCMS/MS 86 (Fandino et al., 2005; Wessels et al., 2009). Furthermore, a BN-PAGE LCMS/MS approach 87 was used to cut high-molecular weight sections (not individual bands) to either validate 88 immunoblotting analyses (Greggio et al., 2017) or decipher the composition of individual 89 complexes through agglomerative clustering based on profile-similarity, namely 90 complexome profiling (Guerrero-Castillo et al., 2017; Heide et al., 2012; Van Strien et al., 91 2019). Thus, while these studies have established a workflow from BN-PAGE to mass 92 spectrometry, this technique has yet to be applied to the analysis of individually targeted 93 supercomplexes. 94 95 Mitochondria are highly plastic organelles, rapidly adapting to the metabolic demands of the 96 cell. Exercise training is a potent stimulus to increase mitochondrial respiration within 97 skeletal muscle (Holloszy, 1967) and, therefore, provides an ideal stimulus to study 98 mitochondrial plasticity and supercomplex formation. Using antibody-based detection, 99 supercomplex formation was recently shown to increase within skeletal muscle following 100 exercise training in humans (Greggio et al., 2017). Altered stoichiometry of respiratory 101 complexes within supercomplexes, particularly a redistribution of CI, CIII, and CIV into 4 bioRxiv preprint doi: https://doi.org/10.1101/860080; this version posted November 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 102 supercomplexes was identified following exercise training (Greggio et al., 2017). Thus, 103 endurance exercise provides an ideal model to study plasticity in mitochondrial 104 supercomplexes. 105 106 In this study we applied an antibody-independent methodology that couples BN-PAGE and 107 LCMS/MS to assess the mitochondrial supercomplexome. Particularly, we utilize exercise 108 training in murine skeletal muscle to study mitochondrial plasticity and supercomplex 109 formation. 110 111 Results and discussion 112 Exercise increases mitochondrial respiratory protein subunits in a non- 113 stoichiometric