Biology subjects

Lazar, J. T.

Publications and source records attributed to Lazar, J. T..

3 recordsLinked to original sources

bioRxiv2026

Cell-free pathway prototyping enables cost-effective biomanufacturing of 1,2,4-butanetriol at the 1-L scale

Biomanufacturing offers sustainable alternatives to chemical synthesis under lower temperatures and pressures than traditional catalytic methods. However, the slow pace and iterative engineering bottlenecks of cell strain development restrict the feasible biological design space. Cell-free systems circumvent these constraints, providing a flexible and high-throughput screening approach to accelerate pathway prototyping and enzyme optimization but are not typically used for manufacturing scale-up. To understand the scalability of cell-free biosynthesis, we establish an end-to-end fully cell-free architecture to discover, develop, and scale the biosynthesis of 1,2,4-butanetriol (BT), a high-value industrial platform chemical. First, we systematically screened ~150 enzymes across the 4-step pathway from xylose to BT to identify highly active homologs for each reaction. Next, we applied statistical Design of Experiments to optimize reaction formulations for cost and titer. Finally, the maximum-titer and minimum-cost formulations were scaled up across five orders of magnitude, from 10-{micro}L to 1-L reactions. This resulted in peak volumetric productivities of ~1 g/L/h and yields over 13 g of BT in a single 1-L reaction, with raw substrate costs totaling just $3.00 per liter. This work expands the diversity of enzymes tested for BT synthesis and establishes a blueprint for advancing industrial biochemical manufacturing fully in vitro.

synthetic biology↗

bioRxiv2026

Machine learning guided cell-free expression maps the biochemical landscape of carbonic anhydrase

Carbonic anhydrases are among the fastest known biocatalysts, reversibly facilitating the hydration of CO2 to HCO3- at rates up to 107 s-1, which warrants their investigation for industrial carbon capture technologies. However, engineering carbonic anhydrases to maintain stability under harsh industrial process conditions remains a key challenge, and sequence-to-function datasets compatible with machine learning to inform forward engineering are lacking. Here, we developed a high-throughput platform that couples cell-free gene expression with a gaseous CO2 colorimetric assay to map the fitness landscapes of carbonic anhydrases. From 96 diverse natural homologs, we identified a robust variant from the Aquificota phylum and conducted an exhaustive mutational scan and functional assessment of this enzyme at 70{degrees}C and 90{degrees}C, covering >99% of all single-amino acid substitutions (totaling 4,365 mutations assayed in 39,285 reactions). This biochemical landscape was used to benchmark 22 zero-shot protein fitness models and identify critical mutations that improved enzyme stability at 90{degrees}C by more than three-fold. We then used both zero-shot protein language models and supervised learning to filter 419 model-generated variants from a ProteinMPNN library of 100,000 sequences, leading to a best-in-class enzyme that retained activity after incubation at 95{degrees}C. This work demonstrates that integrating cell-free enzyme engineering with machine learning enables opportunities for high-throughput experimental measurements to benchmark and improve protein language models, accelerate design loops, and expand functional exploration within protein families where experimental information is limited.

synthetic biology↗

bioRxiv2019

Dynamic control of pathway expression with riboregulated switchable feedback promoters

Dynamic pathway regulation has emerged as a promising strategy in metabolic engineering for improved system productivity and yield, and continues to grow in sophistication. Bacterial stress-response promoters allow dynamic gene regulation using the hosts natural transcriptional networks, but lack the flexibility to control the expression timing and overall magnitude of pathway genes. Here, we report a strategy that uses RNA transcriptional regulators to introduce another layer of control over the output of natural stress-response promoters. This new class of gene expression cassette, called a riboregulated switchable feedback promoter (rSFP), can be modularly activated using a variety of mechanisms, from manual induction to quorum sensing. We develop and apply rSFPs to regulate a toxic cytochrome P450 enzyme in the context of a Taxol precursor biosynthesis pathway and show this leads to 2.4x fold higher titers than from the best reported strain. We envision that rSFPs will become a valuable tool for flexible and dynamic control of gene expression in metabolic engineering, protein and biologic production, and many other applications.

synthetic biology↗