Single cell variability of CRISPR-Cas interference and adaptation

While CRISPR-Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in individual cells have remained unknown. Using a microfluidic device, time-lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multiple generations. We observed that CRISPR...

A thousand needles in a haystack: The search for invading DNA sequences by the CRISPR immune system

Viruses are, as we have seen over the past year, very proficient at invading a host and subsequently reproducing rapidly. Our adaptive immune system, after a first encounter with a virus, can store information about the outside protein shell and use this information to destroy the virus in later encounters. Bacteria have an adaptive immune...

PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems

Background: The adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many aspects of CRISPR-Cas biology, including target requirements such as the protospacer adjacent motif (PAM). However,...

The gRAMP CRISPR-Cas effector is an RNA endonuclease complexed with a caspase-like peptidase

Type III CRISPR-Cas immunity is widespread in prokaryotes and is generally mediated by multisubunit effector complexes. These complexes recognize complementary viral transcripts and can activate ancillary immune proteins. Here, we describe a type III-E effector from Candidatus “Scalindua brodae” (Sb-gRAMP), which is natively encoded by a...

Mechanism for Cas4-assisted directional spacer acquisition in CRISPR–Cas

Prokaryotes adapt to challenges from mobile genetic elements by integrating spacers derived from foreign DNA in the CRISPR array¹. Spacer insertion is carried out by the Cas1–Cas2 integrase complex^2–4. A substantial fraction of CRISPR–Cas systems use a Fe–S cluster containing Cas4 nuclease to ensure that spacers are...

Visualisation of dCas9 target search in vivo using an open-microscopy framework

CRISPR-Cas9 is widely used in genomic editing, but the kinetics of target search and its relation to the cellular concentration of Cas9 have remained elusive. Effective target search requires constant screening of the protospacer adjacent motif (PAM) and a 30 ms upper limit for screening was recently found. To further quantify the rapid...

Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation

CRISPR-Cas systems adapt their immunological memory against their invaders by integrating short DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci. While Cas1 and Cas2 make up the core machinery of the CRISPR integration process, various class I and II CRISPR-Cas systems encode Cas4 proteins for which...