Comparative Genomics of the Late Gene Cluster from Lactobacillus Phages

Desiere, Frank; Pridmore, R. David; Brüssow, Harald

doi:10.1006/viro.2000.0498

Cited by 50 publications

(37 citation statements)

References 37 publications

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“…The 2-Mb chromosome of the gut commensal Lactobacillus johnsonii NCC 533 (Nestlé) contained two prophages showing the genome organization of Sfi11-like pac-site Siphoviridae (54). The lysogeny module of these prophages contained more genes than are commonly found in temperate phages of LAB (128).…”

Section: Lactobacillusmentioning

confidence: 99%

“…Comprehensive research was conducted on two virulent phages of the soil bacterium Bacillus subtilis: phi29, a podovirus, and SPP1, despite its life-style a typical Sfi11-like siphovirus (54) and by far the best-characterized phage of this proposed phage genus (see references 6 and 130 for recent examples and references therein). Much less is known about temperate B. subtilis phages, which have been classified into five groups (231).…”

Section: Bacillusmentioning

confidence: 99%

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Prophage Genomics

Canchaya

Proux

Fournous

et al. 2003

Microbiol Mol Biol Rev

637

621

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The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria

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Section: Lactobacillusmentioning

confidence: 99%

Section: Bacillusmentioning

confidence: 99%

Prophage Genomics

Canchaya

Proux

Fournous

et al. 2003

Microbiol Mol Biol Rev

637

621

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“…Until now only a single Sfi21-like phage was identified in the genus Lactobacillus. L. gasseri phage adh shared deduced amino acid sequence identity up to 61% with phage Sfi21 over the DNA packaging, head, tail, lysogeny, and DNA replication modules (22). The identical organization of the replication and lysogeny modules from L. casei phage A2 and phage Sfi21 (19,28,40,46) suggested that phage A2 is a further member of this group.…”

Section: Resultsmentioning

confidence: 98%

“…An intriguing observation was the fact that distinct Sfi21-like phage isolates were linked by a hierarchy of relatedness when S. thermophilus phages were used as a reference point (11). Sfi21-like phages from S. thermophilus were closely related at the DNA level essentially over the entire genome length (11); those from S. thermophilus and L. lactis shared a smaller degree of DNA identity limited to part of the structural genes (20); S. thermophilus and Lactobacillus gasseri Sfi21-like phages were related by a relatively high level of protein similarity over the structural genes, but significant DNA sequence homology was no longer detected (22). Notably, even Escherichia coli phage HK97 shared a functional gene map with Sfi21-like S. thermophilus phages over the structural genes in the absence of any sequence similarity (11).…”

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confidence: 99%

The Dilemma of Phage Taxonomy Illustrated by Comparative Genomics of Sfi21-LikeSiphoviridaein Lactic Acid Bacteria

et al. 2002

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The complete genome sequences of two dairy phages, Streptococcus thermophilus phage 7201 and Lactobacillus casei phage A2, are reported. Comparative genomics reveals that both phages are members of the recently proposed Sfi21-like genus of Siphoviridae, a widely distributed phage type in low-GC-content gram-positive bacteria. Graded relatedness, the hallmark of evolving biological systems, was observed when different Sfi21-like phages were compared. Across the structural module, the graded relatedness was represented by a high level of DNA sequence similarity or protein sequence similarity, or a shared gene map in the absence of sequence relatedness. This varying range of relatedness was found within Sfi21-like phages from a single species as demonstrated by the different prophages harbored by Lactococcus lactis strain IL1403. A systematic dot plot analysis with 11 complete L. lactis phage genome sequences revealed a clear separation of all temperate phages from two classes of virulent phages. The temperate lactococcal phages share DNA sequence homology in a patchwise fashion over the nonstructural gene cluster. With respect to structural genes, four DNA homology groups could be defined within temperate L. lactis phages. Closely related structural modules for all four DNA homology groups were detected in phages from Streptococcus or Listeria, suggesting that they represent distinct evolutionary lineages that have not uniquely evolved in L. lactis. It seems reasonable to base phage taxonomy on data from comparative genomics. However, the peculiar modular nature of phage evolution creates ambiguities in the definition of phage taxa by comparative genomics. For example, depending on the module on which the classification is based, temperate lactococcal phages can be classified as a single phage species, as four distinct phage species, or as two if not three different phage genera. We propose to base phage taxonomy on comparative genomics of a single structural gene module (head or tail genes). This partially phylogeny-based taxonomical system still mirrors some aspects of the current International Committee on Taxonomy in Virology classification system. In this system the currently sequenced lactococcal phages would be grouped into five genera: c2-, sk1, Sfi11-, r1t-, and Sfi21-like phages.Due to their economic impact on industrial milk fermentation, bacteriophages attacking dairy starter bacteria (Streptococcus thermophilus, Lactococcus lactis, and various species of Lactobacillus) became the focus of substantial research efforts which made them the best-investigated phage group with respect to complete genome sequences (10). Dairy phages are therefore a suitable test case for hypotheses on phage evolution and for a genomics-based phage taxonomy. The comparative analysis of S. thermophilus phage genomes has revealed a rather homogeneous group of phages with substantial DNA sequence sharing between all investigated temperate and virulent phage isolates (11). On the basis of the DNA packaging mechanisms two groups m...

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“…The location of transglycosylase motifs are indicated by the grey boxes. gpR1608 in phi g1e, a minor structural protein , is probably a tail tape measure protein (Desiere et al, 2000) and misannotated as a capsid protein.…”

Section: Morphogenesismentioning

confidence: 99%

Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are bIL170, AF009630; bIL120, AY054975; bIL15, AY054976; bIL191, AY054977; bIL77, AY054978.

et al. 2002

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The complete 31 754 bp genome of bIL170, a virulent bacteriophage of Lactococcus lactis belonging to the 936 group, was analysed. Sixty-four ORFs were predicted and the function of 16 of them was assigned by significant homology to proteins in databases. Three putative homing endonucleases of the HNH family were found in the early region. An HNH endonuclease with zinc-binding motif was identified in the late cluster, potentially being part of the same functional module as terminase. Three putative structural proteins were analysed in detail and show interesting features among dairy phages. Notably, gpl12 (putative fibre) and gpl20 (putative baseplate protein) of bIL170 are related by at least one of their domains to a number of multidomain proteins encoded by lactococcal or streptococcal phages. A 110-to 150-aa-long hypervariable domain flanked by two conserved motifs of about 20 aa was identified. The analysis presented here supports the participation of some of these proteins in host-range determination and suggests that specific adsorption to the host may involve a complex multi-component system. Divergences in the genome of phages of the 936 group, that may have important biological properties, were noted. Insertions/deletions of units of one or two ORFs were the main source of divergence in the early clusters of the two entirely sequenced phages, bIL170 and sk1. An exchange of fragments probably affected the regions containing the putative origin of replication. It led to the absence in bIL170 of the direct repeats recognized in sk1 and to the presence of different ORFs in the ori region. Shuffling of protein domains affected the endolysin (putative cell-wall binding part), as well as gpl12 and gpl20.

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Comparative Genomics of the Late Gene Cluster from Lactobacillus Phages

Cited by 50 publications

References 37 publications

Prophage Genomics

Prophage Genomics

The Dilemma of Phage Taxonomy Illustrated by Comparative Genomics of Sfi21-LikeSiphoviridaein Lactic Acid Bacteria

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