Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Are bacteriophage defence and virulence two sides of the same coin in Campylobacter jejuni?
    Louwen, R. ; Baarlen, P. van - \ 2013
    Biochemical Society Transactions 41 (2013)6. - ISSN 0300-5127 - p. 1475 - 1481.
    guillain-barre-syndrome - provides acquired-resistance - crispr-cas systems - escherichia-coli - pseudomonas-aeruginosa - sialic-acid - genetic elements - envelope stress - immune evasion - protein-a
    The continuous battle for survival in the environment has led to the development or acquisition of sophisticated defence systems in bacteria. These defence systems have contributed to the survival of the bacterial species in the environment for millions of years. Some systems appear to have evolved in a number of pathogenic bacteria towards a role in virulence and host immune evasion. Recently, different bacterial cell envelope components from diverse bacterial species have been linked not only to bacteriophage defence, but also to virulence features. In the present review we focus specifically on the bacterial cell envelope-expressed sialic-acid-containing LOS (lipo-oligosaccharide) structures and Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) genes that both occur in specific Gram-negative pathogens. In Campylobacter jejuni circumstantial evidence points at a potential intertwined dual function between sialylated LOS structures and subtype II-C CRISPR-Cas, i.e. in phage defence and virulence. In the present review we discuss whether a dual functionality of sialylated LOS and subtype II-C CRISPR-Cas is exclusive to C. jejuni only or could be more widespread within the group of Type II CRISPR-Cas-harbouring bacteria. We conclude from the literature that, at least in C. jejuni, circumstantial evidence exists for a complex intertwined dual functionality between sialylated LOS and Type II CRISPR-Cas, and that other bacteria show similar genomic signatures.
    RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements
    Jore, M.M. ; Brouns, S.J.J. ; Oost, J. van der - \ 2012
    Cold Spring Harbor Perspectives in Biology 4 (2012)6. - ISSN 1943-0264
    provides acquired-resistance - thermus-thermophilus hb8 - ray crystal-structure - escherichia-coli - streptococcus-thermophilus - sulfolobus-solfataricus - microbial communities - structural basis - dna - system
    The CRISPR/Cas system in prokaryotes provides resistance against invading viruses and plasmids. Three distinct stages in the mechanism can be recognized. Initially, fragments of invader DNA are integrated as new spacers into the repetitive CRISPR locus. Subsequently, the CRISPR is transcribed and the transcript is cleaved by a Cas protein within the repeats, generating short RNAs (crRNAs) that contain the spacer sequence. Finally, crRNAs guide the Cas protein machinery to a complementary invader target, either DNA or RNA, resulting in inhibition of virus or plasmid proliferation. In this article, we discuss our current understanding of this fascinating adaptive and heritable defense system, and describe functional similarities and differences with RNAi in eukaryotes
    Evolution and classification of the CRISPR-Cas systems
    Makarova, K.S. ; Brouns, S.J.J. ; Oost, J. van der - \ 2011
    Nature Reviews Microbiology 9 (2011)6. - ISSN 1740-1526 - p. 467 - 477.
    provides acquired-resistance - dna-repair system - immune-system - small rna - repeats - prokaryotes - bacteria - defense - archaea - protein
    The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR-Cas systems and Cas proteins. Three major types of CRISPR-Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR-Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR-cas loci
    Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes
    Al-Attar, S. ; Westra, E.R. ; Oost, J. van der; Brouns, S.J.J. - \ 2011
    Biological Chemistry 392 (2011)4. - ISSN 1431-6730 - p. 277 - 289.
    provides acquired-resistance - sulfolobus-solfataricus p2 - thermus-thermophilus hb8 - escherichia-coli - streptococcus-thermophilus - mycobacterium-tuberculosis - horizontal transfer - complete genome - h-ns - dna
    Many prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences (repeats), interspaced by highly variable sequences referred to as spacers. The spacers originate from either phages or plasmids and comprise the prokaryotes' ‘immunological memory’. CRISPR-associated (cas) genes encode conserved proteins that together with CRISPRs make-up the CRISPR/Cas system, responsible for defending the prokaryotic cell against invaders. CRISPR-mediated resistance has been proposed to involve three stages: (i) CRISPR-Adaptation, the invader DNA is encountered by the CRISPR/Cas machinery and an invader-derived short DNA fragment is incorporated in the CRISPR array. (ii) CRISPR-Expression, the CRISPR array is transcribed and the transcript is processed by Cas proteins. (iii) CRISPR-Interference, the invaders' nucleic acid is recognized by complementarity to the crRNA and neutralized. An application of the CRISPR/Cas system is the immunization of industry-relevant prokaryotes (or eukaryotes) against mobile-genetic invasion. In addition, the high variability of the CRISPR spacer content can be exploited for phylogenetic and evolutionary studies. Despite impressive progress during the last couple of years, the elucidation of several fundamental details will be a major challenge in future research
    CRISPR-based adaptive and heritable immunity in prokaryotes
    Oost, J. van der; Jore, M.M. ; Westra, E.R. ; Lundgren, N.M.J. ; Brouns, S.J.J. - \ 2009
    Trends in Biochemical Sciences 34 (2009)8. - ISSN 0968-0004 - p. 401 - 407.
    provides acquired-resistance - thermus-thermophilus hb8 - streptococcus-thermophilus - crystal-structure - rna-interference - dna repeats - defense - protein - sulfolobus - bacteria
    The recently discovered CRISPR (clustered regularly interspaced short palindromic repeat) defense system protects bacteria and archaea against mobile genetic elements. This immunity system has the potential to continuously adjust its reach at the genomic level, implying that both gain and loss of information is inheritable. The CRISPR system consists of typical stretches of interspaced repetitive DNA (CRISPRs) and associated cas genes. Three distinct stages are recognized in the CRISPR defense mechanism: (i) adaptation of the CRISPR via the integration of short sequences of the invaders as spacers; (ii) expression of CRISPRs and subsequent processing to small guide RNAs; and (iii) interference of target DNA by the crRNA guides. Recent analyses of key Cas proteins indicate that, despite some functional analogies, this fascinating prokaryotic system shares no phylogenetic relation with the eukaryotic RNA interference system
    Small CRISPR RNAs guide antiviral defense in prokaryotes
    Brouns, S.J.J. ; Jore, M.M. ; Lundgren, M. ; Westra, E.R. ; Slijkhuis, R.J. ; Snijders, A.P. ; Dickman, M.J. ; Makarova, K.S. ; Koonin, E.V. ; Oost, J. van der - \ 2008
    Science 321 (2008)5891. - ISSN 0036-8075 - p. 960 - 964.
    provides acquired-resistance - streptococcus-thermophilus - repeats - identification - elements - dna - evolutionary - sequence - viruses - system
    Prokaryotes acquire virus resistance by integrating short fragments of viral nucleic acid into clusters of regularly interspaced short palindromic repeats (CRISPRs). Here we show how virus-derived sequences contained in CRISPRs are used by CRISPR-associated (Cas) proteins from the host to mediate an antiviral response that counteracts infection. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation. Our results demonstrate that the formation of mature guide RNAs by the CRISPR RNA endonuclease subunit of Cascade is a mechanistic requirement for antiviral defense
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