Diversity of structure and function of DNA polymerase (gp43) of T4-related bacteriophages

Abstract

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 (approximately 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.

Insertion of a homing endonuclease creates a genes-in-pieces ribonucleotide reductase that retains function

“…Because many characterized homing endonucleases have recognition and cleavage sites within protein-coding genes, transposition of free-standing endonucleases into coding regions by illegitimate DSB repair may occur at an appreciable rate (36)(37)(38). A Seg-like homing endonuclease is found associated with a split gene structure in the family B DNA polymerase (gp43) of Aeromonas salmonicida phage 25 (23,39). Related phage possess a split gene 43 separated by up to Ϸ3 kb of intervening sequence without a Seg-like endonuclease.…”

Multiple Controls Regulate the Expression of mobE , an HNH Homing Endonuclease Gene Embedded within a Ribonucleotide Reductase Gene of Phage Aeh1

“…The genome sequence of phage Aeh1 identified homologs of T4 proteins that function to direct the host RNA polymerase to recognize early and late phage promoters preferentially over host promoters (44,47). One critical difference, however, was the lack of middle-promoter-like promoters in Aeh1 and the absence of the middle-mode transcription factor, MotA, from the genome sequence, suggesting that Aeh1 does not possess a class of transcripts analogous to T4 middle transcripts.…”

Plasticity of the Gene Functions for DNA Replication in the T4-like Phages

“…18 Yet, as we point out here, the gene 43 sequence has diverged widely in evolution, including examples where split (bicistronic) forms of this gene have evolved in the T4-like Aeromonas and Acinetobacter phages. 19 The diversity of intercistronic sequences that we have observed among these split forms suggests that a highly divergent internal sequence of the polymerase gene is a hotspot for mutations, including the invasion by DNA insertion elements, but that modularity and flexibility of the gene product allow for adaptation to the mutational events. Taken together with other studies, 16 the work we describe here points to a remarkable ability of the T4 genome type to diversify in evolution through various mechanisms of genetic recombination and plasticity of its DNA replication machine.…”