CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA

By L. Marraffini, E. Sontheimer. Science, 2008

1,708 citations recorded by the source corpus.

Horizontal gene transfer (HGT) in bacteria and archaea occurs through phage transduction, transformation, or conjugation, and the latter is particularly important for the spread of antibiotic resistance. Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci confer sequence-directed immunity against phages. A clinical isolate of Staphylococcus epidermidis harbors a CRISPR spacer that matches the nickase gene present in nearly all staphylococcal conjugative plasmids. Here we show that CRISPR interference prevents conjugation and plasmid transformation in S. epidermidis. Insertion of a self-splicing intron into nickase blocks interference despite the reconstitution of the target sequence in the spliced mRNA, which indicates that the interference machinery targets DNA directly. We conclude that CRISPR loci counteract multiple routes of HGT and can limit the spread of antibiotic resistance in pathogenic bacteria.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2b375974b7236a45ecae7ef652c34a1c2ecdde74

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Citations in the corpus

Type III CRISPR-Cas Systems: Deciphering the Most Complex Prokaryotic Immune System (2021, background): “characterized a Type III A CRISPR Cas system from Staphylococcus epidermidis as a DNA targeting system [11].”
Biological Diversity of Prokaryotic Type IV Secretion Systems (2009, background): “Staphylococcus epidermidis, wherein a CRISPR sequence matching a relaxase gene that is present in nearly all conjugative plasmids of staphylococci prevents plasmid acquisition during conjugation (184).”
Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. (2011, background): “The extent to which a bacterial cell can limit LGT is determined by the number and type of RNA guides, which in turn varies between individual cells (Marraffini & Sontheimer, 2008).”
sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites (2014, background): “The core endonucleases Cas9 in the type II CRISPR system has been harnessed to achieve gene mutation, DNA deletion and insertion, as well as transcriptional activation and repression, with multiplex targeting ability, just by customizing 20-nt RNA components [1].”
Identifying and visualizing functional PAM diversity across CRISPR-Cas systems (2016, background): “Unlike adaptive immune systems in eukaryotes, CRISPR-Cas systems rely on the base-pairing potential of RNA guides for specific target recognition (Brouns et al., 2008; Garneau et al., 2010; Marraffini and Sontheimer, 2008).”
CRISPR/Cas9 in Genome Editing and Beyond. (2016, background): “In contrast to most known DNA-binding proteins, Cas9 is an RNA-guided nuclease whose sequence specificity largely arises from Watson–Crick base pairing between its guide RNA and the target DNA site, in addition to a direct interaction between Cas9 and a short protospaceradjacent motif (PAM) of DNA (”
Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA (2014, background): “Three types (I–III) of CRISPR-Cas systems have been functionally identified across a wide range of microbial species (Barrangou et al., 2007; Brouns et al., 2008; Marraffini and Sontheimer, 2008), and each contains a cluster of CRISPR-associated (Cas) genes and its corresponding CRISPR array.”
The CRISPR/Cas9 system for plant genome editing and beyond. (2015, background): “The mechanism of this immune system based on RNA-mediated DNA targeting was demonstrated shortly thereafter (Brouns et al., 2008; Deltcheva et al., 2011; Garneau et al., 2010; Marraffini and Sontheimer, 2008).”
The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli (2011, background): “First, the unique SapI restriction endonuclease site was removed from pCRISPR3 plasmid by XbaI-SapI cleavage followed by re-ligation with T4 DNA ligase to generate pCRISPR3-ΔSapI plasmid.”
Regulatory RNAs in Bacteria (2009, background): “CRISPR RNAs A unique class of recently discovered regulatory RNAs is the CRISPR RNAs, which provide resistance to bacteriophage (reviewed in Sorek et al., 2008) and prevent plasmid conjugation (Marraffini and Sontheimer, 2008 ).”