Journal of Molecular Biology
CommunicationA small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution1
Section snippets
Finding dORFs in the sequenced yeast genome
Since the full extent of the dORF complement in yeast is not known at present, here we have defined the yeast dORF pool using a simple homology-based procedure. As described in detail in Figure 1(a), the yeast genome was scanned for significant protein homologies that contain at least one disablement and that do not rely on alignment to a previously annotated ORF in the genomic DNA. That is, if the dORF entails an annotated ORF, the disabled extension to the ORF arises from a significant span
Properties of yeast dORFs
We examined the core pool of dORFs as follows: (1) their distribution of disablements; (2) their homology trends; (3) their prevalent families; and (4) their chromosomal distribution.
Expression of dORFs
We tested a small random sample of 11 dORFs for expression (Figure 2(d)). Four of these showed appreciable expression, even though one has two disablements, and the other three have five or more disablements. Two of these four dORFs are subtelomeric (within 20 kb from chromosome ends), and homologous to putative hypothetical ORFs, representing dORF families of nine or more members. The other two are single dORFs with moderate sequence similarity for two annotated ORFs, both with five or more
A dynamically evolving subtelomeric subproteome and its role in strain-specific variation
The total pool of dORFs and pseudogenic fragments corresponds to only a very small percentage of the total annotated proteome (∼3%). However, the distribution of these dORFs, both in terms of homology and chromosomal position, details an important perspective on yeast proteome evolution.
In the present study, we have found that dORFs are half as likely to be related to a non-yeast protein (∼40% of dORFs) as to the average known yeast protein (80 % of annotated ORFs). This comparison implies that
Website
The dORF annotation data and sequences are available at the website http://genecensus.org/pseudogene (or http://bioinfo.mbb.yale.edu/ genome/pseudogene).
Acknowledgements
We thank Tricia Serio and Zhaolei Zhang for comments on the manuscript. A.K. is supported by a postdoctoral fellowship from the American Cancer Society. M.G. acknowledges support from the NIH protein structure initiative (P50 grant GM62413-01).
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