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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
J Cell Sci. Author manuscript; available in PMC 2017 December 13.
Published in final edited form as:
PMCID: PMC5728373
NIHMSID: NIHMS908696

Mitochondrial Nucleoids Undergo Remodeling in Response to Metabolic Cues

Summary

Mitochondrial DNA is organized as a nucleoprotein complex called the nucleoid. Its major protein components have been identified in different organisms, but it is unknown whether nucleoids undergo any form of remodeling. Using an in organello ChIP on chip assay, we demonstrate that the DNA bending protein Abf2 binds to most of the mitochondrial genome with a preference for GC-rich gene sequences. Thus, Abf2 is a bona fide mitochondrial DNA packaging protein in vivo. Nucleoids form a more open structure under respiring growth conditions in which the ratio of Abf2 to mitochondrial DNA is decreased. Bifunctional nucleoid proteins Hsp60 and Ilv5 are recruited to nucleoids during glucose repression and amino acid starvation, respectively. Thus, mitochondrial nucleoids in yeast are dynamic structures that are remodeled in response to metabolic cues. A mutant form of Hsp60, which exhibits an mtDNA instability phenotype, has altered submitochondrial localization, suggesting that nucleoid remodeling is essential for the maintenance of mitochondrial genome.

Introduction

Genomic DNA is organized as chromatin, a highly dynamic and intricate nucleoprotein structure. Histones are the major protein components of nuclear chromatin where, as an octamer, they wrap and thus condense DNA in the form of nucleosomes. Nucleosome remodeling has emerged as a key strategy for the regulation of gene expression as well as for other chromosomal events including DNA replication, recombination, repair, and segregation (Ehrenhofer-Murray, 2004). Histones are extensively modified, undergoing different posttranslational modifications, depending on their chromosomal location (Saha et al., 2006). As a result, chromatin remodeling is an essential process in eukaryotic cells, playing a crucial role in growth, development, and epigenetic events.

The mitochondrial genomes are packaged with proteins yielding structures, which, by analogy to bacterial chromosomes, are called mitochondrial DNA (mtDNA) nucleoids (Chen and Butow, 2005; Kucej and Butow, 2007; Malka et al., 2006). In contrast to nuclear chromatin, there is less information on the organization and dynamics of mtDNA nucleoids and how these properties might affect mtDNA transactions, including gene expression and inheritance. Initial studies in yeast (Chen et al., 2005; Kaufman et al., 2000; Miyakawa et al., 1987), human (Bogenhagen et al., 2007; Cheng et al., 2005; Garrido et al., 2003; Wang and Bogenhagen, 2006), and frog (Bogenhagen et al., 2003) revealed that in addition to DNA transaction factors, high mobility group (HMG) like proteins plus a set of chaperones and metabolic enzymes are the major nucleoid components. Mitochondrial nucleoids lack histones. Instead, many mitochondrial genomes of different organisms are putatively packaged by HMG like proteins such as Abf2 in the budding yeast, Saccharomyces cerevisiae, and Tfam in animal cells (Chen and Butow, 2005; Kaufman et al., 2007; Malka et al., 2006). These proteins are able to bend and wrap dsDNA in vitro (Brewer et al., 2003; Fisher et al., 1992; Friddle et al., 2004). Abf2 readily associates with DNA without sequence specificity, although it has a decreased affinity for simple polyA sequences (Diffley and Stillman, 1992). This feature causes phased binding, which was found to occur in vitro on replication origins and promoter sequences (Diffley and Stillman, 1991; Fisher et al., 1992). The mtDNA in abf2 mutants is less protected and exhibits increased sensitivity to nuclease attack (Newman et al., 1996) and oxidative stress (O'Rourke et al., 2002). Nucleoids contain an assortment of proteins with no obvious role in mtDNA transactions. These “unexpected” nucleoid proteins, such as aconitase and Ilv5 in yeast, have turned out to be bifunctional with distinct metabolic activities and, as nucleoid proteins, novel activities with respect to their functions in the maintenance of mtDNA (Bateman et al., 2002b; Chen et al., 2007; Chen et al., 2005; Kaufman et al., 2003; Shadel, 2005; Zelenaya-Troitskaya et al., 1995).

Here we demonstrate by chromatin immunoprecipitation (ChIP) that yeast Abf2 is a bona fide mtDNA packaging protein. Due to changes in mtDNA copy number, the ratio of Abf2 to mtDNA varies in different growth conditions, which is accompanied by variable sensitivity of mtDNA to micrococcal nuclease. In addition, other nucleoid proteins like Hsp60 and Ilv5 are recruited to nucleoids during glucose repression and amino acid starvation, respectively. We propose that these protein localization dynamics constitute a mitochondrial nucleoid remodeling. Finally, the nucleoid remodeling seems to be essential for the maintenance of mtDNA, as some mutant forms of nucleoid proteins that destabilize mtDNA, like Hsp60 A144V and previously reported Ilv5 W327R (Bateman et al., 2002a), have perturbed submitochondrial localization.

Results

Mapping Abf2 interactions with the mitochondrial genome

Abf2 is considered to be the major mtDNA packaging protein in yeast, but no comprehensive analysis of Abf2 interaction with mtDNA in situ is available. Therefore, we examined the binding of Abf2 and mtDNA by means of chromatin immunoprecipitation experiments, in which proteins associated with mtDNA were crosslinked to DNA or to each other by formaldehyde treatment of isolated mitochondria (Fig. S1). A strain expressing the fusion protein Abf2-13Myc was constructed for this purpose. Expression of the fusion protein was verified by western blotting with an anti-Myc antibody (Fig. S2). We did not observe any mtDNA instability in the constructed strain, indicating that Abf2-13Myc is functional (data not shown). After formaldehyde treatment, the purified mitochondria were lysed with a non-ionic detergent, sheared by sonication to obtain ~500 bp DNA fragments, and nucleoid complexes were immunoprecipitated with an anti-Myc antibody. The coimmunoprecipitated DNA was first used as a probe for Southern blot hybridization (Fig. 1 A). ChIP DNA was labeled without amplification and hybridized to blots of total mtDNA digested with DraI. We found that the hybridization profile obtained with the ChIP DNA was similar to that obtained when CsCl-purified total mtDNA was used as a probe, indicating that Abf2p binds most regions of mtDNA. The difference in signal intensities between the strains expressing Abf2-13Myc and the untagged Abf2 demonstrates that ChIP with Abf2 was very efficient. As a result, almost all immunoprecipitated DNA from the Myc-tagged strain represented the DNA material specifically bound by Abf2. These observations strongly support the role of Abf2 as a major mtDNA packaging protein.

Fig. 1
Abf2 associates preferentially with complex GC-rich sequences. (A) Southern blot hybridizations of blots of mtDNA digested with DraI with the following probes: CsCl-purified total mtDNA sheared by sonication (left panel), DNA coimmunoprecipitated with ...

To map the association of Abf2 with mtDNA in greater detail, we opted to examine DNA obtained from the ChIP experiments with DNA microarrays. A similar approach was successfully used to identify mtDNA binding sites of Arg5/6 protein in yeast (Hall et al., 2004). However, authors of this study examined mostly mitochondrial gene sequences. We wanted to compare representatives of all features on the yeast mtDNA, including intergenic regions. Therefore, we prepared DNA microarrays of ~550 bp average length mtDNA fragments covering ~70% of a wild-type mitochondrial genome lacking introns, which we used for mitochondrial ChIP-chip (Fig. 1 D). Amplified DNA samples from Abf2-13Myc and untagged Abf2 ChIP experiments were labeled with Cy5; CsCl-purified, ultrasonically sheared total mtDNA, amplified by the same procedure, was used as a Cy3-labeled control (Fig. S1). Microarray hybridization datasets of Abf2-13Myc experimental samples and Abf2 controls (Fig. S3) were compared using a median percentile rank method, as described previously (Buck and Lieb, 2004). When DNA spots with the same median percentile ranks were grouped, a small subset of sequences appeared as a second peak (Fig. 1 B). This group of sequences was represented almost exclusively by long, complex, GC rich sequences located in COX1, COX3, COB, ATP6, ATP9, 15S_rRNA, and 21S_rRNA gene loci (Fig. 1, C and D). Normally, only these enriched sequences would be considered to be bound by an analyzed protein. However, since the amount of crosslinked DNA was much higher in Abf2-13Myc samples compared with Abf2 controls (Fig. 1 A), the correct interpretation is that Abf2 protein binds most of the mtDNA sequences with a relatively higher affinity for GC-rich gene regions.

Abf2 protein-protein interactions in mitochondria

We performed ChIP-chip assays with two additional mitochondrial nucleoid proteins, namely Aco1 in glycerol medium and Ilv5 in medium lacking amino acids. No specific DNA enrichment was observed in these experiments. The most probable cause is very inefficient crosslinking of the examined proteins to mtDNA. When an excessive treatment by formaldehyde was applied mitochondrial chromatin became resistant to DNA fragmentation and thus unusable for ChIP. It has been indeed observed that Aco1, for instance, exhibits only a weak binding to dsDNA (Chen et al., 2007). Also, it is conceivable that some nucleoid proteins are preferentially retained in proximity of mtDNA by protein-protein interactions with other DNA binding proteins. We therefore asked whether we could coimmunoprecipitate such proteins with an mtDNA binding protein, namely Abf2 (Fig. 2). Mitochondria isolated from yeast strains expressing Abf2-13Myc and Abf2 as a control were crosslinked with dithiobis(succinimidylpropionate) (DSP) and lyzed with a non-ionic detergent. The lyzate was treated with DNAseI to prevent detection of protein interactions mediated by DNA (Fig. 2C). Abf2-13Myc protein was immunoprecipitated from the lysate using an anti-Myc antibody. The crosslinks were reversed and coimmunoprecipitated proteins were analyzed by gel electrophoresis (Fig. 2B). The examination of silver-stained bands, specific to the sample from the Abf2-13Myc expressing strain, revealed Aco1, Ald4, Idh1, Idh2, and Kgd1 as the major interacting proteins of Abf2. The proteins identified in this screen have been previously found in purified formaldehyde-fixed nucleoids (Kaufman et al., 2000). Thus, protein crosslinking with DSP further supports the localization of these proteins in nucleoids. Moreover, these proteins directly interact or are in proximity to the major nucleoid protein Abf2.

Fig. 2
Abf2 protein interactions in mitochondria. (A) An approach for identification of mitochondrial Abf2-interacting proteins. The purified mitochondria from yeast strains expressing Abf2 and Abf2-13Myc were crosslinked with DSP. Mitochondrial lysates were ...

Remodeling of mitochondrial nucleoids

Although the composition of mitochondrial nucleoids in yeast has been reasonably well-characterized, there is little information on whether nucleoids undergo structural or compositional remodeling. We therefore examined these issues in cells in which the respiration was repressed by glucose and activated by growth of cells on glycerol. To investigate whether nucleoid remodeling occurs in these conditions, we assessed the sensitivity of selected mtDNA sequences to micrococcal nuclease digestion in toluene-permeabilized mitochondria (Newman et al., 1996). Nucleoids that might be in a more compact structure, or more covered with proteins, should be more resistant to nuclease digestion, whereas nucleoids with a more open structure should be more sensitive to nuclease digestion. Accordingly, we compared three test regions of the mitochondrial genome, the 21S_rRNA region 71, the ATP6 region 33, and the intergenic DNA region 81 (Table S1), for their sensitivity to nuclease digestion. We found that these sequences were more resistant to nuclease attack in mitochondria isolated from glucose grown cells than from glycerol grown cells (Fig. 3, A-C). Thus, the structure of mitochondrial nucleoids differs in these conditions and is more open in glycerol grown cells compared with glucose grown cells.

Fig. 3
Mitochondrial nucleoids undergo remodeling. (A to C) The quantification of micrococcal nuclease sensitivity assays of 21S_rRNA (A), ATP6 (B) and an intergenic region 81 (C) using ~1mg of toluene-permeabilized mitochondria isolated from BY4741 ...

Our ChIP-chip experiments demonstrate that Abf2 binds most of the mtDNA sequences, consistent with it being an mtDNA packaging protein. Using nuclease sensitivity assays, it has been demonstrated previously that Abf2 is the major determinant of mtDNA protection from a nuclease (Newman et al., 1996). Thus, the nucleoid remodeling observed by micrococcal nuclease sensitivity assays could be accomplished by modulation of Abf2 levels, for example, by increasing the amount of Abf2 in glucose medium, or decreasing it in glycerol medium. However, expression of Abf2 was comparable in BY4741 cells grown in both types of media (Fig. 3 D). Notably, mtDNA copy number can vary too, depending on whether cells grow in glucose or on a non-fermentable carbon source (Goldthwaite et al., 1974), providing another means for nucleoid remodeling. Therefore, we measured mtDNA abundance in the BY4741 strain used in this study, and confirmed that mtDNA copy number was ~two-fold higher in glycerol grown cells compared with glucose grown cells (Fig. 3 E). As a result, the Abf2 to mtDNA ratio in whole cells is decreased by a factor of two in glycerol medium. In agreement with this observation, nucleoids in glycerol grown cells were less protected from nuclease digestion.

To examine the possibility that the distribution of Abf2 to nucleoids may vary under these different metabolic conditions, we assessed the submitochondrial localization of Abf2 by sedimentation of mitochondrial lysates in sucrose gradients. Purified mitochondria were lysed with a nonionic detergent and loaded on to stepwise 20%/60%/80% sucrose gradients. MtDNA was found in fractions near the bottom of the gradient (Fig. 4 B), whereas the mitochondrial matrix marker protein, Mdh1, remained near the top (Fig. 4 A). We repeatedly observed that in our experimental conditions, Abf2 largely co-fractionated with mtDNA in cells grown in both glucose and glycerol medium (Fig. 4, A and B). We quantified the amount of mtDNA and Abf2 in the first seven fractions from the bottom, and confirmed that the average Abf2 to mtDNA ratio in glycerol grown cells reaches 59 % ± 21 % of the ratio in glucose grown cells. This approximately reflects changes in the whole cell ratio of Abf2 to mtDNA (Fig. 3, D and E). In summary, because the level of expression and the pattern of distribution of Abf2 between nucleoids and the matrix do not vary, while the copy number of mtDNA does, the amount of Abf2 associated with mtDNA effectively decreases in mitochondrial nucleoids of glycerol grown cells. This provides an explanation for a more open structure of nucleoids detected by micrococcal nuclease.

Fig. 4
Distribution of nucleoid proteins in sucrose gradients. Sucrose gradients of an equal amount of lysed purified mitochondria (~1 mg of proteins) isolated from BY4741 cells grown in glucose and glycerol containing media (A, B) and MCC109 cells grown ...

Recruitment of Hsp60 and Ilv5 to nucleoids

To investigate whether other mitochondrial nucleoid proteins are redistributed under different growth conditions, we assessed the localization of three bifunctional nucleoid proteins: aconitase (Aco1), Ilv5, and the 60 kDa heat shock protein Hsp60 using stepwise sucrose gradients (Fig. 4 B). As expected, the majority of these proteins co-fractionated with mitochondrial matrix marker, Mdh1. However, Aco1, Ilv5, and Hsp60, but not Mdh1, exhibited a dual distribution in the sucrose gradients. A smaller fraction of these proteins was found to co-sediment with mtDNA. Using this rapid and sensitive assay, we found that various nucleoid proteins behaved differently depending on whether mitochondrial lysates were prepared from glucose or glycerol grown cells (Fig. 4 A). For example, we repeatedly found a several-fold increase in the amount of Hsp60 in nucleoids from glucose versus glycerol grown cells. By contrast, the distribution of Aco1 and Ilv5 in nucleoids was comparable in both conditions.

We have previously shown that Ilv5 is required for parsing of mtDNA into a greater number of nucleoids during amino acid starvation (MacAlpine et al., 2000). Therefore, we compared the distribution of Ilv5 and other nucleoid proteins in sucrose gradients of mitochondrial extracts from cells grown in minimal medium with no amino acids, or with isoleucine, leucine, valine as a control (Fig. 4, C and D). We repeatedly found that there was more Ilv5 present in mtDNA-containing fractions of the mitochondria isolated from cells starved for amino acids compared with the control. At the same time, the distribution of other proteins to nucleoids was unchanged, or slightly lower, which could be attributed to decreased expression levels of these proteins in conditions of amino acid starvation. These results suggest underlying functional differences for these nucleoid proteins reflected in the differential responses to growth conditions. Together, these experiments demonstrate that mitochondrial nucleoids undergo specific compositional remodeling in response to various metabolic cues.

Mutant forms of bifunctional Hsp60 and Ilv5 proteins, which exhibit mtDNA instability phenotypes with their “conventional” functions preserved, have been characterized (Bateman et al., 2002b; Kaufman et al., 2003). Molecular functions of Hsp60 and Ilv5 proteins related to the maintenance of mtDNA are not yet understood, but it has been demonstrated that mutants of Ilv5 protein, which exhibit an mtDNA instability phenotype, have altered submitochondrial localization; namely they form protein aggregates in the mitochondrial matrix (Bateman et al., 2002a). We asked whether the A144V mutant form of Hsp60, which is unable to maintain mtDNA, has also impaired submitochondrial localization. We compared the distribution of Hsp60 A144V with the wild type protein in sucrose gradients of mitochondrial lysates (Fig. 5). The levels of the A144V protein that we found associated with mtDNA were substantially elevated compared to that of the wild type protein both in glucose and glycerol growth media. Thus, Hsp60 mutant protein, which causes defects in the mtDNA metabolism, exhibits an altered recruitment to nucleoids.

Fig. 5
Distribution of Hsp60 A144V mutant protein in sucrose gradients. Sucrose gradients of an equal amount of lysed purified mitochondria (~1 mg of proteins) from W303-1B cells expressing the wild type Hsp60 protein or A144V mutant grown in glucose ...

Discussion

Our results show that mtDNA nucleoids are not static structures, but are subject to remodeling, which is linked to metabolic cues like glucose repression or amino acid starvation (Fig. 6). We propose that mitochondrial nucleoids are in a more open state under conditions that are characterized by a decreased Abf2 to mtDNA ratio, and are more compact when this ratio is increased. This scenario is supported by several of our observations.

Fig. 6
A model of mitochondrial nucleoid remodeling. In repressed conditions (growth in glucose media), mitochondrial nucleoids form a more compact conformation with an increased ratio of Abf2 to mtDNA. Hsp60 is recruited to nucleoids. In conditions that activate ...

First, using mitochondrial ChIP-chip, we demonstrate that Abf2 binds most of the mitochondrial genome and is therefore a bona fide mtDNA packaging protein (Fig. 1). Thus, our study supports the hypothesis, which aroused from previous in vitro studies (Brewer et al., 2003; Friddle et al., 2004), that the abundance of Abf2 in nucleoids determines the degree of compaction and the overall structure of nucleoids. In addition, our ChIP-chip experiments revealed a preferential binding of Abf2 to complex GC-rich sequences in vivo. In essence, the yeast mtDNA consists of gene sequences, which are the only complex GC-rich features on the genome, and AT-rich spacers interrupted by short GC clusters. Thus, the Abf2 distribution on the mitochondrial genome may reflect the inability of Abf2 to bind oligoA sequences, which has been demonstrated previously in vitro (Diffley and Stillman, 1992). However, it is conceivable that the observed binding pattern represents an intentional recruitment of Abf2 to gene sequences to ensure better protection, packaging, or other regulatory roles.

Second, we show that the average whole cell ratio of Abf2 to mtDNA is decreased in cells grown in glycerol medium compared to glucose grown cells, due to a two-fold increase in mtDNA copy number, while the expression of Abf2 remains comparable (Fig. 3 D, E). Notably, the distribution of Abf2 between nucleoids and the matrix remains similar both in glucose and glycerol media in our experimental conditions (Fig. 4 A). Therefore, we conclude that there is effectively less Abf2 protein bound per molecule of mtDNA in transcriptionally active nucleoids. Our comparison of nuclease sensitivity of nucleoids in mitochondria isolated from glucose and glycerol grown cells supports this hypothesis, as glucose nucleoids are more resistant to micrococcal nuclease than glycerol nucleoids (Fig. 3 A, B, C). The functional significance of this remodeling is unknown at this point. It is conceivable that Abf2 could regulate the access of other proteins to mtDNA. To test this we examined a mitochondrial RNA polymerase, Rpo41, but found that it is predominantly associated with nucleoids both in glucose and glycerol media (M. Kucej, unpublished data). Although the access of Rpo41 to mtDNA does not seem to be regulated by Abf2 there may be other DNA binding factors that can be affected by the Abf2 abundance on mtDNA.

Although Abf2 is the major mtDNA binding protein, other nucleoid proteins are also likely to contribute to the overall nucleoid structure and DNA protection in various growth conditions. Indeed, we show that the distribution of some nucleoid proteins is connected to metabolic cues. Namely, Hsp60 and Ilv5 are recruited to nucleoids during glucose repression and amino acid starvation, respectively (Fig. 4). It is known that Ilv5 is required for DNA parsing into greater number of nucleoids in media lacking amino acids, however, the role for Hsp60 during glucose repression is less clear. Hsp60 has been proposed to function in nucleoid division (Kaufman et al., 2003). It is conceivable that the recruitment of Hsp60 to nucleoids in glucose grown cells reflects an increased requirement for this protein in order to ensure reliable propagation of mitochondrial nucleoids under conditions, in which loss of mtDNA is not lethal.

Mutants of Ilv5 that exhibit an mtDNA instability phenotype have been previously studied (Bateman et al., 2002a). Some of these mutant Ilv5 proteins cannot perform their function in nucleoids because they form protein aggregates in the mitochondrial matrix. We thought that Hsp60 A144V mutant protein (Kaufman et al., 2003), which cannot maintain mtDNA properly, might be inadequately localized in the mitochondrial nucleoids as well. Surprisingly, we observed that the A144V mutant proteins are associated with mtDNA in a great surplus (Fig. 5). Thus, the mtDNA instability phenotype of A144V mutant may be caused by this excessive presence of Hsp60 in the mitochondrial nucleoids. These two examples of an altered localization of nucleoid proteins suggest that proper recruitment of nucleoid factors and remodeling of mitochondrial nucleoprotein is essential for the maintenance of mtDNA in various metabolic conditions.

Materials and Methods

Mitochondrial ChIP-chip

ChIP-chip analysis was performed using the strain (MCC109) whose mtDNA lacks introns. The ABF2 gene was modified using homologous recombination, with a PCR amplified 13Myc-kanMX6 cassette, so that the Abf2-13Myc fusion protein could be expressed from the ABF2 genomic locus (Longtine et al., 1998). A wild-type untagged strain was used as a negative control throughout the ChIP-chip experiments. Mitochondria were isolated from cells grown in 2L YPG medium (1% yeast extract, 2% peptone, 3% glycerol) and purified on Histodenz™ (Sigma) gradients (Diekert et al., 2001). Approximately 2 mg of mitochondria were crosslinked with 1% formaldehyde for 2 hours at 4°C in 2ml of 0.5M sucrose, 20mM HEPES pH 7.4, 2mM EDTA, 7mM β-mercaptoethanol. After crosslinking, the mitochondria were lysed for 5 min at 4°C in 0.5% Nonidet P40 in the presence of protease inhibitor mix Complete™ (Roche) and 50mM NaCl. The lysed mitochondria were sheared by ultrasound for 10×25 sec with a Branson Sonifier 450 (output 20%, setting 3). An aliquot of the sheared DNA was purified and examined by agarose gel electrophoresis. The size of the resulting DNA fragments ranged from about 400 bp to 2 kbp. Prior to immunoprecipitation the samples were precleared with Protein G agarose (Roche). The extracts were incubated overnight at 4°C with ~2 μg of mouse antibodies against the Myc epitope (Roche). The immunocomplexes were precipitated with Protein G agarose (Roche), as specified by the manufacturer, except that 2mM EDTA was present during all washing steps. The crosslinked DNA was released from the beads by incubating the samples at 65°C overnight in 1% SDS, 50mM Tris Cl, pH 8.0, and 2mM EDTA. The DNA samples were purified with Qiaquick® PCR purification kit and amplified using a linear amplification method (Liu et al., 2003). Briefly, the DNA was dephosphorylated and dT-tailed with terminal transferase. T7 RNA polymerase promoters were incorporated into the extremities of DNA fragments and RNA was synthesized in vitro using the MEGAscript® T7 kit (Ambion). Approximately 0.5-1 μg of synthesized RNA was labeled using the AminoAllyl cDNA labeling kit (Ambion). Cy5 mono NHS ester (Amersham) was used to label the cDNA sample from Abf2p-13Myc and the untagged strains. Cy3 mono NHS ester was conjugated with cDNA amplified identically from CsCl-purified mtDNA from the intronless MCC109 strain. The Cy5 and Cy3 labeled samples were mixed and used for hybridizations with microarrays. Custom microarrays were printed with PCR-amplified regions of intronless mtDNA by the University of Texas Southwestern Medical Center Microarray Core Facility (tab. S1). Since S. cerevisiae mtDNA contains many variable regions, some sequences were amplified from mtDNA of the FY1679 strain, which has been used to determine the complete mtDNA sequence (Foury et al., 1998). For ori5 and VAR1 regions, HS40 that contained the entire ori5 region, and VAR1 petite mtDNAs were used, respectively. In total, about 70% of the genome was covered with representatives of all features: ORFs, rRNAs, tRNA genes, promoters, oris, GC clusters, and AT rich spacer regions. Sequences of all oligonucleotides used for PCR reactions can be found in table S1. The ChIP-chip experiments were repeated 3 times with the Abf2-13Myc expressing strain and 4 times with the wild type strain (Fig. S3). The datasets were analyzed by a median percentile ranking method as previously described (Buck and Lieb, 2004).

Nuclease sensitivity assay

Nuclease sensitivity of mitochondrial nucleoids in organello was assessed as previously described with modifications (Newman et al., 1996). Mitochondria were isolated from 3 L YPD medium (1% yeast extract, 2% peptone, 5% glucose) or 2 L YPG cultures of the strain BY4741 and were further purified on Histodenz™ (Sigma) gradients. Approximately 1 mg of mitochondria was treated with 1% toluene for 15 min at 22°C in 1 ml of 0.5M sucrose, 20mM Tris.Cl pH 7.4, 2mM EDTA. The permeable mitochondria were collected by centrifugation and treated with 0.2U/ml micrococcal nuclease (USB) at 30°C in 0.5M sucrose, 20mM Tris.Cl pH 7.4, 2mM EDTA and 4mM CaCl2. Without the addition of micrococcal nuclease, mtDNA was stable for at least 60 min in the presence of 4mM CaCl2 (Fig. S4 A). The reactions were stopped with 10mM EGTA, pH 8.4. In order to isolate the DNA, the mitochondria were treated for 2 hours at 65°C with 0.2 mg/ml proteinase K in the presence of 1% SDS. The DNA was extracted with phenol and precipitated with isopropanol in the presence of 5μg of linear acrylamide (Ambion). The DNA was digested with HaeIII, separated in agarose gels and transferred to nylon membranes. The blots were hybridized at 62°C in 6×SSC, 0.5% SDS and 5×Denhardt solution with various probes PCR-amplified from mtDNA (21S_rRNA/71, ATP6/33, product 81, tab. S1) labeled with αP32-dATP (Perkin Elmer) using the Random Primed DNA Labeling Kit (Roche). Blots were washed 2 times for 30 min with 6×SSC, 0.5% SDS at 30°C and 2 times for 30 min with 0.1×SSC, 0.5% SDS at 62°C. The signal intensities were quantified using a phosphorimager and ImageQuant software (Molecular Dynamics).

Submitochondrial fractionation

The mitochondria were isolated from 3 L YPD (5% glucose) and 2 L YPG cultures of the BY4741 strain grown at 30°C, 3 L YPD (5% glucose) and 2 L YPG cultures of W303-1B Δhsp60::HIS3 [pRS415-HSP60] and W303-1B Δhsp60::HIS3 [pRS415-hsp60-A144V] (Kaufman et al., 2003) grown at 26°C, and 3 L cultures of the MCC109 strain grown in SD (5% glucose) with or without the addition of 0.5g/l isoleucine, leucine, and valine. The gradient-purified mitochondria (1mg/ml) were lysed in 0.5% Nonidet P40 in 0.5M sucrose, 20mM Tris.Cl pH 7.4, 2mM EDTA, 50mM NaCl, 7mM β-mercaptoethanol, and 1×Complete™ (Roche) for 5 min on ice. The same amount of lysed mitochondria, approximately 1mg of mitochondrial proteins, were loaded on top of a stepwise gradient composed of 4ml of 20%, 2ml of 60%, and 1ml of 80% sucrose solution in 20mM TrisCl, pH 7.4, 2mM EDTA, 50mM NaCl, and 7mM β-mercaptoethanol. After centrifugation at 110,000g for 70 min at 4°C, ~0.5 ml fractions were collected from the bottom of the tubes. The fractions were analyzed for the presence of mtDNA by Southern dot blot hybridizations as follows: 50μl from each fraction were treated overnight with 20 μg Proteinase K (USB) and denatured in 0.1M NaOH for 20 min at 37°C. The DNA was neutralized in 6×SSC and loaded onto nylon membranes using a multi-well manifold blotter (Bio-Rad). The membranes were hybridized at 62°C in 6×SSC, 0.5% SDS, 5×Denhardt solution with ATP6/33 PCR product, labeled with αP32-dATP (Perkin Elmer) using Random Primed DNA Labeling Kit (Roche). The dot blots were washed 2 times for 30 min with 6×SSC, 0.5% SDS at 30°C and 2 times for 30 min with 0.1×SSC, 0.5% SDS at 62°C. For protein analysis, aliquots of 12μl from each fraction were separated in 4%-20% gradient polyacrylamide gels (Bio-Rad), blotted to nitrocellulose membranes, and probed with rabbit polyclonal antibodies against Abf2, Ilv5, Hsp60, Aco1, and Mdh1 and with Goat Anti Rabbit secondary antibodies conjugated with horseradish peroxidase (Bio-Rad). The immunocomplexes were detected by chemiluminescence with ECL™ reagents (Amersham). In order to minimize chemiluminescence variations, membranes were always processed at the same time in one solution and exposed side by side on a single film. Also, a single nitrocellulose membrane, not parallel membranes, was used to detect all proteins. All gradients and Western blots were repeated with essentially identical results.

Mitochondrial DNA copy number

The BY4741 cells were grown in 100 ml of YPD and YPG media. The total DNA was isolated by phenol/glass beads treatment. MtDNA copy number was measured by hybridizations of blots containing HaeIII-cut total cellular DNA. The membranes were hybridized with 21S_rRNA probe 71 and ACT1 probe 117 (Table S1). The hybridization, washing, and detection of DNA blots was carried out as described elsewhere in Methods. The band intensities were quantified using a phosphorimager (Molecular Dynamics) and ImageQuant 5.0 software (Molecular Dynamics).

Abf2 protein interactions

About 1mg of pure mitochondria from YPG-grown MCC109 and MCC109 Abf2-13Myc strains were suspended in 0.6 M sorbitol, 40mM HEPES.KOH pH 7.4 to obtain a total volume of 1 ml. The mitochondria were incubated for 2 hrs on ice with or without 1 mM DSP. In order to stop the crosslinking reaction, 2.5 M glycine was added to the final concentration of 100 mM. The mitochondria were isolated by centrifugation at 4°C, 20,000 × g for 30 min, resuspended in 0.5 M sucrose, 50 mM Tris.Cl pH 7.4, 0.05 M NaCl, 0.5% Nonidet P40, 1 × Complete™, and incubated on ice for 15 min. In order to digest the mtDNA, 100U of DNaseI and MgCl2 to a concentration of 25 mM was added and the suspension was incubated at 30°C for 1 hr. The insoluble material was removed by centrifugation at 20,000 × g for 10 min. About 15 μg of an anti-Myc antibody was added and the samples were incubated on a rocking platform at 4°C for 2 hrs, followed by incubation with a 100 μl of Protein G-Agarose (Roche) at 4°C for 16 hrs. The agarose beads were washed twice in 50 mM Tris.Cl pH 7.4, 0.5 M NaCl, 1% Nonidet P40, 1 × Complete™, twice in 50 mM Tris.Cl pH 7.4, 0.5 M NaCl, 0.1% Nonidet P40, and once in 50 mM Tris.Cl pH 7.4, 0.1% Nonidet P40. In order to reverse the crosslinks, the beads were suspended in ~160 μl of 60 mM Tris.Cl pH 6.8, 2% SDS, 10 % glycerol, 5% β-mercaptoethanol, 0.25% bromophenol blue and incubated at 92°C for 15 min. The proteins separated by SDS-PAGE were stained by silver. The bands of interest were cut out and analyzed by the Protein Chemistry Technology Center of Southwestern Medical Center at Dallas. Briefly, the proteins were in-gel digested by modified porcine trypsin, the peptide extracts were injected into a nano-HPLC/MS/MS system, and mass spectrometric data were searched against the NCBI non-redundant protein sequence database.

Supplementary Material

Fig S1

Fig S2

Fig S3

Fig S4

Support Material

Table S1

Acknowledgments

We thank Julie Covino for editorial advice. This work was supported by grants GM22525, GM33510 from the NIH and grant I0642 from The Robert A. Welch Foundation to R.A.B. Ron Butow passed away on August 8th 2007.

References

  • Bateman JM, Iacovino M, Perlman PS, Butow RA. Mitochondrial DNA instability mutants of the bifunctional protein ilv5p have altered organization in mitochondria and are targeted for degradation by hsp78 and the pim1p protease. J Biol Chem. 2002a;277:47946–53. [PubMed]
  • Bateman JM, Perlman PS, Butow RA. Mutational bisection of the mitochondrial DNA stability and amino acid biosynthetic functions of ilv5p of budding yeast. Genetics. 2002b;161:1043–52. [PubMed]
  • Bogenhagen DF, Rousseau D, Burke S. The layered structure of human mtDNA nucleoids. J Biol Chem. 2008;283:3665–75. [PubMed]
  • Bogenhagen DF, Wang Y, Shen EL, Kobayashi R. Protein components of mitochondrial DNA nucleoids in higher eukaryotes. Mol Cell Proteomics. 2003;2:1205–16. [PubMed]
  • Brewer LR, Friddle R, Noy A, Baldwin E, Martin SS, Corzett M, Balhorn R, Baskin RJ. Packaging of single DNA molecules by the yeast mitochondrial protein Abf2p. Biophys J. 2003;85:2519–24. [PubMed]
  • Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics. 2004;83:349–60. [PubMed]
  • Chen XJ, Butow RA. The organization and inheritance of the mitochondrial genome. Nat Rev Genet. 2005;6:815–25. [PubMed]
  • Chen XJ, Wang X, Butow RA. Yeast aconitase binds and provides metabolically coupled protection to mitochondrial DNA. Proc Natl Acad Sci U S A. 2007;104:13738–43. [PubMed]
  • Chen XJ, Wang X, Kaufman BA, Butow RA. Aconitase couples metabolic regulation to mitochondrial DNA maintenance. Science. 2005;307:714–7. [PubMed]
  • Cheng X, Kanki T, Fukuoh A, Ohgaki K, Takeya R, Aoki Y, Hamasaki N, Kang D. PDIP38 Associates with Proteins Constituting the Mitochondrial DNA Nucleoid. J Biochem (Tokyo) 2005;138:673–8. [PubMed]
  • Diekert K, de Kroon AI, Kispal G, Lill R. Isolation and subfractionation of mitochondria from the yeast Saccharomyces cerevisiae. Methods Cell Biol. 2001;65:37–51. [PubMed]
  • Diffley JF, Stillman B. A close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. Proc Natl Acad Sci U S A. 1991;88:7864–7868. [PubMed]
  • Diffley JFX, Stillman B. DNA binding properties of an HMG1-related protein from yeast mitochondria. J Biol Chem. 1992;267:3368–3374. [PubMed]
  • Ehrenhofer-Murray AE. Chromatin dynamics at DNA replication, transcription and repair. Eur J Biochem. 2004;271:2335–49. [PubMed]
  • Fisher RP, Lisowsky T, Parisi MA, Clayton DA. DNA wrapping and bending by a mitochondrial high mobility group-like transcriptional activator protein. J Biol Chem. 1992;267:3358–3367. [PubMed]
  • Foury F, Roganti T, Lecrenier N, Purnelle B. The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Lett. 1998;440:325–331. [PubMed]
  • Friddle RW, Klare JE, Martin SS, Corzett M, Balhorn R, Baldwin EP, Baskin RJ, Noy A. Mechanism of DNA compaction by yeast mitochondrial protein Abf2p. Biophys J. 2004;86:1632–9. [PubMed]
  • Garrido N, Griparic L, Jokitalo E, Wartiovaara J, Van Der Bliek AM, Spelbrink JN. Composition and dynamics of human mitochondrial nucleoids. Mol Biol Cell. 2003;14:1583–96. [PMC free article] [PubMed]
  • Goldthwaite CD, Cryer DR, Marmur J. Effect of carbon source on the replication and transmission of yeast mitochondrial genomes. Mol Gen Genet. 1974;133:87–104. [PubMed]
  • Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M. Regulation of gene expression by a metabolic enzyme. Science. 2004;306:482–4. [PubMed]
  • Kaufman BA, Durisic N, Mativetsky JM, Costantino S, Hancock MA, Grutter P, Shoubridge EA. The Mitochondrial Transcription Factor TFAM Coordinates the Assembly of Multiple DNA Molecules into Nucleoid-like Structures. Mol Biol Cell. 2007;18:3225–3236. [PMC free article] [PubMed]
  • Kaufman BA, Kolesar JE, Perlman PS, Butow RA. A function for the mitochondrial chaperonin Hsp60 in the structure and transmission of mitochondrial DNA nucleoids in Saccharomyces cerevisiae. J Cell Biol. 2003;163:457–61. [PMC free article] [PubMed]
  • Kaufman BA, Newman SM, Hallberg RL, Slaughter CA, Perlman PS, Butow RA. In organello formaldehyde crosslinking of proteins to mtDNA: identification of bifunctional proteins. Proc Natl Acad Sci U S A. 2000;97:7772–7777. [PubMed]
  • Kucej M, Butow RA. Evolutionary tinkering with mitochondrial nucleoids. Trends Cell Biol. 2007;17:586–92. [PubMed]
  • Liu CL, Schreiber SL, Bernstein BE. Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics. 2003;4:19. [PMC free article] [PubMed]
  • Longtine MS, McKenzie A, 3rd, Demarini DJ, Shah NG, Wach A, Brachat A, Philippsen P, Pringle JR. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast. 1998;14:953–61. [PubMed]
  • MacAlpine DM, Perlman PS, Butow RA. The number of individual mitochondrial DNA molecules and mitochondrial DNA nucleoids in yeast are co-regulated by the general amino acid control pathway. EMBO J. 2000;19:767–775. [PubMed]
  • Malka F, Lombes A, Rojo M. Organization, dynamics and transmission of mitochondrial DNA: focus on vertebrate nucleoids. Biochim Biophys Acta. 2006;1763:463–72. [PubMed]
  • Miyakawa I, Sando N, Kawano K, Nakamura S, Kuroiwa T. Isolation of morphologically intact mitochondrial nucleoids from the yeast, Saccharomyces cerevisiae. J Cell Sci. 1987;88:431–439. [PubMed]
  • Newman SM, Zelenaya-Troitskaya O, Perlman PS, Butow RA. Analysis of mitochondrial DNA nucleoids in wild-type and a mutant strain of Saccharomyces cerevisiae that lacks the mitochondrial HMG box protein Abf2p. Nucleic Acids Res. 1996;24:386–93. [PMC free article] [PubMed]
  • O'Rourke TW, Doudican NA, Mackereth MD, Doetsch PW, Shadel GS. Mitochondrial dysfunction due to oxidative mitochondrial DNA damage is reduced through cooperative actions of diverse proteins. Mol Cell Biol. 2002;22:4086–93. [PMC free article] [PubMed]
  • Roberts GG, Hudson AP. Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling. Mol Genet Genomics. 2006;276:170–86. [PubMed]
  • Saha A, Wittmeyer J, Cairns BR. Chromatin remodelling: the industrial revolution of DNA around histones. Nat Rev Mol Cell Biol. 2006;7:437–47. [PubMed]
  • Shadel GS. Mitochondrial DNA, aconitase ‘wraps’ it up. Trends Biochem Sci. 2005;30:294–6. [PubMed]
  • Wang Y, Bogenhagen DF. Human mitochondrial DNA nucleoids are linked to protein folding machinery and metabolic enzymes at the mitochondrial inner membrane. J Biol Chem. 2006;281:25791–802. [PubMed]
  • Zelenaya-Troitskaya O, Perlman PS, Butow RA. ILV5 encodes a bifunctional mitochondrial protein involved in branched chain amino acid biosynthesis and maintenance of mitochondrial DNA. EMBO J. 1995;14:3268–3276. [PubMed]