Table 3 Genes of the Core Genome of T4-like Viruses

DNA replication, repair and recombination

43 ; 45 ; 44 and 62 ; 41 & 61 ; 59 ; 32 ; 46&47 ; uvsW ; uvsX, uvsY; 30 ; rnh ; 39 + 60 & 52 ; dda ; 49

gp43 ( DNA polymerase); gp45 (trimeric sliding clamp); gp44/gp62 sliding clamp loader complex (gp44 tetramer+gp62 monomer); gp41/ gp61 helicase-primase complex (hexamers of both proteins); gp59 (helicase-primase loader & gp43 regulator); gp32 (single-strand binding protein); gp46-gp47 (subunits of a recombination nuclease complex required for initiation of DNA replication); UvsW protein (recombination DNA-RNA helicase, DNA-dependent ATPase); uvsX (RecA-like recombination protein); uvsY (uvsX helper protein); gp30 (DNA ligase); Rnh (Ribonuclease H); gp39+60 & gp52 (subunits of a Type II DNA topoisomerase); Dda protein (short-range DNA helicase); gp49 (Endonuclease VII, required for recombination & DNA packaging).

Many of the Quasicore genes in this group are absent in one or more T4-related marine cyanophages. In T4, some these genes are not required in certain E. coli hosts or become dispensable in the presence of mutations in specific other genes (intergenic suppression).

Auxiliary metabolism

nrdA&nrdB; nrdC; nrdG; nrdH; 56; cd; frd; td; tk; 1; denA; dexA

NrdA-NrdB (subunits of an aerobic ribonucleotide reductase complex); NrdG & NrdH (subunits of an anaerobic ribonucleotide reductase complex); NrdC (thioredoxin); gp56 (dCTPase-dUTPase); Cd (dCMP deaminase); Frd (DHFR; (dihydrofolate reductase); Td (thymidylate synthetase), Tk (thymidine kinase); gp1 (dNMP kinase); DenA (Endonuclease II); DexA (Exonuclease A).

A combination of at least some of these genes is required to supplement the intracellular pool of nucleotides for phage DNA and RNA synthesis.

Gene expression

33; 55; regA

gp33 (essential protein that mediates gp55-gp45-RNA polymerase interactions in late transcription); gp55 (sigma factor for late transcription); RegA (mRNA-binding translational repressor; also involved in host nucleoid unfolding)

In T4, regA mutations are not lethal, yet all the T4 relatives examined so far encode homologues of this gene.

Phage morphogenesis

2; 3; 4; 5; 6; 8; 13; 14; 15; 16 17; 18; 19; 20; 21; 22; 23; 25; 26; 34; 35; 36; "37"; 49; 53

gp2 (protects ends of packaged DNA against RecBCD nuclease); gp3 (sheath terminator); gp4 (Head completion protein); gp5 (baseplate lysozyme hub component); gp6 (baseplate wedge component); gp8 (baseplate wedge), gp13 (head completion protein ); gp14 ( head completion protein); gp15 (tail completion protein); gp16 &gp17 (subunits of the terminase for DNA packaging); gp18 (tail sheath subunit), gp19 (tail tube subunit); gp20 (head portal vertex protein); gp21 (prohead core protein and protease); gp22 (prohead core protein); gp23 (precursor of major head protein); gp25 (base plate wedge subunit); gp26 (base plate hub subunit); gp34 (proximal tail fiber protein subunit); gp35 (tail fiber hinge protein); gp36 (small distal tail fiber protein subunit); gp37 ( large distal tail fiber protein subunit; heterogeneous among T4 relatives); gp49 (Endo VII; required for DNA packaging); gp53 (baseplate wedge component)

T4 gp2 is not required in recBCD mutant hosts and no gene 2 homologues are detected in some marine cyanophages. Also, the "37" designation means that in some T4 relatives (e.g. the marine cyanophages and the vibriophages), the identification of gene 37 and other tail fiber genes can be difficult or impossible to make by bioinformatic tools because of extensive mosaicism or putative substitutions with non-homologous tail-fiber genes.

Other

rIIA &rIIB

The precise functions of the rIIA and rIIB gene products are not known. In T4, rIIA or rIIB mutations exhibit multiple effects on phage physiology, but are only lethal in the presence of a lambda prophage.

Like many other Quasicore genes, the rIIA and rIIB genes are found in all T4 relatives, except the marine cyanophages. The wide natural distribution of these 2 genes might be a reflection of the distribution of prophages that restrict T4 relatives in various bacterial hosts.