U.S. Department of Energy

Pacific Northwest National Laboratory

Aaron Wright

Biography:

Aaron Wright leads the Chemical Biology & Exposure Sciences Group in the Biological Sciences Division at PNNL.  His highly collaborative and diverse chemical biology research team is focused on gaining an improved functional and mechanistic understanding of biological processes including: (a) spatiotemporal, functional, and interaction dynamics of microbes and microbiomes; (b) oxidative and conjugation metabolism in mammalian liver and lung, particularly with regard to environmental exposures and the effect of developmental stage; and, (c) the coupling of host metabolism to the gut microbiome.  To improve our understanding of biological processes we synthesize chemical probes that are coupled to high sensitivity omics, imaging, and other analytics, in addition to 'traditional' microbiology, genetics, and molecular biology experiments.  Our research team is a talented composite of biologists, chemists, and chemical biologists, and include research staff, post-doctoral and post-bachelor's research associates, graduate students (from Washington State University, WSU) and undergraduate interns working closely together with our PNNL colleagues and external collaborators.  Interested in joining our research team?  Send Dr. Wright an email.

A little more about Dr. Wright:  Aaron is a group lead and senior scientist in the Biological Sciences Division in the Earth and Biological Sciences Directorate at PNNL, and has a joint appointment as a research professor in the Gene and Linda Voiland School of Chemical Engineering and Bioengineering at WSU, and an adjunct faculty appointment with the School of Molecular Biosciences at WSU.   Aaron earned his Ph.D. in Organic Chemistry from the University of Texas at Austin with Prof. Eric Anslyn, performing research on host-guest sensors for small molecules, peptides, and proteins relevant to biomedical applications. Realizing the potential of synthetic chemistry to answer biological questions, Aaron carried out a California Breast Cancer Research Program postdoctoral fellowship with Prof. Benjamin Cravatt at the Scripps Research Institute. While there, his research focused on the general areas of chemical biology and activity-based protein profiling, with an emphasis on cytochrome P450 oxidative metabolism.

Education & Scientific Training:

  • 2000, NSF-Research Experience for Undergraduates, University of Washington, Seattle, WA
  • 2001, B.S., Chemistry, George Fox University, Newberg, OR
  • 2006, Ph.D., Organic Chemistry, University of Texas, Austin, TX
  • 2008, Postdoctoral Research Fellow of the California Breast Cancer Research Program, Chemical Biology, The Scripps Research Institute, La Jolla, CA

*Dr. Wright's CV can be found at the bottom of this webpage.

Research Interests:

Research Overview

Our chemical biology research program is focused on: (1) characterizing the functional, spatial, and temporal dynamics of microbes and microbial communities that impact community composition and interactions and effect properties such as resilience, resistance, and productivity; (2) determining the function of drug/xenobiotic metabolizing enzymes in the mammalian liver, lung, and gut microbiome as a function of environmental exposure and developmental stage; (3) identifying the interplay between host and gut microbiome metabolic activities, and (4) developing novel chemical synthesis and chemoproteomic methodologies.

We develop and deploy active-site, modification-directed, or metabolite-based chemical probes that form irreversible bonds to protein targets in microbes, microbial communities, and mammalian cells and tissues, and subsequently report on probe labeling events by MS-based proteomics, imaging, or flow cytometry. Our team has strengths in synthetic organic chemistry for probe development, chemoproteomics, and environmental and human health biology.  At the simplest level we can summarize our research as such: we apply chemical probes to living biological systems or cellular extracts, then append enrichment moieties or fluorescent groups via click chemistry for subsequent LC-MS or imaging characterization of probe labeling (Scheme 1) resulting in an improved functional and mechanistic understanding of biological processes. Below, you can find descriptions of some of our ongoing projects.  You can also check out two recent reviews we authored in Current Opinion in Chemical Biology and in Biotechnology for Biofuels. These reviews provide a perspective on the role activity-based protein profiling has on understanding the biological functions, interactions, and regulatory dynamics of microbes and microbial communities.

Scheme 1. General strategy for chemical probing of protein functions, interactions, or regulatory modifications. Click chemistry is used to append various reporting moieties to probed proteins for subsequent characterization by imaging, flow cytometry or MS-based proteomics.

[1] The Gut Microbiome - Drug Metabolism and Exposure Perturbations

The gut microbiome is a key player in human health and development. In particular, gut microbes have an impact on the effect of xenobiotics, foreign chemical compounds that we are exposed to throughout life. Many xenobiotics are known to impact the host, but the impact xenobiotics have on the gut microbiome is not well understood. At the same time, gut microbes can also metabolize or alter xenobiotics into different compounds that can have a different impact on the host.

Understanding how host, microbiome, and xenobiotic exposure all interact could guide the development of therapies to mitigate exposure risk or damage. However, the sheer diversity of the gut microbiome makes it difficult to identify the molecular mechanisms underlying specific interactions.

To address this, we are developing an approach to isolate and identify the microbes and proteins involved in different functions using activity-based probes, and to correlate changes to those functions upon perturbation of the gut microbiome. These small molecules can be used to covalently label only active, functional enzymes within a population.

Our goal is to move away from gene- and transcript- based omics and directly measure gut microbiome enzyme activities.  We anticipate our work will provide key information to help develop and guide therapies in the future.  See also a recent review we co-authored with many others on new technologies for characterizing microbiomes (ACS Nano, 2016).

[2] Xenobiotic Metabolism in the Liver and Lung - Ontogeny-Based Function and Response to Xenobiotic Exposure

In collaboration with Jordan Smith and Justin Teeguarden of PNNL, we are engaged in research to understand how oxidative and conjugative (Phase I and II, respectively) metabolic activities in the liver and lung change as a function of age and/or exposures (for example, exposure to polyaromatic hydrocarbons). Specifically, we are researching organ-level response to persistent environmental contaminant exposure, drugs, and diet.

We are also developing novel chemical probes for phase II enzymes, as well as using existing probes for cytochrome P450 enzymes. In an initial study, we determined the effects on P450 functional activity during pregnancy due to exposure to dibenzo[def,p]chrysene in mice (Toxicol Sci. 2013, 135, 48-62). We followed this by characterizing human liver P450 activity in samples ranging from prenatal to old age (Drug Metabolism and Disposition, 2016).

We are getting set to submit a manuscript on research we performed to understand perturbations to P450 activity due to the combination of obesity and smoking. Stay on the lookout!  You can listen to Aaron Wright describe this research here during a recent interview at the 2016 American Chemical Society National Meeting & Exposition.

Our results will inform pharmacokinetic modeling and to understand the metabolic and health implications of individual chemicals and environmentally relevant mixtures.

Figure 1:

 

[3] Microbe and Microbiome Functions, Interactions and Spatial Dynamics - Mechanisms for Nutrient Acquisition and Disposition

Nutrient trafficking is a driving force influencing the biogeochemical networks established by microbial communities under metabolic flux. It promotes unique interdependent relationships among microbial members in thriving ecosystems.  B-vitamin auxotrophy and opportunism is one of many nutrient-dependent mechanisms with the power to elucidate the evolutionary dynamics behind microbial community structure, resilience, and resistance to perturbations.

Using a newly synthesized suite of chemical probes derived from B-type vitamins, our initial probe efforts led to the experimental validation and identification of numerous substrate-specific B-vitamin transporters and novel intracellular enzyme-cofactor protein associations. We used live-cell labeling of the filamentous anoxygenic photoheterotroph, Chloroflexus aurantiacus J-10-fl, known to employ biosynthetic and salvage-based mechanisms for B-vitamin acquisition. See Figure 2. (ACS Chemical Biology 2016).

Our probes provide a unique opportunity to directly link cellular activity and protein function back to native ecosystems and/or host dynamics. The probes do this by targeting protein interactions and vitamin-dependent regulatory functions.

Using tractable probe-based methods in living cells, our efforts include innovative experimental designs for directly measuring how microbes respond and adapt to multiple nutrient conditions. These include fluctuations in light intensity, C and N limitation, vitamin deficiency, and carbohydrate utilization in a static biofilm formation. We also use state-of-the-art bioreactor and flow-cell culture techniques.

We use live-cell activity and affinity-based probes to allow for multimodal downstream techniques that generate high-throughput functional protein data. These probes are parallel to relative global abundance, transcriptomics, confocal laser microscopy, and cell-sorting techniques. They accurately assign function and specificity for a wide range of experimentally unidentified and predicted membrane-embedded transport proteins. As well as the functional characterization of the intracellular vitamin cofactor-dependent pathways they impact.

In February 2017 we published a manuscript in the Proceedings of the National Academy of Sciences (PNAS 2017) describing novel regulatory regulatory roles we identified for Vitamin-B12 (cobalamin) in microbes. Our Vitamin-B12 probe exquisitely mimics natural B12 – so much so that microbes grow solely on the probe.  Stay tuned. Additional exciting publications on Vitamin B12 are coming!

 

Figure 2. B vitamin transport and intracellular metabolic pathways identified by probe-based (star) and global (triangle) proteomics in C. aurantiacus. (A) Thiamine; (B) Riboflavin.  Copyright American Chemical Society.

[4] Soil Microbiomes - Responding to Environmental Change

Soil microbiomes are essential to environmental nutrient cycling, yet their response to perturbations driven by climate change are still incredibly vague. 

We are investigating the roles hydraulic connectivity and spatial structure have on niche differentiation in the context of substrate availability, the distribution of taxa in soil micro-habitats, and the metabolic capacity of community members. We will deploy activity-based protein profiling to target enzymes responsible for organic matter decomposition related to nutrient cycling in the environment. This will tease out community member function in varied conditions. These experiments will be used to inform predictive models of soil microbiomes.  This work builds off our prior experience in characterizing cellulose and protein degradation – for example, Ser and Cys proteases.  (J. Am. Chem. Soc. 2012, 134, 20521-32; Molecular BioSystems, 2013, 9, 2992-3000).  In a brand new project (October 2017) funded by the DOE-BER, we will evaluate soil microbial community mechanisms for C acquisition, how these alter community composition and function, and hwo environmental perturbations impact the communities.

[5] Redox-Based Protein Profiling in Photoautotrophic Cyanobacteria to Characterize Dynamics Associated with Biofuel Production

We are studying the importance of redox regulation and dynamics on cysteine thiols of the proteins involved in key photosynthetic and metabolic modules within the photoautotrophic cyanobacteria, Synechococcus sp. PCC 7002 and Cyanothece sp. 51142.

Cysteine thiols are susceptible to a range of oxidative modifications, which make them a powerful chemical agent for signaling and regulatory processes in microbes. Additionally, cysteine thiol reduction and oxidation (redox) is a common mechanism used by microbes to sense environmental perturbations and initiate responses.

Photosynthetic cyanobacteria are of great interest because of their potential to generate biofuels. But the regulatory redox dynamics of protein cysteine thiols must first be understood in order to fully realize their capacity

We hypothesized that there is widespread regulation of proteins involved in critical metabolic pathways, including those important to the synthesis of high-value small molecules, biofuel precursors, and/or hydrogen. A critical caveat to investigating thiol redox status is the limitation imposed by cell lysis, in which near-immediate oxidation upon lysis destroys the native redox status.

We have developed novel chemical probe strategies for targeting reduced protein cysteine thiols in living cells (Frontiers in Microbiology 2014,5:325; ACS Chemical Biology 2014, 9, 291-300; Molecular Carcinogenesis 2014,Epub ahead of print, PMID:24285572). We used an existing chemical probe to target sulfenic acid formation.

Thus far we have investigated redox dynamics in multiple nutrient conditions including C and N limitation, high light, and oxidative stress. We have also been able to identify changes to cysteine thiol redox status in as little as 30 seconds in living cells following an environmental perturbation.

By parsing proteins that undergo redox reactions and those highly sensitive to ROS stress from the rest of the proteome, we can achieve a fuller understanding of photoautotrophic regulatory dynamics. To validate and extend our redox probing, we have also carried out complementary global proteomic, transcriptomic, confocal laser microscopy (See figure 3), and photophysiology measurements.

In total, our comprehensive approach provides a more thorough understanding of redox signaling that will facilitate optimization of photosynthetic cellular output. Our work in this area was covered in Chemical & Engineering News.  Our most recent manuscript in this area of research describes the alleviation of oxidative stress by the nifHDK complex in Cyanothece during photobiological hydrogen production (Applied & Environmental Microbiology 2016).

[6] Activity-Based Protein Profiling for Lignocellulose-Based Biofuel Applications

Microbial degradation and fermentation of lignocellulosic biomass is a key strategy being investigated in renewable energy research. Cellulolytic microbes and microbial communities are capable of producing β-glucosidases, endo- and exoglucanases, and other glycoside hydrolases to facilitate the degradation of highly recalcitrant cellulose and related plant cell wall polysaccharides. Towards this end, we developed a large suite of activity-based probes for identifying the functional enzymes involved in cellulose deconstruction published in the J. Am. Chem. Soc, 2012. This suite of probes has been applied to characterize the functional assemblage of the cell-adherent cellulosome structure in the anaerobic bacterium Clostridium thermocellum, and to rapidly identify alterations to cellulolytic activity upon industry- and biorefinery-relevant perturbations in the established biofuel platform production fungi Trichoderma reesei (Molecular Biosystems, 2013).  Most recently we have worked closely with Michelle O’Malley of UCSB to perform proteomic analyses of fungal lignocellulose degraders.  This research resulted in a publication in Science 2016 characterizing a fungal cellulosome system. Stay on the lookout for a follow on study that is now in review.  Below, Figure 3, shows a general schematic of how we want to use chemical probes and other experiments to understand microbe and microbiome lignocellulose degrading activities.  This work ties in with the soil studies described above.

Figure 3. To elucidate and annotate the concert of lignocellulose deconstruction, catabolite transport, and intracellular metabolic activities in microbes and microbiomes we develop ABPP approaches coupled to other experimental techniques. To understand lignocellulose deconstruction we can measure extracellular oxidative lignin depolymerizing enzymes (A) and cellulose degrading enzymes (B), the transport mechanisms for aromatic (C) and carbohydrate (D) catabolites, and the intracellular metabolic activities associated with aromatic (E) and carbohydrate (F) catabolites. Critical associations (G) between lignin depolymerization and cellulose degradation are also of high interest to us, as our microbe-microbe interactions that facilitate lignocellulose deconstruction (Pill/Pac-Man shapes indicate proteins and enzymes).

Research Highlights from PNNL:

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