Berkeley Lab researchers have revealed critical genetic secrets of a bacterium that holds potential for removing toxic and radioactive waste from the environment. 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.”
Desulfovibrio vulgaris is an anaerobic bacterium that is present in many ecological niches and serves as a model organism for the study of sulfate-reducing bacteria. The microbe has drawn much attention – both positive and negative – for its ability to metabolize metals. On the positive side, D. vulgaris can generate enzymes that reduce toxic heavy metals and radioactive nuclides into non-hazardous forms. On the negative side, D. vulgaris 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 characterized.”
Bacteria 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.
Mukhopadhyay and her team bypassed the need to know the signal activation conditions and mapped 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.
The DAP-chip strategy used to create this regulatory gene map for D. vulgaris can 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 contaminated environments.