Yeast harbor numerous duplicate genes. For example, 59 of their 78 ribosomal proteins have doubles that differ by only a few amino acids. For more than a decade, researchers thought that these paralogues were interchangeable, in part because knockouts showed no slowing of growth. However, recent work suggested that some so-called backups can't substitute for their counterparts, prompting Komili and colleagues to ask whether duplicate ribosomal proteins have distinct jobs during translation.
The team found that translation of the protein ASH1 went awry in strains lacking certain paralogues, suggesting that these copies were essential for regulating protein synthesis. Loss of paralogues also had broader, often contrasting effects on cell activities. Yeast missing the protein Rpl12a cranked up amino acid metabolism genes, for instance, whereas cells lacking its twin, Rpl12b, shut down genes involved in building the cell wall. “The absence of one copy of a duplicated gene has a very different effect on the cell than the absence of the other copy of the same gene,” says Komili.
Using information from databases and the literature, the team organized ribosomal paralogues by function. They found that the proteins didn't form set teams, in which the same paralogues always collaborate, but instead had shifting lineups. That result suggests that cells build specialized ribosomes, each carrying a different set of paralogues, that perform all the translation required for a certain function, such as spore formation. Other organisms, including humans, have duplicate ribosomal proteins and might show a similar specialization.