Comparative genomics of defense systems in archaea and bacteria

Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing

(2013) Vivek Anantharaman et al.   Biology Direct

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

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

Bacterial Persistence and Toxin-Antitoxin Loci

(2012) Kenn Gerdes et al.   Annual Review of Microbiology

Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

(2012) Kira S Makarova et al.   Biology Direct

Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes

(2012) Kira S Makarova et al.   Biology Direct

Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics

(2012) Dapeng Zhang et al.   Biology Direct

Chromosomal bacterial type II toxin–antitoxin systems

(2012) Mohammad Adnan Syed et al.   CANADIAN JOURNAL OF MICROBIOLOGY

CRISPR Interference Can Prevent Natural Transformation and Virulence Acquisition during In Vivo Bacterial Infection

(2012) David Bikard et al.   Cell Host & Microbe

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

(2012) Xing Zhu et al.   FEBS LETTERS

A vast collection of microbial genes that are toxic to bacteria

(2012) A. Kimelman et al.   GENOME RESEARCH

Native Tandem and Ion Mobility Mass Spectrometry Highlight Structural and Modular Similarities in Clustered-Regularly-Interspaced Shot-Palindromic-Repeats (CRISPR)-associated Protein Complexes FromEscherichia coliandPseudomonas aeruginosa

(2012) Esther van Duijn et al.   MOLECULAR & CELLULAR PROTEOMICS

Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing

(2012) Vivek Anantharaman et al.   Molecular BioSystems

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

(2012) Jing Zhang et al.   MOLECULAR CELL

Dmd of bacteriophage T4 functions as an antitoxin against Escherichia coli LsoA and RnlA toxins

(2012) Yuichi Otsuka et al.   MOLECULAR MICROBIOLOGY

YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli

(2012) Hisako Masuda et al.   MOLECULAR MICROBIOLOGY

A promiscuous antitoxin of bacteriophage T4 ensures successful viral replication

(2012) Francesca L. Short et al.   MOLECULAR MICROBIOLOGY

A CRISPR Approach to Gene Targeting

(2012) Dana Carroll   MOLECULAR THERAPY

Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system

(2012) Joe Bondy-Denomy et al.   NATURE

RNA-guided genetic silencing systems in bacteria and archaea

(2012) Blake Wiedenheft et al.   NATURE

RNA processing enables predictable programming of gene expression

(2012) Lei Qi et al.   NATURE BIOTECHNOLOGY

A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS

(2012) Xiaoxue Wang et al.   Nature Chemical Biology

The wobble nucleotide-excising anticodon nuclease RloC is governed by the zinc-hook and DNA-dependent ATPase of its Rad50-like region

(2012) D. Klaiman et al.   NUCLEIC ACIDS RESEARCH

Solitary restriction endonucleases in prokaryotic genomes

(2012) Anna S. Ershova et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Ido Yosef et al.   NUCLEIC ACIDS RESEARCH

Identification and classification of bacterial Type III toxin–antitoxin systems encoded in chromosomal and plasmid genomes

(2012) Tim R. Blower et al.   NUCLEIC ACIDS RESEARCH

Crystal Structure of the Cysteine Desulfurase DndA from Streptomyces lividans Which Is Involved in DNA Phosphorothioation

(2012) Fukun Chen et al.   PLoS One

CRISPR Typing and Subtyping for Improved Laboratory Surveillance of Salmonella Infections

(2012) Laëtitia Fabre et al.   PLoS One

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Memory of viral infections by CRISPR-Cas adaptive immune systems: Acquisition of new information

(2012) Peter C. Fineran et al.   VIROLOGY

CRISPR: New Horizons in Phage Resistance and Strain Identification

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

Viral Diversity Threshold for Adaptive Immunity in Prokaryotes

(2012) A. D. Weinberger et al.   mBio

Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism

(2012) Tim R. Blower et al.   PLoS Genetics

Gene flow and biological conflict systems in the origin and evolution of eukaryotes

(2012) L. Aravind et al.   Frontiers in Cellular and Infection Microbiology

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

Toxin-Antitoxin Systems in Bacteria and Archaea

(2011) Yoshihiro Yamaguchi et al.   Annual Review of Genetics

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

(2011) Kira S Makarova et al.   Biology Direct

Toxins-antitoxins: diversity, evolution and function

(2011) Finbarr Hayes et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Balancing at survival's edge: the structure and adaptive benefits of prokaryotic toxin–antitoxin partners

(2011) Tim R Blower et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2011) Tomas Sinkunas et al.   EMBO JOURNAL

Mechanistic insights into type III restriction enzymes

(2011) Nidhanapati et al.   Frontiers in Bioscience-Landmark

Nature and Intensity of Selection Pressure on CRISPR-Associated Genes

(2011) N. Takeuchi et al.   JOURNAL OF BACTERIOLOGY

RelE-Mediated Dormancy Is Enhanced at High Cell Density in Escherichia coli

(2011) Y. Tashiro et al.   JOURNAL OF BACTERIOLOGY

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

(2011) K. S. Makarova et al.   JOURNAL OF BACTERIOLOGY

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

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

Regulation of growth and death in Escherichia coli by toxin–antitoxin systems

(2011) Yoshihiro Yamaguchi et al.   NATURE REVIEWS MICROBIOLOGY

Evolution and classification of the CRISPR–Cas systems

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

A reverse transcriptase-related protein mediates phage resistance and polymerizes untemplated DNA in vitro

(2011) Chen Wang et al.   NUCLEIC ACIDS RESEARCH

A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

(2011) Dapeng Zhang et al.   NUCLEIC ACIDS RESEARCH

Diversity of bacterial type II toxin–antitoxin systems: a comprehensive search and functional analysis of novel families

(2011) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus

(2011) Ling Deng et al.   NUCLEIC ACIDS RESEARCH

IS-Linked Movement of a Restriction-Modification System

(2011) Noriko Takahashi et al.   PLoS One

Bacterial persistence by RNA endonucleases

(2011) Etienne Maisonneuve et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lactococcal Abortive Infection Protein AbiV Interacts Directly with the Phage Protein SaV and Prevents Translation of Phage Proteins

(2010) J. Haaber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2010) Adi Stern et al.   BIOESSAYS

Conflicts Targeting Epigenetic Systems and Their Resolution by Cell Death: Novel Concepts for Methyl-Specific and Other Restriction Systems

(2010) K. Ishikawa et al.   DNA RESEARCH

The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea

(2010) Fedor V. Karginov et al.   MOLECULAR CELL

YeeV is an Escherichia coli toxin that inhibits cell division by targeting the cytoskeleton proteins, FtsZ and MreB

(2010) Qian Tan et al.   MOLECULAR MICROBIOLOGY

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

(2010) Josiane E. Garneau et al.   NATURE

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

Abundance of type I toxin–antitoxin systems in bacteria: searches for new candidates and discovery of novel families

(2010) Elizabeth M. Fozo et al.   NUCLEIC ACIDS RESEARCH

A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI)

(2010) Feroz Khan et al.   NUCLEIC ACIDS RESEARCH

Genome comparison and context analysis reveals putative mobile forms of restriction–modification systems and related rearrangements

(2010) Yoshikazu Furuta et al.   NUCLEIC ACIDS RESEARCH

A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella

(2010) Tiegang Xu et al.   NUCLEIC ACIDS RESEARCH

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

Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation

(2010) Marc Uzan et al.   Virology Journal

The Great Billion-year War between Ribosome- and Capsid-encoding Organisms (Cells and Viruses) as the Major Source of Evolutionary Novelties

(2009) Patrick Forterre et al.   Annals of the New York Academy of Sciences

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

Is evolution Darwinian or/and Lamarckian?

(2009) Eugene V Koonin et al.   Biology Direct

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

(2009) Caryn R. Hale et al.   CELL

Crystal Structure of the IrrE Protein, a Central Regulator of DNA Damage Repair in Deinococcaceae

(2009) Andreja Vujičić-Žagar et al.   JOURNAL OF MOLECULAR BIOLOGY

Deciphering the function of lactococcal phage ul36 Sak domains

(2009) Erika Scaltriti et al.   JOURNAL OF STRUCTURAL BIOLOGY

The phage abortive infection system, ToxIN, functions as a protein–RNA toxin–antitoxin pair

(2009) Peter C. Fineran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Blake Wiedenheft et al.   STRUCTURE

CRISPR-based adaptive and heritable immunity in prokaryotes

(2009) John van der Oost et al.   TRENDS IN BIOCHEMICAL SCIENCES

Bacterial Toxin–Antitoxin Systems: More Than Selfish Entities?

(2009) Laurence Van Melderen et al.   PLoS Genetics

MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases

(2008) Lakshminarayan M Iyer et al.   Biology Direct

Comparative Enzymology in the Alkaline Phosphatase Superfamily to Determine the Catalytic Role of an Active-Site Metal Ion

(2008) Jesse G. Zalatan et al.   JOURNAL OF MOLECULAR BIOLOGY

Small Toxic Proteins and the Antisense RNAs That Repress Them

(2008) E. M. Fozo et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Systematic Survey for Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture

(2008) K. K. Kojima et al.   MOLECULAR BIOLOGY AND EVOLUTION

RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase

(2008) Elena Davidov et al.   MOLECULAR MICROBIOLOGY

Structure of the guide-strand-containing argonaute silencing complex

(2008) Yanli Wang et al.   NATURE

Using shotgun sequence data to find active restriction enzyme genes

(2008) Yu Zheng et al.   NUCLEIC ACIDS RESEARCH

Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses

(2008) Jerzy Orlowski et al.   NUCLEIC ACIDS RESEARCH