Cloning and functional analysis of human mTERFL encoding a novel mitochondrial transcription termination factor-like protein

The Molecular Function of Plant mTERFs as Key Regulators of Organellar Gene Expression

The protein family of mTERFs (mitochondrial transcription termination factors) was initially studied in mammalian and insect mitochondria before the first Arabidopsis mTERF mutant was characterized. More than 10 years of research on the function of plant mTERFs in the flowering plants Arabidopsis thaliana, Zea mays and the green microalga Chlamydomonas reinhardtii has since highlighted that mTERFs are key regulators of organellar gene expression (OGE) in mitochondria and in chloroplasts. Additional functions to be fulfilled by plant mTERFs (e.g. splicing) and the fact that the expression of two organellar genomes had to be facilitated have led to a massive expansion of the plant mTERF portfolio compared to that found in mammals. Plant mTERFs are implicated in all steps of OGE ranging from the modulation of transcription to the maturation of tRNAs and hence translation. Furthermore, being regulators of OGE, mTERFs are required for a successful long-term acclimation to abiotic stress, retrograde signaling and interorganellar communication. Here, I review the recent progress in the elucidation of molecular mTERF functions.

A Mitochondrial Transcription Termination Factor, ZmSmk3, Is Required for nad1 Intron4 and nad4 Intron1 Splicing and Kernel Development in Maize

The expression systems of the mitochondrial genes are derived from their bacterial ancestors, but have evolved many new features in their eukaryotic hosts. Mitochondrial RNA splicing is a complex process regulated by families of nucleus-encoded RNA-binding proteins, few of which have been characterized in maize (Zea mays L.). Here, we identified the Zea mays small kernel 3 (Zmsmk3) candidate gene, which encodes a mitochondrial transcription termination factor (mTERF) containing two mTERF motifs, which is conserved in monocotyledon; and the target introns were also quite conserved during evolution between monocotyledons and dicotyledons. The mutations of Zmsmk3 led to arrested embryo and endosperm development, resulting in small kernels. A transcriptome of 12 days after pollination endosperm analysis revealed that the starch biosynthetic pathway and the zein gene family were down-regulated in the Zmsmk3 mutant kernels. ZmSMK3 is localized in mitochondria. The reduced expression of ZmSmk3 in the mutant resulted in the splicing deficiency of mitochondrial nad4 intron1 and nad1 intron4, causing a reduction in complex I assembly and activity, impairing mitochondria structure and activating the alternative respiratory pathway. So, the results suggest that ZmSMK3 is required for the splicing of nad4 intron 1 and nad1 intron 4, complex I assembly and kernel development in maize.

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.

Marek's Disease Virus Infection Induced Mitochondria Changes in Chickens

Mitochondria are crucial cellular organelles in eukaryotes and participate in many cell processes including immune response, growth development, and tumorigenesis. Marek’s disease (MD), caused by an avian alpha-herpesvirus Marek’s disease virus (MDV), is characterized with lymphomas and immunosuppression. In this research, we hypothesize that mitochondria may play roles in response to MDV infection. To test it, mitochondrial DNA (mtDNA) abundance and gene expression in immune organs were examined in two well-defined and highly inbred lines of chickens, the MD-susceptible line 7₂ and the MD-resistant line 6₃. We found that mitochondrial DNA contents decreased significantly at the transformation phase in spleen of the MD-susceptible line 7₂ birds in contrast to the MD-resistant line 6₃. The mtDNA-genes and the nucleus-genes relevant to mtDNA maintenance and transcription, however, were significantly up-regulated. Interestingly, we found that POLG2 might play a potential role that led to the imbalance of mtDNA copy number and gene expression alteration. MDV infection induced imbalance of mitochondrial contents and gene expression, demonstrating the indispensability of mitochondria in virus-induced cell transformation and subsequent lymphoma formation, such as MD development in chicken. This is the first report on relationship between virus infection and mitochondria in chicken, which provides important insights into the understanding on pathogenesis and tumorigenesis due to viral infection.

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.

Emerging functions of mammalian and plant mTERFs

Organellar gene expression (OGE) is crucial for plant development, respiration and photosynthesis, but the mechanisms that control it are still largely unclear. Thus, OGE requires various nucleus-encoded proteins that promote transcription, splicing, trimming and editing of organellar RNAs, and regulate their translation. In mammals, members of the mitochondrial transcription termination factor (mTERF) family play important roles in OGE. Intriguingly, three of the four mammalian mTERFs do not actually terminate transcription, as their designation suggests, but appear to function in antisense transcription termination and ribosome biogenesis. During the evolution of land plants, the mTERF family has expanded to approximately 30 members, but knowledge of their function in photosynthetic organisms remains sparse. Here, we review recent advances in the characterization of mterf mutants in mammals and photosynthetic organisms, focusing particularly on the progress made in elucidating their molecular functions in the last two years. This article is part of a Special Issue entitled: Chloroplast biogenesis.

MTERF1 regulates the oxidative phosphorylation activity and cell proliferation in HeLa cells

The mitochondrial transcription termination factor (MTERF) family is a group of highly conserved DNA-binding proteins composed of four key members, MTERF1-4. To date, several studies have investigated the binding sites of MTERF1 on mitochondrial genome and the regulation of mitochondrial gene transcription, but the more intricate connection between mitochondrial genes transcription regulation, mitochondrial oxidative phosphorylation (OXPHOS), and cell proliferation is still poorly understood. In this study, we constructed over-expression and knockdown vectors of MTERF1 that were transfected into HeLa cells to investigate the functions of MTERF1. Results showed that although MTERF1 is a positive regulatory factor of mitochondrial genes transcription, it had no significant effect on the replication of mitochondrial DNA. Over-expression of MTERF1 increased mitochondrial oxidative phosphorylation activity and promoted ATP synthesis, cyclin D1 expression, and cell proliferation, while its knockdown inhibited ATP synthesis, decreased cyclin D1 expression, and slowed the cell growth. These results suggested that MTERF1 may promote cell proliferation by regulating oxidative phosphorylation activity in HeLa cells. Ultimately, these findings create a foundation for further and more conclusive studies on the physiological functions of MTERF family by providing novel insights into the potential mechanisms underlying cell proliferation regulation.

Expression, purification of recombinant human mitochondrial transcription termination factor 3 (hMTERF3) and preparation of polyclonal antibody against hMTERF3

In mammalian cells, a family of mitochondrial transcription termination factors (MTERFs) regulates mitochondrial gene expression. Mitochondrial transcription termination factor 3 (MTERF3) is the most conserved member of the MTERF family and a negative regulator of mammalian mitochondrial DNA transcription. To create a specific polyclonal antibody against human MTERF3 (hMTERF3), we first cloned hMTERF3 into prokaryotic expression vector pGEX-4T-1, and GST-hMTERF3 was efficiently expressed in Escherichia coli after induction by IPTG. The expressed GST-tagged hMTERF3 fusion protein was purified by passive electro-elution process and then used to immunize BALB/c mice, we obtained anti-GST-hMTERF3 polyclonal antibody purified by protein A column and determined the sensitivity and specificity of the antibody against human MTERF3 by enzyme-linked immunosorbent assay and Western blot assay. Furthermore, the full-length hMTERF3 protein expressed in human embryonic kidney 293T cells was detected by anti-GST-hMTERF3 in western blot analysis and immunofluorescence staining. Taken together, our results demonstrate the functionality of the mouse anti-GST-hMTERF3 polyclonal antibody which will provide a useful tool for further characterization of hMTERF3.

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.

Regulation of the cell cycle via mitochondrial gene expression and energy metabolism in HeLa cells

Human cervical cancer HeLa cells have functional mitochondria. Recent studies have suggested that mitochondrial metabolism plays an essential role in tumor cell proliferation. Nevertheless, how cells coordinate mitochondrial dynamics and cell cycle progression remains to be clarified. To investigate the relationship between mitochondrial function and cell cycle regulation, the mitochondrial gene expression profile and cellular ATP levels were determined by cell cycle progress analysis in the present study. HeLa cells were synchronized in the G0/G1 phase by serum starvation, and re-entered cell cycle by restoring serum culture, time course experiment was performed to analyze the expression of mitochondrial transcription regulators and mitochondrial genes, mitochondrial membrane potential (MMP), cellular ATP levels, and cell cycle progression. The results showed that when arrested G0/G1 cells were stimulated in serum-containing medium, the amount of DNA and the expression levels of both mRNA and proteins in mitochondria started to increase at 2 h time point, whereas the MMP and ATP level elevated at 4 h. Furthermore, the cyclin D1 expression began to increase at 4 h after serum triggered cell cycle. ATP synthesis inhibitor-oligomycin-treatment suppressed the cyclin D1 and cyclin B1 expression levels and blocked cell cycle progression. Taken together, our results suggested that increased mitochondrial gene expression levels, oxidative phosphorylation activation, and cellular ATP content increase are important events for triggering cell cycle. Finally, we demonstrated that mitochondrial gene expression levels and cellular ATP content are tightly regulated and might play a central role in regulating cell proliferation.

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.

Arabidopsis RUGOSA2 encodes an mTERF family member required for mitochondrion, chloroplast and leaf development

Little is known about the mechanisms that control transcription of the mitochondrial and chloroplastic genomes, and their interplay within plant cells. Here, we describe the positional cloning of the Arabidopsis RUG2 gene, which encodes a protein that is dual-targeted to mitochondria and chloroplasts, and is homologous with the metazoan mitochondrial transcription termination factors (mTERFs). In the loss-of-function rug2 mutants, most organs were pale and showed reduced growth, and the leaves exhibited both green and pale sectors, with the latter containing sparsely packed mesophyll cells. Chloroplast and mitochondrion development were strongly perturbed in the rug2-1 mutant, particularly in pale leaf sectors, in which chloroplasts were abnormally shaped and reduced in number, thereby impairing photoautotrophic growth. As expected from the pleiotropic phenotypes caused by its loss-of-function alleles, the RUG2 gene was ubiquitously expressed. In a microarray analysis of the mitochondrial and chloroplastic genomes, 56 genes were differentially expressed between rug2-1 and the wild type: most mitochondrial genes were downregulated, whereas the majority of the chloroplastic genes were upregulated. Quantitative RT-PCR analyses showed that the rug2-1 mutation specifically increases expression of the RpoTp nuclear gene, which encodes chloroplastic RNA polymerase. Therefore, the RUG2 nuclear gene seems to be crucial for the maintenance of the correct levels of transcripts in the mitochondria and chloroplasts, which is essential for optimized functions of these organelles and proper plant development. Our results highlight the complexity of the functional interaction between these two organelles and the nucleus.

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.

hMTERF4 knockdown in HeLa cells results in sub-G1 cell accumulation and cell death

Mitochondrial activity and cell energy status play important roles in the regulation of cell cycle and cell proliferation. Regulation of mitochondrial gene expression is crucial for mitochondrial activity regulation. The mitochondrial transcription termination factor (MTERF) family is a group of important mitochondrial transcription regulatory factors. It has been demonstrated that MTERF1-3 are involved in the regulation of mitochondrial gene transcription and oxidative phosphorylation. However, the function of the newest member MTERF4 has not been characterized. In this study, human MTERF4 full-length open reading frame was cloned, and the protein structure prediction revealed that hMTERF4 protein contained leucine-zipper motifs, which is similar to human MTERF1-3. The expressed pMTERF4-green fluorescence fusion protein in HeLa cells localized the mitochondria. (3(4,5)dimethylthiahiazo(zy1)3,5diphenytetrazoliumromide) (MTT) proliferation assay and flow cytometry analysis showed that hMTERF4 knockdown induced sub-G1 phase cells accumulation, whereas its overexpression promoted cell proliferation. Furthermore, double staining with Annexin V and PI revealed that hMTERF4 knockdown increased necrosis but not apoptosis. In conclusion, our data suggested that hMTERF4 is an essential factor for cell proliferation, which is probably modulated by mitochondrial transcription to promote cell proliferation.

A compendium of human mitochondrial gene expression machinery with links to disease

Mammalian mitochondrial DNA encodes 37 essential genes required for ATP production via oxidative phosphorylation, instability or misregulation of which is associated with human diseases and aging. Other than the mtDNA-encoded RNA species (13 mRNAs, 12S and 16S rRNAs, and 22 tRNAs), the remaining factors needed for mitochondrial gene expression (i.e., transcription, RNA processing/modification, and translation), including a dedicated set of mitochondrial ribosomal proteins, are products of nuclear genes that are imported into the mitochondrial matrix. Herein, we inventory the human mitochondrial gene expression machinery, and, while doing so, we highlight specific associations of these regulatory factors with human disease. Major new breakthroughs have been made recently in this burgeoning area that set the stage for exciting future studies on the key outstanding issue of how mitochondrial gene expression is regulated differentially in vivo. This should promote a greater understanding of why mtDNA mutations and dysfunction cause the complex and tissue-specific pathology characteristic of mitochondrial disease states and how mitochondrial dysfunction contributes to more common human pathology and aging.

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.

Dynamic regulation of genes involved in mitochondrial DNA replication and transcription during mouse brown fat cell differentiation and recruitment

Background

Brown adipocytes are specialised in dissipating energy through adaptive thermogenesis, whereas white adipocytes are specialised in energy storage. These essentially opposite functions are possible for two reasons relating to mitochondria, namely expression of uncoupling protein 1 (UCP1) and a remarkably higher mitochondrial abundance in brown adipocytes.

Methodology/Principal Findings

Here we report a comprehensive characterisation of gene expression linked to mitochondrial DNA replication, transcription and function during white and brown fat cell differentiation in vitro as well as in white and brown fat, brown adipose tissue fractions and in selected adipose tissues during cold exposure. We find a massive induction of the majority of such genes during brown adipocyte differentiation and recruitment, e.g. of the mitochondrial transcription factors A (Tfam) and B2 (Tfb2m), whereas only a subset of the same genes were induced during white adipose conversion. In addition, PR domain containing 16 (PRDM16) was found to be expressed at substantially higher levels in brown compared to white pre-adipocytes and adipocytes. We demonstrate that forced expression of Tfam but not Tfb2m in brown adipocyte precursor cells promotes mitochondrial DNA replication, and that silencing of PRDM16 expression during brown fat cell differentiation blunts mitochondrial biogenesis and expression of brown fat cell markers.

Conclusions/Significance

Using both in vitro and in vivo model systems of white and brown fat cell differentiation, we report a detailed characterisation of gene expression linked to mitochondrial biogenesis and function. We find significant differences in differentiating white and brown adipocytes, which might explain the notable increase in mitochondrial content observed during brown adipose conversion. In addition, our data support a key role of PRDM16 in triggering brown adipocyte differentiation, including mitochondrial biogenesis and expression of UCP1.

MTERF2 is a nucleoid component in mammalian mitochondria

The mammalian MTERF family of proteins has four members, named MTERF1 to MTERF4, which were identified in homology searches using the mitochondrial transcription termination factor, mTERF (here denoted MTERF1) as query. MTERF1 and MTERF3 are known to participate in the control of mitochondrial DNA transcription, but the function of the other two proteins is not known. We here investigate the structure and function of MTERF2. Protein import experiments using isolated organelles confirm that MTERF2 is a mitochondrial protein. Edman degradation of MTERF2 isolated from stably transfected HeLa cells demonstrates that mature MTERF2 lacks a targeting peptide (amino acids 1-35) present in the precursor form of the protein. MTERF2 is a monomer in isolation and displays a non sequence-specific DNA-binding activity. In vivo quantification experiments demonstrate that MTERF2 is relatively abundant, with one monomer present per approximately 265 bp of mtDNA. In comparison, the mtDNA packaging factor TFAM is present at a ratio of one molecule per approximately 10-12 bp of mtDNA. Using formaldehyde cross-linking we demonstrate that MTERF2 is present in nucleoids, and therefore must be located in close proximity to mtDNA. Taken together, our work provides a basic biochemical characterization of MTERF2, paving the way for future functional studies.

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.

Transcriptional paradigms in mammalian mitochondrial biogenesis and function

Mitochondria contain their own genetic system and undergo a unique mode of cytoplasmic inheritance. Each organelle has multiple copies of a covalently closed circular DNA genome (mtDNA). The entire protein coding capacity of mtDNA is devoted to the synthesis of 13 essential subunits of the inner membrane complexes of the respiratory apparatus. Thus the majority of respiratory proteins and all of the other gene products necessary for the myriad mitochondrial functions are derived from nuclear genes. Transcription of mtDNA requires a small number of nucleus-encoded proteins including a single RNA polymerase (POLRMT), auxiliary factors necessary for promoter recognition (TFB1M, TFB2M) and activation (Tfam), and a termination factor (mTERF). This relatively simple system can account for the bidirectional transcription of mtDNA from divergent promoters and key termination events controlling the rRNA/mRNA ratio. Nucleomitochondrial interactions depend on the interplay between transcription factors (NRF-1, NRF-2, PPARalpha, ERRalpha, Sp1, and others) and members of the PGC-1 family of regulated coactivators (PGC-1alpha, PGC-1beta, and PRC). The transcription factors target genes that specify the respiratory chain, the mitochondrial transcription, translation and replication machinery, and protein import and assembly apparatus among others. These factors are in turn activated directly or indirectly by PGC-1 family coactivators whose differential expression is controlled by an array of environmental signals including temperature, energy deprivation, and availability of nutrients and growth factors. These transcriptional paradigms provide a basic framework for understanding the integration of mitochondrial biogenesis and function with signaling events that dictate cell- and tissue-specific energetic properties.

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.

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.