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Molecular and Cellular Biology, August 2004, p. 7249-7259, Vol. 24, No. 16
0270-7306/04/$08.00+0     DOI: 10.1128/MCB.24.16.7249-7259.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Cluster Analysis of Mass Spectrometry Data Reveals a Novel Component of SAGA

David W. Powell,1 Connie M. Weaver,1 Jennifer L. Jennings,1 K. Jill McAfee,1 Yue He,1 P. Anthony Weil,2 and Andrew J. Link1*

Department of Microbiology and Immunology,1 Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-23632

Received 13 February 2004/ Returned for modification 16 March 2004/ Accepted 18 May 2004

The SAGA histone acetyltransferase and TFIID complexes play key roles in eukaryotic transcription. Using hierarchical cluster analysis of mass spectrometry data to identify proteins that copurify with components of the budding yeast TFIID transcription complex, we discovered that an uncharacterized protein corresponding to the YPL047W open reading frame significantly associated with shared components of the TFIID and SAGA complexes. Using mass spectrometry and biochemical assays, we show that YPL047W (SGF11, 11-kDa SAGA-associated factor) is an integral subunit of SAGA. However, SGF11 does not appear to play a role in SAGA-mediated histone acetylation. DNA microarray analysis showed that SGF11 mediates transcription of a subset of SAGA-dependent genes, as well as SAGA-independent genes. SAGA purified from a sgf11{Delta} deletion strain has reduced amounts of Ubp8p, and a ubp8{Delta} deletion strain shows changes in transcription similar to those seen with the sgf11{Delta} deletion strain. Together, these data show that Sgf11p is a novel component of the yeast SAGA complex and that SGF11 regulates transcription of a subset of SAGA-regulated genes. Our data suggest that the role of SGF11 in transcription is independent of SAGA's histone acetyltransferase activity but may involve Ubp8p recruitment to or stabilization in SAGA.

* Corresponding author. Mailing address: Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232-2363. Phone: (615) 343-6823. Fax: (615) 343-7392. E-mail: andrew.link{at}vanderbilt.edu.

Molecular and Cellular Biology, August 2004, p. 7249-7259, Vol. 24, No. 16
0022-538X/04/$08.00+0     DOI: 10.1128/MCB.24.16.7249-7259.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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