Victor De Lorenzo | PubMed Health

PubMed2005

MetaRouter: bioinformatics for bioremediation.

Bioremediation, the exploitation of biological catalysts (mostly microorganisms) for removing pollutants from the environment, requires the integration of huge amounts of data from different sources. We have developed MetaRouter, a system for maintaining heterogeneous information related to bioremediation in a framework that allows its query, administration and mining (application of methods for extracting new knowledge). MetaRouter is an application intended for laboratories working in biodegradation and bioremediation, which need to maintain and consult public and private data, linked internally and with external databases, and to extract new information from it. Among the data-mining features is a program included for locating biodegradative pathways for chemical compounds according to a given set of constraints and requirements. The integration of biodegradation information with the corresponding protein and genome data provides a suitable framework for studying the global properties of the bioremediation network. The system can be accessed and administrated through a web interface. The full-featured system (except administration facilities) is freely available at http://pdg.cnb.uam.es/MetaRouter. Additional material: http://www.pdg.cnb.uam.es/biodeg_net/MetaRouter.

Bacteria↗

PubMed2003

Recruitment of sigma54-RNA polymerase to the Pu promoter of Pseudomonas putida through integration host factor-mediated positioning switch of alpha subunit carboxyl-terminal domain on an UP-like element.

The interactions between the sigma54-containing RNA polymerase (sigma54-RNAP) and the region of the Pseudomonas putida Pu promoter spanning from the enhancer to the binding site for the integration host factor (IHF) were analyzed both by DNase I and hydroxyl radical footprinting. A short Pu region centered at position -104 was found to be involved in the interaction with sigma54-RNAP, both in the absence and in the presence of IHF protein. Deletion or scrambling of the -104 region strongly reduced promoter affinity in vitro and promoter activity in vivo, respectively. The reduction in promoter affinity coincided with the loss of IHF-mediated recruitment of the sigma54-RNAP in vitro. The experiments with oriented-alpha sigma54-RNAP derivatives containing bound chemical nuclease revealed interchangeable positioning of only one of the two alpha subunit carboxyl-terminal domains (alphaCTDs) both at the -104 region and in the surroundings of position -78. The addition of IHF resulted in perfect position symmetry of the two alphaCTDs. These results indicate that, in the absence of IHF, the sigma54-RNAP asymmetrically uses only one alphaCTD subunit to establish productive contacts with upstream sequences of the Pu promoter. In the presence of IHF-induced curvature, the closer proximity of the upstream DNA to the body of the sigma54-RNAP can allow the other alphaCTD to be engaged in and thus favor closed complex formation.

Base Sequence↗