New tool for mining bacterial genome for novel drugs
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| Drug resistant bacteria Klebsiella pneumoniae. (Shutterstock) |
Vanderbilt biochemists have discovered that the process bacteria
undergo when they become drug resistant can act as a powerful tool for drug
discovery. Their findings -- reported this week in the Online Early Edition of
the Proceedings of the National Academy of Sciences -- should give a major boost to natural
products drug discovery -- the process of finding new drugs from compounds
isolated from living organisms -- by substantially increasing the number of
novel compounds that scientists can extract from individual microorganisms.
Bacteria
have traditionally been the source of important drugs such as antibiotics and anticancer
agents. Researchers looking for new bacterially synthesized drugs have long
known that bacterial genomes contain a large number of "silent genes"
that contain the instructions for making drug-like compounds. But, until now,
scientists have found it is very difficult to find ways to turn on the
production of these compounds, known as secondary metabolites.
While
investigating how bacteria develop drug resistance, Vanderbilt biochemists
Brian Bachmann and John McLean discovered that strains of antibiotic-resistant
bacteria express hundreds of compounds not produced by their progenitors, many
of which are potential secondary metabolites.
"It's
as if the bacteria respond to the assault by the antibiotic with a
'save-all-ships' strategy of turning on hundreds of silent genes," said
Bachmann, associate professor chemistry at Vanderbilt.
"This
technique is something like fracking in the natural gas industry. We've known
for a long time that there were large amounts of underground natural gas that
we couldn't extract using conventional methods but now we can, using hydraulic
fracturing technology. In a similar fashion we think we can use bacteria's
antibiotic resistance to intensively mine the bacterial genome for new drug
leads," he said.
The
original purpose of the study was to take the most detailed look yet at what
happens when microbes develop drug resistance. Bachmann is an expert in natural
products drug discovery and McLean, an assistant professor of chemistry, is a
pioneer in the development of analytical instrumentation and chemical
techniques that can identify thousands of different biological compounds
simultaneously, such as ion mobility-mass spectrometry.
"One
of the daunting challenges is to rapidly inventory the tens to hundreds of
thousands of molecules the bacteria construct to live, and then to read this
inventory to understand how the bacteria compensate for their changing
circumstances. To complicate matters further, we are looking for new drug-like
molecules, so by definition we are looking for something that has not been seen
before," said McLean.
Working
with Research Assistant Dagmara Derewacz and graduate students Cody Goodwin and
Ruth McNees, Bachmann and McLean started with the well-characterized soil
bacterium Nocardiopsis. They exposed the bacterium to two different antibiotics
-- streptomycin and rifampicin -- and observed the results.
"The
first thing that happens is almost all of the bacteria die. Less than one cell
in a million survives," said Bachmann.
The
chemists then cultured the survivors (six streptomycin-resistant strains and
five rifampicin-resistant strains) without the antibiotic and used McLean's
instrumental methods to profile the drug-like compounds that they produced.
They
discovered that the differences were much greater than they expected. The
survivors had undergone extensive mutations, not only in the genes that produce
secondary metabolites but also in the housekeeping genes that alter the way
they make RNA and proteins. As a result, they determined that the resistant
strains produced more than 300 compounds that were not expressed by the
original organism.
"The
cells appear to be 'de-repressing' as many of their silent genes as possible.
This seems like a very drastic way to become drug resistant," Bachmann
said.
McLean's
team has developed strategies that allow them to automatically identify and
compare the relative uniqueness and the relative abundance of tens of thousands
of molecules from which the hundreds of novel compounds were found.
"What
we are looking for are new species of molecules in the mutants that are the
most unique and the most abundant," said Bachmann.
In the
antibiotic-resistant Nocardiopsis strains the researchers found a total of five
compounds that were both unique enough and abundant enough to isolate,
determine their molecular structures and test for biological activity.
"Normally,
we only find one compound per organism, so this is a significant improvement in
yield, allowing us to get many new compounds from previously mined
microorganisms," Bachmann said.
Source: Vanderbilt University
Posted by Unknown
on Monday, January 28, 2013.
Filed under
Biology,
Plants And Animals
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