Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Caught in the act

07.03.2011
An analysis of the interactions of a gene-reading enzyme with an inhibitor protein provides surprising insights

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[1].

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

Journal information

[1] 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).

gro-pr | Research asia research news
Further information:
http://www.riken.jp
http://www.researchsea.com

More articles from Life Sciences:

nachricht Ion treatments for cardiac arrhythmia — Non-invasive alternative to catheter-based surgery
20.01.2017 | GSI Helmholtzzentrum für Schwerionenforschung GmbH

nachricht Seeking structure with metagenome sequences
20.01.2017 | DOE/Joint Genome Institute

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Traffic jam in empty space

New success for Konstanz physicists in studying the quantum vacuum

An important step towards a completely new experimental access to quantum physics has been made at University of Konstanz. The team of scientists headed by...

Im Focus: How gut bacteria can make us ill

HZI researchers decipher infection mechanisms of Yersinia and immune responses of the host

Yersiniae cause severe intestinal infections. Studies using Yersinia pseudotuberculosis as a model organism aim to elucidate the infection mechanisms of these...

Im Focus: Interfacial Superconductivity: Magnetic and superconducting order revealed simultaneously

Researchers from the University of Hamburg in Germany, in collaboration with colleagues from the University of Aarhus in Denmark, have synthesized a new superconducting material by growing a few layers of an antiferromagnetic transition-metal chalcogenide on a bismuth-based topological insulator, both being non-superconducting materials.

While superconductivity and magnetism are generally believed to be mutually exclusive, surprisingly, in this new material, superconducting correlations...

Im Focus: Studying fundamental particles in materials

Laser-driving of semimetals allows creating novel quasiparticle states within condensed matter systems and switching between different states on ultrafast time scales

Studying properties of fundamental particles in condensed matter systems is a promising approach to quantum field theory. Quasiparticles offer the opportunity...

Im Focus: Designing Architecture with Solar Building Envelopes

Among the general public, solar thermal energy is currently associated with dark blue, rectangular collectors on building roofs. Technologies are needed for aesthetically high quality architecture which offer the architect more room for manoeuvre when it comes to low- and plus-energy buildings. With the “ArKol” project, researchers at Fraunhofer ISE together with partners are currently developing two façade collectors for solar thermal energy generation, which permit a high degree of design flexibility: a strip collector for opaque façade sections and a solar thermal blind for transparent sections. The current state of the two developments will be presented at the BAU 2017 trade fair.

As part of the “ArKol – development of architecturally highly integrated façade collectors with heat pipes” project, Fraunhofer ISE together with its partners...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Sustainable Water use in Agriculture in Eastern Europe and Central Asia

19.01.2017 | Event News

12V, 48V, high-voltage – trends in E/E automotive architecture

10.01.2017 | Event News

2nd Conference on Non-Textual Information on 10 and 11 May 2017 in Hannover

09.01.2017 | Event News

 
Latest News

Helmholtz International Fellow Award for Sarah Amalia Teichmann

20.01.2017 | Awards Funding

An innovative high-performance material: biofibers made from green lacewing silk

20.01.2017 | Materials Sciences

Ion treatments for cardiac arrhythmia — Non-invasive alternative to catheter-based surgery

20.01.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>