MTERF3, the most conserved member of the mTERF-family, is a modular factor involved in mitochondrial protein synthesis

Suppressing MTERF3 inhibits proliferation of human hepatocellular carcinoma via ROS-mediated p38 MAPK activation

Mitochondrial transcription termination factor 3 (MTERF3) negatively regulates mitochondrial DNA transcription. However, its role in hepatocellular carcinoma (HCC) progression remains elusive. Here, we investigate the expression and function of MTERF3 in HCC. MTERF3 is overexpressed in HCC tumor tissues and higher expression of MTERF3 positively correlates with poor overall survival of HCC patients. Knockdown of MTERF3 induces mitochondrial dysfunction, S-G2/M cell cycle arrest and apoptosis, resulting in cell proliferation inhibition. In contrast, overexpression of MTERF3 promotes cell cycle progression and cell proliferation. Mechanistically, mitochondrial dysfunction induced by MTERF3 knockdown promotes ROS accumulation, activating p38 MAPK signaling pathway to suppress HCC cell proliferation. In conclusion, ROS accumulation induced by MTERF3 knockdown inhibits HCC cell proliferation via p38 MAPK signaling pathway suggesting a promising target in HCC patients.

Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling

MOTIVATION

Recent development of deep-learning methods has led to a breakthrough in the prediction accuracy of 3D protein structures. Extending these methods to protein pairs is expected to allow large-scale detection of protein-protein interactions (PPIs) and modeling protein complexes at the proteome level.

RESULTS

We applied RoseTTAFold and AlphaFold, two of the latest deep-learning methods for structure predictions, to analyze coevolution of human proteins residing in mitochondria, an organelle of vital importance in many cellular processes including energy production, metabolism, cell death and antiviral response. Variations in mitochondrial proteins have been linked to a plethora of human diseases and genetic conditions. RoseTTAFold, with high computational speed, was used to predict the coevolution of about 95% of mitochondrial protein pairs. Top-ranked pairs were further subject to modeling of the complex structures by AlphaFold, which also produced contact probability with high precision and in many cases consistent with RoseTTAFold. Most top-ranked pairs with high contact probability were supported by known PPIs and/or similarities to experimental structural complexes. For high-scoring pairs without experimental complex structures, our coevolution analyses and structural models shed light on the details of their interfaces, including CHCHD4-AIFM1, MTERF3-TRUB2, FMC1-ATPAF2 and ECSIT-NDUFAF1. We also identified novel PPIs (PYURF-NDUFAF5, LYRM1-MTRF1L and COA8-COX10) for several proteins without experimentally characterized interaction partners, leading to predictions of their molecular functions and the biological processes they are involved in.

AVAILABILITY AND IMPLEMENTATION

Data of mitochondrial proteins and their interactions are available at: http://conglab.swmed.edu/mitochondria.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

MTERF3 contributes to MPP+-induced mitochondrial dysfunction in SH-SY5Y cells

Parkinson's disease (PD) is a neurodegenerative disorder causing severe social and economic burdens. The origin of PD has been usually attributed to mitochondrial dysfunction. To this end, mitochondrial transcription regulators become attractive subjects for understanding PD pathogenesis. Previously, we found that the expression of mitochondrial transcription termination factor 3 (MTERF3) was reduced in MPP+-induced mice model of PD. In the present study, we probe the function of MTERF3 and its role in MPP+-induced cellular model of PD. Initially, we observe that MTERF3 expression is also reduced in MPP+-induced cellular model of PD, which can be mainly attributed to the increase of MTERF3 degradation. Next, we examine the effect of MTERF3 knockdown and overexpression on the replication, transcription, and translation of mitochondrial DNA (mtDNA). We show that knockdown and overexpression of MTERF3 have opposite effects on mtDNA transcript level but similar effects on mtDNA expression level, in line with MTERF3's dual roles in mtDNA transcription and translation. In addition, we examine the effect of MTERF3 knockdown and overexpression on mitochondrial function with and without MPP+ treatment, and find that MTERF3 seems to play a generally protective role in MPP+-induced mitochondrial dysfunction. Together, this work suggests a regulatory role of MTERF3 in MPP+-induced cellular model of PD and may provide clues in designing novel therapeutics against PD.

Identification, characterization and functional analysis of grape (Vitis vinifera L.) mitochondrial transcription termination factor (mTERF) genes in responding to biotic stress and exogenous phytohormone

Background

Mitochondrial transcription termination factor (mTERF) is a large gene family which plays a significant role during plant growth under various environmental stresses. However, knowledge of mTERF genes in grapevine (Vitis L.) is limited.

Results

In this research, a comprehensive analysis of grape mTERF (VvmTERF) genes, including chromosome locations, phylogeny, protein motifs, gene structures, gene duplications, synteny analysis and expression profiles, was conducted. As a result, a total of 25 mTERF genes were identified from the grape genome, which are distributed on 13 chromosomes with diverse densities and segmental duplication events. The grape mTERF gene family is classified into nine clades based on phylogenetic analysis and structural characteristics. These VvmTERF genes showed differential expression patterns in response to multiple phytohormone treatments and biotic stresses, including treatments with abscisic acid and methyl jasmonate, and inoculation of Plasmopara viticola and Erysiphe necator.

Conclusions

These research findings, as the first of its kind in grapevine, will provide useful information for future development of new stress tolerant grape cultivars through genetic manipulation of VvmTERF genes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07446-z.

Prognostic roles of mitochondrial transcription termination factors in non-small cell lung cancer

Mitochondrial transcription termination factors (MTERFs) regulate mitochondrial gene transcription and metabolism in numerous types of cells. Previous studies have indicated that MTERFs serve pivotal roles in the pathogenesis of various cancer types. However, the expression and prognostic roles of MTERFs in patients with non-small cell lung cancer (NSCLC) remain elusive. The present study investigated the gene alteration frequency and expression level using Gene Expression Omnibus datasets and reverse transcription-quantitative polymerase chain reaction, and evaluated the prognostic roles of MTERFs in patients with NSCLC using the Kaplan-Meier plotter database. In human lung cancer tissues, it was observed that the mRNA levels of MTERF1, 2, 3 and 4 were positively associated with the copy number of these genes. The mRNA expression levels of MTERF1 and 3 were significantly increased in NSCLC tissues compared with adjacent non-tumor tissues; however, the mRNA expression of MTERF2 was significantly decreased in NSCLC tissues. High mRNA expression levels of MTERF1, 2, 3 and 4 were strongly associated with an improved overall survival rate (OS) in patients with lung adenocarcinoma. Additionally, high mRNA expression levels of MTERF1, 2, 3 and 4 were also strongly associated with an improved OS of patients with NSCLC in the earlier stages of disease (stage I) or patients with negative surgical margins. These results indicate the critical prognostic values of MTERF expression levels in NSCLC. The findings of the present study may be beneficial for understanding the molecular biology mechanism of NSCLC and for generating effective therapeutic approaches for patients with NSCLC.

Mitotype Interacts With Diet to Influence Longevity, Fitness, and Mitochondrial Functions in Adult Female Drosophila

Mitochondrial DNA (mtDNA) and the dietary macronutrient ratio are known to influence a wide range of phenotypic traits including longevity, fitness and energy production. Commonly mtDNA mutations are posited to be selectively neutral or reduce fitness and, to date, no selectively advantageous mtDNA mutations have been experimentally demonstrated in adult female Drosophila. Here we propose that a ND V161L mutation interacted with diets differing in their macronutrient ratios to influence organismal physiology and mitochondrial traits, but further studies are required to definitively show no linked mtDNA mutations are functionally significant. We utilized two mtDNA types (mitotypes) fed either a 1:2 Protein: Carbohydrate (P:C) or 1:16 P:C diet. When fed the former diet, Dahomey females harboring the V161L mitotype lived longer than those with the Alstonville mitotype and had higher climbing, basal reactive oxygen species (ROS) and elevated glutathione S-transferase E1 expression. The short lived Alstonville females ate more, had higher walking speed and elevated mitochondrial functions as suggested by respiratory control ratio (RCR), mtDNA copy number and expression of mitochondrial transcription termination factor 3. In contrast, Dahomey females fed 1:16 P:C were shorter lived, had higher fecundity, walking speed and mitochondrial functions. They had reduced climbing. This result suggests that mtDNA cannot be assumed to be a strictly neutral evolutionary marker when the dietary macronutrient ratio of a species varies over time and space and supports the hypothesis that mtDNA diversity may reflect the amount of time since the last selective sweep rather than strictly demographic processes.

MTERF factors: a multifunction protein family

The MTERF family is a large protein family, identified in metazoans and plants, which consists of four subfamilies, MTERF1, 2, 3 and 4. Mitochondrial localisation was predicted for the vast majority of MTERF family members and demonstrated for the characterised MTERF proteins. The main structural feature of MTERF proteins is the presence of a modular architecture, based on repetitions of a 30-residue module, the mTERF motif, containing leucine zipper-like heptads. The MTERF family includes transcription termination factors: human mTERF, sea urchin mtDBP and Drosophila DmTTF. In addition to terminating transcription, they are involved in transcription initiation and in the control of mtDNA replication. This multiplicity of functions seems to flank differences in the gene organisation of mitochondrial genomes. MTERF2 and MTERF3 play antithetical roles in controlling mitochondrial transcription: that is, mammalian and Drosophila MTERF3 act as negative regulators, whereas mammalian MTERF2 functions as a positive regulator. Both proteins contact mtDNA in the promoter region, perhaps establishing interactions, either mutual or with other factors. Regulation of MTERF gene expression in human and Drosophila depends on nuclear transcription factors NRF-2 and DREF, respectively, and proceeds through pathways which appear to discriminate between factors positively or negatively acting in mitochondrial transcription. In this emerging scenario, it appears that MTERF proteins act to coordinate mitochondrial transcription.

Genome-wide identification, evolution and expression analysis of mTERF gene family in maize

Plant mitochondrial transcription termination factor (mTERF) genes comprise a large family with important roles in regulating organelle gene expression. In this study, a comprehensive database search yielded 31 potential mTERF genes in maize (Zea mays L.) and most of them were targeted to mitochondria or chloroplasts. Maize mTERF were divided into nine main groups based on phylogenetic analysis, and group IX represented the mitochondria and species-specific clade that diverged from other groups. Tandem and segmental duplication both contributed to the expansion of the mTERF gene family in the maize genome. Comprehensive expression analysis of these genes, using microarray data and RNA-seq data, revealed that these genes exhibit a variety of expression patterns. Environmental stimulus experiments revealed differential up or down-regulation expression of maize mTERF genes in seedlings exposed to light/dark, salts and plant hormones, respectively, suggesting various important roles of maize mTERF genes in light acclimation and stress-related responses. These results will be useful for elucidating the roles of mTERF genes in the growth, development and stress response of maize.

Mitochondrial transcription terminator family members mTTF and mTerf5 have opposing roles in coordination of mtDNA synthesis

All genomes require a system for avoidance or handling of collisions between the machineries of DNA replication and transcription. We have investigated the roles in this process of the mTERF (mitochondrial transcription termination factor) family members mTTF and mTerf5 in Drosophila melanogaster. The two mTTF binding sites in Drosophila mtDNA, which also bind mTerf5, were found to coincide with major sites of replication pausing. RNAi-mediated knockdown of either factor resulted in mtDNA depletion and developmental arrest. mTTF knockdown decreased site-specific replication pausing, but led to an increase in replication stalling and fork regression in broad zones around each mTTF binding site. Lagging-strand DNA synthesis was impaired, with extended RNA/DNA hybrid segments seen in replication intermediates. This was accompanied by the accumulation of recombination intermediates and nicked/broken mtDNA species. Conversely, mTerf5 knockdown led to enhanced replication pausing at mTTF binding sites, a decrease in fragile replication intermediates containing single-stranded segments, and the disappearance of species containing segments of RNA/DNA hybrid. These findings indicate an essential and previously undescribed role for proteins of the mTERF family in the integration of transcription and DNA replication, preventing unregulated collisions and facilitating productive interactions between the two machineries that are inferred to be essential for completion of lagging-strand DNA synthesis.

MTERF3 regulates mitochondrial ribosome biogenesis in invertebrates and mammals

Regulation of mitochondrial DNA (mtDNA) expression is critical for the control of oxidative phosphorylation in response to physiological demand, and this regulation is often impaired in disease and aging. We have previously shown that mitochondrial transcription termination factor 3 (MTERF3) is a key regulator that represses mtDNA transcription in the mouse, but its molecular mode of action has remained elusive. Based on the hypothesis that key regulatory mechanisms for mtDNA expression are conserved in metazoans, we analyzed Mterf3 knockout and knockdown flies. We demonstrate here that decreased expression of MTERF3 not only leads to activation of mtDNA transcription, but also impairs assembly of the large mitochondrial ribosomal subunit. This novel function of MTERF3 in mitochondrial ribosomal biogenesis is conserved in the mouse, thus we identify a novel and unexpected role for MTERF3 in coordinating the crosstalk between transcription and translation for the regulation of mammalian mtDNA gene expression.

Expression profile of mouse Mterfd2, a novel component of the mitochondrial transcription termination factor (MTERF) family

Mterfd2 is a component of mitochondria transcription termination factor (MTERF) family which belongs to the MTERF4 subfamily. In this report, we characterized the expression profile of mouse Mterfd2 during embryogenesis by in situ hybridization (ISH), quantitative real-time PCR (qRT-PCR) and northern blot. The whole mount ISH at E9.5, E10.5 and E11.5 showed that Mterfd2 was dynamically expressed in the brain. Besides, at E9.5 and E10.5 stages, Mterfd2 was persistently expressed in the lateral plate mesoderm and heart; at E10.5 and E11.5 stages, it showed an abundant expression in the limb buds. The tissue ISH of E13.5 and E15.5 suggested that Mterfd2 was ubiquitously expressed, and has the higher expression in the forebrain, diencephalon, midbrain, spinal cord, dorsal root ganglion, tongue, lung, liver and kidney. This ubiquitous expression profile in the late embryogenesis was further confirmed by qRT-PCR and northern blot at E12.5, E15.5 and E18.5 stages. Besides, the results of co-location of EGFP-Mterfd2 fusion protein indicated that Mterfd2 was targeted to the mitochondria. Collectively, these data suggested that Mterfd2 showed a dynamic expression pattern during embryogenesis. It might play an important role in the organ differentiation which was probably resulted from its role in the mitochondrial transcription regulation.

Hitting the brakes: termination of mitochondrial transcription

Deficiencies in mitochondrial protein production are associated with human disease and aging. Given the central role of transcription in gene expression, recent years have seen a renewed interest in understanding the molecular mechanisms controlling this process. In this review, we have focused on the mostly uncharacterized process of transcriptional termination. We review how several recent breakthroughs have provided insight into our understanding of the termination mechanism, the protein factors that mediate termination, and the functional relevance of different termination events. Furthermore, the identification of termination defects resulting from a number of mtDNA mutations has led to the suggestion that this could be a common mechanism influencing pathogenesis in a number of mitochondrial diseases, highlighting the importance of understanding the processes that regulate transcription in human mitochondria. We discuss how these recent findings set the stage for future studies on this important regulatory mechanism. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.

Mitochondrial transcription: lessons from mouse models

Mammalian mitochondrial DNA (mtDNA) is a circular double-stranded DNA genome of ~16.5 kilobase pairs (kb) that encodes 13 catalytic proteins of the ATP-producing oxidative phosphorylation system (OXPHOS), and the rRNAs and tRNAs required for the translation of the mtDNA transcripts. All the components needed for transcription and replication of the mtDNA are, therefore, encoded in the nuclear genome, as are the remaining components of the OXPHOS system and the mitochondrial translation machinery. Regulation of mtDNA gene expression is very important for modulating the OXPHOS capacity in response to metabolic requirements and in pathological processes. The combination of in vitro and in vivo studies has allowed the identification of the core machinery required for basal mtDNA transcription in mammals and a few proteins that regulate mtDNA transcription. Specifically, the generation of knockout mouse strains in the last several years, has been key to understanding the basis of mtDNA transcription in vivo. However, it is well accepted that many components of the transcription machinery are still unknown and little is known about mtDNA gene expression regulation under different metabolic requirements or disease processes. In this review we will focus on how the creation of knockout mouse models and the study of their phenotypes have contributed to the understanding of mitochondrial transcription in mammals. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.

Production, purification and characterization of mouse monoclonal antibodies against human mitochondrial transcription termination factor 2 (MTERF2)

Human mitochondrial transcription termination factor 2 (MTERF2) is a member of the mitochondrial transcription termination factors (MTERFs) family and a cell growth inhibitor. To create a specific mouse monoclonal antibody against human MTERF2, the full-length His-tag MTERF2 protein (1-385 aa) was expressed in Escherichia coli, and purified recombinant protein was injected into three BALB/c mice to perform an immunization procedure. Eight stable positive monoclonal cell lines were screened and established. ELISA results demonstrated that all antibody light chains were kappa, while the heavy chains displayed three subtypes IgG1, IgG2a, and IgG2b respectively. The sensitivity and specificity of the monoclonal antibodies against human MTERF2 were determined using immunoblotting, immunoprecipitation and immunofluorescence analyses. Furthermore, serum regulation of human MTERF2 protein expression levels in human glioma U251 cells was examined with these monoclonal antibodies and the results demonstrated that the expression level of MTERF2 protein was dramatically inhibited by the addition of serum to serum-starved cells. Taken together, our results demonstrate the functionality of these mouse anti-human MTERF2 monoclonal antibodies, which may provide a useful tool to elucidate the role of MTERF2 in human mitochondrial transcription as well as other potential activities. To our knowledge, this is the first report on the preparation and characterization of mouse monoclonal antibodies against human MTERF2.

The bicoid stability factor controls polyadenylation and expression of specific mitochondrial mRNAs in Drosophila melanogaster

The bicoid stability factor (BSF) of Drosophila melanogaster has been reported to be present in the cytoplasm, where it stabilizes the maternally contributed bicoid mRNA and binds mRNAs expressed from early zygotic genes. BSF may also have other roles, as it is ubiquitously expressed and essential for survival of adult flies. We have performed immunofluorescence and cell fractionation analyses and show here that BSF is mainly a mitochondrial protein. We studied two independent RNAi knockdown fly lines and report that reduced BSF protein levels lead to a severe respiratory deficiency and delayed development at the late larvae stage. Ubiquitous knockdown of BSF results in a severe reduction of the polyadenylation tail lengths of specific mitochondrial mRNAs, accompanied by an enrichment of unprocessed polycistronic RNA intermediates. Furthermore, we observed a significant reduction in mRNA steady state levels, despite increased de novo transcription. Surprisingly, mitochondrial de novo translation is increased and abnormal mitochondrial translation products are present in knockdown flies, suggesting that BSF also has a role in coordinating the mitochondrial translation in addition to its role in mRNA maturation and stability. We thus report a novel function of BSF in flies and demonstrate that it has an important intra-mitochondrial role, which is essential for maintaining mtDNA gene expression and oxidative phosphorylation.

The majority of the cellular energy currency ATP is formed in a tubular network, termed mitochondria, present within virtually all eukaryotic cells. The mitochondria are unique among cellular organelles in that they contain their own genome, which encodes critical proteins necessary for cellular energy production. However, the vast majority of mitochondrial proteins are encoded in the nucleus and imported into mitochondria. Gene expression thus needs to be coordinated between the two genomes to ensure efficient mitochondrial function and sufficient adaptation to different physiological demands. The regulation of the mitochondrial genome is poorly understood, with many of the basic regulators not yet being characterized. We used RNAi in the fruit fly to study the in vivo function of the bicoid stability factor (BSF), previously thought to be a cytoplasmic and nuclear protein important for fly development. We show here that BSF is mainly localized to mitochondria, where it is essential for mtDNA gene expression, regulating the polyadenylation and maturation of specific mRNAs. Furthermore, BSF coordinates the translation and assembly of mitochondrial peptides in the inner mitochondrial membrane.

Mitochondrial DNA transcription regulation and nucleoid organization

Mitochondrial biogenesis is a complex process depending on both nuclear and mitochondrial DNA (mtDNA) transcription regulation to tightly coordinate mitochondrial levels and the cell's energy demand. The energy requirements for a cell to support its metabolic function can change in response to varying physiological conditions, such as, proliferation and differentiation. Therefore, mitochondrial transcription regulation is constantly being modulated in order to establish efficient mitochondrial oxidative metabolism and proper cellular function. The aim of this article is to review the function of major protein factors that are directly involved in the process of mtDNA transcription regulation, as well as, the importance of mitochondrial nucleoid structure and its influence on mtDNA segregation and transcription regulation. Here, we discuss the current knowledge on the molecular mode of action of transcription factors comprising the mitochondrial transcriptional machinery, as well as the action of nuclear receptors on regulatory regions of the mtDNA.

Mitochondrial transcription termination factor 2 binds to entire mitochondrial DNA and negatively regulates mitochondrial gene expression

Mitochondrial transcription termination factor 2 (mTERF2) is a mitochondrial matrix protein that binds to the mitochondrial DNA. Previous studies have shown that overexpression of mTERF2 can inhibit cell proliferation, but the mechanism has not been well defined so far. This study aimed to present the binding pattern of mTERF2 to the mitochondrial DNA (mtDNA) in vivo, and investigated the biological function of mTERF2 on the replication of mtDNA, mRNA transcription, and protein translation. The mTERF2 binding to entire mtDNA was identified via the chromatin immunoprecipitation analysis. The mtDNA replication efficiency and expression levels of mitochondria genes were significantly inhibited when the mTERF2 was overexpressed in HeLa cells. The inhibition level of mtDNA content was the same with the decreased levels of mRNA and mitochondrial protein expression. Overall, the mTERF2 might be a cell growth inhibitor based on its negative effect on mtDNA replication, which eventually down-regulated all of the oxidative phosphorylation components in the mitochondria that were essential for the cell's energy metabolism.

Effects on mitochondrial transcription of manipulating mTERF protein levels in cultured human HEK293 cells

Background

Based on its activities in vitro, the mammalian mitochondrial transcription termination factor mTERF has been proposed to regulate mitochondrial transcription by favouring termination at its high-affinity binding immediately downstream of the rDNA segment of mitochondrial DNA, and initiation selectively at the PH1 site of the heavy-strand promoter. This defines an rDNA transcription unit distinct from the 'global' heavy-strand transcription unit initiating at PH2. However, evidence that the relative activities of the two heavy-strand transcription units are modulated by mTERF in vivo is thus far lacking.

Results

To test this hypothesis, we engineered human HEK293-derived cells for over-expression or knockdown of mTERF, and measured the steady-state levels of transcripts belonging to different transcription units, namely tRNA^Leu(UUR) and ND1 mRNA for the PH2 transcription unit, and tRNA^Phe plus 12S and 16S rRNA for the PH1 transcription unit. The relative levels of 16S rRNA and ND1 mRNA were the same under all conditions tested, although mTERF knockdown resulted in increased levels of transcripts of 12S rRNA. The amount of tRNA^Phe relative to tRNA^Leu(UUR) was unaffected by mTERF over-expression, altered only slightly by mTERF knockdown, and was unchanged during recovery from ethidium bromide-induced depletion of mitochondrial RNA. mTERF overexpression or knockdown produced a substantial shift (3-5-fold) in the relative abundance of antisense transcripts either side of its high-affinity binding site.

Conclusions

mTERF protein levels materially affect the amount of readthrough transcription on the antisense strand of mtDNA, whilst the effects on sense-strand transcripts are complex, and suggest the influence of compensatory mechanisms.

Helix unwinding and base flipping enable human MTERF1 to terminate mitochondrial transcription

Defects in mitochondrial gene expression are associated with aging and disease. Mterf proteins have been implicated in modulating transcription, replication and protein synthesis. We have solved the structure of a member of this family, the human mitochondrial transcriptional terminator MTERF1, bound to dsDNA containing the termination sequence. The structure indicates that upon sequence recognition MTERF1 unwinds the DNA molecule, promoting eversion of three nucleotides. Base flipping is critical for stable binding and transcriptional termination. Additional structural and biochemical results provide insight into the DNA binding mechanism and explain how MTERF1 recognizes its target sequence. Finally, we have demonstrated that the mitochondrial pathogenic G3249A and G3244A mutations interfere with key interactions for sequence recognition, eliminating termination. Our results provide insight into the role of mterf proteins and suggest a link between mitochondrial disease and the regulation of mitochondrial transcription.

Mitochondrial translation and beyond: processes implicated in combined oxidative phosphorylation deficiencies

Mitochondrial disorders are a heterogeneous group of often multisystemic and early fatal diseases, which are amongst the most common inherited human diseases. These disorders are caused by defects in the oxidative phosphorylation (OXPHOS) system, which comprises five multisubunit enzyme complexes encoded by both the nuclear and the mitochondrial genomes. Due to the multitude of proteins and intricacy of the processes required for a properly functioning OXPHOS system, identifying the genetic defect that underlies an OXPHOS deficiency is not an easy task, especially in the case of combined OXPHOS defects. In the present communication we give an extensive overview of the proteins and processes (in)directly involved in mitochondrial translation and the biogenesis of the OXPHOS system and their roles in combined OXPHOS deficiencies. This knowledge is important for further research into the genetic causes, with the ultimate goal to effectively prevent and cure these complex and often devastating disorders.

Animal models of mitochondrial DNA transactions in disease and ageing

Mitochondrial DNA (mtDNA) transactions, processes that include mtDNA replication, repair, recombination and transcription constitute the initial stages of mitochondrial biogenesis, and are at the core of understanding mitochondrial biology and medicine. All of the protein players are encoded in nuclear genes: some are proteins with well-known functions in the nucleus, others are well-known mitochondrial proteins now ascribed new functions, and still others are newly discovered factors. In this article we review recent advances in the field of mtDNA transactions with a special focus on physiological studies. In particular, we consider the expression of variant proteins, or altered expression of factors involved in these processes in powerful model organisms, such as Drosophila melanogaster and the mouse, which have promoted recognition of the broad relevance of oxidative phosphorylation defects resulting from improper maintenance of mtDNA. Furthermore, the animal models recapitulate many phenotypes related to human ageing and a variety of different diseases, a feature that has enhanced our understanding of, and inspired theories about, the molecular mechanisms of such biological processes.

The Drosophila nuclear factor DREF positively regulates the expression of the mitochondrial transcription termination factor DmTTF

The DREF [DRE (DNA replication-related element)-binding factor], which regulates the transcription of a group of cell proliferation-related genes in Drosophila, also controls the expression of three genes involved in mtDNA (mitochondrial DNA) replication and maintenance. In the present study, by in silico analysis, we have identified DREs in the promoter region of a gene participating in mtDNA transcription, the DmTTF (Drosophila mitochondrial transcription termination factor). Transient transfection assays in Drosophila S2 cells, with mutated versions of DmTTF promoter region, showed that DREs control DmTTF transcription; moreover, gel-shift and ChIP (chromatin immunoprecipitation) assays demonstrated that the analysed DRE sites interact with DREF in vitro and in vivo. Accordingly, DREF knock-down in S2 cells by RNAi (RNA interference) induced a considerable decrease in DmTTF mRNA level. These results clearly demonstrate that DREF positively controls DmTTF expression. On the other hand, mtRNApol (mitochondrial RNA polymerase) lacks DREs in its promoter and is not regulated in vivo by DREF. In situ RNA hybridization studies showed that DmTTF was transcribed almost ubiquitously throughout all stages of Drosophila embryogenesis, whereas mtRNApol was efficiently transcribed from stages 11-12. Territories where transcription occurred mostly were the gut and Malpighi tubes for DmTTF, and the gut, mesoderm, pharyngeal muscle and Malpighi tubes for mtRNApol. The partial overlapping in the temporal and spatial mRNA expression patterns confirms that transcription of the two genes is differentially regulated during embryogenesis and suggests that DmTTF might play multiple roles in the mtDNA transcription process, for which different levels of the protein with respect to mtRNApol are required.

The MTERF family proteins: mitochondrial transcription regulators and beyond

The MTERF family is a wide protein family, identified in Metazoa and plants, which consists of 4 subfamilies named MTERF1-4. Proteins belonging to this family are localized in mitochondria and show a modular architecture based on repetitions of a 30 amino acid module, the mTERF motif, containing leucine zipper-like heptads. The MTERF family includes the characterized transcription termination factors human mTERF, sea urchin mtDBP and Drosophila DmTTF. In vitro and in vivo studies show that these factors play different roles which are not restricted to transcription termination, but concern also transcription initiation and the control of mtDNA replication. The multiplicity of functions could be related to the differences in the gene organization of the mitochondrial genomes. Studies on the function of human and Drosophila MTERF3 factor showed that the protein acts as negative regulator of mitochondrial transcription, possibly in cooperation with other still unknown factors. The complete elucidation of the role of the MTERF family members will contribute to the unraveling of the molecular mechanisms of mtDNA transcription and replication.

The mitochondrial transcription termination factor mTERF modulates replication pausing in human mitochondrial DNA

The mammalian mitochondrial transcription termination factor mTERF binds with high affinity to a site within the tRNA(Leu(UUR)) gene and regulates the amount of read through transcription from the ribosomal DNA into the remaining genes of the major coding strand of mitochondrial DNA (mtDNA). Electrophoretic mobility shift assays (EMSA) and SELEX, using mitochondrial protein extracts from cells induced to overexpress mTERF, revealed novel, weaker mTERF-binding sites, clustered in several regions of mtDNA, notably in the major non-coding region (NCR). Such binding in vivo was supported by mtDNA immunoprecipitation. Two-dimensional neutral agarose gel electrophoresis (2DNAGE) and 5' end mapping by ligation-mediated PCR (LM-PCR) identified the region of the canonical mTERF-binding site as a replication pause site. The strength of pausing was modulated by the expression level of mTERF. mTERF overexpression also affected replication pausing in other regions of the genome in which mTERF binding was found. These results indicate a role for TERF in mtDNA replication, in addition to its role in transcription. We suggest that mTERF could provide a system for coordinating the passage of replication and transcription complexes, analogous with replication pause-region binding proteins in other systems, whose main role is to safeguard the integrity of the genome whilst facilitating its efficient expression.

DNA replication and transcription in mammalian mitochondria

The mitochondrion was originally a free-living prokaryotic organism, which explains the presence of a compact mammalian mitochondrial DNA (mtDNA) in contemporary mammalian cells. The genome encodes for key subunits of the electron transport chain and RNA components needed for mitochondrial translation. Nuclear genes encode the enzyme systems responsible for mtDNA replication and transcription. Several of the key components of these systems are related to proteins replicating and transcribing DNA in bacteriophages. This observation has led to the proposition that some genes required for DNA replication and transcription were acquired together from a phage early in the evolution of the eukaryotic cell, already at the time of the mitochondrial endosymbiosis. Recent years have seen a rapid development in our molecular understanding of these machineries, but many aspects still remain unknown.

MTERF3 is a negative regulator of mammalian mtDNA transcription

Regulation of mammalian mtDNA gene expression is critical for altering oxidative phosphorylation capacity in response to physiological demands and disease processes. The basal machinery for initiation of mtDNA transcription has been molecularly defined, but the mechanisms regulating its activity are poorly understood. In this study, we show that MTERF3 is a negative regulator of mtDNA transcription initiation. The MTERF3 gene is essential because homozygous knockout mouse embryos die in midgestation. Tissue-specific inactivation of MTERF3 in the heart causes aberrant mtDNA transcription and severe respiratory chain deficiency. MTERF3 binds the mtDNA promoter region and depletion of MTERF3 increases transcription initiation on both mtDNA strands. This increased transcription initiation leads to decreased expression of critical promoter-distal tRNA genes, which is possibly explained by transcriptional collision on the circular mtDNA molecule. To our knowledge, MTERF3 is the first example of a mitochondrial protein that acts as a specific repressor of mammalian mtDNA transcription initiation in vivo.

Mitochondrial DNA transcription: regulating the power supply

In this issue of Cell, Park et al. (2007) describe the nuclear encoded protein MTERF3 as a negative regulator of mitochondrial DNA transcription initiation. This study highlights a mechanism by which mitochondrial DNA transcription (and therefore oxidative phosphorylation) may be regulated in response to alterations in the cell's physiological and metabolic demands.

Cloning of the sea urchin mitochondrial RNA polymerase and reconstitution of the transcription termination system

Termination of transcription is a key process in the regulation of mitochondrial gene expression in animal cells. To investigate transcription termination in sea urchin mitochondria, we cloned the mitochondrial RNA polymerase (mtRNAP) of Paracentrotus lividus and used a recombinant form of the enzyme in a reconstituted transcription system, in the presence of the DNA-binding protein mtDBP. Cloning of mtRNAP was performed by a combination of PCR with degenerate primers and library screening. The enzyme contains 10 phage-like conserved motifs, two pentatricopeptide motifs and a serine-rich stretch. The protein expressed in insect cells supports transcription elongation in a promoter-independent assay. Addition of recombinant mtDBP caused arrest of the transcribing mtRNAP when the enzyme approached the mtDBP-binding site in the direction of transcription of mtDNA l-strand. When the polymerase encountered the protein-binding site in the opposite direction, termination occurred in a protein-independent manner, inside the mtDBP-binding site. Pulse-chase experiments show that mtDBP caused true transcription termination rather than pausing. These data indicate that mtDBP acts as polar termination factor and suggest that transcription termination in sea urchin mitochondria could take place by two alternative modes based on protein-mediated or sequence-dependent mechanisms.

Mitochondrial transcription and its regulation in mammalian cells

Human mitochondria contain multiple copies of a small double-stranded DNA genome that encode 13 components of the electron-transport chain and RNA components that are needed for mitochondrial translation. The mitochondrial genome is transcribed by a specialized machinery that includes a monomeric RNA polymerase, the mitochondrial transcription factor A and one of the two mitochondrial transcription factor B paralogues, TFB1M or TFB2M. Today, the components of the basal transcription machinery in mammalian mitochondria are known and their mechanisms of action are gradually being established. In addition, regulatory factors govern transcription levels both at the stage of initiation and termination, but the detailed biochemical understanding of these processes is largely missing.