Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Cell Signaling Classification System Gives Researchers New Tool

05.07.2010
Using ever-growing genome data, scientists with the Department of Energy’s (DOE) Oak Ridge National Laboratory and the University of Tennessee are tracing the evolution of the bacterial regulatory system that controls cellular motility, potentially giving researchers a method for predicting important cellular functions that will impact both medical and biotechnology research.

A new study from the Joint Institute for Computational Sciences, a research venture between ORNL and UT, has demonstrated how knowledge of biological systems can be derived by computational interrogation of genomic sequences. The results have implications for areas ranging from medicine to bioenergy.

“We now have hundreds of millions of DNA sequences from all sorts of organisms deposited in databases. However, our abilities to translate raw genomic data into useful knowledge are still very limited,” said Igor Zhulin, joint faculty professor and principal investigator.

“We applied our computational skills to glean more information about a biological system that has fascinated researchers for more than a century. This is a molecular signal transduction system that allows bacteria to navigate in the environment pretty much in the same way that higher organisms, including humans, do—by detecting signals (e.g., visual or chemical cues) and then moving toward favorable environments and away from dangerous ones.”

In general, signal transduction systems in bacteria are very simple, consisting of only one or two proteins that regulate expression of various genes in response to changes in the environment. The navigation system, however, is significantly more complex and in some bacteria may involve dozens of different proteins.

How such complexity arose was unknown before this study, which has discovered intermediate signaling systems in bacteria that contain elements of both simple systems that regulate gene expression and the complex navigation system. This provides an argument for the gradual evolution of the navigation system from well-known transcriptional regulators that are much simpler in design, Zhulin said.

Because the navigation system of bacteria has been studied by scientists employing the latest advances in genetics, biochemistry, biophysics, structural biology and other traditional biological disciplines, the system has become one of the best understood molecular systems in nature.

“We took advantage of this knowledge,” said Kristin Wuichet, a postdoctoral fellow, who carried out the computational work. “Without it we would be unable to mine the genomic data intelligently.”

Wuichet sifted through trillions of letters of the DNA code to extract sequences encoding each component of this navigation system. Then, Wuichet and Zhulin designed a computational approach to classify these sequences by applying a variety of bioinformatics tools in a logical, step-by-step procedure.

“By using diverse computational methods, this study has revealed in remarkable detail how a simple two-component signaling pathway can evolve into complex systems like the ones that govern bacterial chemotaxis,” said James Anderson of the National Institutes of Health (NIH), who oversees gene regulatory network grants at the NIH’s National Institute of General Medical Sciences, which supported this work. “This computational approach will be of enormous value in uncovering the inner workings of beneficial and pathogenic microorganisms that cannot be studied using traditional laboratory methods.”

The study has revealed more than a dozen versions of this navigation system and assigned hundreds of bacterial species to each of them. “To use a metaphor, one can compare this system to types of cars,” Zhulin explained. “Imagine, if you would have only seen two types of cars in your life, say a small two-door sedan and a mid-size SUV. By comparing the two, you might guess that there can be other types of cars out there, but you wouldn’t know exactly what they are. Prior to our study, we knew exact details of only two types of navigation system from two model organisms. Simply put, our work reveals that there are all kinds of things on the roads—luxury sedans, minivans, roadsters, pick-up trucks, and we know which bug is in which vehicle.”

Zhulin said the findings “will allow predicting how individual bacteria will use their 'vehicle' to get where they want to be, which is very important in order to be able to fight pathogenic organisms that direct their movement toward weak spots of our bodies.”

At the same time, ORNL researchers are making use of the findings in advanced bioenergy research.

“These same issues of microbial ‘navigation,’ or so-called chemotaxis, are important for microbial processing of biofuels,” said Paul Gilna, director of the ORNL-led DOE BioEnergy Science Center (BESC), a DOE Bioenergy Research Center supported by the Department’s Office of Science. “That’s why we were pleased to co-sponsor this research with the National Institutes of Health and leverage NIH resources to learn more about this process.”

BESC is searching for new cost-effective ways, using microbes, to convert plant cellulose to biofuels, a “green” alternative to oil and coal.

“Cellulases from microbial sources are key enzymes in this process and come in different shapes and forms that are difficult to decipher from DNA sequence alone,” said Gilna. “This study gives us a powerful computational approach that we can now use to reveal new types of cellulolytic enzymes, as well as provide us with deeper insights into complex regulatory pathways that control their activity.”

“This work could significantly aid in our goal of producing microbes that are capable of carrying out all the steps in processing fuels from plant feedstocks,” Gilna added. “In this approach, which we term Consolidated BioProcessing, or CBP, we are working to develop microbes that can both deconstruct plant cellulosic components as well as process the released sugars into biofuels. Understanding better how such microbes can locate their respective substrates in a large biofermenter will greatly enable us to tune the efficiency of such processes, which could lead to profound improvements at a national level in the costs of producing biofuels.”

The paper describing this work, titled, “Origins and diversification of a complex signal transduction system in prokaryotes,” appears in the new journal Science Signaling by the publishers of the Science magazine and is available online at http://stke.sciencemag.org.

ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science.

NOTE TO EDITORS: You may read other press releases from Oak Ridge National Laboratory or learn more about the lab at http://www.ornl.gov/news. Additional information about ORNL is available at the sites below:

Twitter - http://twitter.com/oakridgelabnews

RSS Feeds - http://www.ornl.gov/ornlhome/rss_feeds.shtml

Flickr - http://www.flickr.com/photos/oakridgelab

YouTube - http://www.youtube.com/user/OakRidgeNationalLab

LinkedIn - http://www.linkedin.com/companies/oak-ridge-national-laboratory

Facebook - http://www.facebook.com/Oak.Ridge.National.Laboratory

Barbara Penland | Newswise Science News
Further information:
http://www.ornl.gov

More articles from Life Sciences:

nachricht How brains surrender to sleep
23.06.2017 | IMP - Forschungsinstitut für Molekulare Pathologie GmbH

nachricht A new technique isolates neuronal activity during memory consolidation
22.06.2017 | Spanish National Research Council (CSIC)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

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...

Im Focus: Climate satellite: Tracking methane with robust laser technology

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...

Im Focus: How protons move through a fuel cell

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...

Im Focus: A unique data centre for cosmological simulations

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...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

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)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Quantum thermometer or optical refrigerator?

23.06.2017 | Physics and Astronomy

A 100-year-old physics problem has been solved at EPFL

23.06.2017 | Physics and Astronomy

Equipping form with function

23.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>