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CRISPR Immunity Relies on the Consecutive
Binding and Degradation of Negatively Supercoiled
Invader DNA by Cascade and Cas3
Edze R. Westra,1 Paul B.G. van Erp,1 Tim Kunne,1 Shi Pey Wong,1 Raymond H.J. Staals,1 Christel L.C. Seegers,1
Sander Bollen,3 Matthijs M. Jore,1 Ekaterina Semenova,4 Konstantin Severinov,4,5,6 Willem M. de Vos,1,7 Remus T. Dame,3
Renko de Vries,2 Stan J.J. Brouns,1,* and John van der Oost1
1Laboratory
of Microbiology
of Physical Chemistry and Colloid Science
Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
3Leiden Institute of Chemistry, Gorlaeus Laboratories, Laboratory of Molecular Genetics and Cell Observatory, Leiden University,
2300 RA Leiden, The Netherlands
4Waksman Institute, Piscataway, NJ 08854, USA
5Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
6Institutes of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow 119991, Russia
7Department of Bacteriology and Immunology and Department of Veterinary Biosciences, University of Helsinki, FIN-00014 Helsinki, Finland
*Correspondence: stan.brouns@wur.nl
DOI 10.1016/j.molcel.2012.03.018
2Laboratory
SUMMARY
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Gone in 60 Seconds: Cas3 Degrades Invader DNA
could show that Cascade has high affinity for a nSC target
plasmid. At a molar ratio of pUC-l to J3-Cascade of 1:8, all
nSC plasmid containing a CAT PAM was bound by Cascade
(Figure 1A), while a plasmid carrying an escape mutation in the
PAM (CGT) (Semenova et al., 2011) was fully bound only at
a molar ratio of 1:64 (Figure 1B). Cascade carrying the nontargeting crRNA R44 (R44-Cascade) displayed nonspecific binding
at a molar ratio of 1:128 (Figure 1C). The dissociation constant
(KD) of nSC pUC-l was determined to be 13 1.4 nM for
J3-Cascade (see Figure S1A online), while the KD of nSC
pUC-l with the mutated CGT PAM was 55 12 nM (Figure S1B).
The KD of nonspecific pUC-l binding was determined to be
429 152 nM for R44-Cascade (Figure S1C). Interestingly,
J3-Cascade was unable to bind relaxed target DNA with
measurable affinity, such as nicked open circular (OC) (Figure 1D)
or linear pUC-l (Figure 1E), showing that Cascade only has high
affinity for natural dsDNA substrates that have a nSC topology.
To distinguish nonspecific binding from specific binding, we
made use of the BsmI restriction site that is located within
the protospacer to perform a BsmI footprint analysis. While
R44-Cascade does not protect the BsmI site from cleavage (Figure 1F, lane 3), pUC-l is protected from BsmI cleavage in the
presence of J3-Cascade (Figure 1F, lane 7). This shows that
Cascade is able to locate and bind a protospacer sequence in
a physiologically relevant target DNA molecule in the absence
of Cas3.
Based on the observed helicase activity of Cas3 on RNA/DNA
heteroduplexes, Cas3 has been hypothesized to play a role in recycling Cascade, presumably after ssDNA cleavage by its HD
domain (Sinkunas et al., 2011). Since Cascade alone cannot
bind a nicked plasmid with measurable affinity, we investigated
whether Cascade bound to nSC plasmid remains associated
after relaxation of the DNA. To this end, Cascade-bound nSC
pUC-l was nicked with Nt.BspQI, followed by a BsmI footprint
to monitor Cascade dissociation. Nt.BspQI cleaves pUC-l
400 bp downstream of the protospacer, generating pUC-l
with an OC topology. Interestingly, Cascade remains plasmid
bound after single-strand nicking, as can be seen from the
protection of the BsmI site (Figure 1G, compare lanes 4 and 9).
However, in a gel shift assay, Cascade dissociates from the
DNA, indicating that the Cascade-DNA interaction is weakened
by the change in topology (Figure S1D, compare lanes 8 and
10). Similar observations are made when both DNA strands of
pUC-l are cleaved after Cascade binding, both in a BsmI footprint (Figure 1H, compare lanes 4 and 9) and in a gel shift assay
(Figure S1E, compare lanes 8 and 10). This shows that, although
the Cascade-DNA interaction is weakened upon relaxation of the
DNA, Cascade remains bound to the protospacer sequence
after introducing a single- or double-strand break in the nSC
target DNA.
Cascade Induces Bending of Bound Target DNA
In order to corroborate the binding of Cascade to nSC plasmids,
and to investigate the topological consequences of Cascadeinduced R loop formation, we employed scanning force microscopy. Using this approach we visualized complexes formed
between purified Cascade and pUC-l. Specific complexes containing a single bound J3-Cascade complex were formed, while
Molecular Cell
Gone in 60 Seconds: Cas3 Degrades Invader DNA
Molecular Cell
Gone in 60 Seconds: Cas3 Degrades Invader DNA
Molecular Cell
Gone in 60 Seconds: Cas3 Degrades Invader DNA
the Cas3 nuclease and helicase activities during CRISPR interference, we made three HD domain and three helicase domain
mutants. Some of these mutants have been shown to abolish
MjaCas300 and TthCas3HDdom nuclease and SthCas3 nuclease
and helicase activity in vitro (Beloglazova et al., 2011; Mulepati
and Bailey, 2011; Sinkunas et al., 2011). The HD domain mutants
that were tested include two conserved residues that are
involved in metal ion coordination, Cas3 H74A and Cas3 D75A
(corresponding to TthCas3HDdom H69A and D70A, MjaCas300
H66A and D67A), and a conserved residue Cas3 K78A
(TthCas3HDdom K73A, MjaCas300 K70A) that may be involved in
substrate positioning (Mulepati and Bailey, 2011). The helicase
domain mutants that were generated are motif I mutant Cas3
K320N (corresponding to the SthCas3 K316A mutant [Sinkunas
et al., 2011]), motif II mutant Cas3 D452N (SthCas3 D452A [Sinkunas et al., 2011]), and motif III double mutant Cas3 S483A/
T485A. While motifs I and II are thought to be involved in ATP
binding and hydrolysis, motif III is thought to be involved in
Molecular Cell
Gone in 60 Seconds: Cas3 Degrades Invader DNA
deletions of the protospacer (Figure S3), in agreement with previously described escape mutants (Semenova et al., 2011). Cells
expressing any of the other Cas3 mutants or cells expressing
a nontargeting CRISPR did retain the original pUC-l plasmid
(Figure 5B). This illustrates that although some mutants still
show partial resistance against transformation of a single DNA
molecule into the cell (Figure 5A), they are deficient in curing a
high copy number plasmid (Figure 5B).
The HD Domain of Cas3 in the Cascade-Cas3 Effector
Complex Cleaves Target DNA
An in vitro characterization of the catalytic features of Cas3
requires its production and purification in an active state. Despite
various solubilization strategies, Cas3 overproduced in E. coli
BL21 (DE3) was found to be mainly present in inactive aggregates and inclusion bodies (data not shown, and Howard et al.,
2011). This issue was resolved by producing Cas3 as a Cas3Cse1 fusion protein, containing a linker identical to that of the
aforementioned Cas3-Cse1 fusion protein of S. griseus (Figure S4). When coexpressed with CascadeDCse1 and CRISPR
J3, a soluble fusion complex was produced that could be
purified to apparent homogeneity with the same apparent stoi600 Molecular Cell 46, 595605, June 8, 2012 2012 Elsevier Inc.
Molecular Cell
Gone in 60 Seconds: Cas3 Degrades Invader DNA
with a nSC topology. In mesophiles, all circular dsDNA molecules have a nSC topology in vivo, which is essential for compaction of chromosomal DNA into the nucleoid, and for key cellular
processes such as transcription, replication, and recombination
(reviewed in Bates, 2005). The higher affinity of Cascade for nSC
targets is related to the energy required for opening the dsDNA
duplex, which is DNA topology dependent. Negative supercoiling is considered a high-energy DNA conformation, and processes that require strand separation are generally supported
by an nSC topology. A good example is RecA-mediated base
pairing of ssDNA with the complementary strand in a dsDNA
duplex during homologous recombination (reviewed in Bell,
2005; Holthausen et al., 2010), forming a so-called D loop (Kasamatsu et al., 1971). Although relaxed dsDNA can also serve as
a substrate for a RecA-ssDNA filament during ATP-independent
strand exchange, the efficiency of strand exchange is greatly
enhanced when the DNA duplex has a negative supercoiled
topology (Cai et al., 2001).
Type III-B CRISPR/Cas systems have been demonstrated to
target single-stranded nucleic acids (RNA) (Hale et al., 2009,
2012; Zhang et al., 2012). It is possible that type I and type II
CRISPR/Cas systems can also target ssDNA, such as phage
M13 or conjugative plasmid DNA as it enters the cell. While
systems that target single-stranded nucleic acids can readily
access protospacers, systems that require strand opening of
dsDNA require an energy source. For denaturing a stretch of
32 bp in a 3 kb plasmid, approximately half of the energy needed
(90 kJ/mol) is supplied by the free energy of supercoiling. The
preference for nSC target DNA is therefore likely to be a general
characteristic for all mesophilic CRISPR/Cas systems that target
dsDNA in an ATP-independent manner.
The remaining 100 kJ/mol of Gibbs free energy that is
required for denaturing a stretch of 32 bp may be derived from
destabilizing interactions between Cascade and the dsDNA
duplex, from stabilizing interactions between Cascade and the
displaced strand, and from base pairing between the crRNA
and the target strand. Moreover, the recently identified seed
sequence in the crRNA (Semenova et al., 2011) may also
decrease the energetic barrier, because the duplex first needs
Molecular Cell 46, 595605, June 8, 2012 2012 Elsevier Inc. 601
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Gone in 60 Seconds: Cas3 Degrades Invader DNA
J
G
the target DNA. The Cas3 helicase domain has previously been
reported to unwind R loops in vitro (Sinkunas et al., 2011),
indicating that the Cas3 helicase domain may be involved in
recycling of Cascade after relaxation of the nSC target. Moreover, the Cas3 helicase domain has been shown to unwind
dsDNA in the 30 to 50 direction (Beloglazova et al., 2011; Sinkunas
et al., 2011). This dsDNA unwinding activity is essential for
progressive 30 to 50 exonucleolytic degradation of target DNA
by the HD-nuclease domain of Cas3 (this study; Beloglazova
et al., 2011). In accordance with this, both the nuclease and
the helicase activities of Cas3 are essential for CRISPR interference. The double mutant of motif III (S483A/T485A), which is
thought to couple ATP hydrolysis to unwinding activity, was still
functional. Although many SF2 helicases lose their activity when
this motif is mutated (e.g., translation initiation factor eIF-4A
[Pause and Sonenberg, 1992]), other studies have shown that
Molecular Cell
Gone in 60 Seconds: Cas3 Degrades Invader DNA
RNA in vitro and in vivo (Hale et al., 2009, 2012; Zhang et al.,
2012), while the type III-A system of Staphylococcus epidermidis
targets DNA (Marraffini and Sontheimer, 2008), although
cleavage has not yet been demonstrated. Cascade and Cas3
are the key players in the type I CRISPR interference pathway.
This study demonstrates that Cascade carries out ATP-independent DNA surveillance by exploiting the energy stored in nSC
target DNA while Cas3 carries out complete ATP-dependent
destruction of Cascade-marked invader DNA.
EXPERIMENTAL PROCEDURES
Strains, Gene Cloning, Plasmids, and Vectors
E. coli BL21-AI and BL21 (DE3) strains were used throughout the study.
A description of the plasmids used in this study can be found in the Supplemental Information (S5).
Molecular Cell 46, 595605, June 8, 2012 2012 Elsevier Inc. 603
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Gone in 60 Seconds: Cas3 Degrades Invader DNA
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