About

Jonathan M. Conway is an Assistant Professor of Chemical and Biological Engineering at Princeton University. He earned his Ph.D. in Chemical Engineering from North Carolina State University in 2017, along with a Master's degree from the same institution in 2013, and a Bachelor's degree from the University of Notre Dame in 2011. His research focuses on defining and engineering plant-microbe and microbe-microbe interactions at plant-microbe interfaces, which influence plant growth, health, and productivity, as well as the decomposition of plant biomass. Conway's lab employs genetic engineering of non-model bacteria and biomolecular engineering of their products to understand these complex ecosystems and develop new technologies for bio-agriculture, bio-energy, and bio-chemical industries. He has received numerous awards for his mentorship, research, and innovation, including the Excellence in Mentoring Award from Princeton Engineering and the James K. Ferrell Outstanding Ph.D. Graduate Award from NC State.

Research topics

• Biology
• Computer Science
• Genetics
• Computational biology
• Evolutionary biology
• Ecology
• Library science
• Botany
• Neuroscience
• Data science
• World Wide Web
• Astronomy
• Bioinformatics
• Epistemology

Selected publications

• Eastman, Samuel (2026) "Sequencing data"

  Open MIND · 2026-03-06

  datasetSenior author

  Genome sequencing for PsJN derivatives JC012, JC012OC1, JC012OC2, and JC012OC3 performed by Plasmidsaurus. Plasmid sequencing for MF224-reisolated pNoc variants pNocOC1, pNocOC2, pNocOC3, pNocOC4, pNocOC6, and pNocOC9 performed by Azenta.

  DOI

• Eastman, Samuel (2026) "Sequencing data"

  Mendeley Data · 2026-03-06

  datasetOpen accessSenior author

  Genome sequencing for PsJN derivatives JC012, JC012OC1, JC012OC2, and JC012OC3 performed by Plasmidsaurus. Plasmid sequencing for MF224-reisolated pNoc variants pNocOC1, pNocOC2, pNocOC3, pNocOC4, pNocOC6, and pNocOC9 performed by Azenta.

  PublisherDOI

• A robust enzymatic reporter system for the extremely thermophilic anaerobic bacterium Anaerocellum bescii

  Frontiers in Microbiology · 2026-01-29

  articleOpen accessSenior authorCorresponding

  Thermophilic anaerobic organisms, particularly species that can naturally degrade lignocellulosic biomass, show great promise for next generation bioprocessing. This has led to the development of nascent genetic systems to metabolically engineer these non-model organisms. However, a major challenge remains a lack of reliable reporter systems compatible with the combination of thermophilic and anaerobic growth conditions. Additionally, native glycoside hydrolases in these organisms limit the usefulness of traditional glycosidic enzyme reporters (e.g., LacZ) because of the native background activity present on para-nitrophenyl glycoside substrates. Here we describe the development of a robust enzymatic reporter system that overcomes these challenges in Anaerocellum (f. Caldicellulosiruptor ) bescii , an anaerobic, extremely thermophilic (T opt ~ 78 °C), lignocellulolytic bacterium. Our method is based on heterologous expression of hyperthermophilic archaeal galactosidases: an ⍺-galactosidase from Pyroccous furiosus ( Pf ⍺gal), and a β-galactosidase from Caldivirga maquilingensis ( Cm βgal). We show that these reporters produce strong, orthogonal signals on colorimetric substrates at high temperatures (≥90 °C) that eliminate background activity from endogenous galactosidases. We then demonstrate the capability of Cm βgal, the stronger of the two reporters, to distinguish differences in levels of expression between A. bescii promoter sequences, which we verify through qRT-PCR. With its high signal to noise ratio and relative ease of use, this reporter system offers a straightforward and robust method for assessing protein expression in A. bescii and potentially other anaerobic thermophilic organisms, opening doors to improved genetic tools and metabolic engineering applications for industrial biotechnology.

  PublisherOA PDFDOI

• A Straightforward and Robust Enzymatic Reporter System for Anaerobic Thermophiles

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-23

  preprintSenior authorCorresponding

  Abstract Thermophilic anaerobic organisms, particularly species that can naturally degrade lignocellulosic biomass, show great promise for next generation bioprocessing. This has led to the development of nascent genetic systems to metabolically engineer these non-model organisms. However, a major challenge remains a lack of reliable reporter systems compatible with the combination of thermophilic and anaerobic growth conditions. Additionally, native glycoside hydrolases in these organisms limit the usefulness of traditional glycosidic enzyme reporters (e.g. LacZ) because of the native background activity present on para-nitrophenyl glucoside substrates. Here we describe the development of a straightforward and robust enzymatic reporter system that overcomes these challenges in Anaerocellum (f. Caldicellulosiruptor ) bescii, an anaerobic, extremely thermophilic (T opt ∼78 °C), lignocellulolytic bacterium. Our method is based on heterologous expression of hyperthermophilic archaeal galactosidases: an α-galactosidase from Pyroccous furiosus ( Pf αgal), and a β-galactosidase from Caldivirga maquilingensis ( Cm βgal). We show that these reporters produce strong, orthogonal signals on colorimetric substrates at high temperatures (≥90°C) that eliminate background activity from endogenous galactosidases. We then demonstrate the capability of Cm βgal, the stronger of the two reporters, to distinguish differences in levels of expression between A. bescii promoter sequences, which we verify through qRT-PCR. With its high signal to noise ratio and ease of use, this reporter system offers a reliable method for assessing protein expression in anaerobic thermophilic organisms, opening doors to improved genetic tools and metabolic engineering applications for industrial biotechnology.

  PublisherDOI

• Maltodextrin transport in the extremely thermophilic, lignocellulose degrading bacterium <i>Anaerocellum bescii</i> (f. <i>Caldicellulosiruptor bescii</i> )

  Journal of Bacteriology · 2025-05-01 · 3 citations

  articleOpen accessSenior author

  ABSTRACT Sugar transport into microbial cells is a critical, yet understudied step in the conversion of lignocellulosic biomass to metabolic products. Anaerocellum bescii (formerly Caldicellulosiruptor bescii ) is an extremely thermophilic, anaerobic bacterium that readily degrades the cellulose and hemicellulose components of lignocellulosic biomass into a diversity of oligosaccharide substrates. Despite significant understanding of how this microorganism degrades lignocellulose, the mechanisms underlying its highly efficient transport of the released oligosaccharides into the cell are comparatively underexplored. Here, we identify and characterize the ATP-binding cassette (ABC) transporters in A. bescii governing maltodextrin transport. Utilizing past transcriptomic studies on Anaerocellum and Caldicellulosiruptor species, we identify two maltodextrin transporters in A. bescii and express and purify their substrate-binding proteins (Athe_2310 and Athe_2574) for characterization. Using differential scanning calorimetry and isothermal titration calorimetry, we show that Athe_2310 strongly interacts with shorter maltodextrins, such as maltose and trehalose, with dissociation constants in the micromolar range, while Athe_2574 binds longer maltodextrins, with dissociation constants in the sub-micromolar range. Using a sequence-structure-function comparison approach combined with molecular modeling, we provide context for the specificity of each of these substrate-binding proteins. We propose that A. bescii utilizes orthogonal ABC transporters to uptake malto-oligosaccharides of different lengths to maximize transport efficiency. IMPORTANCE Here, we reveal the biophysical and structural basis for oligosaccharide transport by two maltodextrin ATP-binding cassette (ABC) transporters in Anaerocellum bescii . This is the first biophysical characterization of carbohydrate uptake in this organism and establishes a workflow for characterizing other oligosaccharide transporters in A. bescii and similar biomass-degrading thermophiles of interest for lignocellulosic bioprocessing. By deciphering the mechanisms underlying high-affinity sugar uptake in A. bescii , we shed light on an underexplored step between extracellular lignocellulose degradation and intracellular conversion of sugars to metabolic products. This understanding will expand opportunities for harnessing sugar transport in thermophiles to reshape lignocellulose bioprocessing as part of a renewable bioeconomy.

  PublisherDOI

• Structural insights into xyloglucan recognition by an ABC transporter from a Gram-positive, thermophilic bacterium

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-14

  articleOpen accessSenior authorCorresponding

  Abstract Xyloglucan (an α-1,6-xylosyl–substituted β-1,4-glucan) is a major hemicellulose of the primary cell wall of many plants and an important growth substrate for biomass-degrading bacteria in diverse ecological niches, including the gut microbiome and hot springs. In Gram-positive bacteria, xyloglucan is deconstructed into soluble oligosaccharides in the extracytoplasmic space before import by ATP-Binding Cassette (ABC) transporters, but the structural basis for this process remains poorly understood. Here, we identified an ABC transporter for xyloglucan uptake (Athe_2052-2054) in the Gram-positive, plant biomass-degrading thermophile Anaerocellum bescii , which is conserved across the Anaerocellum genus. We solved the apo crystal structure of its extracellular substrate-binding protein (SBP), Athe_2052, revealing a unique tertiary fold found only in a small subset of SBPs that bind complex oligosaccharides. This structure represents the first ABC SBP known to bind xyloglucan oligosaccharides. Biophysical analysis showed that while Athe_2052 binds unsubstituted β-glucan chains, recognition of xyloglucan side chains in the binding pocket markedly increases affinity (K d = 14 nM) for xyloglucan heptasaccharide (XXXG), the principal oligosaccharide released during xyloglucan deconstruction. Molecular modeling revealed that xyloglucan heptasaccharide, owing to its branched substitutions, is bound in a distinct conformation compared to unsubstituted β-glucans. This represents a unique mode of xyloglucan recognition driven by α-linked side-chain interactions rather than β-glucan backbone recognition alone. Together, these findings provide the first structural basis for xyloglucan oligosaccharide recognition by an ABC transporter in Gram-positive bacteria.

  PublisherDOI

• Designing thermophilic, synthetic microbial communities for consolidated bioprocessing

  BioDesign Research · 2025-04-21 · 2 citations

  reviewOpen accessSenior authorCorresponding

  Lignocellulose-derived fuels and chemicals are vital to breaking the world's dependence on fossil fuels. Though plant biomass is notoriously resistant to deconstruction, lignocellulolytic thermophiles are especially adept at degrading its constituent polysaccharides into mono- and oligo-saccharides for catabolism. And many thermophiles, whether lignocellulolytic or not, can be engineered to ferment lignocellulose-derived sugars into valuable fuels and chemicals as part of consolidated bioprocesses. Although the past twenty years have seen major advances in the genetic and metabolic engineering of individual thermophiles, the strategy of co-culturing thermophilic strains as part of synthetic communities has not been well established. Synthetic communities unlock synergistic interactions that outperform monocultures, thereby enhancing product titers, rates, and yields. While limited genetic tools once hindered the development of synthetic thermophilic communities, recent advances now offer robust systems for engineering these industrially relevant organisms. Here, we propose that this expanded genetic malleability enables engineering of 1) transport specialization to reduce substrate competition between strains and 2) division of labor strategies whereby one strain focuses on lignocellulose deconstruction while another strain dedicates metabolic burden for product synthesis. We draw on examples of engineered thermophiles like Clostridium thermocellum, Thermoanaerobacter saccharolyticum, and Anaerocellum bescii to illustrate how these mechanisms have been applied in thermophilic co-cultures. In brief, this perspective outlines design principles to construct effective thermophilic communities for lignocellulose bioprocessing.

  PublisherDOI

• Functional and structural characterization of AtAbf43C: An exo-1,5-α-L-arabinofuranosidase from Acetivibrio thermocellus DSM1313

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-06

  preprintOpen accessSenior authorCorresponding

  The Acetivibrio thermocellus DSM1313 genome codes for seven predicted glycoside hydrolase family 43 (GH43) enzymes, four of which remain uncharacterized. This study describes the function and structure of one such enzyme, AtAbf43C, from GH43 subfamily 26 (GH43_26) which acts as an α-L-arabinofuranosidase (EC 3.2.1.55). AtAbf43C is active on para-nitrophenol-α-L-arabinofuranoside (pNPAra), with optimal activity observed at pH 5.5 and 65 ℃. Multiple crystal structures of AtAbf43C were obtained, in which an N-terminal carbohydrate binding module family 42 (CBM42) domain displays a β-trefoil type fold and the C-terminal GH43 domain displays a canonical 5-bladed β-propeller motif. One structure, which was solved with two L-arabinofuranose molecules bound to β- and γ-subdomains of the CBM42, builds upon previous literature suggesting the α-binding pocket of the AtAbf43C CBM42 is non-functional. Furthermore, structural alignment with the substrate bound structure of a closely homologous GH43_26 exo-α-1,5-arabinofuranosidase, SaAraf43A from Streptomyces avermitilis (PDB 3AKH), allowed for identification of the conserved catalytic triad via site-directed mutagenesis in AtAbf43C, as well as insight into the deep-narrow topology of the AtAbf43C binding pocket that suggested it would be active on similar arabino-oligosaccharide (AOS) substrates as SaAraf43A. Subsequent liquid chromatography-mass spectrometry (LC-MS) analysis of polysaccharides and oligosaccharides hydrolyzed by AtAbf43C provides experimental evidence confirming this enzyme acts in an exo manner primarily towards α-1,5 linked arabino-oligosaccharides.

  PublisherOA PDFDOI

• A highly conserved ABC transporter mediates cello-oligosaccharide uptake in the extremely thermophilic, lignocellulolytic bacterium <i>Anaerocellum bescii</i> (f. <i>Caldicellulosiruptor bescii</i> )

  Applied and Environmental Microbiology · 2025-12-18

  articleOpen accessSenior author

  ABSTRACT Cellulose deconstruction and utilization are foundational to renewable biofuel and biochemical production. Anaerocellum bescii (formerly Caldicellulosiruptor bescii ) is an extremely thermophilic cellulolytic bacterium, notable for its multi-domain cellulases and hemicellulases that efficiently degrade lignocellulosic biomass. However, the mechanisms by which A. bescii transports cello-oligosaccharides released during cellulose degradation into the cell for catabolism remain unclear. Among its 23 ATP-binding cassette (ABC) sugar transporters, we identified a conserved ABC transporter locus ( athe_0595-0598 ) encoding two extracellular binding proteins: Athe_0597 and Athe_0598. Biophysical analyses using differential scanning calorimetry and isothermal titration calorimetry revealed that Athe_0597 binds cello-oligosaccharides of varying lengths (G2-G5), while Athe_0598 is specific to cellobiose (G2). Ligand docking simulations supported these findings and shed light on the subsite configuration of these substrate-binding proteins (SBPs). To assess its physiological importance, we genetically deleted this transporter locus in A. bescii strain HTAB187, which grew poorly on cellobiose and did not grow on cellulose. Comparison of growth with a msmK deletion strain that cannot consume oligosaccharides showed that HTAB187 retains growth on non-cello-oligosaccharides and monosaccharides. Taken together, these results integrate biophysical characterization, structural modeling, and genetic perturbation to elucidate how A. bescii transports cello-oligosaccharides released from cellulose, providing mechanistic insight relevant to consolidated bioprocessing applications. IMPORTANCE Anaerocellum bescii is the most thermophilic lignocellulolytic bacterium known and holds potential for bioprocessing lignocellulosic biomass into renewable fuels. Its diverse ATP-binding cassette (ABC) sugar transporters make it a valuable model for studying thermophilic sugar uptake. Here, we identify a single ABC transporter with two substrate-binding proteins (Athe_0597 and Athe_0598) responsible for cello-oligosaccharide uptake. Genetic deletion of this transporter locus impaired growth on cellobiose and eliminated growth on cellulose. This is the first genetic manipulation in A. bescii to modulate transport of a specific sugar. We also characterize the substrate specificity of the extracytoplasmic binding proteins associated with the locus. One binds various cellodextrins (G2-G5), while the other specifically binds cellobiose (G2). Molecular modeling depicts how each oligosaccharide is docked within the binding pocket of these proteins. Understanding the mechanism of cello-oligosaccharide uptake by A. bescii expands opportunities for its metabolic engineering and furthers our understanding of its carbohydrate utilization systems.

  PublisherDOI

• Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome

  UNC Libraries · 2025-02-01

  articleOpen access
  PublisherDOI

Frequent coauthors

• Jeffery L. Dangl

  University of North Carolina at Chapel Hill

  30 shared

• Robert M. Kelly

  North Carolina State University

  25 shared

• Sara E. Blumer‐Schuette

  Oakland University

  17 shared

• Michael W. W. Adams

  University of Georgia

  15 shared

• Jeffrey V. Zurawski

  North Carolina State University

  14 shared

• Laura L. Lee

  North Carolina State University

  14 shared

• Theresa F. Law

  12 shared

• Omri M. Finkel

  Hebrew University of Jerusalem

  10 shared

Awards & honors

• Excellence in Mentoring Award, Princeton Engineering, 2026
• 250th Anniversary Fund for Innovation in Undergraduate Educa…
• New Investigator, Joint Genome Institute CSP, 2024
• E. Lawrence Keyes, Jr./Emerson Electric Co. Faculty Advancem…
• James K. Ferrell Outstanding Ph.D. Graduate Award, NC State…