Core polymerase

There is a single prokaryotic RNA polymerase that synthesizes all types of RNA in the cell. The core polymerase responsible for making the RNA molecule has the subunit structure Ojpp. A protein factor called sigma (a) is required for the initiation of transcription at a promoter. Sigma factor is released immediately after initiation of transcription. Termination of transcription sometimes requires a protein called rho (p) faaor. This enzyme is inhibited by rifampin. Actinomycin D binds to the DNA preventing transcription. 

The core polymerase continues moving along the template strand in the 3 to 5 direction, synthesizing the mRNA in the 5 to 3 direction. 

DNA polymerase III is much more complex than DNA polymerase I, having ten types of subunits (Table 25-2). Its polymerization and proofreading activities reside in its a and e (epsilon) subunits, respectively. The 6 subunit associates with a and e to form a core polymerase, which can polymerize DNA but with limited processivity. Two core polymerases can be linked by... 

The enzyme without the sigma factor, called core polymerase, retains the capability to synthesize RNA, but it is defective in the ability to bind and initiate transcription at true initiation sites on the DNA. In fact when RNA polymerase was first purified from crude extracts it was missing the a factor. The assay for polymerase involved the use of DNA with single-strand nicks. When a DNA template was used that did not have single-strand nicks, this enzyme was not active. This led to a search for a missing factor. When this factor (cr70) was added back to the purified core enzyme and the uncut DNA template, the enzyme was able to bind... 

The initiator nucleotide binds to the complex and the first phos-phodiester bonds are made, accompanied by release of o. The remaining core polymerase is now in the elongation mode. Several experimental observations support the picture presented in the next figure, namely the fact that less than one a exists in the cell per core enzyme in each cell. 

A FIGURE 11-6 Schematic representation of the subunit structure of the E. coli RNA core polymerase and yeast nuclear RNA polymerases. All three yeast polymerases have five core subunits homologous to the p, p, two a. and co subunits of E. coli RNA polymerase. The largest subunit (RPB1) of RNA polymerase II also contains an essential C-terminal domain (CTD). RNA polymerases I and III contain the same two nonidentical a-like subunits, whereas RNA polymerase II contains two other nonidentical a-like subunits. All three polymerases share the same co-like subunit and four other common subunits. 

The C subunit plays an important role in directing RNA polymerase to bind to template at the proper site for initiation the promoter site—and to select the correct strand for transcription. The addition of <7 to core polymerase reduces the affinity of the enzyme for nonpromoter sites by about 10, thereby increasing the enzyme s specificity for binding to promoters. In at least some cases, gene expression is regulated by having core polymerase interact with different forms of [Pg.110]

Di - PolC gene product. Has polymerase activity. Part of the core polymerase. 

We have seen that prokaryotes have a single RNA polymerase that is responsible for the synthesis of all three kinds of prokaryotic RNA— mRNA, tRNA, and rRNA. The polymerase can switch a factors to interact with different promoters, but the core polymerase stays the same. The transcription process is predictably more complex in eukaryotes than in prokaryotes. Three RNA polymerases with different activities are known to exist. Each one transcribes a different set of genes and recognizes a different set of promoters ... 

DNA polymerase III is an asymmetric dimer. It contains two copies of the core polymerase, snbnnits a, e, and 0. The a subunit has polymerase activity while e is a 3 — 5 proofreading exonuclease. A 2 subunit is associated with one arm and a (55 i/)2 subunit with the other. These serve as the clamp-loading complex. The P2 subunits form ringlike structures that serve as sliding DNA clamps. 

In prokaryotic RNA polymerases, the ct-factor is required for promoter recognition and binding. It is loosely bound to the core complex and released after the nascent RNA chain becomes 8-9 nucleotides long. The core polymerase with <7 -factor has a high affinity for nonspecific DNA. The <7-factor alters the conformation of theholoenzymeso that its affinity for nonspecific DNA is reduced and the specific binding affinity for the promoter is significantly enhanced. 

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