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Biology subjects

Specht, D. A.

Publications and source records attributed to Specht, D. A..

6 recordsLinked to original sources

Thermodynamic, Electrochemical and Practical Constraints on Electromicrobial Formate Assimilation

Electromicrobial production (EMP) technologies aim to combine renewable electricity, CO2, and engineered microbes to make energy-dense molecules at efficiencies exceeding photosynthesis. CO2 can be electrochemically reduced to formate, which is far easier to handle at the bench than H2 or an electrode, but formate carries only two electrons per carbon against the six in a biofuel. The remaining electrons must come from oxidizing additional formate, from H2 oxidation, or from extracellular electron uptake (EEU), and no rigorous comparison of these options coupled to the choice of carbon assimilation pathway currently exists. We calculate upper-limit efficiencies for butanol production by six carbon assimilation pathways, each paired with all three electron delivery mechanisms, using electrochemical parameters drawn from a survey of the recent literature. Electrical to butanol energy conversion efficiencies range from 35.5 to 51.7%, corresponding to solar-to-fuel efficiencies of 11.7 to 17%, so even the least efficient route exceeds the 8% theoretical ceiling of algal photosynthesis. The serine variant of the reductive glycine pathway reaches an electrical energy conversion efficiency of when using H2 oxidation, within 1.9 points of the most efficient pathway, and is the only high-efficiency option that tolerates O2. This makes an EMP system that combines electron delivery by formate coupled with the serine variant of reductive glycine pathway highly attractive, as it presents few barriers to rapid, iterative engineering in the lab, and a high theoretical ceiling. Drawing both carbon and electrons from formate costs 6.2 points against H2 at a state-of-the-art whole-cell voltage (2.2 V). However, this small penalty is amplified three-fold by any rise in the CO2-to-formate cell voltage, and reaches 13.5 points at the highest whole-cell voltages reported for scaled-up CO2-to-formate electrolyzers, where formate-only operation falls to 11.2 electrical-to-fuel and 3.7% solar-to-fuel efficiency, below the ceiling of photosynthesis, against 24.7 and 8.1% for H2 (only just above algal photosynthesis). Our choice between a formate-only system and one coupled to H2 oxidation or EEU therefore depends on our belief about the trajectory of CO2 reduction technology. If whole-cell voltages continue to fall at the rate of the past decade, formate alone is the right target, and the simplicity of its workflow is bought at low cost. However, if that improvement plateaus, the electron delivery mechanism must be swappable, and a system should be designed from the outset so that it can be. At the US Department of Energy SunShot target of 2 cents per kilowatt hour, the electricity to make a US gallon of butanol costs $1.40 for a formate-only system at the state of the art, rising to $5.45 at the highest scaled-up electrolyzer voltage reported, against $1.23 and $2.47 for formate and H2 system.

synthetic biology↗

Efficient Natural Plasmid Transformation of Vibrio natriegens Enables Zero-capital Molecular Biology

The fast-growing microbe Vibrio natriegens is capable of natural transformation where it draws DNA in from media via an active process under physiological conditions. Using an engineered strain with a genomic copy of the master competence regulator tfoX from Vibrio cholera in combination with a new minimal competence media (MCM) that uses acetate as an energy source, we demonstrate naturally competent cells which are created, transformed, and recovered entirely in the same media, without exchange or addition of new media. Cells are naturally competent to plasmids, recombination with linear DNA, and co-transformation of both to select for scarless and markerless genomic edits. The entire process is simple and inexpensive, requiring no capital equipment for an entirely room temperature process (Zero Capital protocol, 104 cfu/{micro}g), or just an incubator (High Efficiency protocol, 105-6 cfu/{micro}g). These cells retain their naturally competent state when frozen and are transformable immediately upon thawing like a typical chemical or electrochemical competent cell. Since the optimized transformation protocol requires only 50 minutes of hands-on time, and V. natriegens grows quickly even on plates, a transformation started at 9 AM yields abundant culturable single colonies by 5 PM. Further, because all stages of transformation occur in the same media, and the process can be arbitrarily scaled in volume, this natural competence strain and media could be ideal for automated directed evolution applications. As a result, naturally competent V. natriegens could compete with E. coli as an excellent chassis for low-cost and highly scalable synthetic biology.

synthetic biology↗

Efficiency Estimates for Electromicrobial Production of Branched-chain Hydrocarbons

Electromicrobial production is a process where microorganisms use electricity as a charge and energy source for the production of complex molecules, often from starting compounds as simple as CO2. The aviation industry is in need for sustainable fuel alternatives that can meet their requirements of high-altitude performance while also meeting 21st century carbon emissions standards. The electromicrobial production of jet fuel components with CO2-derived carbon provides a unique opportunity to generate jet fuel blends that are compatible with modern engines with net-neutral carbon emissions. In this study, we analyze the pathways necessary to generate single- and multi-branched-chain hydrocarbons in vivo utilizing both extracellular electron uptake (EEU) and H2-oxidation as methods for electron delivery, the Calvin cycle for CO2-fixation and the ADO decarboxylation pathway. We find the maximum electrical-to-fuel energy conversion efficiencies for single- and multi-branched chain hydrocarbons are [Formula] and [Formula]. Utilizing this information, as well as previously collected predictions on straight-chain alkane and terpenoid biosynthesis, we calculate the efficiency of electromicrobial production of jet fuel blends containing straight-chain, branched-chain, and terpenoid components. Increasing the fraction of branched-chain alkanes in the blend from zero to 47% only lowers the electrical energy conversion efficiency from [Formula] to [Formula].

synthetic biology↗

Upper Limit Efficiency Estimates for Electromicrobial Production of Drop-In Jet Fuels

Microbes which participate in extracellular electron uptake or H2 oxidation have an extraordinary ability to manufacture organic compounds using electricity as the primary source of metabolic energy. So-called electromicrobial production could be of particular value in the efficient production of hydrocarbon blends for use in aviation. Because of exacting standards for fuel energy density and the costs of new aviation infrastructure, liquid hydrocarbon fuels will be necessary for the foreseeable future, precluding direct electrification. Production of hydrocarbons using electrically-powered microbes employing fatty acid synthesis-based production of alkanes could be an efficient means to produce drop-in replacement jet fuels using renewable energy. Here, we calculate the upper limit electrical-to-energy conversion efficiency for a model jet fuel blend containing 85% straight-chain alkanes and 15% terpenoids. When using the Calvin cycle for carbon-fixation, the energy conversion efficiency is [Formula] when using extracellular electron uptake for electron delivery and [Formula] when using H2-oxidation. The efficiency of production of the jet fuel blend can be raised to [Formula] when using the Formolase formate-assimilation pathway and H2-oxidation, and to [Formula] with the Wood-Ljungdahl pathway. The production efficiency can be further raised by swapping the well-known ADO pathway for alkane termination with for the recently discovered MCH pathway. If these systems were were supplied with electricity with a maximally-efficient silicon solar photovoltaic, even the least efficient would exceed the maximum efficiency of all known forms of photosynthesis.

synthetic biology↗

Overcoming leak sensitivity in CRISPRi circuits using antisense RNA sequestration and regulatory feedback

The controlled binding of the catalytically-dead CRISPR nuclease (dCas) to DNA can be used to create complex, programmable transcriptional genetic circuits, a fundamental goal of synthetic biology. This approach, called CRISPR interference (CRISPRi), is advantageous over existing methods because the programmable nature of CRISPR proteins enables the simultaneous regulation of many different targets without crosstalk. However, such gene circuit elements are limited by 1) the sensitivity to leaky repression of CRISPRi logic gates and 2) retroactive effects owing to a shared pool of dCas proteins. By utilizing antisense RNAs (asRNAs) to sequester guide RNA transcripts, as well as CRISPRi feedback to self-regulate asRNA production, we demonstrate a mechanism that suppresses unwanted CRISPRi repression and improve logical gene circuit function in E. coli. This improvement is particularly pronounced during stationary expression when CRISPRi circuits do not achieve the expected regulatory dynamics. Further, the use of dual CRISPRi/asRNA inverters restores logical performance of layered circuits such as a double inverter. By studying circuit induction at the single cell level in microfluidic channels, we provide insight into the dynamics of antisense sequestration of gRNA and regulatory feedback on dCas-based repression and derepression. These results demonstrate how CRISPRi inverters can be improved for use in more complex genetic circuitry without sacrificing the programmability and orthogonality of dCas proteins.

synthetic biology↗

Massively parallel CRISPRi assays reveal concealed thermodynamic determinants of dCas12a binding

The versatility of CRISPR-Cas endonucleases as a tool for biomedical research has lead to diverse applications in gene editing, programmable transcriptional control, and nucleic acid detection. Most CRISPR-Cas systems, however, suffer from off-target effects and unpredictable non-specific binding that negatively impact their reliability and broader applicability. To better evaluate the impact of mismatches on DNA target recognition and binding, we develop a massively parallel CRISPR interference (CRISPRi) assay to measure the binding energy between tens of thousands of CRISPR RNA (crRNA) and target DNA sequences. By developing a general thermodynamic model of CRISPR-Cas binding dynamics, our results unravel a comprehensive map of the energetic landscape of Francisella novicida Cas12a (FnCas12a) as it searches for its DNA target. Our results reveal concealed thermodynamic factors affecting FnCas12a DNA binding which should guide the design and optimization of crRNA that limit off-target effects, including the crucial role of an extended PAM sequence and the impact of the specific base composition of crRNA-DNA mismatches. Our generalizable approach should also provide a mechanistic understanding of target recognition and DNA binding when applied to other CRISPR-Cas systems.

biophysics↗