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III. Molecular Genetics
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10. Gene Expression: Transcription
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The McGraw Hill Companies, 2001
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TFIIF TFIIB TFIIE TFIIH TFIID TFIIA RNA polymerase II Transcription
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TFIIF TFIIB TFIIE TFIIH TFIID TFIIA RNA polymerase II Transcription
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(a) An RNA polymerase II preinitiation complex at a promoter. TFIID binds to the TATA box (red). The other transcription factors are then recruited with the polymerase. (b) Two activators (yellow) are shown bound at one end (their DNA domains) to enhancers (blue and green) upstream on the DNA. The activators are bound at their other ends (their transcriptional activation domains) to other proteins associated with the polymerase machinery. Phosphorylation of the polymerase initiates activated transcription.
Table 10.4 Putative Roles of the General Transcription Factors of RNA Polymerase II
General Transcription Factor TFIID, TBP TFIID, TAFs TFIIA TFIIB TFIIE TFIIF TFIIH Function Recognizes TATA box Recognizes initiator element and regulatory proteins Stabilizes TFIID Aids in start-site selection by RNA polymerase II Controls TFIIH functions; enhances promoter melting Destabilizes nonspeci c interactions of RNA polymerase II and DNA Melts promoter with helicase activity; activates RNA polymerase II with kinase activity
Source: Data from R. G. Roeder, The Role of General Initiation Factors in Transcription by RNA Polymerase II in Trends in Biochemical Sciences, 21:327 35, 1996.
basal rate of transcription ( g. 10.25). TFIIH also has a role here, since it is also a helicase.Table 10.4 summarizes the postulated roles of the general transcription factors. For activated transcription, a high level of transcription, to take place, other factors are needed that are involved in controlling which promoters are actively transcribed. These other factors are activators or speci c transcription factors that bind to DNA sequences called en-
hancers. Enhancers are often hundreds or thousands of base pairs upstream from the promoter ( g. 10.24b). Note that much of this information has been gathered by footprinting, mutational studies, cloning and isolating the genes and proteins involved, and then reconstituting various puri ed combinations in the test tube. These studies are combined with kinetic research to determine which arrangements are stable, immunological research
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
10. Gene Expression: Transcription
The McGraw Hill Companies, 2001
Ten
Gene Expression: Transcription
to isolate various components with antibodies, and photocrosslinking studies to determine which moities are in contact with each other. These speci c transcriptional activators have domains (regions) that recognize their speci c enhancer sequences, regions that recognize proteins associated with the polymerase (general transcription factors), and regions that allow the joint attachment of other transcription factors ( g. 10.24b). Similar to activators and enhancers, repressors can bind to silencer regions of DNA, often far upstream of the promoters, to repress transcription. Thus, many genes are associated with numerous and complex arrangements of transcription factors, providing elaborate control of transcription (see chapter 16). For speci c transcription factors to attach to both enhancers and the polymerase machinery, possibly thousands of base pairs apart, the DNA must bend to allow them to come into the range of the polymerase. Electron micrographs clearly show this DNA bending and looping ( g. 10.26).
Although RNA polymerases I and III seem to have termination signals similar to rho-independent promoters in prokaryotes, termination of transcription of RNA polymerase II genes is more complex, coupled with further processing of the mRNA. Before we move on, several other points merit discussion. First, unlike prokaryotic RNA polymerases, eukaryotic RNA polymerases do proofread (showing 3 5 exonuclease activity). Second, as we will discuss in chapter 15, eukaryotic DNA is complexed with histone proteins that can interfere with transcription. In turn, part of the RNA polymerase II complex is made up of proteins that can disrupt the histones bound to the DNA. In addition, the RNA polymerase II complex contains proteins that act as mediators between activators and the polymerase holoenzyme. This complex coordination of the initiation of transcription in eukaryotes has been termed combinatorial control; the huge initiation complex may contain 85 or more different polypeptides.
The RNA polymerase II elongation complex with part of the protein structure removed to show the DNA and RNA within the cleft of the protein. The DNA is blue (template strand) and green (nontemplate strand) with the RNA red. The majority of protein is shown as gray; the part in yellow is a domain that appears to open for DNA loading and is in a closed state during elongation, thus acting as a clamp on the DNA and RNA. Closure of the clamp allows for the high stability of transcribing complexes and thus for processivity of the polymerase. The purple part is a helix that crosses the major cleft of the enzyme. The DNA template strand is led over this helix towards the active site. The pink sphere is a magnesium ion in the active site, where RNA synthesis occurs. (P. Cramer, D. A. Bushnell and R. D. Kornberg. RNA polymerase II at 2.8A
(b) Figure 10.26 The interaction between an activator and RNA polymerase (in this case, in prokaryotes). (a) In this system, the RNA polymerase of E. coli (the more heavily stained sphere) is controlled by an activator called NtrC (the more lightly stained sphere). The activator is bound to an enhancer, and the polymerase is bound to the promoter. (b) The activator has bound to the polymerase, causing a looping of the DNA. Compare with gure 10.24. (Courtesy of Sydney Kustu.)
resolution and A. L. Gnatt, P. Cramer, J. Fu, D. A. Bushnell and R. D. Kornberg, Structure of an RNA polymerase II transcribing complex. Reprinted by permission of the authors.)
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