Research

Systems and Synthetic Biology Group

The Systems and Synthetic Biology Group is formed by experimental and computational biologists who use a wide range of expertise to approach cutting-edge problems in biology.  We use multidisciplinary approaches – ranging from molecular biology through proteomics to modeling – to investigate microbes and microbial communities as they respond to different perturbations, including those relevant to emerging issues in bioenergy and pathogenesis.  Our principal unifying objective is to gain a predictive understanding of protein-mediated activities that are critical to cells and their interactions in living systems.

Research Area Highlights

A combinatorial sensor design in Caulobacter crescentus for selective environmental uranium detection 

D. M. Park and M. J. Taffet (2019) ACS Synthetic Biology
Using a systems biology approach, we identified two previously uncharacterized regulatory pathways—UzcRSand UrtAP—that are responsible for mediating U-dependent gene regulation in C. crescentus. Both pathways exhibit distinct, but imperfect selectivity profiles and function independently with respect to U perception. Using a combinatorial approach, we developed a genetic circuit that triggers GFP expression when the cell receives input from both pathways. The resulting whole-cell sensor enables the selective detection of U in ground water samples.

 

Microbe encapsulation for selective rare-earth recovery from electronic waste leachates

A. Brewer, A. Dohnalkova, V. Shutthanandan, L. Kovarik, E. Chang, A. M. Sawvel, H. E. Mason, D. Reed, C. Ye, W. F. Hynes, L. N. Lammers, D. M. Park, and Y. Jiao. (2019) Environmental Science and Technology.

A flow-through, biosorption-based rare earth element (REE) extraction technology was developed by encapsulating a bacterium engineered for enhanced REE adsorption within poly(ethylene glycol) diacrylate hydrogels and using the resulting microbe beads as the stationary phase resin in a packed bed column. The microbe bead columns exhibited high stability over multiple REE extraction cycles and enabled the selective extraction of REEs from an electronic waste leachate (NdBFe magnets from cell phone speakers) in a single column extraction step. 

 

Bioadsorption of rare earth elements through cell surface display of lanthanide binding tags

D. M. Park, D. W. Reed, M. C. Yung, A. Eslamimanesh, M. M. Lencka, A. Anderko, Y. Fujita, R. E. Riman, A. Navrotsky, Y. Jiao (2016) Environmental Science and Technology
Rare earth elements (REE) are widely and increasingly used in renewable-energy, consumer, and defense applications, but supplies are vulnerable. We are developing an innovative biotechnology to sequester and recover rare earth elements from low-grade sources (e.g., mine tailings, geothermal fluids, and recyclable materials). We are advancing a cost-effective approach that relies on environmentally-safe microorganisms (patent pending). We combine native cell physiology with advanced synthetic biology to recover rare earth elements through biosorption. Our engineered microbes exhibit enhanced adsorption capacity and selectivity towards rare earth metals even in the presence of high concentrations of competing metals.

 

The UzcRS two‐component system in Caulobacter crescentus integrates regulatory input from diverse auxiliary regulators 

D. M. ParkK. W. Overton, and Y. Jiao (2018) Molecular Microbiology
Multicomponent signaling pathway governing an extracytoplasmic stress response in Caulobacter. TheUzcRSTCS is the core signaling unit of this multicomponent signaling pathway and functions as a U/Zn/Cu‐dependent global activator of genes encoding extracytoplasmic functions. Arrows are colored based on interactions that occur under normal conditions of growth conditions (i.e. no added inducer; black) or following exposure to U/Zn/Cu (blue) or an unidentified stressor/s (magenta). Dashed lines represent either indirect interactions or unconfirmed direct interactions, and dashed arrows for UzcR reflect a uzcR‐dependent change in transcription, but no upstream ChIP‐seq peak. 

 

Biogeochemistry of Actinides 

Contacts: Nancy Merino and Yongqin Jiao 
Microorganisms influence actinide environmental fate and transport through several mechanisms, such as bioaccumulation, biosorption, and biomineralization. However, the effect of microbial products on actinide mobility remains largely unexplored. At Savannah River Site (SRS) Pond B in South Carolina, we are investigating the role of microbial intracellular and extracellular products on actinide partitioning (Pu, Am, Cs) between the water column and sediments. Pond B received nuclear reactor cooling water between 1961–1964. We are currently measuring several biogeochemical parameters of Pond B over a 1-year period and conducting microcosm experiments under different conditions to ascertain whether specific metabolisms result in different microbial exudates that affect Pu partitioning between the sediment-water interface. 

 

Encapsulin carrier proteins for enhanced expression of antimicrobial peptides

T-H. Lee, T. S. Carpenter, P. D’haeseleer, D. F. Savage, and M. C. Yung. (2019) Biotechnology and Bioengineering, Editor’s Choice Article
Antimicrobial peptides (AMPs) are regarded as attractive alternatives to conventional antibiotics, but their production in microbes remains challenging due to their inherent bactericidal nature. We have engineered a cage‐disrupted encapsulin carrier protein containing multiple TEV protease recognition sites. When fused to AMPs, this engineered encapsulin protein enabled robust AMP expression in Escherichia coli. In contrast to cage‐forming encapsulin proteins, release of AMP from the cage‐disrupted protein by TEV protease was highly efficient, ultimately yielding highly active AMP.

See also: M. C. Yung, F. A. Bourguet, T. S. Carpenter, M. A. Coleman (2017) Microbial Cell Factories

 

Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions

T. J.Samo, J. A. Kimbrel, D. J. Nilson, J. Pett-Ridge, P. K. Weber, X. Mayali (2018) Environmental Microbiology
NanoSIP images and data of the alga Phaeodactylum tricornutumHaliscomenobacter relative, and bacteria showing atom percent excess in phycosphere enrichment. The elongated and 13C‐enriched cells of P. tricornutum (red, orange, yellow) in the left image can be seen among the less enriched bacteria (blue) while filamentous cells of 15N‐enriched Haliscomenobacter relative in the middle image can be seen among the smaller bacteria and alongside the algae in the merged RGB image on the right.

 

Light regimes shape utilization of extracellular organic C and N in a cyanobacterial biofilm

R. K. Stuart, X. Mayali, A. Boaro, A. Zemla, R. C. Everroad, D. Nilson, P.K. Weber, M. Lipton, B. Bebout, J. Pett-Ridge, M. P. Thelen (2016) mBio
Representative NanoSIMS images of cyanobacterium ESFC-1 trichomes and heterotrophs 24 h after addition of 13C-labeled and 15N-labeled extracellular organic matter. Trichomes and associated microbes were identified morphologically by scanning electron microscopy prior to NanoSIMS analysis. Left, images (panels A and C and panel E) are paired images from a light-treated biofilm; Right, images (panels B and D and panel F) are paired images from a dark-treated biofilm. (A and B) Scanning electron microscope images taken prior to NanoSIMSanalysis. White outlines in panels C to F correspond to areas analyzed (ROIs), from which values for individual cells are derived. (C and D13C enrichment images. (E and F) 15N enrichment images. APE, atom percent excess.

 

Proteomic profiling of Burkholderia thailandensis during host infection using Bio-orthogonal Noncanonical Amino Acid Tagging (BONCAT)

M. Franco, P. M. D'haeseleer, S. S. Branda, M. J. Liou, Y. Haider, B. W. Segelke, S. H. El-Etr (2018) Frontiers in Cellular & Infection Microbiology
MetRSNLL incorporates azidonorleucine (Anl) in place of methionine (Met). (Left) Structures of methionine (Met) and azidonorleucine (Anl). The engineered version of E. coli MetRSNLL encodes three point mutations in the Met-binding pocket of methionyl-tRNA synthetase conferring high and preferential affinity for Anl resulting in loading of Anl onto Met-tRNA and into newly synthesized proteins in the place of Met. (Right) Copper catalyzed cycloaddition reaction of Anl-labeled protein with alkyne conjugated to biotin/fluorescent tag resulting in covalently tagged protein.

 

Jungle Express is a versatile repressor system for tight transcriptional control

T. L. Ruegg, J. H. Pereira, J. C. Chen, A. DeGiovanni, P. Novichkov, V. K. Mutalik,  G. P. Tomaleri, S. Singer, N. J. Hillson, B. A. Simmons, P. Adams, M. P. Thelen (2018) Nature Communications
Tightly regulated promoters with strong inducibility and scalability are highly desirable for biological applications. Using bottom up engineering, we have constructed a versatile system for bacterial gene expression that is based on a novel TetR-type repressor. The repressor was discovered in a bacterium isolated from rain forest soils, so we named our system “Jungle Express”. The dimeric repressor maintains control over the expression of an adjacent target gene of interest by binding to an optimized sequence in the operator DNA. The repressor is specifically induced to release from DNA with sub-micromolar concentrations of a common and inexpensive dye, crystal violet (CV). This activates transcription of the target gene. In this figure, the crystal structure of the repressor in complex with DNA is shown. The repressor’s dye binding and DNA binding domains are indicated (C, carboxy terminus; N, amino terminus). Note that because of the dimeric nature of the protein, only one CV molecule is visible in this image. Structural analysis was performed at the LBNL Advanced Light Source by JH Pereira.