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1.  Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity 
The initial stage of CRISPR–Cas immunity involves the acquisition of foreign DNA spacer segments into the host genomic CRISPR locus. The nucleases Cas1 and Cas2 are the only proteins conserved amongst all CRISPR–Cas systems, yet the molecular functions of these proteins during immunity are unknown. Here we show that Cas1 and Cas2 from Escherichia coli form a stable complex that is essential for spacer acquisition and determine the 2.3-Å resolution crystal structure of the Cas1–Cas2 complex. Mutations that perturb Cas1–Cas2 complex formation disrupt CRISPR DNA recognition and spacer acquisition in vivo. Unlike Cas1, active site mutants of Cas2 can still acquire new spacers indicating a non-enzymatic role of Cas2 during immunity. These results reveal the universal roles of Cas1 and Cas2 and suggest a mechanism by which Cas1–Cas2 complexes specify sites of CRISPR spacer integration.
doi:10.1038/nsmb.2820
PMCID: PMC4075942  PMID: 24793649
2.  New tools provide a second look at HDV ribozyme structure, dynamics and cleavage 
Nucleic Acids Research  2014;42(20):12833-12846.
The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.
doi:10.1093/nar/gku992
PMCID: PMC4227795  PMID: 25326328
3.  Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation 
Science (New York, N.Y.)  2014;343(6176):1247997.
Type II CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA–induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.
doi:10.1126/science.1247997
PMCID: PMC4184034  PMID: 24505130
4.  Structures of the RNA-guided surveillance complex from a bacterial immune system 
Nature  2011;477(7365):486-489.
Bacteria and archaea acquire resistance to viruses and plasmids by integrating short fragments of foreign DNA into clustered regularly interspaced short palindromic repeats (CRISPRs). These repetitive loci maintain a genetic record of all prior encounters with foreign transgressors1–6. CRISPRs are transcribed and the long primary transcript is processed into a library of short CRISPR-derived RNAs (crRNAs) that contain a unique sequence complementary to a foreign nucleic-acid challenger7–12. In Escherichia coli, crRNAs are incorporated into a multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defence), which is required for protection against bacteriophages13,14. Here we use cryo-electron microscopy to determine the subnanometre structures of Cascade before and after binding to a target sequence. These structures reveal a sea-horse-shaped architecture in which the crRNA is displayed along a helical arrangement of protein subunits that protect the crRNA from degradation while maintaining its availability for base pairing. Cascade engages invading nucleic acids through high-affinity base-pairing interactions near the 5′ end of the crRNA. Base pairing extends along the crRNA, resultingina series of short helical segments that trigger a concerted conformational change. This conformational rearrangement may serve as a signal that recruits a trans-acting nuclease (Cas3) for destruction of invading nucleic-acid sequences.
doi:10.1038/nature10402
PMCID: PMC4165517  PMID: 21938068
5.  DNA interrogation by the CRISPR RNA-guided endonuclease Cas9 
Nature  2014;507(7490):62-67.
The CRISPR-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA:DNA base-pairing to target foreign DNA in bacteria. Cas9:guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9:RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9:RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9:RNA. DNA strand separation and RNA:DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 employs PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate dsDNA scission.
doi:10.1038/nature13011
PMCID: PMC4106473  PMID: 24476820
6.  RNA-guided assembly of Rev-RRE nuclear export complexes 
eLife  2014;3:e03656.
HIV replication requires nuclear export of unspliced and singly spliced viral transcripts. Although a unique RNA structure has been proposed for the Rev-response element (RRE) responsible for viral mRNA export, how it recruits multiple HIV Rev proteins to form an export complex has been unclear. We show here that initial binding of Rev to the RRE triggers RNA tertiary structural changes, enabling further Rev binding and the rapid formation of a viral export complex. Analysis of the Rev-RRE assembly pathway using SHAPE-Seq and small-angle X-ray scattering (SAXS) reveals two major steps of Rev-RRE complex formation, beginning with rapid Rev binding to a pre-organized region presenting multiple Rev binding sites. This step induces long-range remodeling of the RNA to expose a cryptic Rev binding site, enabling rapid assembly of additional Rev proteins into the RNA export complex. This kinetic pathway may help maintain the balance between viral replication and maturation.
DOI: http://dx.doi.org/10.7554/eLife.03656.001
eLife digest
HIV is a virus that causes the immune system of an infected person to gradually fail, which can eventually result in AIDS. The virus consists of an RNA molecule—which encodes its genetic information—surrounded by coats of proteins. Once HIV enters a host cell, its RNA genome is converted into a DNA molecule, which travels to the nucleus and becomes part of the host's genome. The integrated viral genome can remain dormant for an extended period before the virus starts to replicate.
HIV replication begins with the production of RNA copies of the viral genome. For certain types of viral RNA molecules to be translated and packaged into new virus particles they need to be exported from the nucleus as part of the ‘nuclear–export complex’. This is made up of: a HIV RNA molecule, a HIV protein called Rev, and two host proteins.
Formation of the nuclear–export complex begins with multiple copies of the Rev protein attaching to specific stretches of the viral RNA, but how the Rev proteins assemble on the RNA molecule was previously unclear. Bai et al. have now used both structural and biochemical techniques to dissect the individual steps in this process. First, Rev proteins rapidly bind to a pre-formed region of the RNA molecule where multiple binding sites are compactly organized. This causes the overall shape of the RNA to change, and exposes a previously hidden extra binding site for Rev proteins. More Rev proteins then quickly bind to the newly exposed site, before finally the two host proteins bind and the whole complex is exported from the nucleus.
Bai et al. propose that checkpoints during this two-step assembly process are required to ensure that Rev proteins specifically bind to viral RNAs, and that such checkpoints may be important for controlling viral replication. The findings of Bai et al. may, in future, help to develop new drugs that treat HIV infection by blocking the export of the virus from the nucleus and thus inhibiting HIV replication.
DOI: http://dx.doi.org/10.7554/eLife.03656.002
doi:10.7554/eLife.03656
PMCID: PMC4142337  PMID: 25163983
SHAPE-Seq; HIV RRE-Rev complex; RNA nuclear export; viruses
7.  CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes 
Cell  2013;154(2):442-451.
SUMMARY
The genetic interrogation and reprogramming of cells requires methods for robust and precise targeting of genes for expression or repression. The CRISPR-associated catalytically inactive dCas9 protein offers a general platform for RNA-guided DNA targeting. Here we show that fusion of dCas9 to effector domains with distinct regulatory functions enables stable and efficient transcriptional repression or activation in human and yeast cells with the site of delivey determined solely by a co-expressed short guide (sg)RNA. Coupling of dCas9 to a transcriptional repressor domain can robustly silence expression of multiple endogenous genes RNA-seq analysis indicates that CRISPR interference (CRISPRi)-mediated transcriptional repression is highly specific. Our results establish that the CRISPR system can be used as a modular and flexible DNA-binding platform for the recruitment of proteins to a target DNA sequence and reveal the potential of CRISPRi as a general tool for the precise regulation of gene expression in eukaryotic cells.
doi:10.1016/j.cell.2013.06.044
PMCID: PMC3770145  PMID: 23849981
8.  Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus 
Molecular cell  2013;52(1):135-145.
Summary
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 co-purifies 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.
doi:10.1016/j.molcel.2013.09.013
PMCID: PMC4006948  PMID: 24119403
9.  High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity 
Nature biotechnology  2013;31(9):839-843.
The RNA-programmable Cas9 endonuclease cleaves double-stranded DNA at sites complementary to a 20-base-pair guide RNA. The Cas9 system has been used to modify genomes in multiple cells and organisms, demonstrating its potential as a facile genome-engineering tool. We used in vitro selection and high-throughput sequencing to determine the propensity of eight Cas9:guide RNA complexes to cleave each of 10^12 potential off-target DNA sequences. The selection results predicted five off-target sites in the human genome that were confirmed to undergo genome cleavage in HEK293T cells upon expression of one of two Cas9:guide RNA complexes. In contrast to previous models, our results show that Cas9:guide RNA specificity extends past a 7- to 12-base pair seed sequence. Our results also suggest a tradeoff between activity and specificity both in vitro and in cells as a shorter, less-active guide RNA is more specific then a longer, more-active guide RNA. High concentrations of Cas9:guide RNA complexes can cleave off-target sites containing mutations near or within the PAM that are not cleaved when enzyme concentrations are limiting.
doi:10.1038/nbt.2673
PMCID: PMC3782611  PMID: 23934178
10.  Substrate-specific structural rearrangements of human Dicer 
Dicer plays a central role in RNA interference pathways by cleaving double-stranded RNAs (dsRNAs) to produce small regulatory RNAs. Human Dicer can process long double-stranded and hairpin precursor RNAs to yield short interfering RNAs (siRNAs) or microRNAs (miRNAs), respectively. Previous studies have shown that pre-miRNAs are cleaved more rapidly than pre-siRNAs in vitro and are the predominant natural Dicer substrates. We have used electron microscopy and single particle analysis of Dicer–RNA complexes to gain insight into the structural basis for human Dicer’s substrate preference. Our studies show that Dicer traps pre-siRNAs in a non-productive conformation, while interactions of Dicer with pre-miRNAs and dsRNA binding proteins induce structural changes in the enzyme that enable productive substrate recognition in the central catalytic channel. These findings implicate RNA structure and cofactors in determining substrate recognition and processing efficiency by human Dicer.
doi:10.1038/nsmb.2564
PMCID: PMC3676429  PMID: 23624860
11.  Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity 
Cell reports  2013;3(5):1362-1368.
Summary
Innate immune recognition of foreign nucleic acids induces protective interferon responses. Detection of cytosolic DNA triggers downstream immune signaling through activation of cyclic GMP–AMP synthase (cGAS). We report here the crystal structure of human cGAS, revealing an unanticipated zinc-ribbon DNA-binding domain appended to a core enzymatic nucleotidyl transferase scaffold. The catalytic core of cGAS is structurally homologous to the RNA sensing enzyme, 2′–5′ oligo-adenylate synthase (OAS), and divergent C-terminal domains account for specific ligand-activation requirements of each enzyme. We show that the cGAS zinc-ribbon is essential for STING-dependent induction of the interferon response, and conserved amino acids displayed within the intervening loops are required for efficient cytosolic DNA recognition. These results demonstrate that cGAS and OAS define a new family of innate immunity sensors, and that structural divergence from a core nucleotidyl transferase enables second-messenger responses to distinct foreign nucleic acids.
doi:10.1016/j.celrep.2013.05.008
PMCID: PMC3800681  PMID: 23707061
12.  Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases 
Nucleic Acids Research  2013;42(2):1341-1353.
In many bacteria and archaea, small RNAs derived from clustered regularly interspaced short palindromic repeats (CRISPRs) associate with CRISPR-associated (Cas) proteins to target foreign DNA for destruction. In Type I and III CRISPR/Cas systems, the Cas6 family of endoribonucleases generates functional CRISPR-derived RNAs by site-specific cleavage of repeat sequences in precursor transcripts. CRISPR repeats differ widely in both sequence and structure, with varying propensity to form hairpin folds immediately preceding the cleavage site. To investigate the evolution of distinct mechanisms for the recognition of diverse CRISPR repeats by Cas6 enzymes, we determined crystal structures of two Thermus thermophilus Cas6 enzymes both alone and bound to substrate and product RNAs. These structures show how the scaffold common to all Cas6 endonucleases has evolved two binding sites with distinct modes of RNA recognition: one specific for a hairpin fold and the other for a single-stranded 5′-terminal segment preceding the hairpin. These findings explain how divergent Cas6 enzymes have emerged to mediate highly selective pre-CRISPR-derived RNA processing across diverse CRISPR systems.
doi:10.1093/nar/gkt922
PMCID: PMC3902920  PMID: 24150936
13.  The Crystal Structure of the Signal Recognition Particle in Complex with its Receptor 
Science (New York, N.Y.)  2011;331(6019):881-886.
Co-translational targeting of membrane and secretory proteins is mediated by the universally conserved Signal Recognition Particle (SRP). Together with its receptor (SR), SRP mediates the GTP-dependent delivery of translating ribosomes bearing signal sequences to translocons on the target membrane. Here we present the crystal structure of the SRP:SR complex at 3.9 Å resolution and biochemical data revealing that the activated SRP:SR GTPase complex bind the distal end of the SRP hairpin RNA where GTP hydrolysis is stimulated. Combined with previous findings, these results suggest that the SRP:SR GTPase complex initially assembles at the tetraloop end of the SRP RNA and then relocalizes to the opposite end of the RNA. This rearrangement provides a mechanism for coupling GTP hydrolysis to the handover of cargo to the translocon.
doi:10.1126/science.1196473
PMCID: PMC3758919  PMID: 21330537
14.  Hepatitis C virus 3′UTR regulates viral translation through direct interactions with the host translation machinery 
Nucleic Acids Research  2013;41(16):7861-7874.
The 3′ untranslated region (3′UTR) of hepatitis C virus (HCV) messenger RNA stimulates viral translation by an undetermined mechanism. We identified a high affinity interaction, conserved among different HCV genotypes, between the HCV 3′UTR and the host ribosome. The 3′UTR interacts with 40S ribosomal subunit proteins residing primarily in a localized region on the 40S solvent-accessible surface near the messenger RNA entry and exit sites. This region partially overlaps with the site where the HCV internal ribosome entry site was found to bind, with the internal ribosome entry site-40S subunit interaction being dominant. Despite its ability to bind to 40S subunits independently, the HCV 3′UTR only stimulates translation in cis, without affecting the first round translation rate. These observations support a model in which the HCV 3′UTR retains ribosome complexes during translation termination to facilitate efficient initiation of subsequent rounds of translation.
doi:10.1093/nar/gkt543
PMCID: PMC3763534  PMID: 23783572
15.  Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation 
Nucleic Acids Research  2013;41(15):7512-7521.
The initiation of protein synthesis plays an essential regulatory role in human biology. At the center of the initiation pathway, the 13-subunit eukaryotic translation initiation factor 3 (eIF3) controls access of other initiation factors and mRNA to the ribosome by unknown mechanisms. Using electron microscopy (EM), bioinformatics and biochemical experiments, we identify two highly conserved RNA-binding motifs in eIF3 that direct translation initiation from the hepatitis C virus internal ribosome entry site (HCV IRES) RNA. Mutations in the RNA-binding motif of subunit eIF3a weaken eIF3 binding to the HCV IRES and the 40S ribosomal subunit, thereby suppressing eIF2-dependent recognition of the start codon. Mutations in the eIF3c RNA-binding motif also reduce 40S ribosomal subunit binding to eIF3, and inhibit eIF5B-dependent steps downstream of start codon recognition. These results provide the first connection between the structure of the central translation initiation factor eIF3 and recognition of the HCV genomic RNA start codon, molecular interactions that likely extend to the human transcriptome.
doi:10.1093/nar/gkt510
PMCID: PMC3753635  PMID: 23766293
16.  Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression 
Cell  2013;152(5):1173-1183.
SUMMARY
Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Here, we develop a method for controlling gene expression based on Cas9, an RNA-guided DNA endonuclease from a type II CRISPR system. We show that a catalytically dead Cas9 lacking endonuclease activity, when coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere with transcriptional elongation, RNA polymerase binding, or transcription factor binding. This system, which we call CRISPR interference (CRISPRi), can efficiently repress expression of targeted genes in Escherichia coli, with no detectable off-target effects. CRISPRi can be used to repress multiple target genes simultaneously, and its effects are reversible. We also show evidence that the system can be adapted for gene repression in mammalian cells. This RNA-guided DNA recognition platform provides a simple approach for selectively perturbing gene expression on a genome-wide scale.
doi:10.1016/j.cell.2013.02.022
PMCID: PMC3664290  PMID: 23452860
17.  Differential roles of human Dicer-binding proteins TRBP and PACT in small RNA processing 
Nucleic Acids Research  2013;41(13):6568-6576.
During RNA interference and related gene regulatory pathways, the endonuclease Dicer cleaves precursor RNA molecules to produce microRNAs (miRNAs) and short interfering RNAs (siRNAs). Human cells encode a single Dicer enzyme that can associate with two different double-stranded RNA (dsRNA)-binding proteins, protein activator of PKR (PACT) and trans-activation response RNA-binding protein (TRBP). However, the functional redundancy or differentiation of PACT and TRBP in miRNA and siRNA biogenesis is not well understood. Using a reconstituted system, we show here that PACT and TRBP have distinct effects on Dicer-mediated dsRNA processing. In particular, we found that PACT in complex with Dicer inhibits the processing of pre-siRNA substrates when compared with Dicer and a Dicer–TRBP complex. In addition, PACT and TRBP show non-redundant effects on the production of different-sized miRNAs (isomiRs), which in turn alter target-binding specificities. Experiments using chimeric versions of PACT and TRBP suggest that the two N-terminal RNA-binding domains of each protein confer the observed differences in dsRNA substrate recognition and processing behavior of Dicer–dsRNA-binding protein complexes. These results support the conclusion that in humans, Dicer-associated dsRNA-binding proteins are important regulatory factors that contribute both substrate and cleavage specificity during miRNA and siRNA production.
doi:10.1093/nar/gkt361
PMCID: PMC3711433  PMID: 23661684
18.  Coordinated Activities of Human Dicer Domains in Regulatory RNA Processing 
Journal of molecular biology  2012;422(4):466-476.
Summary
The conserved ribonuclease Dicer generates microRNAs and short interfering RNAs that guide gene silencing in eukaryotes. The specific contributions of human Dicer's structural domains to RNA product length and substrate preference are incompletely understood, due in part to the difficulties of Dicer purification. Here we show that active forms of human Dicer can be assembled from recombinant polypeptides expressed in bacteria. Using this system, we find that three distinct modes of RNA recognition give rise to Dicer's fidelity and product length specificity. The first involves anchoring one end of a dsRNA helix within the PAZ domain, which can assemble in trans with Dicer's catalytic domains to reconstitute an accurate but non-substrate-selective dicing activity. The second entails non-specific RNA binding by the double-stranded RNA binding domain (dsRBD), an interaction that is essential for substrate recruitment in the absence of the PAZ domain. The third mode of recognition involves hairpin RNA loop recognition by the helicase domain, which ensures efficient processing of specific substrates. These results reveal distinct interactions of each Dicer domain with different RNA structural features, and provide a facile system for investigating the molecular mechanisms of human miRNA biogenesis.
doi:10.1016/j.jmb.2012.06.009
PMCID: PMC3461841  PMID: 22727743
Ribonuclease; Dicer; RNAi
19.  Unconventional miR-122 binding stabilizes the HCV genome by forming a trimolecular RNA structure 
Nucleic Acids Research  2013;41(7):4230-4240.
MicroRNAs (miRNAs) typically downregulate protein expression from target mRNAs through limited base-pairing interactions between the 5′ ‘seed’ region of the miRNA and the mRNA 3′ untranslated region (3′UTR). In contrast to this established mode of action, the liver-specific human miR-122 binds at two sites within the hepatitis C viral (HCV) 5′UTR, leading to increased production of infectious virions. We show here that two copies of miR-122 interact with the HCV 5′UTR at partially overlapping positions near the 5′ end of the viral transcript to form a stable ternary complex. Both miR-122 binding sites involve extensive base pairing outside of the seed sequence; yet, they have substantially different interaction affinities. Structural probing reveals changes in the architecture of the HCV 5′UTR that occur on interaction with miR-122. In contrast to previous reports, however, results using both the recombinant cytoplasmic exonuclease Xrn1 and liver cell extracts show that miR-122-mediated protection of the HCV RNA from degradation does not correlate with stimulation of viral propagation in vivo. Thus, the miR-122:HCV ternary complex likely functions at other steps critical to the viral life cycle.
doi:10.1093/nar/gkt075
PMCID: PMC3627571  PMID: 23416544
20.  RNA-programmed genome editing in human cells 
eLife  2013;2:e00471.
Type II CRISPR immune systems in bacteria use a dual RNA-guided DNA endonuclease, Cas9, to cleave foreign DNA at specific sites. We show here that Cas9 assembles with hybrid guide RNAs in human cells and can induce the formation of double-strand DNA breaks (DSBs) at a site complementary to the guide RNA sequence in genomic DNA. This cleavage activity requires both Cas9 and the complementary binding of the guide RNA. Experiments using extracts from transfected cells show that RNA expression and/or assembly into Cas9 is the limiting factor for Cas9-mediated DNA cleavage. In addition, we find that extension of the RNA sequence at the 3′ end enhances DNA targeting activity in vivo. These results show that RNA-programmed genome editing is a facile strategy for introducing site-specific genetic changes in human cells.
DOI: http://dx.doi.org/10.7554/eLife.00471.001
eLife digest
The ability to make specific changes to DNA—such as changing, inserting or deleting sequences that encode proteins—allows researchers to engineer cells, tissues and organisms for therapeutic and practical applications. Until now, such genome engineering has required the design and production of proteins with the ability to recognize a specific DNA sequence. The bacterial protein, Cas9, has the potential to enable a simpler approach to genome engineering because it is a DNA-cleaving enzyme that can be programmed with short RNA molecules to recognize specific DNA sequences, thus dispensing with the need to engineer a new protein for each new DNA target sequence.
Now Jinek et al. demonstrate the capability of RNA-programmed Cas9 to introduce targeted double-strand breaks into human chromosomal DNA, thereby inducing site-specific genome editing reactions. Cas9 assembles with engineered single-guide RNAs in human cells and the resulting Cas9-RNA complex can induce the formation of double-strand breaks in genomic DNA at a site complementary to the guide RNA sequence. Experiments using extracts from transfected cells show that RNA expression and/or assembly into Cas9 is the limiting factor for the DNA cleavage, and that extension of the RNA sequence at the 3′ end enhances DNA targeting activity in vivo.
These results show that RNA-programmed genome editing is a straightforward strategy for introducing site-specific genetic changes in human cells, and the ease with which it can programmed means that it is likely to become competitive with existing approaches based on zinc finger nucleases and transcription activator-like effector nucleases, and could lead to a new generation of experiments in the field of genome engineering for humans and other species with complex genomes.
DOI: http://dx.doi.org/10.7554/eLife.00471.002
doi:10.7554/eLife.00471
PMCID: PMC3557905  PMID: 23386978
Cas9; endonuclease; genome editing; Human
21.  Reconsidering Movement of Eukaryotic mRNAs Between Polysomes and P-bodies 
Molecular cell  2011;44(5):745-758.
SUMMARY
Cell survival in changing environments requires appropriate regulation of gene expression, including post-transcriptional regulatory mechanisms. From reporter gene studies in glucose-starved yeast, it was proposed that translationally silenced eukaryotic mRNAs accumulate in P-bodies and can return to active translation. We present evidence contradicting the notion that reversible storage of non-translating mRNAs is a widespread and general phenomenon. First, genome-wide measurements of mRNA abundance, translation, and ribosome occupancy following glucose withdrawal show that most mRNAs are depleted from the cell coincident with their depletion from polysomes. Second, only a limited sub-population of translationally repressed transcripts, comprising fewer than 400 genes, can be reactivated for translation upon glucose re-addition in the absence of new transcription. This highly selective post-transcriptional regulation could be a mechanism for cells to minimize the energetic costs of reversing gene-regulatory decisions in rapidly changing environments by transiently preserving a pool of transcripts whose translation is rate-limiting for growth.
doi:10.1016/j.molcel.2011.09.019
PMCID: PMC3240842  PMID: 22152478
22.  Mechanism of foreign DNA selection in a bacterial adaptive immune system 
Molecular cell  2012;46(5):606-615.
Summary
In bacterial and archaeal CRISPR immune pathways, DNA sequences from invading bacteriophage or plasmids are integrated into CRISPR loci within the host genome, conferring immunity against subsequent infections. The ribonucleoprotein complex Cascade utilizes RNAs generated from these loci to target complementary “non-self” DNA sequences for destruction, while avoiding binding to “self” sequences within the CRISPR locus. Here we show that CasA, the largest protein subunit of Cascade, is required for non-self target recognition and binding. Combining a 2.3 Å crystal structure of CasA with cryo-EM structures of Cascade, we have identified a loop that is required for viral defense. This loop contacts a conserved 3-base pair motif that is required for non-self target selection. Our data suggest a model in which the CasA loop scans DNA for this short motif prior to target destabilization and binding, maximizing the efficiency of DNA surveillance by Cascade.
doi:10.1016/j.molcel.2012.03.020
PMCID: PMC3397241  PMID: 22521690
23.  Structural and Biochemical Studies of a Fluoroacetyl-CoA-Specific Thioesterase Reveal a Molecular Basis for Fluorine Selectivity†,‡ 
Biochemistry  2010;49(43):9269-9279.
We have initiated a broad-based program aimed at understanding the molecular basis of fluorine specificity in enzymatic systems, and in this context, we report crystallographic and biochemical studies on a fluoroacetyl-coenzyme A (CoA) specific thioesterase (FlK) from Streptomyces cattleya. Our data establish that FlK is competent to protect its host from fluoroacetate toxicity in vivo and demonstrate a 106-fold discrimination between fluoroacetyl-CoA(kcat/KM=5×107M−1 s−1) and acetyl-CoA(kcat/KM=30 M−1 s−1) based on a single fluorine substitution that originates from differences in both substrate reactivity and binding. We show that Thr 42, Glu 50, and His 76 are key catalytic residues and identify several factors that influence substrate selectivity. We propose that FlK minimizes interaction with the thioester carbonyl, leading to selection against acetyl-CoA binding that can be recovered in part by new C=O interactions in the T42S and T42C mutants. We hypothesize that the loss of these interactions is compensated by the entropic driving force for fluorinated substrate binding in a hydrophobic binding pocket created by a lid structure, containing Val 23, Leu 26, Phe 33, and Phe 36, that is not found in other structurally characterized members of this superfamily. We further suggest that water plays a critical role in fluorine specificity based on biochemical and structural studies focused on the unique Phe 36 “gate” residue, which functions to exclude water from the active site. Taken together, the findings from these studies offer molecular insights into organofluorine recognition and design of fluorine-specific enzymes.
doi:10.1021/bi101102u
PMCID: PMC3461317  PMID: 20836570
24.  Reassortment and Mutation of the Avian Influenza Virus Polymerase PA Subunit Overcome Species Barriers 
Journal of Virology  2012;86(3):1750-1757.
The emergence of new pandemic influenza A viruses requires overcoming barriers to cross-species transmission as viruses move from animal reservoirs into humans. This complicated process is driven by both individual gene mutations and genome reassortments. The viral polymerase complex, composed of the proteins PB1, PB2, and PA, is a major factor controlling host adaptation, and reassortment events involving polymerase gene segments occurred with past pandemic viruses. Here we investigate the ability of polymerase reassortment to restore the activity of an avian influenza virus polymerase that is normally impaired in human cells. Our data show that the substitution of human-origin PA subunits into an avian influenza virus polymerase alleviates restriction in human cells and increases polymerase activity in vitro. Reassortants with 2009 pandemic H1N1 PA proteins were the most active. Mutational analyses demonstrated that the majority of the enhancing activity in human PA results from a threonine-to-serine change at residue 552. Reassortant viruses with avian polymerases and human PA subunits, or simply the T552S mutation, displayed faster replication kinetics in culture and increased pathogenicity in mice compared to those containing a wholly avian polymerase complex. Thus, the acquisition of a human PA subunit, or the signature T552S mutation, is a potential mechanism to overcome the species-specific restriction of avian polymerases and increase virus replication. Our data suggest that the human, avian, swine, and 2009 H1N1-like viruses that are currently cocirculating in pig populations set the stage for PA reassortments with the potential to generate novel viruses that could possess expanded tropism and enhanced pathogenicity.
doi:10.1128/JVI.06203-11
PMCID: PMC3264373  PMID: 22090127
25.  Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning 
Structure (London, England : 1993)  2011;19(10):1456-1466.
SUMMARY
Translation of Hepatitis C viral proteins requires an internal ribosome entry site (IRES) located in the 5′ untranslated region of the viral mRNA. The core domain of the Hepatitis C virus (HCV) IRES contains a four-way helical junction that is integrated within a predicted pseudoknot. This domain is required for positioning the mRNA start codon correctly on the 40S ribosomal subunit during translation initiation. Here we present the crystal structure of this RNA, revealing a complex double-pseudoknot fold that establishes the alignment of two helical elements on either side of the four-helix junction. The conformation of this core domain constrains the open reading frame’s orientation for positioning on the 40S ribosomal subunit. This structure, representing the last major domain of HCV-like IRESs to be determined at near-atomic resolution, provides the basis for a comprehensive cryo-electron microscopy-guided model of the intact HCV IRES and its interaction with 40S ribosomal subunits.
doi:10.1016/j.str.2011.08.002
PMCID: PMC3209822  PMID: 22000514

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