Mitochondrial dysfunction leads to nuclear genome instability via an iron-sulfur cluster defect

Abstract

Mutations and deletions in the mitochondrial genome (mtDNA), as well as instability of the nuclear genome, are involved in multiple human diseases. Here, we report that in Saccharomyces cerevisiae, loss of mtDNA leads to nuclear genome instability, through a process of cell-cycle arrest and selection we define as a cellular crisis. This crisis is not mediated by the absence of respiration, but instead correlates with a reduction in the mitochondrial membrane potential. Analysis of cells undergoing this crisis identified a defect in iron-sulfur cluster (ISC) biogenesis, which requires normal mitochondrial function. We found that downregulation of nonmitochondrial ISC protein biogenesis was sufficient to cause increased genomic instability in cells with intact mitochondrial function. These results suggest mitochondrial dysfunction stimulates nuclear genome instability by inhibiting the production of ISC-containing protein(s), which are required for maintenance of nuclear genome integrity. For a video summary of this article, see the PaperFlick file available with the online Supplemental Data.

Figure 1. Loss or damage to the mtDNA results in nuclear genomic instability

(A-B) Forty mother cells were analyzed by pedigree analysis. (A) left: Colonies produced by the 1^st through 37^th daughter of a single representative mother cell are shown (daughter 13 did not produce a colony). Right: The colonies from the left were replicated to media containing lead nitrate, which permits colony color development. Chromosome IV LOH results in a brown color, and chromosome XII LOH results in a red color. (B) The fraction of colonies that had at least a 1/8 sector of colony color are presented as a function of the number of cell divisions the mother cell went through. The data were classified as to whether the colony was normal or petite. Data are shown for LOH events that occurred on either the right arm of chromosome XII or IV. The difference in the LOH frequency between petite and normal cells for divisions 11-30 had a significance of p<0.0001 from chromosome XII and p<0.001 for chromosome IV. (C) A wild-type (WT) strain was treated with or without a transient pulse of ethidium bromide (EtBr), and colonies grown from these cells were transferred to medium allowing visualization of LOH events. A derivative of the wild-type strain containing the dominant negative P_GAL1-MIP1^DN allele under control of the Gal4-EBD-VP16 (GEV) fusion protein was treated with or without a transient pulse of estradiol (E2), and grown as described above. (D) The treatments described in C were carried out on the WT strain or derivatives of this strain that contain the GEV activator, and/or the dominant negative P_GAL1-MIP1^DN as indicated. The percentage of colonies showing at least a 1/8 sector of LOH on chromosome XII and IV are presented. All error bars represent 95% confidence intervals and were calculated using the Poisson distribution.

Figure 2. Loss of the mtDNA leads to a progressive decline in growth rate, cell cycle arrest, and selection for suppressor clones

(A) Growth rate of isogenic strains containing the GEV transcriptional activator, P_GAL1-MIP1^DN or both, following transient treatment with estradiol (E2). (B) Growth rate of the wild-type strain treated with or without a transient pulse of ethidium bromide. (C) The percentage of cells from (A) and (B) able to form a colony of at least 1mm in diameter after 8 days is presented on the left. The percentage of cells arrested as unbudded cells is presented on the right. Error bars represent 95% confidence intervals calculated using the binomial distribution. (D) Spontaneous [ρ⁰] haploid suppressor mutants were back-crossed to isogenic cells with intact mtDNA. After sporulation, haploid [ρ⁺] progeny of these crosses containing each suppressor allele were treated transiently with ethidium bromide and the growth rate was monitored as before.

Figure 3. The absence of respiration is not sufficient to cause the crisis and LOH

(A) Wild-type cells (UCC1899) and derivatives with homozygous deletions for either COX4, RIP1 or CAT5 were treated as described in Figure 2A. (B-D) Growth rate of cells with or without transient treatment with ethidium bromide. Wild-type cells are compared to deletions of CAT5 (B), RIP1 (C) or COX4 (D).

Figure 4. A hyperactive F₁ ATP synthase partially restores mitochondrial protein import and prevents the growth defect and nuclear genomic instability that results from mtDNA loss

(A) Growth rates of a wild-type diploid and a the ATP1-111/ATP1-111 derivative, with or without transient ethidium bromide treatment. (B) The frequency of LOH events in the strains from (A). (C) Localization of proteins to the outer mitochondrial membrane (Tom70-GFP, green) or the mitochondrial matrix (preCox4-Cherry, red) in wild-type cells or ATP1-111/ATP1-111 derivative cells are presented.

Figure 5. Cells show a transcriptional signature of iron starvation following mtDNA loss

Levels of mRNA from WT cells 3, 11, 19 and 27 hours after mtDNA loss were compared to cells with intact mtDNA. mRNA from ATP1-111 mutants collected 27 hours after mtDNA loss was compared to mRNA of the same strain with intact mtDNA. mRNA was isolated from the NAR1 repressible strain 27 hours after a shift from 50 nM estradiol to 2 nM estradiol and compared to the same strain grown in 50 nM estradiol. Genes are arranged in order of their reported magnitude of induction (red) or repression (green) by iron starvation (Puig et al., 2005). Comparisons are made to published array data for depletion of the YAH1 and ATM1 genes (Hausmann et al., 2008).

Figure 6. Reducing ISC protein loading activity in the cytoplasm leads to nuclear genome instability

(A) A strain (UCC3970) with NAR1 expression controlled by estradiol (E2) was plated to media containing either 50 nM (NAR1 expressed) or 2 nM estradiol (NAR1 down-regulated) followed by replication to LOH indicator media. (B) The frequency of colonies showing at least 1/8 sector of LOH following plating of the strain in A (NAR1^EST) and an isogenic strain without the estradiol regulated promoter (WT) to either low (2nM) or high (50nM) estradiol (E2). Error bars represent 95% confidence intervals calculated using the Poisson distribution.

Figure 7. Model to explain nuclear genomic instability following mtDNA loss

A) In normal cells, iron is packaged into iron-sulfur clusters (ISCs) in the mitochondria, and some ISCs are exported into the cytoplasm. The cytoplasmic ISCs inhibit iron regulon induction and are required for the function of proteins that maintain nuclear genome integrity. (B) Upon loss of the mtDNA, the mitochondrial membrane potential (Δψ) is reduced, which compromises mitochondrial iron import, ISC packaging, and/or export. This results in iron regulon induction and nuclear genome instability. (C) Artificially reduced Nar1 function limits packaging of ISCs into proteins involved in nuclear DNA metabolism, leading to nuclear genome instability. In this case mitochondrial function is intact and the iron regulon is not induced.