Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Massive reanalysis of genome data solves case of the lethal genes

22.10.2007
Highlights avenue for new antibiotic discovery

It is better to be looked over than overlooked, Mae West supposedly said. These are words of wisdom for genome data-miners of today. Data that goes unnoticed, despite its widespread availability, can reveal extraordinary insights to the discerning eye.

Such is the case of a systematic analysis by the U.S. Department of Energy Joint Genome Institute (DOE JGI) of the massive backlog of microbial genome sequences from the public databases. The survey identified genes that kill the bacteria employed in the sequencing process and throw a microbial wrench in the works. It also offers a possible strategy for the discovery of new antibiotics. These findings are published in the Oct. 19 edition of the journal Science.

In nature, promiscuous microbes share genetic information so readily that using genes to infer their species position on the evolutionary tree of life was thought to be futile. Now, researchers at DOE JGI have characterized barriers to this gene transfer by identifying genes that kill the recipient bacterium upon transfer, regardless of the type of bacterial donor. These lethal genes also provide better reference points for building phylogenic trees -- the means to verify evolutionary relationships between organisms.

... more about:
»Coli »DNA »DOE »E. coli »JGI »antibiotic »sequence

"At DOE JGI, we are responsible for producing and making publicly available genomes from hundreds of different microbes, most of which are relevant to advancing the frontiers of bioenergy, carbon cycling, and bioremediation," said Eddy Rubin, DOE JGI Director. "We realized that sequencing a genome is like conducting a massive experiment in gene transfer. By checking which genes could not be sequenced, we discovered barriers to transfer."

The industrial-scale "shotgun" DNA sequencing strategy typically involves sheering the organism's DNA into manageable fragments, and then inserting these fragments into a disarmed strain of E. coli, which is used as an enrichment culture -- to grow up vast amounts of the target DNA. The team led by Rubin showed that this sequencing process mimics the transmission of DNA from one organism to another, a mechanism called horizontal gene transfer. This phenomenon occurs in nature, allowing one organism to acquire and use genes from other organisms. While this is an extremely rare event in animals, it does occur frequently in microorganisms and is one of the main sources for the rapid spread of antibiotic resistance among bacteria.

"When you sequence a genome, you never get the whole genome reconstructed in one pass," said Rubin. "You always get gaps in the assembly. This is annoying, expensive, and compels us to close the gaps and finish the puzzle so that we could tell the story behind the sequence. Our breakthrough was in understanding that gaps occur because some genes cannot be transferred to E. coli -- because they are lethal."

So Rubin and his colleagues sifted through more than nine billion nucleotides to assess gaps in 80 different genomes. They found that the same genes, over and over again, caused these gaps, meaning that they could not be transferred into the E. coli.

"We use the bits that people usually throw away, the gaps of information keeping us from finishing an assembly," Rubin said. "We identified a set of genes that, if you add another copy or you tweak its expression, the host dies.

"The genes we categorized, while providing us a lesson in the evolutionary history of the organism, now suggest a short-cut for finishing genomes," Rubin said. "In addition, it offers a new strategy for screening molecules that may represent the next generation of broad-spectrum antibiotics. We expect that many organisms, not just E. coli, are susceptible to being killed if they take up certain genes that are over-expressed. We have strong evidence that most microbes behave like that."

David Gilbert | EurekAlert!
Further information:
http://www.jgi.doe.gov/

Further reports about: Coli DNA DOE E. coli JGI antibiotic sequence

More articles from Life Sciences:

nachricht Study shines light on brain cells that coordinate movement
26.06.2017 | University of Washington Health Sciences/UW Medicine

nachricht New insight into a central biological dogma on ion transport
26.06.2017 | Aarhus University

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

Study shines light on brain cells that coordinate movement

26.06.2017 | Life Sciences

Smooth propagation of spin waves using gold

26.06.2017 | Physics and Astronomy

Switchable DNA mini-machines store information

26.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>