Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Sequencing efforts miss DNA crucial to bacteria's disease causing power

26.06.2014

Genomic sequencing is supposed to reveal the entire genetic makeup of an organism.

For infectious disease specialists, the technology can be used to analyze a disease-causing bacterium to determine how much harm it is capable of causing and whether or not it will be resistant to antibiotics.

But new research at Rockefeller University suggests that current sequencing protocols overlook crucial bits of information: isolated pieces of DNA floating outside the bacterial chromosome, the core of a cell's genetic material.

"Extensive sequencing of chromosomal DNA has been performed for a variety of pathogenic organisms, but these sequences fail to uncover the presence of DNA elements in the cell's cytoplasm. As a result, the DNA profile of a pathogenic bacteria may be incomplete," says Vincent Fischetti, head of the Laboratory of Bacterial Pathogenesis and Immunology. "We have now devised a way to identify these elements."

Extrachromosomal DNA can include bacteria-infecting viruses, known as phages, and strands of self-replicating DNA, known as plasmids, often picked up from other bacteria. These phages and plasmids can easily move between bacterial cells, and scientists have known for some time that, as a result, these so-called mobile genetic elements can play important roles in virulence and antibiotic resistance.

This study focused on phages. Their activity outside the chromosomes has been poorly studied; most research has focused on phages integrated into bacterial chromosomes. Meanwhile, plasmids, which allow bacteria to share genes among themselves, are well studied.

"So far, no one has looked across a variety of strains of bacteria, as we have done with Staphylococcus aureus, to find these extrachromosomal phages that have potential to play an important role in disease," says Bryan Utter a postdoc in the lab and the first author of the research published June 25 in PLoS ONE. Staphylococcus is a common bacterium that can cause serious or even fatal infections under certain circumstances.

Until now, an analysis of this scope wasn't possible, because chromosomal DNA easily fragments and contaminates the sample during the process by which researchers prepare the extrachromosomal DNA, making them virtually impossible to identify and sequence.

"To solve this problem, we borrowed a tool from phages themselves: the enzymes these viruses use to break apart a phage-infected cell to release their progeny," says Douglas Deutsch, a graduate student in the lab. These enzymes, a focus of research in the lab in the development of novel anti-infectives, are now being harnessed to gently extract the chromosomal DNA, while leaving behind any other genetic elements for analysis. Using this technique, they looked for extrachromosomal phages across 24 medically important strains of Staphylococci.

Not only did extrachromosomal phages appear widespread among these strains, but the researchers found evidence that these phages encode genes that can make the bacteria more dangerous.

For example, when the researchers decoded the complete sequence of one extrachromosomal circular phage from a disease-causing Staphylococcus, they identified a number of genes that may help this strain evade a host's immune system and that could readily spread to other Staphylococcus bacteria. The researchers are now studying what role, if any, these viral genes play in this strain's ability to cause disease.

The implications go beyond pathogenicity. Phage elements, including those not integrated into chromosomes, are part of a bacterial system for regulating genes. For instance, some of these phage elements can activate or silence bacterial genes by moving into or out of the chromosome. Within the Staphylococcus strains, the researchers found both transient elements as well as those residing permanently outside the chromosomes.

"By examining the DNA outside the bacterial chromosomes, you may get a better understanding of the dynamics by which these elements may mobilize thereby controlling microbial genes," Fischetti says.

Zach Veilleux | Eurek Alert!
Further information:
http://www.rockefeller.edu

Further reports about: DNA Rockefeller Sequencing Staphylococcus bacteria bacterial bacterium chromosomal chromosomes enzymes genes play strains

More articles from Life Sciences:

nachricht Rainbow colors reveal cell history: Uncovering β-cell heterogeneity
22.09.2017 | DFG-Forschungszentrum für Regenerative Therapien TU Dresden

nachricht The pyrenoid is a carbon-fixing liquid droplet
22.09.2017 | Max-Planck-Institut für Biochemie

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: The pyrenoid is a carbon-fixing liquid droplet

Plants and algae use the enzyme Rubisco to fix carbon dioxide, removing it from the atmosphere and converting it into biomass. Algae have figured out a way to increase the efficiency of carbon fixation. They gather most of their Rubisco into a ball-shaped microcompartment called the pyrenoid, which they flood with a high local concentration of carbon dioxide. A team of scientists at Princeton University, the Carnegie Institution for Science, Stanford University and the Max Plank Institute of Biochemistry have unravelled the mysteries of how the pyrenoid is assembled. These insights can help to engineer crops that remove more carbon dioxide from the atmosphere while producing more food.

A warming planet

Im Focus: Highly precise wiring in the Cerebral Cortex

Our brains house extremely complex neuronal circuits, whose detailed structures are still largely unknown. This is especially true for the so-called cerebral cortex of mammals, where among other things vision, thoughts or spatial orientation are being computed. Here the rules by which nerve cells are connected to each other are only partly understood. A team of scientists around Moritz Helmstaedter at the Frankfiurt Max Planck Institute for Brain Research and Helene Schmidt (Humboldt University in Berlin) have now discovered a surprisingly precise nerve cell connectivity pattern in the part of the cerebral cortex that is responsible for orienting the individual animal or human in space.

The researchers report online in Nature (Schmidt et al., 2017. Axonal synapse sorting in medial entorhinal cortex, DOI: 10.1038/nature24005) that synapses in...

Im Focus: Tiny lasers from a gallery of whispers

New technique promises tunable laser devices

Whispering gallery mode (WGM) resonators are used to make tiny micro-lasers, sensors, switches, routers and other devices. These tiny structures rely on a...

Im Focus: Ultrafast snapshots of relaxing electrons in solids

Using ultrafast flashes of laser and x-ray radiation, scientists at the Max Planck Institute of Quantum Optics (Garching, Germany) took snapshots of the briefest electron motion inside a solid material to date. The electron motion lasted only 750 billionths of the billionth of a second before it fainted, setting a new record of human capability to capture ultrafast processes inside solids!

When x-rays shine onto solid materials or large molecules, an electron is pushed away from its original place near the nucleus of the atom, leaving a hole...

Im Focus: Quantum Sensors Decipher Magnetic Ordering in a New Semiconducting Material

For the first time, physicists have successfully imaged spiral magnetic ordering in a multiferroic material. These materials are considered highly promising candidates for future data storage media. The researchers were able to prove their findings using unique quantum sensors that were developed at Basel University and that can analyze electromagnetic fields on the nanometer scale. The results – obtained by scientists from the University of Basel’s Department of Physics, the Swiss Nanoscience Institute, the University of Montpellier and several laboratories from University Paris-Saclay – were recently published in the journal Nature.

Multiferroics are materials that simultaneously react to electric and magnetic fields. These two properties are rarely found together, and their combined...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

“Lasers in Composites Symposium” in Aachen – from Science to Application

19.09.2017 | Event News

I-ESA 2018 – Call for Papers

12.09.2017 | Event News

EMBO at Basel Life, a new conference on current and emerging life science research

06.09.2017 | Event News

 
Latest News

Rainbow colors reveal cell history: Uncovering β-cell heterogeneity

22.09.2017 | Life Sciences

Penn first in world to treat patient with new radiation technology

22.09.2017 | Medical Engineering

Calculating quietness

22.09.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>