MODOMICS: a database of RNA modification pathways. 2008 update - PubMed (original) (raw)

. 2009 Jan;37(Database issue):D118-21.

doi: 10.1093/nar/gkn710. Epub 2008 Oct 14.

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MODOMICS: a database of RNA modification pathways. 2008 update

Anna Czerwoniec et al. Nucleic Acids Res. 2009 Jan.

Abstract

MODOMICS, a database devoted to the systems biology of RNA modification, has been subjected to substantial improvements. It provides comprehensive information on the chemical structure of modified nucleosides, pathways of their biosynthesis, sequences of RNAs containing these modifications and RNA-modifying enzymes. MODOMICS also provides cross-references to other databases and to literature. In addition to the previously available manually curated tRNA sequences from a few model organisms, we have now included additional tRNAs and rRNAs, and all RNAs with 3D structures in the Nucleic Acid Database, in which modified nucleosides are present. In total, 3460 modified bases in RNA sequences of different organisms have been annotated. New RNA-modifying enzymes have been also added. The current collection of enzymes includes mainly proteins for the model organisms Escherichia coli and Saccharomyces cerevisiae, and is currently being expanded to include proteins from other organisms, in particular Archaea and Homo sapiens. For enzymes with known structures, links are provided to the corresponding Protein Data Bank entries, while for many others homology models have been created. Many new options for database searching and querying have been included. MODOMICS can be accessed at http://genesilico.pl/modomics.

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Figures

Figure 1.

Figure 1.

Contents of the MODOMICS database. (a) Detailed report on the modification mnm5se2U. (b) A fragment of the uridine modification pathway. In addition to A, C, G and U, a separate graph for queuosine is available. (c) Six of 124 modification enzymes, as seen on the web. (d) The methylation of m6A (6A according to the new nomenclature) to the hypermodified base m6,6A (7A). (e) Three out of 28 model structures for modification enzymes: E. coli MnmA; tT.Eco.MnmA according to the new nomenclature); E. coli TruC (tP.Eco.TruC); E. coli Tgt (tG.Eco.Tgt)). (f) New nomenclature for modified bases and modification enzymes. (g) Alignment of tRNAs with modified positions indicated. (h) Chemical structures of the chm5U (36U) and i6A (19A) modifications.

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