Bacteriophage lambda: Early pioneer and still relevant

Abstract

Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid-1950s to mid-1980s was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives has continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle.

Keywords: Bacteriophage; Lambda; Lambdoid phages.

Figure 1. Map of the bacteriophage lambda chromosome

The linear virion chromosome is shown with a scale in kbp below. Rectangles indicate known genes with names and functional regions shown above; red genes are transcribed rightward and green leftward; vertically offset gene rectangles are expressed from reading frames that overlap (CNu3, S107–S105 and sieB-esc in the same reading frame, rz-rz1 in different frames) or by programmed frameshifting (G-T, small arrow in figure). Diamonds (♦) mark regulatory genes. Important DNA sites (e.g., P, promoters; t, terminators) are indicated below the genes. Thick horizontal arrows below indicate mRNAs: black, transcripts made in a lysogen; orange, immediate-early transcripts; green, early transcripts; red, late transcripts; blue, transcripts made in response to high CII levels. Asterisks (✳) mark RNAs with regulatory activity (the detailed role of P_RE-initiated cro antisense message remains unclear (Spiegelman et al., 1972). The chromosome is circularized in the cell during infection, so the P_R'-initiated late transcript is continuous from the lower right to the upper left in the figure.

Figure 2. Lambda regulatory circuits

The figure shows phage lambda-encoded functions (yellow ovals) and host encoded functions (blue ovals) that impact the lysis-lysogeny decision and control the lytic gene expression cascade. Phage P22 (Liao et al., 1987;Wu et al., 1987) and phage 434 (Shkilnyj et al., 2013) genes are pink and orange ovals respectively. Green arrows denote positive (activation) functions and red lines denote inhibitory (repression) functions. Asterisks (*) indicate antisense RNA interactions, hashes (#) indicate translational repression, and daggers (†) indicate mRNA stability controls; other regulatory events are at the level of transcription except IHF and FIS physical participation in the integrase complex that catalyzes the integration of prophage DNA.

Figure 3. The phage lambda virion

A. Negatively stained electron micrograph of the Ur-lambda virion. Micrograph is modified from Hendrix and Duda (1992) and reproduced with permission of publisher. B. Ribbon diagram of the phage HK97 virion MCP subunit. The N- and C-termini of the protein are indicated, and the asterisks mark the locations of K169 and N356 whose side chains are crosslinked to adjacent subunits in the virion (from Helgestrand et al., 2003; protein database code 1OHG with rainbow color depiction by MacPyMOL copyright 2009–2010 Schrodinger, LLC). C. Subnanometer-resolution 3-dimensional cyroelectron microscopic reconstruction of the phage lambda head. Coloration ranges from red to blue with increasing radius, and the black arrowhead indicates the center of a coat protein hexamer as shown in panel D. D. Close up view centered on a major capsid protein hexamer of the head shown in panel C. Six gene D protein trimers are indicated in orange and seven major coat protein (gene E protein) subunits are shown in other colors. These colored subunits form one shell asymmetric unit. Panels C and D are modified from Lander et al. (2008) and reproduced with permission of publisher.

Figure 4. The lambdoid phage diversity menu

A schematic map of the lambda virion chromosome and its major transcripts are shown above (colored as in figure 1). The "menus" of various functional sections are labeled above and listed below the map in colored rectangles. In each section's menu a few lambdoid phages that have very different genes in this region and are best understood in that particular regard are indicated; however, the extant diversity of most sections is larger than shown and remains poorly defined in many cases. In some cases the different phages indicated within one menu section have clearly nonhomologous genes that encode parallel functions (e.g., SfV long contractile, lambda long non-contractile and P22 short tails; lambda Exo, P22 Erf and gifsy-2 RecE type homologous recombination systems), and in some cases the genes are extremely divergent homologues (e.g., portal and MCPs in the procapsid assembly section and probably all the different prophage repressors with different operator binding specificities). Each of the functional sections shown is populated by at least one gene in most lambdoid phages, although there are a few exceptions (e.g., Fels-1 has no nin region genes and HK022 has no N gene). In addition, any given lambdoid phage may have additional scattered accessory genes (e.g., in lambda the lom and rexAB genes between the tail and tail fiber genes and immediately downstream of cI, respectively, and in P22 the rha and ant genes between the lysis and DNA packaging genes and between tail and tailspike genes in P22, respectively).