04/03/2012

Observe DNA-synthesis of bacteria with the naked eye



The Leibniz-Institute DSMZ GmbH is the first scientific facility in Niedersachsen to use the newest sequencing technology. This technology is the sequencing system PacBio RS, a "third generation" sequencing device that utilises an innovative technology of single molecule sequencing (single molecule resolution, SMRT-technology). A similar device was inaugurated at the Max-Delbrück-Center for Molecular Medicine in Berlin by Federal Chancellor Angela Merkel in September 2011. With the PacBio RS-System it is possible to sequence individual DNA molecules in real time and gain more in-depth insight into the gene regulation of micro-organisms. This device will allow us to perform sequencing of genomes and transcriptomes of bacteria and virus sequences in the future and forms the basis of the new genome analysis oriented research at the Leibnitz-Institute DSMZ.

"The quick and cost-effective analysis of genome sequences of micro-organisms with the new sequencer opens up completely new possibilities in diversity research," explains Prof. Overmann, Scientific Director of the Leibniz-Institute DSMZ and head of the research group Microbial Diversity. "The estimated number of bacteria on earth is between one million and one billion. They are not only pathogenic agents but also produce important active agents, play a role in global metabolic cycles, and are relevant for the comprehension of the development and diversity of life. Currently, about 9,400 strains of bacteria have been specified and only about 2,000 more complete or almost complete genome sequences of bacteria are available for research," he says.

"When new types of bacterial genomes are decoded, we can then also discover new gene functions and better understand the interaction of diverse genes during biological processes," Prof. Overmann explains further. "Complete genomic data provide us with information about possible metabolic channels or effective natural compounds that are produced by the microbes. There is still huge potential for medical research, environmental research, and industry."

How is the new sequencing technology different from current methods? "Compared to the technologies available until now, it is possible for the first time to directly sequence individual DNA molecules with the PacBio RS. The new sequencer reads the order, the so-called "sequence" of the DNA building blocks (bases) in real time, and makes the reaction of a single enzyme with a single DNA molecule visible with the assistance of a laser. So to speak, we can observe with the "naked eye" how DNA is synthesized", says Prof. Overmann. "Unusually large fragments of genomic DNS can be sequenced in less than 1.5 hours."

On the average, the device can read more than 3,100 bases uninterrupted and complete a complex, microbial genome sequencing in one day; the same process would have taken one week or more in the past. "Therefore, it will be possible in the future to analyse 300,000 bacterial sequences from complex samples in about eight hours. For an environmental soil sample with an estimated number of 50,000 types of bacteria, for instance, the question as to which bacteria play a role in the fertility of the soil can be answered more quickly," states Prof. Overmann.

Another challenge is the tremendous amount of data (about 2 terabytes raw data) that a sequencing run with the new technology produces - enough to fill two hard drives of a modern computers. This flood of data is analysed by the team of Dr. Boyke Bunk, a computational biologist at the Leibniz-Institute DSMZ with the help of mathematics and computer science and extremely powerful computers.

A new research project based on the new sequencing platform was recently started at the Leibniz-Institut DSMZ. The scientist Dr. Cathrin Spröer analysed several strains of the bacterium sphingomonas, which are known for their ability to break down many different, partly toxic, aromatic compound and therefore could be utilised for soil rehabilitation.

Source: Leibniz-Institut (DSMZ)