Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation.

Abstract:

:Prokaryotes use a mechanism called priming to update their CRISPR immunological memory to rapidly counter revisiting, mutated viruses, and plasmids. Here we have determined how new spacers are produced and selected for integration into the CRISPR array during priming. We show that Cas3 couples CRISPR interference to adaptation by producing DNA breakdown products that fuel the spacer integration process in a two-step, PAM-associated manner. The helicase-nuclease Cas3 pre-processes target DNA into fragments of about 30-100 nt enriched for thymine-stretches in their 3' ends. The Cas1-2 complex further processes these fragments and integrates them sequence-specifically into CRISPR repeats by coupling of a 3' cytosine of the fragment. Our results highlight that the selection of PAM-compliant spacers during priming is enhanced by the combined sequence specificities of Cas3 and the Cas1-2 complex, leading to an increased propensity of integrating functional CTT-containing spacers.

journal_name

Mol Cell

journal_title

Molecular cell

authors

Künne T,Kieper SN,Bannenberg JW,Vogel AI,Miellet WR,Klein M,Depken M,Suarez-Diez M,Brouns SJ

doi

10.1016/j.molcel.2016.07.011

subject

Has Abstract

pub_date

2016-09-01 00:00:00

pages

852-64

issue

5

eissn

1097-2765

issn

1097-4164

pii

S1097-2765(16)30364-1

journal_volume

63

pub_type

杂志文章
  • The nucle(ol)ar Tif6p and Efl1p are required for a late cytoplasmic step of ribosome synthesis.

    abstract::Deletion of elongation factor-like 1 (Efl1p), a cytoplasmic GTPase homologous to the ribosomal translocases EF-G/EF-2, results in nucle(ol)ar pre-rRNA processing and pre-60S subunits export defects. Efl1p interacts genetically with Tif6p, a nucle(ol)ar protein stably associated with pre-60S subunits and required for t...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(01)00403-8

    authors: Senger B,Lafontaine DL,Graindorge JS,Gadal O,Camasses A,Sanni A,Garnier JM,Breitenbach M,Hurt E,Fasiolo F

    更新日期:2001-12-01 00:00:00

  • A role for SIRT1 in the hypoxic response.

    abstract::In this issue of Molecular Cell, Lim et al. (2010) show that SIRT1 deacetylates HIF-1alpha and regulates its ability to respond to hypoxia, revealing yet another important function of SIRT1 and suggesting a connection between HIF function in aging and sirtuin enzymes. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2010.06.015

    authors: Leiser SF,Kaeberlein M

    更新日期:2010-06-25 00:00:00

  • Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center.

    abstract::One of the oldest questions in RNA science is the role of nucleotide modification. Here, the importance of pseudouridine formation (Psi) in the peptidyl transferase center of rRNA was examined by depleting yeast cells of 1-5 snoRNAs that guide a total of six Psi modifications. Translation was impaired substantially wi...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(03)00040-6

    authors: King TH,Liu B,McCully RR,Fournier MJ

    更新日期:2003-02-01 00:00:00

  • PML, SUMO, and RNF4: guardians of nuclear protein quality.

    abstract::In this issue of Molecular Cell, Guo et al. (2014) report that misfolded or aggregated nuclear proteins, such as pathogenic polyQ proteins, are cleared by a SUMO-dependent quality control pathway, which involves the E3 SUMO ligase PML and the SUMO-targeted ubiquitin ligase RNF4. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2014.06.022

    authors: Gärtner A,Muller S

    更新日期:2014-07-03 00:00:00

  • Mechanism of microtubule stabilization by doublecortin.

    abstract::Neurons undertake an amazing journey from the center of the developing mammalian brain to the outer layers of the cerebral cortex. Doublecortin, a component of the microtubule cytoskeleton, is essential in postmitotic neurons and was identified because its mutation disrupts human brain development. Doublecortin stabil...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2004.06.009

    authors: Moores CA,Perderiset M,Francis F,Chelly J,Houdusse A,Milligan RA

    更新日期:2004-06-18 00:00:00

  • A soluble form of the pilus protein FimA targets the VDAC-hexokinase complex at mitochondria to suppress host cell apoptosis.

    abstract::Inhibition of apoptotic response of host cells during an early phase of infection is a strategy used by many enteroinvasive bacterial pathogens to enhance their survival. Here, we report the identification of a soluble form of the pilus protein FimA from the culture supernatants of E. coli K1, Salmonella, and Shigella...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2010.02.015

    authors: Sukumaran SK,Fu NY,Tin CB,Wan KF,Lee SS,Yu VC

    更新日期:2010-03-26 00:00:00

  • Structural Basis for the Modulation of Human KCNQ4 by Small-Molecule Drugs.

    abstract::Among the five KCNQ channels, also known as the Kv7 voltage-gated potassium (Kv) channels, KCNQ2-KCNQ5 control neuronal excitability. Dysfunctions of KCNQ2-KCNQ5 are associated with neurological disorders such as epilepsy, deafness, and neuropathic pain. Here, we report the cryoelectron microscopy (cryo-EM) structures...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2020.10.037

    authors: Li T,Wu K,Yue Z,Wang Y,Zhang F,Shen H

    更新日期:2021-01-07 00:00:00

  • A Functional Mini-Integrase in a Two-Protein-type V-C CRISPR System.

    abstract::CRISPR-Cas immunity requires integration of short, foreign DNA fragments into the host genome at the CRISPR locus, a site consisting of alternating repeat sequences and foreign-derived spacers. In most CRISPR systems, the proteins Cas1 and Cas2 form the integration complex and are both essential for DNA acquisition. M...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2018.12.015

    authors: Wright AV,Wang JY,Burstein D,Harrington LB,Paez-Espino D,Kyrpides NC,Iavarone AT,Banfield JF,Doudna JA

    更新日期:2019-02-21 00:00:00

  • An orphan receptor tyrosine kinase family whose members serve as nonintegrin collagen receptors.

    abstract::Mammalian cells constantly monitor and respond to a myriad of extracellular signals, often by using cell surface receptors. Two important classes of cell surface receptors include the receptor tyrosine kinases, which recognize peptide growth factors such as insulin, and the integrins, which most often mediate binding ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)80004-0

    authors: Shrivastava A,Radziejewski C,Campbell E,Kovac L,McGlynn M,Ryan TE,Davis S,Goldfarb MP,Glass DJ,Lemke G,Yancopoulos GD

    更新日期:1997-12-01 00:00:00

  • Essential Roles of the Smc5/6 Complex in Replication through Natural Pausing Sites and Endogenous DNA Damage Tolerance.

    abstract::The essential functions of the conserved Smc5/6 complex remain elusive. To uncover its roles in genome maintenance, we established Saccharomyces cerevisiae cell-cycle-regulated alleles that enable restriction of Smc5/6 components to S or G2/M. Unexpectedly, the essential functions of Smc5/6 segregated fully and select...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2015.10.023

    authors: Menolfi D,Delamarre A,Lengronne A,Pasero P,Branzei D

    更新日期:2015-12-17 00:00:00

  • A Finer Print Than TADs: PRC1-Mediated Domains.

    abstract::Polycomb proteins are well-known epigenetic repressors with unexplained roles in chromatin folding. In this issue of Molecular Cell, Kundu et al. (2017) investigate the structures of PRC1-mediated domains in stem cells and probe their changes upon differentiation and in PRC knockouts. ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2017.01.028

    authors: Torlai Triglia E,Rito T,Pombo A

    更新日期:2017-02-02 00:00:00

  • Resolving the CSN and CAND1 paradoxes.

    abstract::In this issue of Molecular Cell, Schmidt et al. (2009) untangle the interplay between the COP9 signalosome (CSN), cullin-associated and neddylation-dissociated 1 (CAND1) protein, and cullin-RING ubiquitin ligases (CRLs). ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2009.08.011

    authors: Dubiel W

    更新日期:2009-09-11 00:00:00

  • Akt-mediated phosphorylation of the G protein-coupled receptor EDG-1 is required for endothelial cell chemotaxis.

    abstract::The role of the protein kinase Akt in cell migration is incompletely understood. Here we show that sphingosine-1-phosphate (S1P)-induced endothelial cell migration requires the Akt-mediated phosphorylation of the G protein-coupled receptor (GPCR) EDG-1. Activated Akt binds to EDG-1 and phosphorylates the third intrace...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(01)00324-0

    authors: Lee MJ,Thangada S,Paik JH,Sapkota GP,Ancellin N,Chae SS,Wu M,Morales-Ruiz M,Sessa WC,Alessi DR,Hla T

    更新日期:2001-09-01 00:00:00

  • A core complex of CPSF73, CPSF100, and Symplekin may form two different cleavage factors for processing of poly(A) and histone mRNAs.

    abstract::Metazoan histone mRNAs are unique: their pre-mRNAs contain no introns, and the mRNAs are not polyadenylated, ending instead in a conserved stem-loop structure. In Drosophila, canonical poly(A) signals are located downstream of the normal cleavage site of each histone gene and are utilized when histone 3' end formation...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2009.04.024

    authors: Sullivan KD,Steiniger M,Marzluff WF

    更新日期:2009-05-15 00:00:00

  • Deamidation of Bcl-X(L): a new twist in a genotoxic murder mystery.

    abstract::Bcl-2 proteins are critical regulators of apoptosis following DNA damage. Recent studies have shown that genotoxic stress induces the deamidation of Bcl-X(L), inhibiting its antiapoptotic activities. Remarkably, Rb and p53 are important regulators of this novel modification of Bcl-X(L). ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(02)00693-7

    authors: Johnstone RW

    更新日期:2002-10-01 00:00:00

  • A major conformational change in p97 AAA ATPase upon ATP binding.

    abstract::AAA ATPases play central roles in cellular activities. The ATPase p97, a prototype of this superfamily, participates in organelle membrane fusion. Cryoelectron microscopy and single-particle analysis revealed that a major conformational change of p97 during the ATPase cycle occurred upon nucleotide binding and not dur...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)00144-1

    authors: Rouiller I,Butel VM,Latterich M,Milligan RA,Wilson-Kubalek EM

    更新日期:2000-12-01 00:00:00

  • Regulation of SUMOylation by reversible oxidation of SUMO conjugating enzymes.

    abstract::Posttranslational modification with small ubiquitin-related modifier (SUMO) has emerged as a central regulatory mechanism of protein function. However, little is known about the regulation of sumoylation itself. It has been reported that it is increased after exposure to various stresses including strong oxidative str...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2005.12.019

    authors: Bossis G,Melchior F

    更新日期:2006-02-03 00:00:00

  • Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli.

    abstract::In bacteria, Hfq is a core RNA chaperone that catalyzes the interaction of mRNAs with regulatory small RNAs (sRNAs). To determine in vivo RNA sequence requirements for Hfq interactions, and to study riboregulation in a bacterial pathogen, Hfq was UV crosslinked to RNAs in enterohemorrhagic Escherichia coli (EHEC). Hfq...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2014.05.006

    authors: Tree JJ,Granneman S,McAteer SP,Tollervey D,Gally DL

    更新日期:2014-07-17 00:00:00

  • MitoCPR: Meticulous Monitoring of Mitochondrial Proteostasis.

    abstract::Mitochondrial protein import stress compromises functioning of the organelles, due to inadequate supply of inner mitochondrial proteins. Weidberg and Amon (2018) describe a new monitoring pathway in budding yeast, which restores mitochondrial function following the clearing of accumulated unfolded pre-transported mito...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2018.06.027

    authors: Desai R,Campanella M

    更新日期:2018-07-05 00:00:00

  • Insulin activation of Rheb, a mediator of mTOR/S6K/4E-BP signaling, is inhibited by TSC1 and 2.

    abstract::Tumor suppressor genes evolved as negative effectors of mitogen and nutrient signaling pathways, such that mutations in these genes can lead to pathological states of growth. Tuberous sclerosis (TSC) is a potentially devastating disease associated with mutations in two tumor suppressor genes, TSC1 and 2, that function...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(03)00220-x

    authors: Garami A,Zwartkruis FJ,Nobukuni T,Joaquin M,Roccio M,Stocker H,Kozma SC,Hafen E,Bos JL,Thomas G

    更新日期:2003-06-01 00:00:00

  • E1 on the move.

    abstract::E1 enzymes activate ubiquitin or related proteins and pass them to E2 enzymes. A recent structure and associated biochemical studies (Huang et al., 2005) show how an E1 binds its cognate E2 and indicates that large, conformational changes will be an integral component of the E1 reaction cycle. ...

    journal_title:Molecular cell

    pub_type: 杂志文章,评审

    doi:10.1016/j.molcel.2005.02.004

    authors: VanDemark AP,Hill CP

    更新日期:2005-02-18 00:00:00

  • Histone Deacetylase 3 Couples Mitochondria to Drive IL-1β-Dependent Inflammation by Configuring Fatty Acid Oxidation.

    abstract::Immune cell function depends on specific metabolic programs dictated by mitochondria, including nutrient oxidation, macromolecule synthesis, and post-translational modifications. Mitochondrial adaptations have been linked to acute and chronic inflammation, but the metabolic cues and precise mechanisms remain unclear. ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2020.08.015

    authors: Chi Z,Chen S,Xu T,Zhen W,Yu W,Jiang D,Guo X,Wang Z,Zhang K,Li M,Zhang J,Fang H,Yang D,Ye Q,Yang X,Lin H,Yang F,Zhang X,Wang D

    更新日期:2020-10-01 00:00:00

  • Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs.

    abstract::A paradigm in transcriptional regulation is that graded increases in transcription factor (TF) concentration are translated into on/off transcriptional responses by cooperative TF binding to adjacent sites. Digital transcriptional responses underlie the definition of anatomical boundaries during development. Here we s...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2010.01.016

    authors: Giorgetti L,Siggers T,Tiana G,Caprara G,Notarbartolo S,Corona T,Pasparakis M,Milani P,Bulyk ML,Natoli G

    更新日期:2010-02-12 00:00:00

  • Distinct signals generate repeating striped pattern in the embryonic parasegment.

    abstract::How repeating striped patterns arise across cellular fields is unclear. To address this we examined the repeating pattern of Stripe (Sr) expression across the parasegment (PS) in Drosophila. This pattern is generated in two steps. First, the ligands Hedgehog (Hh) and Wingless (Wg) subdivide the PS into smaller territo...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(01)00163-0

    authors: Hatini V,DiNardo S

    更新日期:2001-01-01 00:00:00

  • Growth factor withdrawal and apoptosis: the middle game.

    abstract::In this issue of Molecular Cell, detail molecular events that trigger apoptosis following growth factor withdrawal, linking irreversible mitochondrial permeabilization to activation of GSK-3 and subsequent phosphorylation, ubiquitinylation, and degradation of the antiapoptotic BCL-2 family member MCL-1. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章,评审

    doi:10.1016/j.molcel.2006.03.005

    authors: Letai A

    更新日期:2006-03-17 00:00:00

  • Interaction of translation initiation factor 3 with the 30S ribosomal subunit.

    abstract::Hydroxyl radical footprinting and directed probing from Fe(II)-derivatized IF3 have been used to map the interaction of IF3 relative to 16S rRNA and tRNA(Met)(f) in the 30S ribosomal subunit. Our results place the two domains of IF3 on opposite sides of the initiator tRNA, with the C domain at the platform interface a...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(01)00356-2

    authors: Dallas A,Noller HF

    更新日期:2001-10-01 00:00:00

  • RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability.

    abstract::Genome instability, a hallmark of cancer progression, is thought to arise through DNA double strand breaks (DSBs). Studies in yeast and mammalian cells have shown that DSBs and instability can occur through RNA:DNA hybrids generated by defects in RNA elongation and splicing. We report that in yeast hybrids naturally f...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2011.10.017

    authors: Wahba L,Amon JD,Koshland D,Vuica-Ross M

    更新日期:2011-12-23 00:00:00

  • Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome.

    abstract::Thousands of cis-elements in genomes are predicted to have vital functions. Although conservation, activity in surrogate assays, polymorphisms, and disease mutations provide functional clues, deletion from endogenous loci constitutes the gold-standard test. A GATA-2-binding, Gata2 intronic cis-element (+9.5) required ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2015.05.020

    authors: Hewitt KJ,Kim DH,Devadas P,Prathibha R,Zuo C,Sanalkumar R,Johnson KD,Kang YA,Kim JS,Dewey CN,Keles S,Bresnick EH

    更新日期:2015-07-02 00:00:00

  • Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development.

    abstract::The methylcytosine oxidase TET proteins play important roles in DNA demethylation and development. However, it remains elusive how exactly they target substrates and execute oxidation. Interestingly, we found that, in mice, the full-length TET1 isoform (TET1e) is restricted to early embryos, embryonic stem cells (ESCs...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2016.10.030

    authors: Zhang W,Xia W,Wang Q,Towers AJ,Chen J,Gao R,Zhang Y,Yen CA,Lee AY,Li Y,Zhou C,Liu K,Zhang J,Gu TP,Chen X,Chang Z,Leung D,Gao S,Jiang YH,Xie W

    更新日期:2016-12-15 00:00:00

  • Caspase-mediated cleavage, IAP binding, and ubiquitination: linking three mechanisms crucial for Drosophila NF-kappaB signaling.

    abstract::Innate immune responses are critical for the immediate protection against microbial infection. In Drosophila, infection leads to the rapid and robust production of antimicrobial peptides through two NF-kappaB signaling pathways-IMD and Toll. The IMD pathway is triggered by DAP-type peptidoglycan, common to most Gram-n...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2009.12.036

    authors: Paquette N,Broemer M,Aggarwal K,Chen L,Husson M,Ertürk-Hasdemir D,Reichhart JM,Meier P,Silverman N

    更新日期:2010-01-29 00:00:00