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Anomalous peroxidase activity of cytochrome c is the primary pathogenic target in Barth syndrome

Nature Metabolism volume 5, pages 2184–2205 (2023)Cite this article

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Abstract

Barth syndrome (BTHS) is a life-threatening genetic disorder with unknown pathogenicity caused by mutations in TAFAZZIN (TAZ) that affect remodeling of mitochondrial cardiolipin (CL). TAZ deficiency leads to accumulation of mono-lyso-CL (MLCL), which forms a peroxidase complex with cytochrome c (cyt c) capable of oxidizing polyunsaturated fatty acid-containing lipids. We hypothesized that accumulation of MLCL facilitates formation of anomalous MLCL–cyt c peroxidase complexes and peroxidation of polyunsaturated fatty acid phospholipids as the primary BTHS pathogenic mechanism. Using genetic, biochemical/biophysical, redox lipidomic and computational approaches, we reveal mechanisms of peroxidase-competent MLCL–cyt c complexation and increased phospholipid peroxidation in different TAZ-deficient cells and animal models and in pre-transplant biopsies from hearts of patients with BTHS. A specific mitochondria-targeted anti-peroxidase agent inhibited MLCL–cyt c peroxidase activity, prevented phospholipid peroxidation, improved mitochondrial respiration of TAZ-deficient C2C12 myoblasts and restored exercise endurance in a BTHS Drosophila model. Targeting MLCL–cyt c peroxidase offers therapeutic approaches to BTHS treatment.

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Fig. 1: Electronic and structural rearrangements occurring in MLCL–cyt c peroxidase complexes.
Fig. 2: Simulations reveal close association of M80 with MLCLs driving the opening of the heme-binding pocket.
Fig. 3: Peroxidase activity of the MLCL–cyt c complex causes phospholipid peroxidation in vitro and induces changes in the lipidome and oxy-lipidome of genetically manipulated yeast.
Fig. 4: TAZ deficiency induces changes in the phospholipidome of mouse and human cells and tissues.
Fig. 5: Effect of TPP–IOA on the structure of MLCL–cyt c peroxidase complexes, lipid oxidation.
Fig. 6: TAZ deficiency induces changes in Drosophila endurance and the Drosophila lipidome.
Fig. 7: Bioenergetic characteristics, mitochondrial membrane potential of WT and TAZ-KO cells and the effect of treatment with MLCL–cyt c peroxidase complex inhibitor IOA.

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Data availability

Source data for Figs. 1–7 and Extended Data Figs. 4–8 are provided with the manuscript. Raw flow cytometry data can be accessed from the FlowRepository database (repository ID FR-FCM-Z6XG). MS data are available upon request. Source data are provided with this paper.

Code availability

No custom code was generated for this study.

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Acknowledgements

The study was supported by the National Institutes of Health grant GM134715 (to V.E.K. and M.L.G.), HL117880 (M.L.G.), NS076511 (V.E.K. and H.B.) and AG059683 (R.W.), the Polish National Science Centre (2019/35/D/ST4/02203 to K.M.-R) and the Natural Sciences and Engineering Research Council of Canada (RGPIN/5368-2019 to G.M.H). G.M.H. is the Canada Research Chair in Molecular Cardiolipin Metabolism.

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Authors and Affiliations

  1. Department of Environmental and Occupational Health, Center for Free Radical and Antioxidant Health, School of Public Health, Children’s Neuroscience Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

    Valerian E. Kagan, Yulia Y. Tyurina, Alexander A. Kapralov, Vladimir A. Tyurin, Andrew A. Amoscato, Svetlana N. Samovich, Austin B. Souryavong, Haider H. Dar, Georgy K. Vladimirov, Margarita A. Artyukhova & Jim Peterson

  2. Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Toruń, Poland

    Karolina Mikulska-Ruminska

  3. Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA

    Deena Damschroder & Robert Wessells

  4. Department of Pediatrics, Genetic and Genomic Medicine Division, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA

    Eduardo Vieira Neto & Jerry Vockley

  5. Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands

    Alessia Lasorsa, Pushpa Rampratap & Patrick C. A. van der Wel

  6. Department of Biological Sciences, Wayne State University, Detroit, MI, USA

    Abu Ramim, Zhuqing Liang, Pablo Lazcano, Jiajia Ji, Michael W. Schmidtke & Miriam L. Greenberg

  7. Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA

    Kirill Kiselyov

  8. Department of Pediatrics, Division of Critical Care and Hospital Medicine, Redox Health Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA

    Aybike Korkmaz & Hülya Bayir

  9. Department of Pharmacology and Therapeutics, University of Manitoba, Children’s Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada

    Laura K. Cole & Grant M. Hatch

  10. Department of Pediatrics, Pediatric Institute for Heart Regeneration and Therapeutics, University of Pittsburgh, Pittsburgh, PA, USA

    Ammanamanchi Niyatie & Bernhard Kühn

  11. Department of Chemistry & Centre for Biotechnology, Brock University, St Catharines, Ontario, Canada

    Emma-Kate Baker & Jeffrey Atkinson

  12. Laufer Center for Physical Quantitative Biology and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, New York, NY, USA

    Ivet Bahar

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Contributions

Conceptualization was the responsibility of V.E.K., H.B. and M.L.G. Methodology was the responsibility of V.E.K., Y.Y.T., V.A.T., A.A.K., A.A.A., J.P., J.J., R.W., M.L.G., P.C.A.W., A.L., G.M.H. and E.V.N. Software was the responsibility of Y.Y.T., K.M.-R. and P.C.A.W. Validation was carried out by V.E.K. and M.L.G. Formal analysis was conducted by Y.Y.T., V.A.T., A.A.K., A.A.A., S.N.S., M.A.A., G.K.V., E.-K.B., D.D., J.J. and A.R. Computational modeling was carried out by K.M.-R. and I.B. Investigation was conducted by Y.Y.T., V.A.T., A.A.K., M.A.A., S.N.S., H.H.D., A.B.S., A.K., Z.L., D.D., J.J., A.R., P.L., A.L., P.R., L.K.C., E.V.N. and K.K. Resources were the responsibility of K.M.-R., M.W.S., B.K., G.M.H., A.N., H.B., J.A. and J.V. Data curation was carried out by Y.Y.T., K.M.-R. and P.C.A.W. Writing of the original draft was carried out by V.E.K., H.B. and M.L.G. Review and editing was carried out by Y.Y.T., K.M.-R., P.C.A.W., M.W.S., I.B., G.M.H. and E.V.N. Visualization was the responsibility of Y.Y.T., K.M.-R., A.R. and A.L. Supervision was the responsibility of V.E.K., R.W., M.L.G., P.C.A.W. and J.V. Project administration was the responsibility of V.E.K. and M.L.G. Funding acquisition was the responsibility of V.E.K. and M.L.G.

Corresponding authors

Correspondence to Valerian E. Kagan, Hülya Bayir or Miriam L. Greenberg.

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Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Metabolism thanks Steven M. Claypool, Rafael Radi and the other, anonymous, reviewers for their contribution to the peer review of this work. Primary Handling Editor: Yanina-Yasmin Pesch, in collaboration with the Nature Metabolism team.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 SSNMR analysis of structural and dynamic rearrangements in the cyt c peroxidase complex with MLCL.

a, Region from the 2D CP-DARR spectrum of 15N,13C-labeled cyt c bound to DOPC:MLCL(L)3 (1:1; blue). Overlaid red contours show simulated peak patterns constructed from the solution NMR shifts of the N- and C-terminal α-helices (BMRB ID 25908). b, 2D 15N-13C NCA ssNMR spectrum of the same sample, along with a corresponding simulated spectrum for the N- and C-terminal α-helices. The simulated peaks from the blue foldon coincide with strong peaks in the experimental ssNMR spectra. c, 2D (CP-based) 15N-13C NCA ssNMR spectrum of membrane-bound cyt c, alongside the analogous simulated spectrum (d) for cyt c in solution (BMRB ID 25908). Key resonances missing in the experimental spectrum (c) are indicated with green circles; these mostly belong to the Ω-loop D (for example Met80 and Ile81). These 2D NCA ssNMR spectra were acquired at 253 K and 10 kHz MAS. e, 1D 13C INEPT, CP, and direct excitation spectra of 15N,13C-labeled cyt c bound to DOPC:MLCL(L)3 (1:1), measured at 278K. These ssNMR spectra detect flexible (INEPT), rigid (CP), or both (direct excitation) sample components. The liquid crystalline lipids contribute many peaks to the INEPT spectrum (marked with blue arrows), while the labeled protein dominates the other two spectra. f, Overlay of 2D INEPT-TOBSY spectra for 15N,13C-labeled cyt c bound to MLCL/DOPC (blue) and CL/DOPC (red) vesicles. Cross-peaks stem from the labeled protein and must reflect flexible residues. Many more (and stronger) peaks are seen for MLCL-bound cyt c.

Extended Data Fig. 2 31P ssNMR analysis of MLCL-induced structural and dynamic changes in the lipid membrane.

a, 1D 31P ssNMR static spectra of DOPC:MLCL (1:1) (blue) and DOPC:CL (1:1) (red) vesicles with bound cyt c. b, Analogous 31P NMR spectra in absence of cyt c. Panels (a,b) show that the presence of MLCL results in a narrower extra component, that is neither isotropic nor reflects a typical non-bilayer phase. As previously discussed23, these signals reflect MLCL in the liquid crystalline bilayer, undergoing distinct, increased dynamics (of the phosphate groups) compared to normal CL. c, 1D 31P ssNMR MAS spectra of DOPC:MLCL (1:1) at 10 kHz (blue curve) and 1.8 kHz (light blue curve) MAS rates. d, Zoomed-in region from (C) showing the isotropic peak (left) and first sideband (at 1.8 kHz MAS). Peak assignments are indicated, based on prior publications13,23. Note that in the side bands, the PC signals are strong, one MLCL signal is partly retained and one MLCL signal is attenuated or missing. This is consistent with the shown assignments and cited literature.

Extended Data Fig. 3 Final shapshots from simulations of cyt c – membrane interactions and superposition of the conformations of cyt c reached after 100 ns runs.

a, Final shapshots from simulations of cyt c – membrane interactions, and residues making frequent contacts with MLCL. Final conformations of cyt c reached after 100 ns in twenty independent MD trajectories. Red labels denote the systems which were further extended to 300 ns. The colors of the components of the membrane are following: DOPC – in orange, DOPE – in green, MLCL – in transparent blue. b, Superposition of the conformations of cyt c reached after 100 ns runs, in a system without membrane which contained Fe-S bond (sharp structure) and two independent runs where the bond was drastically weakened (transparent structures). All final conformations of heme group are displayed as grey shadow balls-sticks. c, Final conformations of cyt c after association with the membrane, observed in four runs MD1-MD4 (labeled). The white arrow in the upper left panel shows the residue M80 which inserted deep into the membrane, being trapped by several MLCL molecules, also shown in Fig. 2b.

Extended Data Fig. 4 Peroxidase activity of cyt c–MLCL complex causes phospholipid peroxidation in vitro and induces changes in lipidome and oxy-lipidome of genetically manipulated yeast.

MS/MS spectra of (a) HOO-MLCL(L)3 (left panel) and oxidatively truncated ONA-MLCL(L)3 (right panel), (b) PC(18:0/18:2-OOH) (left panel) and PE(18:0/18:2-OOH) (right panel), (c) PC(18:0/ONA) (left panel) and PE(18:0/ONA) (right panel). Possible structures of oxidation products are inserted. ONA- 9-oxo nonanoic acid. d, Typical MS spectra of CL (upper panels) and MLCL (lower panels) obtained from yeast cells. e, Effect of D12desaturase on composition of CL (left panel) and MLCL (right panel) in WT and taz1D yeasts. SFA – saturated fatty acids, MUFA – monounsaturated fatty acids, PUFA – polyunsaturated fatty acids. f, Content of PC (upper panels) and PE (lower panels) molecular species in WT and D12/taz1D cells. Data are presented as mean values ± SD. Each data point represents a biologically independent sample. Upper panels: left ****P < 0.0001, middle ****P < 0.0001, ***P = 0.0004, right *P = 0.0202, ***P = 0.0001. ****P < 0.0001. One-way ANOVA, Tukey’s multiple comparison test. Lower panels; left ****P < 0.0001, middle **P = 0.0115. ***P = 0.0006, unpaired two-tailed t-test, ***P < 0.0001, ****P < 0.0001, One-way ANOVA, Tukey’s multiple comparison test. right ***P = 0.0056, unpaired two-tailed t-test, ****P < 0.0001, One-way ANOVA, Tukey’s multiple comparison test. g, OPLS-DA analysis showing the differences in oxy-lipidomes of D12 and D12/taz1D yeast cells; h, Pie plots showing the number of oxidatively modified phospholipid species. In total, 60 oxygenated phospholipid species were detected in yeast cells.

Source data

Extended Data Fig. 5 TAZ deficiency induces the changes in phospholipidome of mouse myoblasts and human lymphoblasts in vitro and mouse and human heart in vivo.

a, Table: Human heart biopsy sample description. Typical spectra of MLCL (left panels) and CL (right panels) obtained from WT and TAZ-KO C2C12 cells (b), WT and TAZ-KD mice (c), human lymphoblasts (d) and heart biopsy samples from control, non-BTHS-associated heart failure (NBHF) and BTHS-associated heart failure (BTHS) patients (e). TAZ deficiency in cells and mice and TAZ mutation in human results in a decrease of MLCL molecular species with C18:2 and appearance of MLCL molecular species containing C20:4 (shown in red); (f) Pie plots showing the total number of MLCL species in C2C12 cells, mouse heart, human lymphoblasts and heart samples from BTHD patients. (g) The score plots of OPLS-DA analysis show the differences in oxy-lipidomes in WT and TAZ-KO cells, WT and TAZ-KD mice, human control and BTHS lymphoblasts and control heart samples and BTHS heart samples.

Source data

Extended Data Fig. 6 Content of PE and PC species in cells, mouse heart, human lymphoblasts and human heart biopsy samples.

C2C12 cells (a-d): a, Total content of diacyl-PC (left panel) and its molecular species (right panel). b, Total content of plasmalogen-PC (left panel) and its molecular species (right panel). c, Total content of diacyl-PE (left panel) and its molecular species (right panel). d, Total content of plasmalogen-PE (left panel) and its molecular species (right panel). Mouse heart (e-h): e, Total content of diacyl-PC (left panel) and its molecular species (right panel). f, Total content of plasmalogen-PC (left panel) and its molecular species (right panel). g, Total content of diacyl-PE (left panel) and its molecular species (right panel). h, Total content of plasmalogen-PE (left panel) and its molecular species (right panel). Human lymphocytes (i-l): i, Total content of diacyl-PC (left panel) and its molecular species (right panel). j, Total content of plasmalogen-PC (left panel) and its molecular species (right panel). k, Total content of diacyl-PE (left panel) and its molecular species (right panel). l, Total content of plasmalogen-PE (left panel) and its molecular species (right panel). Human heart biopsy samples (m-p): m, Total content of diacyl-PC (left panel) and its molecular species (right panel). n, Total content of plasmalogen-PC (left panel) and its molecular species (right panel). o, Total content of diacyl-PE (left panel) and its molecular species (right panel). p, Total content of plasmalogen-PE (left panel) and its molecular species (right panel). *P < 0.05, **P < 0.01. DB - double bond number.

Source data

Extended Data Fig. 7 Effect of TPP-IOA on structure of cyt c–MLCL peroxidase complex, with MLCL, lipid oxidation and the endurance of Drosophila melanogaster.

Effect of TPP-imidazole-oleic acid (TPP-IOA) on MLCL(L)3-dependent formation of heme iron high-spin forms assessed by absorbance at 620 nm (a) and absorbace at 695 nm (b). Right: the differential absorption spectra (a) and representative absorption spectra (b) of MLCL–cyt c with or without TPP-IOA. Data are presented as mean values ± SD. Each data point represents a biologically independent sample. ****p < 0.0001, One-way ANOVA, Tukey’s multiple comparison test. (a) N = 8 (control), N = 6 (TPP-IOA–cyt c = 2/1), N = 6 (TPP-IOA–cyt c = 4/1). (b) N = 8 (control), N = 10 (TPP-IOA–cyt c = 2/1), N = 9 (TPP-IOA–cyt c = 4/1).(c) TPP-IOA inhibits accumulation of HOO-PE (left panel) and oxidatively truncated PE (right panel) species formed in MLCL(L)3–cyt c-driven reaction. Data are presented as mean values ± SD. N = 3. Each data point represents a biologically independent sample. Right panel: *p = 0.0287, ****p < 0.0001, Left panel: ***p = 0.0007, ****p < 0.0001. One-way ANOVA, Tukey’s multiple comparison test. (d) Normalized peak intensity values from 13C-13C ssNMR spectra of cyt c bound to DOPC:MLCL(L)3 (1:1; blue), or DOPC:MLCL(L)3 (2:1) LUVs in the absence (black) and presence (orange) of a four-fold excess of IOA with respect to protein (1:40 P/L ratio). Shown are the Cα/Cβ (open) and Cβ/Cα (closed) peaks for Thr residues. Each residue shows two data points: one for either side of the diagonal: see Fig. 5e). Increasing the ratio of MLCL (over PC) caused a net decrease in peak intensities, signifying increased protein motion. Addition of the IOA inhibitor had a much more modest effect on the Thr peak volumes.

Source data

Extended Data Fig. 8 TAZ deficiency induces changes in Drosophila melanogaster lipidome.

Typical mass spectra of MLCL (a) and CL (b) obtained from control (W1118) and (TAZ889) mutant flies. Content MLCL containing C18:2 (c) and C18:3 (d) in control W1118 and TAZ889 deficient flies. Lipidomics analysis was performed using 6 vials (n = 20 fly torsos per vial). (c) *P = 0.0401, **P < 0.0015, ***P = 0.0005 unpaired two-tailed t-test. (d) *P = 0.0378, **P < 0.0019, ****p < 0.0001 unpaired two-tailed t-test. (e) TPP-IOA did not significantly affect the endurance of control flies. Endurance was measure using 8 vials (N = 20 flies) and significance was determined by log-rank analysis., ns = not significant. (f) Content of CL (left panel) and MLCL (right panel) in control W1118 flies after feeding with TPP-IOA. Lipidomics analysis was performed using 6 vials (n = 20 fly torsos per vial). For all violin plots presented, individual points including maximal and minimal are shown as black circles. Dashed black line indicates median and doted lines indicate quartiles.

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Kagan, V.E., Tyurina, Y.Y., Mikulska-Ruminska, K. et al. Anomalous peroxidase activity of cytochrome c is the primary pathogenic target in Barth syndrome. Nat Metab 5, 2184–2205 (2023). https://doi.org/10.1038/s42255-023-00926-4

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