User:Ketan Mathavan/Sandbox 1

spinqualitylabelsall models Human mitochondrial RNA polymerase (PDB: 3SPA) scene= Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.

Transcription and the human mitochondrial RNA polymeraseTranscription and the human mitochondrial RNA polymerase

The central dogma of biology in which genetic information is transferred from DNA to RNA, and subsequently into protein, is fundamental to life. A key player in this process is the DNA-dependent RNA polymerase. RNA polymerase produces RNA in the presence of a DNA template under tight control by the cell. In the Martin lab, our goal is to elucidate the energetics and thermodynamics of this complicated process. As a model, we use T7 bacteriophage RNA polymerase (PDB:1QLN). This single-subunit polymerase can transcribe DNA without assistance from other proteins, making it an ideal model to understand transcription. Likewise, it is representative of all other known RNA polymerases in that it initiates at unique positions along the DNA, undergoes abortive cycling, transitions to a stable elongation complex, and terminates transcription at specific sequences.

Related to the T7 RNA polymerase is the human mitochondrial RNA polymerase . Recent crystallization of this enzyme by Temiakov et al. has revealed structural similarity between the two polymerases. The C-terminal contains the active site for RNA synthesis. The N-terminal (NTD) contains the promoter-binding domain (PBD) essential for DNA binding and start site specificity. Key structures of the NTD include the specificity , intercalating , and AT-recognition .

One very big difference between the two polymerases is in the form of two transcription factors, TFB2M and TFAM. Human mtRNA polymerase requires these two proteins for binding and melting of promoter DNA. TFAM binds 15-40 base pairs upstream while TFB2M binds more proximal to the transcription start site (1-3). The requirement of these transcription factors coupled with the discrepancy of PBD orientation between T7 (Fig. 2; salmon) and human mtRNA polymerase (Fig. 2; grey) suggests a role in enzyme remodeling for the transcription factors, namely, TFB2M. By studying the structural changes and differences between the two polymerases, we can better under the energetics that governed transcription.

ReferencesReferences

1. Ekstrand, M. I. Mitochondrial transcription factor A regulates mtDNA copy number in mammals. Hum. Mol. Genet. 13, 935-944 (2004). Pubmed
2. Dairaghi, D. J., Shadel, G. S., Clayton, D. A. Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim. Biophys. Acta 1271, 127-134 (1995). Pubmed
3. Sologub, M., Litonin, D., Anikin, M., Mustaev, A., Temiakov, D. TFB2 is a transient component of the catalytic site of the human mitochondrial RNA polymerase. Cell 139, 934-944 (2009).ﾠPubmed

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I was unable to create Jmol scenes to illustrate structures of the human mitochondrial RNA polymerase due to a "java.security.AccessControlException: access denied" problem regardless of the computer or web browser I use.

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