Genetic insertions and diversification of the PolB-type DNA polymerase (gp43) of T4-related phages

J Mol Biol. 2010 Jan 22;395(3):457-74. doi: 10.1016/j.jmb.2009.10.054. Epub 2009 Nov 5.


In Escherichia coli phage T4 and many of its phylogenetic relatives, gene 43 consists of a single cistron that encodes a PolB family (PolB-type) DNA polymerase. We describe the divergence of this phage gene and its protein product (gp43) (gene product 43) among 26 phylogenetic relatives of T4 and discuss our observations in the context of diversity among the widely distributed PolB enzymes in nature. In two T4 relatives that grow in Aeromonas salmonicida phages 44RR and 25, gene 43 is fragmented by different combinations of three distinct types of DNA insertion elements: (a) a short intercistronic untranslated sequence (IC-UTS) that splits the polymerase gene into two cistrons, 43A and 43B, corresponding to N-terminal (gp43A) and C-terminal (gp43B) protein products; (b) a freestanding homing endonuclease gene (HEG) inserted between the IC-UTS and the 43B cistron; and (c) a group I intron in the 43B cistron. Phage 25 has all three elements, whereas phage 44RR has only the IC-UTS. We present evidence that (a) the split gene of phage 44RR encodes a split DNA polymerase consisting of a complex between gp43A and gp43B subunits; (b) the putative HEG encodes a double-stranded DNA endonuclease that specifically cleaves intron-free homologues of the intron-bearing 43B site; and (c) the group I intron is a self-splicing RNA. Our results suggest that some freestanding HEGs can mediate the homing of introns that do not encode their own homing enzymes. The results also suggest that different insertion elements can converge on a polB gene and evolve into a single integrated system for lateral transfer of polB genetic material. We discuss the possible pathways for the importation of such insertion elements into the genomes of T4-related phages.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aeromonas salmonicida / virology
  • Amino Acid Sequence
  • Bacteriophage T4 / classification
  • Bacteriophage T4 / enzymology*
  • Bacteriophage T4 / genetics*
  • Base Sequence
  • DNA Transposable Elements
  • DNA, Viral / genetics
  • DNA-Directed DNA Polymerase / biosynthesis
  • DNA-Directed DNA Polymerase / chemistry
  • DNA-Directed DNA Polymerase / genetics*
  • Evolution, Molecular
  • Genes, Viral
  • Genetic Variation
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phylogeny
  • Polymorphism, Genetic
  • Protein Conformation
  • RNA Splicing
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Sequence Homology, Amino Acid
  • Sequence Homology, Nucleic Acid
  • Species Specificity
  • Viral Proteins / biosynthesis
  • Viral Proteins / chemistry
  • Viral Proteins / genetics*


  • DNA Transposable Elements
  • DNA, Viral
  • RNA, Viral
  • Recombinant Proteins
  • Viral Proteins
  • gene 43 protein, Enterobacteria phage T4
  • DNA-Directed DNA Polymerase