Regulation of defective mitochondrial DNA accumulation and transmission in C. elegans by the programmed cell death and aging pathways
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa Barbara, United States
- Computational Biology Unit, Institute for Informatics, University of Bergen, Norway
Figures
Figure 1 with 2 supplements
Analysis of the impact of mtDNAuaDf5 on fitness parameters.
(A) Diagram of C. elegans mtDNA. Black bars with arrows indicate the locations of genes and direction of transcription. Black lines with letters indicate the locations of tRNAs. Green bars show the …
Figure 1—figure supplement 1
Characterization of the uaDf5 allele.
(A) The percentage of reads that mapped to the w47 insertion in uaDf5 samples (red) and wildtype samples (blue). Error bars represent standard deviation of the mean (SEM). (B) Table outlining the …
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Figure 1—figure supplement 1—source data 1
ddPCR reads of mitochondrial DNA.
- https://cdn.elifesciences.org/articles/79725/elife-79725-fig1-figsupp1-data1-v1.xlsx
Figure 1—figure supplement 2
Lifespan analysis of the impact of uaDf5.
Lifespan analysis of N2-bearing uaDf5 compared to wildtype N2. Day 1 is defined as the day starved L1s are plated on food. Box plots show median and IQR, and the diamond indicates the mean. …
Figure 2 with 4 supplements
Regulators of programmed cell death (PCD) act on mutant mtDNA.
(A–C) Digital-droplet PCR (ddPCR) analysis of the steady-state molar ratio of mtDNAuaDf5 in 200 worm populations of day 1 adults of various PCD mutant backgrounds. (A) PCD mutants that result in a …
Figure 2—figure supplement 1
Reproducibility of digital-droplet PCR (ddPCR) measurement of uaDf5.
Analysis of the steady state of uaDf5 in a wildtype nuclear background shows highly stable steady-state levels. Trials were done months apart on different thaws. Dots represent biological …
Figure 2—figure supplement 2
Programmed cell death (PCD) signaling pathway.
(A) Signaling pathway for PCD. The canonical pathway is shown with black arrows, the non-canonical pathway is shown with green arrows, and the downstream engulfment pathway is shown with blue …
Figure 2—figure supplement 3
Analysis of the ced-3 alleles.
(A) Locations and consequences of the four tested ced-3 alleles, as well as the measured fractional abundance of uaDf5. (B) Diagram showing the locations of the mutations for each allele.
Figure 2—figure supplement 4
Analysis of the impact of uaDf5 on fitness parameters in programmed cell death (PCD) mutants.
(A) Brood size analysis of PCD mutants. (B) Lifespan analysis shows that uaDf5 does not affect lifespan in both wildtype background and in PCD mutant backgrounds. (C) Lifespan analysis shows that uaD…
Figure 3 with 1 supplement
mtDNAuaDf5 accumulates in the germline of aging adults, and evidence of purifying selection between mother and offspring.
(A) Analysis of the molar ratio of mtDNAuaDf5 in aging adults in a wildtype nuclear background. Average wildtype mtDNA copy number ± standard deviation is shown in the graph below. (B) Analysis of …
Figure 3—figure supplement 1
uaDf5 accumulation in individual lines of adults and progeny.
(A) Analysis of uaDf5 accumulation in individual lines of aging P0 adults shows a consistent accumulation trend as adults age. (B) Analysis of uaDf5 accumulation in individual lines of F1-L1 progeny …
Figure 4 with 3 supplements
Lifespan mutants have both a lower steady-state level and accumulation rate of mtDNAuaDf5.
(A–C) Analysis of molar ratio of mtDNAuaDf5 in day 1 adults of various mutant backgrounds. Average wildtype mtDNA copy number ± standard deviation is shown in the graph below in each panel. (A) …
Figure 4—figure supplement 1
Insulin/IGF-1 signaling (IIS) pathway.
Insulin-like peptides (ILPs) bind to DAF-2 and activate the PI3P pathway which prevents nuclear translocation of DAF-16. AAK-2 may phosphorylate and activate DAF-16 transcriptional activity. Loss of …
Figure 4—figure supplement 2
Analysis of the accumulation of mtDNAuaDf5 in programmed cell death (PCD) and lifespan mutants.
Analysis of the normalized fractional abundance uaDf5 [(% uaDf5 day x − % uaDf5 day 1) × % uaDf5 day 1] in steady-state populations, showing the accumulation rate of mtDNAuaDf5 as worms age from day …
Figure 4—figure supplement 3
uaDf5 differentially impacts fitness parameters in lifespan-affecting mutants.
(A, B) Brood size analysis showing how uaDf5 differentially impacts brood size in lifespan mutant backgrounds. uaDf5 has no negative impact on the long-lived mutant clk-1 but has a modestly larger …
Figure 5
Evidence for late adulthood-specific mechanisms for removal of mtDNAuaDf5.
(A) Subtracting uaDf5:WT in progeny from day 1 adults from progeny of day 4 adults shows that day 4 F1-L1s tend to have higher mtDNAuaDf5 burden than their day 1 siblings, but this is no longer the …
Figure 6
Regulation of mtDNAuaDf5 accumulation and transmission by the programmed cell death (PCD) and aging pathways.
(A) Our results suggest that CED-3 and CSP-1, which are activated by BH-3 only protein CED-13, function cooperatively to promote mitochondrial purifying selection, independent of CED-9 and the CED-4 …
Additional files
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Supplementary file 1
A summary of all mutants analyzed in the PCD pathway, including their known homologs, whether they are part of the core PCD machinery, if they are pro- or anti-apoptotic, whether they are mitochondrial proteins, and molecular details of the alleles analyzed.
- https://cdn.elifesciences.org/articles/79725/elife-79725-supp1-v1.docx
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Supplementary file 2
Wildtype and mutant mtDNA levels in the different cell death and aging pathway mutants.
(mean of 3 replicates ± standard deviation).
- https://cdn.elifesciences.org/articles/79725/elife-79725-supp2-v1.docx
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Supplementary file 3
A summary of all lifespan mutants analyzed, including their known homologs, cellular pathways they are known to act in, whether the mutant extends or reduces lifespan, and molecular details of the alleles analyzed.
- https://cdn.elifesciences.org/articles/79725/elife-79725-supp3-v1.docx
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Supplementary file 4
C. elegans strains used in this study.
- https://cdn.elifesciences.org/articles/79725/elife-79725-supp4-v1.docx
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MDAR checklist
- https://cdn.elifesciences.org/articles/79725/elife-79725-mdarchecklist1-v1.pdf
