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  1. Article ; Online: The action of Escherichia coli CRISPR-Cas system on lytic bacteriophages with different lifestyles and development strategies.

    Strotskaya, Alexandra / Savitskaya, Ekaterina / Metlitskaya, Anastasia / Morozova, Natalia / Datsenko, Kirill A / Semenova, Ekaterina / Severinov, Konstantin

    Nucleic acids research

    2017  Volume 45, Issue 4, Page(s) 1946–1957

    Abstract: CRISPR-Cas systems provide prokaryotes with adaptive defense against bacteriophage infections. Given an enormous variety of strategies used by phages to overcome their hosts, one can expect that the efficiency of protective action of CRISPR-Cas systems ... ...

    Abstract CRISPR-Cas systems provide prokaryotes with adaptive defense against bacteriophage infections. Given an enormous variety of strategies used by phages to overcome their hosts, one can expect that the efficiency of protective action of CRISPR-Cas systems against different viruses should vary. Here, we created a collection of Escherichia coli strains with type I-E CRISPR-Cas system targeting various positions in the genomes of bacteriophages λ, T5, T7, T4 and R1-37 and investigated the ability of these strains to resist the infection and acquire additional CRISPR spacers from the infecting phage. We find that the efficiency of CRISPR-Cas targeting by the host is determined by phage life style, the positions of the targeted protospacer within the genome, and the state of phage DNA. The results also suggest that during infection by lytic phages that are susceptible to CRISPR interference, CRISPR-Cas does not act as a true immunity system that saves the infected cell but rather enforces an abortive infection pathway leading to infected cell death with no phage progeny release.
    MeSH term(s) Bacteriolysis ; Bacteriophage lambda/genetics ; Bacteriophages/physiology ; CRISPR-Cas Systems ; Escherichia coli/physiology ; Escherichia coli/virology ; Gene Targeting ; Genetic Variation ; Genome, Viral ; T-Phages/genetics
    Language English
    Publishing date 2017-01-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkx042
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
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  2. Article ; Online: Highly efficient primed spacer acquisition from targets destroyed by the Escherichia coli type I-E CRISPR-Cas interfering complex.

    Semenova, Ekaterina / Savitskaya, Ekaterina / Musharova, Olga / Strotskaya, Alexandra / Vorontsova, Daria / Datsenko, Kirill A / Logacheva, Maria D / Severinov, Konstantin

    Proceedings of the National Academy of Sciences of the United States of America

    2016  Volume 113, Issue 27, Page(s) 7626–7631

    Abstract: Prokaryotic clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated (Cas) immunity relies on adaptive acquisition of spacers-short fragments of foreign DNA. For the type I-E CRISPR-Cas system from Escherichia coli, efficient " ... ...

    Abstract Prokaryotic clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated (Cas) immunity relies on adaptive acquisition of spacers-short fragments of foreign DNA. For the type I-E CRISPR-Cas system from Escherichia coli, efficient "primed" adaptation requires Cas effector proteins and a CRISPR RNA (crRNA) whose spacer partially matches a segment (protospacer) in target DNA. Primed adaptation leads to selective acquisition of additional spacers from DNA molecules recognized by the effector-crRNA complex. When the crRNA spacer fully matches a protospacer, CRISPR interference-that is, target destruction without acquisition of additional spacers-is observed. We show here that when the rate of degradation of DNA with fully and partially matching crRNA targets is made equal, fully matching protospacers stimulate primed adaptation much more efficiently than partially matching ones. The result indicates that different functional outcomes of CRISPR-Cas response to two kinds of protospacers are not caused by different structures formed by the effector-crRNA complex but are due to the more rapid destruction of targets with fully matching protospacers.
    MeSH term(s) Adaptation, Biological ; CRISPR-Associated Proteins/metabolism ; CRISPR-Cas Systems ; DNA, Intergenic ; Endodeoxyribonucleases/metabolism ; Endonucleases/metabolism ; Escherichia coli/physiology ; Escherichia coli Proteins/metabolism
    Chemical Substances CRISPR-Associated Proteins ; DNA, Intergenic ; Escherichia coli Proteins ; Cas2 protein, E coli (EC 3.1.-) ; Endodeoxyribonucleases (EC 3.1.-) ; Endonucleases (EC 3.1.-) ; YgbT protein, E coli (EC 3.1.-)
    Language English
    Publishing date 2016--05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1602639113
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    Zs.A 1148: Show issues Location:
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  3. Article ; Online: Isolation and characterization of a novel indigenous intestinal N4-related coliphage vB_EcoP_G7C.

    Kulikov, Eugene / Kropinski, Andrew M / Golomidova, Alla / Lingohr, Erika / Govorun, Vadim / Serebryakova, Marina / Prokhorov, Nikolai / Letarova, Maria / Manykin, Anatolij / Strotskaya, Alexandra / Letarov, Andrey

    Virology

    2012  Volume 426, Issue 2, Page(s) 93–99

    Abstract: Lytic coliphage vB_EcoP_G7C and several other highly related isolates were obtained repeatedly from the samples of horse feces held in the same stable thus representing a component of the normal indigenous intestinal communities in this population of ... ...

    Abstract Lytic coliphage vB_EcoP_G7C and several other highly related isolates were obtained repeatedly from the samples of horse feces held in the same stable thus representing a component of the normal indigenous intestinal communities in this population of animals. The genome of G7C consists of 71,759 bp with terminal repeats of about 1160 bp, yielding approximately 73 kbp packed DNA size. Seventy-eight potential open reading frames, most of them unique to N4-like viruses, were identified and annotated. The overall layout of functional gene groups was close to that of the original N4 phage, with some important changes in late gene area including new tail fiber proteins containing hydrolytic domains. Structural proteome analysis confirmed all the predicted subunits of the viral particle. Unlike N4 itself, phage G7C did not exhibit a lysis-inhibited phenotype.
    MeSH term(s) Animals ; Bacteriophage N4/classification ; Bacteriophage N4/genetics ; Bacteriophage N4/isolation & purification ; Coliphages/classification ; Coliphages/genetics ; Coliphages/isolation & purification ; Coliphages/physiology ; Feces/virology ; Genome, Viral ; Horses ; Host Specificity ; Intestines/virology ; Molecular Sequence Data ; Open Reading Frames
    Language English
    Publishing date 2012-05-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2012.01.027
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    Ud II Zs.172: Show issues Location:
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  4. Article: Isolation and characterization of a novel indigenous intestinal N4-related coliphage vB_EcoP_G7C

    Kulikov, Eugene / Kropinski, Andrew M / Golomidova, Alla / Lingohr, Erika / Govorun, Vadim / Serebryakova, Marina / Prokhorov, Nikolai / Letarova, Maria / Manykin, Anatolij / Strotskaya, Alexandra / Letarov, Andrey

    Virology. 2012 May 10, v. 426, no. 2

    2012  

    Abstract: Lytic coliphage vB_EcoP_G7C and several other highly related isolates were obtained repeatedly from the samples of horse feces held in the same stable thus representing a component of the normal indigenous intestinal communities in this population of ... ...

    Abstract Lytic coliphage vB_EcoP_G7C and several other highly related isolates were obtained repeatedly from the samples of horse feces held in the same stable thus representing a component of the normal indigenous intestinal communities in this population of animals. The genome of G7C consists of 71,759bp with terminal repeats of about 1160bp, yielding approximately 73 kbp packed DNA size. Seventy-eight potential open reading frames, most of them unique to N4-like viruses, were identified and annotated. The overall layout of functional gene groups was close to that of the original N4 phage, with some important changes in late gene area including new tail fiber proteins containing hydrolytic domains. Structural proteome analysis confirmed all the predicted subunits of the viral particle. Unlike N4 itself, phage G7C did not exhibit a lysis-inhibited phenotype.
    Keywords DNA ; coliphages ; feces ; genes ; horses ; open reading frames ; phenotype ; proteins ; proteome ; virion
    Language English
    Dates of publication 2012-0510
    Size p. 93-99.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 200425-2
    ISSN 1096-0341 ; 0042-6822
    ISSN (online) 1096-0341
    ISSN 0042-6822
    DOI 10.1016/j.virol.2012.01.027
    Database NAL-Catalogue (AGRICOLA)

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