▲ FIGURE 11-47 Transcription-control elements in genes transcribed by RNA polymerase III. Both tRNA and 5S-rRNA genes contain internal promoter elements (yellow) located downstream from the start site and named A-, B-, and C-boxes, as indicated. Assembly of transcription initiation complexes on these genes begins with the binding of Pol Ill-specific general transcription factors TFIIIA, TFIIIB, and TFIIIC to these control elements. Green arrows indicate strong, sequence-specific protein-DNA interactions. Blue arrows indicate interactions between general transcription factors. Purple arrows indicate interactions between general transcription factors and Pol III. [From L. Schramm and N. Hernandez, 2002, Genes Dev. 16:2593.]


Mitochondrial and Chloroplast DNAs Are Transcribed by Organelle-Specific RNA Polymerases

As discussed in Chapter 10, mitochondria and chloroplasts probably evolved from bacteria that were endocytosed into ancestral cells containing a eukaryotic nucleus. In modern-day eukaryotes, both organelles contain distinct circular DNAs that encode some of the proteins essential to their specific functions. The RNA polymerases that transcribe mitochondrial (mt) DNA and chloroplast DNA are similar to polymerases from bacteria and bacteriophages.

Mitochondrial RNA Polymerase The RNA polymerase that transcribes mtDNA is encoded in nuclear DNA. After synthesis of the enzyme in the cytosol, it is imported into the mitochondrial matrix by mechanisms described in Chapter 16. The mitochondrial RNA polymerases from cerevisiae and the frog Xenopus laevis both consist of a large subunit with ribonucleotide-polymerizing activity and a small subunit, or specificity factor, essential for initiating transcription at the start sites in mtDNA used in the cell. The large subunit of yeast mitochondrial RNA polymerase clearly is related to the monomeric RNA polymerases of bacte-riophage T7 and similar bacteriophages. However, the mitochondrial enzyme is functionally distinct from the bac-teriophage enzyme in its dependence on the small subunit for transcription from the proper start sites. This small subunit is related to the ct factors in bacterial RNA polymerases, which interact with promoter DNA and function as initiation factors. Thus mitochondrial RNA polymerase appears to be a hybrid of the simple bacteriophage RNA polymerases and the multisubunit bacterial RNA poly-merases of intermediate complexity.

The promoter sequences recognized by mitochondrial RNA polymerases include the transcription start site. These promoter sequences, which are rich in A residues, have been characterized in the mtDNA from yeast, plants, and animals. The circular, human mitochondrial genome contains two related 15-bp promoter sequences, one for the transcription of each strand. Each strand is transcribed in its entirety; the long primary transcripts are then processed to yield mito-chondrial mRNAs, rRNAs, and tRNAs. A small basic protein called mtTFl, which binds immediately upstream from the two mitochondrial promoters, greatly stimulates transcription. A homologous protein found in yeast mitochondria is required for maintenance of mtDNA and probably performs a similar function.

Chloroplast RNA Polymerase In contrast to mitochondr-ial RNA polymerase, the enzyme that transcribes chloro-plast DNA is encoded in the chloroplast genome itself. This RNA polymerase has subunits with considerable ho-mology to the E. coli RNA polymerase a, ß, and ß' sub-units, but apparently lacks a subunit equivalent to the E. coli ct factor.

Some chloroplast promoters are quite reminiscent of the E. coli a70-promoter, with similar sequences in the — 10 and — 35 regions. Transcription from one chloroplast promoter, however, depends on sequences from about —20 to +60, quite different from most E. coli promoters. This promoter may be recognized by a second RNA polymerase, which most likely is encoded in the nuclear genome and imported into the organelle. Analysis of chloroplast transcription is still in its infancy, but at this point it is clear that at least one transcription system is highly homologous to transcription in E. coli and other bacteria from which chloro-plasts evolved.

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