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Proteins that are essential for starting replication at the origin of E. coli and Activities and function of DNA Polymerases.

  • Proteins that are essential for starting replication at the origin of E. coli.

Dna A Protein

Recognizes Ori C sequence, Open duplex at specific sites in Origin

Dna B Protein (Helicase)

Unwinds DNA

Dna C Protein

Required for Dna B Binding at origin

Primase (Dna G)

 Synthesizes RNA Primers

Single-stranded DNA binding protein (SSB)

 Binds single-stranded DNA

DNA Gyrase (Topoisomerase-II)

 Relieves torsional strain generated by DNA unwinding.


  • Activities and function of DNA Polymerases


Prokaryotic (E. coli)

Number of subunits

Function

Pol I

1

RNA primer removal, DNA repair,

Pol II (Din A)

1

DNA repair

Pol III Core

3

Chromosome replication

Pol III Holoenzyme

9

Chromosome replication

Pol IV (Din B)

1

DNA repair, Trans Lesion Synthesis (TLS)

Pol V (Umu C, UmuD2 C)

3

TLS



Eukaryotic

Number of subunits

Function

Pol α

4

Primer synthesis during DNA replication

Pol β

1

Base excision repair

Pol γ

3

Mitochondrial DNA replication and repair

Pol δ

2-3

DNA replication, nucleotide and base excision repair

Pol ε

4

DNA replication, nucleotide and base excision repair

Pol θ

1

DNA Repair of crosslinks

Pol ζ

1

Translesion synthesis

Pol λ

1

Meiosis-associated DNA repair

Pol μ

1

Somatic hypermutation

Pol n

1

Relatively accurate TLS past cis-syn cyclobutene dimers

 

 

 

Source: Data from Sutton and Walker, 2001 

DNA polymerases play a central role in the efficient and accurate replication of the genome, which is why cells possess multiple specialized DNA polymerases. For instance, E. coli has at least five distinct DNA polymerases, each characterized by unique enzymatic properties, subunit compositions, and levels of abundance.

DNA polymerase III (DNA Pol III) is the primary enzyme responsible for chromosome replication. The complete 4.6 Mb E. coli genome is replicated at two replication forks, requiring DNA Pol III to be highly processive. To meet this demand, DNA Pol III is usually a component of a larger entity known as the DNA Pol III holoenzyme, which enhances its processivity.

In contrast, DNA polymerase I (DNA Pol I) specializes in removing the RNA primers that initiate DNA synthesis. To accomplish this, DNA Pol I possesses a 5' exonuclease, which enables it to eliminate RNA or DNA that is immediately upstream of the DNA synthesis site. Unlike DNA Pol III, DNA Pol I is not highly processive and adds only 20–100 nucleotides during each binding event. This limited processivity is ideal for removing RNA primers and synthesizing DNA across the resulting single-stranded DNA (ssDNA) gap. Furthermore, the 5' exonuclease of DNA Pol I can effectively remove the RNA-DNA linkage, which is resistant to RNase H. The short synthesis capability of DNA Pol I is well-suited for replacing the brief region previously occupied by RNA primers, typically less than 10 nucleotides.

Both DNA Pol I and DNA Pol III are essential for DNA replication and must operate with high accuracy. Consequently, both enzymes are equipped with associated proofreading exonucleases. The remaining three DNA polymerases in E. coli are specialized for DNA repair tasks and do not possess proofreading activities.
Eukaryotic cells contain multiple DNA polymerases, with a typical cell having more than 15 different types. Among these, three are essential for genome duplication: DNA Pol α/primase, DNA Pol ε, and DNA Pol δ. Each of these eukaryotic DNA polymerases is made up of multiple subunits 

DNA Pol α/primase plays a key role in initiating new DNA strands. This four-subunit protein complex consists of a two-subunit DNA Pol α and a two-subunit primase. Once the primase synthesizes an RNA primer, the resulting RNA primer-template junction is quickly transferred to the associated DNA Polα to begin DNA synthesis. Due to its relatively low processivity, DNA Pol α/primase is rapidly replaced by the more processive DNA polymerases, DNA Pol δ and DNA Pol ε. This exchange of DNA Pol α/primase for DNA Pol δ or ε is known as polymerase switching and allows three different DNA polymerases to operate at the eukaryotic replication fork. Similar to bacterial cells, most of the other eukaryotic DNA polymerases are involved in DNA repair.

REFERENCE:
  • Steitz T.A. 1998. A mechanism for all polymerases. Nature 391: 231-232.
  • Sutton M.D. and Walker G.C. 2001. Managing DNA polymerases: Coordinating DNA replication, DNA repair, and DNA recombination. Proc. Nat/. Acad. Sci. 98: 8342-8349. 

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