Search for: All records

Abstract The tenets of intelligent biological systems are (i) scalable decision-making, (ii) inheritable memory, and (iii) communication. This study aims to increase the complexity of decision-making operations beyond standard Boolean logic, while minimizing the metabolic burden imposed on the chassis cell. To this end, we present a new platform technology for constructing genetic circuits with multiple OUTPUT gene control using fewer INPUTs relative to conventional genetic circuits. Inspired by principles from quantum computing, we engineered synthetic bidirectional promoters, regulated by synthetic transcription factors, to construct 1-INPUT, 2-OUTPUT logical operations—i.e. biological QUBIT and PAULI-X logic gates—designed as compressed genetic circuits. We then layered said gates to engineer additional quantum-inspired logical operations of increasing complexity—e.g. FEYNMAN and TOFFOLI gates. In addition, we engineered a 2-INPUT, 4-OUTPUT quantum operation to showcase the capacity to utilize the entire permutation INPUT space. Finally, we developed a recombinase-based memory operation to remap the truth table between two disparate logic gates—i.e. converting a QUBIT operation to an antithetical PAULI-X operation in situ. This study introduces a novel and versatile synthetic biology toolkit, which expands the biocomputing capacity of Transcriptional Programming via the development of compressed and scalable multi-INPUT/OUTPUT logical operations. 

Abstract Synthetic biologists seek to engineer intelligent living systems capable of decision-making, communication, and memory. Separate technologies exist for each tenet of intelligence; however, the unification of all three properties in a living system has not been achieved. Here, we engineer completely intelligentEscherichia colistrains that harbor six orthogonal and inducible genome-integrated recombinases, forming Molecularly Encoded Memory via an Orthogonal Recombinase arraY (MEMORY). MEMORY chassis cells facilitate intelligence via the discrete multi-input regulation of recombinase functions enabling inheritable DNA inversions, deletions, and genomic insertions. MEMORY cells can achieve programmable and permanent gain (or loss) of functions extrachromosomally or from a specific genomic locus, without the loss or modification of the MEMORY platform – enabling the sequential programming and reprogramming of DNA circuits within the cell. We demonstrate all three tenets of intelligence via a probiotic (Nissle 1917) MEMORY strain capable of information exchange with the gastrointestinal commensalBacteroides thetaiotaomicron. 

Abstract Here we present a technology to facilitate synthetic memory in a living system via repurposing Transcriptional Programming (i.e., our decision-making technology) parts, to regulate (intercept) recombinase function post-translation. We show that interception synthetic memory can facilitate programmable loss-of-function via site-specific deletion, programmable gain-of-function by way of site-specific inversion, and synthetic memory operations with nested Boolean logical operations. We can expand interception synthetic memory capacity more than 5-fold for a single recombinase, with reconfiguration specificity for multiple sites in parallel. Interception synthetic memory is ~10-times faster than previous generations of recombinase-based memory. We posit that the faster recombination speed of our next-generation memory technology is due to the post-translational regulation of recombinase function. This iteration of synthetic memory is complementary to decision-making via Transcriptional Programming – thus can be used to develop intelligent synthetic biological systems for myriad applications. 

Allosteric function is a critical component of many of the parts used to construct gene networks throughout synthetic biology. In this review, we discuss an emerging field of research and education, biomolecular systems engineering, that expands on the synthetic biology edifice—integrating workflows and strategies from protein engineering, chemical engineering, electrical engineering, and computer science principles. We focus on the role of engineered allosteric communication as it relates to transcriptional gene regulators—i.e., transcription factors and corresponding unit operations. In this review, we ( a) explore allosteric communication in the lactose repressor LacI topology, ( b) demonstrate how to leverage this understanding of allostery in the LacI system to engineer non-natural BUFFER and NOT logical operations, ( c) illustrate how engineering workflows can be used to confer alternate allosteric functions in disparate systems that share the LacI topology, and ( d) demonstrate how fundamental unit operations can be directed to form combinational logical operations.