MICROBIOLOGICAL REVIEWS, Sept. 1978, p. 577-591 Vol.42, No. 3 0146-0749/78/0042-0577$02.00/0 Copyright © 1978 American Society for Microbiology Printed in U.S.A. Genetic Map of Bacteriophage Lambda HARRISON ECHOLS* AND HELIOS MURIALDO Department ofMolecular Biology, University of California, Berkeley, California 94720, * and Department of Medical Genetics, University of Toronto, Toronto M5S 1A8, Canada INTRODUCTION .5..577 PHYSICAL STATES AND ACTIVITY OF THE A GENOME 577 GENETIC MAP OF THE A GENOME .577 ACTIITrY MAP OF THE A GENOME .583 COMMENTS ON GENETIC ORGANIZATION ...........5*583 LITERATURE CITED .584 INTRODUCTION that are the obligatory precursors for the The study of bacteriophage A has been a cen- cleaved, linear molecules packaged into a phage tral endeavor of molecular biology for a number head (Fig. 1). The lysogenic pathway involves a of years. Phage A has been the creature of choice repression of transcription and a site-specific for many investigators interested in deoxyribo- recombination event that inserts A DNA into nucleic acid (DNA) transcription, replication, the host Escherichia coli genome. This integra- and recombination, in nucleoprotein assembly, tive recombination between the phage and host and in the organization of these processes into attachment sites (att) generates a genetic struc- temporally regulated pathways. As a result of ture that is permuted from the linear order this intensive study, a great deal of information found in the phage particle because the phage is now available about A genes and how they attachment site (a a' or P P) is approximately work; however, the communication of this in the center of the mature DNA molecule (Fig. knowledge is sometimes hindered by a "culture 1). The prophage has structurally distinct at- gap" between "lambdologists" and those lacking tachment sites: a left attL site (b a' or B P') an understanding ofthe array ofgene names and and a right attR site (a b' or P B'); these in sites for protein activity. In an effort to remedy turn can recombine to detach the prophage this difficulty, we present an annotated genetic DNA when the virus is induced to lytic devel- map of phage A. We begin with a brief summary opment, regenerating the phage attP site (a a' of the A life cycle; present two maps, one of gene or P P') and the original host attB site (b b' or order and one of gene activity; and conclude B B'). with a short on the More detailed descriptions of the diverse life- commentary genetic orga- styles of phage A can be found in the general nization. review articles by Echols (47; in J. R. Sokatch PHYSICAL STATES AND ACTIVITY OF and L. N. Ornston, ed., The Bacteria, in press) THE X GENOME and Herskowitz (88). The lysogenic pathway has been recently reviewed by Weisberg et al. (233); The genome of phage A is a double-stranded the lytic pathway has not been selectively re- DNA molecule about 47,000 base pairs in length. viewed for some time, but the general features In the phage particle, A DNA has single- are covered in the review Echols stranded, complementary ends 12 bases in by (46). length, termed mature or cohesive ends m and m'. Within an infected cell, A DNA forms a circle GENETIC MAP OF THE X GENOME through pairing ofthe single-stranded DNA, and The order of genes along the linear A DNA is replicated and transcribed as a circular mole- molecule is shown in the upper part of Fig. 2; cule during the replication-oriented early phase the function of certain gene clusters is indicated of A development. below the map. The lower part of Fig. 2 gives a After this early stage, A development may blowup of the right half of the A map, designed proceed along the productive (or lytic) pathway to focus on the activity sites for the develop- or along the alternative lysogenic pathway. The mental events noted in the preceding section. encapsulation-oriented late stage of the produc- To construct Fig. 2, we used three principal tive pathway involves a transcription switch to types of information: (i) "traditional" genetic synthesis of head, tail, and lysis proteins and a mapping; (ii) physical mapping by heteroduplex replication switch to a rolling-circle mode that analysis of genetically characterized deletion generates multimeric A genomes (concatemers) mutations; and (iii) molecular weights of gene 577 578 ECHOLS AND MURIALDO MICROBIOL. REV. DNA encapsulation Phage Late proteins Monomer DNA on Injected DNA replicotion mm' Eor1yEorly~~~~~~~mm' f" proteinsEoff K> proteins o mmmiil ° C ) Lytic DNA integration Prophoge proteins mm o,f fI _110. bo' mm' oab' Integrotion on b bI FIG. 1. Developmental pathways for bacteriophage A. The injected DNA forms a covalently closed circle through pairing of the mature ends, m and mi', followed by ligation. After an early phase common to both pathways, viral development may follow the productive or lysogenic pathways. In the productive pathway, synthesis of encapsulation and lysis proteins is turned on, synthesis of early proteins is turned off, and replication switches to a rolling-circle mode that generates the multimeric DNA used as a substrate for encapsulation of linear DNA with free mature ends. In the lysogenic pathway, synthesis of lytic proteins is turned off, and the circular viral DNA is inserted into the host genome by a specific recombination event. GENETIC MAP Nu! P.u3 Ef Fl Fl z U V G rt L K i uooint xis redX redB gem i! ciiicralrox cro cl OP S R mAmtXW W-t;tX'lCO]D 4g4HS2 /aD?J 4+ 1~~~~'V ClII o$g lm 0 10 20 30 40 50 60 70 80 90 100 Phage heod Phoge tail Integration, Replication sis excision, and ReglatonRegulation Late recombination regulationlateo GENE ACTIVITY MAP Through heod and toil 00 PL CI PR CrO fg1 Cl 'np 0 or P fe2 P's int xis cmIII ILAN9 0 m 50 60 70 2 80 90 too Pt SOL! PM Pt FIG. 2. Genetic map of bacteriophage A. The genes that code forproteins of defined function are shown in the upper part of the figure; the vertical line marks the approximate center of the genes (see Table 1). The b region is silent in terms of defined viral functions, although it does code for several proteins (see text and Table 1). The regulatory sites and their function are indicated in the lower part of the figure; these are described in the text and in Table 1. The different stages of transcriptional activity and the DNA regions involved are indicated by the arrows; the actual length of DNA transcribed can be determined from the intersection of the promoter (p) and terminator (t) lines with the horizontal calibrated line representing the A genome. products. The principles (and examples) are examples of this type of overestimate exist (e.g., given in the articles by Campbell (20), Davidson the V protein has an electrophoretic estimate of and Szybalski (38), and Szybalski and Szybalski 32,000 daltons, but a calculated value from (211). The functions of the genes and sites are amino acid composition of 26,000 daltons). summarized with references in Table 1. Based on this assessment, we have reduced the Based on the physical mapping data of Par- size of some genes (3 to 10%) to conform to the kinson and Davis (156) and the estimated mo- physical map; these reduced values are used for lecular weights of the gene products (Table 1), the "Coordinates" column of Table 1. The mo- the head and tail region is "oversaturated" lecular weight values originally reported for the (codes for more amino acids than available nu- proteins are given in the "Gene function and/or cleotides). We believe that the discrepancy most protein activity" column. likely results from overestimates of protein size Most readers of this article are aware already by the standard method of polyacrylamide gel that A nomenclature has not evolved in a logi- electrophoresis in sodium dodecyl sulfate, rather cally consistent way. Genes for proteins essential than from overlapping genes, because several to productive growth were originally given up- VOL. 42, 1978 GENETIC MAP OF PHAGE LAMBDA 579 TABLE 1. Genes ofphage A and their function co- Gene symbol Approxordinatesamap Gene function and/or protein activity Referencesb m 0 Left cohesive end of the mature DNA mol- 13,31,38,57,60,61,69,87,146, ecule; the first 12 nucleotides of the 5' 147, 151, 206, 218, 228, 229, end of the I (transcribed leftward) strand 237,238 protrude as a single-stranded chain, complementary to m'. Nul 0/0.5 Involved in DNA packaging and cohesive 8, 145, D end formation; may activate A protein. A 0.5/4.7 DNA packaging into proheads and forma- 5-7, 19, 67,90, 96, 103, 109-111, tion of cohesive ends; protein is 79,000 132, 139, 144, 145, 155, 197, daltons (79K). 204, 206, 210, 226, 229, 231 w 4.7/5.0 Modifies DNA-filled heads in an unknown 28, 93, 132, 155, 205, 226 way to allow FII action; protein is 5-10K. B 5.0/8.3 Structural component of the capsid; B pro- 7, 19, 67, 85, 86, 91, 120, 139, tein and a cleaved derivative B form 140, 141, 142, 145, 155, 169, the head-tail connector-, B is 59-62K; B" 204, 223, 231, 242 is 53-56K. C 8.3/11.3 Structural component of capsid; the 7, 19, 67, 84-86, 91, 120, 139, 56-61K C protein is present in the capsid 140, 141, 142, 144, 145, 155, as two cleaved derivatives, fused to a 169, 204, 223, 231, 242 cleaved derivative of E; the two cleav- age-fusion products, termed Xl and X2, are 29 and 27K, respectively.