MODOMICS: a database of RNA modification pathways. 2008 update

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.

Unexpected expansion of tRNA substrate recognition by the yeast m1G9methyltransferase Trm10

“…4); percentage modification determined by intensity of primer extension stop before G 9 compared to intensity of total primer extension products for each tRNA. c From references Czerwoniec et al (2009) andJühling et al (2009). d (NA) not applicable; tRNA already fully modified with m 1 G 9 .…”

“…tRNA species from all three domains of life contain numerous post-transcriptional modifications to nucleotide bases and ribose sugars (Grosjean et al 1995;Grosjean and Benne 1998;Czerwoniec et al 2009;Jühling et al 2009;Phizicky and Hopper 2010;Jackman and Alfonzo 2013;Machnicka et al 2013). Nucleotide modifications found in tRNAs range in complexity from single methyl groups to large chemical groups, such as wybutosine.…”

NSUN 3 and ABH 1 modify the wobble position of mt‐t RNA Met to expand codon recognition in mitochondrial translation

“…More than a hundred different chemical modifications of ribonucleosides have been identified in cellular RNAs (Czerwoniec et al , 2009; Motorin & Helm, 2011). Modifications regulate the biogenesis, structure and function of the corresponding RNAs and RNA–protein complexes (RNPs).…”

rRNA Methyltransferases and their Role in Resistance to Antibiotics

“…While the biolo gical significance of r-protein modifi cations by methylation is poorly understood (10), the im portance of methylations of rRNAs that carry out 'housekeeping' roles essential for the general functioning of rRNA, during protein synthesis, has been recognized. Bacterial rRNAs can contain over thirty 'housekeeping' modifications, all of which are added posttranscriptionally (11). The sites of 'house-keeping' methylations have been most accurately mapped in Escherichia coli.…”