Pseudomonas Phage MD8: Genetic Mosaicism and Challenges of Taxonomic Classification of Lambdoid Bacteriophages.

Pseudomonas phage MD8 is a temperate phage isolated from the freshwater lake Baikal. The organisation of the MD8 genome resembles the genomes of lambdoid bacteriophages. However, MD8 gene and protein sequences have little in common with classified representatives of lambda-like phages. Analysis of phage genomes revealed a group of other Pseudomonas phages related to phage MD8 and the genomic layout of MD8-like phages indicated extensive gene exchange involving even the most conservative proteins and leading to a high degree of genomic mosaicism. Multiple horizontal transfers and mosaicism of the genome of MD8, related phages and other λ-like phages raise questions about the principles of taxonomic classification of the representatives of this voluminous phage group. Comparison and analysis of various bioinformatic approaches applied to λ-like phage genomes demonstrated different efficiency and contradictory results in the estimation of genomic similarity and relatedness. However, we were able to make suggestions for the possible origin of the MD8 genome and the basic principles for the taxonomic classification of lambdoid phages. The group comprising 26 MD8-related phages was proposed to classify as two close genera belonging to a big family of λ-like phages.

Taxonomic parsing of bacteriophages using core genes and in silico proteome-based CGUG and applications to small bacterial genomes.

A combined genomics and in situ proteomics approach can be used to determine and classify the relatedness of organisms. The common set of proteins shared within a group of genomes is encoded by the "core" set of genes, which is increasingly recognized as a metric for parsing viral and bacterial species. These can be described by the concept of a "pan-genome", which consists of this "core" set and a "dispensable" set, i.e., genes found in one or more but not all organisms in the grouping. "CoreGenesUniqueGenes" (CGUG) is a web-based tool that determines this core set of proteins in a set of genomes as well as parses the dispensable set of unique proteins in a pair of viral or small bacterial genomes. This proteome-based methodology is validated using bacteriophages, aiding the reevaluation of current classifications of bacteriophages. The utility of CGUG in the analysis of small bacterial genomes and the annotation of hypothetical proteins is also presented.

Conservation and diversity in the immunity regions of wild phages with the immunity specificity of phage lambda.

The gene regulatory circuitry of phage lambda is among the best-understood circuits. Much of the circuitry centres around the immunity region, which includes genes for two repressors, CI and Cro, and their cis-acting sites. Related phages, termed lambdoid phages, have different immunity regions, but similar regulatory circuitry and genome organization to that of lambda, and show a mosaic organization, arising by recombination between lambdoid phages. We sequenced the immunity regions of several wild phages with the immunity specificity of lambda, both to determine whether natural variation exists in regulation, and to analyse conservation and variability in a region rich in well-studied regulatory elements. CI, Cro and their cis-acting sites are almost identical to those in lambda, implying that regulatory mechanisms controlled by the immunity region are conserved. A segment adjacent to one of the operator regions is also conserved, and may be a novel regulatory element. In most isolates, different alleles of two regulatory proteins (N and CII) flank the immunity region; possibly the lysis-lysogeny decision is more variable among isolates. Extensive mosaicism was observed for several elements flanking the immunity region. Very short sequence elements or microhomologies were also identified. Our findings suggest mechanisms by which fine-scale mosaicism arises.

Genomic structure of the Salmonella enterica serovar Typhimurium DT 64 bacteriophage ST64T: evidence for modular genetic architecture.

The complete sequence of the double-stranded DNA genome of a serotype-converting temperate bacteriophage, ST64T, was determined. The 40,679-bp genomic sequence of ST64T has an overall GC content of 47.5% and was reminiscent of a number of lambdoid phages, in particular, P22. Inferred proteins of ST64T which exhibited a high degree of sequence similarity to P22 proteins (>90%) included the functional serotype conversion cassette, integrase, excisionase, Abc1, Abc2, early antitermination (gp24), NinD, NinH, NinZ, packaging (gp3 and gp2), head (with the exception of gp26, gp7, gp20, and gp16), and tail proteins. The putative immunity genes were highly related to those of Salmonella enterica serotype Typhimurium phage L, whereas the lysis genes were almost identical to those of S. enterica serovar Typhimurium PS3.

[Attenuation of bacteriophage phi80 repression]. / Oslablenie repressii bakteriofaga phi80.

Data are obtained suggesting the involvement of the cor gene of the [symbol: see text] 80 phage in regulation of phage operons. Mutations in the cor gene, which is located outside the region of phage [symbol: see text] 80 immunity, cause disturbances in the establishment and maintenance of the phage lysogenic state. The cor gene was shown to affect RecA-inactivation of the phage repressor induced by UV-irradiation. A model suggesting cor gene involvement in [symbol: see text] 80 operon regulation is discussed.

A generalized transducing bacteriophage for Serratia marcescens.

Using Serratia marcescens 2170 harbouring plasmid pTroy11 (encoding for LamB), and lambda (lambda:: Tn5) we constructed a collection of 25 auxotrophic mutations induced by Tn5 insertions. These mutants permitted the use an easy screening method for generalized transducing bacteriophages. Out of twelve bacteriophages isolated from natural sources only one (phage 3M) was able to transduce all Tn5 insertions tested. The preliminary characterization of bacteriophage 3M indicates that it belongs to the Myoviridae family.

Restriction fragment analysis for differentiation of indistinguishable temperate coliphages.

DNA of lambda and seven related phages was digested with restriction endonuclease, EcoRI. Seven different fragment patterns were observed, only two of the eight phages showing identical profiles. Restriction enzyme fragment analysis is thus shown to be a sensitive tool for the differentiation of biologically indistinguishable phages.

Temperate coliphages: classification and correlation with habitats.

Temperate coliphages were recovered from sewage, mammalian feces, and lysogenic strains of Escherichia coli. A total of 32 phages of independent origin were divided into six groups by applying the criteria of host range, antigenic homology, and the ultraviolet inducibility of the prophage. The demonstration of genetic interactions in some cases has confirmed the classification scheme. Nine phages were assigned to the P2 family and 19 to the lambda family. The remaining four isolates may represent some novel phylogenetic types. Phages recovered from the lysogenic strains of E. coli were all found to be P2 related, whereas a majority of the phages recovered as cell-free plaque-forming units were assignable to the lambda family. It is proposed that the biological attributes of the phages belonging to the two principal families are reflected in the distribution patterns observed. The virions of phage HK256 show multiple tail fibers and may thus represent a "new" virion form among the temperate coliphages.