Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.

The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of singleguide RNAs (sgRNAs) to enable genome editing1–10. Here, we characterize SpCas9 targeting specificity in human cells to inform the selection of target sites and avoid off-target effects. Our study evaluates >700 guide RNA variants and SpCas9-induced indel mutation levels at >100 predicted genomic off-target loci in 293T and 293FT cells. We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. We also show that SpCas9-mediated cleavage is unaffected by DNA methylation and that the dosage of SpCas9 and sgRNA can be titrated to minimize off-target modification. To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses.

The targeting of nucleases to specific DNA sequences facilitates genome editing. Recent work demonstrated that the CRISPR-associated (Cas) nuclease Cas9 can be targeted to sequences in vitro simply by modifying a short7 CRISPR RNA (crRNA) guide. Here we use this CRISPR-Cas system to introduce marker-free mutations in Streptococcus pneumoniae and Escherichia coli. The approach involves re-programming Cas9 by using a crRNA complementary to a target chromosomal locus and introducing a template DNA harboring a desired mutation and an altered crRNA recognition site for recombination with the target locus. We exhaustively analyze Cas9 target requirements to define the range of targetable sequences and show strategies for editing sites that do not meet these requirements. Alone or together with recombineering, CRISPR assisted editing induces recombination at the targeted locus and kills non-edited cells leading to a recovery of close to a 100% of edited cells. Multiple crRNA can be used to modify several loci simultaneously. Our results show that CRISPR-mediated genome editing only requires programming of the crRNA and template sequences and thus constitutes a useful tool for genetic engineering.

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. C lustered, regularly interspaced, short palindromic repeat (CRISPR) loci are present in~40% of eubacterial genomes and nearly all archaeal genomes sequenced to date and consist of short (~24 to 48 nucleotides) repeats separated by similarly sized unique spacers (1, 2). They are generally flanked by a set of CRISPR-associated (cas) protein-coding genes (3-5). The CRISPR spacers and repeats are transcribed and processed into small CRISPR RNAs (crRNAs) (4, 6-8) that specify acquired immunity against bacteriophage infection by a mechanism that relies on the strict identity between CRISPR spacers and phage targets (3, 4).The rise of hospital-and communityacquired methicillin-and vancomycin-resistant Staphylococcus aureus (MRSA and VRSA, respectively) is directly linked to the horizontal transfer of antibiotic resistance genes by plasmid conjugation (9, 10). S. aureus and S. epidermidis strains are the most common causes of nosocomial infections (11-13), and conjugative plasmids can spread from one species to the other. Although the S. epidermidis strain American Type Culture Collection (ATCC) 12228 (14) lacks CRISPR sequences, the clinically isolated strain RP62a (15) contains a CRISPR locus (Fig. 1A and fig. S1A) that includes a spacer (spc1) that is homologous to a region of the nickase (nes) gene found in all sequenced staphylococcal conjugative plasmids ( fig. S1B), including those from MRSA and VRSA strains (9,16,17).To test whether spc1 prevents plasmid conjugation into S. epidermidis RP62a, we disrupted the sequence match by introducing nine silent mutations into the nes target in the conjugative plasmid pG0400 (18), generating pG0(mut) (Fig. 1B) (19). We tested whether both wild-type and mutant pG0400 transferred from S. aureus strain RN4220 (20) into either of the two S. epidermidis strains (Fig. 1D and fig. S1C). Although the conjugation frequency of both plasmids was similar for the CRISPR-negative ATCC 12228 strain, only pG0(mut) was transferred into the CRISPR-positive RP62a strain and with a frequency similar to that of wild-type pG0400 in the control ATCC 12228 strain. These r...

The ability to artificially control transcription is essential both to the study of gene function and to the construction of synthetic gene networks with desired properties. Cas9 is an RNA-guided double-stranded DNA nuclease that participates in the CRISPR-Cas immune defense against prokaryotic viruses. We describe the use of a Cas9 nuclease mutant that retains DNA-binding activity and can be engineered as a programmable transcription repressor by preventing the binding of the RNA polymerase (RNAP) to promoter sequences or as a transcription terminator by blocking the running RNAP. In addition, a fusion between the omega subunit of the RNAP and a Cas9 nuclease mutant directed to bind upstream promoter regions can achieve programmable transcription activation. The simple and efficient modulation of gene expression achieved by this technology is a useful asset for the study of gene networks and for the development of synthetic biology and biotechnological applications.

Antibiotics target conserved bacterial cellular pathways or growth functions and therefore cannot selectively kill specific members of a complex microbial population. Here, we develop programmable, sequence-specific antimicrobials using the RNA-guided nuclease Cas91, 2 delivered by a bacteriophage. We show that Cas9 re-programmed to target virulence genes kills virulent, but not avirulent, Staphylococcus aureus. Re-programming the nuclease to target antibiotic resistance genes destroys staphylococcal plasmids that harbor antibiotic resistance genes3, 4 and immunizes avirulent staphylococci to prevent the spread of plasmid-borne resistance genes. We also demonstrate the approach in vivo, showing its efficacy against S. aureus in a mouse skin colonization model. This new technology creates opportunities to manipulate complex bacterial populations in a sequence-specific manner.

Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. The importance of such pathways is highlighted by the extensive study of RNA interference (RNAi) and related processes in eukaryotes. In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. CRISPR sequences provide an adaptive, heritable record of past infections and express CRISPR RNAs -small RNAs that target invasive nucleic acids. Here, we review the mechanisms of CRISPR interference and its roles in microbial physiology and evolution. We also discuss potential applications of this novel interference pathway.The acquisition of new genes that confer a selective advantage is an important factor in genome evolution. Considerable proportions of bacterial and archaeal genomes consist of genes derived from the exchange of genetic material among related or unrelated species 1 , which is known as horizontal gene transfer (HGT). HGT occurs by uptake of environmental DNA (transformation) or by the incorporation of heterologous DNA carried on mobile genetic elements, such as plasmids (conjugation) and bacteriophages (transduction) 2 .However, only a miniscule fraction of acquired genes confers an immediate selective advantage. Therefore bacteria and archaea have developed many mechanisms to prevent HGT, such as DNA restriction and surface exclusion 2 . Recently, arrays of clustered, regularly interspaced short palindromic repeats (CRISPRs) have been identified as determinants of a novel genetic interference pathway that limits at least two major routes of HGT -conjugation and transduction. Like eukaryotic RNA interference (RNAi) and Competing interests statementThe authors declare no competing financial interests. DATABASES NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript related pathways (with which CRISPR interference is analogous but not homologous), CRISPR interference provides the host with an efficient antiviral defence mechanism.In contrast to other gene transfer and phage defence mechanisms, CRISPR interference is an adaptive immune system that can be reprogrammed to reject invading DNA molecules that have not been previously encountered. CRISPRs are separated by short spacer sequences that match bacteriophage or plasmid sequences and specify the targets of interference. Upon phage infection, CRISPR arrays can acquire new repeat-spacer units that match the challenging phage. Cells with this extended CRISPR locus will survive phage infection and thrive. Therefore the spacer content of CRISPR arrays reflects the many different phages and plasmids that have been encountered by the host, and these spacers can be expanded rapidly in response to new invasions. Accordingly, CRISPRs constitute a 'genetic memory' that ensures the rejection of new, returning and ever-present invading DNA m...

SUMMARY The cell wall envelopes of gram-positive bacteria represent a surface organelle that not only functions as a cytoskeletal element but also promotes interactions between bacteria and their environment. Cell wall peptidoglycan is covalently and noncovalently decorated with teichoic acids, polysaccharides, and proteins. The sum of these molecular decorations provides bacterial envelopes with species- and strain-specific properties that are ultimately responsible for bacterial virulence, interactions with host immune systems, and the development of disease symptoms or successful outcomes of infections. Surface proteins typically carry two topogenic sequences, i.e., N-terminal signal peptides and C-terminal sorting signals. Sortases catalyze a transpeptidation reaction by first cleaving a surface protein substrate at the cell wall sorting signal. The resulting acyl enzyme intermediates between sortases and their substrates are then resolved by the nucleophilic attack of amino groups, typically provided by the cell wall cross bridges of peptidoglycan precursors. The surface protein linked to peptidoglycan is then incorporated into the envelope and displayed on the microbial surface. This review focuses on the mechanisms of surface protein anchoring to the cell wall envelope by sortases and the role that these enzymes play in bacterial physiology and pathogenesis.