Origin and properties of non-coding ORFs in the yeast genome

Abstract

In a recent paper we have estimated the total number of protein coding open reading frames (ORFs) in the Saccharomyces cerevisiae genome, based on their properties, at about 4800. This number is much smaller than the 5800-6000 which is widely accepted. In this paper we analyse differences between the set of ORFs with known phenotypes annotated in the Munich Information Centre for Protein Sequences (MIPS) database and ORFs for which the probability of coding, counted by us, is very low. We have found that many of the latter ORFs have properties of antisense sequences of coding ORFs, which suggests that they could have been generated by duplication of coding sequences. Since coding sequences generate ORFs inside themselves, with especially high frequency in the antisense sequences, we have looked for homology between known proteins and hypothetical polypeptides generated by ORFs under consideration in all the six phases. For many ORFs we have found paralogues and orthologues in phases different than the phase which had been assumed in the MIPS database as coding.

Schizosaccharomyces pombe Essential Genes: A Pilot Study

“…1). The budding yeast class V proteins may be too high by ∼10% because of overestimation of the total number of proteins in S. cerevisiae, especially those that are not conserved (Mackiewicz et al 1999(Mackiewicz et al , 2002Blandin et al 2000;Wood et al 2001). …”

ORF organization and gene recognition in the yeast genome

“…The numbers of the three kinds of overlapping genes were obtained from direct enumeration in each chromosome. Note that if a shorter ORF overlaps fully with a part of another longer ORF in the same frame, then the shorter one was not enumerated in this study (Dujon et al, 1994;Mackiewicz et al, 1999). However, shorter ORFs contained in alternative reading frames of the same strand or in any of the three reading frames of the opposite strand should be enumerated as well.…”

“…Many theoretical investigations have been carried out to search for the information hidden in the sequence. (Dujon, 1996;Dujon et al, 1994;Termier et al, 1996;Velculescu et al, 1997;Mackiewicz et al, 1999;Blandin et al, 2000;Cliften et al, 2001;Wood et al, 2001). One of the central problems in bioinformatics is gene recognition (International Humun Genome Sequencing Consortium, 2001;Stormo, 2000;Guigo et al, 2000;Karlin, 1998, 1997;Claverie, 1997;Gelfand et al, 1996;Burset and Guigo, 1996;Krogh et al, 1994).…”

Reverse Transcriptase-Polymerase Chain Reaction Validation of 25 “Orphan” Genes from Escherichia coli K-12 MG1655

“…A strong selection pressure would then exist against the maintenance of nonphysiological ORFs in the genome of proteobacteria (with the exception of intracellular parasites such a R. prowazekii (Andersson et al 1998)). The situation appears to be different in a unicellular eukaryote such as yeast, where up to 76% of annotated ORFs might not be expressed (Mackiewicz et al 1999). The intolerance for fake ORFs in prokaryote genomes might be related to the direct coupling between transcription and translation that is characteristic of these organisms.…”

“…Like ORFing, homology searches and functional assignments also involve different programs, target databases, and empirical significance thresholds. The classification of genes into the uncharacterized and orphan categories is thus subject to change Ouzounis et al 1995;Fisher and Eisenberg 1999;Mackiewicz et al 1999).…”