Ribosomal Paralogs not Redundant Afterall
In the budding yeast Saccharomyces cerevisiae, 59 of the 79 cytoplasmic ribosomal proteins are encoded by two genes, stemming from an ancient genome duplication event. Komili et al. (2007) now report that these paralogous genes are not functionally equivalent, suggesting the possible existence of a “ribosome code.”1
Yeast and mammalian genomes are riddled with apparently duplicated genes, differing in only a few amino acids from one paralogue to its clone. Because they’re so nearly identical, most researchers assume some degree of redundancy in such circumstances, and attempt to ascertain the function of only one of the two. If there is any difference in function between two paralogues, the difference might be unimportant, or just too difficult to tease apart experimentally.
As we gain more and more insight into how the cell works, such minutiae might be a curious area to study up on. In the case of the yeast S. cerevisiae, it turns out that 59 of their 78 ribosomal proteins have doubles that differ by only a few amino acids. Suzanne Komili, Pamela Silver (Harvard Medical School, Boston, MA), and colleagues2 make an intriguing argument that only rarely are individual members of a paralogous gene pair functionally identical, despite this strong sequence similarity.
The team found that translation of the protein ASH1 could be altered in strains lacking certain paralogues, suggesting that these copies were essential for regulating protein synthesis. These effects were found to be neither dependent on the expression level of the duplicate genes nor are they suppressed by overexpression of the other gene, suggesting that the paralogous proteins are performing different functions. So what patterns of translational functionality can we infer? Komili et al. offer a possibility:
Our data supports a model in which there are many different forms of functionally distinct ribosomes in yeast, where the functional specificity is determined by the combination of duplicated ribosomal proteins present…. This model of translational regulation bears a striking resemblance to the canonical model for transcriptional regulation. The transcriptional activity of a given region of DNA is regulated by the structure of the surrounding chromatin, which is largely determined by the types of associated histones and their posttranslational modifications. As with ribosomal proteins, histone genes are duplicated in yeast…. Our data support a similar level of complexity for the process of translation in which different combinations of ribosomal protein paralogs, posttranslational modifications of ribosomal proteins, different forms of rRNA, and modifications to the rRNA allow calibrated translation of specific mRNAs. As with the histone code, this “ribosome code” would provide a new level of complexity in the regulation of gene expression.
A “ribosome code?” Maybe - but the more concise description might be that this finding represents just another level of regulation of gene expression. Layers upon layers.
- McIntosh KB, Warner JR. Yeast Ribosomes: Variety Is the Spice of Life. Cell 2 Nov 2007, 131(3):450-451. doi:10.1016/j.cell.2007.10.028
- Komili S, Farny NG, Roth FP, Silver PA. Functional Specificity among Ribosomal Proteins Regulates Gene Expression. Cell 2 Nov 2007, 131(3):557-571. doi:10.1016/j.cell.2007.08.037
About the Author
Dan Rhoads
Dan is an American working in industry in a small Mediterranean country. He has a BSc in Molecular Biology and a PhD in Cancer Pharmacology and Biochemistry.
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