Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Working in concert

06.12.2010
RIKEN biochemists decipher how the precisely choreographed activity of a pair of enzymes helps protein synthesis move forward

As cells go about the process of building new proteins, each amino acid gets delivered individually to the protein-synthesizing machinery of the ribosome by a specialized transfer RNA (tRNA) molecule. This process is generally facilitated by a variety of RNA synthetase enzymes, with each type of amino acid-attached tRNA formed as the product of a distinct synthetase.

However, archaea and most bacteria lack the capacity to directly synthesize every necessary tRNA-amino acid conjugate. For example, the glutamine-linked tRNA (Gln-tRNAGln) in such species is instead produced via a two-step process, a synthetic pathway that is initiated by glutamyl-tRNA synthetase (GluRS), the enzyme normally responsible for producing the glutamate-bearing tRNA (Glu-tRNAGlu).

In this case, however, GluRS needs to make a ‘wrong move’ in order to produce an unusual hybrid tRNA, Glu-tRNAGln, which serves as an essential intermediate in the Gln-tRNAGln production process. This pathway has proven baffling to biochemists such as Shigeyuki Yokoyama, director of the RIKEN Systems and Structural Biology Center (SSBC) in Yokohama. “This mechanism has the possibility of forming harmful byproducts, including Gln-tRNAGlu and Glu-tRNAGln, which can cause serious errors in protein synthesis,” he says. “We wanted to know how such a risky system functions efficiently.”

To further add to the mysteries surrounding Gln-tRNAGln production, the complex responsible for the second step in this process, GatCAB, has been proposed to interact with the same region of Glu-tRNAGln as GluRS. This has left it unclear how these two enzymes are able to effectively partner with their common substrate in a manner that enables the two stages of synthesis to flow seamlessly without interfering with one another or potentially releasing toxic intermediates into the cellular environment.

Taking turns

Yokoyama recently teamed up with SSBC colleague Takuhiro Ito in an effort to tackle these various mysteries, collecting high-resolution structural data from the bacterial species Thermotoga maritima for both the GluRS-tRNAGln complex as well as the ‘glutamine transamidosome’—the ternary complex containing tRNAGln, GluRS and GatCAB. They confirmed that the latter is indeed a stable complex (Fig. 1), indicating that some mechanism must exist that prevents the two enzymes from simultaneously occupying the same space and disrupting each other’s function. Yokoyama and Ito have published their findings in the science journal Nature1.

Comparison of the two structures revealed that tRNAGln undergoes structural changes when assembled within the glutamine transamidosome, interacting with GatCAB via structural elements that are absent in tRNAGlu. In order to confirm this mechanism, Yokoyama and Ito constructed a series of hybrid tRNAGlu molecules that contain various elements from tRNAGln and examined the extent to which they could successfully be processed to yield Gln-tRNAGlu. Based on these experiments, they were able to confirm that the region in question—also known as the D loop—is an essential structural feature in this process, revealing the mechanism by which this complex avoids introducing inappropriate modifications to Glu-tRNAGlu. “Our structure clearly shows how GatCAB recognizes tRNAGln without inhibiting the reaction by GluRS,” says Yokoyama.

Their analysis also revealed a number of flexible ‘hinge’ segments in both GatCAB and GluRS that appear to contribute to their capacity to perform modifications in a stepwise manner (Fig. 2). Each of these factors initially binds to a different segment of tRNAGln, with the GatCAB interaction contributing the discrimination mechanism revealed by Yokoyama and Ito. GluRS subsequently transfers a glutamate amino acid to the tRNA and undergoes a structural rearrangement that frees the newly modified ‘acceptor arm’ domain of the tRNAGln molecule. GatCAB then executes a pivoting motion that brings its own catalytic domain in contact with the glutamate-bound acceptor arm, at which point it initiates the amidation chemical reaction necessary to transform this amino acid into a glutamine residue. “This structure itself is very unique and interesting,” says Yokoyama. “One substrate tRNA is bound by two different enzymes working consecutively.”

Protein evolution—past and future

Based on the unusual mechanism that they identified, the researchers hypothesize that this process of tRNA modification may have emerged relatively recently in the evolution of protein synthesis. As such, glutamine and asparagine—another amino acid whose synthesis is also the result of a two-step synthesis in a number of bacterial and archaeal species—could represent late additions to the genetic code.

In other work, Yokoyama and colleagues have explored methods for producing proteins whose characteristics have been selectively modified through the inclusion of atypical or synthetic amino acids, typically by inducing cells to express altered versions of tRNA synthetase enzymes that exclusively work with these alternative amino acids. However, the pathway described here could provide a useful model for future engineering efforts. “It might be possible to incorporate a new unnatural amino acid into the genetic code via this mechanism—modifying amino acids after tRNA formation, but before they are transferred to the ribosome,” explains Yokoyama.

However, all of the data presented in their study of Gln-tRNAGln represent deductions drawn from only a relatively small number of structural ‘snapshots’, based on a transamidosome complex that was essentially trapped in the first stage of Gln-tRNAGln synthesis. In order to further understand the detailed operation of this cellular machine, Yokoyama now intends to collect additional structural data that will help fill in the gaps and provide additional confirmation for the model that he and Ito have developed. “We have not succeeded yet, but we would like to continue our trials to crystallize the amidation form of the transamidosome,” he says.

About the Researcher
Shigeyuki Yokoyama
Shigeyuki Yokoyama was born in Tokyo, Japan, in 1953. He received his BS and PhD degrees from The University of Tokyo in 1975 and 1981, and following completion of five years of postdoctoral work, became an associate professor in 1986 and a professor in 1991 in the Department of Biophysics and Biochemistry, The University of Tokyo. In 1993, he was appointed chief scientist of the RIKEN Cellular Signaling Laboratory, and later project director of the Protein Research Group in the Genomic Sciences Center. He played a pivotal role as science director of the RIKEN Structural Genomics / Proteomics Initiative (RSGI). Since 2008, he has acted as director of the Systems and Structural Biology Center (SSBC) at the RIKEN Yokohama Institute.
Journal information
Ito, T. & Yokoyama, S. Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions. Nature 467, 612–616 (2010).

gro-pr | Research asia research news
Further information:
http://www.riken.jp
http://www.researchsea.com/html/article.php/eml/1/aid/5676/cid/1

More articles from Life Sciences:

nachricht Navigational view of the brain thanks to powerful X-rays
18.10.2017 | Georgia Institute of Technology

nachricht Separating methane and CO2 will become more efficient
18.10.2017 | KU Leuven

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Neutron star merger directly observed for the first time

University of Maryland researchers contribute to historic detection of gravitational waves and light created by event

On August 17, 2017, at 12:41:04 UTC, scientists made the first direct observation of a merger between two neutron stars--the dense, collapsed cores that remain...

Im Focus: Breaking: the first light from two neutron stars merging

Seven new papers describe the first-ever detection of light from a gravitational wave source. The event, caused by two neutron stars colliding and merging together, was dubbed GW170817 because it sent ripples through space-time that reached Earth on 2017 August 17. Around the world, hundreds of excited astronomers mobilized quickly and were able to observe the event using numerous telescopes, providing a wealth of new data.

Previous detections of gravitational waves have all involved the merger of two black holes, a feat that won the 2017 Nobel Prize in Physics earlier this month....

Im Focus: Smart sensors for efficient processes

Material defects in end products can quickly result in failures in many areas of industry, and have a massive impact on the safe use of their products. This is why, in the field of quality assurance, intelligent, nondestructive sensor systems play a key role. They allow testing components and parts in a rapid and cost-efficient manner without destroying the actual product or changing its surface. Experts from the Fraunhofer IZFP in Saarbrücken will be presenting two exhibits at the Blechexpo in Stuttgart from 7–10 November 2017 that allow fast, reliable, and automated characterization of materials and detection of defects (Hall 5, Booth 5306).

When quality testing uses time-consuming destructive test methods, it can result in enormous costs due to damaging or destroying the products. And given that...

Im Focus: Cold molecules on collision course

Using a new cooling technique MPQ scientists succeed at observing collisions in a dense beam of cold and slow dipolar molecules.

How do chemical reactions proceed at extremely low temperatures? The answer requires the investigation of molecular samples that are cold, dense, and slow at...

Im Focus: Shrinking the proton again!

Scientists from the Max Planck Institute of Quantum Optics, using high precision laser spectroscopy of atomic hydrogen, confirm the surprisingly small value of the proton radius determined from muonic hydrogen.

It was one of the breakthroughs of the year 2010: Laser spectroscopy of muonic hydrogen resulted in a value for the proton charge radius that was significantly...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ASEAN Member States discuss the future role of renewable energy

17.10.2017 | Event News

World Health Summit 2017: International experts set the course for the future of Global Health

10.10.2017 | Event News

Climate Engineering Conference 2017 Opens in Berlin

10.10.2017 | Event News

 
Latest News

Osaka university researchers make the slipperiest surfaces adhesive

18.10.2017 | Materials Sciences

Space radiation won't stop NASA's human exploration

18.10.2017 | Physics and Astronomy

Los Alamos researchers and supercomputers help interpret the latest LIGO findings

18.10.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>