Abstract
FUGOID is a web-based, taxonomically broad organelle intron database that collects and integrates various functional and structural data on organellar (mitochondrial and chloroplast) introns. The main information provided by FUGOID includes intron sequence, subclass, resident ORF, self-splicing capability, host gene, protein factor(s) involved in splicing, mobility, insertion site, twintron, seminal references and taxonomic position of host organism. It is implemented in a relational database management system, allowing sophisticated, user-friendly searching, data entry and revision. Users can access the database by any common web browser using a variety of operating systems. The main page of the database is available at http://wnt.cc.utexas.edu/~ifmr530/introndata/main.htm.
INTRODUCTION
Unlike prokaryotes and archaea, eukaryotic cells contain a variety of subcellular, membrane-bound organelles. Chloroplasts and mitochondria are prominent organelles that have their own distinct genetic systems, and although there are significant differences between them, there are also striking similarities, such as their evolution from prokaryotes, the types of genes they contain, uniparental inheritance and their dependence on nuclear genes for biogenesis (1).
A distinguishing feature of organellar genomes is the presence of characteristic introns. There are three recognized classes of organellar introns: (i) Group I, (ii) Group II and (iii) Group III (2–4). Group III introns are phylogenetically restricted in their distribution, and are related to Group II introns, from which they may have evolved (3). Organellar introns differ significantly from nuclear mRNA (and tRNA) introns in both structure and function, although splicing of Group II and III introns shares some mechanistic features (and very limited structural similarity) with nuclear mRNA introns (2,3).
Introns of Groups I and II have attracted considerable attention, because of two remarkable properties of at least some members of these groups: the ability to self-splice (2,4,5), and the ability to invade intronless alleles in a process known as intron homing (6–8). In vivo, splicing of even the self-splicing introns probably requires protein factors, which can be encoded within the intron itself, or as separate genes that may also have other functions, such as tRNA charging (9,10). Intron homing is a complicated process that is initiated by an intron-encoded protein whose structure and function differs significantly between mobile Group I and II introns (10). There is also increasing evidence for these introns moving horizontally between genomes over evolutionary time, although the mechanisms responsible are enigmatic (8).
A large amount of functional as well as structural data on organellar introns has been generated over the last two decades; however, the information is widely dispersed and time-consuming to retrieve. Thus, this database, FUGOID, for Functional Genomics of Organellar Introns Database, is established as a single, user-friendly resource to facilitate exploitation of existing and future data on the functions of organellar introns.
DATABASE CONSTRUCTION AND CONTENT
FUGOID contains information primarily on mitochondrial and chloroplast introns for which there is functional (e.g. self-splicing) and/or expression data. However, there are some entries for which there is only structural information, although there was no attempt to be exhaustive in this regard. FUGOID is available at http://wnt.cc.utexas.edu/~ifmr530/introndata/main.htm. The current version includes: intron definition, classification, size, sequence, host gene, ORF, self-splicing ability, intron-encoded protein, mobility, splicing factor(s), insertion site, twintron, initial references and general taxonomic information. To date, the database has information on 354 organellar introns.
FUGOID is a relational database. The web interface and search facility were developed using ColdFusion 5 (Macromedia, 2001), and the data is stored in a Microsoft Access database engine. The intron sequences and taxonomic information were drawn from the NCBI Entrez system (11).The other information was retrieved from the scientific literature.
Links are provided to two other databases that have information related to organellar introns, the Group I Intron Database (12), which focuses on secondary structure models of selected Group I introns, and GOBASE (13), which specializes in taxonomic comparison of introns. FUGOID is unique because it collects and integrates functional data on organellar introns, elements which are not found in these other databases. FUGOID is also searchable by partial or full intron sequence, and by other properties, such as subclass, splicing or homing properties, insertion site, twintron, initial references, etc.
DATABASE ACCESS
FUGOID can be accessed with any web browser; however, certain features, such as wrapping of the sequence and reference fields, may work better with later versions of Internet Explorer (at least 5.5) or Netscape (6.0). There are two general ways to query the database: one is using intron information, the other is using a reference query. With the former, one can search with intron sequence, name, genus, species, host gene, size, intron-encoded protein, self-splicing ability, nuclear splicing factor, twintron, insertion site or some combination of these. For the reference query, an author, reference title and/or name of a journal can be entered.
A query first returns a list of introns with limited information. The user can then obtain more detailed information about a specific intron by selecting it in the return list. Detailed user instructions can also be found on the database homepage.
DATA SUBMISSION AND UPDATING
FUGOID has data submitting and updating systems; however, only authorized individuals can access these editors. Researchers who want to submit or update intron data may contact the authors (lifei@mail.utexas.edu or dlherrin@utxvms.cc.utexas.edu).
FUTURE DIRECTIONS
One of the goals for this database is to expand it to add nuclear rRNA and prokaryotic introns that are related to organellar introns, and for which there is functional/expression data. Further planned developments include adding homology searching capability and a password-protected security access so that authorized researchers can submit or revise data directly on the web.
Acknowledgments
ACKNOWLEDGEMENTS
We thank Dr O. W. Odom for helpful discussions and critical reading of the manuscript. This research was supported by grants from the R.A. Welch Foundation (F-1164) and the USDA (NRICGP 99-35301-7847).
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