2,850
Views
30
CrossRef citations to date
0
Altmetric
Review

Deazaguanine derivatives, examples of crosstalk between RNA and DNA modification pathways

, ORCID Icon & ORCID Icon
Pages 1175-1184 | Received 03 Oct 2016, Accepted 19 Nov 2016, Published online: 29 Dec 2016

References

  • Forterre P, Grosjean H. The interplay between RNA and DNA modifications. Back to the RNA world. In DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution, H Grosjean, Ed. Landes Bioscience, 2009; pp 259-274.
  • Weigele P, Raleigh EA. Biosynthesis and function of modified bases in Bacteria and their viruses. Chemical Rev 2016; 116(20):12655-87; PMID:27319741; http://dx.doi.org/10.1021/acs.chemrev.6b00114
  • Grosjean H. Nucleic Acids are not boring long polymers of only four types of nucleotides. In DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution, H Grosjean, Ed. Landes Bioscience, 2009; pp 1-18.
  • Warren RA. Modified bases in bacteriophage DNAs. Ann Rev Microbiol 1980; 34:137-58; PMID:7002022; http://dx.doi.org/10.1146/annurev.mi.34.100180.001033
  • Perche-Letuvee P, Molle T, Forouhar F, Mulliez E, Atta M. Wybutosine biosynthesis: structural and mechanistic overview. RNA Biol 2014; 11:1508-18; PMID:25629788; http://dx.doi.org/10.4161/15476286.2014.992271
  • Gilbert WV, Bell TA, Schaening C. Messenger RNA modifications: Form, distribution, and function. Science 2016; 352:1408-1412; PMID:27313037; http://dx.doi.org/10.1126/science.aad8711
  • Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, Peer E, Kol N, Ben-Haim MS, Dai Q, Di Segni A, Salmon-Divon M, Clark WC, et al. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature 2016; 530:441-446; PMID:26863196; http://dx.doi.org/10.1038/nature16998
  • Lovejoy AF, Riordan DP, Brown PO. Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS ONE 2014; 9:e110799; PMID:25353621; http://dx.doi.org/10.1371/journal.pone.0110799
  • Auxilien S, Rasmussen A, Rose S, Brochier-Armanet C, Husson C, Fourmy D, Grosjean H, Douthwaite S. Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases. RNA 2011; 17:45-53; PMID:21051506; http://dx.doi.org/10.1261/rna.2323411
  • Jurkowska RZ, Jurkowski TP, Jeltsch A. Structure and function of mammalian DNA methyltransferases. Chembiochem 2011; 12:206-22; PMID:21243710; http://dx.doi.org/10.1002/cbic.201000195
  • Jeltsch A, Ehrenhofer-Murray A, Jurkowski TP, Lyko F, Reuter G, Ankri S, Nellen W, Schaefer M, Helm M. Mechanism and biological role of Dnmt2 in nucleic acid methylation. RNA biology 2016; 1-16; PMID:27232191; http://dx.doi.org/10.1080/15476286.2016.1191737
  • Salter JD, Bennett RP, Smith HC. The APOBEC protein family: united by structure, divergent in function. Trends Biochem Sci 2016; 41:578-594; PMID:27283515; http://dx.doi.org/10.1016/j.tibs.2016.05.001
  • Rubio MAT, Pastar I, Gaston KW, Ragone FL, Janzen CJ, Cross GAM, Papavasiliou FN, Alfonzo JD. An adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U deamination of DNA. Proc Natl Acad Sci USA 2007; 104:7821-7826; PMID:17483465; http://dx.doi.org/10.1073/pnas.0702394104
  • Fedeles BI, Singh V, Delaney JC, Li D, Essigmann JM. The AlkB family of Fe(II)/α-ketoglutarate-dependent dioxygenases: repairing nucleic acid alkylation damage and beyond. J Biol Chem 2015; 290:20734-20742; PMID:26152727; http://dx.doi.org/10.1074/jbc.R115.656462
  • van den Born E, Vagbo CB, Songe-Moller L, Leihne V, Lien GF, Leszczynska G, Malkiewicz A, Krokan HE, Kirpekar F, Klungland A, et al. ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA. Nat Commun 2011; 2:172; PMID:21285950; http://dx.doi.org/10.1038/ncomms1173
  • Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, Yi C, Lindahl T, Pan T, Yang YG, et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 2011; 7:885-7; PMID:22002720; http://dx.doi.org/10.1038/nchembio.687
  • Thiaville JJ, Kellner SM, Yuan Y, Hutinet G, Thiaville PC, Jumpathong W, Mohapatra S, Brochier-Armanet C, Letarov AV, Hillebrand R, et al. Novel genomic island modifies DNA with 7-deazaguanine derivatives. Proc Natl Acad Sci USA 2016; 113:E1452-E1459; PMID:26929322; http://dx.doi.org/10.1073/pnas.1518570113
  • Okada N, Noguchi S, Kasai H, Shindo-Okada N, Ohgi T, Goto T, Nishimura S. Novel mechanism of post-transcriptional modification of tRNA. Insertion of bases of Q precursors into tRNA by a specific tRNA transglycosylase reaction. J Biol Chem 1979; 254:3067-73; PMID:372186
  • Meier F, Suter B, Grosjean H, Keith G, Kubli E. Queuosine modification of the wobble Base in tRNAHis influences ‘in vivo’ decoding properties. EMBO J 1985; 4:823-827; PMID:2988936
  • Manickam N, Nag N, Abbasi A, Patel K, Farabaugh PJ. Studies of translational misreading in vivo show that the ribosome very efficiently discriminates against most potential errors. RNA 2014; 20:9-15; PMID:24249223; http://dx.doi.org/10.1261/rna.039792.113
  • Manickam N, Joshi K, Bhatt MJ, Farabaugh PJ. Effects of tRNA modification on translational accuracy depend on intrinsic codon-anticodon strength. Nucleic Acids Res 2016; 44:1871-81; PMID:26704976; http://dx.doi.org/10.1093/nar/gkv1506
  • Zallot R, Brochier-Armanet C, Gaston KC, Forouhar F, Limbach PA, Hunt JF, De Crécy Lagard V. The plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. ACS Chem Biol 2014; 9:1812-25; PMID:24911101; http://dx.doi.org/10.1021/cb500278k
  • Noguchi S, Nishimura Y, Hirota Y, Nishimura S. Isolation and characterization of an Escherichia coli mutant lacking tRNA-guanine transglycosylase. Function and biosynthesis of queuosine in tRNA. J Biol Chem 1982; 257:6544-50; PMID:6804468
  • Thibessard A, Borges F, Fernandez A, Gintz B, Decaris B, Leblond-Bourget N. Identification of Streptococcus thermophilus CNRZ368 genes involved in defense against superoxide stress. Appl EnvironMicrobiol 2004; 70:2220-9; PMID:15066816
  • Durand JM, Dagberg B, Uhlin BE, Björk GR. Transfer RNA modification, temperature and DNA superhelicity have a common target in the regulatory network of the virulence of Shigella flexneri: the expression of the virF gene. Mol Microbiol 2000; 35:924-35; PMID:10692168; http://dx.doi.org/10.1046/j.1365-2958.2000.01767.x
  • Marchetti M, Capela D, Poincloux R, Benmeradi N, Auriac MC, Le Ru A, Maridonneau-Parini I, Batut J, Masson-Boivin C. Queuosine biosynthesis is required for Sinorhizobium meliloti-induced cytoskeletal modifications on HeLa Cells and symbiosis with Medicago truncatula. PLoS ONE 2013; 8:e56043; PMID:23409119; http://dx.doi.org/10.1371/journal.pone.0056043
  • Vinayak M, Pathak C. Queuosine modification of tRNA: its divergent role in cellular machinery. Bioscience Rep 2010; 30:135-48; PMID:19925456; http://dx.doi.org/10.1042/BSR20090057
  • Marks T, Farkas WR. Effects of a diet deficient in tyrosine and queuine on germfree mice. Biochem Bioph Res Com 1997; 230:233-237; PMID:9016755; http://dx.doi.org/10.1006/bbrc.1996.5768
  • Rakovich T, Boland C, Bernstein I, Chikwana VM, Iwata-Reuyl D, Kelly VP. Queuosine deficiency in eukaryotes compromises tyrosine production through increased tetrahydrobiopterin oxidation. J Biol Chem 2011; 286:19354-63; PMID:21487017; http://dx.doi.org/10.1074/jbc.M111.219576
  • Zaborske JM, Bauer DuMont JL, Wallace EWJ, Pan T, Aquadro CF, Drummond DA. A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein encoding across and animal genus. Plos Biol 2014; 12:e1002015; PMID:25489848; http://dx.doi.org/10.1371/journal.pbio.1002015
  • Müller M, Hartmann M, Schuster I, Bender S, Thüring KL, Helm M, Katze JR, Nellen W, Lyko F, Ehrenhofer-Murray AE. Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine. Nucleic Acids Res 2015; 43:10952-10962; PMID:26424849; http://dx.doi.org/10.1093/nar/gkv980
  • Gregson JM, Crain PF, Edmonds CG, Gupta R, Hashizume T, Phillipson DW, McCloskey JA. Structure of Archaeal transfer RNA nucleoside G*-15 (2-Amino-4,7-dihydro-4-oxo-7-b-D-ribofuranosyl-1H-pyrrolo[2,3-d]pyrimidine-5-carboximidamide (Archaeosine)). J Biol Chem 1993; 268:10076-10086; PMID:7683667
  • Kawamura T, Hirata A, Ohno S, Nomura Y, Nagano T, Nameki N, Yokogawa T, Hori H. Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon. Nucleic Acids Res 2016; 44:1894-1908; PMID:26721388; http://dx.doi.org/10.1093/nar/gkv1522
  • Oliva R, Tramontano A, Cavallo L. Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs. RNA 2007; 13:1427-1436; PMID:17652139; http://dx.doi.org/10.1261/rna.574407
  • Blaby IK, Phillips G, Blaby-Haas CE, Gulig KS, El Yacoubi B, de Crécy-Lagard V. Towards a systems approach in the genetic analysis of Archaea: Accelerating mutant construction and phenotypic analysis in Haloferax volcanii. Archaea 2010; 2010; 426239; PMID:21234384; http://dx.doi.org/10.1155/2010/426239
  • Reader JS, Metzgar D, Schimmel P, de Crécy-Lagard V. Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. J Biol Chem 2004; 279:6280-5; PMID:14660578; http://dx.doi.org/10.1074/jbc.M310858200
  • McCarty RM, Somogyi Ard, Lin G, Jacobsen NE, Bandarian V. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of preQ0 from guanosine 5′-triphosphate in four steps. Biochemistry 2009; 48:3847-3852; PMID:19354300; http://dx.doi.org/10.1021/bi900400e
  • Phillips G, El Yacoubi B, Lyons B, Alvarez S, Iwata-Reuyl D, de Crécy-Lagard V. Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: a new role for GTP Cyclohydrolase I. J Bacteriol 2008; 190:7876-7884; PMID:18931107; http://dx.doi.org/10.1128/JB.00874-08
  • Colloc'h N, Poupon A, Mornon JP. Sequence and structural features of the T-fold, an original tunnelling building unit. Proteins 2000; 39:142-54; PMID:10737935; http://dx.doi.org/10.1002/(SICI)1097-0134(20000501)39:2%3c142::AID-PROT4%3e3.0.CO;2-X
  • Sankaran B, Bonnett SA, Shah K, Gabriel S, Reddy R, Schimmel P, Rodionov DA, de Crécy-Lagard V, Helmann JD, Iwata-Reuyl D, et al. Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB. J Bacteriol 2009; 191:6936-49; PMID:19767425; http://dx.doi.org/10.1128/JB.00287-09
  • McCarty RM, Somogyi Ard, Bandarian V. Escherichia coli QueD is a 6-Carboxy-5,6,7,8-tetrahydropterin synthase. Biochemistry 2009; 48:2301-2303; PMID:19231875; http://dx.doi.org/10.1021/bi9001437
  • Phillips G, Grochowski LL, Bonnett S, Xu H, Bailly M, Blaby-Haas C, El Yacoubi B, Iwata-Reuyl D, White RH, de Crécy-Lagard V. Functional promiscuity of the COG0720 family. ACS Chem Biol 2012; 7:197-209; PMID:21999246; http://dx.doi.org/10.1021/cb200329f
  • Miles ZD, Roberts SA, McCarty RM, Bandarian V. Biochemical and structural studies of 6-Carboxy-5,6,7,8-tetrahydropterin synthase reveal the molecular basis of catalytic promiscuity within the Tunnel-fold superfamily. J Biol Chem 2014; 289:23641-23652; PMID:24990950; http://dx.doi.org/10.1074/jbc.M114.555680
  • Zallot R, Harrison K, Kolaczkowski B, de Crécy-Lagard V. Functional annotations of paralogs: a blessing and a curse. Life 2016; 6:39; PMID:27618105; http://dx.doi.org/10.3390/life6030039
  • Bandarian V, Drennan CL. Radical-mediated ring contraction in the biosynthesis of 7-deazapurines. Curr Opin Struc Biol 2015; 35:116-124; PMID:26643180; http://dx.doi.org/10.1016/j.sbi.2015.11.005
  • Nelp MT, Bandarian VA. single enzyme transforms a carboxylic acid into a nitrile through an amide Intermediate. Angew Chem Int Ed Engl 2015; 54:10627-10629; PMID:26228534; http://dx.doi.org/10.1002/anie.201504505
  • Auerbach G, Herrmann A, Bracher A, Bader G, Gutlich M, Fischer M, Neukamm M, Garrido-Franco M, Richardson J, Nar H, et al. Zinc plays a key role in human and bacterial GTP cyclohydrolase I. Proc Natl Acad Sci USA 2000; 97:13567-72; PMID:11087827; http://dx.doi.org/10.1073/pnas.240463497
  • Cicmil N, Huang RH. Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis. Proteins 2008; 72:1084-8; PMID:18491386; http://dx.doi.org/10.1002/prot.22098
  • Dowling DP, Bruender NA, Young AP, McCarty RM, Bandarian V, Drennan CL. Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism. Nature Chem Biol 2014; 10:106-12; PMID:24362703; http://dx.doi.org/10.1038/nchembio.1426
  • Kim Y, Zhou M, Moy S, Morales J, Cunningham MA, Joachimiak A. High-Resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism. J Mol Biol 2010; 404:127-137; PMID:20875425; http://dx.doi.org/10.1016/j.jmb.2010.09.042
  • Chikwana VM, Stec B, Lee BWK, de Crécy-Lagard V, Iwata-Reuyl D, Swairjo MA. Structural basis of biological nitrile reduction. J Biol Chem 2012; 287:30560-30570; PMID:22787148; http://dx.doi.org/10.1074/jbc.M112.388538
  • Van Lanen SG, Reader JS, Swairjo MA, de Crécy-Lagard V, Lee B, Iwata-Reuyl D. From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc Natl Acad Sci USA 2005; 102:4264-9; PMID:15767583; http://dx.doi.org/10.1073/pnas.0408056102
  • Lee BWK, Van Lanen SG, Iwata-Reuyl D. Mechanistic studies of Bacillus subtilis QueF, the nitrile oxidoreductase involved in Queuosine biosynthesis. Biochemistry 2007; 46:12844-12854; PMID:17929836; http://dx.doi.org/10.1021/bi701265r
  • Romier C, Reuter K, Suck D, Ficner R. Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase reveal aspartate 102 as the active site nucleophile. Biochemistry 1996; 35:15734-9; PMID:8961936; http://dx.doi.org/10.1021/bi962003n
  • Ritschel T, Atmanene C, Reuter K, Van Dorsselaer A, Sanglier-Cianferani S, Klebe G. An integrative approach combining noncovalent mass spectrometry, enzyme kinetics and X-ray crystallography to decipher Tgt protein-protein and protein-RNA interaction. J Mol Biol 2009; 393:833-847; PMID:19627989; http://dx.doi.org/10.1016/j.jmb.2009.07.040
  • Stengl B, Reuter K, Klebe G. Mechanism and substrate specificity of tRNA-Guanine transglycosylases (TGTs): tRNA-modifying enzymes from the three different kingdoms of life share a common catalytic mechanism. Chem Bio Chem 2005; 6:1926-1939; PMID:16206323; http://dx.doi.org/10.1002/cbic.200500063
  • Biela I, Tidten-Luksch N, Immekus F, Glinca S, Nguyen TXP, Gerber H-D, Heine A, Klebe G, Reuter K. Investigation of specificity determinants in bacterial tRNA-guanine transglycosylase reveals queuine, the substrate of Its eucaryotic counterpart, as inhibitor. PLoS ONE 2013; 8:e64240; PMID:23704982; http://dx.doi.org/10.1371/journal.pone.0064240
  • Romier C, Reuter K, Suck D, Ficner R. Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange. Embo J 1996; 15:2850-2857; PMID:8654383
  • Van Lanen SG, Iwata-Reuyl D. Kinetic Mechanism of the tRNA-Modifying Enzyme S-Adenosylmethionine:tRNA Ribosyltransferase-Isomerase (QueA). Biochemistry 2003; 42:5312-5320; PMID:12731872; http://dx.doi.org/10.1021/bi034197u
  • Frey B, McCloskey JA, Kersten W, Kersten H. New function of vitamin B12: cobamide-dependent reduction of epoxyqueuosine to queuosine in tRNAs of Escherichia coli and Salmonella typhimurium. J Bacteriol 1988; 170:2078-2082; PMID:3129401; http://dx.doi.org/10.1128/jb.170.5.2078-2082.1988
  • Miles ZD, McCarty RM, Molnar G, Bandarian V. Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification. Proc Natl Acad Sci USA 2011; 108:7368-7372; PMID:21502530; http://dx.doi.org/10.1073/pnas.1018636108
  • Ishitani R, Nureki O, Fukai S, Kijimoto T, Nameki N, Watanabe M, Kondo H, Sekine M, Okada N, Nishimura S, et al. Crystal structure of archaeosine tRNA-guanine transglycosylase. J Mol Biol 2002; 318:665-77; PMID:12054814; http://dx.doi.org/10.1016/S0022-2836(02)00090-6
  • Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S. Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell 2003; 113:383-94; PMID:12732145; http://dx.doi.org/10.1016/S0092-8674(03)00280-0
  • Phillips G, Chikwana VM, Maxwell A, El-Yacoubi B, Swairjo MA, Iwata-Reuyl D, de Crécy-Lagard V. Discovery and characterization of an amidinotransferase involved in the modification of archaeal tRNA. J Biol Chem 2010; 285:12706-12713; PMID:20129918; http://dx.doi.org/10.1074/jbc.M110.102236
  • Phillips G, Swairjo MA, Gaston KW, Bailly M, Limbach PA, Iwata-Reuyl D, de Crécy Lagard V. Diversity of archaeosine synthesis in crenarchaeota. ACS Chem Biol 2012; 7:300-5; PMID:22032275; http://dx.doi.org/10.1021/cb200361w
  • Mei X, Alvarez J, Ramos AB, Samanta U, Iwata-Reuyl D, Swairjo MA. Crystal structure of the archaeosine synthase QueF-Like - insights into amidino transfer and tRNA Recognition by the tunnel fold. Proteins 2016; PMID:25884661; http://dx.doi.org/10.3390/nu7042897
  • Fergus C, Barnes D, Alqasem M, Kelly V. The Queuine micronutrient: charting a course from microbe to man. Nutrients 2015; 7:2897; PMID:25884661; http://dx.doi.org/10.3390/nu7042897
  • Boland C, Hayes P, Santa-Maria I, Nishimura S, Kelly VP. Queuosine formation in eukaryotic tRNA occurs via a mitochondria-localized heteromeric transglycosylase. J Biol Chem 2009; 284:18218-18227; PMID:19414587; http://dx.doi.org/10.1074/jbc.M109.002477
  • Biela I, Tidten-Luksch N, Immekus F, Glinca S, Nguyen TX, Gerber HD, Heine A, Klebe G, Reuter K. Investigation of specificity determinants in bacterial tRNA-guanine transglycosylase reveals queuine, the substrate of its eucaryotic counterpart, as inhibitor. PLoS ONE 2013; 8:e64240; PMID:23704982; http://dx.doi.org/10.1371/journal.pone.0064240
  • de Crécy-Lagard V, Olson G. RNA modification subsystems in the SEED database In DNA and RNA editing enzymes: comparative structure, mechanism, functions, cellular interactions and evolution, H Grosjean, Ed. Landes Bioscience: Austin, 2009; pp 624-228.
  • Xu D, Ma M, Liu Y, Zhou T, Wang K, Deng Z, Hong K. PreQ0 base, an unusual metabolite with anti-cancer activity from Streptomyces qinglanensis 172205. Anticancer Agents Med Chem 2015; 15:285-90; PMID:25353335; http://dx.doi.org/10.2174/1871520614666141027144653
  • McCarty RM, Bandarian V. Biosynthesis of pyrrolopyrimidines. Bioorg Chem 2012; 43:15-25; PMID:22382038; http://dx.doi.org/10.1016/j.bioorg.2012.01.001
  • Watanabe M, Matsuo M, Tanaka S, Akimoto H, Asahi S, Nishimura S, Katze JR, Hashizume T, Crain PF, McCloskey JA, et al. Biosynthesis of archaeosine, a novel derivative of 7-deazaguanosine specific to archaeal tRNA, proceeds via a pathway involving base replacement on the tRNA polynucleotide chain. J Biol Chem 1997; 272:20146-51; PMID:9242689; http://dx.doi.org/10.1074/jbc.272.32.20146
  • Rodionov DA, Hebbeln P, Eudes A, ter Beek J, Rodionova IA, Erkens GB, Slotboom DJ, Gelfand MS, Osterman AL, Hanson AD, et al. A novel class of modular transporters for vitamins in prokaryotes. J Bacteriol 2009; 191:42-51; PMID:18931129; http://dx.doi.org/10.1128/JB.01208-08
  • Zallot R, De Crécy Lagard V. Comparative genomics of bacterial queuosine salvage identify COG1738 as a preQ0 transporter. Biomolecules 2017, submitted.
  • Iyer LM, Zhang D, Maxwell Burroughs A, Aravind L. Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Nucleic Acids Res 2013; 41:7635-7655; PMID:23814188; http://dx.doi.org/10.1093/nar/gkt573
  • Sabri M, Häuser R, Ouellette M, Liu J, Dehbi M, Moeck G, García E, Titz B, Uetz P, Moineau S. Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent Phage Dp-1. J Bacteriol 2011; 193:551-562; PMID:21097633; http://dx.doi.org/10.1128/JB.01117-10
  • Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, Jacobs-Sera D, Falbo J, Gross J, Pannunzio NR, et al. Origins of highly mosaic Mycobacteriophage genomes. Cell 2003; 113:171-182; PMID:12705866; http://dx.doi.org/10.1016/S0092-8674(03)00233-2
  • Kulikov E, Golomidova A, Letarova M, Kostryukova E, Zelenin A, Prokhorov N, Letarov A. Genomic sequencing and biological characteristics of a novel Escherichia coli bacteriophage 9g, a putative representative of a new Siphoviridae genus. Viruses 2014; 6:5077; PMID:25533657; http://dx.doi.org/10.3390/v6125077
  • Moreno Switt AI, den Bakker HC, Cummings CA, Rodriguez-Rivera LD, Govoni G, Raneiri ML, Degoricija L, Brown S, Hoelzer K, Peters JE, et al. Identification and characterization of novel Salmonella mobile elements involved in the dissemination of genes linked to virulence and transmission. PLoS One 2012; 7:e41247; PMID:22911766; http://dx.doi.org/10.1371/journal.pone.0041247
  • Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Research 2014; 42:D206-14; PMID:24293654; http://dx.doi.org/10.1093/nar/gkt1226
  • Wang L, Chen S, Xu T, Taghizadeh K, Wishnok JS, Zhou X, You D, Deng Z, Dedon PC. Phosphorothioation of DNA in bacteria by dnd genes. Nat Chem Biol 2007; 3:709-710; PMID:17934475; http://dx.doi.org/10.1038/nchembio.2007.39
  • He W, Huang T, Tang Y, Liu Y, Wu X, Chen S, Chan W, Wang Y, Liu X, Chen S, et al. Regulation of DNA phosphorothioate modification in Salmonella enterica by DndB. Scientific Reports 2015; 5:12368; PMID:26190504; http://dx.doi.org/10.1038/srep12368
  • Gorbalenya AE, Koonin EV. Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain. FEBS Letters 1991; 291:277-81; PMID:1657645; http://dx.doi.org/10.1016/0014-5793(91)81301-N
  • Carstens AB, Kot W, Hansen LH. Complete genome sequences of four novel Escherichia coli bacteriophages belonging to new phage groups. Genome Announc 2015; 3; PMID:26184932; http://dx.doi.org/10.1128/genomeA.00741-15
  • McCarty RM, Bandarian V. Deciphering deazapurine biosynthesis: pathway for pyrrolopyrimidine nucleosides toyocamycin and sangivamycin. Chem & Biol 2008; 15:790-8; http://dx.doi.org/10.1016/j.chembiol.2008.07.012
  • Hurt JK, Olgen S, Garcia GA. Site-specific modification of Shigella flexneri virF mRNA by tRNA-guanine transglycosylase in vitro. Nucleic Acids Res 2007; 35:4905-13; PMID:17626052; http://dx.doi.org/10.1093/nar/gkm473
  • Nonekowski ST, Kung FL, Garcia GA. The Escherichia coli tRNA-guanine transglycosylase can recognize and modify DNA. J Biol Chem 2002; 277:7178-82; PMID:11751936; http://dx.doi.org/10.1074/jbc.M111077200