In stationary phase bacteria cells, Dps (DNA binding protein from starved cells) is the most abundant protein component of the nucleoid. Dps compacts DNA into a dense structure, and the deletion of Dps has wide-ranging effects on the levels of protein expression in stationary cells. We have applied RNA-Seq techniques to measure the global effects on transcription associated with Dps-induced compaction of DNA. Strikingly, we found virtually no significant changes in mRNA levels in stationary-phase cells. Additionally, we measured the in vitro activity of RNA polymerase on DNA compacted by Dps, and we found no meaningful change in either transcriptional initiation or transcriptional elongation. We are therefore forced to conclude that Dps does not affect stationary-phase transcription either directly or indirectly in the cell. Instead, Dps provides a mechanism to compact and protect DNA that is orthogonal to transcription, and changes in protein expression associated with Dps must be caused by changes in translation or degradation of these proteins.
Recently, the Meyer lab has started a new line of research targeted at re-engineering bacteria to synthesize bio-inspired materials with improved properties. This approach has the potential to replace traditional chemical approaches that require extreme environmental conditions, expensive equipment, and the generation of hazardous waste. As a first step we have targeted bacterial production of patterned artificial nacre, a biomineralized material lining seashells that combines high mechanical strength with high fracture toughness. We are currently able to deposit layers of crystallized calcium carbonate via bacterial action in alternation with bacterially-synthesized organic polymers. Our visibly layered composite materials represent a breakthrough in the fabrication of tunable, environmentally-friendly materials. Combination of our biological materials-producing systems with our newly developed 3D bacterial printers will allow the rapid and straight-forward production of spatially structured biomaterials.