Biology subjects

Ducat, D.

Publications and source records attributed to Ducat, D..

5 recordsLinked to original sources

bioRxiv2025

Uncovering the Design Rules for Sustainable Growth of Mineralized Mycomaterials

Mycomaterials, materials made from filamentous fungi, have several advantages over traditional materials, such as their genetic programmability and self-healing properties. However, their lack of mechanical strength and cost of production often constrain the applications they can be used in. In this work, we take inspiration from natural systems to overcome these challenges by elucidating design principles for mineralization-based enhancement of mechanical strength and synthetic lichen-based low-cost growth. We demonstrate that surface display of an enzyme from sea sponges, silicatein , on the hyphae of the filamentous fungus Aspergillus niger enables mineralization of polysilicate and that this does not impact fungal growth. We also show that this strategy can be extended to other silicatein variants and characterize how the degree of mineralization can be modulated. We then demonstrate that mineralization enhances the mechanical properties of the mycelium, including its tensile strength, modulus, and toughness. Finally, we show how these reinforced mycelia can be grown without external carbon sources using a synthetic lichen-based co-culture to facilitate low cost biomanufacturing. Together, our results lay the groundwork for the sustainable production of mineralized mycomaterials and create a new model system to study how mineralization impacts growth and mechanical properties. Significance StatementMaterials made from filamentous fungi, called mycomaterials, have several advantages over traditional materials, but their poor mechanical properties and relatively high production costs have limited their application. We elucidated design principles to enable tunable mineralization of fungal mycelium and have shown that it does not impact growth but significantly enhances mechanical strength. We have also shown that these reinforced mycelia can be grown without any external carbon in a synthetic lichen like consortia to minimize production costs. This work creates a novel experimental system to study how mineralization impacts growth and mechanical properties and will facilitate the broader application of mycomaterials in the future.

synthetic biology↗

bioRxiv2025

HIGH CO2 LEVELS OVERCOME THE NIGHTTIME LETHALITY OF CIRCADIAN MUTANTS IN CYANOBACTERIA

Cyanobacteria have adapted to daily fluctuations in light intensity through a circadian clock that aligns their physiology and metabolism to the external daytime. In the model cyanobacterium Synechococcus elongatus PCC 7942, the rhythm generated by a molecular pacemaker is converted into a global transcriptional oscillation by the central regulator RpaA. Mutants in RpaA and other components have been instrumental in elucidating the clocks molecular architecture and physiological role. Extensive evidence suggests that one of the central functions of circadian regulation is to prevent the accumulation of reactive oxygen species (ROS) during nighttime. However, circadian mutants are unable to grow under natural day/night cycles and require constant illumination, hindering our ability to study the clock function during the night, a phase where circadian regulation is critical for redox homeostasis. Here, we show that the darkness lethality phenotype of circadian mutants can be overcome by high CO2 levels. When grown under a 3% CO2 atmosphere, RpaA-null mutants exhibited growth rates similar to the wt. An analysis of the ROS levels under different CO2 and light intensity conditions revealed carbon scarcity to be the most significant contributor to redox stress. Nighttime ROS accumulation can be modulated by CO2 abundance, an observation that will allow the characterization of heretofore lethal mutants in circadian regulation. The dispensability of the circadian clock in a high CO2 environment suggests that the clock may have evolved as an adaptation to the decrease in atmospheric CO2 levels that occurred after the Great Oxygenation Events, in the Paleoproterozoic era. IMPORTANCECyanobacterial circadian clocks are considered essential for survival under natural day/night conditions, and many circadian mutants are lethal under diel cycles. Results presented here challenge this assumption, showing that these mutants grow normally when CO2 is abundant. This suggests that the major adaptive role of the clock is to manage the redox stress caused by carbon limitation. By separating the effects of carbon availability from circadian control, we identify a key environmental factor that shaped the evolution of biological timekeeping. Using high CO2 to bypass clock dependency will allow the study of circadian function in otherwise lethal mutants. These findings reframe the clock as a specific adaptation to atmospheric carbon, stressing its key role in the regulation of the redox balance.

microbiology↗

bioRxiv2025

Autoinduction expression systems by AHL-mediated quorum-sensing circuits in Synechococcus elongatus PCC 7942

Despite significant potential for cyanobacteria as sustainable bioproduction chases, there are limited examples of scaled cyanobacterial bioproduction. In part, this is because most cyanobacterial species are poorly adapted to bioreactor cultivation conditions and lack features that facilitate biomass growth and harvesting at scale. We explored quorum sensing (QS) pathways derived from heterotrophic microbes as a method for autoinduction of gene expression circuits coordinated to population density in cyanobacteria. Here, we integrated genetic modules designed to produce and detect the diffusible QS signal, acyl-homoserine lactones (AHLs), in the cyanobacterial model, Synechococcus elongatus PCC 7942 (S. elongatus). We demonstrate that S. elongatus heterologously produces sufficient AHL signals to activate gene expression in a dose-dependent and population density-responsive manner. A hybrid combination of AHL synthesis enzyme from Vibrio fischeri (Lux system) with the transcription factor receiver from Pseudomonas aeruginosa (Las system) provides an ideal activation ratio and mitigates toxicity observed with some AHL systems. As a proof of concept, we coupled the QS pathway to the expression of a cell division inhibitory gene, cdv3, facilitating late-phase cell elongation, cell sedimentation, and improved biomass recovery. Our findings provide a foundation for the development of auto-induction systems leverageable to improve cyanobacterial biotechnology applications.

microbiology↗

bioRxiv2021

Investigating the growth of an engineered strain of Cyanobacteria with an Agent-Based Model and a Recurrent Neural Network

A computational framework combining Agent-Based Models (ABMs) and Deep Learning techniques was developed to help design microbial communities that convert light and CO2 into useful bioproducts. An ABM that accounts for CO2, light, sucrose export rate and cell-to-cell mechanical interactions was used to investigate the growth of an engineered sucrose-exporting strain of Synechococcus elongatus PCC 7942. The ABM simulations produced population curves and synthetic images of colony growth. The curves and the images were analyzed, and growth was correlated to nutrients availability and colonies initial spatial distribution. To speed up the ABM simulations, a metamodel based on a Recurrent Neural Network, RNN, was trained on the synthetic images of growth. This metamodel successfully reproduced the population curves and the images of growth at a lower computational cost. The computational framework presented here paves the road towards designing microbial communities containing sucrose-exporting Synechococcus elongatus PCC 7942 by exploring the solution space in silico first.

microbiology↗

bioRxiv2018

Current production as a rapid response expression reporter under micro-oxic and anoxic conditions

Inducible gene expression is crucial for regulating cellular processes and production of compounds within cellular pathways. Yet, inducing gene expression is only the first step to utilizing cellular processes for an applied purpose such as biosensors. Detecting when gene expression occurs is central to understanding the overall mechanism of the process as well as maximizing the process. Fluorescent proteins have been established as the primary tool for detecting gene expression in inducible systems. This study proposes electricity production as an alternate tool in reporting gene expression. Using a model organism for electricity production, Shewanella oneidensis MR-1, current was shown to be an efficient reporter for gene expression and comparable to superfolder green fluorescent protein (GFP). Through regulation of the lac operator and T7 promoter, current production was induced by isopropyl {beta}-D-1-thiogalactopyranoside (IPTG) addition. IPTG addition induced translation of GFP and the MtrB protein, which complemented a {triangleup}mtrB strain of S. oneidensis MR-1 and restored current production. This inducible system generated reproducible current in 18 minutes in both micro-oxic and anoxic conditions. These results show that current is a fast reporter for gene expression.\n\nFinancial DisclosureThe team was supported by the following departments and colleges at Michigan State University: College of Natural Science, College of Engineering, Biochemistry and Molecular Biology Department and Plant Research Laboratory. The team also received support from the DOE Great Lakes Bioenergy Research Center (DOE Office of Science BER DE-FC02-07ER64494) and startup funding from the Department of Molecular Biology and Biochemistry, Michigan State University and support from Michigan State University AgBioResearch (MICL02454) (to B.H.). This work was also supported by NSF CAREER (Award #1254238) to T.A.W. MSU Alpha Chi Sigma also supported the team.\n\nCompeting InterestsThe authors declare that no competing interests exist.\n\nEthics StatementN/A\n\nData AvailabilityAll data will be supplied upon request by the corresponding author.\n\nThis work was assessed during the iGEM/PLOS Realtime Peer Review Jamboree on 23rd February 2018 and has been revised in response to the reviewers comments.

synthetic biology↗