The enigmatic epitranscriptome of bacteriophages: putative RNA modifications in viral infections.

[1]  A. Bernheim,et al.  The highly diverse antiphage defence systems of bacteria , 2023, Nature Reviews Microbiology.

[2]  Sandro Bottaro,et al.  Hepatitis C virus RNA is 5′-capped with flavin adenine dinucleotide , 2023, Nature.

[3]  Stan J. J. Brouns,et al.  Phage tRNAs evade tRNA-targeting host defenses through anticodon loop mutations , 2023, eLife.

[4]  R. Lavigne,et al.  Assessing the Orthogonality of Phage-Encoded RNA Polymerases for Tailored Synthetic Biology Applications in Pseudomonas Species , 2023, International journal of molecular sciences.

[5]  Chuan-Yun Li,et al.  Host-mediated RNA editing in viruses , 2023, Biology Direct.

[6]  Yina Gao,et al.  Molecular basis of RADAR anti-phage supramolecular assemblies , 2023, Cell.

[7]  M. Liao,et al.  N6-methyladenosine modification of viral RNA and its role during the recognition process of RIG-I-like receptors , 2022, Frontiers in Immunology.

[8]  Frederik Sommer,et al.  A Cyanophage MarR-Type Transcription Factor Regulates Host RNase E Expression during Infection , 2022, Microorganisms.

[9]  Timo Glatter,et al.  Integrated Omics Reveal Time-Resolved Insights into T4 Phage Infection of E. coli on Proteome and Transcriptome Levels , 2022, Viruses.

[10]  Hugh E. Olsen,et al.  Advances in nanopore direct RNA sequencing , 2022, Nature Methods.

[11]  Katharina Höfer,et al.  NAD-capped RNAs - a redox cofactor meets RNA. , 2022, Trends in biochemical sciences.

[12]  Gil Amitai,et al.  Cryo-EM structure of the RADAR supramolecular anti-phage defense complex , 2022, Cell.

[13]  Nan Dai,et al.  N1-methyl-pseudouridine is incorporated with higher fidelity than pseudouridine in synthetic RNAs , 2022, Scientific Reports.

[14]  Gil Amitai,et al.  Antiviral activity of bacterial TIR domains via immune signalling molecules , 2021, Nature.

[15]  Yi-Tao Yu,et al.  The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines , 2021, Frontiers in Cell and Developmental Biology.

[16]  O. Namy,et al.  The Importance of the Epi-Transcriptome in Translation Fidelity , 2021, Non-coding RNA.

[17]  Kathryn M. Kauffman,et al.  Degradation of host translational machinery drives tRNA acquisition in viruses. , 2021, Cell systems.

[18]  Katharina Höfer,et al.  Shaping the Bacterial Epitranscriptome—5′‐Terminal and Internal RNA Modifications , 2021, Advanced biology.

[19]  H. Urlaub,et al.  A viral ADP-ribosyltransferase attaches RNA chains to host proteins , 2021, bioRxiv.

[20]  Wei Zhou,et al.  Structural insights into dpCoA-RNA decapping by NudC , 2021, RNA biology.

[21]  B. Cullen,et al.  Mapping of pseudouridine residues on cellular and viral transcripts using a novel antibody-based technique , 2021, bioRxiv.

[22]  L. Aravind,et al.  An RNA Repair Operon Regulated by Damaged tRNAs , 2020, Cell reports.

[23]  J. Vogel,et al.  Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ , 2020, RNA biology.

[24]  M. Sokolova,et al.  Multisubunit RNA Polymerases of Jumbo Bacteriophages , 2020, Viruses.

[25]  F. Tian,et al.  A-to-I RNA editing in bacteria increases pathogenicity and tolerance to oxidative stress , 2020, PLoS pathogens.

[26]  V. de Crécy-Lagard,et al.  Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity. , 2020, Trends in microbiology.

[27]  L. Tong,et al.  Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs , 2020, Nucleic acids research.

[28]  Xianqun Fan,et al.  Novel insight into the regulatory roles of diverse RNA modifications: Re-defining the bridge between transcription and translation , 2020, Molecular Cancer.

[29]  Christine L. Sun,et al.  Clades of huge phages from across Earth’s ecosystems , 2020, Nature.

[30]  Peter C. Fineran,et al.  A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity , 2019, Nature Microbiology.

[31]  Feng-Ting Huang,et al.  Klebsiella Phage KP34 RNA Polymerase and Its Use in RNA Synthesis , 2019, Front. Microbiol..

[32]  C. Wolz,et al.  The 5′ NAD Cap of RNAIII Modulates Toxin Production in Staphylococcus aureus Isolates , 2019, bioRxiv.

[33]  K. Severinov,et al.  Xenogeneic Regulation of the Bacterial Transcription Machinery. , 2019, Journal of molecular biology.

[34]  M. Waldor,et al.  The RNA degradosome promotes tRNA quality control through clearance of hypomodified tRNA , 2019, Proceedings of the National Academy of Sciences.

[35]  Zhike Lu,et al.  N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation , 2018, Nature Chemical Biology.

[36]  R. Linhardt,et al.  Bacteriophage T7 transcription system: an enabling tool in synthetic biology. , 2018, Biotechnology advances.

[37]  V. Kaberdin,et al.  RNA polyadenylation and its consequences in prokaryotes , 2018, Philosophical Transactions of the Royal Society B: Biological Sciences.

[38]  S. Borkotoky,et al.  The highly efficient T7 RNA polymerase: A wonder macromolecule in biological realm. , 2018, International journal of biological macromolecules.

[39]  W. Haefeli,et al.  Identification, Biosynthesis, and Decapping of NAD-Capped RNAs in B. subtilis. , 2018, Cell reports.

[40]  C. Hill,et al.  RNA Phage Biology in a Metagenomic Era , 2018, Viruses.

[41]  I. Ruiz-Trillo,et al.  Codon adaptation to tRNAs with Inosine modification at position 34 is widespread among Eukaryotes and present in two Bacterial phyla , 2018, RNA biology.

[42]  Deanne M. Taylor,et al.  “CapZyme-Seq” comprehensively defines promoter-sequence determinants for RNA 5’ capping with NAD+ , 2017, bioRxiv.

[43]  Y. Pilpel,et al.  RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system , 2017, Genome research.

[44]  A. Serganov,et al.  A Novel RNA Phosphorylation State Enables 5' End-Dependent Degradation in Escherichia coli. , 2017, Molecular cell.

[45]  Shuai Le,et al.  Corrigendum: Characterization of the first double-stranded RNA bacteriophage infecting Pseudomonas aeruginosa , 2017, Scientific Reports.

[46]  Yulia Yuzenkova,et al.  Bacterial RNA polymerase caps RNA with various cofactors and cell wall precursors , 2017, Nucleic acids research.

[47]  E. S. Miller,et al.  Vibrio Phage KVP40 Encodes a Functional NAD+ Salvage Pathway , 2017, Journal of bacteriology.

[48]  D. Agard,et al.  Assembly of a nucleus-like structure during viral replication in bacteria , 2017, Science.

[49]  Tingting Zou,et al.  Structural basis of prokaryotic NAD-RNA decapping by NudC , 2016, Cell Research.

[50]  E. Koonin,et al.  The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases. , 2016, Virology.

[51]  D. Patel,et al.  Structure and function of the bacterial decapping enzyme NudC , 2016, Nature chemical biology.

[52]  Craig D. Kaplan,et al.  The mechanism of RNA 5′ capping with NAD+, NADH, and desphospho-CoA , 2016, Nature.

[53]  V. Volchkov,et al.  RNA Editing of the GP Gene of Ebola Virus is an Important Pathogenicity Factor. , 2015, The Journal of infectious diseases.

[54]  D. Qi,et al.  Rapid Degradation of Host mRNAs by Stimulation of RNase E Activity by Srd of Bacteriophage T4 , 2015, Genetics.

[55]  Xin Deng,et al.  Widespread occurrence of N6-methyladenosine in bacterial mRNA , 2015, Nucleic acids research.

[56]  C. Richardson,et al.  Synthesis of 2′-Fluoro RNA by Syn5 RNA polymerase , 2015, Nucleic acids research.

[57]  Eric C. Keen.  A century of phage research: Bacteriophages and the shaping of modern biology , 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

[58]  Hana Cahová,et al.  NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs , 2014, Nature.

[59]  Michael Bott,et al.  A chromosomally encoded T7 RNA polymerase-dependent gene expression system for Corynebacterium glutamicum: construction and comparative evaluation at the single-cell level , 2014, Microbial biotechnology.

[60]  Haiquan Yang,et al.  Transcription regulation mechanisms of bacteriophages , 2014, Bioengineered.

[61]  Magnar Bjørås,et al.  Inosine in DNA and RNA. , 2014, Current opinion in genetics & development.

[62]  Schraga Schwartz,et al.  Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs , 2013, PLoS genetics.

[63]  J. King,et al.  The RNA Polymerase of Marine Cyanophage Syn5* , 2012, The Journal of Biological Chemistry.

[64]  P. Sergiev,et al.  The last rRNA methyltransferase of E. coli revealed: the yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA. , 2012, RNA.

[65]  M. Rodnina,et al.  Impact of methylations of m2G966/m5C967 in 16S rRNA on bacterial fitness and translation initiation , 2012, Nucleic acids research.

[66]  Martha R. J. Clokie,et al.  Phages in nature , 2011, Bacteriophage.

[67]  M. Uzan,et al.  Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation , 2010, Virology Journal.

[68]  M. Helm,et al.  tRNA stabilization by modified nucleotides. , 2010, Biochemistry.

[69]  E. Westhof,et al.  Toward predicting self-splicing and protein-facilitated splicing of group I introns. , 2008, RNA.

[70]  H. Čelešnik,et al.  The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal , 2008, Nature.

[71]  P. Sergiev,et al.  The ybiN gene of Escherichia coli encodes adenine-N6 methyltransferase specific for modification of A1618 of 23 S ribosomal RNA, a methylated residue located close to the ribosomal exit tunnel. , 2008, Journal of molecular biology.

[72]  Massimo Vergassola,et al.  Causes for the intriguing presence of tRNAs in phages. , 2007, Genome research.

[73]  A. Bowie,et al.  The family of five: TIR-domain-containing adaptors in Toll-like receptor signalling , 2007, Nature Reviews Immunology.

[74]  R. Depping,et al.  The mono-ADP-ribosyltransferases Alt and ModB of bacteriophage T4: target proteins identified. , 2005, Biochemical and biophysical research communications.

[75]  Houping Ni,et al.  Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA. , 2005, Immunity.

[76]  T. Yonesaki,et al.  Phage-induced change in the stability of mRNAs. , 2004, Virology.

[77]  R. Depping,et al.  ModA and ModB, Two ADP-Ribosyltransferases Encoded by Bacteriophage T4: Catalytic Properties and Mutation Analysis , 2004, Journal of bacteriology.

[78]  Thomas A Steitz,et al.  The Structural Mechanism of Translocation and Helicase Activity in T7 RNA Polymerase , 2004, Cell.

[79]  Fumio Arisaka,et al.  Bacteriophage T4 Genome , 2003, Microbiology and Molecular Biology Reviews.

[80]  F. Huang,et al.  Efficient incorporation of CoA, NAD and FAD into RNA by in vitro transcription. , 2003, Nucleic acids research.

[81]  Stanley N Cohen,et al.  The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[82]  P. Gauss,et al.  The Gene e.1 (nudE.1) of T4 Bacteriophage Designates a New Member of the Nudix Hydrolase Superfamily Active on Flavin Adenine Dinucleotide, Adenosine 5′-Triphospho-5′-adenosine, and ADP-ribose* , 2002, The Journal of Biological Chemistry.

[83]  W. Mcallister,et al.  Cloning and purification of bacteriophage K11 RNA polymerase. , 1999, BioTechniques.

[84]  D. Steege,et al.  Roles of polyadenylation and nucleolytic cleavage in the filamentous phage mRNA processing and decay pathways in Escherichia coli. , 1999, RNA.

[85]  R. Sousa,et al.  Efficient synthesis of nucleic acids heavily modified with non-canonical ribose 2'-groups using a mutantT7 RNA polymerase (RNAP). , 1999, Nucleic acids research.

[86]  D. Steege,et al.  Appropriate Expression of Filamentous Phage f1 DNA Replication Genes II and X Requires RNase E-Dependent Processing and Separate mRNAs , 1998, Journal of bacteriology.

[87]  P. Shen,et al.  Bacteriophage T7 mRNA is polyadenylated , 1998, Molecular microbiology.

[88]  W. Mcallister,et al.  The phage RNA polymerases are related to DNA polymerases and reverse transcriptases , 1993, Molecular microbiology.

[89]  D. Belin,et al.  Processing of unstable bacteriophage T4 gene 32 mRNAs into a stable species requires Escherichia coli ribonuclease E. , 1988, The EMBO journal.

[90]  Y. Hirota,et al.  Isolation and characterization of an Escherichia coli mutant lacking tRNA-guanine transglycosylase. Function and biosynthesis of queuosine in tRNA. , 1982, The Journal of biological chemistry.

[91]  S. C. Falco,et al.  Virion-associated RNA polymerase required for bacteriophage N4 development. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[92]  W. Summers,et al.  Control of Template Specificity of E. coli RNA Polymerase by a Phage-coded Protein , 1969, Nature.

[93]  J. Marmur,et al.  Replacement of Thymidylic Acid by Deoxyuridylic Acid in the Deoxyribonucleic Acid of a Transducing Phage for Bacillus subtilis , 1963, Nature.

[94]  OUP accepted manuscript , 2021, Nucleic Acids Research.

[95]  M. Uzan.  RNA processing and decay in bacteriophage T4. , 2009, Progress in molecular biology and translational science.

[96]  A. McLennan,et al.  The Nudix hydrolase superfamily , 2005, Cellular and Molecular Life Sciences CMLS.

[97]  R. Depping,et al.  Overexpression, purification, and partial characterization of ADP-ribosyltransferases modA and modB of bacteriophage T4. , 1999, Gene expression.

[98]  T. Koch,et al.  Overexpression, purification, and characterization of the ADP-ribosyltransferase (gpAlt) of bacteriophage T4: ADP-ribosylation of E. coli RNA polymerase modulates T4 "early" transcription. , 1995, Gene expression.

[99]  D. Melton,et al.  In vitro RNA synthesis with SP6 RNA polymerase. , 1987, Methods in enzymology.