Augmenter of liver regeneration (alr) promotes liver outgrowth during zebrafish hepatogenesis

Augmenter of Liver Regeneration (ALR) is a sulfhydryl oxidase carrying out fundamental functions facilitating protein disulfide bond formation. In mammals, it also functions as a hepatotrophic growth factor that specifically stimulates hepatocyte proliferation and promotes liver regeneration after liver damage or partial hepatectomy. Whether ALR also plays a role during vertebrate hepatogenesis is unknown. In this work, we investigated the function of alr in liver organogenesis in zebrafish model. We showed that alr is expressed in liver throughout hepatogenesis. Knockdown of alr through morpholino antisense oligonucleotide (MO) leads to suppression of liver outgrowth while overexpression of alr promotes liver growth. The small-liver phenotype in alr morphants results from a reduction of hepatocyte proliferation without affecting apoptosis. When expressed in cultured cells, zebrafish Alr exists as dimer and is localized in mitochondria as well as cytosol but not in nucleus or secreted outside of the cell. Similar to mammalian ALR, zebrafish Alr is a flavin-linked sulfhydryl oxidase and mutation of the conserved cysteine in the CxxC motif abolishes its enzymatic activity. Interestingly, overexpression of either wild type Alr or enzyme-inactive Alr(C131S) mutant promoted liver growth and rescued the liver growth defect of alr morphants. Nevertheless, alr(C131S) is less efficacious in both functions. Meantime, high doses of alr MOs lead to widespread developmental defects and early embryonic death in an alr sequence-dependent manner. These results suggest that alr promotes zebrafish liver outgrowth using mechanisms that are dependent as well as independent of its sulfhydryl oxidase activity. This is the first demonstration of a developmental role of alr in vertebrate. It exemplifies that a low-level sulfhydryl oxidase activity of Alr is essential for embryonic development and cellular survival. The dose-dependent and partial suppression of alr expression through MO-mediated knockdown allows the identification of its late developmental role in vertebrate liver organogenesis.

Alrp, a survival factor that controls the apoptotic process of regenerating liver after partial hepatectomy in rats

Augmenter of Liver Regeneration (Alrp) enhances, through unknown mechanism/s, hepatocyte proliferation only when administered to partially hepatectomized (PH) rats. Liver resection, besides stimulating hepatocyte proliferation, induces reactive oxygen species (ROS), triggering apoptosis. To clarify the role of Alrp in the process of liver regeneration, hepatocyte proliferation, apoptosis, ROS-induced parameters and morphological findings of regenerating liver were studied from PH rats Alrp-treated for 72 h after the surgery. The same parameters, evaluated on regenerating liver from albumin-treated PH rats, were used as control. The results demonstrated that Alrp administration induces the anti-apoptotic gene expression, inhibits hepatocyte apoptosis and reduces ROS-induced cell damage. These and similar data from in vitro studies and the presence of 'Alrp homologous proteins' in viruses as well as in mammals (i) allow to hypothesize that Alrp activity/ies may not be exclusive for regenerating liver and (ii) suggest the use of Alrp in the treatment of oxidative stress-related diseases.

Protective effect of augmenter of liver regeneration on hydrogen peroxide-induced apoptosis in SH-SY5Y human neuroblastoma cells

BACKGROUND

Hydrogen peroxide, as other reactive oxygen species (ROS) produced during redox processes, induces lipid membrane peroxidation and protein degeneration causing cell apoptosis. ROS are recently considered as messengers in cell signalling processes, which, through reversible protein disulphide bridges formation, activate regulatory factors of cell proliferation and apoptosis. Disulphide bridges formation is catalysed by sulphydryl oxidase enzymes.

AIM

The neuroprotective effect of ALR protein (Alrp), a sulphydryl oxidase enzyme, on H(2)O(2)-induced apoptosis in SH-SY5Y cells has been evaluated.

METHODS

Cell viability, flow cytometric evaluation of apoptotic cells, fluorescent changes of nuclear morphology, immunocytochemistry Alrp detection, Western blot evaluation of mitochondrial cyt c release and mitochondrial swelling were determined.

RESULTS

Alrp prevents the H(2)O(2)-induced cell viability loss, apoptotic cell death and mitochondrial swelling in SH-SY5Y cells in culture.

CONCLUSIONS

The data demonstrate that Alrp improves SH-SY5Y cells survival in H(2)O(2)-induced apoptosis. It is speculated that this effect could be related to the Alrp enzymatic activity.

Gain of Function in an ERV/ALR Sulfhydryl Oxidase by Molecular Engineering of the Shuttle Disulfide

The ERV/ALR sulfhydryl oxidase domain is a versatile module adapted for catalysis of disulfide bond formation in various organelles and biological settings. Its four-helix bundle structure juxtaposes a Cys-X-X-Cys dithiol/disulfide motif with a bound flavin adenine dinucleotide (FAD) cofactor, enabling transfer of electrons from thiol substrates to non-thiol electron acceptors. ERV/ALR family members contain an additional di-cysteine motif outside the four-helix-bundle core. Although the location and context of this "shuttle" disulfide differs among family members, it is proposed to perform the same basic function of mediating electron transfer from substrate to the enzyme active site. We have determined by X-ray crystallography the structure of AtErv1, an ERV/ALR enzyme that contains a Cys-X4-Cys shuttle disulfide and oxidizes thioredoxin in vitro, and compared it to ScErv2, which has a Cys-X-Cys shuttle and does not oxidize thioredoxin at an appreciable rate. The AtErv1 shuttle disulfide is in a region of the structure that is disordered and thus apparently mobile and exposed. This feature may facilitate access of protein substrates to the shuttle disulfide. To test whether the shuttle disulfide region is modular and can confer on other enzymes oxidase activity toward new substrates, we generated chimeric enzyme variants combining shuttle disulfide and core elements from AtErv1 and ScErv2 and monitored oxidation of thioredoxin by the chimeras. We found that the AtErv1 shuttle disulfide region could indeed confer thioredoxin oxidase activity on the ScErv2 core. Remarkably, various chimeras containing the ScErv2 Cys-X-Cys shuttle disulfide were found to function efficiently as well. Since neither the ScErv2 core nor the Cys-X-Cys motif is therefore incapable of participating in oxidation of thioredoxin, we conclude that wild-type ScErv2 has evolved to repress activity on substrates of this type, perhaps in favor of a different, as yet unknown, substrate.

Erv1 mediates the Mia40-dependent protein import pathway and provides a functional link to the respiratory chain by shuttling electrons to cytochrome c

Unlike matrix-targeted or inner membrane proteins, those that are targeted to the mitochondrial intermembrane space (IMS) do not require ATP or the inner membrane electrochemical potential. Their import is mediated primarily by the essential IMS protein Mia40/Tim40. Here, we show that the mitochondrial flavin adenine dinucleotide (FAD)-linked sulfhydryl oxidase Erv1 (essential for respiration and vegetative growth 1) plays a central role in the biogenesis of small, cysteine proteins of the IMS that are import substrates for Mia40. In a temperature-sensitive strain of Erv1, steady-state levels of small translocases of the inner membrane (Tims) are specifically affected when cells are grown at the non-permissive temperature. Furthermore, mitochondria isolated from the erv1-ts show a specific import and assembly defect for the small Tims but not in any other protein import pathway. Erv1 does not directly oxidise the small Tims, as thiol trapping assays show that the small Tims can still be oxidised in erv1-ts cells grown at the non-permissive temperature and in isolated mitochondria from this strain. Moreover, addition of pure Erv1 into erv1-ts mitochondria lacking the endogenous protein restores import and assembly of the small Tims only to an extent, arguing for a cascade of interactions with Erv1 rather than for a direct interaction of Erv1 with the small Tims. Cytochrome c (cyt c) is the in vivo oxidase for Erv1, as yeast cells mutated in cyt c cannot grow under anaerobic conditions. Therefore, Erv1 functionally links the Mia40-dependent import pathway to the Mia40-independent cyt c import pathway transferring electrons from the incoming precursors to cyt c as an acceptor. In this context, the protein import process is linked to the respiratory chain via the communication of Erv1 with cyt c.

Expression of the sulfhydryl oxidase ALR (Augmenter of Liver Regeneration) in adult rat brain

Mammalian Augmenter of Liver Regeneration protein (ALR) was first identified as a secondary growth factor involved in liver regeneration. Its sulfhydryl oxidase activity and involvement in iron homeostasis have been recently demonstrated. ALR is expressed in a broad range of peripheral organs, and initial experiments gave also evidence for the occurrence of this protein in brain. In the present study, we investigated in detail the expression of ALR in rat brain sections and determined its cellular and subcellular localizations using biomolecular and immunohistochemical procedures. As shown by Northern blot, ALR is differentially expressed throughout the rat brain, with the highest mRNA levels in the cerebellum and diencephalon. High protein levels were also detected in the brain and cerebellum by Western blot. ALR immunoreactivity was found in neurons and glial cells throughout brain rostrocaudal extent. Labeled astrocytes were particularly abundant in the white matter, and immunoreactive neurons were observed in several regions including the olfactory bulb, isocortex, hippocampal formation, amygdala, thalamus, hypothalamus, some nuclei of the brainstem and cerebellum. In neurons, immunoelectron microscopy showed the protein in the nucleus and mainly in mitochondria. These subcellular localizations may correlate with the occurrence of two ALR protein isoforms in the brain. In the central nervous system, the enzyme might be of importance in heavy metal homeostasis whose dysregulation can induce neurodegenerative disorders.

Unique Features of Plant Mitochondrial Sulfhydryl Oxidase

The yeast and human mitochondrial sulfhydryl oxidases of the Erv1/Alr family have been shown to be essential for the biogenesis of mitochondria and the cytosolic iron sulfur cluster assembly. In this study we identified a likely candidate for the first mitochondrial flavin-linked sulfhydryl oxidase of the Erv1-type from a photosynthetic organism. The central core of the plant enzyme (AtErv1) exhibits all of the characteristic features of the Erv1/Alr protein family, including a redox-active YPCXXC motif, noncovalently bound FAD, and sulfhydryl oxidase activity. Transient expression of fusion proteins of AtErv1 and the green fluorescence protein in plant protoplasts showed that the plant enzyme preferentially localizes to the mitochondria. Yet AtErv1 has several unique features, such as the presence of a CXXXXC motif in its carboxyl-terminal domain and the absence of an amino-terminally localized cysteine pair common to yeast and human Erv1/Alr proteins. In addition, the dimerization of AtErv1 is not mediated by its amino terminus but by its unique CXXXXC motif. In vitro assays with purified protein and artificial substrates demonstrate a preference of AtErv1 for dithiols with a defined space between the thiol groups, suggesting a thioredoxin-like substrate.

The N-terminal cysteine pair of yeast sulfhydryl oxidase Erv1p is essential for in vivo activity and interacts with the primary redox centre

Yeast Erv1p is a ubiquitous FAD-dependent sulfhydryl oxidase, located in the intermembrane space of mitochondria. The dimeric enzyme is essential for survival of the cell. Besides the redox-active CXXC motif close to the FAD, Erv1p harbours two additional cysteine pairs. Site-directed mutagenesis has identified all three cysteine pairs as essential for normal function. The C-terminal cysteine pair is of structural importance as it contributes to the correct arrangement of the FAD-binding fold. Variations in dimer formation and unique colour changes of mutant proteins argue in favour of an interaction between the N-terminal cysteine pair with the redox centre of the partner monomer.

Accumulation of the mitochondrial form of the sulphydryl oxidase Erv1p/Alrp during the early stages of spermatogenesis

In this study, we investigated the expression of the mammalian FAD-dependent sulphydryl oxidase Erv1p/Alrp in the rat and mouse and during mouse spermatogenesis. Up to three forms of Alrp were identified in protein extracts from different tissues and organs, but very little enzyme was present in blood samples. The three forms of Alrp represent the full-length protein of 23 kDa and fragments of 21 kDa and 15 kDa. All forms of Alrp were assembled into dimers in vivo. In contrast to samples from other organs, the protein analysis of mouse testis identified predominantly full-length 23 kDa Alrp. This finding prompted us to investigate in more detail the expression of Alrp during spermatogenesis. Testis samples of individual mice from postnatal days 13-29 were probed with an antibody specific for mammalian Alrp. In addition, cells from whole testis preparations were fractionated on a bovine serum albumin column gradient. Protein expression of mouse Alrp was compared with those of testis-specific cyritestin, the cytoskeleton marker actin and mitochondrial subunit Vb of cytochrome oxidase and cytochrome c. These studies demonstrated a specific accumulation of full-length mouse Alrp during the early stages of spermatogenesis. The highest levels of Alrp were found in spermatogonia and primary spermatocytes. Levels of expression of Alrp did not correlate with the synthesis of components of the respiratory chain,indicating that full-length Alrp in the mitochondria of spermatogonia and spermatocytes has another function in addition to its role in oxidative phosphorylation.

The C-terminal region of mitochondrial single-subunit RNA polymerases contains species-specific determinants for maintenance of intact mitochondrial genomes

Functional conservation of mitochondrial RNA polymerases was investigated in vivo by heterologous complementation studies in yeast. It turned out that neither the full-length mitochondrial RNA polymerase of Arabidopsis thaliana, nor a set of chimeric fusion constructs from plant and yeast RNA polymerases can substitute for the yeast mitochondrial core enzyme Rpo41p when expressed in Deltarpo41 yeast mutants. Mitochondria from mutant cells, expressing the heterologous mitochondrial RNA polymerases, were devoid of any mitochondrial genomes. One important exception was observed when the carboxyl-terminal domain of Rpo41p was exchanged with its plant counterpart. Although this fusion protein could not restore respiratory function, stable maintenance of mitochondrial petite genomes (rho(-))(-) was supported. A carboxyl-terminally truncated Rpo41p exhibited a comparable activity, in spite of the fact that it was found to be transcriptionally inactive. Finally, we tested the carboxyl-terminal domain for complementation in trans. For this purpose the last 377 amino acid residues of yeast mitochondrial Rpo41p were fused to its mitochondrial import sequence. Coexpression of this fusion protein with C-terminally truncated Rpo41p complemented the Deltarpo41 defect. These data reveal the importance of the carboxyl-terminal extension of Rpo41p for stable maintenance of intact mitochondrial genomes and for distinct species-specific intramolecular protein-protein interactions.

An essential function of the mitochondrial sulfhydryl oxidase Erv1p/ALR in the maturation of cytosolic Fe/S proteins

Biogenesis of Fe/S clusters involves a number of essential mitochondrial proteins. Here, we identify the essential Erv1p of Saccharomyces cerevisia mitochondria as a novel component that is specifically required for the maturation of Fe/S proteins in the cytosol, but not in mitochondria. Furthermore, Erv1p was found to be important for cellular iron homeostasis. The homologous mammalian protein ALR ('augmenter of liver regeneration'), also termed hepatopoietin, can functionally replace defects in Erv1p and thus represents the mammalian orthologue of yeast Erv1p. Previously, a fragment of ALR was reported to exhibit an activity as an extracellular hepatotrophic growth factor. Both Erv1p and full-length ALR are located in the mitochondrial intermembrane space and represent the first components of this compartment with a role in the biogenesis of cytosolic Fe/S proteins. It is likely that Erv1p/ALR operates downstream of the mitochondrial ABC transporter Atm1p/ABC7/Sta1, which also executes a specific task in this essential biochemical process.

Yeast ERV2p is the first microsomal FAD-linked sulfhydryl oxidase of the Erv1p/Alrp protein family

Saccharomyces cerevisiae Erv2p was identified previously as a distant homologue of Erv1p, an essential mitochondrial protein exhibiting sulfhydryl oxidase activity. Expression of the ERV2 (essential for respiration and vegetative growth 2) gene from a high-copy plasmid cannot substitute for the lack of ERV1, suggesting that the two proteins perform nonredundant functions. Here, we show that the deletion of the ERV2 gene or the depletion of Erv2p by regulated gene expression is not associated with any detectable growth defects. Erv2p is located in the microsomal fraction, distinguishing it from the mitochondrial Erv1p. Despite their distinct subcellular localization, the two proteins exhibit functional similarities. Both form dimers in vivo and in vitro, contain a conserved YPCXXC motif in their carboxyl-terminal part, bind flavin adenine dinucleotide (FAD) as a cofactor, and catalyze the formation of disulfide bonds in protein substrates. The catalytic activity, the ability to form dimers, and the binding of FAD are associated with the carboxyl-terminal domain of the protein. Our findings identify Erv2p as the first microsomal member of the Erv1p/Alrp protein family of FAD-linked sulfhydryl oxidases. We propose that Erv2p functions in the generation of microsomal disulfide bonds acting in parallel with Ero1p, the essential, FAD-dependent oxidase of protein disulfide isomerase.

Mammalian augmenter of liver regeneration protein is a sulfhydryl oxidase

BACKGROUND

Augmenter of Liver Regeneration is an important secondary hepatic growth factor. Augmenter of liver regeneration protein has been shown to control mitochondrial gene expression and the lytic activity of liver-resident Natural Killer cells through the levels of interferon-gamma, but the precise enzymatic function of this protein is unknown.

AIMS

To define the enzymatic activity of augmenter of liver regeneration protein. The carboxy terminus of augmenter of liver regeneration protein contains a special CXXC motif characteristic for redox proteins and with faint homologies to the redox-active site of sulfhydryl oxidases. Tests were, therefore, carried out to establish whether isolated augmenter of liver regeneration protein can also function in the formation of sulfur bridges.

METHODS

Purified augmenter of liver regeneration proteins from rat and human were tested in enzyme assays for the ability to introduce disulfide bonds into protein substrates. The isolated proteins were tested for the formation of dimers and the presence of bound FAD was investigated spectroscopically. The function of the conserved CXXC motif was investigated by in vitro mutagenesis experiments and subsequent enzyme assays.

RESULTS

In this study, we demonstrate that rat and human augmenter of liver regeneration protein are flavin-linked sulfhydryl oxidases that catalyze the formation of disulfide bonds in reduced protein substrates. A flavin moiety is firmly but not covalently attached to the protein. In human cell cultures augmenter of liver regeneration protein is expressed in a long and short form that both exist as covalently linked dimers. The active site of the enzyme is associated with a conserved CXXC motif in the carboxy-terminal domain, that is present in the homologous proteins from yeast to humans and also in the human Q6 growth regulator protein. In vitro mutagenesis of one cysteine residue in the CXXC motif results in loss of enzymatic function and the mutated protein no longer binds FAD.

CONCLUSIONS

For the first time, these data assign an enzymatic activity to the important hepatic growth factor augmenter of liver regeneration protein. The finding that augmenter of liver regeneration protein acts as a FAD-linked sulfhydryl oxidase is essential to identify the molecular targets inside liver cells and to elucidate the precise role of mammalian augmenter of liver regeneration protein in hepatic cell growth, liver disease and regeneration.

The augmenter of liver regeneration induces mitochondrial gene expression in rat liver and enhances oxidative phosphorylation capacity of liver mitochondria

BACKGROUND

The mammalian augmenter of liver regeneration gene encodes a protein involved in the unique process of liver regeneration. The augmenter of liver regeneration respective protein stimulates hepatocyte proliferation in hepatectomized rats and inhibits cytotoxic activity of liver-derived Natural Killer cells from intact rats. Augmenter of liver regeneration protein shares homology with a Saccharomyces Cerevisiae protein essential for the viability, oxidative phosphorylation and cell-division cycle.

AIMS

To demonstrate if augmenter of liver regeneration protein, like the homologous in the yeast, plays a role in the regulation of biogenesis of mitochondria.

METHODS

Augmenter of liver regeneration protein was injected in intact rats and, in the hepatic tissue, the expression of two genes located in two different regions of the mitochondrial genome, mitochondrial ATPase 6/8, and ND1 subunit, and of a nuclear gene, mitochondrial Transcription Factor A, were considered. In addition, cytochrome content and oxidative phosphorylation capacity of liver-derived mitochondria were evaluated.

RESULTS

The augmenter of liver regeneration protein administration induces an increase in the mitochondrial gene expression and enhances cytochrome content and oxidative phosphorylation capacity of liver-derived mitochondria.

CONCLUSIONS

The present data demonstrate a comparable role in the regulation of mitochondria biogenesis in the eukaryotic cell like the yeast protein. This phenomenon could be part of the complex mechanism through which augmenter of liver regeneration regulates hepatocyte proliferation.

Erv1p from Saccharomyces cerevisiae is a FAD-linked sulfhydryl oxidase

The yeast ERV1 gene encodes a small polypeptide of 189 amino acids that is essential for mitochondrial function and for the viability of the cell. In this study we report the enzymatic activity of this protein as a flavin-linked sulfhydryl oxidase catalyzing the formation of disulfide bridges. Deletion of the amino-terminal part of Erv1p shows that the enzyme activity is located in the 15 kDa carboxy-terminal domain of the protein. This fragment of Erv1p still binds FAD and catalyzes the formation of disulfide bonds but is no longer able to form dimers like the complete protein. The carboxy-terminal fragment contains a conserved CXXC motif that is present in all homologous proteins from yeast to human. Thus Erv1p represents the first FAD-linked sulfhydryl oxidase from yeast and the first of these enzymes that is involved in mitochondrial biogenesis.

A screen of yeast respiratory mutants for sensitivity against the mycotoxin citrinin identifies the vacuolar ATPase as an essential factor for the toxicity mechanism

In countries with a hot climate the mycotoxin citrinin represents a serious problem in fungal food-poisoning. In humans the renal system is affected the most and the mitochondrial respiratory chain was identified as a possible sensitive target for this toxin. In addition, citrinin has an antifungal activity that also inhibits the growth of the yeast Saccharomyces cerevisiae. So far the precise mode of action and the subcellular targets for citrinin have not been identified. Therefore, we decided to use the model organism yeast for a genetic approach to identify genes that play a role in the sensitivity against this mycotoxin. A large collection of conditional respiratory deficient yeast mutants was screened for sensitivity against citrinin. One special pet-ts mutant was identified that exhibited a higher sensitivity against citrinin. The genetic system of yeast allowed the isolation of the respective wild-type gene. This yeast gene encodes the Vph2p subunit that is essential for the correct assembly of the vacuolar ATPase. Isolation of the mutated gene and gene-disruption experiments of VPH2 and the partially overlapping small YKL118W gene verified this finding. The wild-type VPH2 gene restores all defects of the mutants. In contrast to this, YKL118W gave no complementation and the null mutant showed no phenotype. Thereby the yeast vacuolar ATPase was found to be important for the toxic effect of citrinin in yeast cells. The consequences of this finding for the molecular mechanism of citrinin action and its relation to the mitochondrial respiratory chain are discussed.

Molecular mechanisms of augmenter of liver regeneration as immunoregulator: its effect on interferon-gamma expression in rat liver

BACKGROUND

We have shown that the administration of exogenous Augmenter of Liver Regeneration protein in intact rats i) regulates mitochondrial gene expression by inducing the transcription and translation of the nuclear-encoded mitochondrial transcription factor A, and ii) inhibits the lytic activity of liver-resident Natural Killer cells.

AIMS

The present investigation was carried out to study the effect, in intact rats, of exogenous administration of Augmenter of Liver Regeneration protein on Interferon-gamma, a cytokine produced by activated Natural Killer cells and known to control the expression of mitochondrial transcription factor A, a nuclear gene responsible for mitochondrial metabolism.

METHODS

Interferon-gamma was measured as messenger RNA in liver-derived mononuclear leukocytes and as protein in liver-derived Natural Killer cells after a single injection of Augmenter of Liver Regeneration protein.

RESULTS

The data obtained demonstrate that: i) in intact rats, Augmenter of Liver Regeneration protein administration induces a reduction of Interferon-gamma in the liver-resident Natural Killer cells and ii) the administration of Interferon-gamma in 70% hepatectomized rats is followed by a significant reduction both of the mitochondrial transcription factor A expression and of liver regeneration.

CONCLUSIONS

These data demonstrate the pivotal role of Augmenter of Liver Regeneration as Growth Factor and as immunoregulator by controlling, through Interferon-gamma levels, the mitochondrial transcription factor A expression and the lytic activity of liver-resident Natural Killer cells.

A mutant for the yeast scERV1 gene displays a new defect in mitochondrial morphology and distribution

The yeast scERV1 gene is the best characterized representative of a new gene family found in different lower and higher eukaryotes. The gene product is essential for the yeast cell and has a complex influence on different aspects of mitochondrial biogenesis. The homologous mammalian ALR(Augmenter of Liver Regeneration) genes from man, mouse and rat are important at different developmental stages of the organism as, for example, in spermatogenesis and liver regeneration. In this study the influence of scERV1 on the morphology of mitochondria and its submitochondrial localization are investigated. A temperature-sensitive mutant of the gene was stained with a mitochondria-specific dye and fluorescence was inspected at the permissive and restrictive temperature. A new phenotype for morphological defects of mitochondria was identified. Already at the permissive temperature mitochondrial vesicles accumulate at defined positions in the cell. After shift to the restrictive temperature, morphological changes, and finally complete loss of mitochondrial structures, are observed. Ultrastructural studies confirm these findings and demonstrate the loss of the mitochondrial inner membrane and at the final stage a drastic reduction or complete absence of mitochondria from the cell. GFP fusion experiments with the scERV1 gene and subcellular localization by fractionation experiments identify the gene product inside mitoplasts and the cytosol. Re-investigation of the mutant phenotype demonstrates that after longer incubation of the mutant at the restrictive temperature an irreversible defect of the cells, even on glucose complete medium, is found that is in accordance with a complete loss or irreversible damage of mitochondria.

A mutant for the yeast scERV1 gene displays a new defect in mitochondrial morphology and distribution

The yeast scERV1 gene is the best characterized representative of a new gene family found in different lower and higher eukaryotes. The gene product is essential for the yeast cell and has a complex influence on different aspects of mitochondrial biogenesis. The homologous mammalian ALR(Augmenter of Liver Regeneration) genes from man, mouse and rat are important at different developmental stages of the organism as, for example, in spermatogenesis and liver regeneration. In this study the influence of scERV1 on the morphology of mitochondria and its submitochondrial localization are investigated. A temperature-sensitive mutant of the gene was stained with a mitochondria-specific dye and fluorescence was inspected at the permissive and restrictive temperature. A new phenotype for morphological defects of mitochondria was identified. Already at the permissive temperature mitochondrial vesicles accumulate at defined positions in the cell. After shift to the restrictive temperature, morphological changes, and finally complete loss of mitochondrial structures, are observed. Ultrastructural studies confirm these findings and demonstrate the loss of the mitochondrial inner membrane and at the final stage a drastic reduction or complete absence of mitochondria from the cell. GFP fusion experiments with the scERV1 gene and subcellular localization by fractionation experiments identify the gene product inside mitoplasts and the cytosol. Re-investigation of the mutant phenotype demonstrates that after longer incubation of the mutant at the restrictive temperature an irreversible defect of the cells, even on glucose complete medium, is found that is in accordance with a complete loss or irreversible damage of mitochondria.

Expression studies and promoter analysis of the nuclear gene for mitochondrial transcription factor 1 (MTF1) in yeast

The basal mitochondrial transcription apparatus of Saccharomyces cerevisiae consists of the core enzyme for mitochondrial RNA polymerase and the specificity factor. The core enzyme is homologous to those of bacteriophages T3, T7 and SP6 whereas the specificity factor shows similarities with bacterial sigma factors. Recently it was shown that the bacteriophage-type core enzyme is widespread among the eukaryotic lineage and a common picture for the mitochondrial transcription apparatus in eukaryotic cells is now emerging. In contrast to the situation for the core enzyme, the gene for the specificity factor has only been identified from S. cerevisiae and more recently from two other yeast species. As the specificity factor is the key component for initiation of transcription at the mitochondrial promoter we wanted to study in more detail gene expression, regulation, and the function of the promoter of the nuclear MTF1 gene. For this purpose the messenger RNA level for scMTF1 was investigated under a large number of different growth conditions and thereby exhibited a very low, but regulated and carbon source-dependent, expression. Deletion experiments identify the minimal promoter for functional complementation in yeast. To evaluate the functional conservation of the promoter elements the homologous MTF1 gene from the closely related yeast Saccharomyces douglasii was isolated and tested in heterologous complementation experiments. In spite of a highly conserved protein sequence these studies demonstrate that at low-copy number sdMTF1 is not able to substitute for scMTF1 in S. cerevisiae. Promoter exchange experiments with MTF1 from S. cerevisiae and S. douglasii demonstrate that differences in gene expression are responsible for the failure in heterologous complementation. This finding prompted us to compare the promoter regions of MTF1 from four different yeast species. For this purpose the sequences of the 5' regions from S. douglasii, S. kluyveri and Kluyveromyces lactis were determined. A comparison of these sequences identifies significant differences and rapid changes in the intergenic regions, even between closely related yeast species.

From yeast to man--from mitochondria to liver regeneration: a new essential gene family

The purpose of this review is to bring to the attention of the reader the latest developments in research on an important new emerging gene family. The respective genes are found in eukaryotes from yeast to man and even on the genome of some doubled-stranded DNA viruses. They have essential functions in the biogenesis of mitochondria, the cell division cycle and, in higher eukaryotes, in the development of organs like liver and testis. The most important medical implication is their probable role in liver regeneration that will, therefore, be addressed in detail. Aspects of molecular biology, medical implications and problems of developmental biology reflect the complexity of the functions of these proteins and the subjects of the respective research. This is just the beginning of an interdisciplinary effort directed towards the elucidation of the precise function of these essential factors inside the eukaryotic cell. In the general part of this review, we will concentrate on the history of the discovery of these genes and on a summary of their characteristic features. In the more specialized section, the specific role as augmenter of liver regeneration will be addressed in detail.

Identification of human GC-box-binding zinc finger protein, a new Krüppel-like zinc finger protein, by the yeast one-hybrid screening with a GC-rich target sequence

A new human zinc finger DNA-binding protein was identified by using a yeast one-hybrid selection system. Two versions of the cDNA, encoding the same protein, were detected that differ for a 584 bp extension at the 5' region. Sequence analysis showed that the longer clone is a full length version containing part of the 5' untranslated region. The smaller version was fused in frame with the yeast GAL4 activation domain whereas the 5' region of the longer clone displayed a stop codon interrupting the fusion with the GAL4 domain. Nevertheless, this clone activated the yeast HIS3 reporter gene with the same efficiency as the smaller version. Sequence comparison of the derived protein with the database showed that it belongs to a family of zinc finger DNA-binding proteins which regulate the expression of genes involved in cell proliferation. Expression of the protein in an in vitro system, DNA-binding studies and genetic experiments identify this factor as a new zinc finger DNA-binding protein which binds GC-rich sequences and contains a domain probably functioning as a transcriptional activator. The new human protein identified in this study was therefore named GC-box-binding zinc finger protein).

Highly divergent amino termini of the homologous human ALR and yeast scERV1 gene products define species specific differences in cellular localization

The yeast scERV1 gene product is involved in the biogenesis of mitochondria and is indispensable for viability and regulation of the cell cycle. Recently the general importance of this gene for the eukaryotic cell was shown by the identification of a structural and functional human homologue. The homologous mammalian ALR (Augmenter of Liver Regeneration) genes from man, mouse and rat are involved in the phenomenon of liver regeneration. A low expression rate of the genes is found in all investigated cells and mammalian tissues but it is specifically induced after damage of liver organs and is especially high during spermatogenesis. The alignment of the different proteins identifies a highly conserved carboxy terminus with more than 40% identical amino acids between yeast and mammals. The conserved carboxy terminus is functionally interchangeable between distantly related species like yeast and man. In contrast, the amino terminal parts of the proteins display a high degree of variability and significant differences even among closely related species. This finding leads to the problem whether the amino termini have comparable or divergent functions in different species. In this study we demonstrate by heterologous complementation experiments in yeast that the complete human ALR protein with its own amino terminus is not able to substitute for the yeast scERV1 protein. Fusion proteins of Alrp and scErv1p with the green fluorescence protein were created to investigate the respective subcellular localizations of these homologous proteins in yeast and human cells. In yeast cells human Alrp accumulates in the cytoplasm in contrast to yeast scErv1p that is preferentially associated with yeast mitochondria. Comparable studies with human cells clearly show that the homologous human Alrp is located in the cytosol of these cells. Fractionation experiments and antibody tests with yeast and human mitochondria and cellular extracts verify these findings.

Azf1p is a nuclear-localized zinc-finger protein that is preferentially expressed under non-fermentative growth conditions in Saccharomyces cerevisiae

In previous studies the AZF1 gene has been identified as a second high-copy number suppressor for a special mutant of the gene for the mitochondrial core enzyme of RNA polymerase. The first high-copy number suppressor of this mutant turned out to be the specificity factor MTF1 for mitochondrial transcription. Up to now, the influence of AZF1 on mitochondrial transcription, its precise localization in the cell and the regulation of its expression has not been determined. The putative protein contains a long stretch of poly-asparagine amino acids and a typical zinc-finger domain for DNA binding. These characteristic structural features were used to create the abbreviation AZF1 (Asparagine-rich Zinc Finger protein). An initial computer analysis of the sequence gave no conclusive results for the presence of a mitochondrial import sequence or a typical nuclear-targeting sequence. A recent more-detailed analysis identified a possible nuclear localization signal in the middle of the protein. Disruption of the gene shows no effect on plates with glucose-rich medium or glycerol. In this report a specific polyclonal antibody against Azf1p was prepared and used in cell-fractionation experiments and in electron-microscopic studies. Both of these clearly demonstrate that the AZF1 protein is localized exclusively in the nucleus of the yeast cell. Northern analysis for the expression of the AZF1 messenger RNA under different growth conditions was therefore performed to obtain new insights into the regulation of this gene. Together with the respective protein-expression analysis these data demonstrate that Azf1p is preferentially synthezised in higher amounts under non-fermentable growth conditions. Over-expression of Azf1p in the yeast cell does not influence the expression level of the mitochondrial transcription factor Mtf1p, indicating that the influence of Azf1p on the suppression of the special mitochondrial RNA polymerase mutant is an indirect one. Subcellular investigation of the deletion mutant by electron microscopy identifies specific ultrastructural cell-division defects in comparison to the wild-type.

Functional comparison of the yeast scERV1 and scERV2 genes

The yeast scERV1 gene is the first representative of a new emerging gene family. Its gene product is essential for the yeast cell and is involved in the biogenesis of mitochondria and the regulation of the cell cycle. Recently the general importance of the gene for the eukaryotic cell was shown by the identification of a structural and functional human homologue. The homologous mammalian ALR (augmenter of liver regeneration) genes from man, mouse and rat are important for different developmental stages of the organism as for example in spermatogenesis and the regeneration of damaged liver organs. Latest research identified an intron with an unusual 3' branch site in the 5' region of the yeast scERV1 gene. Analysis of the now available complete genome sequence from Saccharomyces cerevisiae identified a second yeast gene with homologies to scERV1 on chromosome 16. The corresponding gene product has a length of 196 amino acids similar to the 189 residues of the scERV1 protein and exhibits 30% identical amino acid residues in the highly conserved carboxy-terminal part of the polypeptides. Because of the structural similarities the new gene will be termed scERV2 from now on. For the scERV1 gene product it has just been shown that it is associated with yeast mitochondria. Analysis of the amino-terminal part of the putative scERV2 protein also identifies a typical leader sequence for import into mitochondria. The comparison of cDNA and genomic DNA from the scERV2 gene shows that no intron is present in this gene. To investigate the functional relation between the two yeast genes disruption experiments and complementation studies of mutants from scERV1 were performed. In addition the expression of messenger RNA under 15 different growth conditions was investigated by detailed Northern hybridization studies. Both genes show a complex and distinct expression pattern for their transcripts and are highly regulated under different physiological conditions. Moreover correct and efficient splicing of the transcript from the scERV1 gene was found to vary with the physiological state of the yeast cell, as further verified by reverse transcription-polymerase chain reaction analysis of transcripts from galactose-grown yeast cells.

Functional comparison of the yeast scERV1 and scERV2 genes

The yeast scERV1 gene is the first representative of a new emerging gene family. Its gene product is essential for the yeast cell and is involved in the biogenesis of mitochondria and the regulation of the cell cycle. Recently the general importance of the gene for the eukaryotic cell was shown by the identification of a structural and functional human homologue. The homologous mammalian ALR (augmenter of liver regeneration) genes from man, mouse and rat are important for different developmental stages of the organism as for example in spermatogenesis and the regeneration of damaged liver organs. Latest research identified an intron with an unusual 3' branch site in the 5' region of the yeast scERV1 gene. Analysis of the now available complete genome sequence from Saccharomyces cerevisiae identified a second yeast gene with homologies to scERV1 on chromosome 16. The corresponding gene product has a length of 196 amino acids similar to the 189 residues of the scERV1 protein and exhibits 30% identical amino acid residues in the highly conserved carboxy-terminal part of the polypeptides. Because of the structural similarities the new gene will be termed scERV2 from now on. For the scERV1 gene product it has just been shown that it is associated with yeast mitochondria. Analysis of the amino-terminal part of the putative scERV2 protein also identifies a typical leader sequence for import into mitochondria. The comparison of cDNA and genomic DNA from the scERV2 gene shows that no intron is present in this gene. To investigate the functional relation between the two yeast genes disruption experiments and complementation studies of mutants from scERV1 were performed. In addition the expression of messenger RNA under 15 different growth conditions was investigated by detailed Northern hybridization studies. Both genes show a complex and distinct expression pattern for their transcripts and are highly regulated under different physiological conditions. Moreover correct and efficient splicing of the transcript from the scERV1 gene was found to vary with the physiological state of the yeast cell, as further verified by reverse transcription-polymerase chain reaction analysis of transcripts from galactose-grown yeast cells.

Removal of an intron with unique 3' branch site creates an amino-terminal protein sequence directing the scERV1 gene product to mitochondria

The yeast scERV1 gene is of special interest because it has a dual function in mitochondrial biogenesis and in the regulation of the cell cycle. The recent discovery that the yeast scERV1 gene has a structural and functional human homologue initiated a detailed comparison of the genes and their structures. In addition the homologous ALR (augmenter of liver regeneration) genes from rat and mouse have just been identified and it has been found that the mammalian proteins have a specific function in liver regeneration and in spermatogenesis. It now turns out that the organization of the 5' regions of these genes is much more complicated than expected. The latest research has discovered an additional intron in the 5' region of the mouse gene and possible amino-terminal extensions of the reading frames. In this work, reinvestigation of the 5' region of the yeast gene identifies a putative intron with an unusual 3' branch site. It is shown that a small intron of 83 nucleotides is present in this genomic region. Analysis of cDNA clones demonstrates that the intron is correctly removed from the messenger RNA and that therefore the unusual 3' branch site is probably functional. Furthermore, studies with antibodies directed against recombinant scERV1 protein demonstrate that the gene product is associated with mitochondria, in agreement with its involvement in mitochondrial biogenesis. Complementation experiments with mutants and different 5' deletions of the gene identify the corresponding promotor for transcription and the start codon for translation.

Removal of an intron with unique 3' branch site creates an amino-terminal protein sequence directing the scERV1 gene product to mitochondria

The yeast scERV1 gene is of special interest because it has a dual function in mitochondrial biogenesis and in the regulation of the cell cycle. The recent discovery that the yeast scERV1 gene has a structural and functional human homologue initiated a detailed comparison of the genes and their structures. In addition the homologous ALR (augmenter of liver regeneration) genes from rat and mouse have just been identified and it has been found that the mammalian proteins have a specific function in liver regeneration and in spermatogenesis. It now turns out that the organization of the 5' regions of these genes is much more complicated than expected. The latest research has discovered an additional intron in the 5' region of the mouse gene and possible amino-terminal extensions of the reading frames. In this work, reinvestigation of the 5' region of the yeast gene identifies a putative intron with an unusual 3' branch site. It is shown that a small intron of 83 nucleotides is present in this genomic region. Analysis of cDNA clones demonstrates that the intron is correctly removed from the messenger RNA and that therefore the unusual 3' branch site is probably functional. Furthermore, studies with antibodies directed against recombinant scERV1 protein demonstrate that the gene product is associated with mitochondria, in agreement with its involvement in mitochondrial biogenesis. Complementation experiments with mutants and different 5' deletions of the gene identify the corresponding promotor for transcription and the start codon for translation.

A new point mutation in the nuclear gene of yeast mitochondrial RNA polymerase, RPO41, identifies a functionally important amino-acid residue in a protein region conserved among mitochondrial core enzymes

The core enzyme of mitochondrial RNA polymerase in yeast is homologous to those of bacteriophages T3, T7 and SP6. In previous studies the identification of the first conditional yeast mutant for this enzyme helped to identify the corresponding specificity factor and to elucidate their interaction inside mitochondria. In the present study we report the identification of a second nuclear mutation located in the gene for mitochondrial RNA polymerase. A comparison of the two temperature-sensitive mutants demonstrates that the new mutant has a phenotype distinct from the first one and characterizes a new important domain of the enzyme. Two different suppressor genes which both rescue the first mutant do not abolish the defect of the second one and, in addition, an extremely high instability of mitochondrial genomes is observed in the new mutant. The enzymatic defect is caused by a single nucleotide exchange which results in the replacement of the serine938 residue by phenylalanine. This amino acid is located in the middle part of the protein in an as yet poorly characterized region that is not highly conserved between mitochondrial core enzymes and bacteriophage-type RNA polymerases. However, the affected amino acid and the respective protein domain are specific for mitochondrial RNA polymerase core enzymes and may help to define enzymatic functions specific for the mitochondrial transcription apparatus.

Different respiratory-defective phenotypes of Neurospora crassa and Saccharomyces cerevisiae after inactivation of the gene encoding the mitochondrial acyl carrier protein

The nuclear genes (acp-1, ACP1) encoding the mitochondrial acyl carrier protein were disrupted in Neurospora crassa and Saccharomyces cerevisiae. In n. crassa acp-1 is a peripheral subunit of the respiratory NADH : ubiquinone oxidoreductase (complex I). S. cerevisiae lacks complex I and its ACP1 appears to be located in the mitochondrial matrix. The loss of acp-1 in N. crassa causes two biochemical lesions. Firstly, the peripheral part of complex I is not assembled, and the membrane part is not properly assembled. The respiratory ubiquinol : cytochrome c oxidoreductase (complex III) and cytochrome c oxidase (complex IV) are made in normal amounts. Secondly, the lysophospholipid content of mitochondrial membranes is increased four-fold. In S. cerevisiae, the loss of ACP1 leads to a pleiotropic respiratory deficient phenotype.

A new human gene located in the PKD1 region of chromosome 16 is a functional homologue to ERV1 of yeast

A new human gene has been identified on chromosome 16 in the interval containing the locus for polycystic kidney disease (PKD1) by analysis of a genomic cosmid clone and cDNAs. The gene contains at least one intron and is actively transcribed in tissues from kidney and brain. The putative gene product is predicted to be homologous to the yeast scERV1 protein by virtue of the high degree of identity (42%) over the entire length of the polypeptides. In former studies the yeast scERV1 gene was found to be essential for oxidative phosphorylation, the maintenance of mitochondrial genomes, and the cell-division cycle. In this study a yeast expression vector with a chimeric reading frame coding for the first 21 amino acids of the yeast protein and the terminal 100 amino acid residues of the human factor was transformed into yeast mutants with two different defects for scERV1. The chimeric human gene product was able to complement the yeast mutants and restored near normal viability. This identifies the human gene as a structural and functional homologue of the scERV1 gene.

ERV1 is involved in the cell-division cycle and the maintenance of mitochondrial genomes in Saccharomyces cerevisiae

In former studies it was found that the ERV1 gene is essential for cell viability and for the biogenesis of functional mitochondria. A temperature-sensitive nuclear mutant exhibits a severe reduction in all the mitochondrial transcripts. Elimination of the gene leads to growth arrest after a few cell divisions. The putative gene product bears the characteristics of a regulatory factor since it has low expression rate and a high content of charged amino acids. In this study it is further verified that the ERV1 gene alone is responsible for the observed cellular and mitochondrial defects. The 5' region of the gene is analysed by DNA deletions and complementation studies. Expression of the gene under the control of the GAL1-10 promoter in a disruption strain of ERV1 allows a more detailed specification ot its influence on mitochondrial and cellular functions. Immediate and complete loss of mitochondrial genomes is observed after the promoter has been shut off, whereas the yeast cells are still able to grow for a limited time under these conditions. Analysis of the cells by in-vivo DNA fluorescence demonstrates a specific arrest in the cell-division cycle as the terminal phenotype. To further characterize the temperature-sensitive allele of ERV1 the mutated gene has been isolated and sequenced. A single point mutation which leads to the exchange of a single amino acid is found in the reading frame.

A new nuclear suppressor system for a mitochondrial RNA polymerase mutant identifies an unusual zinc-finger protein and a polyglutamine domain protein in Saccharomyces cerevisiae

A yeast strain with a point mutation in the nuclear gene for the core subunit of mitochondrial RNA polymerase was used to isolate new extragenic suppressors. Spontaneously occurring phenotypical revertants were analysed by crosses with the wild-type and tetrad dissection. One of the new nuclear suppressor mutants was characterized by temperature-sensitive growth on non-fermentable carbon sources. This mutant was transformed with a genomic yeast library. Two independent types of DNA clones were isolated which both complemented the temperature-sensitive defect. Subcloning and DNA sequencing identified two novel yeast genes which code for proteins with the characteristic features of transcription factors. Both factors exhibit highly structured protein domains consisting of runs and clusters of asparagine and glutamine residues. One of the proteins contains in addition zinc-finger domains of the C2H2-type. Therefore the genes are proposed to be named AZF1 (asparagine-rich zinc-finger protein) and PGD1 (polyglutamine domain protein). Gene disruption of both reading frames has no detectable influence on the vegetative growth on complete glucose or glycerol media, indicating that the genes may act as high copy number suppressors of the mutant defect. Additional transformation experiments showed that AZF1 is also an efficient suppressor for the original defect in the core subunit of mitochondrial RNA polymerase.

A high copy number of yeast gamma-glutamylcysteine synthetase suppresses a nuclear mutation affecting mitochondrial translation

A new temperature-sensitive nuclear mutant affecting the biogenesis of functional mitochondria has been identified. This pet mutant was formerly characterized by a complete block of mitochondrial translation at the restrictive temperature. The analysis of mitochondrial transcripts demonstrates the accumulation of precursors for the small ribosomal RNA. Transformation of the mutant with plasmids from gene banks identified a chromosomal DNA fragment which can restore growth at the restrictive temperature. A reading frame of 2034 base pairs was found to be responsible for complementation of the mutant phenotype. Sequence analysis identified this gene as the gamma-glutamylcysteine synthetase of yeast. This enzyme catalyses the first reaction in the gamma-glutamyl cycle for the synthesis of glutathione. Disruption of yeast gamma-glutamylcysteine synthetase causes a drastic reduction of growth on glucose medium. The insertion mutants were not able to grow on plates with glycerol as the sole carbon source indicating the special dependence of mitochondria on this substance. Crosses between the pet-ts mutant and the disruption mutant produced diploid cells with a complementation of all their genetic defects indicating that the pet-ts mutation and the insertion mutation are located in different genes. This finding demonstrates that the cloned yeast gene acts as an extragenic suppressor when present on a high-copy-number plasmid inside the pet mutant.

Nuclear control of the messenger RNA expression for mitochondrial ATPase subunit 9 in a new yeast mutant

A new temperature-sensitive nuclear mutant of Saccharomyces cerevisiae altered in the expression of the mitochondrially encoded ATPase 9 gene was identified. Analysis of several mitochondrial transcripts reveals the selective loss of the messenger RNA for the ATPase 9 subunit under restrictive temperature conditions. This defect results in a respiratory deficiency of the yeast cells. RNA synthesis studied with isolated mitochondria gives first evidence that the mitochondrial transcription process does not react in a temperature-sensitive way. Therefore, it is concluded that the loss of the transcript is due to specific posttranscriptional degradation. Further on it is demonstrated that all the observed effects in the mutant are caused by only one mutated nuclear gene. The mutant strain was transformed with a genomic yeast library and a complementary DNA fragment was obtained. Molecular characterization of the respective DNA clone identified a new gene, which we propose to call NCA1 (Nuclear Control of ATPase messenger RNA expression). Complete inactivation of this gene by insertion mutagenesis in the chromosome leads to a permanent respiratory defect of the cell. Localization of the insertion locus in the yeast genome and complementation studies with the temperature-sensitive mutant indicate that the two mutations are allelic.

An yeast nuclear mutation conferring temperature-sensitivity to the mitochondrial tryptophanyl-tRNA synthetase

The conditional respiratory-deficient Saccharomyces cerevisiae mutant pet-ts2281 was complemented by an yeast genomic DNA library. The gene thus isolated was sequenced and proved to be identical to the known MSW1 sequence encoding mitochondrial tryptophanyl-tRNA synthetase (Myers and Tzagoloff 1985). Compared to the wild-type, the ts2281 mutant allele of MSW1 contained a single T----C transition leading to a Leu----Ser replacement at position 294 of the protein sequence. In addition to this mutational alteration, our sequence data for the wild-type gene differ from the originally published MSW1 sequence at five other DNA positions which affect two locally restricted regions of the polypeptide chain. As expected, at the non-permissive temperature ts2281 cells are specifically defective in mitochondrial trp-tRNA formation and, thus, in overall mitochondrial protein synthesis. In addition, the patterns of cytochrome b mRNA maturation intermediates were distinctly different in ts2281 and wild-type yeast cells. The mutational effect of the observed amino-acid substitution in ts2281 is discussed in terms of weakened hydrogen bonding in the C-terminal half of the MSW1-encoded protein.

Dual function of a new nuclear gene for oxidative phosphorylation and vegetative growth in yeast

A new gene essential for cell viability and indispensable for the biogenesis of a functional respiratory chain in Saccharomyces cerevisiae was isolated by complementing a temperature-sensitive mutant. This conditional nuclear mutation selectively affects oxidative phosphorylation at restrictive temperatures. At the molecular level a severe and complex defect inside mitochondria is observed, with drastically reduced levels of mitochondrial transcripts. Surprisingly a null mutation in this nuclear gene in a haploid yeast strain leads to cell death. Spores containing a disrupted copy of the gene exhibit a severe growth defect and cell division stops irreversibly after 3 to 4 days. It is shown that the null and conditional mutants are indeed allelic. This finding demonstrates a dual function of the gene product in oxidative phosphorylation and vegetative growth. The putative protein product, as deduced from the sequence of the relevant reading frame is characterized by a low molecular weight of approximately 14 kDa, a high content of charged amino acids and a very low codon bias index. A transcript of low abundance and with a length of about 600 nucleotides can be assigned to this gene.

DNA wrapping and bending by a mitochondrial high mobility group-like transcriptional activator protein

Mitochondrial transcription factor 1 (mtTF1) is the only accessory protein known to be required for accurate and efficient promoter recognition by mammalian mitochondrial RNA polymerase. It activates transcription by binding immediately upstream of transcriptional start sites and shows an inherent flexibility in primary DNA sequence requirement. By application of a purification strategy designed for human and mouse mtTF1, a protein resembling mtTF1 was recently isolated from yeast mitochondria; its size (19 kDa), DNA-binding properties, and amino acid composition suggest identity to HM, a previously described abundant protein of yeast mitochondria. Both human and yeast proteins show a general ability to wrap or condense and unwind DNA in vitro and bend DNA at specific sequences. Recent determinations of the amino acid sequences of the human and yeast proteins reveal that both contain domains homologous to the nuclear high mobility group (HMG) proteins which have been implicated in diverse functions such as chromatin compaction and transcription stimulation. The ability to unwind and bend DNA may be fundamental to the documented roles of the mammalian protein in mitochondrial DNA transcription and replication priming and suggests a similar function for the yeast protein in yeast mitochondria.

A rapid, efficient method for purifying DNA-binding proteins. Denaturation-renaturation chromatography of human and yeast mitochondrial extracts

We describe a novel method for the purification of DNA-binding proteins. Isolated mitochondria were lysed in boiling sodium dodecyl sulfate-containing buffer, the extracts were chromatographed on hydroxylapatite in the presence of sodium dodecyl sulfate, and DNA-binding activities were identified after adding a large excess of nonionic detergent (Triton X-100) and assaying fractions by a gel retardation procedure. Fractions containing DNA-binding activity were bulk renatured and chromatographed on phosphocellulose in the presence of Triton X-100. When applied to human mitochondria, the technique resulted in the purification to homogeneity of fully functional mitochondrial transcription factor 1 (mtTF1), the major activator of mammalian mitochondrial transcription. Moreover, the yield of mtTF1 purified by this method was at least 25 times higher than that obtained by conventional nondenaturing chromatographies. When yeast mitochondria were subjected to the same protein isolation scheme, a 19-kilodalton putative yeast homologue of mtTF1 was purified to homogeneity. These results suggest that the denaturation-renaturation approach may be a valuable general method for the identification and high yield purification of DNA-binding proteins.

Molecular analysis of the mitochondrial transcription factor mtf2 of Saccharomyces cerevisiae

The nuclear gene for a new mitochondrial transcription factor (mtf2) was isolated by transformation of mutant pet-ts3504. It was localized on a 6.4 kb fragment of yeast genomic DNA by subcloning and complementation tests. Sequencing of a 1.7 kb DNA fragment revealed an open reading frame of 1320 bp. A transcript of 1400 nucleotides can be assigned to this region. Gene disruption of this reading frame in a wild-type yeast strain created a stable pet phenotype. Further analysis of this insertion mutation showed that it is allelic to the mutated gene of pet-ts3504. Comparison of the 5' upstream regions of MTF2 and a previously characterized mitochondrial transcription factor (MTF1) revealed common sequence motifs which may be important for coordinated regulation of gene expression.

Mutations in the genes for mitochondrial RNA polymerase and a second mitochondrial transcription factor of Saccharomyces cerevisiae

In our previous work (Lisowsky et al. 1987; Lisowsky and Michaelis 1988) we have identified two nuclear pet genes of yeast that are required for mitochondrial transcription. In this report we show that one of these pet mutations, pet-ts798, maps in the RP041 gene encoding mitochondrial RNA polymerase. The temperature-sensitive lesion of mutant pet-ts798 can be suppressed by a second nuclear gene RF1023 (mtf1) when inserted into a high copy number plasmid. Our assumption that mtf1 codes for a 40 kDa mitochondrial transciription factor is supported by the fact that the cloned gene acts as an intergenic suppressor of a temperature-sensitive RNA polymerase mutant. A third nuclear gene (mtf2) for mitochondrial transcription was identified by analysing mutant pet-ts3504. The in vitro transcriptional activity of isolated mutant mitochondria is temperature sensitive suggesting the presence of an altered component of transcription inside mitochondria. The defect was confirmed by studies with a transcriptionally active DNA-protein complex and by testing the DNA-binding ability of mitochondrial proteins.

A nuclear gene essential for mitochondrial replication suppresses a defect of mitochondrial transcription in Saccharomyces cerevisiae

A genomic DNA fragment from yeast was isolated by transforming a temperature sensitive pet mutant. This mutant, pet-ts 798, has previously been characterized by its altered mitochondrial transcription apparatus. Subcloning and DNA sequencing of the genomic DNA fragment identified a reading frame responsible for the restoration of the pet-ts phenotype. The reading frame of 1023 bp is transcribed as an RNA of about 1100 nucleotides. The putative protein of 40 kDa possesses a hydrophobic amino-terminus and acidic and basic domains characteristic of recently described transcriptional activators. The inactivation of the functional gene by the introduction of an insertion fragment into the reading frame, leads to a stable pet phenotype. Further analysis of this mutant created by gene disruption makes clear that the respiratory defect is caused by the complete loss of mitochondrial DNA. Experimental evidence is given that the cloned gene acts as an intergenic suppressor of the mutant pet-ts 798. Therefore, the isolated gene represents a new factor involved in the regulation of mitochondrial replication and transcription.

A nuclear mutation affecting mitochondrial transcription in Saccharomyces cerevisiae

Mitochondrial transcription was studied in a nuclear temperature-sensitive pet mutant of Saccharomyces cerevisiae. The mitochondrial RNA levels in vivo and the in vitro transcriptional activities of isolated mitochondria were analysed. In comparison to the wild-type an overall reduction of mitochondrial gene expression together with a changed expression pattern was observed for the mutant, indicating a defect in mitochondrial RNA synthesis. These findings were supported by studies with a purified DNA-protein complex from yeast mitochondria. This complex was able to synthesize ribosomal and messenger RNAs in an in vitro system. Proteins from wild-type and mutant transcription complexes were tested for their DNA-binding abilities; one of the proteins identified in the wild type had either lost this ability or was absent in the mutant.