CellWhere: graphical display of interaction networks organized on subcellular localizations.

Given a query list of genes or proteins, CellWhere produces an interactive graphical display that mimics the structure of a cell, showing the local interaction network organized into subcellular locations. This user-friendly tool helps in the formulation of mechanistic hypotheses by enabling the experimental biologist to explore simultaneously two elements of functional context: (i) protein subcellular localization and (ii) protein-protein interactions or gene functional associations. Subcellular localization terms are obtained from public sources (the Gene Ontology and UniProt-together containing several thousand such terms) then mapped onto a smaller number of CellWhere localizations. These localizations include all major cell compartments, but the user may modify the mapping as desired. Protein-protein interaction listings, and their associated evidence strength scores, are obtained from the Mentha interactome server, or power-users may upload a pre-made network produced using some other interactomics tool. The Cytoscape.js JavaScript library is used in producing the graphical display. Importantly, for a protein that has been observed at multiple subcellular locations, users may prioritize the visual display of locations that are of special relevance to their research domain. CellWhere is at http://cellwhere-myology.rhcloud.com.

In situ characterization of mycobacterial growth inhibition by lytic enzymes expressed in vectorized E. coli.

The emergence of extremely drug resistant Mycobacterium tuberculosis necessitates new strategies to combat the pathogen. Engineered bacteria may serve as vectors to deliver proteins to human cells, including mycobacteria-infected macrophages. In this work, we target Mycobacterium smegmatis, a nonpathogenic tuberculosis model, with E. coli modified to express trehalose dimycolate hydrolase (TDMH), a membrane-lysing serine esterase. We show that TDMH-expressing E. coli are capable of lysing mycobacteria in vitro and at low pH. Vectorized E. coli producing TDMH were found suppress the proliferation of mycobacteria in infected macrophages.

Silencing of antibiotic resistance in E. coli with engineered phage bearing small regulatory RNAs.

In response to emergent antibiotic resistance, new strategies are needed to enhance the effectiveness of existing antibiotics. Here, we describe a phagemid-delivered, RNA-mediated system capable of directly knocking down antibiotic resistance phenotypes. Small regulatory RNAs (sRNAs) were designed to specifically inhibit translation of chloramphenicol acetyltransferase and kanamycin phosphotransferase. Nonlytic phagemids coding for sRNA expression were able to infect and restore chloramphenicol and kanamycin sensitivity to populations of otherwise resistant E. coli. This modular system could easily be extended to other bacteria with resistance profiles that depend on specific transcripts.