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One of the most comprehensive reviews that covers essentially every enzyme involved in prokaryotic replication. A must-read for anyone in the field. A supplementary compendium of replication enzymes might be also very useful for reference.
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Weigel C., and Seitz H. Bacteriophage replication modules. FEMS Microbiol Rev 30 (2006) 321-381. One of the most comprehensive reviews that covers essentially every enzyme involved in prokaryotic replication. A must-read for anyone in the field. A supplementary compendium of replication enzymes might be also very useful for reference.
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To the best of our knowledge, this work shows the first examples of bacteriophage-encoded inhibitors of host replicase other than inhibitors of replication initiation. Based on this work, it is likely that additional phage-derived inhibitors will be identified and their cellular targets and mechanisms of action will be described. In addition, the work has practical application, suggesting strategies for designing antibacterial drugs.
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This outstanding paper not only demonstrates large-scale phage-induced genomic rearrangements in the host as a novel mechanism of dealing with virus threat, but also shows that such rearrangements can lead to phage resistance.
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Scott A.E., Timms A.R., Connerton P.L., Loc Carrillo C., Adzfa Radzum K., and Connerton I.F. Genome dynamics of Campylobacter jejuni in response to bacteriophage predation. PLoS Pathog 3 (2007) e119. This outstanding paper not only demonstrates large-scale phage-induced genomic rearrangements in the host as a novel mechanism of dealing with virus threat, but also shows that such rearrangements can lead to phage resistance.
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This work shows that bacteria could respond to phage threat by acquiring the mutator phenotype, which confers a competitive advantage to the host specifically in the presence of viral threat. Findings of this work provide an important clue as to why mutation rates that are too low might be deleterious to organisms, and highlight that the life span of a species might be determined by a fine compromise between fidelity of replication and survival in the presence of various threats.
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Pal C., Maciá M.D., Oliver A., Schachar I., and Buckling A. Coevolution with viruses drives the evolution of bacterial mutation rates. Nature 450 (2007) 1079-1081. This work shows that bacteria could respond to phage threat by acquiring the mutator phenotype, which confers a competitive advantage to the host specifically in the presence of viral threat. Findings of this work provide an important clue as to why mutation rates that are too low might be deleterious to organisms, and highlight that the life span of a species might be determined by a fine compromise between fidelity of replication and survival in the presence of various threats.
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Nature
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Pal, C.1
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This work proposes that carrying host metabolism genes might be beneficial to the phage, in that these genes might provide a metabolism boost to the host during phage infection. In a long run, these phage-borne host metabolism genes enjoy a faster rate of evolution, which might benefit the bacterial host as well. Thus, 'outsourcing' evolution of metabolism genes to the phage might be a novel aspect of phage-host relationship.
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Lindell D., Jaffe J.D., Coleman M.L., Futschik M.E., Axmann I.M., Rector T., Kettler G., Sullivan M.B., Steen R., Hess W.R., et al. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 449 (2007) 83-86. This work proposes that carrying host metabolism genes might be beneficial to the phage, in that these genes might provide a metabolism boost to the host during phage infection. In a long run, these phage-borne host metabolism genes enjoy a faster rate of evolution, which might benefit the bacterial host as well. Thus, 'outsourcing' evolution of metabolism genes to the phage might be a novel aspect of phage-host relationship.
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Nature
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This work suggests the existence of an evolutionary arms race between the phage and host. Resulting from this race, both sides accumulate elaborate DNA modifications and proprietary enzymes evolved to counteract these modifications, both of which are gratuitous in other environments. These increasingly elaborate but ultimately futile arms races might be general phenomena pertinent to co-evolution of binary systems.
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Bair C.L., Rifat D., and Black L.W. Exclusion of glucosyl-hydroxymethylcytosine DNA containing bacteriophages is overcome by the injected protein inhibitor IPI*. J Mol Biol 366 (2007) 779-789. This work suggests the existence of an evolutionary arms race between the phage and host. Resulting from this race, both sides accumulate elaborate DNA modifications and proprietary enzymes evolved to counteract these modifications, both of which are gratuitous in other environments. These increasingly elaborate but ultimately futile arms races might be general phenomena pertinent to co-evolution of binary systems.
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38949214103
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Diversity, activity and evolution of CRISPR loci in Streptococcus thermophilus
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This important work provides an essential confirmation that acquisition of foreign sequences by CRISPR loci is indeed a general phenomenon. This work reinforces the notion that CRISPR loci are part of the bacterial immune system.
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Horvath P., Romero D.A., Coûté-Monvoisin A.C., Richards M., Deveau H., Moineau S., Boyaval P., Fremaux C., and Barrangou R. Diversity, activity and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 190 (2008) 1401-1412. This important work provides an essential confirmation that acquisition of foreign sequences by CRISPR loci is indeed a general phenomenon. This work reinforces the notion that CRISPR loci are part of the bacterial immune system.
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(2008)
J Bacteriol
, vol.190
, pp. 1401-1412
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Horvath, P.1
Romero, D.A.2
Coûté-Monvoisin, A.C.3
Richards, M.4
Deveau, H.5
Moineau, S.6
Boyaval, P.7
Fremaux, C.8
Barrangou, R.9
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41
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38949123143
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Phage response to CRISPR-encoded resistance in Streptococcus thermophilus
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This important work provides experimental clues to the molecular mechanisms of CRISPR function. In particular, the work shows that generation of genetic 'memory' in Streptococcus thermophilus is accomplished by incorporating foreign sequence fragments into the existing CRISPR locus. The work also indicates that incorporation of these sequences might involve recognition of phage sequences immediately outside of the incorporated sequence.
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Deveau H., Barrangou R., Garneau J.E., Labonté J., Fremaux C., Boyaval P., Romero D.A., Horvath P., and Moineau S. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 190 (2008) 1390-1400. This important work provides experimental clues to the molecular mechanisms of CRISPR function. In particular, the work shows that generation of genetic 'memory' in Streptococcus thermophilus is accomplished by incorporating foreign sequence fragments into the existing CRISPR locus. The work also indicates that incorporation of these sequences might involve recognition of phage sequences immediately outside of the incorporated sequence.
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(2008)
J Bacteriol
, vol.190
, pp. 1390-1400
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Deveau, H.1
Barrangou, R.2
Garneau, J.E.3
Labonté, J.4
Fremaux, C.5
Boyaval, P.6
Romero, D.A.7
Horvath, P.8
Moineau, S.9
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42
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38149061877
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Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses
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This important work provides evidence that CRISPR loci are rapidly changing and adapting to local environments in natural bacterial populations.
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Tyson G.W., and Banfield J.F. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10 (2008) 200-207. This important work provides evidence that CRISPR loci are rapidly changing and adapting to local environments in natural bacterial populations.
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(2008)
Environ Microbiol
, vol.10
, pp. 200-207
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Tyson, G.W.1
Banfield, J.F.2
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43
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39049150896
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A bacterial metapopulation adapts locally to phage predation despite global dispersal
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This important work analyses the variability in bacterial genome caused primarily by specifics of the local environment, and independently shows that CRISPR loci are among the most highly variable genomic regions.
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Kunin V., He S., Warnecke F., Peterson S.B., Garcia Martin H., Haynes M., Ivanova N., Blackall L.L., Breitbart M., Rohwer F., et al. A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res 18 (2008) 293-297. This important work analyses the variability in bacterial genome caused primarily by specifics of the local environment, and independently shows that CRISPR loci are among the most highly variable genomic regions.
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(2008)
Genome Res
, vol.18
, pp. 293-297
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Kunin, V.1
He, S.2
Warnecke, F.3
Peterson, S.B.4
Garcia Martin, H.5
Haynes, M.6
Ivanova, N.7
Blackall, L.L.8
Breitbart, M.9
Rohwer, F.10
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45
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33846975418
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PILER-CR: fast and accurate identification of CRISPR repeats
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Edgar R.C. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinform 8 (2007) 18
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(2007)
BMC Bioinform
, vol.8
, pp. 18
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Edgar, R.C.1
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46
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34447644810
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CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
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Bland C., Ramsey T.L., Sabree F., Lowe M., Brown K., Kyrpides N.C., and Hugenholtz P. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinform 8 (2007) 209
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(2007)
BMC Bioinform
, vol.8
, pp. 209
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Bland, C.1
Ramsey, T.L.2
Sabree, F.3
Lowe, M.4
Brown, K.5
Kyrpides, N.C.6
Hugenholtz, P.7
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