Nijmegen (Radboud Universiteit).
Daarnaast druk met publicaties in diverse wetenschappelijke tijdschriften. Veel daarvan zijn o.a. terug te vinden op de website van PubMed. Klik maar op: Publicaties Raymond Staals
De volledige tekst van de verschillende publicaties is niet beschikbaar voor iedereen. Daarvoor moet betaald worden. De korte samenvattingen (Abstracts; zie hieronder) zijn gratis. De afgedrukte voorbeelden zijn van 2014 (no.1 en no.2), en van 2013 (no.3). Mijn volledige lijst van wetenschappelijke publicaties (vanaf 2005) is natuurlijk veel langer. Het is maar om even een indruk te geven.no.1 Proc Natl Acad Sci U S A. 2014 Apr 7. [Epub ahead of print]
Degenerate target sites mediate rapid primed CRISPR adaptation.
Fineran PC1, Gerritzen MJ, Suárez-Diez M, Künne T, Boekhorst J, van Hijum SA, Staals RH, Brouns SJ.
Abstract
Prokaryotes encode adaptive immune systems, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated), to provide resistance against mobile invaders, such as viruses and plasmids. Host immunity is based on incorporation of invader DNA sequences in a memory locus (CRISPR), the formation of guide RNAs from this locus, and the degradation of cognate invader DNA (protospacer). Invaders can escape type I-E CRISPR-Cas immunity in Escherichia coli K12 by making point mutations in the seed region of the protospacer or its adjacent motif (PAM), but hosts quickly restore immunity by integrating new spacers in a positive-feedback process termed "priming." Here, by using a randomized protospacer and PAM library and high-throughput plasmid loss assays, we provide a systematic analysis of the constraints of both direct interference and subsequent priming in E. coli. We have defined a high-resolution genetic map of direct interference by Cascade and Cas3, which includes five positions of the protospacer at 6-nt intervals that readily tolerate mutations. Importantly, we show that priming is an extremely robust process capable of using degenerate target regions, with up to 13 mutations throughout the PAM and protospacer region. Priming is influenced by the number of mismatches, their position, and is nucleotide dependent. Our findings imply that even outdated spacers containing many mismatches can induce a rapid primed CRISPR response against diversified or related invaders, giving microbes an advantage in the coevolutionary arms race with their invaders.
PMID: 24711427 [PubMed - as supplied by publisher]
no.2 Microbiol Mol Biol Rev. 2014 Mar;78(1):74-88. doi: 10.1128/MMBR.00039-13. The role of CRISPR-Cas systems in virulence of pathogenic bacteria.
Louwen R1, Staals RH, Endtz HP, van Baarlen P, van der Oost J.
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. The discovery that CRISPR spacers are often identical to sequence fragments of mobile genetic elements was a major breakthrough that eventually led to the elucidation of CRISPR-Cas as an adaptive immunity system. Key elements of this unique prokaryotic defense system are small CRISPR RNAs that guide nucleases to complementary target nucleic acids of invading viruses and plasmids, generally followed by the degradation of the invader. In addition, several recent studies have pointed at direct links of CRISPR-Cas to regulation of a range of stress-related phenomena. An interesting example concerns a pathogenic bacterium that possesses a CRISPR-associated ribonucleoprotein complex that may play a dual role in defense and/or virulence. In this review, we describe recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular.
PMID: 24600041 [PubMed - in process] PMCID: PMC3957734 [Available on 2015/3/1]
no.3 Mol Cell. 2013 Oct 10;52(1):135-45. doi: 10.1016/j.molcel.2013.09.013. Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus.
Staals RH1, Agari Y, Maki-Yonekura S, Zhu Y, Taylor DW, van Duijn E, Barendregt A, Vlot M, Koehorst JJ, Sakamoto K, Masuda A, Dohmae N, Schaap PJ, Doudna JA, Heck AJ, Yonekura K, van der Oost J, Shinkai A.Abstract
The CRISPR-Cas system is a prokaryotic host defense system against genetic elements. The Type III-B CRISPR-Cas system of the bacterium Thermus thermophilus, the TtCmr complex, is composed of six different protein subunits (Cmr1-6) and one crRNA with a stoichiometry of Cmr112131445361:crRNA1. The TtCmr complex copurifies with crRNA species of 40 and 46 nt, originating from a distinct subset of CRISPR loci and spacers. The TtCmr complex cleaves the target RNA at multiple sites with 6 nt intervals via a 5' ruler mechanism. Electron microscopy revealed that the structure of TtCmr resembles a "sea worm" and is composed of a Cmr2-3 heterodimer "tail," a helical backbone of Cmr4 subunits capped by Cmr5 subunits, and a curled "head" containing Cmr1 and Cmr6. Despite having a backbone of only four Cmr4 subunits and being both longer and narrower, the overall architecture of TtCmr resembles that of Type I Cascade complexes.Copyright © 2013 Elsevier Inc. All rights reserved.
Same same but different: new structural insight into CRISPR-Cas complexes. [Mol Cell. 2013]PMID: 24119403 [PubMed - indexed for MEDLINE]
De afbeelding hiernaast werd ontworpen door mijn vader, en werd gebruikt door het tijdschrift Molecular Cell waarin het bovengenoemde artikel (no. 3) werd geplaatst, oktober 2013.
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