Proceedings of the National Academy of Sciences of the United States of America | 2019
Proteome-wide observation of the phenomenon of life on the edge of solubility
Abstract
Significance More than a decade ago, we put forward the “life on the edge of solubility” hypothesis, according to which proteins are expressed in the cellular environment at levels close to their solubility limits. This observation was based on the analysis of a small number of proteins for which solubility and cellular concentration information was available at the time. To confirm this hypothesis we have now taken advantage of recent advances in mass spectrometry that have enabled the proteome-wide analysis of protein concentrations in both the soluble and insoluble forms. We have been able to show in this way that the vast majority of proteins in a model organism are indeed expressed above their solubility limits, and to investigate the consequences of this phenomenon. To function effectively proteins must avoid aberrant aggregation, and hence they are expected to be expressed at concentrations safely below their solubility limits. By analyzing proteome-wide mass spectrometry data of Caenorhabditis elegans, however, we show that the levels of about three-quarters of the nearly 4,000 proteins analyzed in adult animals are close to their intrinsic solubility limits, indeed exceeding them by about 10% on average. We next asked how aging and functional self-assembly influence these solubility limits. We found that despite the fact that the total quantity of proteins within the cellular environment remains approximately constant during aging, protein aggregation sharply increases between days 6 and 12 of adulthood, after the worms have reproduced, as individual proteins lose their stoichiometric balances and the cellular machinery that maintains solubility undergoes functional decline. These findings reveal that these proteins are highly prone to undergoing concentration-dependent phase separation, which on aging is rationalized in a decrease of their effective solubilities, in particular for proteins associated with translation, growth, reproduction, and the chaperone system.