1022-7954/05/4104- © 2005 Pleiades Publishing, Inc. 0356 Russian Journal of Genetics, Vol. 41, No. 4, 2005, pp. 356–365. Translated from Genetika, Vol. 41, No. 4, 2005, pp. 455–465. Original Russian Text Copyright © 2005 by Krylov, Pleteneva, Lavigne, Hertveldt, Volckaert, Sernova, Georgopoulos, Korchevskii, Kurochkina, Mesyanzhinov. INTRODUCTION Many genes with unknown functions are contained in the genomes of large DNA bacteriophages such as T4 of Escherichia coli [1] or ϕKZ of Pseudomonas aeruginosa [2]. It is rather difficult to elucidate whether these genes are essential, or represent genetic noise, or are nonfunctional genes captured as a result of gene exchange with unrelated organisms (including eukary- otes), or are waste genes that have lost their original function as a result of mutation accumulation. To establish whether the function of a particular gene is essential for a given organism (i.e., the gene is a component of the minimal genome), it is possible to compare gene products of phylogenetically related organisms. A convenient model for such analysis is pro- vided by ϕKZ [2–9] and EL [10], P. aeruginosa giant ϕKZ-like phages of the family Myoviridae that lack appreciable DNA homology. Phages EL and ϕKZ are similar in several phenotypic characters (the size and morphology of phage particles and the developmental strategy allowing a high phage yield). Comparison of gene products for these phages has revealed conserved genes representing the minimal genome of the given phage group. Infection with P. aeruginosa develops in some immunosuppressive patients. Phages of the ϕKZ family have been used as components of therapeutic formula- tions for a long time [11–13], because many of them infect P. aeruginosa strains resistant to other phages [14] as well as some Burkhodleria cepacia strains (our observations). The intracellular development of numer- ous ϕKZ-like phages often takes place in the presence of P. aeruginosa plasmids that suppress the growth of phages of other species [15]. MATERIALS AND METHODS Bacteriophages. We compared the genomes of bac- teriophages ϕKZ and EL, which were described earlier [9, 10]. These phages are distinguished for the large sizes of their particles and DNAs (the ϕKZ genome packed in the head is 280 334 bp and harbors 306 open reading frames (ORFs)), accumulation to considerable Comparison of the Genome for Phylogenetically Related Bacteriophages jKZ and EL of Pseudomonas aeruginosa: Evolutionary Aspects and Minimal Genome Size V. N. Krylov 1 , E. A. Pleteneva 1 , R. Lavigne 2 , K. Hertveldt 2 , G. Volckaert 2 , N. V. Sernova 3, 4 , C. Georgopoulos 3 , R. V. Korchevskii 4 , L. P. Kurochkina 4 , and V. V. Mesyanzhinov 4 1 State Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545 Russia; e-mail: krylov@genetika.ru 2 Laboratory of Gene Technology, Katholieke Universiteit Leuven, Leuven, B-3001 Belgium; e-mail: guido.volckaert@agr.kuleuven.ac.be 3 Department of Microbiology and Molecular Medicine, Centre Médical Universitaire, Universite Geneva, Geneva, Switzerland; e-mail: natalia.sernova@medecine.unige.ch 4 Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117991 Russia; e-mail: vvm@ibch.ru Received November 26, 2004 Abstract—Bacteriophages of the family Myoviridae represent one of the most widespread domains of the bio- sphere substantially affecting the ecological balance of microorganisms. Interestingly, sequence analysis of genomic DNAs of large bacteriophages revealed many genes coding for proteins with unknown functions. A new approach is proposed to improve the functional identification of genes. This approach is based on com- paring the genome sequence for phylogenetically and morphologically related phages showing no considerable homology at the level of genomic DNA. It is assumed that gene functions essential for the development of phages of a given family are conserved and that the corresponding genes code for similar orthologous proteins even when lacking sequence homology. The genome was sequenced and compared for two Pseudomonas aeruginosa giant bacteriophages, ϕKZ and EL, which belong to a group of ϕKZ-related phages. A substantial difference in genome organization was observed, suggesting specific features of phage evolution. In addition, the problem of the minimal genome of the superfamily is discussed on the basis of the difference in size and structure between the ϕKZ and EL genomes. THEORETICAL PAPERS AND REVIEWS