Multiplicity of DNA and RNA Polymerases

Multiple DNA and RNA polymerases are present in both eukaryotes and prokaryotes, which evolved to fulfill distinct roles in the cell. In E. coli, DNA polymerases I (Pol I), II (Pol II), and III (Pol III) account for most DNA polymerase activity. Pol I has the highest enzymatic activity and was the first DNA polymerase to be discovered by A Kornberg. However, Pol III is responsible for cellular DNA replication, while Pol I is involved in gap filling necessary during normal DNA replication (to fill in the space of degraded RNA primers) and also during repair of DNA damage. Pol II and two other DNA polymerases, Din B and UmuD/C, are responsible for replication of damaged DNA when it remains unrepaired.

Eukaryotic cells express five different DNA polymerases, α, β, γ , δ, and ε, for normal DNA replication and repair. Pol α is involved in synthesis of primers for DNA replication; Pol β and possibly Pol ε are involved in repair replication of damaged DNA. Pol δ (and possibly Pol ε) are responsible for replication of the nuclear genome. Pol γ found in the mitochondria is responsible for replication of the mitochondrial genome. Several additional DNA polymerases recently identified and characterized are involved in replication of unrepaired damaged bases, like the E. coli DinB and UmuD/C (Table II).

E. coli has only one RNA polymerase, while eukaryotes have three distinct RNA polymerases, Pol I, Pol II, and Pol III, which transcribe different types of genes.RNA Pol I makes only ribosomal RNAs, which constitute the largest fraction of totalRNAand, in fact, a significant fraction of the cellular mass. Pol III transcribes small RNAs, including transfer RNAs, which function as carriers of cognate amino acids and are required for protein synthesis. RNA Pol II transcribes all genes to generate mRNA, which encodes all proteins. Thus, this enzyme recognizes the most diverse group of genes. All of these RNA classes are initially synthesized as longer precursors that require extensive, often regulated, processing to yield the mature RNA product.

RNA and DNApolymerases encoded by virus and other episomal genomes are, in general, smaller and have fewer subunits than the cellular polymerases. Cellular polymerase holoenzymes are rather complex with multiple subunits which may have distinct functions. These will be discussed later.

TABLE II Cellular DNA Polymerases

Prokaryote (E. coli)	In vivo function
Pol I	Nonreplicative removal of 5´ primer of Okazaki fragments
Pol II	Nonreplicative, damage responsive polymerase
Pol III	Replicative synthesis
Din B	Lesion bypass DNA synthesis
UmuC	Lesion bypass DNA synthesis
Eukaryote
Pol α	RNA primer synthesis
Pol β	Repair synthesis
Pol δ	Replicative (repair) synthesis
Pol ε	Replicative (repair) synthesis
Pol ζ	Damage bypass synthesis
Pol η	Damage bypass synthesis
Pol θ	Damage bypass synthesis
Pol ι	Damage bypass synthesis
Pol γ	Mitochondrial DNA synthesis