Characterization and genomic analysis of phage asccphi28, a phage of the family Podoviridae infecting Lactococcus lactis
| Autor: | Gaëtan K. Y. Limsowtin, Barrie E. Davidson, Steven Kotsonis, Ian B. Powell, Christopher J. Pillidge, Alan J. Hillier |
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| Rok vydání: | 2008 |
| Předmět: |
Streptococcus Phages
Genes Viral viruses Molecular Sequence Data Genetics and Molecular Biology Bacillus Phages DNA-Directed DNA Polymerase Genome Viral Viral Plaque Assay Biology Applied Microbiology and Biotechnology Genome Synteny DNA sequencing Microbiology Bacteriophage Siphoviridae Podoviridae Open Reading Frames Viral Proteins Microscopy Electron Transmission Gene Order Phage typing Genetics Ecology Sequence Homology Amino Acid Lactococcus lactis Terminal Repeat Sequences Virion Sequence Analysis DNA biology.organism_classification DNA-Binding Proteins Lytic cycle DNA Viral Electrophoresis Polyacrylamide Gel Food Science Biotechnology |
| Zdroj: | Applied and environmental microbiology. 74(11) |
| ISSN: | 1098-5336 |
| Popis: | Bacteriophage infection of Lactococcus lactis starter cultures used in cheese making and in other dairy fermentations affects product quality and can result in fermentation failure. Because of these worldwide industrial and financial consequences, phages infecting L. lactis are among the best-studied and most commonly isolated phages infecting any bacterial species (1, 6, 9, 20). As occurs with several well-studied bacterial species (such as Escherichia coli and Bacillus subtilis), a diverse range of phage types has been found to infect L. lactis. Taxonomic classification of lactococcal phages continues to be an area of debate. All L. lactis phages documented so far are double-stranded DNA phages, and the vast majority have a Siphoviridae morphotype (long noncontractile tail, Bradley morphotypes B1 and B2). Using mainly morphology and DNA-DNA hybridization data, Jarvis et al. (20) divided these phages into 11 or 12 species. The status of the T187 group of phages was doubtful because of DNA homology between it and phage BK5-T (34). Later, Proux et al. (33) reported recognizable modular similarities among phages infecting a range of gram-positive bacteria and proposed five genera of lactococcal phages in a phage classification scheme (not confined to lactococcal phages) partially based on the phylogeny of phage genome modules deduced from DNA sequence comparisons. However, this scheme included only phage types for which whole-genome sequence data were available. No sequence information is available for some phage types, so they cannot yet be classified in this way. Moreover, some reported types (e.g., RZh and P107) are possibly extinct (9, 20), at least in the formal taxonomic sense that reference examples are no longer available. In the latest review of the biodiversity and classification of lactococcal phages, Deveau et al. (9) revised the species scheme proposed by Jarvis et al. (20) so that it included eight species, and they added two novel species belonging to the family Siphoviridae (1706 and Q54). The 936 (small isometric-headed) and c2 (prolate-headed) phage species each comprise only lytic phages. There is a high degree of genetic conservation within each of these two different species. By contrast, the P335 species, which contains both temperate and lytic phages, has greater genome diversity (9, 11, 28, 33). Based on an apparent high degree of genetic exchange between the formerly recognized 1483, T187, BK5-T, and P335 species, Deveau et al. (9) proposed merging these species into a revised P335 species. Recent DNA sequencing has confirmed that phages Q54 (11) and 1706 (14) are new phage species. Most L. lactis phages isolated from dairy fermentations belong to the 936 (most common), c2, or P335 species (9, 19, 20, 23, 31). It is no coincidence, therefore, that most publicly available L. lactis phage genome sequences belong to one of these species (9). The reported ratio of phage species isolated in the dairy industry varies, perhaps depending on the geographical region, the types of starter strains used (L. lactis subsp. lactis or L. lactis subsp. cremoris), and the criteria employed for strain selection. Distinct from these common phage types, one of the least-studied species is P034 (family Podoviridae, Bradley C2 morphotype), which is characterized by a prolate head and short tail with prominent whiskers emanating from the head-tail interface region. Historically, this species has comprised on average less than 1% of the phages isolated from dairy fermentations (1, 6). A “dot blot” DNA hybridization survey of Australian phage isolates using probes derived from reference phages detected only 3 P034 species phages, compared with 100 936 species phages, 34 P335 species phages (including the BK5-T and 1483 phage groups), and 13 c2 species phages. A further 49 phages were not classified unambiguously in that study (23). In this study, we describe phage asccφ28 and its complete genome sequence and present evidence showing that this phage has genetic and functional similarities to the φ29-like phages of B. subtilis (30) and phage Cp-1 of Streptococcus pneumoniae (29, 35). This is the first such analysis of an L. lactis phage belonging to the P034 species. In structure, genome sequence, and mode of replication this phage species is distinctly different from other phage species infecting L. lactis. |
| Databáze: | OpenAIRE |
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