Scientists from The Scripps Research Institute have shed new light on a molecular switch that turns genes on or off in response to a cell's energy needs.
The study—published February 13, 2011 in an Advance Online Publication of the journal Nature Structural and Molecular Biology—shows these recently discovered RNA "riboswitches" are capable of more complex functions than originally thought. In addition, because riboswitches so far have been found primarily in bacteria, the study may have implications for designing new antibiotics against harmful bacteria.
"The study provides new insights into how a single RNA molecule can integrate both positive and negative signals from a cell," said senior author Martha Fedor, an associate professor and member of the Skaggs Institute for Chemical Biology at Scripps Research. "It extends the known capabilities of riboswitches."
Riboswitches respond to the concentrations of molecules produced by a cell's metabolism—the process of creating or using energy—to regulate genes' activities. The new study shows that a particular riboswitch does not respond to just a single metabolite, as had been assumed, but rather to many such compounds.
Switching Genes On and Off
Each gene serves as a recipe for building a protein molecule. When a particular protein is needed by the cell, the corresponding gene, made of DNA, is turned "on," or transcribed into a messenger RNA, which then carries the "protein recipe" to the protein-making machinery of the cell.
For many years scientists thought proteins, unlike DNA and RNA, were the only molecules in a cell capable of accomplishing sophisticated tasks, such as regulating the activities of genes or carrying out chemical reactions. But in the past couple of decades, researchers have discovered that certain types of RNA molecules are adept at performing feats worthy of their protein counterparts. Riboswitches are one such example.
Discovered only about eight years ago, riboswitches are short stretches of RNA that reside within the messenger RNAs of proteins involved in a cell's metabolism. These riboswitches bind certain metabolites and, depending on how much binding occurs, the riboswitches turn the production of the corresponding proteins on or off.
Until now, most researchers had assumed a single riboswitch was specific for a single metabolite. But the new study by Fedor's group shows a riboswitch can incorporate signals from many metabolites at once.
A Self-Destructing Riboswitch
Fedor's group was interested in studying the function of a type of riboswitch that binds to a metabolite called glucosamine-6-phosphate. This amino sugar, a building block for many glyosides and glycans, is required for the cell wall and other vital structures in bacterial cells.
This particular riboswitch resides in the messenger RNA that carries instructions for the enzyme responsible for the production of glucosamine-6-phosphate, called GlmS. It was known that when glucosamine-6-phosphate is abundant in a cell, the riboswitch stops production of the GlmS enzyme by destroying itself and its messenger RNA. This self-destruction functions to shut off any more production of glucosamine-6-phosphate.
On the other hand, when glucosamine-6-phosphate concentrations are low, the glmS riboswitch does not self-destruct, keeping the messenger RNA functioning.
A Puzzling Observation
Fedor and graduate student Peter Watson had designed an assay to measure the amounts of the glmS riboswitch in yeast cells as they added increasing concentrations of glucosamine. But the scientists stumbled on a puzzling finding.
If they grew their yeast in energy-rich broth that contained glycerol, a 3-carbon energy source, the riboswitch behaved as they expected, shutting off the glmS messenger RNA in response to increasing glucosamine concentrations. However, if bacteria was grown in a broth containing glucose, a 6-carbon energy source, the riboswitch no longer self-destructed.
"At first we thought something was wrong with our system," said Fedor.
But Fedor and Watson solved the puzzle. They discovered this riboswitch can bind both glucosamine-6-phosphate and glucose-6-phosphate. Each compound, however, produces opposite results. Binding glucosamine-6-phosphate induces self-destruction of the riboswitch and turns the glmS gene off; binding glucose-6-phosphate prevents self-destruction and keeps the glmS gene turned on.
"Scientists had long focused on the ability of riboswitches to recognize a single compound, but we have now found that riboswitches, or at least this one, can recognize multiple ones," said Watson.
"When glucose concentrations are high in a cell, it means that energy is abundant," explained Watson. "That is when cells would want to grow and divide and make more glucosamine-6-phosphate to build new cell walls. But when glucosamine-6-phosphate concentrations are high, then cells know to stop making more of this compound."
The glmS riboswitch function thus depends upon a balance between these two—and possibly additional—competing signals. "This kind of complex signaling had long thought to be the domain of just proteins," said Fedor. "This is another example of a function thought to belong only to proteins that we now know that RNA can do."
Fedor and Watson are now testing whether other types of riboswitches use this same mechanism. Unlike the glmS riboswitch, which self-destructs, most known riboswitches regulate the activities of their respective messenger RNAs by changing their three-dimensional structures in response to metabolite binding. The new shapes act to prevent the transcription of messenger RNA or translation of messenger RNA into protein.
Although riboswitches have not yet been found in humans, Fedor believes this discovery is just a matter of time. "The great thing about the field of RNA is that we are always coming across unexpected findings," she said.
Research for the paper entitled "The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo" was funded by the National Institutes of Health and a graduate fellowship from The Skaggs Institute for Chemical Biology
About The Scripps Research Institute
The Scripps Research Institute is one of the world's largest independent, non-profit biomedical research organizations, at the forefront of basic biomedical science that seeks to comprehend the most fundamental processes of life. Scripps Research is internationally recognized for its discoveries in immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune, cardiovascular, and infectious diseases, and synthetic vaccine development. An institution that evolved from the Scripps Metabolic Clinic founded by philanthropist Ellen Browning Scripps in 1924, Scripps Research currently employs approximately 3,000 scientists, postdoctoral fellows, scientific and other technicians, doctoral degree graduate students, and administrative and technical support personnel. Headquartered in La Jolla, California, the institute also includes Scripps Florida, whose researchers focus on basic biomedical science, drug discovery, and technology development. Scripps Florida is located in Jupiter, Florida.
Mika Ono | EurekAlert!
For a chimpanzee, one good turn deserves another
27.06.2017 | Max-Planck-Institut für Mathematik in den Naturwissenschaften (MPIMIS)
New method to rapidly map the 'social networks' of proteins
27.06.2017 | Salk Institute
An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.
Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...
Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.
Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...
Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.
As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...
Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.
With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...
Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine
Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...
19.06.2017 | Event News
13.06.2017 | Event News
13.06.2017 | Event News
27.06.2017 | Power and Electrical Engineering
27.06.2017 | Information Technology
27.06.2017 | Physics and Astronomy