Green Design

A Step Forward for Bioremediation

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.

(Berkeley Lab)