Fungal Zuotin Proteins Evolved from MIDA1-like Factors by Lineage-Specific Loss of MYB Domains

Molecular Biology and Evolution, Vol. 18, pp. 1401-1412

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Fungal Zuotin Proteins Evolved from MIDA1-like Factors by Lineage-Specific Loss of MYB Domains

Edward L. Braun* and Erich Grotewold

Department of Plant Biology and Plant Biotechnology Center, Ohio State University, Columbus, Ohio 43210 (both authors);
E.L.B. is currently in the Department of Zoology at the University of Florida.

Proteins are often characterized by the presence of multiple domains, which make specific contributions to their cellular function. While the gain of domains in proteins by duplication and shuffling is well established, domain loss is poorly documented. Here, we provide evidence thatdomain loss has played an important role in the evolution of protein architecture and function by demonstrating that fungal Zuotin proteins evolved from MIDA1-like proteins, present in animals and plants, by complete loss of the carboxyl-terminal MYB domains. Phylogenetic analyses of the DnaJ motif (the J domain) present in both Zuotin and MIDA1 proteins were complicated by the limited length and profound differences in evolutionary rates exhibited by this domain. To rigorously examine J domain phylogeny, we combined the nonparametricbootstrap with Monte Carlo simulation. This method, which we have designated the resampled parametric bootstrap, allowed us to assess type I and type II error associated with these analyses. These results revealed significant support for domain loss rather than domain gain or gene loss involving paralogs. The absence of sequences related to the MIDA1 MYB domains in Saccharomyces cerevisiae further indicates that the domains have been completely lost, consistent with known functional differences between Zuotin and MIDA1 proteins. These analysessuggest that the description of additional examples of complete domain loss may provide a method to identify orthologous proteins exhibiting functional differences using genomic sequence data.


This work was supported by grants from the USDA (1999-01582 to E.L.B.), the National Science Foundation (grant MCB-9896111 to E.G.), and Pioneer Hi-Bred International (to E.G.) and the Ohio State University Office of Research (to E.G.).

* Corresponding author