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A feedback loop engaging propionate catabolism intermediates controls mitochondrial morphology

Nature Cell Biology volume 24, pages 526–537 (2022)Cite this article

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Abstract

d-2-Hydroxyglutarate (D-2HG) is an α-ketoglutarate-derived mitochondrial metabolite that causes d-2-hydroxyglutaric aciduria, a devastating developmental disorder. How D-2HG adversely affects mitochondria is largely unknown. Here, we report that in Caenorhabditis elegans, loss of the D-2HG dehydrogenase DHGD-1 causes D-2HG accumulation and mitochondrial damage. The excess D-2HG leads to a build-up of 3-hydroxypropionate (3-HP), a toxic metabolite in mitochondrial propionate oxidation, by inhibiting the 3-HP dehydrogenase HPHD-1. We demonstrate that 3-HP binds the MICOS subunit MIC60 (encoded by immt-1) and inhibits its membrane-binding and membrane-shaping activities. We further reveal that dietary and gut bacteria affect mitochondrial health by modulating the host production of 3-HP. These findings identify a feedback loop that links the toxic effects of D-2HG and 3-HP on mitochondria, thus providing important mechanistic insights into human diseases related to D-2HG and 3-HP.

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Fig. 1: Loss of dhgd-1 function damages mitochondrial structure and functions.
Fig. 2: dhgd-1 and hphd-1 function in the same genetic pathway.
Fig. 3: 3-HP is responsible for the mitochondrial defects in hphd-1 and dhgd-1 mutants.
Fig. 4: D-2HG binds to and inhibits HPHD-1.
Fig. 5: 3-HP binds to IMMT-1 and inhibits its membrane-binding and membrane-shaping activities.
Fig. 6: Reinforced expression of IMMT-1 restores mitochondrial structure in hphd-1 and dhgd-1 mutants.
Fig. 7: K12-type E. coli strains ameliorate the mitochondrial defects in dhgd-1 and hphd-1 mutants.

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Data availability

The genome sequencing data that support the findings of this study have been deposited in the Sequence Read Archive (SRA) under the accession code PRJNA808177. Protein structure predictions were downloaded from the AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/). All other data supporting the findings of this study are available from the authors on reasonable request. Source data are provided with this paper.

References

  1. Wajner, M. & Goodman, S. I. Disruption of mitochondrial homeostasis in organic acidurias: insights from human and animal studies. J. Bioenerg. Biomembr. 43, 31–38 (2011).

    Article  CAS  PubMed  Google Scholar 

  2. Vaidyanathan, K., Narayanan, M. P. & Vasudevan, D. M. Organic acidurias: an updated review. Indian J. Clin. Biochem. 26, 319–325 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Park, K. C., Krywawych, S., Richard, E., Desviat, L. R. & Swietach, P. Cardiac complications of propionic and other inherited organic acidemias. Front. Cardiovasc. Med. 7, 617451 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Struys, E. A. et al. Kinetic characterization of human hydroxyacid-oxoacid transhydrogenase: relevance to d-2-hydroxyglutaric and γ-hydroxybutyric acidurias. J. Inherit. Metab. Dis. 28, 921–930 (2005).

    Article  CAS  PubMed  Google Scholar 

  5. Kranendijk, M., Struys, E. A., Salomons, G. S., Van der Knaap, M. S. & Jakobs, C. Progress in understanding 2-hydroxyglutaric acidurias. J. Inherit. Metab. Dis. 35, 571–587 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Kranendijk, M. et al. IDH2 mutations in patients with d-2-hydroxyglutaric aciduria. Science 330, 336 (2010).

    Article  CAS  PubMed  Google Scholar 

  7. Dang, L. & Su, S. M. Isocitrate dehydrogenase mutation and (R)-2-hydroxyglutarate: from basic discovery to therapeutics development. Annu. Rev. Biochem. 86, 305–331 (2017).

    Article  CAS  PubMed  Google Scholar 

  8. Laurence, M. G., Boulay, K., Topisirovic, I., Huot, M. E. & Mallette, F. A. Oncogenic activities of IDH1/2 mutations: from epigenetics to cellular signaling. Trends Cell Biol. 27, 738–752 (2017).

    Article  Google Scholar 

  9. Su, R. et al. R-2HG exhibits anti-tumor activity by targeting FTO/m6A/MYC/CEBPA signaling. Cell 172, 90–105.e23 (2018).

    Article  CAS  PubMed  Google Scholar 

  10. Losman, J. A. et al. (R)-2-hydroxyglutarate is sufficient to promote leukemogenesis and its effects are reversible. Science 339, 1621–1625 (2013).

    Article  CAS  PubMed  Google Scholar 

  11. Ando, T., Rasmussen, K., Nyhan, W. L. & Hull, D. 3-Hydroxypropionate: significance of β-oxidation of propionate in patients with propionic acidemia and methylmalonic acidemia. Proc. Natl Acad. Sci. USA 69, 2807–2811 (1972).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Sbai, D. et al. Contribution of odd-chain fatty acid oxidation to propionate production in disorders of propionate metabolism. Am. J. Clin. Nutr. 59, 1332–1337 (1994).

    Article  CAS  PubMed  Google Scholar 

  13. Schwab, M. A. et al. Secondary mitochondrial dysfunction in propionic aciduria: a pathogenic role for endogenous mitochondrial toxins. Biochem. J. 398, 107–112 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Deodato, F., Boenzi, S., Santorelli, F. M. & Dionisi-Vici, C. Methylmalonic and propionic aciduria. Am. J. Med Genet C Semin. Med. Genet. 142C, 104–112 (2006).

    Article  CAS  PubMed  Google Scholar 

  15. Shchelochkov, O. A., Carrillo, N. & Venditti, C. In GeneReviews (eds Adam, M. P. et al.) NBK92946 (Univ. Washington, 2016).

  16. Tang, R. et al. Defective arginine metabolism impairs mitochondrial homeostasis in Caenorhabditis elegans. J. Genet Genomics 47, 145–156 (2020).

    Article  PubMed  Google Scholar 

  17. Youle, R. J. & van der Bliek, A. M. Mitochondrial fission, fusion, and stress. Science 337, 1062–1065 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Zhou, J. et al. The lysine catabolite saccharopine impairs development by disrupting mitochondrial homeostasis. J. Cell Biol. 218, 580–597 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Qi, B. & Han, M. Microbial siderophore enterobactin promotes mitochondrial iron uptake and development of the host via interaction with ATP synthase. Cell 175, 571–582.e11 (2018).

    Article  CAS  PubMed  Google Scholar 

  20. Han, B. et al. Microbial genetic composition tunes host longevity. Cell 169, 1249–1262.e13 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. McGee, M. D. et al. Loss of intestinal nuclei and intestinal integrity in aging C. elegans. Aging Cell 10, 699–710 (2011).

    Article  CAS  PubMed  Google Scholar 

  22. Portal-Celhay, C., Bradley, E. R. & Blaser, M. J. Control of intestinal bacterial proliferation in regulation of lifespan in Caenorhabditis elegans. BMC Microbiol. 12, 49 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Ma, T. et al. A pair of transporters controls mitochondrial Zn2+ levels to maintain mitochondrial homeostasis. Protein Cell https://doi.org/10.1007/s13238-021-00881-4 (2022).

  24. Watson, E. et al. Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans. eLife https://doi.org/10.7554/eLife.17670 (2016).

  25. Achouri, Y. et al. Identification of a dehydrogenase acting on d-2-hydroxyglutarate. Biochem. J. 381, 35–42 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Kaufman, E. E., Nelson, T., Fales, H. M. & Levin, D. M. Isolation and characterization of a hydroxyacid-oxoacid transhydrogenase from rat kidney mitochondria. J. Biol. Chem. 263, 16872–16879 (1988).

    Article  CAS  PubMed  Google Scholar 

  27. Le, T. T. et al. Development and validation of a simple LC–MS/MS method for the simultaneous quantitative determination of trimethylamine-N-oxide and branched chain amino acids in human serum. Anal. Bioanal. Chem. 411, 1019–1028 (2019).

    Article  CAS  PubMed  Google Scholar 

  28. Sivanand, S. & Vander Heiden, M. G. Emerging roles for branched-chain amino acid metabolism in cancer. Cancer Cell 37, 147–156 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Elshaghabee, F. M. et al. Ethanol production by selected intestinal microorganisms and lactic acid bacteria growing under different nutritional conditions. Front. Microbiol. 7, 47 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  30. Tarasenko, D. et al. The MICOS component Mic60 displays a conserved membrane-bending activity that is necessary for normal cristae morphology. J. Cell Biol. 216, 889–899 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Hessenberger, M. et al. Regulated membrane remodeling by Mic60 controls formation of mitochondrial crista junctions. Nat. Commun. 8, 15258 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Pfanner, N. et al. Uniform nomenclature for the mitochondrial contact site and cristae organizing system. J. Cell Biol. 204, 1083–1086 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Harner, M. et al. The mitochondrial contact site complex, a determinant of mitochondrial architecture. EMBO J. 30, 4356–4370 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Kondadi, A. K., Anand, R. & Reichert, A. S. Cristae membrane dynamics—a paradigm change. Trends Cell Biol. 30, 923–936 (2020).

    Article  CAS  PubMed  Google Scholar 

  35. Head, B. P., Zulaika, M., Ryazantsev, S. & van der Bliek, A. M. A novel mitochondrial outer membrane protein, MOMA-1, that affects cristae morphology in Caenorhabditis elegans. Mol. Biol. Cell 22, 831–841 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Mun, J. Y. et al. Caenorhabditis elegans mitofilin homologs control the morphology of mitochondrial cristae and influence reproduction and physiology. J. Cell. Physiol. 224, 748–756 (2010).

    Article  CAS  PubMed  Google Scholar 

  37. Fujiki, Y., Hubbard, A. L., Fowler, S. & Lazarow, P. B. Isolation of intracellular membranes by means of sodium carbonate treatment: application to endoplasmic reticulum. J. Cell Biol. 93, 97–102 (1982).

    Article  CAS  PubMed  Google Scholar 

  38. Cani, P. D. et al. Microbial regulation of organismal energy homeostasis. Nat. Metab. 1, 34–46 (2019).

    Article  CAS  PubMed  Google Scholar 

  39. Koh, A., De Vadder, F., Kovatcheva-Datchary, P. & Backhed, F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 165, 1332–1345 (2016).

    Article  CAS  PubMed  Google Scholar 

  40. Urrutia, A. et al. Bacterially produced metabolites protect C. elegans neurons from degeneration. PLoS Biol. 18, e3000638 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Revtovich, A. V., Lee, R. & Kirienko, N. V. Interplay between mitochondria and diet mediates pathogen and stress resistance in Caenorhabditis elegans. PLoS Genet. 15, e1008011 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. da Silva, C. G. et al. Inhibition of creatine kinase activity from rat cerebral cortex by d-2-hydroxyglutaric acid in vitro. Neurochem. Int. 44, 45–52 (2004).

    Article  PubMed  Google Scholar 

  43. Kolker, S. et al. NMDA receptor activation and respiratory chain complex V inhibition contribute to neurodegeneration in d-2-hydroxyglutaric aciduria. Eur. J. Neurosci. 16, 21–28 (2002).

    Article  PubMed  Google Scholar 

  44. Haijes, H. A., Jans, J. J. M., Tas, S. Y., Verhoeven-Duif, N. M. & van Hasselt, P. M. Pathophysiology of propionic and methylmalonic acidemias. Part 1: complications. J. Inherit. Metab. Dis. 42, 730–744 (2019).

    Article  CAS  PubMed  Google Scholar 

  45. Haijes, H. A., van Hasselt, P. M., Jans, J. J. M. & Verhoeven-Duif, N. M. Pathophysiology of propionic and methylmalonic acidemias. Part 2: treatment strategies. J. Inherit. Metab. Dis. 42, 745–761 (2019).

    Article  PubMed  Google Scholar 

  46. Louis, P., Hold, G. L. & Flint, H. J. The gut microbiota, bacterial metabolites and colorectal cancer. Nat. Rev. Microbiol. 12, 661–672 (2014).

    Article  CAS  PubMed  Google Scholar 

  47. Davis, M. W. et al. Rapid single nucleotide polymorphism mapping in C. elegans. BMC Genomics 6, 118 (2005).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Neve, I. A. A. et al. Escherichia coli metabolite profiling leads to the development of an RNA interference strain for Caenorhabditis elegans. G3 (Bethesda) 10, 189–198 (2020).

    Article  CAS  Google Scholar 

  49. Meng, X. et al. Actin polymerization and ESCRT trigger recruitment of the fusogens syntaxin-2 and EFF-1 to promote membrane repair in C. elegans. Dev. Cell 54, 624–638.e5 (2020).

    Article  CAS  PubMed  Google Scholar 

  50. Koopman, M. et al. A screening-based platform for the assessment of cellular respiration in Caenorhabditis elegans. Nat. Protoc. 11, 1798–1816 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Fiehn, O., Kopka, J., Trethewey, R. N. & Willmitzer, L. Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry. Anal. Chem. 72, 3573–3580 (2000).

    Article  CAS  PubMed  Google Scholar 

  52. Bitencourt-Ferreira, G. & de Azevedo, W. F. Jr. Molegro virtual docker for docking. Methods Mol. Biol. 2053, 149–167 (2019).

    Article  CAS  PubMed  Google Scholar 

  53. Song, J. W. et al. Omics-driven systems interrogation of metabolic dysregulation in COVID-19 pathogenesis. Cell Metab. 32, 188–202.e5 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This research was supported by the grant 2021YFA1300302 from the National Basic Research Program of China, grants 91954204, 31730053 (to C.Y.) and 32000531 (to M.D.) from the National Science Foundation of China, and grant 202001BB050077 from the Yunnan Province Science and Technology Department. C.Y. is supported by Program of Yunnan Province Leading Talents in Science and Technology. We thank I. Hanson for proofreading the manuscript and S. Mitani and the Caenorhabditis Genetics Center for the C. elegans strains used in this study.

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  1. These authors contributed equally: Junxiang Zhou, Mei Duan, Xin Wang.

Authors and Affiliations

  1. State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China

    Junxiang Zhou, Mei Duan, Xin Wang, Hejiang Zhou, Tengfei Ma, Qiuyuan Yin, Jie Zhang, Fei Tian & Chonglin Yang

  2. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

    Fengxia Zhang & Guodong Wang

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Contributions

C.Y. supervised the study. J.Z. and M.D. performed most of the experiments and interpreted the data (with C.Y.). X.W. performed the TEM experiments and analysis. F.Z. and G.W. performed the metabolite measurements. H.Z., T.M., Q.Y., J. Zhang and F.T. contributed to the experiments and materials. J.Z., M.D. and C.Y. prepared the manuscript with discussion between all authors.

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Correspondence to Mei Duan or Chonglin Yang.

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Nature Cell Biology thanks Martina Wallace, Meng Wang, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Characterization of the dhgd-1 and hphd-1 genes.

a, Diagram of the dhgd-1 gene (top) and the encoded protein (bottom). In the gene, filled boxes and thin lines represent exons and introns, respectively. The locations of the tm6671 deletion and the yq169 point mutation are indicated. In the protein, the positions of the tm6671 deletion and the yq169 point mutation are indicated with the red bracket and the red asterisk, respectively. Orange and blue boxes indicate FAD-binding and FAD-oxidase domains, respectively. The similarity of the indicated domains between C. elegans DHGD-1 and mouse or human D2HGDH is indicated. b, Representative images of mitochondria in the intestine in dhgd-1(tm6671) mutants. Bars, 5 μm. c, Expression of DHGD-1::GFP driven by the dhgd-1 promoter (Pdhgd-1dhgd-1::gfp) in a whole worm expressing TOMM-20::RFP (Ptomm-20tomm-20::rfp) (top), Bars, 50 μm. The bottom rows show enlarged images of hypodermis, muscle, and intestine within the boxed region. Bars, 5 μm. d, Diagram of the hphd-1 gene (top) and the encoded protein (bottom). Filled boxes and thin lines represent exons and introns, respectively. The ok3580 deletion and the yq367 point mutation of hphd-1 are indicated with red lines. Blue boxes indicate the Fe-ADH (Fe-containing alcohol dehydrogenase) domains. The similarity of the indicated domains between C. elegans HPHD-1 and mouse or human ADHFE1 is indicated. e, Representative images of mitochondria in the intestine in hphd-1(ok3580) mutants. Bars, 5 μm. f, Expression of the hphd-1 gene. HPHD-1::GFP driven by the hphd-1 promoter (Phphd-1hphd-1::gfp) in a whole worm expressing TOMM-20::RFP (Ptomm-20tomm-20::rfp) (top), Bars, 50 μm. The bottom rows show enlarged images of hypodermis, muscle, and intestine within the boxed region. Bars, 5 μm. g, Left: Representative images of mitochondria with general RNAi of dhgd-1 and hphd-1 in N2 animals. Right: Representative images of mitochondria with hypodermis-specific RNAi of dhgd-1 and hphd-1 in rde-1(ne219);juIs346(Pcol-19rde-1) worms. RNAi was performed using RNAi-competent OP50 E. coli. Mitochondria were stained with Mito-CMXRos. Bars, 5 μm.

Extended Data Fig. 2 Profiling of 3-HP in C. elegans of the indicated genotypes by liquid chromatography-electrospray ionization-mass spectrometry.

a-c, Representative chromatograms of 3-HP in N2, hphd-1 (ok3580) and dhgd-1 (tm6671) animals grown on E. coli OP50 without (a) or with VB12 (b), and on E. coli HT115 (c). The arrows indicate the expected elution time of 7.006 min for MTBSTFA-derivatized 3-HP, based on similar derivatization of a commercial 3-HP standard. d, Mass spectrum of the 3-HP metabolite peak eluting at 7.006 min in hphd-1 (ok3580) mutants. m/z- indicates the mass (in atomic mass units) to charge ratio for fragments generated by electron impact ionization.

Extended Data Fig. 3 Characterization of mitochondrial defects and metabolites in C. elegans mutants affecting propionate breakdown.

a, Representative images of hypodermal mitochondria in hphd-1(ok3580) and dhgd-1(tm6671) mutants grown on E. coli OP50 without or with addition of VB1, VB6, and VC. Bars, 5 μm. b-d, Left: Quantification of Val (b), Ile (c) and Leu (d) in N2, dhgd-1(tm6671) and hphd-1(ok3580) animals fed on E. coli OP50. Right: Representative chromatograms of each amino acid in the indicated worms. Worms grown on 20 NGM plates (10 cm in diameter) were analyzed for each genotype. n = 4 independent experiments for N2 and dhgd-1(tm6671) and n = 3 independent experiments for hphd-1(ok3580). e, Left: Quantification of KMP (top) and KMV (bottom) in N2, dhgd-1(tm6671) and hphd-1(ok3580) animals fed on E. coli OP50. Right: Representative chromatograms of KMP and KMV in the indicated worms. Worms grown on 20 NGM plates (10 cm in diameter) were analyzed for each genotype. n = 4 independent experiments for N2 and dhgd-1(tm6671) and n = 3 independent experiments for hphd-1(ok3580). f, Representative images of mitochondria in the hypodermis of N2, pcca-1(ok2282) mutants, control RNAi-, mce-1 RNAi- and mmcm-1 RNAi-treated worms fed on E. coli OP50. RNAi was performed using RNAi-competent OP50 E. coli. Bars, 5 μm. g, Representative images of mitochondria in the hypodermis of N2, acdh-1(ok1489), alh-8(ww48), control RNAi-, ech-6 RNAi- and hach-1 RNAi-treated worms fed on E. coli OP50. RNAi was performed using RNAi-competent E. coli OP50. Bars, 5 μm. h, Representative images of mitochondria in the hypodermis of N2, acdh-1(ok1489) and dhgd-1(tm6671) single mutants and acdh-1;dhgd-1 double mutants fed on E. coli OP50. Bars, 5 μm. i. Quantification of propionate in worms with the indicated genotype. Worms grown on 20 NGM plates (10 cm in diameter) were analyzed for each genotype. n = 3 independent experiments. For statistical analyses, P values were determined using one-way ANOVA (i) and two-sided Student’s t-test (b, c, d and e). Individual data points (mean ± s.e.m. and exact P value) are shown. ****P < 0.0001; ***P < 0.001; **P < 0.01; *P < 0.05. Source numerical data are available in source data.

Source data

Extended Data Fig. 4 Characterization of the D-2HG-HPHD-1 interaction.

a, Predication of D-2HG binding to HPHD-1. HPHD-1 structure is predicted using alpha-Fold (https://alphafold.ebi.ac.uk/). D-2HG (in green and orange) docking on HPHD-1 (in blue) is predicted using the Molegro Virtual Docker (http://molexus.io/molegro-virtual-docker/). Amino acid residues involved in binding with D-2HG are labeled in orange. b, Left: Graphic depiction of HPHD-1 truncations (top) and gel images showing recombinant HPHD-1 proteins (bottom). Right: Binding curves of D-2HG with HPHD-1 proteins using MST assays. Data (mean) are from two independent experiments. c, Top: Schematic depiction of the forward reaction of HPHD-1 dehydrogenase using isopropanol and NAD+ as substrates. Bottom: HPHD-1 dehydrogenase activity without or with D-2HG was measured at the reaction times 0.5 h (left) and 1.5 h (right) by quantifying the production of NADH as in Fig. 4e. n = 3 independent experiments. d, Top: Schematic depiction of the reverse reaction catalyzed by HPHD-1 using 2-propanone and NADH as substrates. HPHD-1 activity without or with D-2HG at the indicated reaction time points was measured by quantifying the reduction of NADH. The B. licheniformis NADH Oxidase (B.l. Oxidase) was used as positive control. n = 3 independent experiments. For statistical analyses, P values were determined using one-way ANOVA (c and d). Individual data points (mean ± s.e.m. and exact P value) are shown. ****P < 0.0001; ***P < 0.001; ns, P > 0.05. Source numerical data and unprocessed gels are available in source data.

Source data

Extended Data Fig. 5 Characterization of dhgd-1, hphd-1, and immt-1 mutants, expression of MICOS components, and 3-HP biding with IMMT-1.

a, Representative TEM images of mitochondria in the hypodermis and muscle cells in N2, dhgd-1(tm6671) and hphd-1(ok3580) animals grown on E. coli OP50. Bars, 2 μm. Quantifications of abnormal mitochondria are shown on the right. ≥6 mitochondria in each cell type in animals of each genotype were examined, the exact number of mitochondria is provided as source data. n = 3 independent biological samples. b, Graphic depiction of the MICOS complex. SAM, sorting and assembly machinery. c, Diagram of the immt-1 gene and the encoded protein. Filled boxes and thin lines represent exons and introns, respectively. The yq160 point mutation is indicated with a red line. In the protein, blue, red, green and purple boxes indicate the transmembrane domain (TM), the coiled-coil domain, the lipid binding sites (LBS), and the mitofilin domain, respectively. d, Representative images of mitochondria in the hypodermis of immt-1(yq160) mutants. Mitochondria are labeled with Mito-GFP and TOMM-20::mCh. Bars, 5 µm. e, Representative TEM images of mitochondria in hypodermal and muscle cells in immt-1(yq160) mutants grown on E. coli OP50. Red and yellow arrows indicate vacuoles and inner membrane stacks, respectively. Bars, 2 μm. Quantifications of hypodermal (top) and muscle (bottom) mitochondria containing only vacuoles (Vacuole only), only inner membrane stacks (Stack only), or both (Vacuole + Stack) are shown on the right. The indicated numbers of mitochondria were analyzed in n = 8 independent immt-1(yq160) animals. f, Relative mRNA levels of immt-1, immt-2, chch-3 (Mic19) and F54A3.5 (Mic10) in N2, hphd-1(ok3580) and dhgd-1(tm6671) animals. 300 animals were examined for each genotype. n = 3 independent experiments. g, Immunoblotting of IMMT-1 in N2, immt-1(yq160), hphd-1(ok3580) and dhgd-1(tm6671) animals. Quantification of IMMT-1 protein levels from two independent experiments with similar results is shown at the bottom. h, Left: Graphic depiction of the full-length and truncated IMMT-1 (top) and the corresponding His6-tagged proteins (indicated with *) used for MST assays. Right: Binding curves of 3-HP with the different His6-tagged IMMT-1 proteins shown in the left panel. Data (mean) are from two independent experiments. For statistical analyses, P values were determined using one-way ANOVA (a and g) and two-way ANOVA (f). Individual data points (mean ± s.e.m. and exact P value) are shown. ****P < 0.0001; ns, P > 0.05. Source numerical data and unprocessed gels and blots are available in source data.

Source data

Extended Data Fig. 6 Characterization of IMMT-1-lipid interaction and analysis of the rescuing effect of IMMT-1 mutants, MICOS components, and IMMT-2 on defective mitochondria in hphd-1, dhgd-1 and aass-1 mutants.

a, Gel image of the His6-tagged recombinant IMMT-1 proteins illustrated in Fig. 5f. b, Representative EM images of liposome tubulation (red arrows) induced by the IMMT-1 proteins shown in (a) in the absence or presence of 3-HP or D-2HG. Bars, 0.5 µm. c, 3-HP does not extract IMMT-1 from pre-formed IMMT-1 proteoliposomes. Pre-formed His6-IMMT-1 proteoliposomes were incubated with 3-HP or Na2CO3 for 30 min and spun down. The pellets and supernatants were collected and immuno-blotted with anti-His6 antibody. d, Reinforced expression of IMMT-1ΔLBS::GFP (PY37A1B.5immt-1ΔLBS::gfp) in hphd-1(ok3580) or dhgd-1(tm6671) mutants. Bars, 5 µm. e, f, Representative images of TOMM-20::mCh-labeled mitochondria in the hypodermis in hphd-1(ok3580) and dhgd-1(tm6671) adults expressing F54A3.5(Mic10)::GFP (PY37A1B.5F54A3.5::gfp) (e) or CHCH-3(Mic19)::GFP (P Y37A1B.5chch-3::gfp) (f). Bars, 5 µm. g, Representative images of TOMM-20::mCh-labeled mitochondria in the hypodermis in hphd-1(ok3580) and dhgd-1(tm6671) adults expressing IMMT-2::GFP (P Y37A1B.5immt-2::gfp). Bars, 5 µm. h, Representative images of TOMM-20::mCh-labeled mitochondria in the hypodermis in aass-1(yq170) mutants expressing IMMT-1::GFP (P Y37A1B.5immt-1::gfp). Bars, 5 µm. Source unprocessed gels and blots are available in source data.

Source data

Extended Data Fig. 7 Analysis of free fatty acids and branched-chain amino acids in OP50 and HT115 E. coli.

a, Representative images (left) and quantification (right) of hypodermal mitochondria in dhgd-1(tm6671) and hphd-1(ok3580) mutants fed on a mixture of bacteria with the indicated HT115/OP50 ratio. 100 animals were examined for each treatment. n = 3 independent experiments. Bars, 5 µm. b, c, Heat maps reflecting the content of free fatty acids (b) and BCAAs (c) are shown for E. coli OP50 and HT115. Bacteria collected from 250 ml of liquid bacterial culture with OD600 = 1.0 were analyzed for each strain, n = 4 independent experiments. The color bar on the right of the heat map indicates standard deviations from the mean value. For statistical analyses in (a), P values were determined using the two-way ANOVA and individual data points (mean ± s.e.m. and exact P value) are shown. ****P < 0.0001; **P < 0.01; ns, P > 0.05. Source numerical data are available in source data.

Source data

Extended Data Fig. 8 Profiling of 3-HP in worms with the indicated genotypes fed on E. coli OP50 or HT115 supplied without or with Val (250 mM) or Ile (100 mM) by gas chromatography-electrospray ionization-mass spectrometry.

3-HP levels were measured in N2 (a), pcca-1(ok2282) (b), dhgd-1(tm6671) (c), and dhgd-1;pcca-1 (d) animals.

Extended Data Fig. 9 Graphic summary of the mitochondrion-damaging D-2HG-3-HP feedback loop and its interaction with dietary/gut bacteria.

C. elegans animals grown on OP50 (B-type E. coli) produce propionyl-CoA and 3-HP through the VB12-independent pathway in mitochondria. HPHD-1 converts 3-HP and α-KG to MSA and D-2HG, which is converted back to α-KG by DHGD-1 (top). Loss of DHGD-1 function causes accumulation of D-2HG, which binds to HPHD-1 and inhibits its dehydrogenase activity, leading to 3-HP buildup. Accumulated 3-HP in turn binds to Mic60/IMMT-1 and inhibits its membrane-binding and -shaping activities, causing mitochondrial damage (middle). E. coli HT115 (K12-type) alleviates the buildup of 3-HP by providing lower levels of propionyl-CoA precursors (for example BCAAs), and activating VB12-dependent degradation of propionyl-CoA, thus protecting mitochondria from 3-HP-induced impairment (bottom).

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Supplementary Tables

Supplementary Table 1: Strains used in this study. Supplementary Table 2: Expression vectors. Supplementary Table 3: Oligonucleotides used for real-time quantitative PCR.

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Unprocessed western blots and gels with Coomassie blue staining.

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Zhou, J., Duan, M., Wang, X. et al. A feedback loop engaging propionate catabolism intermediates controls mitochondrial morphology. Nat Cell Biol 24, 526–537 (2022). https://doi.org/10.1038/s41556-022-00883-2

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