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NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin

Nature Metabolism volume 2, pages 387–396 (2020)Cite this article

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Abstract

Mitochondria are multidimensional organelles whose activities are essential to cellular vitality and organismal longevity, yet underlying regulatory mechanisms spanning these different levels of organization remain elusive1,2,3,4,5. Here we show that Caenorhabditis elegans nuclear transcription factor Y, beta subunit (NFYB-1), a subunit of the NF-Y transcriptional complex6,7,8, is a crucial regulator of mitochondrial function. Identified in RNA interference (RNAi) screens, NFYB-1 loss leads to perturbed mitochondrial gene expression, reduced oxygen consumption, mitochondrial fragmentation, disruption of mitochondrial stress pathways, decreased mitochondrial cardiolipin levels and abolition of organismal longevity triggered by mitochondrial impairment. Multi-omics analysis reveals that NFYB-1 is a potent repressor of lysosomal prosaposin, a regulator of glycosphingolipid metabolism. Limiting prosaposin expression unexpectedly restores cardiolipin production, mitochondrial function and longevity in the nfyb-1 background. Similarly, cardiolipin supplementation rescues nfyb-1 phenotypes. These findings suggest that the NFYB-1–prosaposin axis coordinates lysosomal to mitochondria signalling via lipid pools to enhance cellular mitochondrial function and organismal health.

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Fig. 1: Mitochondrial regulation during ARD and upon recovery.
Fig. 2: NFYB-1 regulates mitochondrial function and longevity.
Fig. 3: Multi-omics analyses indicate that NFYB-1 regulates organellar functions and stress response.
Fig. 4: Lysosomal SPP-8 rescues mitochondrial function.

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Data availability

RNA-seq data have been deposited in Gene Expression Omnibus (GEO) under accession code GSE127917. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD013233. Source data for Extended Data Figs. 1, 2 and 4 are presented with the paper.

References

  1. Nunnari, J. & Suomalainen, A. Mitochondria: in sickness and in health. Cell 148, 1145–1159 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Quirós, P. M., Mottis, A. & Auwerx, J. Mitonuclear communication in homeostasis and stress. Nat. Rev. Mol. Cell Biol. 17, 213–226 (2016).

    Article  PubMed  CAS  Google Scholar 

  3. D’Amico, D., Sorrentino, V. & Auwerx, J. Cytosolic proteostasis networks of the mitochondrial stress response. Trends Biochem. Sci. 42, 712–725 (2017).

    Article  PubMed  CAS  Google Scholar 

  4. Melber, A. & Haynes, C. M. UPR mt regulation and output: a stress response mediated by mitochondrial–nuclear communication. Cell Res. 28, 281–295 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Durieux, J. & Dillin, A. Mitochondria and aging: dilution is the solution. Cell Metab. 6, 427–429 (2007).

    Article  CAS  PubMed  Google Scholar 

  6. Donati, G., Imbriano, C. & Mantovani, R. Dynamic recruitment of transcription factors and epigenetic changes on the ER stress response gene promoters. Nucleic Acids Res. 34, 3116–3127 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Donati, G. et al. An NF-Y-dependent switch of positive and negative histone methyl marks on CCAAT promoters. PLoS ONE 3, 2006 (2008).

    Article  CAS  Google Scholar 

  8. Ceribelli, M. et al. The histone-like NF-Y Is a bifunctional transcription factor. Mol. Cell. Biol. 28, 2047–2058 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. McCarroll, S. A. et al. Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat. Genet. 36, 197–204 (2004).

    Article  CAS  PubMed  Google Scholar 

  10. Ventura-Clapier, R., Garnier, A. & Veksler, V. Transcriptional control of mitochondrial biogenesis: the central role of PGC-1α. Cardiovasc. Res. 79, 208–217 (2008).

    Article  CAS  PubMed  Google Scholar 

  11. Angelo, G. & Van Gilst, M. R. Starvation protects germline stem cells c extends reproductive longevity in C. elegans. Science 326, 954–958 (2009).

    Article  CAS  PubMed  Google Scholar 

  12. Gerisch, B. et al. HLH-30/TFEB is a master regulator of reproductive quiescence. Dev. Cell https://doi.org/10.1016/j.devcel.2020.03.014 (2020).

    Article  PubMed  CAS  Google Scholar 

  13. Mair, W. et al. Lifespan extension induced by AMPK and calcineurin is mediated by CRTC-1 and CREB. Nature 470, 404–408 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Nargund, A. M., Pellegrino, M. W., Fiorese, C. J., Baker, B. M. & Haynes, C. M. Mitochondrial import efficiency of ATFS-1 regulates mitochondrial UPR activation. Science 337, 587–590 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Blackwell, T. K., Steinbaugh, M. J., Hourihan, J. M., Ewald, C. Y. & Isik, M. SKN-1/Nrf, stress responses, and aging in Caenorhabditis elegans. Free Radic. Biol. Med. 88, 290–301 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Zhang, K. et al. Endoplasmic reticulum stress activates cleavage of CREBH to induce a systemic inflammatory response. Cell 124, 587–599 (2006).

    Article  CAS  PubMed  Google Scholar 

  17. Merkwirth, C. et al. Two conserved histone demethylases regulate mitochondrial stress-induced longevity. Cell 165, 1209–1223 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Durieux, J., Wolff, S. & Dillin, A. The cell-non-autonomous nature of electron transport chain-mediated longevity. Cell 144, 79–91 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Haynes, C. M. & Ron, D. The mitochondrial UPR — protecting organelle protein homeostasis. J. Cell Sci. 123, 3849–3855 (2010).

    Article  CAS  PubMed  Google Scholar 

  20. Pellegrino, M. W., Nargund, A. M. & Haynes, C. M. Signaling the mitochondrial unfolded protein response. Biochim. Biophys. Acta Mol. Cell Res. 1833, 410–416 (2013).

    Article  CAS  Google Scholar 

  21. Kim, H. E. et al. Lipid biosynthesis coordinates a mitochondrial-to-cytosolic stress response. Cell 166, 1539–1552.e16 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Baruah, A. et al. CEP-1, the Caenorhabditis elegans p53 Homolog, mediates opposing longevity outcomes in mitochondrial electron transport chain mutants. PLoS Genet. 10, e1004097 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Tiku, V. et al. Small nucleoli are a cellular hallmark of longevity. Nat. Commun. 8, 16083 (2016).

  24. Elleder, M. et al. Prosaposin deficiency — a rarely diagnosed, rapidly progressing, neonatal neurovisceral lipid storage disease. Neuropediatrics 36, 171–180 (2005).

    Article  CAS  PubMed  Google Scholar 

  25. Vaccaro, A. M. et al. Effect of saposins A and C on the enzymatic hydrolysis of liposomal glucosylceramide. J. Biol. Chem. 16862–16867 (1997).

    Article  CAS  PubMed  Google Scholar 

  26. Paradies, G., Paradies, V., De Benedictis, V., Ruggiero, F. M. & Petrosillo, G. Functional role of cardiolipin in mitochondrial bioenergetics. Biochim. Biophys. Acta 1837, 408–417 (2014).

    Article  CAS  PubMed  Google Scholar 

  27. Okino, N. et al. The reverse activity of human acid ceramidase. J. Biol. Chem. 278, 1621 (2003).

    Article  CAS  Google Scholar 

  28. Buschlen, S. et al. The S. cerevisiae HAP complex, a key regulator of mitochondrial function, coordinates nuclear and mitochondrial gene expression. Comp. Funct. Genomics 4, 37–46 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Benatti, P. et al. NF-Y activates genes of metabolic pathways altered in cancer cells. Oncotarget 7, 1633–1650 (2016).

    Article  PubMed  Google Scholar 

  30. Liu, Y., Samuel, B. S., Breen, P. C. & Ruvkun, G. Caenorhabditis elegans pathways that surveil and defend mitochondria. Nature 508, 406–410 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Schuette, C. G., Pierstorff, B., Huettler, S. & Sandhoff, K. Sphingolipid activator proteins: proteins with complex functions in lipid degradation and skin biogenesis. Glycobiology 11, 81–90 (2001).

    Article  Google Scholar 

  32. Dupre, T. V. et al. Inhibiting glucosylceramide synthase exacerbates cisplatin-induced acute kidney injury. J. Lipid Res. 58, 1439–1452 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hage-Sleiman, R., Esmerian, M. O., Kobeissy, H. & Dbaibo, G. p53 and ceramide as collaborators in the stress response. Int. J. Mol. Sci. 322, 14–5012 (2013).

    Google Scholar 

  34. Deng, X. et al. Ceramide biogenesis is required for radiation-induced apoptosis in the germ line of C. elegans. Science 322, 110–115 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Houtkooper, R. H. & Vaz, F. M. Cardiolipin, the heart of mitochondrial metabolism. Cell. Mol. Life Sci. 65, 2493–2506 (2008).

    Article  CAS  PubMed  Google Scholar 

  36. Dudek, J. Role of cardiolipin in mitochondrial signaling pathways. Front. Cell Dev. Biol. 5, 1–17 (2017).

    Article  Google Scholar 

  37. Diogo, C. V., Yambire, K. F., Fernández Mosquera, L., Branco, F. T. & Raimundo, N. Mitochondrial adventures at the organelle society. Biochem. Biophys. Res. Commun. 500, 87–93 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Elbaz-Alon, Y. et al. A dynamic interface between vacuoles and mitochondria in yeast. Dev. Cell 30, 95–102 (2014).

    Article  CAS  PubMed  Google Scholar 

  39. Gottschling, D. E. & Nyström, T. The upsides and downsides of organelle interconnectivity. Cell 169, 24–34 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Hughes, A. L. & Gottschling, D. E. An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast. Nature 492, 261–265 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Kim, N. Y., Woo, A. M., Kim, J. R. & Lee, C. Exploration of senescence-associated genes by differential display reverse transcription polymerase chain reaction: prosaposin as a novel senescence-associated gene. Arch. Pharm. Res. 32, 737–745 (2009).

    Article  CAS  PubMed  Google Scholar 

  42. Boutros, M. & Ahringer, J. The art and design of genetic screens: RNA interference. Nat. Rev. Genet. 9, 554–566 (2008).

    Article  CAS  PubMed  Google Scholar 

  43. Gerisch, B., Weitzel, C., Kober-Eisermann, C., Rottiers, V. & Antebi, A. A hormonal signaling pathway influencing C. elegans metabolism, reproductive development, and life span. Dev. Cell 1, 841–851 (2001).

    Article  CAS  PubMed  Google Scholar 

  44. Bratic, I., Hench, J. & Trifunovic, A. Caenorhabditis elegans as a model system for mtDNA replication defects. Methods 51, 437–443 (2010).

    Article  CAS  PubMed  Google Scholar 

  45. 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 

  46. Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Dagda, R. K. et al. Loss of PINK1 function promotes mitophagy through effects on oxidative stress and mitochondrial fission. J. Biol. Chem. 284, 13843–13855 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Bolte, S. & Cordelières, F. P. A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213–232 (2006).

    Article  CAS  PubMed  Google Scholar 

  49. Nakamura, S. et al. Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals. Nat. Commun. 7, 10944 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Dodt, M., Roehr, J. T., Ahmed, R. & Dieterich, C. FLEXBAR-flexible barcode and adapter processing for next-generation sequencing platforms. Biology (Basel). 1, 895–905 (2012).

    PubMed  PubMed Central  Google Scholar 

  51. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).

    Article  CAS  PubMed  Google Scholar 

  52. Cox, J. et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794–1805 (2011).

    Article  CAS  PubMed  Google Scholar 

  53. Cox, J. et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics 10, 1794–1805 (2014).

    Google Scholar 

  54. Ritchie, M. E. et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Alexa, A. & Rahnenfuhrer, J. topGO: Enrichment Analysis for Gene Ontology. R package version 2.26.0 (R Foundation for Statistical Computing, 2016).

  56. Alexa, A., Rahnenführer, J. & Lengauer, T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22, 1600–1607 (2006).

    Article  CAS  PubMed  Google Scholar 

  57. Carlson, M. org.Hs.eg.db: Genome wide annotation for Human. R package version 3.1.2 (R Foundation for Statistical Computing, 2015).

  58. Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2009).

  59. Le’, S., Josse, J. & Husson, F. FactoMineR: an R package for multivariate analysis. J. Stat. Softw. 25, 1–18 (2008).

    Google Scholar 

  60. Kassambara, A. & Mundt, F. Factoextra: Extract and Visualize the Results of Multivariate Data Analyses. R package version 1.0.7 (R Foundation for Statistical Computing, 2017).

  61. Annibal, A. et al. A novel EI-GC/MS method for the accurate quantification of anti-aging compound oleoylethanolamine in C. elegans. Anal. Methods 22, 2551–2559 (2018).

    Article  Google Scholar 

  62. Hu, C. et al. RPLC-lon-trap-FTMS method for lipid profiling of plasma: method validation and application to p53 mutant mouse model. J. Proteome Res. 7, 4982–4991 (2008).

    Article  CAS  PubMed  Google Scholar 

  63. Sparagna, G. C., Johnson, C. A., McCune, S. A., Moore, R. L. & Murphy, R. C. Quantitation of cardiolipin molecular species in spontaneously hypertensive heart failure rats using electrospray ionization mass spectrometry. J. Lipid Res. 46, 1196–1204 (2005).

    Article  CAS  PubMed  Google Scholar 

  64. Scherer, M., Schmitz, G. & Liebisch, G. Simultaneous quantification of cardiolipin, bis(monoacylglycero)phosphate and their precursors by hydrophilic interaction LC-MS/MS including correction of isotopic overlap. Anal. Chem. 82, 8794–8799 (2010).

    Article  CAS  PubMed  Google Scholar 

  65. Garrett, T. A., Kordestani, R. & Raetz, C. R. H. Quantification of cardiolipin by liquid chromatography–electrospray ionization mass spectrometry. Methods in Enzymology 433, 213–230 (2007).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank the CGC (University of Minnesota), A. Trifunovic (University of Cologne), C. Haynes (University of Massachusetts), A. Dillin (University of California, Berkeley) and SunyBiotech for strains. Our proteomics bioinformatic and microscopy cores for assistance (MPI-AGE), T. Vicar and T. Langer (MPI-AGE) for manuscript comments, C. Geisen and C. Calabrese for scientific input, and C. Latza for lipidomics. This work was funded by the Max Planck Society.

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Authors and Affiliations

  1. Max Planck Institute for Biology of Ageing, Cologne, Germany

    Rebecca George Tharyan, Andrea Annibal, Isabelle Schiffer, Raymond Laboy, Ilian Atanassov, Anna Luise Weber, Birgit Gerisch & Adam Antebi

  2. CECAD, University of Cologne, Cologne, Germany

    Isabelle Schiffer, Raymond Laboy & Adam Antebi

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Contributions

A. Antebi and R.G.T. designed experiments and wrote the paper. R.G.T. carried out all experiments. I.A. performed proteomics and multi-omics analysis. A. Annibal performed lipidomic analysis and cardiolipin staining. I.S. constructed and generated spp-8 reporter, and R.L. performed co-localization and LysoTracker stainning experiments. A.L.W. gave technical assistance and B.G. aided with ARD induction and formulated the ARD recovery RNAi screen idea.

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Correspondence to Adam Antebi.

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Extended data

Extended Data Fig. 1 NFYB-1 regulates mitochondrial function and longevity (Related to Fig. 2).

a, Mini lifespan screen of WT and isp-1(qm150) upon RNAi knockdown of candidate genes from egg on in comparison to luci RNAi control bacteria (N = 1, n = 120 per condition). b, Representative image of mKate2::NFYB-1 nuclear (nuc) localization in various tissues of AL day 1 adults, scale bar = 10 μm. c, Representative immunoblot of mKate2::NFYB-1 levels over age in AL WT (day 1, 3, 5, 9 and 13 as mentioned, n = 200 worms per repeat per condition), with quantitation and histone loading control. d-e, nfyb-1(cu13) mutations leads to a decrease in pcco-1::gfp expression in AL day 1 at 25 °C. d, Representative images of ca. n = 10–20 worms, scale bar = 75 μm, e, pcco-1::gfp expression levels normalised to (Time of Flight) TOF quantitated using biosorter (n ≥ 400). f, nfyb-1(cu13) mutation results in a decrease in relative basal oxygen consumption rate (OCR) compared to WT, and in germline-less glp-4(bn2);nfyb-1(cu13) compared to glp-4(bn2) animals at 25 °C, upon ARD recovery (n = 900 worms). g, Kaplan–Meier survival curves of WT, nfyb-1(cu13) upon ARD recovery shows that nfyb-1 loss leads to decrease in survival (n = 120 per repeat, per condition). h, i, Percentage decrease in mean and median survival of nfyb-1(cu13) in comparison to WT in AL and upon ARD recovery. j, cco-1 mRNA levels are reduced in nfyb-1(cu13). k, mRNA levels of nfyb-1 mitochondrial regulated genes, l, loss of nfyb-1 does not affect mRNA levels of atfs-1, dve-1 and skn-1, j-l quantitation by qPCR at AL day 1 (n ≥ 1000). b-l, All data represent N = 3 independent biological replicates, n = total worms per condition from three replicates unless stated otherwise. Error bar shows mean± s.e.m., statistics determined by c, j, l one-way ANOVA and e, f, k two-sided t-test, ns: not significant, *P < 0.5, **P < 0.01, ***P < 0.001. a, g-i, Two-sided Mantel–Cox log-rank test, refer to Supplementary Table 2 for statistics. d-f, ARD day 10 worm recovered for 1day.

Source Data

Extended Data Fig. 2 NFYB-1 partially regulates UPRmt factors and MCSR (Related to Fig. 2).

a–c, nfyb-1(cu13) loss leads to reduction in nuclear localization of pdve-1::dve-1::gfp upon mitochondrial stress induced by exposure to cco-1i (pointed by white arrow), AL day 1 adults a, microscopy images scale bar = 10 μm, b, quantitation of pdve-1::dve-1::gfp expression using biosorter (n ≥ 400) and c, representative immunoblot of pdve-1::dve-1::gfp, with quantitation of DVE-1::GFP and histone loading control (N = 4, n = 100 per repeat, per condition). d, Kaplan–Meier survival curve of isp-1(qm150) and isp-1(qm150); nfyb-1(cu13) shows that dve-1i does not further reduce isp-1;nfyb-1 lifespan (n = 120 per repeat, per condition). e, nfyb-1(cu13) mutation reduces nuclear localization of patfs-1::atfs-1::gfp upon mitochondrial stress induced by hsp-6i, L3-L4 larvae, scale bar = 10 μm (n ~ 30). f, nfyb-1(cu13) shows no significant (ns) effect on publ-5::gfp expression upon exposure to cco-1i or control luci, day 1 adult (n ≥ 400). g, nfyb-1(cu13) loss only partially reduces phsp-6::gfp expression upon cco-1i induced mitochondrial stress, day 1 adult (n ≥ 400). h, i nfyb-1(cu13) reduces phsp-16::gfp expression upon exposure to hsp-6i from day 1 to day 3, showing a requirement for MCSR. h, microscopy images, scale bar = 75 μm, i, quantitation of phsp-16::gfp expression using biosorter (n ≥ 200). j, k, nfyb-1(cu13) leads to a reduction in lipids by BODIPY staining from day 1 to day 3. j, microscopy images, scale bar = 10 μm, k, quantitation of expression using biosorter (n ≥ 200). a-k, under all WT conditions, cco-1i and hsp-6i induce the mitochondrial stress response. b, d, e-g, i, k All data represent N = 3 independent biological replicates, n = total worms per condition from three replicates unless stated otherwise. Error bar shows mean ± s.e.m, b, e-g, i, k statistics determined by one-way ANOVA and c, two-sided t-test. *P < 0.5, **P < 0.01, ***P < 0.001. d, Two-sided Mantel–Cox log-rank test, refer to Supplementary Table 2 for statistics.

Source Data

Extended Data Fig. 3 NFYB-1 omics analyses, ER genes only weakly modulate mitochondrial longevity (Related to Fig. 3).

a, Workflow of transcriptomics and proteomics analysis for indicated genotypes on AL day 1 adult worms. Heat maps represent log2-fold change of differentially expressed transcripts and proteins (P < 0.05). b, Averaged PCA (Principal Component Analysis) of most variable differentially expressed genes in transcriptomics and proteomics of day 1 adults for genotypes WT, nfyb-1(cu13), isp-1(qm150) and isp-1(qm150);nfyb-1(cu13), (Omics: transcriptomics N = 3, proteomics N ≥ 5 independent biological replicates. n ≥ 5000 worms per condition per repeat). c, Mean lifespan of isp-1(qm150) and isp-1(qm150);nfyb-1(cu13) upon RNAi knockdown of differentially expressed proteins or luciferase control RNAi (luci) (n = 120 per repeat, per condition), spp-8i shows the most prominent rescue of lifespan. d, nfyb-1(cu13) elevates expression of UPRER marker, phsp-4::gfp, which is dependent on UPRER factors ire-1 and xbp-1, day 1 adult, quantitation by biosorter (n ≥ 400). e, Kaplan–Meier survival curve of isp-1(qm150);nfyb-1(cu13) upon RNAi knockdown of UPRER factors show no significant regulation of lifespan (N = 2 independent biological replicates, n = 120 per repeat, per condition). c, d, All data represent N = 3 independent biological replicates unless stated otherwise, n = total worms per condition from three replicates unless stated otherwise. Error bar shows mean ± s.e.m, d, statistics determined by one-way ANOVA, *P < 0.5, **P < 0.01, ***P < 0.001. c, e, Two-sided Mantel–Cox log-rank test, refer Supplementary Table 2 for statistics.

Extended Data Fig. 4 Lysosomal SPP-8 suppresses NFYB-1 dependent mitochondrial dysfunction (Related to Fig. 4).

a, spp-8i modestly increases WT and nfyb-1(cu13) lifespan (N = 2, n = 120 per repeat, per condition). b, spp-8 mRNA levels are unaffected by nfya-1 and nfyc-1 knockdown AL day 1, quantitated by qPCR (n ≥ 1000). c, skn-1 and dve-1 knockdown diminished elevated spp-8 mRNA in nfyb-(cu13) AL day 1, quantitated by qPCR (n ≥ 1000). d, e, Representative immunoblot of 1 kb pspp-8::NLS::GFP, shows skn-1 dependent regulation of spp-8 in nfyb-1(cu13) compared to AL WT day 1 (n = 100 per repeat, per condition) with quantitation and actin loading control. f, g, spp-8i rescues the reduced mitochondrial circularity and cross-sectional area of nfyb-1(cu13) mutants in AL day 5 (n ~ 30), quantitated47. h, spp-8i has no effect on phsp-4::gfp expression in indicated genotypes, quantitation by biosorter, AL day 1 (n ≥ 400). i, spp-8i has no effect on nfyb-1(cu13) regulated ER genes, quantitated by qPCR, AL day 1 (n ≥ 1000). j, k, Confocal microscopy images show endogenously tagged mKate2::NFYB-1 in intestine, co-localizes with LMP-1::GFP, AL day 1. Percentage colocalization as measured using Manders Colocalizaton Coefficient (Costes significance test was done for colocalization, refer method section for detail), AL day 1, scale bar = 10 μm (n ~ 30). l, nfyb-1(cu13) mutation leads to less acidified lysosomes in comparison WT, stained with LysoTracker Red in AL day 1 (n ~ 30). b-l, All data represent N = 3 independent biological replicates, n = total worms per condition from three replicates unless stated otherwise. Error bar shows mean ± s.e.m, statistics determined by b-c, e-h, one-way ANOVA, i and l, two-sided t-test ns: not significant, *P < 0.5, **P < 0.01, ***P < 0.001. a, Two-sided Mantel–Cox log-rank test, refer Supplementary Table 2 for statistics.

Source Data

Extended Data Fig. 5 NFYB-1 regulates specific lipid species via SPP-8 (Related to Fig. 4).

a, Absolute levels of respective ceramides species normalized to protein levels detected by targeted lipidomic analysis of day 1 isp-1(qm150) and isp-1(qm150);nfyb-1(cu13) on control and upon spp-8i in AL day 1 (N = 4, n ≥ 5000 per repeat per condition) (box plot represents line at median, using minimum and maximum of all of the data, error bar shows standard deviation above and below the mean of the data). b, Abundance of exogenously supplemented CER (ceramides) and CL (cardiolipins) as detected by Mass-spectrometry in AL day 1 (N = 1, n ≥ 1000). c, spp8i increases nonyl-acridine orange staining in AL day 1, indicating increased cardiolipin levels, quantitation by biosorter (n ≥ 400). d, Relative fold change in mRNA levels of cardiolipin synthesis genes measured by qPCR in indicated genotypes AL day1 (n ≥ 1000), e, Cardiolipin (CL) synthesis pathway. c-d, All data represent N = 3 independent biological replicates, n = total worms per condition from three replicates unless stated otherwise. Error bar shows mean ± s.e.m, statistics determined by a and c, one-way ANOVA and d, two-sided t-test ns: not significant, *P < 0.5, **P < 0.01, ***P < 0.001. f, NFYB-1 coordinates organellar activities: Transcription factor NFYB-1 promotes nuclear localization of UPRmt factors DVE-1 and ATFS-1, maintains cardiolipin levels and facilitates the mitochondria to cytosolic stress response (MCSR). Concurrently NFYB-1 limits ER associated genes, ER stress and lysosomal prosaposin. This state results in normal mitochondrial function and longevity. nfyb-1 loss (NFYB-1 KO) activates ER stress, partially disrupts UPRmt factors, and MCSR. NFYB-1 activates lysosomal prosaposin/SPP-8, leading to fragmented mitochondria, reduction of oxygen consumption, altered ceramide (CER) and cardiolipin (CL) levels, resulting in abolishment of mitochondrial longevity.

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Source Data Extended Data Fig. 1c

Supplementary Fig 1c: Immunoblots of WT; mKate2::NFYB-1

Source Data Extended Data Fig. 2c

Supplementary Fig. 2c: Immunoblots of pdve-1::DVE-1::GFP

Source Data Extended Data Fig. 4d

Supplementary Fig 4d: Immunoblots of 1 kb pspp-8::NLS::GFP (4X NLS)

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Tharyan, R.G., Annibal, A., Schiffer, I. et al. NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin. Nat Metab 2, 387–396 (2020). https://doi.org/10.1038/s42255-020-0200-2

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