Within the cells, the RNA polymerase (RNAP) protein complex clutches DNA like a crab claw, scanning across gene-coding regions and transcribing these sequences into the messenger RNA molecules that will ultimately provide the blueprint for protein production.
Figure 1: In the RNAP-Gfh1 protein complex the transcription factor (purple) inserts itself in the channel where nucleotides (NTPs) enter (red). This can only happen when the channel has expanded by a ratcheting motion that alters the relative position of the core module (gray) and shelf and clamp modules (light). Copyright : 2011 Shigeyuki Yokoyama
This process can be impaired or assisted through interactions with proteins known as transcription factors, but understanding how these factors influence RNAP function can pose a serious challenge for structural biologists. “It is very difficult to crystallize RNAP, which is an unusually large enzyme,” says Shigeyuki Yokoyama, director of the RIKEN Systems and Structural Biology Center in Yokohama. “In particular, no crystal structures of bacterial RNAP-transcription factor complexes have ever been reported.” Recently, however, Yokoyama and colleagues successfully obtained a crystal structure that captures RNAP in the midst of transcription while bound to Gre factor homologue 1 (Gfh1), a transcription factor from the bacterium Thermus thermophilus.
RNAP consists of several discrete modules connected by flexible linker regions, with most of the enzymatic machinery residing in the ‘shelf’ and ‘core’ modules that serve as the main body of the RNAP ‘claw’. In their structure, the researchers uncovered a never-before-seen arrangement of the RNAP modules, where some sort of ‘ratcheting’ action has created notable displacement between the shelf and core relative to its normal structure.
In fact, the binding of Gfh1 appears to lock RNAP into this configuration. This transcription factor—a known inhibitor—inserts itself into a channel on the complex that normally accepts nucleotides for addition onto newly synthesized RNA molecules (Fig. 1). However, such insertion would be impossible with the normal RNAP complex, where the channel is too narrow. This suggests that RNAP executes this unexpected ratcheting motion as part of its normal behavior, which in turn leaves it vulnerable to Gfh1 inhibition. “This conformational change was most surprising,” says Yokoyama. “It was simply impossible to predict this before the structure of RNAP-Gfh1 was solved.”
In subsequent biochemical experiments, he and his colleagues managed to essentially catch RNAP in the act of ratcheting, providing further evidence that this behavior occurs spontaneously in nature and is likely to contribute directly to the enzyme’s transcriptional activity. “We hypothesize that RNAP uses this ratcheted state to slide along DNA chains as an intermediate step in the course of normal transcription,” says Yokoyama. “This state may also be used an intermediate for transcriptional termination, in which the [RNA] dissociates from the RNAP.” He adds that validating these and other hypotheses will be top priorities for future experimental efforts.
The corresponding author for this highlight is based at the RIKEN Systems and Structural Biology Center
 Tagami, S., Sekine, S., Kumarevel, T., Hino, N., Murayama, Y., Kamegamori, S., Yamamoto, M., Sakamoto, K. & Yokoyama, S. Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein. Nature 468, 978–982 (2010).
‘Farming’ bacteria to boost growth in the oceans
24.10.2016 | Max-Planck-Institut für marine Mikrobiologie
Calcium Induces Chronic Lung Infections
24.10.2016 | Universität Basel
Terahertz excitation of selected crystal vibrations leads to an effective magnetic field that drives coherent spin motion
Controlling functional properties by light is one of the grand goals in modern condensed matter physics and materials science. A new study now demonstrates how...
Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.
"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...
In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.
A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...
By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.
"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...
COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.
In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...
14.10.2016 | Event News
14.10.2016 | Event News
12.10.2016 | Event News
24.10.2016 | Earth Sciences
24.10.2016 | Life Sciences
24.10.2016 | Physics and Astronomy