Electron Microscopy reconstruction of the yeast vacuolar ATPase. Ribbon models for individual protein subunits have been fit to the electron density.
From the lab of Stephan Wilkens, PhD.
Bruce Knutson, PhD
- Assistant Professor of Biochemistry and Molecular Biology
Research Programs and Affiliations
- Biochemistry and Molecular Biology
- Biomedical Sciences Program
RNA polymerase I transcription (structure, assembly, regulation), nucleolar biology, macromolecular architecture, crosslinking, proteomics, bioinformatics, modeling, molecular genetics, biochemistry, model systems
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A century old hallmark of cancer is an enlarged nucleolus (Fig.1), a unique nuclear sub compartment where RNA polymerase I (Pol I) transcription and ribosome biogenesis take place. Pol I transcription is unregulated in cancer cells and drives cell proliferation, making it an attractive anti-cancer therapeutic target. The major focus of our research is to elucidate the molecular mechanism of Pol I transcription and how its dysregulation leads to cancer and disease. Our research uses an innovative cross-organismal and interdisciplinary approach that integrates bioinformatics, biochemistry, computational biology, genetics, proteomics and structural biology in yeast and human model system.
Molecular architecture of the Pol I preinitiation complex (PIC)
Pol I transcription begins with the formation of the PIC (Fig.2), a macromolecular assemblage of more than 20 different proteins that function coordinately to accurately position Pol I at the promoter and to help initiate transcription. We are interested in the key structural facets of Pol I PIC formation and how it's altered in cancer and diseased cells. Our lab uses an integrated combination of sophisticated protein-protein interaction mapping technologies such as combined chemical crosslinking/mass spectrometry to determine the spatial orientation of Pol I PIC components and how they change during the transcription cycle and in diseased states.
Pol I and craniofacial dysmorphology. Mutations in Pol I cause an autosomal dominant craniofacial abnormality called Treacher Collins Syndrome (TCS). TCS is characteried by an underdeveloped lower jaw and cheekbones that is treated by an extensive multi-stage surgical reconstruction from childhood to early adulthood. We are interested in how these Pol I mutations cause TCS, how they affect Pol I activity, and how they can be suppressed to prevent the disease. Currently, there are no known cures for TCS and other related craniofacial dysmorphologies.
Pol I dysregulation in cancer. The upregulation of Pol I transcription in cancer cells coincides with activating mutations in many oncogenes and loss of function mutations in tumor suppressors that are believed to directly regulate Pol I activity (Fig.3). However, their bona fide Pol I targets and sites of interaction remain unclear. To understand how these cancer proteins target the Pol I complex, we use a combination of protein crosslinking technologies coupled of molecular genetics and biochemistry to identify and characterize the direct and functionally relevant in vivo Pol I targets. These studies will illuminate new strategies to control aberrant Pol I activity.
Graduate research in the Knutson Lab. Interested students should directly contact Bruce Knutson to discuss available research opportunities.
Smith ML, Cui W, Jackobel AJ, Walker-Kopp N, Knutson. Reconstitution of RNA Polymerase I Upstream Activating Factor and the Roles of Histones H3 and H4 in Complex Assembly. J Mol Biol. 2018 Epub
Jackobel AJ, Han Y, He Y, Knutson BA. Breaking the mold: structures of the RNA polymerase I transcription complex reveal a new path for initiation. Transcription. 2018 Jan 15:1-7
Walker-Kopp N, Jackobel AJ, Pannafino GN, Morocho PA, Xu X, Knutson BA. Treacher Collins syndrome mutations in Saccharomyces cerevisiae destabilize RNA polymerase I and III complex integrity. Hum Mol Genet. 2017 Nov 1;26(21):4290-4300.
Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I, Knutson BA, He Y. Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. Elife. 2017 Jun 17;6.
Knutson BA, Smith ML, Walker-Kopp N, Xu X. Super elongation complex contains a TFIIF-related subcomplex. Transcription. 2016. 7(4):133-40
Knutson BA, Lui J, Ranish J. Hahn S. Architecture of the S.cerevisiae RNA polymerase I Core Factor complex. Nature Structural and Molecular Biology. 2014. 21(9): 810-816
Knutson BA, Hahn S. TFIIB-related factors in RNA polymerase I transcription. Biochem Biophys Acta. 2013. 1829(3-4): 265-273
Knutson BA. Emergence and expansion of TFIIB-like factors in the plant kingdom. Gene. 2013. 526(1): 30-38
Knutson BA, Hahn S. Yeast Rrn7 and human TAF1B are TFIIB-related RNA polymerase I general transcription factors. Science. 2011. 33(6049): 1637-40
Knutson BA, Hahn S. Domains of Tra1 important for activator recruitment and transcription coactivator functions of SAGA and NuA4 complexes. Mol Cell Biol. 2011. 31(4): 818-831
Knutson BA. Insights into the domain and repeat architecture of target of rapamycin. J Struct Biol. 2010. 170(2): 354-63
SUNY Distinguished Professor Emeritus
- Richard Cross, PhD
- David Turner, PhD