U-insertion/deletion Edited Sequence Database

doi:10.1093/nar/26.1.170

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Nucleic Acids Research Pages 170-176

U-insertion/deletion Edited Sequence Database
Introduction
Description Of Database
Availability
Acknowledgements
References

U-insertion/deletion Edited Sequence Database

Larry Simpson^1,2,3,*, Shirley H. Wang¹, Otavio H. Thiemann², Juan D. Alfonzo¹, Dmitri A. Maslov⁴, Herbert A. Avila⁵

¹Howard Hughes Medical Institute, ²Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, CA 90095-1662, USA, ³Department of Medical Microbiology and Immunology, UCLA School of Medicine, Los Angeles, CA, USA, ⁴Department of Biology, University of California, Riverside, CA 92521, USA and ⁵Department of Biochemistry, University of Kentucky Medical Center, Lexington, KY 40536-0084, USA

Received August 20, 1997; Revised and Accepted October 3, 1997

ABSTRACT

Uridine insertion/deletion RNA editing is a post-transcriptional RNA modification occurring in the mitochondria of kinetoplastid protozoa. The U-insertion/deletion Edited Sequence Database is a compilation of mitochondrial genes and edited mRNAs from five kinetoplastid species. It contains separate files with the DNA, mRNA (both unedited and edited) and predicted protein sequences, as well as alignments of the Leishmania tarentolae and Trypanosoma brucei protein sequences from edited and unedited genes. The sequence files are in GCG format. A `map' sequence file showing the location of U-deletions, U-insertions and the translated amino acid sequences is also provided for each gene. Genomic maps for each species are also provided with clickable genes, including maxicircle-encoded gRNAs. Sets of aligned nuclear rRNA sequences from kinetoplastid protozoa are also provided, which were used for phylogenetic reconstructions in an analysis of the origin of RNA editing. The database is available through the World Wide Web as an HTML document at the URL http://www.lifesci.ucla.edu/RNA/trypanosome/database.html

INTRODUCTION

Multiple mRNAs from the maxicircle mitochondrial genome of kinetoplastid protozoa undergo uridine (U)-insertion/deletion RNA editing (1-5). In this process, Us are inserted and deleted at precise sites, usually within coding regions. Editing provides a mechanism for the alteration of the reading frame and, in some cases, the creation of translation initiation codons (6-8). Genes whose transcripts are modified by RNA editing are termed `cryptogenes' (6), and the region in which editing occurs is termed the `pre-edited region' or the `editing domain'. In several instances, editing is so extensive as to take an unrecognizable G-rich cryptogene and render it into an open reading frame; this is termed `pan-editing'. The resulting edited RNAs are homologous to sequences encoding known mitochondrial proteins (9-16).

The information for the precise insertion and deletion events in a cryptogene transcript is provided by guide RNAs (gRNAs). Guide RNAs can base-pair to the pre-edited mRNAs just downstream of the region to be edited, thereby forming the `anchor duplex' (17). A single gRNA mediates the editing of a `block' of sequence. Frequently, an editing domain consists of multiple overlapping gRNAs. The 3[prime]->5[prime] polarity of editing-site selection within a domain is caused by the creation of anchor sequences for upstream gRNAs by downstream editing (18).

The maxicircle molecules correspond to the informational DNA molecules in other organisms, and encode two rRNAs, 18 structural genes and a few gRNAs (4,19,20). The minicircle molecules encode the majority of the gRNAs. The kinetoplastid protozoa consist of at least two major lineages, the trypanosomatids and the bodonids/cryptobiids (21,22). The trypanosomatids, which are the best studied organisms, contain a single network consisting of thousands of catenated minicircles and maxicircles situated within the single mitochondrion adjacent to the basal body of the flagellum. Only one example of the second major lineage has been studied in detail. The cryptobiid, Trypanoplasma borreli, contains two types of circular mitochondrial DNA molecules: the 40-80 kb circles contain rRNA genes, structural genes and cryptogenes, and the 180-200 kb circles contain gRNA genes (23-25).

We describe here a database of mitochondrial genes, cryptogenes, and edited mRNA sequences from kinetoplastid protozoa.

DESCRIPTION OF DATABASE

This database (Fig. 1) is a compilation of mitochondrial sequences from four trypanosomatid species: Leishmania tarentolae (Fig. 2A), Trypanosoma brucei (Fig. 2B), Trypanosoma cruzi (not included as a clickable map), Crithidia fasciculata (Fig. 2C), and one cryptobiid species, Trypanoplasma borreli (Fig. 2D). The database contains files of the 9S and 12S mitochondrial rRNA sequences, the sequences of unedited structural genes, pre-edited cryptogenes, fully edited mRNAs, and the predicted peptide sequences encoded by the unedited genes and the fully edited mRNAs. All files are HTML documents, with the sequences in GCG format, which can be accessed either by clicking the name of the gene in a Table (Fig. 3), or the gene itself in a genomic map (Fig. 2A-D). Preceding each sequence is the gene name, the species, the accession number in GenBank, and notes on sequence corrections or 5[prime] end localizations.

Nucleic Acids Research