An E1–E2 fusion protein primes antiviral immune signalling in bacteria

[1]  M. Laub,et al.  A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome , 2022, Nature Microbiology.

[2]  T. A. Nagy,et al.  Bacterial NLR-related proteins protect against phage , 2022, Cell.

[3]  L. Aravind,et al.  Discovering Biological Conflict Systems Through Genome Analysis: Evolutionary Principles and Biochemical Novelty. , 2022, Annual review of biomedical data science.

[4]  Gil Amitai,et al.  An expanding arsenal of immune systems that protect bacteria from phages , 2022, bioRxiv.

[5]  E. Rocha,et al.  Phages and their satellites encode hotspots of antiviral systems , 2022, Cell host & microbe.

[6]  R. Sorek,et al.  Effector-mediated membrane disruption controls cell death in CBASS antiphage defense. , 2021, Molecular cell.

[7]  D. Hassabis,et al.  Protein complex prediction with AlphaFold-Multimer , 2021, bioRxiv.

[8]  Gil Amitai,et al.  Cyclic CMP and cyclic UMP mediate bacterial immunity against phages , 2021, Cell.

[9]  S. Ovchinnikov,et al.  ColabFold: making protein folding accessible to all , 2022, Nature Methods.

[10]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[11]  A. Govande,et al.  Molecular basis of CD-NTase nucleotide selection in CBASS anti-phage defense. , 2021, Cell reports.

[12]  R. Sorek,et al.  STING cyclic dinucleotide sensing originated in bacteria. , 2020, Nature.

[13]  Jonathan L. Schmid-Burgk,et al.  Diverse enzymatic activities mediate antiviral immunity in prokaryotes , 2020, Science.

[14]  Gil Amitai,et al.  Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems , 2020, Nature Microbiology.

[15]  P. J. Kranzusch,et al.  CBASS Immunity Uses CARF-Related Effectors to Sense 3′–5′- and 2′–5′-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection , 2020, Cell.

[16]  L. Marraffini,et al.  Faculty Opinions recommendation of HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity. , 2020, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

[17]  Yulong Niu,et al.  The ubiquitin-like modification by ThiS and ThiF in Escherichia coli. , 2019, International journal of biological macromolecules.

[18]  Gil Amitai,et al.  Cyclic GMP–AMP signalling protects bacteria against viral infection , 2019, Nature.

[19]  P. J. Kranzusch,et al.  Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity , 2019, bioRxiv.

[20]  P. J. Kranzusch,et al.  Bacterial cGAS-like enzymes synthesize diverse nucleotide signals , 2019, Nature.

[21]  B. Damania,et al.  cGAS and STING: At the intersection of DNA and RNA virus-sensing networks , 2018, PLoS pathogens.

[22]  C. Waters,et al.  Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae , 2018, Proceedings of the National Academy of Sciences.

[23]  Rotem Sorek,et al.  Systematic discovery of antiphage defense systems in the microbial pangenome , 2018, Science.

[24]  Randy J. Read,et al.  Real-space refinement in PHENIX for cryo-EM and crystallography , 2018, bioRxiv.

[25]  Christopher J. Williams,et al.  MolProbity: More and better reference data for improved all‐atom structure validation , 2018, Protein science : a publication of the Protein Society.

[26]  N. Robinson,et al.  Functional reconstruction of a eukaryotic-like E1/E2/(RING) E3 ubiquitylation cascade from an uncultured archaeon , 2017, Nature Communications.

[27]  Joseph H. Davis,et al.  Addressing preferred specimen orientation in single-particle cryo-EM through tilting , 2017, Nature Methods.

[28]  D. Agard,et al.  MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy , 2017, Nature Methods.

[29]  C. Lima,et al.  Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism , 2017, Chemical reviews.

[30]  David J. Fleet,et al.  cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination , 2017, Nature Methods.

[31]  Zhao‐Qing Luo,et al.  Ubiquitination independent of E1 and E2 enzymes by bacterial effectors , 2016, Nature.

[32]  Hongbo Hu,et al.  Ubiquitin signaling in immune responses , 2016, Cell Research.

[33]  L. Aravind,et al.  Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling , 2015, Nucleic acids research.

[34]  Nathaniel Echols,et al.  EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy , 2015, Nature Methods.

[35]  A. Sebé-Pedrós,et al.  The Eukaryotic Ancestor Had a Complex Ubiquitin Signaling System of Archaeal Origin , 2014, Molecular biology and evolution.

[36]  J. Berger,et al.  Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity , 2014, Cell.

[37]  E. Strieter,et al.  Insights into the Mechanism of Deubiquitination by JAMM Deubiquitinases from Cocrystal Structures of the Enzyme with the Substrate and Product , 2014, Biochemistry.

[38]  H. Schindelin,et al.  Structure of the ubiquitin-activating enzyme loaded with two ubiquitin molecules. , 2014, Acta crystallographica. Section D, Biological crystallography.

[39]  Nieves Peltzer,et al.  Ubiquitin in the immune system , 2013, EMBO reports.

[40]  Philip R. Evans,et al.  How good are my data and what is the resolution? , 2013, Acta crystallographica. Section D, Biological crystallography.

[41]  F. Inagaki,et al.  Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7 , 2012, Nature Structural &Molecular Biology.

[42]  Olga Vitek,et al.  A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet , 2012, BMC Bioinformatics.

[43]  D. Klionsky,et al.  Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7–Atg3 and Atg7–Atg10 structures , 2012, Nature Structural &Molecular Biology.

[44]  H. Song,et al.  Structure of the autophagic E2 enzyme Atg10. , 2012, Acta crystallographica. Section D, Biological crystallography.

[45]  M. Kikkert,et al.  Regulation of the innate immune system by ubiquitin and ubiquitin-like modifiers , 2012, Cytokine & Growth Factor Reviews.

[46]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[47]  J. Mekalanos,et al.  Coordinated Regulation of Accessory Genetic Elements Produces Cyclic Di-Nucleotides for V. cholerae Virulence , 2012, Cell.

[48]  P. Zwart,et al.  Towards automated crystallographic structure refinement with phenix.refine , 2012, Acta crystallographica. Section D, Biological crystallography.

[49]  D. Durocher,et al.  OTUB1 co-opts Lys48-linked ubiquitin recognition to suppress E2 enzyme function. , 2012, Molecular cell.

[50]  Joonhee Kim,et al.  Insights into noncanonical E1 enzyme activation from the structure of autophagic E1 Atg7 with Atg8 , 2011, Nature Structural &Molecular Biology.

[51]  Michal Hammel,et al.  Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the autophagy pathway. , 2011, Molecular cell.

[52]  K. Ogura,et al.  Structural basis of Atg8 activation by a homodimeric E1, Atg7. , 2011, Molecular cell.

[53]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[54]  Derek S. Tan,et al.  Active site remodeling accompanies thioester bond formation in the SUMO E1 , 2009, Nature.

[55]  L. Aravind,et al.  Natural history of the E1‐like superfamily: Implication for adenylation, sulfur transfer, and ubiquitin conjugation , 2009, Proteins.

[56]  J. Wade Harper,et al.  Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways , 2009, Nature Reviews Molecular Cell Biology.

[57]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[58]  Tadhg P Begley,et al.  Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis. , 2006, Biochemistry.

[59]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[60]  Huilin Zhou,et al.  Global Analyses of Sumoylated Proteins in Saccharomyces cerevisiae , 2004, Journal of Biological Chemistry.

[61]  D. Wolf,et al.  The ubiquitin-proteasome system: past, present and future. , 2004, Cellular and molecular life sciences : CMLS.

[62]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[63]  H. Koseki,et al.  Cell-autonomous involvement of Mab21l1 is essential for lens placode development , 2003, Development.

[64]  John F. Heidelberg,et al.  Comparative genomic analysis of Vibrio cholerae: Genes that correlate with cholera endemic and pandemic disease , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[65]  H. Schindelin,et al.  Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB–MoaD complex , 2001, Nature.

[66]  D. Belin,et al.  Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter , 1995, Journal of bacteriology.

[67]  D. Waugh,et al.  Removal of Affinity Tags with TEV Protease. , 2017, Methods in molecular biology.

[68]  L. Aravind,et al.  The natural history of ubiquitin and ubiquitin-related domains. , 2012, Frontiers in bioscience.

[69]  E. Lingohr,et al.  Enumeration of bacteriophages by double agar overlay plaque assay. , 2009, Methods in molecular biology.

[70]  P. Evans,et al.  Scaling and assessment of data quality. , 2006, Acta crystallographica. Section D, Biological crystallography.

[71]  L. Comstock,et al.  The tac promoter: a functional hybrid derived from the trp and lac promoters. , 1983, Proceedings of the National Academy of Sciences of the United States of America.