Research Overview

The Wilson Research Laboratory at Georgia Institute of Technology - School of Chemical and Biomolecular Engineering, seeks to engineer novel, non-natural biological systems of bespoke function for high impact applications — while advancing our fundamental knowledge of protein and genetic structure-function relationships. The Wilson lab leverages a unique blend of iterative protein engineering and genetic engineering to design novel synthetic biological systems (i.e., biomolecular systems engineering). Our current focus is in the area of engineering cooperative systems of functional proteins and cognate genetic elements. To accomplish our goals, we employ workflows that involve rational protein design, synthetic biology, computational modeling, and laboratory evolution. These studies represent the most rigorous test of our understanding of structure-function and phylogenetic relationships; in addition to, promoting the development of novel biological tools that will benefit society.

Project Descriptions

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Project 1

Engineering Advanced Logical Operations for Gene Control.

Description

The control of gene expression is an important tool for metabolic engineering, the design of synthetic gene networks, gene-function analysis, drug discovery and biopharmaceutical manufacturing. Several strategies have been developed to regulate gene expression and target protein production at different biosynthetic levels. The most widely used regulatory elements focus on blocking or activating mRNA synthesis by inducible coupling of transcriptional repressors or activators to constitutive or minimal promoters. Our long-term goal is to rationally design a new class of proteins that regulate gene expression, in which we can confer modulated DNA binding function that is responsive to specific exogenous cues and logical operations. This goal will require the complementary understanding and design of allosteric communication and functional molecular interactions (i.e., protein-ligand, protein-protein, and protein-DNA). To date we have engineered a set of novel gene regulatory proteins with antilac function (i.e., the inverse of wild-type function); this work was recently reported in the journal Protein Engineering Design & Selection (Protein Engineering Design & Selection (2013) 26, 433-443). In addition, in our most recent effort we have engineered alternate allosteric communication in the LacI scaffold creating 14 novel anti-lacs with variable ligand sensitivity and temporal gene regulation, (Richards, D.H, et al. 2017 – ACS Synthetic Biology PMID: 27598336). The aforementioned work was summarized (in the context of other work) in a Review Article we recently published (Davey and Wilson (2017) WIREs Nanomedicine & Nanobiotechnology). This project has been supported by federal funds from the National Science Foundation [CBET Award No. 1133834 (2011-2014)] and National Institute of Health [GM008283-26 (2013-2015)].

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Project 2

Examining the Origins of Engineered Allosteric Networks.

Description

The means by which proteins communicate with their environment is critical to many life processes and will be required for the development of next-generation biotechnologies. Allosteric communication is the principal means by which proteins translate an environmental signal into a useful response (e.g., gene expression). Understanding the detailed mechanism of allostery is a vexing problem. Despite more than three decades of study this fundamental mode of biological communication remains unsolved at the molecular level. A thorough understanding of allosteric communication will facilitate the development of new protein design rules. The design of bespoke allosteric functions promises to revolutionize biotechnology, namely with regard to the development of more competent biological drugs, diagnostic tools, and industrial processes. These technological advances will be achieved by enabling precise and predictable biological communication in response to desired environmental cues. The goal of this study is to decipher the underlying molecular mechanism by which the allosteric signal traverses the scaffold across a number of engineered transcription variants with alternate allosteric control. This study will be accomplished by the construction and characterization of a synthetic phylogenetic tree of alternate allosteric networks. To complement inferred evolutionary relationships, experimental maps of communication will be constructed for two or more linages. Members of a given linage will be evaluated biophysically to decipher the underlying molecular mechanism. Phylogenetic and biophysical data will be leveraged to design alternate allosteric routes in certain engineered transcription scaffold in which we confer precise performance metrics (i.e., tuned dynamic range, ligand sensitivity and temporal responsiveness). This study will enable us to identify whether allostery in the LacI scaffold can be conferred via multiple networks of residues, or whether allostery requires a single conserved network of residues. Upon completion, this study will enable us to test our assertions with regard to the origin and molecular mechanics of alternate allosteric communication via the development of design rules for specific allosteric operations. In turn this algorithm will produce novel transcription factors for use in a broad range of biotechnological applications, specifically in the area of synthetic biology. In addition, this study will significantly broaden our fundamental understanding of allosteric communication.

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Project 3

Engineering Intelligent Microbes.

Description

Human stem cells have emerged as one of the most exciting resources in biotechnology, promising to revolutionize the treatment of heart disease, diabetes in addition to other diseases that require organ and tissue replacement. Stem cells have the unique ability to become specialized cells (e.g., muscle, neurological, immune) through a process called differentiation. Stem cells (or progenitor cells) differentiate into specific cell types with disparate functions via timing and order of transcription factor activation. In contrast, bacteria cells lack the ability to differentiate, thus cannot be induced to become specialized. However, through iterative protein and genetic engineering the edifice for the development of synthetic microbial “stem cells” can be realized. The engineering workflow to confer microbial differentiation will require the development of a synthetic memory structure to facilitate long term storage of information, and the design of complementary decision-making genetic programs that will enable the activation of bespoke genetic networks. The specific goal of this project is to create synthetic microbial stem cells. This objective will require the development of a genetic MEMORY structure that can rapidly rearrange genetic control infrastructures, resulting in genetic structural changes that persist in forward generations of the cell line - even after the initiation stimuli are removed. In addition, this goal will require the development of a dynamic synthetic transcriptional programming edifice that can generate two or more different combinational logical operations (i.e., programs) that are differentially responsive to INPUT signal combinations, facilitating two or more non-synonymous states of specialization. Successful completion of the proposed work will result in a significant paradigm shift in biomolecular systems engineering, and the development of schema and workflows for scalable genetic MEMORY structures and dynamic systems programming. The resulting biomolecular systems engineering edifice will revolutionize synthetic biology and metabolic engineering via the production of bespoke microbial progenitor cells that can evolve on cue, producing two or more states of disparate specialization.

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Project 4

The Rational Design of Energy Transfer Protein Systems.

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Project 5

Generalized Concepts for the Engineering of Protein Structural and Functional Stability.

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