Desulfovibrio vulgaris is an anaerobic sulfate-eating microbe that can also consume toxic and radioactive waste, making it a prime candidate for bioremediation of contaminated environments. Photo: Lawrence Berkeley National Laboratory
Critical genetic secrets of a bacterium that holds
potential for removing toxic and radioactive waste from the environment have
been revealed in a study by researchers with the U.S. Department of Energy
(DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab). The researchers
have provided the first ever map of the genes that determine how these bacteria
interact with their surrounding environment.
“Knowing how bacteria respond to environmental
changes is crucial to our understanding of how their physiology tracks with
consequences that are both good, such as bioremediation, and bad, such as
biofouling,” says Aindrila Mukhopadhyay, a chemist with Berkeley Lab’s Physical
Biosciences Division, who led this research. “We have reported the first
systematic mapping of the genes in a sulfate-reducing bacterium—Desulfovibrio
vulgaris—that regulate the mechanisms by which the bacteria perceive and
respond to environmental signals.”
Mukhopadhyay, who also holds an appointment with
the Joint BioEnergy Institute (JBEI), a DOE Bioenergy
is the corresponding author of a paper that describes this research in Genome
Biology. The paper is titled “Systematic mapping of two component response
regulators to gene targets in a model sulfate reducing bacterium.”
Desulfovibrio vulgaris is an anaerobic
bacterium that is present in numerous ecological niches and serves as a model
organism for the study of sulfate-reducing bacteria. The microbe has drawn much
attention—both good and bad—for its unique ability to metabolize metals. On the
good side, D. vulgaris can generate enzymes that reduce toxic heavy
metals and radioactive nuclides into non-hazardous forms. On the bad side, D.
vulgaris is also notorious as a pest that corrodes the metals used in oil
drilling and storage operations.
“For all of these reasons, it is important that we
understand the molecular signaling systems by which D. vulgaris interacts
with and survives in its many different environments,” says Mukhopadhyay. “Yet,
after more than seven decades of study, not a single one of the approximately
70 known molecular signaling systems in D. vulgaris had been
As humans, it is customary to think of us
interacting with our environment through the five senses—sight, sound, smell,
touch, and taste. However, this information processing actually takes place
through molecular signaling systems. Bacteria also process signals at the
molecular level but they utilize a two-component system in which one protein—a
histidine kinase—senses an environmental signal, which it then transfers to a
second protein—a response regulator—that controls the reaction.
“These microbial systems are difficult to identify
and study because they don’t become active until they sense a specific
environmental signal and we don’t know what most of those signals are,”
Mukhopadhyay says. “We had to figure a way around this conundrum.”
Mukhopadhyay and her co-authors were able to bypass
the need to know the signal activation conditions and map virtually the entire D.
vulgaris gene response network through genome-wide in vitro experimental
determinations. They accomplished this using a “DNA-Affinity-Purified-chip
(DAP-chip) strategy” they devised, in which purified response regulator
proteins are incubated with genomic DNA and used to enrich DNA regions
that bind to them. Both the enriched and the starting input DNA are amplified,
pooled, and hybridized in a customized D. vulgaris microarray to
determine enriched gene targets.
“To our knowledge, this is the first extensive use
of a genome-wide method to map all bacterial two component system response
regulator binding sites in a single study,” Mukhopadhyay says.
Mukhopadhyay and her colleagues have already used
their new gene map to predict the functions of several response regulators in D.
vulgaris that include key processes of carbon, nitrogen and energy
metabolism, cell motility and biofilm formation. They have also predicted
responses to stresses such as nitrite, low potassium, and phosphate starvation.
“For several response regulators we predicted and
experimentally verified the binding site motifs, most of which were discovered
as part of this study,” Mukhopadhyay says. “In the future this gene map should
help guide the development of bioremediation methods that do not exacerbate
existing problems, and also help guide field practices that will enhance
The DAP-chip strategy used to create this
regulatory gene map for D. vulgaris can also be used to create similar
gene maps for any microbe whose genome has been sequenced. Given that the
regulatory network of a microbe is often a reflection of the environments in
which it thrives and the biogeochemical processes it can mediate, such gene
maps should have an important role in future clean-ups of a wide range of
“Our study is inherently foundational and the
regulatory networks we discovered not only inform us about the bacterial
response to heavy metals but also allows us to correlate microbial activity to
other biofouling phenomena as well,” says Mukhopadhyay.