Escape of mitochondrial DNA to the nucleus in yme1 yeast is mediated by vacuolar-dependent turnover of abnormal mitochondrial compartments

Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae

Pexophagy, peroxysome autophagy, is regulated in Saccharomyces cerevisiae by Atg36 by direct binding to peroxysome regulator Pex3, Atg8 and Atg11 of the core autophagy machinery.

Peroxisomes undergo rapid, selective autophagic degradation (pexophagy) when the metabolic pathways they contain are no longer required for cellular metabolism. Pex3 is central to the formation of peroxisomes and their segregation because it recruits factors specific for these functions. Here, we describe a novel Saccharomyces cerevisiae protein that interacts with Pex3 at the peroxisomal membrane. We name this protein Atg36 as its absence blocks pexophagy, and its overexpression induces pexophagy. We have isolated pex3 alleles blocked specifically in pexophagy that cannot recruit Atg36 to peroxisomes. Atg36 is recruited to mitochondria if Pex3 is redirected there, where it restores mitophagy in cells lacking the mitophagy receptor Atg32. Furthermore, Atg36 binds Atg8 and the adaptor Atg11 that links receptors for selective types of autophagy to the core autophagy machinery. Atg36 delivers peroxisomes to the preautophagosomal structure before being internalised into the vacuole with peroxisomes. We conclude that Pex3 recruits the pexophagy receptor Atg36. This reinforces the pivotal role played by Pex3 in coordinating the size of the peroxisome pool, and establishes its role in pexophagy in S. cerevisiae.

The many faces of mitochondrial autophagy: making sense of contrasting observations in recent research

Research into the selective autophagic degradation of mitochondria—mitophagy—has intensified in recent years, yielding significant insights into the function, mechanism, and regulation of this process in the eukaryotic cell. However, while some molecular players in budding yeast, such as Atg32p, Uth1p, and Aup1p, have been identified, studies further interrogating the mechanistic and regulatory features of mitophagy have yielded inconsistent and sometimes conflicting results. In this review, we focus on the current understanding of mitophagy mechanism, induction, and regulation in yeast, and suggest that differences in experimental conditions used in the various studies of mitophagy may contribute to the observed discrepancies. Consideration and understanding of these differences may help place the mechanism and regulation of mitophagy in context, and further indicate the intricate role that this essential process plays in the life and death of eukaryotic cells.

Mitochondrial morphology in mitophagy and macroautophagy

Mitochondria are critical organelles in energy conversion, metabolism and amplification of signalling. They are however also major sources of reactive oxygen species and when dysfunctional they consume cytosolic ATP. Maintenance of a cohort of healthy mitochondria is therefore crucial for the overall cell fitness. Superfluous or damaged organelles are mainly degraded by mitophagy, a selective process of autophagy. In response to the triggers of mitophagy, mitochondria fragment: this morphological change accompanies the exposure of "eat-me" signals, resulting in the engulfment of the organelle by the autophagosomes. Conversely, during macroautophagy mitochondria fuse to be spared from degradation and to sustain ATP production in times of limited nutrient availability. Thus, mitochondrial shape defines different types of autophagy, highlighting the interplay between morphology of the organelle and complex cellular responses. This article is part of a Special Issue entitled: Mitochondrial dynamics and physiology.

Mitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system

Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA-DNA interactions between the mitochondrial and nuclear genomes (Mito-nDNA) in Saccharomyces cerevisiae cells grown under three different metabolic conditions. The interactions that form between mitochondrial and nuclear loci are dependent on the metabolic state of the yeast. Moreover, the frequency of specific mitochondrial - nuclear interactions (i.e. COX1-MSY1 and Q0182-RSM7) showed significant reductions in the absence of mitochondrial encoded reverse transcriptase machinery. Furthermore, these reductions correlated with increases in the transcript levels of the nuclear loci (MSY1 and RSM7). We propose that these interactions represent an inter-organelle DNA mediated communication system and that reverse transcription of mitochondrial RNA plays a role in this process.

Cellular homeostasis in fungi: impact on the aging process

Cellular quality control pathways are needed for maintaining the biological function of organisms. If these pathways become compromised, the results are usually highly detrimental. Functional impairments of cell components can lead to diseases and in extreme cases to organismal death. Dysfunction of cells can be induced by a number of toxic by-products that are formed during metabolic activity, like reactive oxygen and nitrogen species, for example. A key source of reactive oxygen species (ROS) are the organelles of oxidative phosphorylation, mitochondria. Therefore mitochondrial function is also directly affected by ROS, especially if there is a compromised ROS-scavenging capacity. Biological systems therefore depend on several lines of defence to counteract the toxic effects of ROS and other damaging agents. The first level is active at the molecular level and consists of various proteases that bind and degrade abnormally modified and / or aggregated mitochondrial proteins. The second level is concerned with maintaining the quality of whole mitochondria. Among the pathways of this level are mitochondrial dynamics and autophagy (mitophagy). Mitochondrial dynamics describes the time-dependent fusion and fission of mitochondria. It is argued that this kind of organellar dynamics has the power to restore the function of impaired organelles by content mixing with intact organelles. If the first and second lines of defence against damage fail and mitochondria become damaged too severely, there is the option to remove affected cells before they can elicit more damage to their surrounding environment by apoptosis. This form of programmed cell death is strictly regulated by a complex network of interacting components and can be divided into mitochondria-dependent and mitochondria-independent modes of action. In this review we give an overview on various biological quality control systems in fungi (yeasts and filamentous fungi) with an emphasis on autophagy (mitophagy) and apoptosis and how these pathways allow fungal organisms to maintain a balanced cellular homeostasis.

Unmasking a temperature-dependent effect of the P. anserina i-AAA protease on aging and development

Different molecular pathways involved in maintaining mitochondrial function are of fundamental importance to control cellular homeostasis. Mitochondrial i-AAA protease is part of such a surveillance system and PaIAP is the putative ortholog in the fungal aging model Podospora anserina. Here we investigated the role of PaIAP in aging and development. Deletion of the gene encoding PaIAP resulted in a specific phenotype. When incubated at 27°C, spore germination and fruiting body formation are not different from that of the corresponding wild-type strain. Unexpectedly, the lifespan of the deletion strain is strongly increased. In contrast, cultivation at an elevated temperature of 37°C leads to impairments in spore germination and fruiting body formation, and to a reduced lifespan. The higher PaIAP abundance in wild-type strains of the fungus grown at elevated temperature and the phenotype of the deletion strain unmasks a temperature-related role of the protein. The protease appears to be part of a molecular system that has evolved to allow survival under changing temperatures as they characteristically occur in nature.

Two MAPK-signaling pathways are required for mitophagy in Saccharomyces cerevisiae

The MAP kinase Slt2 is required for both mitophagy and pexophagy, whereas the MAP kinase Hog1 acts specifically in mitophagy.

Macroautophagy (hereafter referred to simply as autophagy) is a catabolic pathway that mediates the degradation of long-lived proteins and organelles in eukaryotic cells. The regulation of mitochondrial degradation through autophagy plays an essential role in the maintenance and quality control of this organelle. Compared with our understanding of the essential function of mitochondria in many aspects of cellular metabolism such as energy production and of the role of dysfunctional mitochondria in cell death, little is known regarding their degradation and especially how upstream signaling pathways control this process. Here, we report that two mitogen-activated protein kinases (MAPKs), Slt2 and Hog1, are required for mitophagy in Saccharomyces cerevisiae. Slt2 is required for the degradation of both mitochondria and peroxisomes (via pexophagy), whereas Hog1 functions specifically in mitophagy. Slt2 also affects the recruitment of mitochondria to the phagophore assembly site (PAS), a critical step in the packaging of cargo for selective degradation.

Mitophagy in yeast is independent of mitochondrial fission and requires the stress response gene WHI2

Dysfunctional mitochondria show a reduced capacity for fusion and, as mitochondrial fission is maintained, become spatially separated from the intact network. By that mechanism, dysfunctional mitochondria have been proposed to be targeted for selective degradation by mitophagy, thereby providing a quality control system for mitochondria. In yeast, conflicting results concerning the role of mitochondrial dynamics in mitophagy have been reported. Here, we investigate the effects on mitophagy of altering mitochondrial fission and fusion, using biochemical, as well as fluorescence-based, assays. Rapamycin-induced mitophagy was shown to depend upon the autophagy-related proteins Atg11, Atg20 and Atg24, confirming that a selective type of autophagy occurred. Both fragmentation of mitochondria and inhibition of oxidative phosphorylation were not sufficient to trigger mitophagy, and neither deletion of the fission factors Dnm1, Fis1, Mdv1 or Caf4 nor expression of dominant-negative variants of Dnm1 impaired mitophagy. The diminished mitophagy initially observed in a Δfis1 mutant was not due to the absence of Fis1 but rather due to a secondary mutation in WHI2, which encodes a factor reported to function in the general stress response and the Ras-protein kinase A (PKA) signaling pathway. We propose that, in yeast, mitochondrial fission is not a prerequisite for the selective degradation of mitochondria, and that mitophagy is linked to the general stress response and the Ras-PKA signaling pathway.

Hsp90 and mitochondrial proteases Yme1 and Yta10/12 participate in ATP synthase assembly in Saccharomyces cerevisiae

Hsc82 and Hsp82, the Hsp90 family proteins of yeast, are both required for fermentative growth at 37°C. Inactivation of either of the mitochondrial AAA proteases, Yme1 or Yta10/12, allows fermentative growth of hsc82∆ or hsp82∆ strains at 37°C. Genetic evidence indicates interaction of Hsc82/Hsp82 with the Yme1 and Yta10/Yta12 complexes in promoting F(1)F(o)-ATPase activity, with Hsc82 specifically required for F(1)-ATPase assembly. A previously reported mutation in Rpt3, one of the six ATPases of the proteasome, suppresses yme1∆ phenotypes and increases transcription of HSC82 but not HSP82. These genetic interactions describe a functional role for Hsp90 proteins in mitochondrial biogenesis.

Mitophagy in yeast: actors and physiological roles

Mitochondria are essential for oxidative energy production in aerobic eukaryotic cells, where they are also required for multiple biosynthetic pathways to take place. Mitochondria also monitor and evaluate complex information from the environment and intracellular milieu, including the presence or absence of growth factors, oxygen, reactive oxygen species, and DNA damage. It follows that disturbances of the integrity of mitochondrial function lead to the disruption of cell function, expressed as disease, aging, or cell death. It has been assumed that the degradation of damaged mitochondria by an autophagy-related pathway specific to mitochondria (mitophagy), recently found to be strictly regulated, is a fundamental process essential for cell homeostasis. Until now, the main role of mitophagy has been tentatively defined as a 'house-cleaning' pathway that allows to eliminate altered mitochondria, but mitophagy may also play a role in the adaptation of the number and quality of mitochondria to new environmental conditions. In yeast, recent data defined two categories of mitophagy actors: ones constitutively required for mitophagy and those with mitophagy-regulatory functions. Situations were also uncovered in normal physiology in which cells utilize mitophagy to eliminate damaged, dysfunctional, and superfluous mitochondria to adjust to changing physiological demands.

Role of intercompartmental DNA transfer in producing genetic diversity

In eukaryotic cells, genes are found in three compartments-the nucleus, mitochondria, and plastids-and extensive gene transfer has occurred between them. Most organellar genes in the nucleus migrated there long ago, but transfer is ongoing and ubiquitous. It now generates mostly noncoding nuclear DNA, can also disrupt gene functions, and reshape genes by adding novel exons. Plastid or nuclear sequences have also contributed to the formation of mitochondrial tRNA genes. It is now clear that organelle-to-nucleus DNA transfer involves the escape of DNA molecules from the organelles at times of stress or at certain developmental stages, and their subsequent incorporation at sites of double-stranded breaks in nuclear DNA by nonhomologous recombination. Intercompartmental DNA transfer thus appears to be an inescapable phenomenon that has had a broad impact on eukaryotic evolution, affecting DNA repair, gene and genome evolution, and redirecting proteins to different target compartments.

Mitophagy and Parkinson's disease: the PINK1-parkin link

The study of rare, inherited mutations underlying familial forms of Parkinson's disease has provided insight into the molecular mechanisms of disease pathogenesis. Mutations in these genes have been functionally linked to several key molecular pathways implicated in other neurodegenerative disorders, including mitochondrial dysfunction, protein accumulation and the autophagic-lysosomal pathway. In particular, the mitochondrial kinase PINK1 and the cytosolic E3 ubiquitin ligase parkin act in a common pathway to regulate mitochondrial function. In this review we discuss the recent evidence suggesting that the PINK1/parkin pathway also plays a critical role in the autophagic removal of damaged mitochondria–mitophagy. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.

Yeast chromosomal interactions and nuclear architecture

Biology is essentially the study of networks of interactions within or between organisms. The study of chromosomal interactions, while still in its infancy, is providing insights that enable us to study genome biology as a network of inter-linked systems and not simply as the isolated loci we were previously restricted to. Recent work has highlighted how chromosomal interactions, nuclear position and genomic function are inter-linked. This review will start by outlining how chromosomal interactions are determined. It will continue to discuss recent observations of intra-chromosomal and inter-chromosomal interactions in yeast, interactions involving foreign DNA and the formation of chromosomal interactions. The review will then conclude with a model to explain the formation of yeast chromosomal interactions and consequently yeast interphase nuclear structure.

Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes

The natural transfer of DNA from mitochondria to the nucleus generates nuclear copies of mitochondrial DNA (numts) and is an ongoing evolutionary process, as genome sequences attest. In humans, five different numts cause genetic disease and a dozen human loci are polymorphic for the presence of numts, underscoring the rapid rate at which mitochondrial sequences reach the nucleus over evolutionary time. In the laboratory and in nature, numts enter the nuclear DNA via non-homolgous end joining (NHEJ) at double-strand breaks (DSBs). The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency. Polymorphic numts in humans link maternally inherited mitochondrial genotypes to nuclear DNA haplotypes during the past, offering new opportunities to associate nuclear markers with mitochondrial markers back in time.

Autophagy and the degradation of mitochondria

The cellular process of macromolecular degradation known as macroautophagy has long been known to play a role in the elimination of mitochondria. Over the past decade, much progress has been made in the development of systems by which the nature and mechanism of mitochondria degradation may be studied. Recent findings imply that the degradation of mitochondria via autophagy may be more specific and more tightly regulated than originally thought, and have led to designation of this specific type of autophagy as "mitophagy". In this review we provide a brief history of the development of mitophagy models and their associated discoveries.

Mitochondrial protein quality control systems in aging and disease

Preserving the integrity of proteins, biomolecules prone to molecular damage, is a fundamental function of all biological systems. Impairments in protein quality control (PQC) may lead to degenerative processes, such as aging and various disorders and diseases. Fortunately, cells contain a hierarchical system of pathways coping protein damage. Specific molecular pathways detect misfolded proteins and act either to unfold or degrade them. Degradation of proteins generates peptides and amino acids that can be used for remodelling of impaired pathways and cellular functions. At increased levels of cellular damage whole organelles can be removed via autophagy, a process that depends on the activity oflysosomes. In addition, cells may undergo apoptosis, a form of programmed cell death, which in single-cellular and lower multicellular organisms can lead to death of the individual. Molecular damage of cellular compartments is mainly caused by reactive oxygen species (ROS). ROS is generated via different cellular pathways and frequently arises in the mitochondrial electron transport chain as a by-product of oxygenic energy transduction. Consequently, mitochondrial proteins are under high risk to become damaged. Perhaps for this reason mitochondria contain a very efficient PQC system that keeps mitochondrial proteins functional as long as damage does not reach a certain threshold and the components of this system themselves are not excessively damaged. The mitochondrial PQC system consists of chaperones that counteract protein aggregation through binding and refolding misfolded polypeptides and of membrane-bound and soluble ATP-dependent proteases that are involved in degradation of damaged proteins. During aging and in neurodegenerative diseases components of this PQC system, including Lon protease present in the mitochondrial matrix, become functionally impaired. In this chapter we summarise the current knowledge of cellular quality control systems with special emphasis on the role of the mitochondrial PQC system and its impact on biological aging and disease.

A genomic screen for yeast mutants defective in selective mitochondria autophagy

Mitophagy is the process of selective mitochondrial degradation via autophagy, which has an important role in mitochondrial quality control. Very little is known, however, about the molecular mechanism of mitophagy. A genome-wide yeast mutant screen for mitophagy-defective strains identified 32 mutants with a block in mitophagy, in addition to the known autophagy-related (ATG) gene mutants. We further characterized one of these mutants, ylr356wDelta that corresponds to a gene whose function has not been identified. YLR356W is a mitophagy-specific gene that was not required for other types of selective autophagy or macroautophagy. The deletion of YLR356W partially inhibited mitophagy during starvation, whereas there was an almost complete inhibition at post-log phase. Accordingly, we have named this gene ATG33. The new mutants identified in this analysis will provide a useful foundation for researchers interested in the study of mitochondrial homeostasis and quality control.

Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy

Mitochondria are essential organelles that produce most of the energy for a cell, but concomitantly accumulate oxidative damage. Degradation of damaged mitochondria is critical for cell homeostasis, and this process is thought to be mediated by mitophagy, an autophagy-related pathway specific for mitochondria. However, whether mitochondria are selectively degraded, and how the autophagic machinery is targeted to mitochondria, remain largely unknown. Here we demonstrate that, in post-log phase cells under respiratory conditions, a substantial fraction of mitochondria are exclusively sequestered as cargoes and transported to the vacuole, a lytic compartment in yeast, in an autophagy-dependent manner. Interestingly, we found Atg32, a mitochondria-anchored protein essential for mitophagy that is induced during respiratory growth. In addition, our data suggest that Atg32 interacts with Atg8 and Atg11, autophagy-related proteins critical for recognition of cargo receptors. We propose that Atg32 acts as a mitophagy-specific receptor and regulates selective degradation of mitochondria.

Turnover of organelles by autophagy in yeast

Efficient detection and removal of superfluous or damaged organelles are crucial to maintain cellular homeostasis and to assure cell survival. Growing evidence shows that organelles or parts of them can be removed by selective subtypes of otherwise unselective macroautophagy and microautophagy. This requires both the adaptation of the core autophagic machinery and sophisticated mechanisms to recognize organelles destined for turnover. We review the current knowledge on autophagic removal of peroxisomes, mitochondria, ER and parts of the nucleus with an emphasis on yeasts as a model eukaryote.

Selective types of autophagy in yeast

Autophagy is the process through which cytosol and organelles are sequestered into a double-membrane vesicle called an autophagosome and delivered to the vacuole/lysosome for breakdown and recycling. One of its primary roles in unicellular organisms is to regulate intracellular homeostasis and to adjust organelle numbers in response to stress such as changes in nutrient availability. In higher eukaryotes, autophagy plays also an important role in stress-response, development, cell differentiation, immunity and tumor suppression. Importantly, a misregulation in this catabolic pathway is associated with diseases such as cancer, neurodegeneration and myopathies. For a long time, starvation-induced autophagy has been considered a non-selective pathway, however, numerous recent observations revealed that autophagy can also selectively eliminate specific proteins, protein complexes and organelles. Most of these studies used yeast Saccharomyces cerevisiae as a model organism. In this compendium, we will review what is known about the mechanisms and roles of selective types of autophagy in yeast and highlight possible connections of these pathways with human diseases. In addition, we will discuss some selective types of autophagy, which have so far only been described in higher eukaryotes.

DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis

In eukaryotes, DNA is exchanged between endosymbiosis-derived compartments (mitochondria and chloroplasts) and the nucleus. Organelle-to-nucleus DNA transfer involves repair of double-stranded breaks by nonhomologous end-joining, and resulted during early organelle evolution in massive relocation of organelle genes to the nucleus. A large fraction of the products of the nuclear genes so acquired are retargeted to their ancestral compartment; many others now function in new subcellular locations. Almost all present-day nuclear transfers of mitochondrial or plastid DNA give rise to noncoding sequences, dubbed nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs). Some of these sequences were recruited as exons, thus introducing new coding sequences into preexisting nuclear genes by a novel mechanism. In organisms derived from secondary or tertiary endosymbiosis, serial gene transfers involving nucleus-to-nucleus migration of DNA have also occurred. Intercompartmental DNA transfer therefore represents a significant driving force for gene and genome evolution, relocating and refashioning genes and contributing to genetic diversity.

Monitoring mitophagy in yeast

Cellular degradative processes including proteasomal and vacuolar/lysosomal autophagic degradation, as well as the activity of proteases (both cytosolic and mitochondrial), provide for a continuous turnover of damaged and obsolete macromolecules and organelles. Mitochondria are essential for oxidative energy production in aerobic eukaryotic cells, where they are also required for multiple biosynthetic pathways to take place. Mitochondrial homeostasis also plays a crucial role in aging and programmed cell death, and recent data have suggested that mitochondrial degradation is a strictly regulated process. A recent study has shown that in yeast cells subjected to nitrogen starvation, degradation of mitochondria by autophagy occurs by both a selective process (termed mitophagy) and a nonselective process. This chapter provides an overview of the techniques that enable the study of mitophagy. Fluorescent proteins targeted to mitochondria can be used to follow mitochondrial sequestration within vacuoles. Degradation of mitochondria can be assayed using a mitochondrially targeted alkaline phosphatase (ALP) reporter test in which the delivery of mitochondrial N-terminal truncated Pho8Delta60 to the vacuole results from mitophagy. Degradation of mitochondrial proteins can also be followed by Western immunoblot analyses. Finally, electron microscopy observations permit the discrimination between selective mitophagy and nonselective mitochondrial degradation.

The quantitative Pho8Delta60 assay of nonspecific autophagy

The measurement of autophagic flux is critical in understanding the regulation of autophagy. The Pho8Delta60 assay employs a very sensitive enzymatic assay that provides a high signal-to-noise ratio and allows for precise quantification of autophagic flow in yeast. Pho8, alkaline phosphatase, is a resident vacuolar enzyme that is delivered to the vacuole membrane through a portion of the secretory pathway. The assay utilizes a genetically engineered version of Pho8 that lacks the N-terminal transmembrane domain that allows for translocation into the endoplasmic reticulum. Accordingly, Pho8Delta60 remains in the cytosol and is delivered to the vacuole only through autophagy. Once in the vacuole lumen, the C-terminal propeptide is proteolytically removed, which results in activation. Thus, the alkaline phosphatase activity reflects the amount of the cytosol delivered to the vacuole through nonspecific autophagy.

Metabolic implications for the mechanism of mitochondrial endosymbiosis and human hereditary disorders

The endosymbiosis of proto-mitochondrial prokaryotes (PMP) into proto-eukaryotic host-cells was a major advance in eukaryotic evolution. The nature of the initial relationship remains the subject of controversy. Various conceptual models have been proposed, but none has definitive support. We construct a model of inter-species interactions based upon well-established respiratory pathways, describing the respective energy gain of host-cell and PMP resulting from varying levels of cooperation. The model demonstrates conflicting evolutionary strategies ("Prisoner's Dilemmas") in the interspecies molecular transfers. Nevertheless, we show that coercion and iterated, multilevel selection on both species encourage endosymbiosis. Mutualism is favored if host-cells are significantly more effective than PMPs at gathering food. Otherwise, an unambiguous asymmetry between host-cell and PMP benefits implies that the initial relationship consisted of the host-cell deriving a reproductive advantage at the PMPs' expense-a cellular version of farming. Other initial relationships such as oxygen-detoxification mutualism and parasitism are not strongly supported by the model. We compare the model behavior with experiments on mutant human mitochondria and find the model predicts proliferation rates consistent with that data. We derive from the evolutionary dynamics counter-intuitive therapeutic targets for two human hereditary mitochondrial disorders that reflect the ongoing effect of short-term selection at the mitochondrial level.

Mitochondrial DNA fragments released through the permeability transition pore correspond to specific gene size

In the present work, we show that after induction of mitochondrial damage by oxidative stress, in the presence of calcium, matrix DNA content decreased to 42+/-6%. Mitochondrial damage was analyzed by measuring aconitase activity, a marker enzyme of mitochondrial oxidative stress. The genes were identified by amplifying them through the polymerase chain reaction (PCR), using specific primers for each mitochondrial gene (MTCO1, MTCO2, MTCO3, MTND3, MTND5, MTATP6, MTATP8, and MTCYB). The results show that after oxidative stress, the amount of MTCO1, MTND3, and MTCYB genes in the mitochondria approximately decreased by 46, 22, and 54%, respectively. This effect was inhibited in the presence of cyclosporin A. These genes were found outside the mitochondria after permeability transition was induced. Mitochondrial integrity was evaluated by observing the activity of adenylate kinase and malate dehydrogenase.

Aup1p, a yeast mitochondrial protein phosphatase homolog, is required for efficient stationary phase mitophagy and cell survival

Autophagy is a catabolic membrane-trafficking process that occurs in all eukaryotic cells and leads to the hydrolytic degradation of cytosolic material in the vacuolar or lysosomal lumen. Mitophagy, a selective form of autophagy targeting mitochondria, is poorly understood at present. Several recent reports suggest that mitophagy is a selective process that targets damaged mitochondria, whereas other studies imply a role for mitophagy in cell death processes. In a screen for protein phosphatase homologs that functionally interact with the autophagy-dedicated protein kinase Atg1p in yeast, we have identified Aup1p, encoded by Saccharomyces cerevisiae reading frame YCR079w. Aup1p is highly similar to a family of protein phosphatase homologs in animal cells that are predicted to localize to mitochondria based on sequence analysis. Interestingly, we found that Aup1p localizes to the mitochondrial intermembrane space and is required for efficient mitophagy in stationary phase cells. Viability studies demonstrate that Aup1p is required for efficient survival of cells in prolonged stationary phase cultures, implying a pro-survival role for mitophagy under our working conditions. Our data suggest that Aup1p may be part of a signal transduction mechanism that marks mitochondria for sequestration into autophagosomes.

Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris)

Using oligonucleotide primers designed to match hypervariable segments I (HVS-1) of Panthera tigris mitochondrial DNA (mtDNA), we amplified two different PCR products (500 bp and 287 bp) in the tiger (Panthera tigris), but got only one PCR product (287 bp) in the leopard (Panthera pardus). Sequence analyses indicated that the sequence of 287 bp was a D-loop-like nuclear mitochondrial sequence (Numts), indicating a nuclear transfer that occurred approximately 4.8-17 million years ago in the tiger and 4.6-16 million years ago in the leopard. Although the mtDNA D-loop sequence has a rapid rate of evolution, the 287-bp Numts are highly conserved; they are nearly identical in tiger subspecies and only 1.742% different between tiger and leopard. Thus, such sequences represent molecular 'fossils' that can shed light on evolution of the mitochondrial genome and may be the most appropriate outgroup for phylogenetic analysis. This is also proved by comparing the phylogenetic trees reconstructed using the D-loop sequence of snow leopard and the 287-bp Numts as outgroup.

Mitochondrial signal peptidases of yeast: the rhomboid peptidase Pcp1 and its substrate cytochrome C peroxidase

The rhomboid peptidase Pcp1 of yeast is the first mitochondrial enzyme of this new class of serine peptidases. Pcp1 is an integral part of the inner membrane and was identified by its signal peptidase activity responsible for processing of the intermediate of cytochrome c peroxidase (iCcp1) to the mature enzyme. Here we describe studies on the expression of the PCP1 gene. Proteolytic processing of Pcp1 itself was found. The precursor and the intermediate of Ccp1 were localized to the inner membrane. The results confirm our previous report on a two-step processing pathway of cytochrome c peroxidase and the identification of the signal peptidases involved.

Origin, evolution and genetic effects of nuclear insertions of organelle DNA

In eukaryotes, nuclear genomes are subject to an influx of DNA from mitochondria and plastids. The nuclear insertion of organellar sequences can occur during the illegitimate repair of double-stranded breaks. After integration, nuclear organelle DNA is modified by point mutations, and by deletions. Insertion of organelle DNA into nuclear genes is not rare and can potentially have harmful effects. In humans, some insertions of nuclear mitochondrial DNA are associated with heritable diseases. It remains to be determined whether nuclear organelle DNA can contribute beneficially to gene evolution.

Capture of extranuclear DNA at fission yeast double-strand breaks

Proper repair of DNA double-strand breaks (DSBs) is necessary for the maintenance of genomic integrity. Here, a new simple assay was used to study extrachromosomal DSB repair in Schizosaccharomyces pombe. Strikingly, DSB repair was associated with the capture of fission yeast mitochondrial DNA (mtDNA) at high frequency. Capture of mtDNA fragments required the Lig4p/Pku70p nonhomologous end-joining (NHEJ) machinery and its frequency was highly increased in fission yeast cells grown to stationary phase. The fission yeast Mre11 complex Rad32p/Rad50p/Nbs1p was also required for efficient capture of mtDNA at DSBs, supporting a role for the complex in promoting intermolecular ligation. Competition assays further revealed that microsatellite DNA from higher eukaryotes was preferentially captured at yeast DSBs. Finally, cotransformation experiments indicated that, in NHEJ-deficient cells, capture of extranuclear DNA at DSBs was observed if homologies--as short as 8 bp--were present between DNA substrate and DSB ends. Hence, whether driven by NHEJ, microhomology-mediated end-joining, or homologous recombination, DNA capture associated with DSB repair is a mutagenic process threatening genomic stability.

Trs85 (Gsg1), a Component of the TRAPP Complexes, Is Required for the Organization of the Preautophagosomal Structure during Selective Autophagy via the Cvt Pathway

Autophagosomes and Cvt vesicles are limited by two membrane layers. The biogenesis of these unconventional vesicles and the origin of their membranes are hardly understood. Here we identify in Saccharomyces cerevisiae Trs85, a nonessential component of the TRAPP complexes, to be required for the biogenesis of Cvt vesicles. The TRAPP complexes function in endoplasmic reticulum-to-Golgi and Golgi trafficking. Growing trs85delta cells show a defect in the organization of the preautophagosomal structure. Although proaminopeptidase I is normally recruited to the preautophagosomal structure, the recruitment of green fluorescent protein-Atg8 depends on Trs85. Autophagy proceeds in the absence of Trs85, albeit at a reduced rate. Our electron microscopic analysis demonstrated that the reduced autophagic rate of trs85delta cells does not result from a reduced size of the autophagosomes. Growing and starved cells lacking Trs85 did not show defects in vacuolar biogenesis; mature vacuolar proteinase B and carboxypeptidase Y were present. Also vacuolar acidification was normal in these cells. It is known that mutations impairing the integrity of the ER or Golgi block both autophagy and the Cvt pathway. But the phenotypes of trs85delta cells show striking differences to those seen in mutants with defects in the early secretory pathway. This suggests that Trs85 might play a direct role in the Cvt pathway and autophagy.

PpATG9 encodes a novel membrane protein that traffics to vacuolar membranes, which sequester peroxisomes during pexophagy in Pichia pastoris

When Pichia pastoris adapts from methanol to glucose growth, peroxisomes are rapidly sequestered and degraded within the vacuole by micropexophagy. During micropexophagy, sequestering membranes arise from the vacuole to engulf the peroxisomes. Fusion of the sequestering membranes and incorporation of the peroxisomes into the vacuole is mediated by the micropexophagy-specific membrane apparatus (MIPA). In this study, we show the P. pastoris ortholog of Atg9, a novel membrane protein is essential for the formation of the sequestering membranes and assembly of MIPA. During methanol growth, GFP-PpAtg9 localizes to multiple structures situated near the plasma membrane referred as the peripheral compartment (Atg9-PC). On glucose-induced micropexophagy, PpAtg9 traffics from the Atg9-PC to unique perivacuolar structures (PVS) that contain PpAtg11, but lack PpAtg2 and PpAtg8. Afterward, PpAtg9 distributes to the vacuole surface and sequestering membranes. Movement of the PpAtg9 from the Atg9-PC to the PVS requires PpAtg11 and PpVps15. PpAtg2 and PpAtg7 are essential for PpAtg9 trafficking from the PVS to the vacuole and sequestering membranes, whereas trafficking of PpAtg9 proceeds independent of PpAtg1, PpAtg18, and PpVac8. In summary, our data suggest that PpAtg9 transits from the Atg9-PC to the PVS and then to the sequestering membranes that engulf the peroxisomes for degradation.

Impairing the bioenergetic status and the biogenesis of mitochondria triggers mitophagy in yeast

Autophagy, a highly regulated programme found in almost all eukaryotes, is mainly viewed as a catabolic process that degrades nonessential cellular components into molecular building blocks, subsequently available for biosynthesis at a lesser expense than de novo synthesis. Autophagy is largely known to be regulated by nutritional conditions. Here we show that, in yeast cells grown under nonstarving conditions, autophagy can be induced by mitochondrial dysfunction. Electron micrographs and biochemical studies show that an autophagic activity can result from impairing the mitochondrial electrochemical transmembrane potential. Furthermore, mitochondrial damage-induced autophagy results in the preferential degradation of impaired mitochondria (mitophagy), before leading to cell death. Mitophagy appears to rely on classical macroautophagy machinery while being independent of cellular ATP collapse. These results suggest that in this case, autophagy can be envisioned either as a process of mitochondrial quality control, or as an ultimate cellular response triggered when cells are overwhelmed with damaged mitochondria.

The permeability transition pore as a pathway for the release of mitochondrial DNA

This study shows that under oxidative stress DNA from liver mitochondria (mtDNA) can be released through the non-specific permeability transition pore. Pore opening was induced after the addition of Fe2+ and hydrogen peroxide, in the presence of calcium ions. Under these conditions mitochondria undergo large extent swelling, accompanied by the generation of thiobarbituric acid-reactive substances. It was observed that mtDNA was hydrolyzed after the oxidative stress, and it is proposed that some of the fragments were released from the matrix, in such a way that approximately 12% of the total mtDNA remained in the mitochondria. The remaining genetic material was analyzed, after its extraction in an agarose gel. The fragments released were smaller that 1000 bp, by analysis in a native 8% polyacrilamide gel. The presence of cyclosporin A, that inhibited permeability transition, also inhibited mtDNA release by roughly 52%.

Uth1p: a yeast mitochondrial protein at the crossroads of stress, degradation and cell death

UTH1 is a yeast aging gene that has been identified on the basis of stress resistance and longer life span of mutants. It was also shown to participate in mitochondrial biogenesis. The absence of Uth1p was found to trigger resistance to autophagy induced by rapamycin. Uth1p is therefore the first mitochondrial protein proven to be required for the autophagic degradation of mitochondria. Since this protein is also involved in yeast cell death induced by heterologous expression of the pro-apoptotic protein Bax, the results are discussed in the light of evidence suggesting a co-regulation of apoptosis and autophagy in mammalian cells.

Analysis of the functional domains of the mismatch repair homologue Msh1p and its role in mitochondrial genome maintenance

Mitochondrial DNA (mtDNA) repair occurs in all eukaryotic organisms and is essential for the maintenance of mitochondrial function. Evidence from both humans and yeast suggests that mismatch repair is one of the pathways that functions in overall mtDNA stability. In the mitochondria of the yeast Saccharomyces cerevisiae, the presence of a homologue to the bacterial MutS mismatch repair protein, MSH1, has long been known to be essential for mitochondrial function. The mechanisms for which it is essential are unclear, however. Here, we analyze the effects of two point mutations, msh1-F105A and msh1-G776D, both predicted to be defective in mismatch repair; and we show that they are both able to maintain partial mitochondrial function. Moreover, there are significant differences in the severity of mitochondrial disruption between the two mutants that suggest multiple roles for Msh1p in addition to mismatch repair. Our overall findings suggest that these additional predicted functions of Msh1p, including recombination surveillance and heteroduplex rejection, may be primarily responsible for its essential role in mtDNA stability.

Uth1p is involved in the autophagic degradation of mitochondria

The absence of the outer mitochondrial membrane protein Uth1p was found to induce resistance to rapamycin treatment and starvation, two conditions that induce the autophagic process. Biochemical studies showed the onset of a fully active autophagic activity both in wild-type and Deltauth1 strains. On the other hand, the disorganization of the mitochondrial network induced by rapamycin treatment or 15 h of nitrogen starvation was followed in cells expressing mitochondria-targeted green fluorescent protein; a rapid colocalization of green fluorescent protein fluorescence with vacuole-selective FM4-64 labeling was observed in the wild-type but not in the Deltauth1 strain. Degradation of mitochondrial proteins, followed by Western blot analysis, did not occur in mutant strains carrying null mutations of the vacuolar protease Pep4p, the autophagy-specific protein Atg5p, and Uth1p. These data show that, although the autophagic machinery was fully functional in the absence of Uth1p, this protein is involved in the autophagic degradation of mitochondria.

Atg21 is required for effective recruitment of Atg8 to the preautophagosomal structure during the Cvt pathway

Atg21 and Atg18 are homologue yeast proteins. Whereas Atg18 is essential for the Cvt pathway and autophagy, a lack of Atg21 only blocks the Cvt pathway. Our proteinase protection experiments now demonstrate that growing atg21Delta cells fail to form proaminopeptidase I-containing Cvt vesicles. Quantitative measurement of autophagy in starving atg21Delta cells showed only 35% of the wild-type rate. This suggests that Atg21 plays a nonessential role in improving the fidelity of autophagy. The intracellular localization of Atg21 is unique among the Atg proteins. In cells containing multiple vacuoles, Atg21-yellow fluorescent protein clearly localizes to the vertices of the vacuole junctions. Cells with a single vacuole show most of the protein at few perivacuolar punctae. This distribution pattern is reminiscent to the Vps class C(HOPS) (homotypic fusion and vacuolar protein sorting) protein complex. In growing cells, Atg21 is required for effective recruitment of Atg8 to the preautophagosomal structure. Consistently, the covalent linkage of Atg8 to the lipid phosphatidylethanolamine is significantly retarded. Lipidated Atg8 is supposed to act during the elongation of autophagosome precursors. However, despite the reduced autophagic rate and the retardation of Atg8 lipidation, electron microscopy of starved atg21Delta ypt7Delta double mutant cells demonstrates the formation of normally sized autophagosomes with an average diameter of 450 nm.

How big is the iceberg of which organellar genes in nuclear genomes are but the tip?

As more and more complete bacterial and archaeal genome sequences become available, the role of lateral gene transfer (LGT) in shaping them becomes more and more clear. Over the long term, it may be the dominant force, affecting most genes in most prokaryotes. We review the history of LGT, suggesting reasons why its prevalence and impact were so long dismissed. We discuss various methods purporting to measure the extent of LGT, and evidence for and against the notion that there is a core of never-exchanged genes shared by all genomes, from which we can deduce the "true" organismal tree. We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes.

The product of the UTH1 gene, required for Bax-induced cell death in yeast, is involved in the response to rapamycin

A yeast mutant was isolated that was resistant to Bax-induced cell death. It supports a mutation leading to decreased amounts of the protein Uth1p. A strain in which the UTH1 gene is disrupted also exhibits resistance to Bax expression. The absence of Uth1p does not change the mitochondrial localization of Bax, its insertion in the mitochondrial outer membrane or its cytochrome c-releasing activity. On the other hand, the absence of Uth1p does prevent the appearance of other hallmarks related to Bax expression in yeast, such as oxidation of mitochondrial lipid, production of reactive oxygen species and maintenance of plasma membrane properties after ethanol stress. The absence of Uth1p was also found to induce resistance to rapamycin, a specific inducer of autophagy. This resistance only appears when cells are grown under respiratory conditions, but not under fermentative conditions, suggesting that Uth1p acts in an autophagic pathway involving mitochondria, in accordance with its main localization in the outer mitochondrial membrane. Taken together, these data show that Bax is able to activate a death pathway related to autophagy in yeast, which also exhibits typical hallmarks of apoptosis, revealing a possible dual function of Bax in both types of death. This hypothesis is discussed in the light of observations suggesting a co-regulation of apoptosis and autophagy in mammalian cells.

Maintenance of mitochondrial morphology is linked to maintenance of the mitochondrial genome in Saccharomyces cerevisiae

In the yeast Saccharomyces cerevisiae, certain mutant alleles of YME4, YME6, and MDM10 cause an increased rate of mitochondrial DNA migration to the nucleus, carbon-source-dependent alterations in mitochondrial morphology, and increased rates of mitochondrial DNA loss. While single mutants grow on media requiring mitochondrial respiration, any pairwise combination of these mutations causes a respiratory-deficient phenotype. This double-mutant phenotype allowed cloning of YME6, which is identical to MMM1 and encodes an outer mitochondrial membrane protein essential for maintaining normal mitochondrial morphology. Yeast strains bearing null mutations of MMM1 have altered mitochondrial morphology and a slow growth rate on all carbon sources and quantitatively lack mitochondrial DNA. Extragenic suppressors of MMM1 deletion mutants partially restore mitochondrial morphology to the wild-type state and have a corresponding increase in growth rate and mitochondrial DNA stability. A dominant suppressor also suppresses the phenotypes caused by a point mutation in MMM1, as well as by specific mutations in YME4 and MDM10.

Yeast Mon1p/Aut12p functions in vacuolar fusion of autophagosomes and cvt-vesicles

Here we identify Mon1p as being essential for the cvt-pathway and autophagy. Thus, mon1Delta cells are impaired in proaminopeptidase I maturation and homozygous diploid mon1Delta cells do not sporulate. Quantitative autophagy measurements suggest a complete autophagy block. The autophagosomal marker protein GFP-Aut7p accumulates in mon1Delta cells at punctate structures outside the vacuole. Furthermore, proaminopeptidase I accumulates in mon1Delta cells in a proteinase-protected form. Our data demonstrate that mon1Delta cells are defective in the fusion of cvt-vesicles and autophagosomes with the vacuole. Consistent with this, GFP-Mon1p localizes to the cytosol and to punctate structures within the cytosol.

Autophagy in yeast: mechanistic insights and physiological function

Unicellular eukaryotic organisms must be capable of rapid adaptation to changing environments. While such changes do not normally occur in the tissues of multicellular organisms, developmental and pathological changes in the environment of cells often require adaptation mechanisms not dissimilar from those found in simpler cells. Autophagy is a catabolic membrane-trafficking phenomenon that occurs in response to dramatic changes in the nutrients available to yeast cells, for example during starvation or after challenge with rapamycin, a macrolide antibiotic whose effects mimic starvation. Autophagy also occurs in animal cells that are serum starved or challenged with specific hormonal stimuli. In macroautophagy, the form of autophagy commonly observed, cytoplasmic material is sequestered in double-membrane vesicles called autophagosomes and is then delivered to a lytic compartment such as the yeast vacuole or mammalian lysosome. In this fashion, autophagy allows the degradation and recycling of a wide spectrum of biological macromolecules. While autophagy is induced only under specific conditions, salient mechanistic aspects of autophagy are functional in a constitutive fashion. In Saccharomyces cerevisiae, induction of autophagy subverts a constitutive membrane-trafficking mechanism called the cytoplasm-to-vacuole targeting pathway from a specific mode, in which it carries the resident vacuolar hydrolase, aminopeptidase I, to a nonspecific bulk mode in which significant amounts of cytoplasmic material are also sequestered and recycled in the vacuole. The general aim of this review is to focus on insights gained into the mechanism of autophagy in yeast and also to review our understanding of the physiological significance of autophagy in both yeast and higher organisms.

Expression of green fluorescent protein from a recoded gene inserted into Saccharomyces cerevisiae mitochondrial DNA

To generate a visible reporter of mitochondrial gene expression, we have synthesized a DNA fragment that specifies an enhanced variant of the green fluorescent protein (GFP) in the Saccharomyces cerevisiae mitochondrial genetic code. This reporter gene, GFP(m)-3, was inserted into mtDNA at the eighth codon of the COX3 gene. Mitochondria containing this mtDNA could be detected by fluorescence microscopy. Mitochondrially encoded GFP accumulated as soluble matrix protein, whose level could be measured both immunologically and fluorometrically. Quantitation of relative fluorescence by flow cytometry confirmed that cox3 :: GFP(m)-3 expression was affected by carbon source and dependent upon COX3 mRNA-specific translational activation. GFP(m)-3 will be a valuable tool for studying mitochondrial gene regulation and the intracellular fates of mitochondrially synthesized proteins.

Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway

Cvt19 is specifically required for the transport of resident vacuolar hydrolases that utilize the cytoplasm-to-vacuole targeting (Cvt) pathway. Autophagy (Apg) and pexophagy, processes that use the majority of the same protein components as the Cvt pathway, do not require Cvt19. Cvt19GFP is localized to punctate structures on or near the vacuole surface. Cvt19 is a peripheral membrane protein that binds to the precursor form of the Cvt cargo protein aminopeptidase I (prAPI) and travels to the vacuole with prAPI. These results suggest that Cvt19 is a receptor protein for prAPI that allows for the selective transport of this protein by both the Cvt and Apg pathways.

Mitochondria are selectively eliminated from eukaryotic cells after blockade of caspases during apoptosis

Pan caspase inhibitors are potentially powerful cell-protective agents that block apoptosis in response to a wide variety of insults that cause tissue degeneration. In many conditions, however, the blockade of apoptosis by caspase inhibitors does not permit long-term cell survival, but the reasons are not entirely clear. Here we show that the blockade of apoptosis by Boc.Aspartyl(O-methyl)CH2F can result in the highly selective elimination of the entire cohort of mitochondria, including mitochondrial DNA, from both neurons and HeLa cells, irrespective of the stimulus used to trigger apoptosis. In cells that lose their mitochondria, the nuclear DNA, Golgi apparatus, endoplasmic reticulum, centrioles, and plasma membrane remain undamaged. The capacity to remove mitochondria is both specific and regulated since mitochondrial loss in neurons is completely prevented by the expression of the antiapoptotic protein Bcl-2 and partially suppressed by the autolysosomal inhibitor bafilomycin. Cells without mitochondria are more tolerant to an anaerobic environment but are essentially irreversibly committed to death. Prevention of mitochondrial loss may be crucial for the long-term regeneration of tissues emerging from an apoptotic episode in which death was prevented by caspase blockade.