Signal transduction via the PTS in Sinorhizobium meliloti
S. meliloti can grow in the soil as free-living organisms, but can also live as nitrogen-fixing symbionts inside root nodules of plants belonging to the family Leguminosae. Free-living S. meliloti can utilize a wide variety carbon sources including sugars, amino acids and TCA cycle intermediates. A large body of evidence shows that C4 TCA cycle intermediates are used to fuel and provide reducing equivalents for symbiotic forms of Sinorhizobium meliloti. In addition, these compounds are favored carbon and energy sources for free-living S. melilot, and are used in preference to many other carbon sources. The phenomenon of utilizing succinate, and other C4-dicarboxylic acids, in preference to other compounds in S. meliloti, is called succinate-mediated catabolite repression (SMCR) (pdf) (pdf).  SMCR is deeply integrated into the physiology of S. meliloti and the the genes that regulate SMCR also regulate: carbon storage, growth and survival, exopolysaccharide synthesis, symbiosis and nitrogen fixation. SMCR is regulated by both the phosphotransferase system (PTS) and by a two-component system (pdf) (pdf). Two PTS proteins are particularly important: Hpr and EIIANtr. Hpr is the central regulator through which all phosphorylation signals travel, and it integrates information about the S. meliloti’s physiological state via PTS proteins EINtr and HprK. EIIANtr appears to be the main PTS output signal regulating SMCR and symbiotic functions. Recent work shows that regulation of SMCR is connected to the synthesis of polyhydroxybutyrate (PHB) and that PHB has global effects on gene expression and physiology of S. meliloti.

Signal transduction via two-component sytstems in Sinorhizobium meliloti
Signaling in prokaryotes consists of a chain of events that begins with the detection of signal and ends with a physiological response that is usually adaptive. Two component signaling systems (TCSs) are one of the most common signal transduction systems in prokaryotes. The typical TCS consists of a histidine kinase (HK) and a cognate response regulator (RR), which work together to modulate a physiological response. Recently a new family of HKs associated with two component systems was described. These HKs, called HWE kinases, are notable because their kinase domains are different from previously known domains and often signal in response to light, energy, redox or small molecules. HWE kinases work with RRs that are similar to each other at the sequence level and together define a RR subgroup. One goal of our lab is to better understand physiological and structural aspects of HWE_HK/RR signaling using a model set of proteins, Sma0113(HWE_HK) and Sma0114(RR). These two proteins are encoded in the genome of Sinorhizobium meliloti, and together regulate catabolite repression and carbon storage (PHB synthesis) (pdf). We are combining genetic, computational and structural approaches to establish the Sma0113/114 pair as a model for HWE kinases and their response regulators (pdf).

Termites and their symbionts
Our lab is working as part of a NSF-funded EFRI (Emerging Frontiers in Research and Innovation) group to study signaling and the dynamics of the symbiotic gut community in the Northeastern termite Reticulitermes flavipes. The community under study consists of bacteria, archaea and protists. These organisms exist symbiotically within the termite gut, and together with the termite convert wood to fuel (acetate). We think the capabilities of the termite depend on the composition, spatial distribution and structure of the community in its gut and we think that the community is regulated through a complex signaling network composed of cell-cell contact dependent signaling and intercellular chemical signaling. We are trying to replicate microscale physical and chemical features of a lower termite gut using molecular biology and engineered, microfluidic microhabitats. The work under way right now focuses on:
1. Metagenomics: Used to evaluate the gut community composition of R. flavipes and the genes it    expresses
2. Signaling: We are studying cell-cell communication that takes place when community members come    in contact with each other
3. Modeling: We are carrying out mathematical analysis to determine signaling network structure and modulate functionality.
4. Engineering: We are developing a microfluidic culture array mimicking the microhabitat of the R.    flavipes gut allowing physicochemical control and real time monitoring.
 5. Integration: Ultimately we expect to establish, maintain, and control a functional termite microbiome    in vitro.

The group of labs working on this project: Dr. Daniel Gage, Dr. Joerg Graf, Dr. Jared Leadbetter, Dr. William Mustain, Dr. Ken Noll, Dr. Leslie Shor and Dr. Ranjan Srivastava.
 

Microbial ecology of complex environments such as the rhizosphere
Identifying types, and distributions, of nutrients found around plant roots is needed in order to better understand forces driving plant/microbe interactions (pdf) (pdf). However, nutrients near the root are difficult to study: they are hard to extract from soil, they are readily used by microorganisms and thus rapidly disappear, and it is difficult to sample the root region without disrupting nutrient distributions. We have overcome some of these problems by constructing and deploying bacterial reporters which fluoresce when particular nutrients are present in the root/soil environment. The reporters are simply inoculated into environmental chambers containing plants, and the root systems in the chambers are later observed by microscopy. The locations of fluorescing bacteria indicate regions where particular nutrients are detected by the biosensing bacteria. Using this technology, nutrients and their locations in time and space can be observed around plant roots, and in soil. We are applying the technology to study how sugars, organic acids, bulk carbon and water potential support growth of bacteria around the roots of a variety plant species (pdf) (pdf). Ultimately we hope to use these biosensors to investigate how carbon flow into the rhizosphere is modified in response to changes in plant physiology. This work is multidisciplinary and is being done in collaboration with Dr. Zoe Cardon at the Marine Biology Lab at Woods Hole.