Genomic sequences of bacteriophages HK97 and HK022: Pervasive genetic mosaicism in the lambdoid bacteriophages

We report the complete genome DNA sequences of HK97 (39,732 bp) and HK022 ( 40,751 bp), double-stranded DNA bacteriophages of Escherichia coli and memb ers of the lambdoid or h-like group of phages. We provide a comparative ana lysis of these sequences with each other and with two previously determined lambdoid family genome sequences, those of E. coli phage lambda and Salmon ella typhimurium phage P22. The comparisons confirm that these phages are genetic mosaics, with mosaic segments separated by sharp transitions in the sequence. The mosaicism prov ides clear evidence that horizontal exchange of genetic material is a major component of evolution for these viruses. The data suggest a model for evo lution in which diversity is generated by a combination of illegitimate and homologous recombination and mutational drift, and selection for function produces a population in which most of the surviving mosaic boundaries are located at gene boundaries or, in some cases, at protein domain boundaries within genes. Comparisons of these genomes highlight a number of difference s that allow plausible inferences of specific evolutionary scenarios for so me parts of the genome. The comparative analysis also allows some inferences about function of gene s or other genetic elements. We give examples for the generalized recombina tion genes of HK97, HK022 and P22, and for a putative head-tail adaptor pro tein of HK97 and HK022. We also use the comparative approach to identify a new class of genetic elements, the morons, which consist of a protein-codin g region flanked by a putative sigma(70);promoter and a putative factor-ind ependent transcription terminator, all located between two genes that may b e adjacent in a different phage. We argue that morons are autonomous geneti c modules that are expressed from the repressed prophage. Sequence composit ion of the morons implies that they have entered the phages' genomes by hor izontal transfer in relatively recent evolutionary time. (C) 2000 Academic Press.