CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

The CRISPRs, They Are A-Changin': How Prokaryotes Generate Adaptive Immunity

(2012) Edze R. Westra et al.   Annual Review of Genetics

Low Species Barriers in Halophilic Archaea and the Formation of Recombinant Hybrids

(2012) Adit Naor et al.   CURRENT BIOLOGY

Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA

(2012) Rachel E Haurwitz et al.   EMBO JOURNAL

MULTISCALE MODEL OF CRISPR-INDUCED COEVOLUTIONARY DYNAMICS: DIVERSIFICATION AT THE INTERFACE OF LAMARCK AND DARWIN

(2012) Lauren M. Childs et al.   EVOLUTION

Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems

(2012) Xing Zhu et al.   FEBS LETTERS

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

The CRISPR/Cas Adaptive Immune System of Pseudomonas aeruginosa Mediates Resistance to Naturally Occurring and Engineered Phages

(2012) K. C. Cady et al.   JOURNAL OF BACTERIOLOGY

Characterization of the CRISPR/Cas Subtype I-A System of the Hyperthermophilic Crenarchaeon Thermoproteus tenax

(2012) A. Plagens et al.   JOURNAL OF BACTERIOLOGY

Crystal Structure of the Largest Subunit of a Bacterial RNA-guided Immune Complex and Its Role in DNA Target Binding

(2012) Sabin Mulepati et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The crystal structure of the CRISPR-associated protein Csn2 from Streptococcus agalactiae

(2012) Philipp Ellinger et al.   JOURNAL OF STRUCTURAL BIOLOGY

Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs

(2012) B. Bolduc et al.   JOURNAL OF VIROLOGY

CRISPR adaptive immunity systems of prokaryotes

(2012) K. S. Pougach et al.   MOLECULAR BIOLOGY

Structure and Mechanism of the CMR Complex for CRISPR-Mediated Antiviral Immunity

(2012) Jing Zhang et al.   MOLECULAR CELL

Essential Features and Rational Design of CRISPR RNAs that Function with the Cas RAMP Module Complex to Cleave RNAs

(2012) Caryn R. Hale et al.   MOLECULAR CELL

CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3

(2012) Edze R. Westra et al.   MOLECULAR CELL

Mechanism of Foreign DNA Selection in a Bacterial Adaptive Immune System

(2012) Dipali G. Sashital et al.   MOLECULAR CELL

RNA-guided genetic silencing systems in bacteria and archaea

(2012) Blake Wiedenheft et al.   NATURE

Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli

(2012) Ido Yosef et al.   NUCLEIC ACIDS RESEARCH

Crystal Structure of Streptococcus pyogenes Csn2 Reveals Calcium-Dependent Conformational Changes in Its Tertiary and Quaternary Structure

(2012) Yoon Koo et al.   PLoS One

CRISPR Interference Directs Strand Specific Spacer Acquisition

(2012) Daan C. Swarts et al.   PLoS One

Phage-Induced Expression of CRISPR-Associated Proteins Is Revealed by Shotgun Proteomics in Streptococcus thermophilus

(2012) Jacque C. Young et al.   PLoS One

Target Motifs Affecting Natural Immunity by a Constitutive CRISPR-Cas System in Escherichia coli

(2012) Cristóbal Almendros et al.   PLoS One

The CRISPR Associated Protein Cas4 Is a 5′ to 3′ DNA Exonuclease with an Iron-Sulfur Cluster

(2012) Jing Zhang et al.   PLoS One

The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex

(2012) Ruiying Wang et al.   PROTEIN SCIENCE

The mysterious RAMP proteins and their roles in small RNA-based immunity

(2012) Ruiying Wang et al.   PROTEIN SCIENCE

Cascade-mediated binding and bending of negatively supercoiled DNA

(2012) Edze R. Westra et al.   RNA Biology

A genome-wide view of the expression and processing patterns of Thermus thermophilus HB8 CRISPR RNAs

(2012) S. Juranek et al.   RNA

Mechanism of substrate selection by a highly specific CRISPR endoribonuclease

(2012) S. H. Sternberg et al.   RNA

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Structure of the Cmr2 Subunit of the CRISPR-Cas RNA Silencing Complex

(2012) Alexis I. Cocozaki et al.   STRUCTURE

Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System

(2012) Ki Hyun Nam et al.   STRUCTURE

CRISPR: New Horizons in Phage Resistance and Strain Identification

(2012) Rodolphe Barrangou et al.   Annual Review of Food Science and Technology

Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system

(2012) Kirill A. Datsenko et al.   Nature Communications

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

(2012) Ariel D. Weinberger et al.   PLoS Computational Biology

Diverse CRISPRs Evolving in Human Microbiomes

(2012) Mina Rho et al.   PLoS Genetics

Characterization of the multiple CRISPR loci on Streptomyces linear plasmid pSHK1

(2011) Peng Guo et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

Innate and adaptive immunity in bacteria: mechanisms of programmed genetic variation to fight bacteriophages

(2011) David Bikard et al.   CURRENT OPINION IN IMMUNOLOGY

Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference

(2011) Natalia Beloglazova et al.   EMBO JOURNAL

Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system

(2011) Tomas Sinkunas et al.   EMBO JOURNAL

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

The CRISPR/Cas Immune System Is an Operon Regulated by LeuO, H-NS, and Leucine-Responsive Regulatory Protein in Salmonella enterica Serovar Typhi

(2011) L. Medina-Aparicio et al.   JOURNAL OF BACTERIOLOGY

Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca2+-dependent Double-stranded DNA Binding Activity

(2011) Ki Hyun Nam et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural and Biochemical Analysis of Nuclease Domain of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Protein 3 (Cas3)

(2011) Sabin Mulepati et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)

(2011) Nathanael G. Lintner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Targeted Bacterial Immunity Buffers Phage Diversity

(2011) J. O. Haerter et al.   JOURNAL OF VIROLOGY

Genomic island variability facilitates Prochlorococcus–virus coexistence

(2011) Sarit Avrani et al.   NATURE

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

Structures of the RNA-guided surveillance complex from a bacterial immune system

(2011) Blake Wiedenheft et al.   NATURE

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Recognition and maturation of effector RNAs in a CRISPR interference pathway

(2011) Emily M Gesner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3

(2011) Dipali G Sashital et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

(2011) Matthijs M Jore et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli

(2011) Rimantas Sapranauskas et al.   NUCLEIC ACIDS RESEARCH

Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site

(2011) A. Hatoum-Aslan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions

(2011) B. Wiedenheft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

(2011) E. Semenova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteria-Phage Antagonistic Coevolution in Soil

(2011) P. Gomez et al.   SCIENCE

Interaction of the Cas6 Riboendonuclease with CRISPR RNAs: Recognition and Cleavage

(2011) Ruiying Wang et al.   STRUCTURE

Structure of a CRISPR-associated protein Cas2 fromDesulfovibrio vulgaris

(2010) Poulami Samai et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

CRISPR/Cas System and Its Role in Phage-Bacteria Interactions

(2010) Hélène Deveau et al.   Annual Review of Microbiology

Evolutionary Dynamics of Clustered Irregularly Interspaced Short Palindromic Repeat Systems in the Ocean Metagenome

(2010) V. A. Sorokin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Oxidative stress protection and the repair response to hydrogen peroxide in the hyperthermophilic archaeon Pyrococcus furiosus and in related species

(2010) Kari R. Strand et al.   ARCHIVES OF MICROBIOLOGY

The phage-host arms race: Shaping the evolution of microbes

(2010) Adi Stern et al.   BIOESSAYS

A divalent switch drives H-NS/DNA-binding conformations between stiffening and bridging modes

(2010) Y. Liu et al.   GENES & DEVELOPMENT

Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time

(2010) D. T. Pride et al.   GENOME RESEARCH

The Structure of the CRISPR-Associated Protein Csa3 Provides Insight into the Regulation of the CRISPR/Cas System

(2010) Nathanael G. Lintner et al.   JOURNAL OF MOLECULAR BIOLOGY

Diversity of CRISPR loci in Escherichia coli

(2010)   MICROBIOLOGY-SGM

Dangerous weapons: a cautionary tale of CRISPR defence

(2010) Mike Dyall-Smith   MOLECULAR MICROBIOLOGY

Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers

(2010) Soley Gudbergsdottir et al.   MOLECULAR MICROBIOLOGY

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair

(2010) Mohan Babu et al.   MOLECULAR MICROBIOLOGY

Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli

(2010) Ritsdeliz Perez-Rodriguez et al.   MOLECULAR MICROBIOLOGY

Transcription, processing and function of CRISPR cassettes in Escherichia coli

(2010) Ksenia Pougach et al.   MOLECULAR MICROBIOLOGY

Identification and characterization ofE. coliCRISPR-caspromoters and their silencing by H-NS

(2010) Ümit Pul et al.   MOLECULAR MICROBIOLOGY

H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO

(2010) Edze R. Westra et al.   MOLECULAR MICROBIOLOGY

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

(2010) Josiane E. Garneau et al.   NATURE

Self versus non-self discrimination during CRISPR RNA-directed immunity

(2010) Luciano A. Marraffini et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

Heterogeneous Diversity of Spacers within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

(2010) Jiankui He et al.   PHYSICAL REVIEW LETTERS

CRISPR Associated Diversity within a Population of Sulfolobus islandicus

(2010) Nicole L. Held et al.   PLoS One

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities

(2010) V. J. Denef et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleases: diversity of structure, function and mechanism

(2010) Wei Yang   QUARTERLY REVIEWS OF BIOPHYSICS

Binding and cleavage of CRISPR RNA by Cas6

(2010) J. Carte et al.   RNA

Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease

(2010) Rachel E. Haurwitz et al.   SCIENCE

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Self-targeting by CRISPR: gene regulation or autoimmunity?

(2010) Adi Stern et al.   TRENDS IN GENETICS

Multidrug-Resistant Enterococci Lack CRISPR-cas

(2010) K. L. Palmer et al.   mBio

Nasty Viruses, Costly Plasmids, Population Dynamics, and the Conditions for Establishing and Maintaining CRISPR-Mediated Adaptive Immunity in Bacteria

(2010) Bruce R. Levin   PLoS Genetics

CRISPI: a CRISPR interactive database

(2009) C. Rousseau et al.   BIOINFORMATICS

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

(2009) Kira S Makarova et al.   Biology Direct

RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex

(2009) Caryn R. Hale et al.   CELL

Viral biogeography revealed by signatures inSulfolobus islandicusgenomes

(2009) Nicole L. Held et al.   ENVIRONMENTAL MICROBIOLOGY

Characterization of the endonuclease SSO2001 fromSulfolobus solfataricusP2

(2009) Dong Han et al.   FEBS LETTERS

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

Transcription Profile of Thermus thermophilus CRISPR Systems after Phage Infection

(2009) Yoshihiro Agari et al.   JOURNAL OF MOLECULAR BIOLOGY

Analysis of CRISPR in Streptococcus mutans suggests frequent occurrence of acquired immunity against infection by M102-like bacteriophages

(2009)   MICROBIOLOGY-SGM

Short motif sequences determine the targets of the prokaryotic CRISPR defence system

(2009)   MICROBIOLOGY-SGM

CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties

(2009) Reidun K. Lillestøl et al.   MOLECULAR MICROBIOLOGY

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes

(2009) John F. Heidelberg et al.   PLoS One

Local Adaptation of Bacteriophages to Their Bacterial Hosts in Soil

(2009) M. Vos et al.   SCIENCE

Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense

(2009) Blake Wiedenheft et al.   STRUCTURE

Bacteriophages as model organisms for virus emergence research

(2009) John J. Dennehy   TRENDS IN MICROBIOLOGY

(p)ppGpp: Still Magical?

(2008) Katarzyna Potrykus et al.   Annual Review of Microbiology

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

(2008) J. Carte et al.   GENES & DEVELOPMENT

A Novel Family of Sequence-specific Endoribonucleases Associated with the Clustered Regularly Interspaced Short Palindromic Repeats

(2008) Natalia Beloglazova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanism of homologous recombination from the RecA–ssDNA/dsDNA structures

(2008) Zhucheng Chen et al.   NATURE

X-ray crystal structure of a CRISPR-associated RAMP superfamily protein, Cmr5, fromThermus thermophilusHB8

(2008) Keiko Sakamoto et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus

(2008) C. Hale et al.   RNA

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

(2008) S. J. J. Brouns et al.   SCIENCE

CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA

(2008) Luciano A. Marraffini et al.   SCIENCE

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

(2008) A. F. Andersson et al.   SCIENCE