Complete genome sequence of the Lactococcus lactis temperate phage φLC3: comparative analysis of φLC3 and its relatives in lactococci and streptococci

Blatny, Janet Martha; Godager, Linda H.; Lunde, Merete; Nes, Ingolf F.

doi:10.1016/j.virol.2003.09.019

Cited by 29 publications

(25 citation statements)

References 52 publications

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“…The lower disk protein, ORF49, is the most unique protein of the TP901-1 tail module, since it displays full-length similarity to only a single protein encoded by phage LC3 (Table 3). Because TP901-1 and LC3 have overlapping host ranges (they both infect the L. lactis strains 3107 and Wg2 [4,15]), this suggests that the baseplate is a host interaction element and that the lower disk protein, ORF49, is responsible for host receptor recognition. In an effort to prove this thesis experimentally, further studies of ORF49 and TP901-1 host interaction are in progress.…”

Section: Discussionmentioning

confidence: 99%

Structural Characterization and Assembly of the Distal Tail Structure of the Temperate Lactococcal Bacteriophage TP901-1

Vegge

Brøndsted

Neve³

et al. 2005

J Bacteriol

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The tail structures of bacteriophages infecting gram-positive bacteria are largely unexplored, although the phage tail mediates the initial interaction with the host cell. The temperate Lactococcus lactis phage TP901-1 of the Siphoviridae family has a long noncontractile tail with a distal baseplate. In the present study, we investigated the distal tail structures and tail assembly of phage TP901-1 by introducing nonsense mutations into the late transcribed genes dit (orf46), tal TP901-1 (orf47), bppU (orf48), bppL (orf49), and orf50. Transmission electron microscopy examination of mutant and wild-type TP901-1 phages showed that the baseplate consisted of two different disks and that a central tail fiber is protruding below the baseplate. Evaluation of the mutant tail morphologies with protein profiles and Western blots revealed that the upper and lower baseplate disks consist of the proteins BppU and BppL, respectively. Likewise, Dit and Tal TP901-1 were shown to be structural tail proteins essential for tail formation, and Tal TP901-1 was furthermore identified as the tail fiber protein by immunogold labeling experiments. Determination of infection efficiencies of the mutant phages showed that the baseplate is fundamental for host infection and the lower disk protein, BppL, is suggested to interact with the host receptor. In contrast, ORF50 was found to be nonessential for tail assembly and host infection. A model for TP901-1 tail assembly, in which the function of eight specific proteins is considered, is presented.

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Section: Discussionmentioning

confidence: 99%

Structural Characterization and Assembly of the Distal Tail Structure of the Temperate Lactococcal Bacteriophage TP901-1

Vegge

Brøndsted

Neve³

et al. 2005

J Bacteriol

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“…Thus, the strain rotation practice in dairy fermentation is very likely a factor that stimulates LAB phage evolution by horizontal gene transfer, plausibly contributing to the observed genetic mosaicism (2,6,10,11,33,37). With respect to managing the risks of phage-mediated fermentation failure in dairy industry, our work suggests that an undesirable long-term outcome of the strain rotation practice may actually be the appearance of highly promiscuous hybrid "super-phages" with an expanded host range, a phenomenon encountered in the industry (20,29,43 …”

Section: Discussionmentioning

confidence: 99%

“…The most frequently encountered are two groups of small isometric-headed phages named 936 and P335 and one group with prolate-headed phage named c2 (28,38). Recent largescale sequence analyses of bacteriophages of LAB indicate that exchange of functional modules by recombination is widespread among these phages (2,6,10,11,33,37).…”

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confidence: 99%

Isolation of Lactococcal Prolate Phage-Phage Recombinants by an Enrichment Strategy Reveals Two Novel Host Range Determinants

2005

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Virulent lactococcal prolate (or c2-like) phages are the second most common phage group that causes fermentation failure in the dairy industry. We have mapped two host range determinants in two lactococcal prolate phages, c2 and 923, for the host strains MG1363 and 112. Each phage replicates on only one of the two host strains: c2 on MG1363 and 923 on 112. Phage-phage recombinants that replicated on both strains were isolated by a new method that does not require direct selection but rather employs an enrichment protocol. After initial mixed infection of strain 112, two rotations, the first of which was carried out on strain MG1363 and the second on 112, permitted continuous amplification of double-plating recombinants while rendering one of the parent phages unamplified in each of the two rotations. Mapping of the recombination endpoints showed that the presence of the N-terminal two-thirds of the tail protein L10 of phage c2 and a 1,562-bp cosR-terminal fragment of phage 923 genome overcame blocks of infection in strains MG1363 and 112, respectively. Both infection inhibition mechanisms act at the stage of DNA entry; in strain MG1363, the infection block acts early, before phage DNA enters the cytoplasm, and in strain 112, it acts late, after most of the DNA has entered the cell but before it undergoes cos-end ligation. These are the first reported host range determinants in bacteriophage of lactic acid bacteria required for overcoming inhibition of infection at the stage of DNA entry and cos-end ligation.Acquisition and exchange of functional modules by recombination has been proposed as the major mechanism of viral evolution, based on analyses of arrangements of conserved and nonconserved segments along the genomes of lambdoid phage and functional analysis of the recombinants (hybrids) between distant members of the family comprising phage P22 of Salmonella enterica serovar Typhimurium and phage of Escherichia coli K12 (3, 5, 22, 23, 55). The selective pressure for generating phage-phage recombinants in nature is most likely the ability to replicate on an increased number of hosts.Bacteriophages of Lactococcus lactis, a lactic acid bacterium (LAB) used in dairy fermentation, are numerous and diverse. The most frequently encountered are two groups of small isometric-headed phages named 936 and P335 and one group with prolate-headed phage named c2 (28, 38). Recent largescale sequence analyses of bacteriophages of LAB indicate that exchange of functional modules by recombination is widespread among these phages (2, 6, 10, 11, 33, 37).Prolate-headed (or prolate) phages are the secondmost common group isolated after fermentation failure in New Zealand dairy plants. This is a relatively conserved group with an exclusively lytic life style. The two prolate phages (c2 and bIL67) whose genome sequences have been determined to date have an overall identity of 80% (36,54). Both 20-to 22-kbp double-stranded DNA (dsDNA) genomes code for two blocks of divergently oriented open reading frames (ORFs), transcribed early and ...

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“…Among the available genomes, only members of the three main groups of L. lactis phages are represented, namely, the 936, c2, and P335 species. Ten of the genomes are from phages of the P335 species (4,9,15,40,50,68,74,75), whereas only four sequences are from 936-and c2-like phages, namely, bIL170 and sk1 (936 species) as well as c2 and bIL67 (c2 species) (12,18,48,67). The lack of genome sequences from the less frequently isolated phage species is probably explained by the higher industrial incidences of failed fermentations due to the members of the three above predominant species (37, 39).…”

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confidence: 99%

“…On the other hand, the P335 group of phages, comprising both temperate and lytic members, is less conserved and has a polythetic nature. Indeed, several P335-like phages share conserved modules, but there is no single ORF shared by all members of this group (4,9,15,23,24,40). Comparative genomics of these P335-like phages thus revealed a highly mosaic structure, defining functional modules that are exchangeable through homologous recombination, in addition to point mutations and indels (15,23,57).…”

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confidence: 99%

Genome Sequence and Global Gene Expression of Q54, a New Phage Species Linking the 936 and c2 Phage Species ofLactococcus lactis

2006

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The lytic lactococcal phage Q54 was previously isolated from a failed sour cream production. Its complete genomic sequence (26,537 bp) is reported here, and the analysis indicated that it represents a new Lactococcus lactis phage species. A striking feature of phage Q54 is the low level of similarity of its proteome (47 open reading frames) with proteins in databases. A global gene expression study confirmed the presence of two early gene modules in Q54. The unusual configuration of these modules, combined with results of comparative analysis with other lactococcal phage genomes, suggests that one of these modules was acquired through recombination events between c2-and 936-like phages. Proteolytic cleavage and cross-linking of the major capsid protein were demonstrated through structural protein analyses. A programmed translational frameshift between the major tail protein (MTP) and the receptor-binding protein (RBP) was also discovered. A "shifty stop" signal followed by putative secondary structures is likely involved in frameshifting. To our knowledge, this is only the second report of translational frameshifting (؉1) in double-stranded DNA bacteriophages and the first case of translational coupling between an MTP and an RBP. Thus, phage Q54 represents a fascinating member of a new species with unusual characteristics that brings new insights into lactococcal phage evolution.Lactococcus lactis is a low-GϩC gram-positive bacterium extensively used by the dairy industry for its ability to convert sugars into lactic acid, leading to various fermented milk products. However, L. lactis strains are susceptible to attacks by lytic bacteriophages with concomitant low-quality products and economic losses (56). Different strategies have been developed over the past 70 years with the aim of better controlling the indigenous phage population within the dairy environment (54, 71). Nevertheless, the phage population is constantly evolving and new phage isolates are still frequently isolated. Some of these phages are emerging due to current manufacturing practices (49).Classification of the phages is still controversial, and different propositions have been made in recent years (10,65,74). Previous classification studies relied on the comparison of virus morphology and DNA-DNA hybridizations using whole genomes. According to these criteria, 12 lactococcal phage species representing distinct phage groups were proposed (37, 38). This classification of lactococcal phages was recently revisited, and 10 genetically diverse groups of phages, sharing very limited nucleotide similarities, were proposed (26). Among these, two new species were identified, one of which was the type phage Q54.Phage genomics has considerably expanded in the last 5 years, and as of June 2006, 362 complete genomes are available at GenBank. Of those, 14 are from lactococcal phages. Among the available genomes, only members of the three main groups of L. lactis phages are represented, namely, the 936, c2, and P335 species. Ten of the genomes are from phage...

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Complete genome sequence of the Lactococcus lactis temperate phage φLC3: comparative analysis of φLC3 and its relatives in lactococci and streptococci

Cited by 29 publications

References 52 publications

Structural Characterization and Assembly of the Distal Tail Structure of the Temperate Lactococcal Bacteriophage TP901-1

Structural Characterization and Assembly of the Distal Tail Structure of the Temperate Lactococcal Bacteriophage TP901-1

Isolation of Lactococcal Prolate Phage-Phage Recombinants by an Enrichment Strategy Reveals Two Novel Host Range Determinants

Genome Sequence and Global Gene Expression of Q54, a New Phage Species Linking the 936 and c2 Phage Species ofLactococcus lactis

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