Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Researchers Create New Method for Uncovering Natural Products from Mystery 'Orphan Genes'

29.01.2007
Approach leads to identification of compound with potential benefits in agriculture through crop protection

Microorganisms have a proven track record for producing powerful molecules useful in antibiotics, as anticancer agents and in treating human diseases.At times, researchers studying the genomes of these microorganisms have come across sections of DNA for which scientists cannot determine what is ultimately produced. It's not clear what might be created from these so-called "orphan gene clusters" and if those end products might carry beneficial qualities.

Scientists at Scripps Institution of Oceanography at UC San Diego have devised a new method for identifying the mysterious products of orphan gene clusters.

"In this new age of genomics, microorganisms have even more capacity to make exotic natural product molecules than we ever realized," said William Gerwick, a professor in Scripps Oceanography's Center for Marine Biotechnology and Biomedicine and the Skaggs School of Pharmacy and Pharmaceutical Sciences at UC San Diego. "However, sometimes we don't know how to find these products. We can see them in the genomic information but we can't necessarily find the resulting organic substances."

The method developed by Gerwick and his colleagues employs a novel combination of genomic sequence analysis and isotope labeling. The new "genomisotopic approach" is described in the new issue of Chemistry & Biology as the journal's featured cover paper.

Gerwick says the key to the genomisotopic approach lies in the combined power of bioinformatics—computer programming to predict the proteins as well as the component building blocks they will use to make the new mystery product—with the ability to provide building blocks containing distinctive isotope labels to cultures producing the mystery compound. The microorganism assimilates the isotope-tagged precursors, incorporates them into the mystery compound, thus enabling the researchers to "find" the mystery compound simply by looking for the isotope signature. According to the paper, the approach represents a valuable complement to existing genome "mining" strategies.

"This technique allows us to methodically and with a very well-defined strategy figure out and isolate the compounds that are produced from those orphan gene clusters," said Gerwick. "With the genomisotopic approach we're mapping out a metabolic process. We're watching the incorporation of the amino acid into a more complex natural products structure and visualizing it at the end by a combination of mass spectrometry and nuclear magnetic resonance spectroscopy."

The genomisotopic approach was born out of a failed experiment in Gerwick's laboratory. A student had attempted to clone the biosynthetic gene cluster for a certain compound. The student sequenced a stretch of DNA that initially appeared promising as the correct gene cluster, but ultimately proved not to be.

"So with that big stretch of DNA we scratched our heads and wondered, if it didn't make the compound we thought it did, what did it make?" said Gerwick. "We brainstormed and thought we could come up with an approach for finding out."

In addition to describing the genomisotopic approach, the Chemistry & Biology paper describes the identification of a compound of a previously unknown natural product discovered through the new method. Gerwick and his colleagues applied the approach and found what is now known as orfamide A, a new natural product that may prove beneficial in agriculture and crop protection due to its potential in suppressing plant diseases.

Gerwick says the new approach will now be applied to various organisms derived from the ocean, including marine bacteria.

In addition to Gerwick, the paper's coauthors include Harald Gross (Scripps and Oregon State University), Virginia Stockwell (Oregon State University), Marcella Henkels (U.S. Department of Agriculture), Brian Nowak-Thompson (Northland College) and Joyce Loper (U.S. Department of Agriculture).

The study was funded by the National Institutes of Health and the Microbial Genomic Sequencing Program of the U.S. Department of Agriculture Cooperative State Research, Education and Extension Service.

Mario Aguilera | EurekAlert!
Further information:
http://www.ucsd.edu

Further reports about: approach compound genomisotopic microorganism

More articles from Life Sciences:

nachricht For a chimpanzee, one good turn deserves another
27.06.2017 | Max-Planck-Institut für Mathematik in den Naturwissenschaften (MPIMIS)

nachricht New method to rapidly map the 'social networks' of proteins
27.06.2017 | Salk 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: 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

Touch Displays WAY-AX and WAY-DX by WayCon

27.06.2017 | Power and Electrical Engineering

Drones that drive

27.06.2017 | Information Technology

Ultra-compact phase modulators based on graphene plasmons

27.06.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>