Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

Structures of AAA protein translocase Bcs1 suggest translocation mechanism of a folded protein

(2020) Wai Kwan Tang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Highly-regulated, diversifying NTP-based biological conflict systems with implications for emergence of multicellularity

(2020) Gurmeet Kaur et al.   eLife

Phage G Structure at 6.1 Å Resolution, Condensed DNA, and Host Identity Revision to a Lysinibacillus

(2020) Brenda Gonzalez et al.   JOURNAL OF MOLECULAR BIOLOGY

Gp4 is a nuclease required for morphogenesis of T4-like bacteriophages

(2020) Sean Benler et al.   VIROLOGY

The Bacterial Ro60 Protein and Its Noncoding Y RNA Regulators

(2020) Soyeong Sim et al.   Annual Review of Microbiology

Intracellular Organization by Jumbo Bacteriophages

(2020) Jingwen Guan et al.   JOURNAL OF BACTERIOLOGY

Identification of uncharacterized components of prokaryotic immune systems and their diverse eukaryotic reformulations

(2020) A. Maxwell Burroughs et al.   JOURNAL OF BACTERIOLOGY

The Phage-Encoded N-Acetyltransferase Rac Mediates Inactivation of Pseudomonas aeruginosa Transcription by Cleavage of the RNA Polymerase Alpha Subunit

(2020) Pieter-Jan Ceyssens et al.   Viruses-Basel

Multisubunit RNA Polymerases of Jumbo Bacteriophages

(2020) Maria L. Sokolova et al.   Viruses-Basel

A Membrane-Associated DHH-DHHA1 Nuclease Degrades Type III CRISPR Second Messenger

(2020) Ruiliang Zhao et al.   Cell Reports

(p)ppGpp: Magic Modulators of Bacterial Physiology and Metabolism

(2020) Wieland Steinchen et al.   Frontiers in Microbiology

Investigating the Concept and Origin of Viruses

(2020) Arshan Nasir et al.   TRENDS IN MICROBIOLOGY

Megaphages infect Prevotella and variants are widespread in gut microbiomes

(2019) Audra E. Devoto et al.   Nature Microbiology

Bacterial cGAS-like enzymes synthesize diverse nucleotide signals

(2019) Aaron T. Whiteley et al.   NATURE

Viral and metazoan poxins are cGAMP-specific nucleases that restrict cGAS–STING signalling

(2019) James B. Eaglesham et al.   NATURE

An NAD+ Phosphorylase Toxin Triggers Mycobacterium tuberculosis Cell Death

(2019) Diana Mendes Freire et al.   MOLECULAR CELL

(Ph)ighting Phages: How Bacteria Resist Their Parasites

(2019) Jakob T. Rostøl et al.   Cell Host & Microbe

Emerging RNA-binding roles in the TRIM family of ubiquitin ligases

(2019) Felix Preston Williams et al.   BIOLOGICAL CHEMISTRY

The Origin and Evolution of Release Factors: Implications for Translation Termination, Ribosome Rescue, and Quality Control Pathways

(2019) A. Maxwell Burroughs et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Oxidative opening of the aromatic ring: tracing the natural history of a large superfamily of dioxygenase domains and their relatives

(2019) A. Maxwell Burroughs et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

TIR domains of plant immune receptors are NAD+-cleaving enzymes that promote cell death

(2019) Li Wan et al.   SCIENCE

A novel jumbo Tenacibaculum maritimum lytic phage with head-fiber-like appendages

(2019) Yasuhiko Kawato et al.   ARCHIVES OF VIROLOGY

Second messengers and divergent HD‐GYP phosphodiesterases regulate 3′,3′‐cGAMP signaling

(2019) Todd A. Wright et al.   MOLECULAR MICROBIOLOGY

Atomic structures of the RNA end-healing 5′-OH kinase and 2′,3′-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor

(2019) Ankan Banerjee et al.   NUCLEIC ACIDS RESEARCH

Structures of GapR reveal a central channel which could accommodate B-DNA

(2019) Michael J. Tarry et al.   Scientific Reports

A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases

(2019) Senén D. Mendoza et al.   NATURE

PhoH2 proteins couple RNA helicase and RNAse activities

(2019) Emma S. V. Andrews et al.   PROTEIN SCIENCE

A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity

(2019) Lucia M. Malone et al.   Nature Microbiology

CRISPR-based reagents to study the influence of the epigenome on gene expression

(2018) Paul Lavender et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

TIR Domain Proteins Are an Ancient Family of NAD + -Consuming Enzymes

(2018) Kow Essuman et al.   CURRENT BIOLOGY

Direct activation of a phospholipase by cyclic GMP-AMP in El TorVibrio cholerae

(2018) Geoffrey B. Severin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Erwinia amylovora phage vB_EamM_Y3 represents another lineage of hairy Myoviridae

(2018) Colin Buttimer et al.   RESEARCH IN MICROBIOLOGY

Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes

(2018) Genki Yoshikawa et al.   Scientific Reports

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Larger Than Life: Isolation and Genomic Characterization of a Jumbo Phage That Infects the Bacterial Plant Pathogen, Agrobacterium tumefaciens

(2018) Hedieh Attai et al.   Frontiers in Microbiology

In vitro reconstitution of DNA replication initiated by genetic recombination: a T4 bacteriophage model for a type of DNA synthesis important for all cells

(2018) Jack Barry et al.   MOLECULAR BIOLOGY OF THE CELL

The RES domain toxins of RES-Xre toxin-antitoxin modules induce cell stasis by degrading NAD+

(2018) Ragnhild Bager Skjerning et al.   MOLECULAR MICROBIOLOGY

The role of SLX4 and its associated nucleases in DNA interstrand crosslink repair

(2018) Wouter S Hoogenboom et al.   NUCLEIC ACIDS RESEARCH

Cap-specific terminal N6-methylation of RNA by an RNA polymerase II–associated methyltransferase

(2018) Shinichiro Akichika et al.   SCIENCE

Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements

(2017) Lakshminarayan M. Iyer et al.   JOURNAL OF BACTERIOLOGY

Vibrio Phage KVP40 Encodes a Functional NAD + Salvage Pathway

(2017) Jae Yun Lee et al.   JOURNAL OF BACTERIOLOGY

Structural analyses of the MazEF4 toxin-antitoxin pair inMycobacterium tuberculosisprovide evidence for a unique extracellular death factor

(2017) Do-Hwan Ahn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A microtubule bestiary: structural diversity in tubulin polymers

(2017) Sami Chaaban et al.   MOLECULAR BIOLOGY OF THE CELL

Type III CRISPR–Cas systems produce cyclic oligoadenylate second messengers

(2017) Ole Niewoehner et al.   NATURE

Non-homologous DNA end joining and alternative pathways to double-strand break repair

(2017) Howard H. Y. Chang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The SARM1 Toll/Interleukin-1 Receptor Domain Possesses Intrinsic NAD + Cleavage Activity that Promotes Pathological Axonal Degeneration

(2017) Kow Essuman et al.   NEURON

Capsids and Genomes of Jumbo-Sized Bacteriophages Reveal the Evolutionary Reach of the HK97 Fold

(2017) Jianfei Hua et al.   mBio

Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB

(2017) Colin Buttimer et al.   Frontiers in Microbiology

Jumbo Bacteriophages: An Overview

(2017) Yihui Yuan et al.   Frontiers in Microbiology

Macrodomains: Structure, Function, Evolution, and Catalytic Activities

(2016) Johannes Gregor Matthias Rack et al.   Annual Review of Biochemistry

Bacterial GCN5-Related N-Acetyltransferases: From Resistance to Regulation

(2016) Lorenza Favrot et al.   BIOCHEMISTRY

Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses

(2016) Peter Weigele et al.   CHEMICAL REVIEWS

Too much of a good thing: regulated depletion of c-di-AMP in the bacterial cytoplasm

(2016) TuAnh Ngoc Huynh et al.   CURRENT OPINION IN MICROBIOLOGY

Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly

(2016) Julie A. Thomas et al.   JOURNAL OF VIROLOGY

Transcription initiation complex structures elucidate DNA opening

(2016) C. Plaschka et al.   NATURE

RNA damage in biological conflicts and the diversity of responding RNA repair systems

(2016) A. Maxwell Burroughs et al.   NUCLEIC ACIDS RESEARCH

Dynamics of Open DNA Sliding Clamps

(2016) Aaron J. Oakley   PLoS One

The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases

(2016) Daria Lavysh et al.   VIROLOGY

Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography

(2016) Ludovic Sauguet et al.   Nature Communications

A Minimal Threshold of c-di-GMP Is Essential for Fruiting Body Formation and Sporulation in Myxococcus xanthus

(2016) Dorota Skotnicka et al.   PLoS Genetics

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

(2015) Lakshminarayan M. Iyer et al.   BIOESSAYS

The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications

(2015) A Maxwell Burroughs et al.   Biology Direct

Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel bastille-like group of phages in the subfamily Spounavirinae

(2015) Paul Tetteh Asare et al.   BMC GENOMICS

The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond

(2015) Bogdan I. Fedeles et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteasomal Control of Cytokinin Synthesis Protects Mycobacterium tuberculosis against Nitric Oxide

(2015) Marie I. Samanovic et al.   MOLECULAR CELL

Phage T4-induced DNA breaks activate a tRNA repair-defying anticodon nuclease

(2015) Lital Bitton et al.   MOLECULAR MICROBIOLOGY

A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage

(2015) Maria Yakunina et al.   NUCLEIC ACIDS RESEARCH

Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling

(2015) A. Maxwell Burroughs et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The mycobacterial PhoH2 proteins are type II toxin antitoxins coupled to RNA helicase domains

(2015) Emma S.V. Andrews et al.   TUBERCULOSIS

Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution

(2015) Lei Sun et al.   Nature Communications

Battling Phages: How Bacteria Defend against Viral Attack

(2015) Kimberley D. Seed   PLoS Pathogens

Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses

(2015) Venigalla B. Rao et al.   Annual Review of Virology

Intragenus generalized transduction in Staphylococcus spp. by a novel giant phage

(2014) Jumpei Uchiyama et al.   ISME Journal

Translocation and Rotation of tRNA during Template-Independent RNA Polymerization by tRNA Nucleotidyltransferase

(2014) Seisuke Yamashita et al.   STRUCTURE

CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems

(2014) Kira S. Makarova et al.   Frontiers in Genetics

Structure of the Tubulin/FtsZ-Like Protein TubZ from Pseudomonas Bacteriophage ΦKZ

(2013) Christopher H.S. Aylett et al.   JOURNAL OF MOLECULAR BIOLOGY

Cyclic GMP-AMP Containing Mixed Phosphodiester Linkages Is An Endogenous High-Affinity Ligand for STING

(2013) Xu Zhang et al.   MOLECULAR CELL

PAAR-repeat proteins sharpen and diversify the type VI secretion system spike

(2013) Mikhail M. Shneider et al.   NATURE

Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA

(2013) Lakshminarayan M. Iyer et al.   NUCLEIC ACIDS RESEARCH

Klebsiella Phage vB_KleM-RaK2 — A Giant Singleton Virus of the Family Myoviridae

(2013) Eugenijus Šimoliūnas et al.   PLoS One

Protein Similarity Networks Reveal Relationships among Sequence, Structure, and Function within the Cupin Superfamily

(2013) Richard Uberto et al.   PLoS One

Homologous 2',5'-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity

(2013) R. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

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

Recent structures, evolution and mechanisms of glycosyltransferases

(2012) Christelle Breton et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions

(2012) Robson Francisco de Souza et al.   Molecular BioSystems

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

Extensive proteolysis of head and inner body proteins by a morphogenetic protease in the giantPseudomonas aeruginosaphage φKZ

(2012) Julie A. Thomas et al.   MOLECULAR MICROBIOLOGY

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

Tubulin homolog TubZ in a phage-encoded partition system

(2012) M. A. Oliva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The T4 Phage SF1B Helicase Dda Is Structurally Optimized to Perform DNA Strand Separation

(2012) Xiaoping He et al.   STRUCTURE

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

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

The N-end rule pathway: From recognition by N-recognins, to destruction by AAA+proteases

(2011) D.A. Dougan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Analysis of DBC1 and its homologs suggests a potential mechanism for regulation of Sirtuin domain deacetylases by NAD metabolites

(2011) Vivek Anantharaman et al.   CELL CYCLE

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids

(2011) Lakshminarayan M. Iyer et al.   CELL CYCLE

Atomic Structure of Bacteriophage Sf6 Tail Needle Knob

(2011) Anshul Bhardwaj et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RtcB Is the RNA Ligase Component of anEscherichia coliRNA Repair Operon

(2011) Naoko Tanaka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Insights from the architecture of the bacterial transcription apparatus

(2011) Lakshminarayan M. Iyer et al.   JOURNAL OF STRUCTURAL BIOLOGY

Chaperone Role for Proteins p618 and p892 in the Extracellular Tail Development of Acidianus Two-Tailed Virus

(2011) U. Scheele et al.   JOURNAL OF VIROLOGY

Crystal structure of the bacteriophage T4 late-transcription coactivator gp33 with the  -subunit flap domain of Escherichia coli RNA polymerase

(2011) K.-A. F. Twist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA

(2011) K. S. Winther et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophages and their genomes

(2011) Graham F Hatfull et al.   Current Opinion in Virology

2′,3′-cAMP hydrolysis by metal-dependent phosphodiesterases containing DHH, EAL, and HD domains is non-specific: Implications for PDE screening

(2010) Feng Rao et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Determinants of Affinity and Activity of the Anti-Sigma Factor AsiA

(2010) Joshua M. Gilmore et al.   BIOCHEMISTRY

Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily

(2010) Katarzyna H. Kaminska et al.   CELL CYCLE

Receiver domain structure and function in response regulator proteins

(2010) Robert B Bourret   CURRENT OPINION IN MICROBIOLOGY

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments

(2010) Matthew B. Sullivan et al.   ENVIRONMENTAL MICROBIOLOGY

RNA 3′-Phosphate Cyclase (RtcA) Catalyzes Ligase-like Adenylylation of DNA and RNA 5′-Monophosphate Ends

(2010) Anupam K. Chakravarty et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Pseudomonas aeruginosa generalized transducing phage  PA3 is a new member of the  KZ-like group of 'jumbo' phages, and infects model laboratory strains and clinical isolates from cystic fibrosis patients

(2010) R. Monson et al.   MICROBIOLOGY-SGM

Social networking between mobile introns and their host genes

(2010) Barry Stoddard et al.   MOLECULAR MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Mobile DNA elements in T4 and related phages

(2010) David R Edgell et al.   Virology Journal

Transcriptional control in the prereplicative phase of T4 development

(2010) Deborah M Hinton   Virology Journal

Diversity and evolution of chromatin proteins encoded by DNA viruses

(2009) Robson F. de Souza et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Structure-based Mechanism of ADP-ribosylation by Sirtuins

(2009) William F. Hawse et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

YybT Is a Signaling Protein That Contains a Cyclic Dinucleotide Phosphodiesterase Domain and a GGDEF Domain with ATPase Activity

(2009) Feng Rao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins

(2009) Lakshminarayan M. Iyer et al.   Molecular BioSystems

Predicted poxvirus FEN1-like nuclease required for homologous recombination, double-strand break repair and full-size genome formation

(2009) T. G. Senkevich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis

(2009) L. Sorci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Convergent evolution of metabolic roles in bacterial co-symbionts of insects

(2009) J. P. McCutcheon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Searching protein structure databases with DaliLite v.3

(2008) L. Holm et al.   BIOINFORMATICS

A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases

(2008) Lakshminarayan M Iyer et al.   Biology Direct

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

(2008) Timo Lassmann et al.   NUCLEIC ACIDS RESEARCH

X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase

(2008) Katsuhiko S. Murakami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA topoisomerases: harnessing and constraining energy to govern chromosome topology

(2008) Allyn J. Schoeffler et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Structure of RapA, a Swi2/Snf2 Protein that Recycles RNA Polymerase During Transcription

(2008) Gary Shaw et al.   STRUCTURE