David T. Auble

Education

  • AB, Bowdoin College
  • PhD, Case Western Reserve University
  • Postdoc, Fred Hutchinson Cancer Research Center

Primary Appointment

  • Professor, Biochemistry and Molecular Genetics

Contact

Research Interest(s)

Molecular Mechanisms of Transcription Initiation and DNA Repair

Research Description

We are interested in understanding the mechanisms of action and in vivo functions of proteins belonging to a large evolutionarily-conserved family of nuclear ATPases (called the Snf2/Swi2 family). Snf2/Swi2 family members are involved in transcriptional regulation, DNA repair, recombination, and chromosome segregation, but how these proteins work is not well understood, nor is it understood what roles most of these proteins play in vivo. To better understand them, we are applying biochemical and genetic approaches to define the activities of Snf2/Swi2-related proteins in the yeast Saccharomyces cerevisiae.

Our work focuses on the Snf2/Swi2-related protein Mot1. Mot1 is an essential protein that can regulate transcription by a remarkable mechanism: it disrupts TATA-binding protein (TBP)-DNA complexes in an ATP-dependent manner. This disruption prevents the formation of transcription complexes and can thereby inhibit transcription in vitro. We are employing biochemical approaches using purified components to determine how Mot1 recognizes TBP-DNA complexes and how ATP hydrolysis leads to TBP-DNA complex dissociation. The activities of mutant Mot1 proteins and the effects of other proteins that interact with TBP are also being explored. In vivo, the effects of Mot1 on transcription appear to be complex. While some genes are repressed by Mot1, others are apparently unaffected, or paradoxically, activated by Mot1. Using a combination of genetic and molecular biological approaches, we are characterizing genes that are regulated by Mot1 and we are developing strategies to determine how Mot1 functions in vivo to give rise to complex patterns of gene expression.

Several of the yeast Snf2/Swi2 family members are involved in DNA repair, but how they function is unknown. The biochemical activity of Mot1 suggests that they disrupt or rearrange protein-DNA complexes as an obligate part of the repair process. Using our knowledge of how Mot1 functions, genetic and biochemical experiments are in progress to identify the protein targets of two of these repair proteins, and biochemical approaches will be used to characterize their mechanisms of action.

Selected Publications

  • Viswanathan R, Auble D. One small step for Mot1; one giant leap for other Swi2/Snf2 enzymes? Biochimica et biophysica acta. 2011;1809(9): 488-96. PMID: 21658482 | PMCID: PMC3171519
  • Wade S, Auble D. The Rad23 ubiquitin receptor, the proteasome and functional specificity in transcriptional control. Transcription. 2011;1(1): 22-6. PMID: 21327160 | PMCID: PMC3035185
  • Poorey K, Sprouse R, Wells M, Viswanathan R, Bekiranov S, Auble D. RNA synthesis precision is regulated by preinitiation complex turnover. Genome research. 2010;20(12): 1679-88. PMID: 20855454 | PMCID: PMC2989994
  • Wade S, Poorey K, Bekiranov S, Auble D. The Snf1 kinase and proteasome-associated Rad23 regulate UV-responsive gene expression. The EMBO journal. 2009;28(19): 2919-31. PMID: 19680226 | PMCID: PMC2760106
  • The dynamic personality of TATA-binding protein. Trends in biochemical sciences. 2008;34(2): 49-52. PMID: 19038550 | PMCID: PMC2933749
  • Basu D, Walkiewicz M, Frieman M, Baric R, Auble D, Engel D. Novel influenza virus NS1 antagonists block replication and restore innate immune function. Journal of virology. 2008;83(4): 1881-91. PMID: 19052087 | PMCID: PMC2643796
  • Sprouse R, Karpova T, Mueller F, Dasgupta A, McNally J, Auble D. Regulation of TATA-binding protein dynamics in living yeast cells. Proceedings of the National Academy of Sciences of the United States of America. 2008;105(36): 13304-8. PMID: 18765812 | PMCID: PMC2533185
  • Sprouse R, Shcherbakova I, Cheng H, Jamison E, Brenowitz M, Auble D. Function and structural organization of Mot1 bound to a natural target promoter. The Journal of biological chemistry. 2008;283(36): 24935-48. PMID: 18606810 | PMCID: PMC2529012
  • Sprouse R, Wells M, Auble D. TATA-binding protein variants that bypass the requirement for Mot1 in vivo. The Journal of biological chemistry. 2008;284(7): 4525-35. PMID: 19098311 | PMCID: PMC2640957
  • Dasgupta A, Sprouse R, French S, Aprikian P, Hontz R, Juedes S, Smith J, Beyer A, Auble D. Regulation of rRNA synthesis by TATA-binding protein-associated factor Mot1. Molecular and cellular biology. 2007;27(8): 2886-96. PMID: 17296733 | PMCID: PMC1899949
  • Sprouse R, Brenowitz M, Auble D. Snf2/Swi2-related ATPase Mot1 drives displacement of TATA-binding protein by gripping DNA. The EMBO journal. 2006;25(7): 1492-504. PMID: 16541100 | PMCID: PMC1440317