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Abstract Background Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank. Results Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR) and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs) that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases. Conclusion Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes.

Research was conducted to examine the hypothesis that the Bacillus subtilis nucleotidyltransferase is a tRNA CCA-adding enzyme. The poly(A) polymerase (papS)gene was overexpressed and characterized to demonstrate that it is a tRNA nucleotidyltransferase. Results provide evidence that cca is the only gene encoding an Ntr protein despite earlier suggestions that B. subtilis has a PAP similar to E. coli PAP I.

The phage ndd gene induces the rapid decimation of the structure of the Escherichia coli nucleoid during the early phase of bacteriophage T4 infection. The Ndd protein is highly toxic to cells even in very small quantities. In uninfected E. coli, overexpression of the cloned ndd gene causes disruption of the nucleoid that is similar to that seen after T4 infection. A preliminary characterization of the protein shows that it has a double-stranded DNA binding activity with preference for bacterial DNA.

Ribonuclease E has been shown to organize protein interactions in the Escherichia coli RNA degradosome, which is the prototype of a newly discovered family of multiprotein mechanisms involved in the processing and degradation of RNA. A model for regulation of Rh1B RNA helicase activity has emerged. RNase E appears to be a very complex multidomain protein. The carboxy-terminal half (CTH) of ribonuclease E (RNase E) contains binding sites for the three other major degradosomal parts, enolase, polynucleotide phosphorylase (PNPase) and dead-box RNA helicase Rh1B.

Enolase and RhlB, a member of the DEAD-box family of ATP-dependent RNA helicases, are novel components of RNA degradosome. RhlB most likely unwinds distinct RNA structures in the presence of ATP to facilitate mRNA degradation by PNPase as shown by the RNAs failure to degrade when RhlB is blocked by an affinity-purified antibody even if ATP is added. Enolase's purpose in degradosome is still unknown.

Sedimentation and immunoprecipitation analyses confirm the copurification of Escherichia coli ribonuclease E(RNAase E) and polynucleotide phosphorylase (PNPase) and a specific association between these enzymes that is essential for RNA processing and degradation. Responsiveness of the enzyme to proteolysis during purification is responsible for size differences observed in RNAase E.