1. Initiation and Beyond: Multiple Functions of the Human Mitochondrial Transcription Machinery 
Nicholas D. Bonawitz, David A. Clayton, Gerald S. Shadel 
Molecular Cell 
Volume 24, Issue 6, Pages (December 2006)
DOI: /j.molcel
Copyright © 2006 Elsevier Inc. Terms and Conditions

2. Figure 1 Human mtDNA: Genes, Transcripts, and cis-Acting Elements
Shown is the circular human mtDNA molecule with the heavy (H) and light (L) strand transcripts on the outside and inside of the circle, respectively. At the top of the molecule is the hallmark displacement loop (D loop), a stable, three-stranded structure found in many mtDNA molecules in vivo. The D loop region is the major noncoding portion of the molecule and harbors the L strand promoter (LSP), one of the H strand promoters (HSP1), and the origin of H strand synthesis (OH). The major L strand origin (OL) is located in the “WANCY” cluster of tRNAs. The second H strand promoter (HSP2) is located in tRNAPhe (F) immediately upstream of the 12S rRNA gene. Genes transcribed from the H strand promoters (H strand is the template strand) or the LSP (L strand is the template strand) are labeled on the outside or inside of the mtDNA molecule, respectively. Semicircular arcs connected to the mtDNA molecule by dashed lines represent the major mitochondrial primary transcripts, with those emanating from LSP and HSP2 typically being near genome length and those from HSP1 preferentially terminating at a specific termination site (TERM) downstream of the 16S rRNA in tRNALeu (L1). The mtDNA-encoded genes are color coded as follows: rRNAs, purple; complex I/NADH dehydrogenase, green; complex III/ubiquinol-cytochrome c oxidoreductase, blue; complex IV/cytochrome c oxidase, red; and complex V/ATP synthase, yellow. Black boxes labeled with capital letters denote tRNAs for specific amino acids according to standard one-letter nomenclature. There are two tRNAs for serine and leucine, which are labeled S1 and S2 or L1 and L2, respectively.
Molecular Cell  , DOI: ( /j.molcel )
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3. Figure 2 The Core Human Mitochondrial Transcription Machinery
The four primary components required for human mitochondrial transcription are shown: mtRNA polymerase, POLRMT; HMG-box transcription factor, h-mtTFA; and two transcription factors/rRNA methyltransferases, h-mtTFB1 and h-mtTFB2. The salient features and domains of these proteins are indicated, and we have attempted to represent their gross physical structure. Our representation of POLRMT is based on the known structure of the bacteriophage T7 RNA polymerase (which resembles an inverted right hand). The “palm,” “fingers,” and “thumb” regions are indicated. The location of the amino-terminal domain (ATD), containing the two pentatricopeptide repeat (PPR) domains, is unknown, and our placement is arbitrary. Our representation of h-mtTFA is based on the “L shaped” three-dimensional structure of an HMG-box domain. The two HMG boxes are shown connected by a linker and followed by the C-terminal tail, the latter being critical for efficient transcriptional activation and binding to h-mtTFB1 and h-mtTFB2. Similarly, the structures of h-mtTFB1 and h-mtTFB2 are not known, but our approximations are based on the known structures of Saccharomyces cerevisiae mtTFB and bacterial methyltransferases, which use S-adenosylmethionine (SAM) as a cofactor. The protrusions shown extending from the “methyltransferase core” on h-mtTFB1 and h-mtTFB2 (marked with asterisks) are not present in bacterial methyltransferases and likely represent regions involved in their transcription factor function, consistent with mutational analysis in yeast (Cliften et al., 1997).
Molecular Cell  , DOI: ( /j.molcel )
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4. Figure 3
Proposed Models of Human Mitochondrial Transcription Initiation
Promoter recognition and transcription initiation at human mitochondrial promoters requires the simultaneous presence of h-mtTFA and POLRMT complexed with either h-mtTFB1 or h-mtTFB2 (see text for details). However, the precise contribution of each factor to the key steps required for initiation has not yet been fully delineated. Nonetheless, we propose two speculative models that are consistent with the available data in the literature. In model 1 (top two panels), h-mtTFA bound at its high-affinity site upstream of the promoter induces a uniquely bent or unwound state of the surrounding DNA (above the arrow in model 1). Specific sequences in this topologically distorted promoter are then recognized by POLRMT in a complex with either h-mtTFB1 or h-mtTFB2 (or by POLRMT alone, data not shown). In this model, h-mtTFB1/2 promotes the formation and/or stabilization of an open DNA complex, bridges the h-mtTFA/POLRMT interaction at the promoter, or both. Once all of the transcription components are present at the promoter, transcription initiation proceeds (below the arrow in model 1). In model 2 (bottom three panels), the POLRMT/mtTFB heterodimer (or POLRMT alone, data not shown) recognizes the double-stranded promoter in the absence of any physical deformation of the DNA. Having formed this preinitiation complex, the entire basal transcription machinery actively distorts the promoter, with any or all of the components contributing to the formation of a stable open complex and subsequent initiation. In this model, the role of h-mtTFA could be either to aid in promoter opening after all of the core machinery is present or to stabilize the binding of POLRMT/mtTFB complexes to the promoter via the interaction between its C-terminal tail and the mtTFB factors. The role of the mtTFB factors is the same as described in model 1.
Molecular Cell  , DOI: ( /j.molcel )
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