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  1. Article: Contemporary Phage Biology: From Classic Models to New Insights

    Ofir, Gal / Rotem Sorek

    Cell. 2018 Mar. 08, v. 172, no. 6

    2018  

    Abstract: Bacteriophages, discovered about a century ago, have been pivotal as models for understanding the fundamental principles of molecular biology. While interest in phage biology declined after the phage “golden era,” key recent developments, including ... ...

    Abstract Bacteriophages, discovered about a century ago, have been pivotal as models for understanding the fundamental principles of molecular biology. While interest in phage biology declined after the phage “golden era,” key recent developments, including advances in phage genomics, microscopy, and the discovery of the CRISPR-Cas anti-phage defense system, have sparked a renaissance in phage research in the past decade. This review highlights recently discovered unexpected complexities in phage biology, describes a new arsenal of phage genes that help them overcome bacterial defenses, and discusses advances toward documentation of the phage biodiversity on a global scale.
    Keywords bacteriophages ; biodiversity ; genes ; genomics ; microscopy ; models ; molecular biology
    Language English
    Dates of publication 2018-0308
    Size p. 1260-1270.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2017.10.045
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  2. Article: Vesicles Spread Susceptibility to Phages

    Ofir, Gal / Rotem Sorek

    Cell. 2017 Jan. 12, v. 168

    2017  

    Abstract: Extracellular membrane vesicles from bacteria are now shown to transfer phage receptors from susceptible to resistant cells, thus making them transiently sensitive to phage infection (Tzipilevich et al.). ...

    Abstract Extracellular membrane vesicles from bacteria are now shown to transfer phage receptors from susceptible to resistant cells, thus making them transiently sensitive to phage infection (Tzipilevich et al.).
    Keywords bacteria ; bacteriophages ; virus receptors
    Language English
    Dates of publication 2017-0112
    Size p. 13-15.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2016.12.035
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  3. Article: Regulation of antibiotic-resistance by non-coding RNAs in bacteria

    Dar, Daniel / Rotem Sorek

    Current opinion in microbiology. 2017 Apr., v. 36

    2017  

    Abstract: Antibiotic resistance genes are commonly regulated by sophisticated mechanisms that activate gene expression in response to antibiotic exposure. Growing evidence suggest that cis-acting non-coding RNAs play a major role in regulating the expression of ... ...

    Abstract Antibiotic resistance genes are commonly regulated by sophisticated mechanisms that activate gene expression in response to antibiotic exposure. Growing evidence suggest that cis-acting non-coding RNAs play a major role in regulating the expression of many resistance genes, specifically those which counteract the effects of translation-inhibiting antibiotics. These ncRNAs reside in the 5′UTR of the regulated gene, and sense the presence of the antibiotics by recruiting translating ribosomes onto short upstream open reading frames (uORFs) embedded in the ncRNA. In the presence of translation-inhibiting antibiotics ribosomes arrest over the uORF, altering the RNA structure of the regulator and switching the expression of the resistance gene to ‘ON’. The specificity of these riboregulators is tuned to sense-specific classes of antibiotics based on the length and composition of the respective uORF. Here we review recent work describing new types of antibiotic-sensing RNA-based regulators and elucidating the molecular mechanisms by which they function to control antibiotic resistance in bacteria.
    Keywords antibiotic resistance ; antibiotics ; bacteria ; gene expression ; genes ; genetic resistance ; non-coding RNA ; open reading frames ; ribosomes ; translation (genetics)
    Language English
    Dates of publication 2017-04
    Size p. 111-117.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2017.02.005
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  4. Article ; Online: Optimality and sub-optimality in a bacterial growth law

    Benjamin D. Towbin / Yael Korem / Anat Bren / Shany Doron / Rotem Sorek / Uri Alon

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Volume 8

    Abstract: Organisms improve their fitness by adjusting their gene expression to the environment, for example bacteria scale the expression of metabolic enzymes near linearly to their growth rate. Here, the authors show that such linear scaling often maximizes ... ...

    Abstract Organisms improve their fitness by adjusting their gene expression to the environment, for example bacteria scale the expression of metabolic enzymes near linearly to their growth rate. Here, the authors show that such linear scaling often maximizes growth rate, but that linear scaling is suboptimal under some conditions.
    Keywords Science ; Q
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Evidence for a cytoplasmic pool of ribosome-free mRNAs encoding inner membrane proteins in Escherichia coli.

    Daniel Benhalevy / Ido Biran / Elena S Bochkareva / Rotem Sorek / Eitan Bibi

    PLoS ONE, Vol 12, Iss 8, p e

    2017  Volume 0183862

    Abstract: Translation-independent mRNA localization represents an emerging concept in cell biology. In Escherichia coli, mRNAs encoding integral membrane proteins (MPRs) are targeted to the membrane where they are translated by membrane associated ribosomes and ... ...

    Abstract Translation-independent mRNA localization represents an emerging concept in cell biology. In Escherichia coli, mRNAs encoding integral membrane proteins (MPRs) are targeted to the membrane where they are translated by membrane associated ribosomes and the produced proteins are inserted into the membrane co-translationally. In order to better understand aspects of the biogenesis and localization of MPRs, we investigated their subcellular distribution using cell fractionation, RNA-seq and qPCR. The results show that MPRs are overrepresented in the membrane fraction, as expected, and depletion of the signal recognition particle-receptor, FtsY reduced the amounts of all mRNAs on the membrane. Surprisingly, however, MPRs were also found relatively abundant in the soluble ribosome-free fraction and their amount in this fraction is increased upon overexpression of CspE, which was recently shown to interact with MPRs. CspE also conferred a positive effect on the membrane-expression of integral membrane proteins. We discuss the possibility that the effects of CspE overexpression may link the intriguing subcellular localization of MPRs to the cytosolic ribosome-free fraction with their translation into membrane proteins and that the ribosome-free pool of MPRs may represent a stage during their targeting to the membrane, which precedes translation.
    Keywords Medicine ; R ; Science ; Q
    Subject code 571
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Repeat Size Determination by Two Molecular Rulers in the Type I-E CRISPR Array

    Moran G. Goren / Shany Doron / Rea Globus / Gil Amitai / Rotem Sorek / Udi Qimron

    Cell Reports, Vol 16, Iss 11, Pp 2811-

    2016  Volume 2818

    Abstract: Prokaryotic adaptive immune systems are composed of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins. These systems adapt to new threats by integrating short nucleic acids, termed spacers, into the ... ...

    Abstract Prokaryotic adaptive immune systems are composed of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins. These systems adapt to new threats by integrating short nucleic acids, termed spacers, into the CRISPR array. The functional motifs in the repeat and the mechanism by which a constant repeat size is maintained are still elusive. Here, through a series of mutations within the repeat of the CRISPR-Cas type I-E, we identify motifs that are crucial for adaptation and show that they serve as anchor sites for two molecular rulers determining the size of the new repeat. Adaptation products from various repeat mutants support a model in which two motifs in the repeat bind to two different sites in the adaptation complex that are 8 and 16 bp away from the active site. This model significantly extends our understanding of the adaptation process and broadens the scope of its applications.
    Keywords adaptation ; spacer integration ; elongated repeat ; shortened repeat ; anchor site ; Biology (General) ; QH301-705.5
    Subject code 006
    Language English
    Publishing date 2016-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA

    Mellin, J. R / Daniel Dar / Marie-Anne Nahori / Mikael Koutero / Pascale Cossart / Rotem Sorek

    Science. 2014 Aug. 22, v. 345, no. 6199

    2014  

    Abstract: A dual-action RNA switch for expression Riboswitches are short segments of RNA that bind small molecules and switch between two different conformations, thereby regulating gene expression (see the Perspective by Chen and Gottesman). DebRoy et al. and ... ...

    Abstract A dual-action RNA switch for expression Riboswitches are short segments of RNA that bind small molecules and switch between two different conformations, thereby regulating gene expression (see the Perspective by Chen and Gottesman). DebRoy et al. and Mellin et al. find a new class of riboswitches—in two different species of bacteria—that are both part of and regulate the production of a noncoding RNA. Each riboswitch ensures that a particular metabolic pathway is only activated in the presence of an essential small-molecule cofactor. In the absence of the cofactor, the full-length non-coding RNA is made and binds a regulator protein, preventing the regulator protein from inappropriately activating the metabolic pathway. Science , this issue p. 937 and p. 940; see also p. 876
    Keywords biochemical pathways ; gene expression ; non-coding RNA
    Language English
    Dates of publication 2014-0822
    Size p. 940-943.
    Publishing place American Association for the Advancement of Science
    Document type Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.1255083
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  8. Article ; Online: A global transcriptional switch between the attack and growth forms of Bdellovibrio bacteriovorus.

    Iris Karunker / Or Rotem / Mally Dori-Bachash / Edouard Jurkevitch / Rotem Sorek

    PLoS ONE, Vol 8, Iss 4, p e

    2013  Volume 61850

    Abstract: Bdellovibrio bacteriovorus is an obligate predator of bacteria ubiquitously found in the environment. Its life cycle is composed of two essential phases: a free-living, non-replicative, fast swimming attack phase (AP) wherein the predator searches for ... ...

    Abstract Bdellovibrio bacteriovorus is an obligate predator of bacteria ubiquitously found in the environment. Its life cycle is composed of two essential phases: a free-living, non-replicative, fast swimming attack phase (AP) wherein the predator searches for prey; and a non-motile, actively dividing growth phase (GP) in which it consumes the prey. The molecular regulatory mechanisms governing the switch between AP and GP are largely unknown. We used RNA-seq to generate a single-base-resolution map of the Bdellovibrio transcriptome in AP and GP, revealing a specific "AP" transcriptional program, which is largely mutually exclusive of the GP program. Based on the expression map, most genes in the Bdellovibrio genome are classified as "AP only" or "GP only". We experimentally generated a genome-wide map of 140 AP promoters, controlling the majority of AP-specific genes. This revealed a common sigma-like DNA binding site highly similar to the E. coli flagellar genes regulator sigma28 (FliA). Further analyses suggest that FliA has evolved to become a global AP regulator in Bdellovibrio. Our results also reveal a non-coding RNA that is massively expressed in AP. This ncRNA contains a c-di-GMP riboswitch. We suggest it functions as an intracellular reservoir for c-di-GMP, playing a role in the rapid switch from AP to GP.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2013-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

    Brigitte T. Hofmeister / Johanna Denkena / Maria Colomé-Tatché / Yadollah Shahryary / Rashmi Hazarika / Jane Grimwood / Sujan Mamidi / Jerry Jenkins / Paul P. Grabowski / Avinash Sreedasyam / Shengqiang Shu / Kerrie Barry / Kathleen Lail / Catherine Adam / Anna Lipzen / Rotem Sorek / Dave Kudrna / Jayson Talag / Rod Wing /
    David W. Hall / Daniel Jacobsen / Gerald A. Tuskan / Jeremy Schmutz / Frank Johannes / Robert J. Schmitz

    Genome Biology, Vol 21, Iss 1, Pp 1-

    2020  Volume 27

    Abstract: Abstract Background Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local ... ...

    Abstract Abstract Background Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials. Results Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions. Conclusion Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.
    Keywords Mutation rate ; Epimutation rate ; Epigenetics ; Poplar ; DNA methylation ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Subject code 580
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Evolutionary conservation of sequence and secondary structures in CRISPR repeats

    Kunin, Victor / Philip Hugenholtz / Rotem Sorek

    Genome biology. 2007 June, v. 8, no. 4

    2007  

    Abstract: BACKGROUND: Clustered regularly interspaced short palindromic repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in approximately 40% of bacterial and most archaeal genomes ... ...

    Abstract BACKGROUND: Clustered regularly interspaced short palindromic repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in approximately 40% of bacterial and most archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CASs), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes. RESULTS: Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. Some of the clusters present stable, highly conserved RNA secondary structures, while others lack detectable structures. Stable secondary structures exhibit multiple compensatory base changes in the stem region, indicating evolutionary and functional conservation. CONCLUSION: We show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification, including specific relationships between CRISPR and CAS subtypes.
    Keywords genes ; germplasm conservation ; prokaryotic cells ; RNA ; sequence homology ; viruses
    Language English
    Dates of publication 2007-06
    Size p. 1543.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/gb-2007-8-4-r61
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