Coevolution of gene expression among interacting proteins

Journal Article · Mon Mar 01 04:00:00 EST 2004 · Proceedings Of The National Academy of Sciences

DOI:https://doi.org/10.1073/pnas.0402591101· OSTI ID:860470

Fraser, Hunter B; Hirsh, Aaron E; Wall, Dennis P; Eisen, Michael B

Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well documented and has been used to predict interacting proteins, domains, and amino acids. Interacting proteins are also often precisely coexpressed with one another, presumably to maintain proper stoichiometry among interacting components. Here, we show that the expression levels of physically interacting proteins coevolve. We estimate average expression levels of genes from four closely related fungi of the genus Saccharomyces using the codon adaptation index and show that expression levels of interacting proteins exhibit coordinated changes in these different species. We find that this coevolution of expression is a more powerful predictor of physical interaction than is coevolution of amino acid sequence. These results demonstrate previously uncharacterized coevolution of gene expression, adding a different dimension to the study of the coevolution of interacting proteins and underscoring the importance of maintaining coexpression of interacting proteins over evolutionary time. Our results also suggest that expression coevolution can be used for computational prediction of protein protein interactions.

• Research Organization: Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE; National Science Foundation
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 860470
• Report Number(s): LBNL--55192; BnR: 600305000
• Journal Information: Proceedings Of The National Academy of Sciences, Journal Name: Proceedings Of The National Academy of Sciences Journal Issue: 24 Vol. 101
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
AMINO ACID SEQUENCE
AMINO ACIDS
CODONS
DIMENSIONS
FORECASTING
FUNGI
GENES
PROTEINS
SACCHAROMYCES
STOICHIOMETRY