yibd

Welcome to

YIDB: the Yeast Intron DataBase

By Pascal J. Lopez and Bertrand Séraphin

EMBL, Meyerhofstrasse 1, D-69117, Germany.

Postdoctoral positions available

Content

The Yeast Intron DataBase (YIDB) contains currently available information about all introns encoded in the nuclear and mitochondrial genomes of the yeast Saccharomyces cerevisiae. Introns are divided according to their mechanisms of excision as:

pre-mRNA introns

tRNA introns

the HAC1 intron

group I introns

group II introns

Information about the host genome, the type of RNA in which they are inserted and their primary structure are provided together with references. For nuclear pre-mRNA introns transcription frequencies, as determined by microarray experiments, have also been included.

Introns and splicing

Introns are sequences present in various types of genes that need to be removed from primary transcripts to allow the formation of functional RNAs. Introns are present in all classes of RNA (rRNA, tRNA, mRNA, etc…) and have been found in various genomes (eukaryotic, prokaryotic, organelles, viruses, etc…). Intron sequences have to be precisely recognized and eliminated from pre-RNA to allow for functional protein or RNA synthesis. In a few cases, introns are involved in the regulation of the expression of their host genes, are alternatively spliced, correspond to mobile genetic elements or code themselves for protein or functional RNA. They constitue therefore a remarkable evolutionary tool.

Yeast introns

Introns are classified according to their excision mechanisms. In yeast, five different classes can be distinguished:

Group I introns are spliced via two guanosine-initiated transesterification reactions. Some of these introns are autocatalytic. Group I introns share limited sequence similarity but have conserved secondary and tertiary structures (8).

Group II introns are spliced via two transesterification reactions similar to the ones occurring for nuclear pre-mRNA introns. Some group II introns are also autocatalytic. They have conserved 5’ and 3’ extremities as well as secondary and tertiary structures (7). In vivo splicing of group I and II introns often dependents on proteins (5).

Splicing of nuclear spliceosomal introns also involves two transesterification reactions. This process is catalyzed by a large ribonucleoprotein machinery named the spliceosome. This complex and dynamic enzyme is made by the ordered assembly onto the intron of 5 snRNPs (small nuclear RiboNucloProteins) as well as non-snRNP proteins; in total more than 100 proteins may contribute to the spliceosome (2). Conserved sequences are present at the 5’ and 3’ end of spliceosomal introns, at their branchpoint and, to a lesser extent, in flanking exon sequences.

tRNA introns are found in nuclear tRNA genes. They show little sequence conservation but are always inserted at the same location in tRNAs. The removal of these introns is is catalyzed by proteins (1).

Finally, a special type of intron is found in the nuclear HAC1 gene. Splicing of this intron is catalyzed by protein factors, some of which are shared with tRNA introns. The splicing of this intron is highly regulated (10).

The following table provides an overview of yeast introns, their number, type of host RNA, corresponding genomes and frequencies. Further information about each type of intron can be found by following the appropriate links.

Intron type	Intron Number (3, 6, 9)	Number of host genes	Number of intron per gene	Type of host gene	Host genome	Number of genes of this type in the host genome (3, 4, 9)
Spliceosomal	255	250	1 or 2	mRNA	nuclear	ca. 6100
tRNA	61	61	1	tRNA	nuclear	274
HAC1	1	1	1	mRNA	nuclear	ca. 6100
Group I	9	3	1-4	mRNA rRNA	mitochondrial	8 2
Group II	4	2	1-3	mRNA	mitochondrial	8

Why a database

A compilation of intron sequences can help not only to analyze the chromosomal organization of yeast genomes, but also to define consensus sequences and nucleotide contents, features that are crucial for systematic gene identification. Moreover, the database can help, by taking into account quantitative data about expression such as transcription levels, to gain a better insight into cellular processes (see 6).

Database availability and citation

The YIDB database is freely available for academic usage. User of the database should cite "Lopez, P.J. and B. Séraphin. 2000. YIBD: the Yeast Intron DataBase. Nucleic Acids Research 28, 85-86"; as a reference. Comments, corrections and new entries are welcome.

References

1. Abelson, J., C. R. Trotta, and H. Li. 1998. tRNA splicing. J. Biol. Chem. 273, 12685-12688.

2. Burge, C. B., T. Tuschl, and P. A. Sharp. 1999. Splicing of Precursors to mRNAs by the Spliceosomes. In R. F. Gesteland, T. R. Cech, and J. F. Atkins (ed.), The RNA world, Second edition ed. Cold Spring Harbourg Labortory Press, Cold Spring Harbor.

3. Foury, F., T. Roganti, N. Lecrenier, and B. Purnelle. 1998. The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Lett. 440, 325-331.

4. Goffeau, A., B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philippsen, H. Tettelin, and S. G. Oliver. 1996. Life with 6000 genes. Science 274, 563-567.

5. Lambowitz, A. M., and M. Belfort. 1993. Introns as mobile genetic elements. Annu. Rev. Biochem. 62, 587-622.

6. Lopez, P. J., and B. Séraphin. 1999. Genomic-scale quantitative analysis of yeast pre-mRNA splicing: implications for splice site recognition. RNA 5, 1135-1137.

7. Michel, F., and J. L. Ferat. 1995. Structure and activities of group II introns. Annu. Rev. Biochem. 64, 435-461.

8. Michel, F., and E. Westhof. 1990. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216, 585-610.

9. Percudani, R., A. Pavesi, and S. Ottonello. 1997. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol. 268, 322-330.

10. Sidrauski, C., J.S. Cox, and P. Walter. 1996. tRNA ligase is required for regulated mRNA splicing in the unfolded protein response. Cell 87, 405-413.

Author: Séraphin@embl-heidelberg.de Last Modified, August 16, 2000