Acidic residues and a predicted, highly conserved α-helix are critical for the endonuclease/strand separation functions of bacteriophage λ's TerL

DNA Packaging Specificity in the λ-Like Phages: Gifsy-1

DNA viruses recognize viral DNA and package it into virions. Specific recognition is needed to distinguish viral DNA from host cell DNA. The λ-like Escherichia coli phages are interesting and good models to examine genome packaging by large DNA viruses. Gifsy-1 is a λ-like Salmonella phage. Gifsy-1's DNA packaging specificity was compared with those of closely related phages λ, 21, and N15. In vivo packaging studies showed that a Gifsy-1-specific phage packaged λ DNA at ca. 50% efficiency and λ packages Gifsy-1-specific DNA at ~30% efficiency. The results indicate that Gifsy-1 and λ share the same DNA packaging specificity. N15 is also shown to package Gifsy-1 DNA. Phage 21 fails to package λ, N15, and Gifsy-1-specific DNAs; the efficiencies are 0.01%, 0.01%, and 1%, respectively. A known incompatibility between the 21 helix-turn-helix motif and cosBλ is proposed to account for the inability of 21 to package Gifsy-1 DNA. A model is proposed to explain the 100-fold difference in packaging efficiency between λ and Gifsy-1-specific DNAs by phage 21. Database sequences of enteric prophages indicate that phages with Gifsy-1's DNA packaging determinants are confined to Salmonella species. Similarly, prophages with λ DNA packaging specificity are rarely found in Salmonella. It is proposed that λ and Gifsy-1 have diverged from a common ancestor phage, and that the differences may reflect adaptation of their packaging systems to host cell differences.

Hybrid Vigor: Importance of Hybrid λ Phages in Early Insights in Molecular Biology

Laboratory-generated hybrids between phage λ and related phages played a seminal role in establishment of the λ model system, which, in turn, served to develop many of the foundational concepts of molecular biology, including gene structure and control. Important λ hybrids with phages 21 and 434 were the earliest of such phages. To understand the biology of these hybrids in full detail, we determined the complete genome sequences of phages 21 and 434. Although both genomes are canonical members of the λ-like phage family, they both carry unsuspected bacterial virulence gene types not previously described in this group of phages. In addition, we determined the sequences of the hybrid phages λ imm21, λ imm434, and λ h434 imm21. These sequences show that the replacements of λ DNA by nonhomologous segments of 21 or 434 DNA occurred through homologous recombination in adjacent sequences that are nearly identical in the parental phages. These five genome sequences correct a number of errors in published sequence fragments of the 21 and 434 genomes, and they point out nine nucleotide differences from Sanger's original λ sequence that are likely present in most extant λ strains in laboratory use today. We discuss the historical importance of these hybrid phages in the development of fundamental tenets of molecular biology and in some of the earliest gene cloning vectors. The 434 and 21 genomes reinforce the conclusion that the genomes of essentially all natural λ-like phages are mosaics of sequence modules from a pool of exchangeable segments.

Enteric Chromosomal Islands: DNA Packaging Specificity and Role of λ-like Helper Phage Terminase

The phage-inducible chromosomal islands (PICIs) of Gram-negative bacteria are analogous to defective prophages that have lost the ability to propagate without the aid of a helper phage. PICIs have acquired genes that alter the genetic repertoire of the bacterial host, including supplying virulence factors. Recent work by the Penadés laboratory elucidates how a helper phage infection or prophage induction induces the island to excise from the bacterial chromosome, replicate, and become packaged into functional virions. PICIs lack a complete set of morphogenetic genes needed to construct mature virus particles. Rather, PICIs hijack virion assembly functions from an induced prophage acting as a helper phage. The hijacking strategy includes preventing the helper phage from packaging its own DNA while enabling PICI DNA packaging. In the case of recently described Gram-negative PICIs, the PICI changes the specificity of DNA packaging. This is achieved by an island-encoded protein (Rpp) that binds to the phage protein (TerS), which normally selects phage DNA for packaging from a DNA pool that includes the helper phage and host DNAs. The Rpp–TerS interaction prevents phage DNA packaging while sponsoring PICI DNA packaging. Our communication reviews published data about the hijacking mechanism and its implications for phage DNA packaging. We propose that the Rpp–TerS complex binds to a site in the island DNA that is positioned analogous to that of the phage DNA but has a completely different sequence. The critical role of TerS in the Rpp–TerS complex is to escort TerL to the PICI cosN, ensuring appropriate DNA cutting and packaging.