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Overview on RNA Editing database

RNA editing is a post-transcriptional process whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions and deletions. It is widely frequent in some unicellular organisms, viruses and very different species of eukaryotes, including animals and plants [1]. However, the RNA editing has a major impact on genes and genomes of mitochondria and chloroplasts [2]. The translation of mitochondrial mRNAs in kinetoplastids is, indeed, impossible without massive RNA editing of the transcripts by insertion and deletion of Us [3]. Moreover, in some kinetoplastid genes, editing creates over 90% of the amino acid codons and because of this post-transcriptional proof-reading action, the corresponding DNA copies are barely recognizable and sometimes called "cryptogenes" [3].
The impact of RNA editing can still be large even in cases where the physical extend of editing is small. For instance, in plant mitochondrial and chloroplast transcripts the replacement of a limited number of cytidine (C) by uridine (U) results in the translation of functionally competent and evolutionarily conserved polypeptides [4]. Therefore, the RNA editing appears to be a basic post-transcriptional process to promote a reliable gene expression in a wide range of organisms [1, 2].
Nonetheless, in current primary databases editing sites are sometimes omitted or the annotations contain a lot of errors. Indeed, present day primary databases do not contain or provide a specific and appropriate field to correctly and unambiguously store RNA editing alterations.
Given the physiological importance of RNA editing and the importance to collect sequences subjected to editing to:

promote and facilitate evolutionary studies

improve the work of research groups directed to the identification and discovery of new cis-acting elements involved in the biochemical process of RNA editing [5]

make easy the comparison of editing patterns from genes connected to specific diseases (different editing might be required by some mitochondrial genes of CMS plants)

test computational methods to simulate or predict editing sites [6, 7]

we decided to recover from primary databases and literature all sequences post-transcriptionally modified by RNA editing and insert them in a specialized database called REDIdb (RNA Editing database).
The REDIdb is a relational database in which all editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored and maintained in ad hoc designed textual flat files (for details about REDIdb flat file structure see the "structure" page). Individual gene of interest can be searched by appropriate query strings containing the gene name or the intracellular location or the molecular type (as tRNA, rRNA, intron) or the organism or a combination of the previous terms. Moreover, each record of the REDIdb database can be also retrieved according to its specific accession number (more help on how to perform a REDIdb search is available at the “help” page). To make easier the browsing of each REDIdb entry and quicker the identification of editing sites, two alternative but complementary facilities have been provided either to graphically display genomic and cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are shown by mousing over. A complete overview of the REDIdb web site is shown in the picture below.


REDIdb Web Site








In this first release, REDIdb is limited to RNA editing events of organellar genes and genomes, even though the database is ready to receive edited sequences from nuclear and viral genomes as well. The REDIdb has been created and will be maintained at the University of Calabria (Italy). It is currently and freely available at the following web address:
http://biologia.unical.it/py_script/search.html.
If you need more help on specific questions not described in these web pages, please, contact us using the form at the "contact" page.

Thank you very much for using REDIdb database.

The REDIdb staff

Axel Brennicke
Ernesto Picardi
Carla Quagliariello
Teresa M.R. Regina


Acknowledgements


The REDIdb staff gratefully acknowledges J.P. Mower for providing an useful compilation of manually cured edited plant mitochondrial genes. A special thank is also addressed to the Centro di Eccellenza per il Calcolo ad Alte Prestazioni for making available computing facilities and the Area Informatica e Telematica (in particular Fabrizio Di Maio) of the Università della Calabria for providing technical support about the MySQL server. The REDIdb staff acknowledges also the people of the Molekulare Botanik Laboratory at the Universität Ulm for valuable and useful suggestions on REDIdb web interface.



References


[1] Brennicke, A., Marchfelder, A., Binder, S., (1999) RNA editing. FEMS Microbiol 23: 297-316 [Pubmed]

[2] Gray, M.W., (2003) Diversity and evolution of mitochondrial RNA editing systems. IUBMB Life 55: 227-233 [Pubmed]

[3] Horton, T.L., Landweber, L.F., (2002) Rewriting the information in DNA: RNA editing in kinetoplastids and myxomycetes. Curr Opin Microbiol 5: 620-626 [Pubmed]

[4] Regina, T.M.R., Lopez, L., Picardi, E., Quagliariello, C., (2002) Striking differences in RNA editing requirements to express the rps4 gene in magnolia and sunflower mitochondria. Gene 286: 33-41 [Pubmed]

[5] van der Merwe, J.A., Takenaka, M., Neuwirt, J., Verbitskiy, D., Brennicke, A., (2006) RNA editing sites in plant mitochondria can share cis-elements. FEBS Lett 580: 268-72 [Pubmed]

[6] Picardi, E., Quagliariello, C., (2006) EdiPy: a resource to simulate the evolution of plant mitochondrial genes under the RNA editing. Comput Biol Chem 30: 77-80 [Pubmed]

[7] Mower, J.P., (2005) PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinformatics 6: 96 [Pubmed]




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Copyright ©2006-2007 Ernesto Picardi