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MODOMICS


NAR Molecular Biology Database Collection entry number 840
Czerwoniec, A.1, Dunin-Horkawicz, S.2, Purta, E.3,4, Kaminska, K.H.3, Kasprzak, J.M.1, Bujnicki, J.M.1,3, Grosjean, H.5, and Rother, K.3
1Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
2Max Planck Institute for Developmental Biology, Department 1, Protein Evolution Spemannstr. 35, 72076 Tuebingen, Germany
3Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Ks. Trojdena 4, PL-02-190 Warsaw, Poland
4Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw
5IGM, Univ. Paris-Sud, UMR 8621, Orsay, F 91405, France

Database Description

MODOMICS ('omics' approach to RNA modification) integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions. MODOMICS also provides literature information, and links to other databases, including the available protein sequence and structure data. MODOMICS can be queried by the type of nucleoside, type of RNA, position of a particular nucleoside, type of reaction (e.g. methylation, thiolation, deamination, etc.), and name or sequence of an enzyme of interest. The contents of MODOMICS can be accessed through the World Wide Web at http://genesilico.pl/modomics/.

Recent Developments

The field has developed rapidly. Modifications have been found to occur in microRNAs. New modifications have been found, and biosynthesis pathways of known modifications have been elucidated. In many cases, the biochemical and physiological roles of modifications have been found, e.g. in the decoding process for modifications in tRNA. Finally, numerous new RNA-modifying enzymes have been identified, including a number of rRNA methyltransferases.
To adequately represent this rapid accumulation of knowledge, we have added both to the variety and volume of data in the MODOMICS database. The most significant improvements are addition of modifications in rRNA with their positions, updates of the according modification enzymes and pathways, 3D structures of modifications, and structures of many modification enzymes, including a collection of homology models for enzymes with no experimental structure available.
Options for data presentation include graphs of pathways, multiple sequence alignments of RNA sequences and tabular forms with enzyme and literature data. The data has been formalized to a higher extent, resulting in development of an ontology for modified bases, and flat file parsers that make the data more accessible for batch download and further analyses.

Acknowledgements

We would like to thank Rich Roberts, Stephen Douthwaite, Adrian Ferre D'Amare, Jef Rozenski, Saulius Klimasauskas, Xiaodong Cheng, and Tim Bestor for their contribution and intense discussion of the modification and enzyme nomenclature system.
This work was supported by Polish Ministry of Science and Higher Education (Ph.D. grant to A.C., [number N301 010 31/0219]). K.R. was supported by the Marie Curie 6th EU-6FP Research Training Network “DNA Enzymes” [grant number MRTNCT-2005-019566]. J.M.B. was supported by the EU-6FP Network of Excellence “EURASNET” [grant number LSHG-CT-2005-518238].

References

1. Bujnicki, J.M., Droogmans, L., Grosjean, H., Purushothaman, S.K., Lapeyre, B. (2004) Bioinformatics-guided identification and experimental characterization of novel RNA methyltransferases. In Nucleic Acids and Molecular Biology series, "Practical Bioinformatics". Editor: Bujnicki, J.M. Springer-Verlag
2. Dunin-Horkawicz, S., Czerwoniec, A., Gajda, M.J., Feder, M., Grosjean, H., and Bujnicki, J.M. (2006) MODOMICS: a database of RNA modification pathways. Nucleic Acids Res. 34, D145-9
3. Czerwoniec, A., Dunin-Horkawicz, S., Purta, E., Kaminska, K.H., Kasprzak, J.M., Bujnicki, J.M., Grosjean, H., and Rother, K. (2009) MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res. 37, D118-21

Subcategory: Metabolic pathways

Go to the abstract in the NAR 2009 Database Issue.
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