Prokaryotic polymerases

DNA polymerases (Pol) have restricted properties so that the information encoded in DNA can be faithfully copied. The properties of prokaryotic polymerases (Komberg and Baker, 1992) can be summarized as ... 

The inhibitors of RNA polymerase, which generates RNA from DNA, inhibit a crucial step in gene expression. Inhibition of the eukaryotic form of RNA polymerase is used in cancer chemotherapy and is also an important experimental tool. For example, actinomy-cin D binds to the guanine residues in DNA and blocks the movement of the eukaryotic RNA polymerase. Specific inhibitors of bacterial RNA polymerase can be used as antibacterial agents. Most of these inhibitors like rifamycin bind to the prokaryotic enzyme. 

There s not just one DNA polymerase there s a whole army. DNA replication actually occurs in large complexes containing many proteins and sometimes many polymerases. In eukaryotic cells we have to replicate both mitochondrial and nuclear DNA, and there are specific DNA polymerases for each. In addition to DNA replication, you have to make new DNA when you repair. Consequently, the function may be specialized for repair or replication. There can also be specialization for making the leading or lagging strand. Some of the activities of DNA polymerases from eukaryotes and prokaryotes are shown in the table on the next page. 

Eukaryotes have a specific signal for termination of transcription however, prokaryotes seem to have lost this mechanism. Once started, RNA polymerase keeps going, making a primary transcript [pre-mRNA or hnRNA (for heterogeneous nuclear)] until far past the end of the final mRNA message. 

Enzyme-stabilized single-stranded DNA (known as the open complex) is the first intermediate formed in transcription initiation of RNA polymerases its formation is the rate-limiting step. Designing molecules which bind specifically to the open complex is a strategy for generating potent transcription inhibitors. The redox-stable complex of Cu(I) with 1,2-dimethyl- 1,10-phenanthroline is an example of such a strategy (405). The Cu(I) complex binds specifically to the single-stranded DNA of transcriptional open complexes and is an effective inhibitor of eukaryotic and prokaryotic transcription. 

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. 

RNA polymerase eventually reaches a transcription termination signal, at which point it will stop transcription and release the completed mRNA molecule. There are two kinds of transcription terminators commonly found in prokaryotic genes ... 

The nomenclature for transcription factors is confusing. Depending on their mode of action, various terms are in use both for the proteins themselves and for the DNA sequences to which they bind. If a factor blocks transcription, it is referred to as a repressor otherwise, it is called an inducer. DNA sequences to which regulatory proteins bind are referred to as control elements. In prokaryotes, control elements that serve as binding sites for RNA polymerases are called promoters, whereas repressor-binding sequences are usually called operators. Control elements that bind activating factors are termed enhancers, while elements that bind inhibiting factors are known as silencers. 

B. Prokaryotic DNA replication is accomplished by DNA polymerases, large multienzyme complexes that move out bidirectionally from the origin of replication. 

Figure 11-2. The prokaryotic DNA replication fork. A schematic representation of semi-conservative replication of DNA by different mechanisms on the leading and lagging strands by DNA polymerase III (DNA pol III) is shown. Other enzymes and accessory proteins that participate in initiation, elongation, and ligation phases of the process are indicated, with DNA pol I depicted as having just dissociated from a completed Okasaki fragment. SSBs, single-stranded DNA binding proteins.

Like DNA polymerases, prokaryotic RNA polymerase (RNA pol) is a multiprotein complex that operates only in the 5 to 3 direction as it copies the template. 

Figure 11-3. The prokaryotic RNA transcription bubble. RNA pol II, RNA polymerase II hnRNA, heterogeneous nuclear RNA.

C. Eukaryotic transcription is more complex than in prokaryotes, mainly in terms of the nature of the RNA polymerases, the assembly of the pre-initiation complex, and the need for processing eukaryotic RNAs. 

In prokaryotes and eukaryotes, the expression of individual genes is controlled by activation or inhibition of RNA polymerase on each gene by transcription factors. 

Eick, D., Wedel,A. and Heumann, H. From initiation to elongation comparison of transcription by prokaryotic and eukaryotic RNA polymerases (1994) Trends Gen. 10, 292-296... 

Goodman, M.F. (2002) Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 71, 17-50. Review of a class of DNA polymerases that continues to grow. 

The sequences of eukaryotic promoters are more variable than their prokaryotic counterparts (see Fig. 26-8). The three eukaryotic RNA polymerases usually require an array of general transcription factors in order to bind to a promoter. Yet, as with prokaryotic gene expression, the basal level of transcription is determined by the effect of promoter sequences on the function of RNA polymerase and its associated transcription factors. 

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