Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages

HK620 is a temperate lambdoid bacteriophage that adsorbs to the O-antigen o f its host, Escherichia coli H. The genome of a temperature-sensitive clear -plaque mutant consists of 38,297 nucleotides in which we recognize 60 open reading frames (orfs). Eighteen of these lie in a region of the genome tha t we call the virion structure domain. The other 42 orfs lie in what we cal l the metabolic domain. Virions of HK620 resemble those of phage P22. The virion structural orfs en code three kinds of putative proteins relative to the virion proteins of P2 2: (1) those that are nearly (about 90%) identical; (2) those that are weak ly (about 30%) identical; and (3) those composed of nearly and weakly ident ical segments. We hypothesize that these composite proteins form bridges be tween the virion proteins of the other two kinds. Three of the putative virion proteins that are only weakly identical to P22 proteins are 71, 60 and 79% identical to proteins encoded by the phage APS E-1, whose virions also resemble those of P22. Because the hosts of APSE-1 and HK620 have been separated from each other by an estimated 200 My, we pr opose using the amino acid differences that have accumulated in these prote ins to estimate a biological clock for temperate lambdoid phages. The putative transcriptional regulatory gene circuitry of HK620 seems to re semble that of phage lambda. Integration, on the other hand, resembles that of satellite phage P4 in that the attP sequence lies between the leftward promoter and int rather than downstream of int. Comparing the metabolic domains of several lambdoid phage genomes reveals s even short conserved sequences roughly defining boundaries of functional mo dules. We propose that these boundary sequences are foci of genetic recombi nation that serve to assort the modules and make the metabolic domain highl y mosaic genetically. (C) 2001 Academic Press.