A key process in cells that affects immunity and circadian rhythms is illuminated in detail for the first time.
Scientists at Scripps Research have clarified the molecular workings of an important signaling mechanism involved in a host of biological processes including immunity, cholesterol metabolism, and circadian rhythms.
The discovery, reported January 27 in the journal Science Advances, is a significant advance in basic cell biology, and opens up the possibility of designing drug molecules that target this mechanism to treat diseases.
The signaling mechanism illuminated in the study includes an iron-containing molecule called heme, and two molecular switches called REV-ERBα and REV-ERBβ, which work deep within cells to control the activities of large groups of genes. The scientists resolved a long-running conundrum in the field by showing in detail how heme triggers the activation of these switches.
“The REV-ERB receptors are critical regulators of many biological processes and knowing at last how heme interacts with them enables us to start thinking about the design of drugs to target that interaction, potentially to treat sleep disorders, diabetes, atherosclerosis, autoimmune diseases, perhaps even cancers,” says study senior author Douglas Kojetin, PhD, associate professor in the Department of Integrative Structural and Computational Biology at Scripps Research’s Florida campus.
Scientists have known since 2007 that REV-ERB receptors can be activated by heme, a distinctively four-cornered, red-tinted molecule that contains an iron atom and—though it has many functions in mammals—is best known for its oxygen-carrying role in red blood cells.
Knowing the molecular details of how heme switches on the REV-ERBs would, in principle, enable researchers to engineer drugs to enhance or disrupt the interaction. But those molecular details have been elusive. To work properly, the REV-ERBs have to bind to another protein called NCoR, and experiments to illuminate how heme helps the REV-ERBs hook up with NCoR have yielded conflicting results. In particular, tests using fluorescent tags on the molecules have suggested confusingly that heme prevents the REV-ERBs from coupling to NCoR.
In the new study, Kojetin and colleagues, including first author Sarah Mosure, a PhD candidate in the Kojetin lab who performed most of the experiments, found a flaw in the standard fluorescence-based tests that had caused so much confusion: Heme’s unusual optical properties result in a big distortion of the fluorescence readout and essentially a false picture of heme’s effects. Using two alternative, non-fluorescence-based methods, Mosure showed that heme does in fact help bring REV-ERB and NCoR together.
The team also used X-ray crystallography to reveal at atomic scale how heme and NCoR bind to a REV-ERB receptor.
The experiments used REV-ERBβ, but the researchers expect essentially the same results for the sister receptor REV-ERBα.
“We were able in this study to make sense of more than a decade’s contradictory experiments, by demonstrating the detailed structural basis for this three-way interaction,” Mosure says.
The results mean that the Kojetin lab and other investigators can start designing molecules to interrupt or otherwise alter heme-based activation of the REV-ERBs, to aid the study of this process and its role in disease, and pave the way for future drugs that target it.
Based on the success of this research so far, Mosure has been awarded a two-year predoctoral fellowship from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) to study the heme-REV-ERB role in inflammatory disorders.
“Structural basis for heme-dependent NCoR binding to the transcriptional repressor REV-ERBβ” was co-authored by Sarah Mosure, Timothy Strutzenberg, Jinsai Shang, Paola Munoz-Tello, Laura Solt, Patrick Griffin, and Douglas Kojetin.
Funding was provided by the National Institutes of Health (R01GM114420, F31GM126842, R01AI116885, and R01CA241816) and a Richard and Helen DeVos graduate fellowship award.
Featured image: The three-dimensional structure of REV-ERB-beta protein (yellow) bound to heme (red ball and sticks) and NCoR (blue) reveals the molecular basis for a three-way interaction that affects transcription of genes involved in sleep, immunity, and more. Visualizing the complex enables scientists to design potential medicines to affect the interaction.
Provided by SCRIPPS