[Show abstract][Hide abstract] ABSTRACT: Study of two recently isolated giant bacteriophages Lu11 and OBP that are active on Pseudomonas putida var. Manila and Pseudomonas fluorescens, respectively, demonstrated their similarity in morphotype, genome size, and size of phage particles, with giant bacteriophages
of Pseudomonas aeruginosa assigned to the supergroup of ϕKZ-like phages of the family Myoviridae. This supergroup was designated in this manner according
to the best studied phage ϕKZ that belongs to the species of this group widely distributed in nature. Comparison of major
polypeptide sizes of mature particles suggests similarity of certain proteins in the phages examined. In OBP particles visualized
with an electron microscope, an “inner body” was detected, which points to specific DNA package intrinsic to phages of ϕKZ
group. In the meantime, phages Lu11 and OBP do not exhibit resemblance among themselves or with any of earlier described ϕKZ-like
phages in respect to detectable DNA homology. Note that phage Lu11 of P. putida var. Manila exhibits very slight homology with phage Lin68 of the family of P. aeruginosa ϕKZ-like phages detected only in blot hybridization. This suggests the possible involvement of these phages in interspecies
recombination (“gene shuffling”) between phages of various bacterial species. Results of partial sequencing of phage genomes
confirmed the phylogenetic relatedness of phage OBP to phages of the ϕKZ supergroup, whereas phage Lu11 most probably belongs
to a novel species that is not a member of supergroup ϕKZ composition. The results of the study are discussed in terms of
the evolution of these phages.
Russian Journal of Genetics 01/2006; 42(8):877-885. · 0.41 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: To study the genome diversity of bacteriophages from geographically distant natural populations, new giant KZ-like Pseudomonas aeruginosa phages isolated in two different regions were compared with earlier known phages of three species (KZ, Lin68, EL). A broad spectrum of lytic activity was demonstrated for all KZ-like phages. Phages of the KZ species proved to be common in natural populations of various regions, while EL- and Lin68-related phages were extremely rare. Most KZ-related phages had unique DNA restriction patterns, but the differences between these were only minor, and the genomes did not contain nonhomologous fragments. The spectrum of capsid polypeptides proved to be conserved in each species, and was proposed as a character necessary and sufficient for express classification of phages with an accuracy of species. Phages isolated in different geographical regions showed no substantial difference. Some phages only slightly differing in DNA restriction pattern from KZ may be used to study the origin of KZ genes coding for orthologs of proteins of unrelated species (other phages, pathogenic bacteria, eukaryotes).
Russian Journal of Genetics 01/2004; 40(4):363-368. · 0.41 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Recently we have accomplished the entire DNA sequence of bacteriophage phiKZ, a giant virus infecting Pseudomonas aeruginosa. The 280334-bp of phiKZ genome is a linear, circularly permutated and terminally redundant, AT-rich dsDNA molecule that contains no sites for NotI, PstI, SacI, SmaI, XhoI and XmaIII endonucleases. Limited homology to other bacteriophages on the DNA and protein levels indicated that phiKZ represents a distinct branch of the Myoviridae family. In this work, we analyzed a group of six P. aeruginosa phages (Lin68, Lin21, PTB80, NN, EL, and RU), which are morphologically similar to phiKZ, have similar genome size and low G+C content. All phages have a broad host range among P. aeruginosa strains, and they are resistant to the inhibitory action of many P. aeruginosa plasmids. The analysis of the genomic DNA by restriction enzymes and DNA-DNA hybridization shows that phages are representative of three phiKZ-like species: phiKZ-type (phiKZ, Lin21, NN and PTB80), EL-type (EL and RU) and Lin68 which has a shorter tail than other phages. Except for related phages EL and RU, all phiKZ-like phages have identical N-terminal amino acid sequences of the major capsid protein. Random genome sequencing shows that the EL and RU phages have no homology to the phiKZ-like phages on DNA level. We propose that the phiKZ, Lin21, NN, PTB80 and Lin68 phages can be included in a new phiKZ genus, and that the EL and RU phages belong to a separate genus within the Myoviridae family. Based on the resistance to many restriction enzymes and the transduction ability, there are indications that over the long pathway of evolution, the phiKZ-like phages probably inherited the capacity to infect different bacterial species.
Research in Microbiology 06/2003; 154(4):269-75. · 2.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Bacteriophage phiKZ is a giant virus that efficiently infects Pseudomonas aeruginosa strains pathogenic to human and, therefore, it is attractive for phage therapy. We present here the complete phiKZ genome sequence and a preliminary analysis of its genome structure. The 280,334 bp genome is a linear, circularly permutated and terminally redundant, A+T-rich double-stranded DNA molecule. The phiKZ DNA has no detectable sequence homology to other viruses and microorganisms, and it does not contain NotI, PstI, SacI, SmaI, XhoI, and XmaIII endonuclease restriction sites. The genome has 306 open reading frames (ORFs) varying in size from 50 to 2237 amino acid residues. According to the orientation of transcription, ORFs are apparently organized into clusters and most have a clockwise direction. The phiKZ genome also encodes six tRNAs specific for Met (AUG), Asn (AAC), Asp (GAC), Leu (TTA), Thr (ACA), and Pro (CCA). A putative promoter sequence containing a TATATTAC block was identified. Most potential stem-loop transcription terminators contain the tetranucleotide UUCG loops. Some genes may be assigned as phage-encoded RNA polymerase subunits. Only 59 phiKZ gene products exhibit similarity to proteins of known function from a diversity of organisms. Most of these conserved gene products, such as dihydrofolate reductase, ribonucleoside diphosphate reductase, thymidylate synthase, thymidylate kinase, and deoxycytidine triphosphate deaminase are involved in nucleotide metabolism. However, no virus-encoded DNA polymerase, DNA replication-associated proteins, or single-stranded DNA-binding protein were found based on amino acid homology, and they may therefore be strongly divergent from known homologous proteins. Fifteen phiKZ gene products show homology to proteins of pathogenic organisms, including Mycobacterium tuberculosis, Haemophilus influenzae, Listeria sp., Rickettsia prowazakeri, and Vibrio cholerae that must be considered before using this phage as a therapeutic agent. The phiKZ coat contains at least 40 polypeptides, and several proteins are cleaved during virus assembly in a way similar to phage T4. Eleven phiKZ-encoded polypeptides are related to proteins of other bacteriphages that infect a variety of hosts. Among these are four gene products that contain a putative intron-encoded endonuclease harboring the H-N-H motif common to many double-stranded DNA phages. These observations provide evidence that phages infecting diverse hosts have had access to a common genetic pool. However, limited homology on the DNA and protein levels indicates that bacteriophage phiKZ represents an evolutionary distinctive branch of the Myoviridae family.
Journal of Molecular Biology 04/2002; 317(1):1-19. · 3.96 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The article continues a study of pseudolysogeny in Pseudominas aeruginosa infected with phiKZ-like phages of the EL species. Analysis was performed for several newly isolated vir mutants of EL phages
(EL and RU) that were virulent (capable of causing lysis of bacteria infected with the wild-type phage) and a lower extent
of opalescence of negative colonies (NCs). Wile-type recombinants were detected in crosses of virulent mutants of phages EL
and RU to confirm the polygenic control of virulence. Since a deletion mutation was found in one of the virulent EL mutants
and high genetic instability was characteristic of another mutant, a mobile genetic element was assumed to play a role in
mutagenesis. Pseudolysogeny of bacteria provides for horizontal gene transfer between different bacterial strains. Hence,
sequencing of the phage genome and demonstration of the lack of toxic gene products are insufficient for the phage to be included
into a therapeutic mixture. To use live phages, it is essential to study in detail the possible consequences of their interaction
with host bacteria.
Russian Journal of Genetics 47(2):162-167. · 0.41 Impact Factor