Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States; Department of Microbiology and Immunology, University of California, San Francisco, United States
Amanda N Johnson
Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States; Department of Microbiology and Immunology, University of California, San Francisco, United States
Candace S Britton
Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States; Department of Microbiology and Immunology, University of California, San Francisco, United States
Kyle R Fowler
Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States; Department of Microbiology and Immunology, University of California, San Francisco, United States
Jordan T Feigerle
Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
P Anthony Weil
Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
Alexander D Johnson
Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States; Department of Microbiology and Immunology, University of California, San Francisco, United States
Convergent evolutionary events in independent lineages provide an opportunity to understand why evolution favors certain outcomes over others. We studied such a case where a large set of genes—those coding for the ribosomal proteins—gained cis-regulatory sequences for a particular transcription regulator (Mcm1) in independent fungal lineages. We present evidence that these gains occurred because Mcm1 shares a mechanism of transcriptional activation with an ancestral regulator of the ribosomal protein genes, Rap1. Specifically, we show that Mcm1 and Rap1 have the inherent ability to cooperatively activate transcription through contacts with the general transcription factor TFIID. Because the two regulatory proteins share a common interaction partner, the presence of one ancestral cis-regulatory sequence can ‘channel’ random mutations into functional sites for the second regulator. At a genomic scale, this type of intrinsic cooperativity can account for a pattern of parallel evolution involving the fixation of hundreds of substitutions.
