Mitochondrial transcription and its regulation in mammalian cells

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Mitochondrial transcription and its regulation in mammalian cells Jordi Asin-Cayuela and Claes M. Gustafsson Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86, Stockholm, Sweden

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. The mitochondrial genome in mammalian cells Human mitochondria contain a circular double-stranded DNA genome (mtDNA) of 16 600 base pairs (bp). The genome encodes two rRNAs, 22 tRNAs and 13 of the 90 different proteins present in the respiratory chain. The remaining components of the respiratory chain are encoded by nuclear genes and are imported to the mitochondrion via specialized import systems [1]. The genome lacks introns; the only long, non-coding region of the genome contains the control elements for transcription and replication of mtDNA (Figure 1). The individual strands of the mtDNA molecules are denoted heavy (H) and light (L) strand because of their different buoyant densities in a cesium chloride gradient. L-strand transcription is initiated from one single promoter (LSP), whereas H-strand transcription is initiated from two specific and differentially regulated sites, HSP1 (H1) and HSP2 (H2) [2]. The HSP2 transcription-initiation site is located close to the 50 end of the 12S rRNA gene and produces a polycistronic molecule that corresponds to almost the entire H strand, covering the two rRNA genes and 12 mRNA-encoding genes. The HSP1 transcription-initiation site is located 100 bp upstream of HSP2 and produces a transcript that covers the two rRNA genes and terminates at the end of the 16S rRNA-encoding gene [3]. The polycistronic precursor RNAs are processed to produce the individual tRNA and mRNA molecules [4–6]. All of the protein and rRNA genes are immediately flanked by at least one tRNA gene. Excision of tRNA molecules from the polycistronic transcripts is used to produce mature mRNA and rRNA molecules. Corresponding author: Gustafsson, C.M. ([email protected]). Available online 8 February 2007. www.sciencedirect.com

This mode of RNA processing is known as the ‘tRNA punctuation model’ [7]. According to the widely accepted endosymbiotic theory, the mitochondrion developed from an a-proteobacterium [8]. Over time, ancestral bacterial genes have transferred to the nuclear genome, as is evident from the presence of orthologous genes in the mitochondrial genome in some species and in the nuclear genome of other species [9]. Gene transfer explains why all proteins necessary for mtDNA replication and transcription, and translation of mtDNAencoded genes are encoded in the nucleus. However, it is not known why the mitochondrion still retains a separate genome. It is possible that regulated expression of mitochondrial genes is important for metabolic control in eukaryotic cells [10]. The molecular machines governing mitochondrial gene expression could perhaps be directly influenced by components of the respiratory chain. In support of this notion, chloroplast gene transcription is directly affected by the reduction or oxidation status of the organelle [11]. Despite its crucial importance for respiratory-chain function and cell physiology, surprisingly little is known about the mechanisms of mitochondrial transcription and how the levels of transcription are regulated in response to the metabolic need of the eukaryotic cell. In recent years, several new findings have been reported, such as the presence of a family of putative transcription termination factors, and there is a growing interest in the mechanisms and regulation of mitochondrial transcription. Mitochondrial RNA polymerase The existence of a single subunit RNA polymerase (RNAP) in mitochondria was first reported in yeast [12,13] and later in human cells [14]. The mitochondrial RNAP (mtRNAP) from yeast (Rpo41) and human cells (POLRMT, also known as h-mtRPOL) display high sequence similarity to the C-terminal part of RNA polymerases encoded by the T-odd lineage of bacteriophages (e.g. T7 and T3) [14,15]. The mitochondrial RNA polymerases contain a unique N-terminal extension (Figure 2). In yeast, deletion of amino acids 1–185 in Rpo41 results in decreased stability and eventual loss of the mitochondrial genome [16]. Mitochondrial transcription initiation in vivo is largely unaffected by this mutation and expression of the Nterminal portion of the protein in trans partially suppresses the mitochondrial defect. This indicates that the N-terminal extension of the enzyme harbours an independent functional domain that is required for mtDNA replication and/or stability. In support of this, the domain

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Figure 1. Map of human mtDNA, the circular double-stranded DNA genome of mitochondria. The genes encoding the 13 proteins, 22 tRNAs and two rRNAs are mapped. The two strands of the mtDNA are termed heavy and light. Heavy-strand transcription is initiated from two sites, HSP1 and HSP2. The HSP1 transcript terminates at the 30 end of the 16S rRNA, in a region bound by the mTERF protein. A second binding site for mTERF (mTERF*) has recently been identified and is important for stimulation of transcription from HSP1. The HSP2 transcript produces a polycistronic molecule that corresponds to almost the entire heavy strand, including 12 mRNA molecules (blue). Transcription from the light-strand promoter (LSP) produces the ND6 mRNA molecule (yellow) and primers for initiation of DNA synthesis at the heavy-strand origin of DNA replication (OH). Noncoding regions are indicated in green.

interacts specifically with Nam1, a protein originally identified as a high-copy suppressor of mtDNA point mutations that affect splicing of introns in budding yeast [17,18]. The N-terminal domain might, therefore, couple factors involved in additional aspects of RNA metabolism directly to the transcription machinery. Splicing does not occur in mammalian mitochondria, but human POLRMT still retains an N-terminal region of unknown function that contains two 35-amino-acid pentatricopeptide repeat (PPR) motifs [18]. PPR-containing proteins have been described as site-specific, RNA-binding adaptor proteins that mediate interactions between RNA substrates and the enzymes that act on them. PPR-containing proteins have direct roles in RNA editing, processing, splicing and translation. In fact, many genes encoding PPR-containing proteins seem to be key regulators of plant mitochondrial gene expression [19]. The functional importance of the PPR motifs in POLRMT remains to be established. Accessory factors needed for POLRMT function The bacteriophage T7 RNAP interacts directly with promoter elements and can initiate transcription on its own. By contrast, POLRMT requires the assistance of mitochondrial transcription factor A (TFAM) and one of the mitochondrial transcription factor B paralogues, TFB1M or TFB2M. www.sciencedirect.com

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TFAM contains two tandem high-mobility group (HMG) box domains separated by a 27-amino-acid residue-linker region and followed by a 25-residue C-terminal tail. Biochemical characterization of TFAM has revealed that the tail region is important for specific DNA recognition and is essential for transcriptional activation [20]. The mechanisms of transcription initiation might differ between budding yeast and mammalian mitochondria because the yeast TFAM homologue, Abf2, lacks the C-terminal tail domain and is not required for transcription in yeast, but instead has a role in mtDNA packaging and maintenance. The transcription machinery in budding yeast contains one single transcription factor B (TFB) homologue, denoted mt-TFB (or Mtf1). In Saccharomyces cerevisiae, Rpo41 and mt-TFB form a heterodimer that recognizes mitochondrial promoters and initiates transcription [21,22]. The first indication of a mt-TFB homologue in metazoans came with the identification of a mt-TFB-like activity from Xenopus laevis [23]. In 2002, mammalian cells were shown to encode two paralogues to mt-TFB, denoted TFB1M (or mt-TFB1) [24,25] and TFB2M (or mt-TFB2) [24]. The genes encoding TFB1M and TFB2M are ubiquitously expressed with the highest mRNA levels detected in heart, skeletal muscle and liver, which is consistent with the expression patterns of other nucleus-encoded components of the mitochondrial transcription machinery. Both TFB1M and TFB2M can form a heterodimeric complex with POLRMT [24]. TFB1M and TFB2M are closely related to a family of rRNA methyltransferases, members of which dimethylate two adjacent adenosine bases near the 30 end of the small subunit rRNA during ribosome biogenesis [24,25]. This relationship is also supported by the X-ray structure of yeast mt-TFB that is structurally homologous to the rRNA methyltransferase ErmC’ [26]. It seems that an RNAmodifying enzyme was recruited during evolution to function as a mitochondrial transcription factor. In fact, phylogenetic analysis indicates that TFB1M and TFB2M are derived from the rRNA dimethyltransferase of the mitochondrial endosymbiont [27]. TFB1M and TFB2M are dual-function proteins that not only support mitochondrial transcription in vitro but also act as rRNA methyltransferases in vivo [28,29]. The methyltransferase activity is not absolutely required for transcription because single amino acid changes that inactivate the rRNA methyltransferase activity of TFB1M do not affect the ability of the protein to stimulate transcription in vitro [30]. Human mtDNA transcription can be reconstituted in a pure in vitro system consisting of a promoter-containing DNA fragment and recombinant TFAM, POLRMT, and TFB1M or TFB2M [24]. In this system, TFB2M is at least two orders of magnitude more active than TFB1M in basal transcription. TFB2M might, in fact, have evolved to be a specialized transcription factor in the mitochondria of higher eukaryotes, whereas TFB1M is responsible for rRNA methylation [31]. In support of this, RNAi knock-down of Drosophila melanogaster TFB2M in cell culture results in a two-to-eight-times reduction in the abundance of specific mitochondrial RNA transcripts [32]. By contrast, RNAi knock-down of D. melanogaster TFB1M does not change the abundance of specific mitochondrial RNA transcripts but, instead, reduces mitochondrial protein synthesis,

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Figure 2. The basal transcription machinery in yeast and mammalian cells. (a) The C-terminal of POLRMT display sequence similarity to bacteriophage RNA polymerases. The N-terminal extension of mammalian POLRMT has not been characterized but contains a PPR motif, which is found in many plant organelle proteins involved in RNA processing and translation. No PPR motif has been identified in the yeast Rpo41 protein. (b) TFB1M and TFB2M are dual-function proteins that also have rRNA dimethyltransferase activity. The only TFB homologue in yeast, sc-mt-TFB, is not an active methyltransferase, but has retained a sequence motif needed for binding to the methyl donor S-adenosyl-L-methionine (SAM). (c) TFAM is a member of the HMG protein family and contains two HMG boxes. TFAM has two distinct sequence motifs not found in the yeast homologue, Abf2, a linker region between the two HMG boxes (27 amino acids), and a C-terminal tail region (25 amino acids) The positively charged tail region is required for full mitochondrial transcription and has been shown to interact directly with TFB1M and TFB2M. Abf2 is not required for mitochondrial transcription in yeast. For all proteins, the mitochondrial targeting sequence is indicated in red.

suggesting a primary role for TFB1M in modulating translation [33]. These results are intriguing but cannot rule out that TFB1M might also have a role in the regulation of transcription of a particular set of transcripts or only in specific conditions. Manipulation of TFB1M and TFB2M expression in the mouse will shed further light on the individual roles of these two factors. Mechanisms of promoter recognition and transcription initiation How the mammalian mitochondrial transcription machinery recognizes promoter sequences is not fully understood. POLRMT in complex with TFB1M or TFB2M cannot initiate transcription in the absence of TFAM. One possible role for TFAM might be to introduce specific structural alterations in mtDNA, for example, unwinding of the promoter region, which can facilitate transcription initiation [34]. The sequence-specific binding of a TFAM upstream of HSP and LSP might enable the protein to introduce these structural alterations at a precise position in the promoter region and, perhaps, partially unwind the start site for transcription. This model might explain why the exact distance between the TFAM-binding site and the start site for LSP transcription is crucial [35]. Direct TFAM interactions have also been demonstrated for both TFB1M and TFB2M and these protein–protein contacts might contribute to the recruitment of TFBM–POLRMT complexes to mitochondrial promoters [30]. Arguing against an important role for TFAM in promoter recognition is the extreme abundance of the protein. TFAM www.sciencedirect.com

is present in a ratio of about one molecule per 15–20 bp of mtDNA and has been reported to wrap mtDNA entirely [36]. Based on this observation it seems highly unlikely that TFAM alone is responsible for promoter recognition. Recently, a functional approach was used to investigate LSP recognition in mammals by taking advantage of species-specific differences [34]. In lysates, the mouse mitochondrial transcription machinery cannot recognize a human promoter sequence and initiate transcription [37]. TFAM is not responsible for this species specificity because mouse and human TFAM proteins can substitute for one another in an in vitro transcription reaction. Similarly, TFB2M can be exchanged between the two systems. By contrast, mouse POLRMT cannot replace the human polymerase and seems to be largely responsible for speciesspecific promoter recognition, interacting functionally with several nucleotides immediately adjacent to the transcription start site [34]. Promoter recognition by the structurally related T7 RNAP is achieved by the insertion of a ‘specificity loop’ into the DNA major groove at position 8 to 12 relative the transcription start site [38]. Primary sequence analysis indicates that POLRMT also contains a specificity loop [26] and footprinting analyses have demonstrated that the POLRMT–TFB2M heterodimer protects the +10 to 4 region of LSP [34]. Findings in S. cerevisiae also support the notion that POLRMT recognizes specific promoter elements because Rpo41 can initiate promoter-specific transcription on negatively supercoiled templates in the absence of S. cerevisiae mt-TFB (sc-mt-TFB) [39]. On pre-melted templates addition

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of sc-mt-TFB actually inhibits the promoter-specific activity of mt-RNAP. The finding that sc-mt-TFB is required on closed but not open templates led to the suggestion that sc-mt-TFB facilitates DNA strand separation but not recognition of promoters. Studies of the yeast transcription machinery have also revealed that sc-mt-TFB dissociates from mt-RNAP early in the transcription process [22]. After the formation of a 13-nucleotide transcript, sc-mt-TFB is no longer associated with mt-RNAP on the DNA. Detailed mechanistic studies of the function of mammalian TFB1M and TFB2M in mitochondrial transcription have not yet been reported, but a close functional relationship between the mammalian and yeast transcription systems is likely. A fundamental, and yet unanswered, question is why an RNA-modifying protein is recruited to the mitochondrial transcription machinery. One possible role for the TFBMs could be to bind newly synthesized RNA and prevent the formation of an RNA–DNA hybrid at the promoter, which could inhibit further rounds of transcription initiation (Figure 3a). Alternatively, TFBMs could bind single-stranded DNA and stabilize a partially unwound promoter during transcription initiation (Figure 3b). This function would be in agreement with the finding that sc-mt-TFB is required on closed but not open templates. So far, however, direct interactions between TFBMs and single-stranded DNA have not been demonstrated at a mitochondrial promoter. A third possibility is that specific RNA molecules might interact with TFB1M and TFB2M, thereby influencing the activity of the transcription machinery (Figure 3c) Such a mechanism could create positive or negative feedback loops that would directly affect the levels of mitochondrial transcription. These

Figure 3. Putative models for TFB1M and TFB2M function. TFB1M and TFB2M are accessory factors for the mt-RNAP POLRMT. Currently, their mode of action and nature of their interaction with POLMRT is unknown. Three models for how these accessory factors might function in mitochondrial transcription are shown. (a) TFB1M or TFB2M (green) binds to the newly synthesized RNA (red) and prevents the formation of an RNA–DNA hybrid at the promoter. (b) TFB1M or TFB2M interacts with single-stranded DNA and stabilizes the transcription bubble at the promoter. (c) TFB1M or TFB2M interacts with regulatory RNA molecules that directly influence levels of mitochondrial transcription. www.sciencedirect.com

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and alternative explanations need to be addressed experimentally in the years to come. A nuclear isoform of POLRMT Recent findings indicate that the gene encoding POLRMT specifies two single-polypeptide polymerases [termed single-polypeptide RNA polymerases-IV (spRNAP-IV)], one that is targeted to the mitochondria and one that has a function in the nucleus [40]. The nuclear spRNAPIV lacks the N-terminal 262 amino acids that are present in the mitochondrial form and is produced via alternative splicing. This observation, therefore, indicates that the mitochondrial transcription machinery can directly influence nuclear gene transcription. However, the relevance for the mitochondrial function of sp-RNAP-IV remains obscure. Even if spRNAP-IV has been shown to regulate a distinct set of nuclear genes, these genes do not seem to be of special importance for mitochondrial function. Therefore, the nuclear and mitochondrial functions of spRNAP-IV might be completely separate. Moreover, the mechanisms of spRNAP-IV transcription remain unclear. In mitochondria, POLRMT is strictly dependent on the TFAM and TFB1M or TFB2M proteins for initiation of transcription. The ability of spRNAP-IV to initiate transcription in the absence of these factors remains to be demonstrated. Furthermore, spRNAP-IV must be able to transcribe genes that are covered by nucleosomes. A complicated machinery of chromatin-remodeling and transcription-elongation factors assists RNAP II as it transcribes through chromatin. Whether the same machinery supports spRNAP-IV transcription, remains to be investigated. Regulation of transcriptional initiation How mitochondrial transcription is regulated in response to the metabolic needs of the eukaryotic cell is largely unknown. In yeast, Rpo41 is involved in the coordinated control of nuclear and mitochondrial transcription. There is a direct correlation between in vivo changes in mitochondrial transcript abundance and in vitro sensitivity of mitochondrial promoters to ATP concentration [41]. It seems that the Rpo41 itself senses in vivo ATP levels and that shifting cellular pools of ATP might influence mitochondrial transcription. Whether a similar mechanism exists in mammalian mitochondria is not known. Reports from many different laboratories suggest that gene-specific transcription factors might directly influence gene transcription in mammalian mitochondria [42]. Transcription factors identified in mitochondria include the tumour suppressor p53, retinoid-X receptor (RXR) and the thyroid hormone receptor (TR) [43–45]. TR binds directly to regulatory regions in the mitochondrial genome and, supposedly, confers hormone-dependent activation of the mitochondrial genome [46]. Even if thyroid hormone stimulates mitochondrial transcription when added to an in organello mitochondrial system, the mechanisms of activation remain obscure. Nucleotide sequences with homology to hormone-responsive elements have been identified in mtDNA, but there have been no reports demonstrating that TR can influence transcription in a defined in vitro system for mitochondrial transcription. Furthermore, the direct physiological targets of TR in

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the mitochondrial transcription machinery have not been identified [47]. To establish a molecular model for TR in mitochondrial gene expression, it seems necessary to identify them. Such progress will provide interesting possibilities for novel therapeutic approaches in the treatment of metabolic disorders. It should be noted that some transcription factors might have targets outside the transcription machinery. Recently, p53 has been implicated in the maintenance of mitochondrial genetic stability owing to its ability to translocate to mitochondria and interact with mtDNA polymerase g in response to mtDNA damage [48]. Regulation of transcription termination There are three mitochondrial transcription units (those starting at HSP1, HSP2 and LSP), but only the one starting at HSP1 has a clearly established termination site, which is located at the end of the 16S rRNA-encoding gene [3]. Transcription termination of the HSP1 unit at this site is widely believed to be mediated by mTERF, a 39-kDa protein that binds to a 28-bp region at the 30 end of the tRNALeu(UUR) gene in a sequence-specific manner [49,50]. The mTERF protein can terminate transcription in vitro, but the functional role of the protein in vivo remains to be established. A mutation in the mTERF-binding site at the tRNALeu(UUR) gene is associated with a human disease known as MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes). The MELAS mutation reduces the binding affinity for mTERF, but does not change the ratio between H1 and H2 transcripts [51]. This finding might indicate that the main role of mTERF is not to regulate transcription termination from HSP. In fact, mTERF seems to be more effective at blocking L-strand transcription [52,53], which makes mTERF a potential candidate for the protein responsible for termination of L-strand transcription. This possibility is supported by the observation that heterologous RNAPs are stopped only in the L-strand direction of transcription and that no genes are located downstream of the mTERF-binding site in the L-strand. To firmly establish the functional role of mTERF for regulation mitochondrial transcription it seems absolutely necessary to disrupt the mouse gene for mTERF and investigate the functional consequences for mitochondrial transcription and mtDNA replication. Recently, mTERF has been shown to interact with an additional site in mtDNA that is located close to the HSP1 transcription start site [54]. Binding of mTERF to this site activates transcription in vitro and electron microscopy has demonstrated that a DNA loop is formed between the two mTERF binding sites (Figure 1). The mTERF protein might, therefore, control the expression of the HSP1 transcript by creating a loop that brings both ends of the transcription unit into close proximity, thereby facilitating reinitiation of transcription. Interestingly, mTERF stimulation of HSP1 transcription is not observed in a highly purified in vitro system for transcription, suggesting that additional cellular factors are required for this stimulation to occur [52]. More work is clearly needed to establish the mechanistic details of mTERF-dependent stimulation of mitochondrial transcription. Regulation of transcription termination in mammalian mitochondria might not be limited to the mTERF-binding www.sciencedirect.com

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site. A termination site for the H2 transcript unit has been identified just beyond the control region, immediately upstream of the tRNAPhe-encoding gene. Two proteins of 45 and 70 kDa associate with this region, but their identities have not been reported [55]. Furthermore, similarity searches and phylogenetic analyses have identified three novel genes in vertebrates coding for proteins homologous to mTERF, all of them with predicted mitochondrial localization [56]. This family of transcription factors has been denoted MTERF1–F4, with MTERF1 corresponding to the previously characterized human mTERF protein. The MTERF1 and MTERF2 proteins seem to be unique to vertebrates, whereas MTERF3 and MTERF4 also have paralogues in worms and insects. So far, only two reports have been published about the new members of the MTERF family of proteins. The mitochondrial localization of human MTERF2 (mTERFL) has been confirmed and gene expression analysis has shown high expression in heart, liver and skeletal muscle, a pattern typical for a mitochondrial protein [57]. Expression of MTERF2 is inhibited by the addition of serum in serum-starved cells, whereas the expression pattern of MTERF1 was the exact opposite. The actual function of MTERF2 remains to be elucidated but this observation indicates that the expression of these two members of the MTERF family is tightly coordinated. RNAi has been used to knock-down D. melanogaster MTERF3 in D.MeL-2 cells [58]. The depletion of D. melanogaster MTERF3 (D-MTERF3) results in decreased synthesis of some proteins encoded by mtDNA but the levels of mitochondrial mRNAs remain unaltered. These observations have led to the suggestion that DMTERF3 is involved in mitochondrial translation, possibly bridging the mitochondrial transcription and translation apparatus [58]. The characterization of the MTERF family of proteins is just emerging, and interesting progress can be expected in the coming years. Advances in this direction will contribute to the definition of the mechanisms for the control of mtDNA transcription, and might even force some of the generally accepted models for transcriptional regulation to be revisited. Concluding remarks The basal components of the mitochondrial transcription machinery are known, but the mechanisms of mitochondrial gene transcription are poorly understood. The close structural relationship that exists between POLRMT and the T7 RNAP, suggests that previous studies of phage transcription might prove essential for a molecular understanding of the mitochondrial transcription machinery. Furthermore, many regulatory aspects of mitochondrial transcription, including the question of how it is regulated in response to the metabolic requirements of the mammalian cell remain to be established. The existence of two homologous transcription factors, TFB1M and TFB2M, is intriguing but the physiological importance of this increased complexity in mammalian cells is still not understood. Characterization of the newly identified MTERF family of proteins should provide important insights into regulation of transcriptional termination. Most certainly, there must also be other

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Acknowledgements Space limitations have precluded the inclusion of many appropriate publications and we apologize to those authors. This work was supported by grants from the Swedish Research Council, the Swedish Cancer Society, European Commission (fp6 EUMITOCOMBAT) and the Swedish Foundation for Strategic Research. J.A-C. is a recipient of a Marie Curie Intra-European Fellowships from the European Commission (CEIF-CT-2005–011078).

References 1 Mokranjac, D. and Neupert, W. (2005) Protein import into mitochondria. Biochem. Soc. Trans. 33, 1019–1023 2 Montoya, J. et al. (1982) Identification of initiation sites for heavystrand and light-strand transcription in human mitochondrial DNA. Proc. Natl. Acad. Sci. U. S. A. 79, 7195–7199 3 Christianson, T.W. and Clayton, D.A. (1988) A tridecamer DNA sequence supports human mitochondrial RNA 30 -end formation in vitro. Mol. Cell. Biol. 8, 4502–4509 4 Clayton, D.A. (1991) Replication and transcription of vertebrate mitochondrial DNA. Annu. Rev. Cell Biol. 7, 453–478 5 Montoya, J. et al. (1981) Distinctive features of the 50 -terminal sequences of the human mitochondrial mRNAs. Nature 290, 465–470 6 Ojala, D. and Attardi, G. (1980) Fine mapping of the ribosomal RNA genes of HeLa cell mitochondrial DNA. J. Mol. Biol. 138, 411–420 7 Ojala, D. et al. (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature 290, 470–474 8 Gray, M.W. et al. (1999) Mitochondrial evolution. Science 283, 1476– 1481 9 Andersson, S.G. et al. (2003) On the origin of mitochondria: a genomics perspective. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358, 165–177 10 Allen, J.F. (1993) Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J. Theor. Biol. 165, 609–631 11 Pfannschmidt, T. et al. (1999) Photosynthetic control of chloroplast gene expression. Nature 397, 625–628 12 Greenleaf, A.L. et al. (1986) Yeast RPO41 gene product is required for transcription and maintenance of the mitochondrial genome. Proc. Natl. Acad. Sci. U. S. A. 83, 3391–3394 13 Kelly, J.L. and Lehman, I.R. (1986) Yeast mitochondrial RNA polymerase. Purification and properties of the catalytic subunit. J. Biol. Chem. 261, 10340–10347 14 Tiranti, V. et al. (1997) Identification of the gene encoding the human mitochondrial RNA polymerase (h-mtRPOL) by cyberscreening of the Expressed Sequence Tags database. Hum. Mol. Genet. 6, 615– 625 15 Masters, B.S. et al. (1987) Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell 51, 89– 99 16 Wang, Y. and Shadel, G.S. (1999) Stability of the mitochondrial genome requires an amino-terminal domain of yeast mitochondrial RNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 96, 8046–8051 17 Dujardin, G. et al. (1980) Long range control circuits within mitochondria and between nucleus and mitochondria. I. Methodology and phenomenology of suppressors. Mol. Gen. Genet. 179, 469–482 18 Rodeheffer, M.S. et al. (2001) Nam1p, a protein involved in RNA processing and translation, is coupled to transcription through an interaction with yeast mitochondrial RNA polymerase. J. Biol. Chem. 276, 8616–8622 19 Chase, C.D. (2007) Cytoplasmic male sterility: a window to the world of plant mitochondrial-nuclear interactions. Trends Genet. 23, 81–90 20 Dairaghi, D.J. et al. (1995) Addition of a 29 residue carboxyl-terminal tail converts a simple HMG box-containing protein into a transcriptional activator. J. Mol. Biol. 249, 11–28 21 Cliften, P.F. et al. (1997) Identification of three regions essential for interaction between a sigma-like factor and core RNA polymerase. Genes Dev. 11, 2897–2909 22 Mangus, D.A. et al. (1994) Release of the yeast mitochondrial RNA polymerase specificity factor from transcription complexes. J. Biol. Chem. 269, 26568–26574 www.sciencedirect.com

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23 Bogenhagen, D.F. (1996) Interaction of mtTFB and mtRNA polymerase at core promoters for transcription of Xenopus laevis mtDNA. J. Biol. Chem. 271, 12036–12041 24 Falkenberg, M. et al. (2002) Mitochondrial transcription factors B1 and B2 activate transcription of human mtDNA. Nat. Genet. 31, 289–294 25 McCulloch, V. et al. (2002) A human mitochondrial transcription factor is related to RNA adenine methyltransferases and binds S-adenosylmethionine. Mol. Cell. Biol. 22, 1116–1125 26 Schubot, F.D. et al. (2001) Crystal structure of the transcription factor sc-mtTFB offers insights into mitochondrial transcription. Protein Sci. 10, 1980–1988 27 Shutt, T.E. and Gray, M.W. (2006) Homologs of mitochondrial transcription factor B, sparsely distributed within the eukaryotic radiation, are likely derived from the dimethyladenosine methyltransferase of the mitochondrial endosymbiont. Mol. Biol. Evol. 23, 1169–1179 28 Seidel-Rogol, B.L. et al. (2003) Human mitochondrial transcription factor B1 methylates ribosomal RNA at a conserved stem-loop. Nat. Genet. 33, 23–24 29 Cotney, J. and Shadel, G.S. (2006) evidence for an early gene duplication event in the evolution of the mitochondrial transcription factor b family and maintenance of rRNA methyltransferase activity in human mtTFB1 and mtTFB2. J. Mol. Evol. 63, 707–717 30 McCulloch, V. and Shadel, G.S. (2003) Human mitochondrial transcription factor B1 interacts with the C-terminal activation region of h-mtTFA and stimulates transcription independently of its RNA methyltransferase activity. Mol. Cell. Biol. 23, 5816–5824 31 Rantanen, A. et al. (2003) Characterization of the mouse genes for mitochondrial transcription factors B1 and B2. Mamm. Genome 14, 1–6 32 Matsushima, Y. et al. (2004) Drosophila mitochondrial transcription factor B2 regulates mitochondrial DNA copy number and transcription in Schneider cells. J. Biol. Chem. 279, 26900–26905 33 Matsushima, Y. et al. (2005) Drosophila mitochondrial transcription factor B1 modulates mitochondrial translation but not transcription or DNA copy number in Schneider cells. J. Biol. Chem. 280, 16815–16820 34 Gaspari, M. et al. (2004) The mitochondrial RNA polymerase contributes critically to promoter specificity in mammalian cells. EMBO J. 23, 4606–4614 35 Dairaghi, D.J. et al. (1995) Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127–134 36 Alam, T.I. et al. (2003) Human mitochondrial DNA is packaged with TFAM. Nucleic Acids Res. 31, 1640–1645 37 Fisher, R.P. et al. (1989) Flexible recognition of rapidly evolving promoter sequences by mitochondrial transcription factor 1. Genes Dev. 3, 2202–2217 38 Cheetham, G.M. and Steitz, T.A. (2000) Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases. Curr. Opin. Struct. Biol. 10, 117–123 39 Matsunaga, M. and Jaehning, J.A. (2004) Intrinsic promoter recognition by a ‘core’ RNA polymerase. J. Biol. Chem. 279, 44239– 44242 40 Kravchenko, J.E. et al. (2005) Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. Nature 436, 735–739 41 Amiott, E.A. and Jaehning, J.A. (2006) Mitochondrial transcription is regulated via an ATP ‘sensing’ mechanism that couples RNA abundance to respiration. Mol. Cell 22, 329–338 42 Psarra, A.M. et al. (2006) The mitochondrion as a primary site of action of steroid and thyroid hormones: presence and action of steroid and thyroid hormone receptors in mitochondria of animal cells. Mol. Cell. Endocrinol. 246, 21–33 43 Marchenko, N.D. et al. (2000) Death signal-induced localization of p53 protein to mitochondria. A potential role in apoptotic signalling. J. Biol. Chem. 275, 16202–16212 44 Wrutniak, C. et al. (1995) A 43-kDa protein related to c-ErbAa1 is located in the mitochondrial matrix of rat liver. J. Biol. Chem. 270, 16347–16354 45 Lin, X.F. et al. (2004) RXRa acts as a carrier for TR3 nuclear export in a 9-cis retinoic acid-dependent manner in gastric cancer cells. J. Cell Sci. 117, 5609–5621 46 Enriquez, J.A. et al. (1999) Direct regulation of mitochondrial RNA synthesis by thyroid hormone. Mol. Cell. Biol. 19, 657–670

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47 Casas, F. et al. (1999) A variant form of the nuclear triiodothyronine receptor c-ErbAa1 plays a direct role in regulation of mitochondrial RNA synthesis. Mol. Cell. Biol. 19, 7913–7924 48 Achanta, G. et al. (2005) Novel role of p53 in maintaining mitochondrial genetic stability through interaction with DNA Pol g. EMBO J. 24, 3482–3492 49 Kruse, B. et al. (1989) Termination of transcription in human mitochondria: identification and purification of a DNA binding protein factor that promotes termination. Cell 58, 391–397 50 Fernandez-Silva, P. et al. (1997) The human mitochondrial transcription termination factor (mTERF) is a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions. EMBO J. 16, 1066–1079 51 Chomyn, A. et al. (1992) MELAS mutation in mtDNA binding site for transcription termination factor causes defects in protein synthesis and in respiration but no change in levels of upstream and downstream mature transcripts. Proc. Natl. Acad. Sci. U. S. A. 89, 4221–4225 52 Asin-Cayuela, J. et al. (2005) The human mitochondrial transcription termination factor (mTERF) is fully active in vitro in the nonphosphorylated form. J. Biol. Chem. 280, 25499–25505

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53 Shang, J. and Clayton, D.A. (1994) Human mitochondrial transcription termination exhibits RNA polymerase independence and biased bipolarity in vitro. J. Biol. Chem. 269, 29112–29120 54 Martin, M. et al. (2005) Termination factor-mediated DNA loop between termination and initiation sites drives mitochondrial rRNA synthesis. Cell 123, 1227–1240 55 Camasamudram, V. et al. (2003) Transcription termination at the mouse mitochondrial H-strand promoter distal site requires an A/T rich sequence motif and sequence specific DNA binding proteins. Eur. J. Biochem. 270, 1128–1140 56 Linder, T. et al. (2005) A family of putative transcription termination factors shared amongst metazoans and plants. Curr. Genet. 48, 265– 269 57 Chen, Y. et al. (2005) Cloning and functional analysis of human mTERFL encoding a novel mitochondrial transcription termination factor-like protein. Biochem. Biophys. Res. Commun. 337, 1112– 1118 58 Roberti, M. et al. (2006) MTERF3, the most conserved member of the mTERF-family, is a modular factor involved in mitochondrial protein synthesis. Biochim. Biophys. Acta 1757, 1199–1206

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