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PMID: 29106616 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

MODOMICS: a database of RNA modification pathways. 2017 update.

Nucleic acids research ·Vol. 46 ·No. D1 ·2018-00-04 ·Pages D303-D307

Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki TK, de Crécy-Lagard V, Ross R, Limbach PA, Kotter A, Helm M, Bujnicki JM

Abstract

MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. In the current database version, we included the following new features and data: extended mass spectrometry and liquid chromatography data for modified nucleosides; links between human tRNA sequences and MINTbase - a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments; new, machine-friendly system of unified abbreviations for modified nucleoside names; sets of modified tRNA sequences for two bacterial species, updated collection of mammalian tRNA modifications, 19 newly identified modified ribonucleosides and 66 functionally characterized proteins involved in RNA modification. Data from MODOMICS have been linked to the RNAcentral database of RNA sequences. MODOMICS is available at http://modomics.genesilico.pl.

MeSH Terms
Chromatography, Liquid Databases, Genetic Humans Mass Spectrometry RNA/chemistry,metabolism RNA, Transfer/chemistry,metabolism Ribonucleosides/chemistry,metabolism Terminology as Topic
Chemicals
Ribonucleosides RNA RNA, Transfer
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Boccaletto Pietro
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
Machnicka Magdalena A
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. | Institute of Informatics, University of Warsaw, Banacha 2, PL-02-097 Warsaw, Poland.
Purta Elzbieta
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
Piatkowski Pawel
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
Baginski Blazej
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
Wirecki Tomasz K
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.
de Crécy-Lagard Valérie
Microbiology and Cell Science Department, University of Florida, Gainesville, FL 32611, USA.
Ross Robert
Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA.
Limbach Patrick A
Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA.
Kotter Annika
Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany.
Helm Mark
Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany.
Bujnicki Janusz M
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. | Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland.
References (25)
25 references, click to expand
  1. The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis.
    Mol Biol Cell. 2015 Jun 1;26(11):2080-95 PMID: 25851604
  2. Methylation of 12S rRNA is necessary for in vivo stability of the small subunit of the mammalian mitochondrial ribosome.
    Cell Metab. 2009 Apr;9(4):386-97 PMID: 19356719
  3. The RNA Modification Database, RNAMDB: 2011 update.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D195-201 PMID: 21071406
  4. NSUN4 is a dual function mitochondrial protein required for both methylation of 12S rRNA and coordination of mitoribosomal assembly.
    PLoS Genet. 2014 Feb 06;10(2):e1004110 PMID: 24516400
  5. Discovery and biological characterization of geranylated RNA in bacteria.
    Nat Chem Biol. 2012 Nov;8(11):913-9 PMID: 22983156
  6. Systematic identification of tRNAome and its dynamics in Lactococcus lactis.
    Mol Microbiol. 2014 Sep;93(5):944-56 PMID: 25040919
  7. A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition.
    Hum Genet. 2016 Jul;135(7):707-13 PMID: 27055666
  8. RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data.
    Nucleic Acids Res. 2016 Jan 4;44(D1):D259-65 PMID: 26464443
  9. MODOMICS: a database of RNA modification pathways--2013 update.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D262-7 PMID: 23118484
  10. RNAcentral: an international database of ncRNA sequences.
    Nucleic Acids Res. 2015 Jan;43(Database issue):D123-9 PMID: 25352543
  11. Identification of 2-methylthio cyclic N6-threonylcarbamoyladenosine (ms2ct6A) as a novel RNA modification at position 37 of tRNAs.
    Nucleic Acids Res. 2017 Feb 28;45(4):2124-2136 PMID: 27913733
  12. Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3.
    Nat Commun. 2016 Jun 30;7:12039 PMID: 27356879
  13. NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs.
    RNA. 2015 Sep;21(9):1532-43 PMID: 26160102
  14. The RNA modification landscape in human disease.
    RNA. 2017 Dec;23 (12 ):1754-1769 PMID: 28855326
  15. RNA modifications and structures cooperate to guide RNA-protein interactions.
    Nat Rev Mol Cell Biol. 2017 Mar;18(3):202-210 PMID: 28144031
  16. A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs.
    Nucleic Acids Res. 2014 Jun;42(11):7346-57 PMID: 24831542
  17. ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches.
    Nucleic Acids Res. 2001 Apr 1;29(7):1647-52 PMID: 11266569
  18. MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments.
    Bioinformatics. 2016 Aug 15;32(16):2481-9 PMID: 27153631
  19. Enhanced detection of post-transcriptional modifications using a mass-exclusion list strategy for RNA modification mapping by LC-MS/MS.
    Anal Chem. 2015 Aug 18;87(16):8433-40 PMID: 26176336
  20. Pseudouridine in the Anticodon of Escherichia coli tRNATyr(QΨA) Is Catalyzed by the Dual Specificity Enzyme RluF.
    J Biol Chem. 2016 Oct 14;291(42):22327-22337 PMID: 27551044
  21. m6A in mRNA: An Ancient Mechanism for Fine-Tuning Gene Expression.
    Trends Genet. 2017 Jun;33(6):380-390 PMID: 28499622
  22. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  23. Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs.
    RNA. 2014 Feb;20(2):177-88 PMID: 24344322
  24. A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress.
    PLoS Genet. 2010 Dec 16;6(12):e1001247 PMID: 21187895
  25. Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons.
    Nucleic Acids Res. 2016 Jan 29;44(2):509-23 PMID: 26681692
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkx1030
Published
2018-00-04
Pages
D303-D307
Language
English
Region
England
NLM ID
0411011
PMCID
PMC5753262
Grants
NIGMS NIH HHS · R01 GM058843 · United States
NIGMS NIH HHS · R01 GM070641 · United States
External Links
PubMed source DOI: 10.1093/nar/gkx1030 PMC Full Text View journal details
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