Keith Yamamoto delivers 2012 Rodbell Lecture
By Brant Hamel
Keith Yamamoto, Ph.D., continued an annual tradition of outstanding Rodbell lectures with his seminar April 10, titled “Cell-, Gene-, and Physiology-Specific Regulation by the Glucocorticoid Receptor.” Yamamoto’s talk explored the specificity of transcriptional regulation by the glucocorticoid receptor (GR), which he explained integrates signals from multiple contexts to direct its regulation of gene expression.
Yamamoto (http://yamamotolab.ucsf.edu/keith.html) is the vice chancellor for research, executive vice dean of the school of medicine, and a professor of cellular and molecular pharmacology at the University of California, San Francisco (UCSF), who has published more than 150 articles greatly increasing the understanding of nuclear receptor structure and function. Just as importantly, Yamamoto is very involved in improving the scientific enterprise through his service on multiple committees exploring science training and education, scientific policy, and the peer review process at NIH.
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Multiple levels of signals converge to determine GR signaling
The GR is a member of the nuclear receptor family of transcription factors, which binds to steroids to regulate many physiological processes ranging from glucose signaling to the anti-inflammatory response. A key enigma is that the GR is highly variable in how it regulates gene expression in different types of cells. Yamamoto explained this, in large part, is due to the complexity of the macromolecular complex that it organizes, which may contain up to 100 different polypeptides that vary from cell to cell and gene to gene.
Yamamoto detailed how signals converge on the receptor from multiple levels, including gene-specific sequences provided by the sequence of the GR-DNA binding site; cell-specific signals, such as the identity of coregulators expressed in a given cell; and physiological signals, including those that result in post-translational modifications of the receptor. He explained that instead of thinking of the receptor as having a specific intrinsic activity, it is more appropriate to think of it as a signal integrator that results in a receptor complex with different activities that are highly dependent upon gene, cell, and physiological context.
Regulatory logic circuits allow complex gene activation patterns
To better understand the mechanism of cell-specific regulation by the GR, Yamamoto searched for genes that were induced in one cell type, but repressed in another, in response to glucocorticoid treatment. One of the genes discovered, ANKRD1, displayed an intriguing kinetic profile in osteosarcoma cells of a very brief activation followed by a prolonged repression. Yamamoto found that ANKRD1 and 29 other genes all followed a logic circuit known as an incoherent feed-forward loop type I, in which the initial activation of gene expression is quenched after a gene-specific inhibitory threshold is reached. He is now searching for the mechanism that results in this kinetic profile in certain cell types, but not others.
DNA is an allosteric effector of GR
Although it has long been known that the binding of varying ligands results in differing conformational changes of the GR, Yamamoto provided the unexpected finding that DNA itself can act allosterically to alter the structure of the receptor. Using X-ray crystallography, Yamamoto solved the structure of the DNA binding domain of the GR bound to a variety of different DNA sequences. Even alterations in bases that do not directly contact the receptor were found to lead to structural changes in the receptor that might be expected to alter its activity or bind to other co-regulatory proteins. Yamamoto was not content to stop at the static pictures provided by crystallography and expanded the study through the use of nuclear magnetic resonance spectroscopy, to show that the shifts induced by DNA binding follow an allosteric path that extends all the way to the dimerization interface. Conversely, mutation of the dimerization interface leads to alterations in DNA binding capability through the same allosteric pathway working in reverse.
Yamamoto’s talk was co-hosted by NIEHS Laboratory of Molecular Carcinogenesis head Trevor Archer, Ph.D., who introduced the speaker and moderated the question and answer session, and NIEHS Laboratory of Signal Transduction head John Cidlowski, Ph.D.
(Brant Hamel, Ph.D., is an Intramural Research Training Award fellow in the NIEHS Laboratory of Signal Transduction.)