Diversity of Structure and Function of DNA Polymerase (gp43) of T4-Related Bacteriophages

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V. M. Petrov and J. D. Karam^*

Tulane University Health Sciences Center, Department of Biochemistry SL43, 1430 Tulane Avenue, New Orleans, LA 70112-2699, USA; fax: 504-988-1611; E-mail: karamoff@tulane.edu

^* To whom correspondence should be addressed.

Received July 29, 2004

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The replication DNA polymerase (gp43) of the bacteriophage T4 is a member of the pol B family of DNA polymerases, which are found in all divisions of life in the biosphere. The enzyme is a modularly organized protein that has several activities in one polypeptide chain (~900 amino acid residues). These include two catalytic functions, POL (polymerase) and EXO (3´-exonuclease), and specific binding activities to DNA, the mRNA for gp43, deoxyribonucleotides (dNTPs), and other T4 replication proteins. The gene for this multifunctional enzyme (gene 43) has been preserved in evolution of the diverse group of T4-like phages in nature, but has diverged in sequence, organization, and specificity of the binding functions of the gene product. We describe here examples of T4-like phages where DNA rearrangements have created split forms of gene 43 consisting of two cistrons instead of one. These gene 43 variants specify separate gp43A (N-terminal) and gp43B (C-terminal) subunits of a split form of gp43. Compared to the monocistronic form, the interruption in contiguity of the gene 43 reading frame maps in a highly diverged sequence separating the code for essential components of two major modules of this pol B enzyme, the FINGERS and PALM domains, which contain the dNTP binding pocket and POL catalytic residues of the enzyme. We discuss the biological implications of these gp43 splits and compare them to other types of pol B splits in nature. Our studies suggest that DNA mobile elements may allow genetic information for pol B modules to be exchanged between organisms.

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KEY WORDS: DNA polymerase, pol B family, gp43, molecular evolution, DNA binding proteins, RNA binding proteins, DNA replication, multifunctional proteins, modular proteins, microbial diversity, bacteriophages

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