Biology subjects

Engle, N. L.

Publications and source records attributed to Engle, N. L..

4 recordsLinked to original sources

bioRxiv2026

Switchgrass Root Cell Wall Composition and Anatomy Vary with Depth, Suggesting Approaches for Trait Enhancement

Plant root cellular architecture and cell wall composition influence plant productivity, stress resilience, biotic interactions, and potentially soil carbon accumulation. This study establishes comprehensive compositional parameters for roots of a lowland switchgrass genotype, DVR3. Root traits were analyzed in 12.5 cm depth segments, from Zone 1 near the surface to Zone 4 down to 50 cm. Mean abundance (g/mg) for major cell wall components included cellulose 470 {+/-} 20, xylose 250 {+/-} 20, lignin 170 {+/-} 15, and total suberin 35 {+/-} 5. Composition and cellular anatomy varied with depth, in a partially coordinated manner. Cross sections showed extensive aerenchyma in mature root regions despite greater root mass density, corresponding to abundant lignin and cellulose. Deep roots were enriched for pectin-associated traits, including arabinogalactan II, homogalacturonan, and arabinose-associated linkages. Suberin content did not vary significantly, though Casparian strip formation, endoderm and exoderm thickening, and suberin surface staining progressed with development. Similar trends in root lignin and specific root length were observed for another lowland switchgrass genotype, AP13. These results suggest that it may be possible to genetically enhance native switchgrass root chemistry to promote soil penetration and below-ground carbon accumulation by reducing variability with development, potentially via cell-type specific adjustments.

plant biology↗

bioRxiv2025

Manipulation of in planta ethylene levels modulates the metabolome of Populus tremula x tremuloides in a microbial-dependent manner.

BackgroundThe assembly of tree microbiota is a dynamic process that varies across space and time, influenced by both biotic and abiotic factors. Plants have developed defence strategies, mediated by phytohormones such as ethylene, to manage its interactions with pathogens and, in certain non-perennials, interactions with the commensal microbiota. However, whether and how ethylene regulation affects the assembly of tree microbiota is unknown. ResultsWe investigated the assembly of fungal and bacterial communities in poplars (P. tremula x. P. tremuloides T89), altered either in ethylene biosynthesis (ACO1), or in ethylene perception (etr1.1), by combining high-throughput amplicon sequencing with confocal microscopy. In parallel, we characterised root exudates, as well as root and shoot metabolomes of the different poplar lines grown on sterile soil and in the presence of microbiota using GC-MS. Alteration of ethylene levels had little impact on the metabolome of sterile poplars, but led to differential primary and secondary metabolic responses in the root and shoots of poplars colonised by microorganisms. These metabolomic changes were associated with a decrease in fungal colonisation of shoots, particularly by saprophytes in the early stages, whereas reduced ethylene stimulated root colonisation by fungi. Conversely, arbuscular mycorrhizal fungal and bacterial communities, as well as root exudation, were little affected by changes in ethylene production. ConclusionThe findings of this study suggest a potential dual role for ethylene in poplar, whereby its levels may either promote or inhibit microbial growth and activity, depending on the concentration, microbial trophic guild, and poplar organ.

plant biology↗

bioRxiv2020

Development of a clostridia-based cell-free system for prototyping genetic parts and metabolic pathways

Gas fermentation by autotrophic bacteria, such as clostridia, offers a sustainable path to numerous bioproducts from a range of local, highly abundant, waste and low-cost feedstocks, such as industrial flue gases or syngas generated from biomass or municipal waste. Unfortunately, designing and engineering clostridia remains laborious and slow. The ability to prototype individual genetic parts, gene expression, and biosynthetic pathway performance in vitro before implementing them in cells could help address these bottlenecks by speeding up design. Unfortunately, a high-yielding cell-free gene expression (CFE) system from clostridia has yet to be developed. Here, we report the development and optimization of a high-yielding (236 {+/-} 24 {micro}g/mL) batch CFE platform from the industrially relevant anaerobe, Clostridium autoethanogenum. A key feature of the platform is that both circular and linear DNA templates can be applied directly to the CFE reaction to program protein synthesis. We demonstrate the ability to prototype gene expression, and quantitatively map cell-free metabolism in lysates from this system. We anticipate that the C. autoethanogenum CFE platform will not only expand the protein synthesis toolkit for synthetic biology, but also serve as a platform in expediting the screening and prototyping of gene regulatory elements in non-model, industrially relevant microbes.

synthetic biology↗

bioRxiv2018

Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis

Metabolic pathways are frequently transferred between bacterial strains in the environment through horizontal gene transfer (HGT), yet laboratory engineering to introduce new metabolic pathways often fails. Successful use of a pathway requires co-evolution of both pathway and host, and these interactions may be disrupted upon transfer to a new host. Here we show that two different pathways for catabolism of coumarate failed to function when initially transferred into Escherichia coli. Using laboratory evolution, we elucidated the factors limiting activity of the newly-acquired pathways and the modifications required to overcome these limitations. Both pathways required mutations to the host to enable effective growth with coumarate, but the necessary mutations differed depending on the chemistry and intermediates of the pathways. In one case, an intermediate inhibited purine nucleotide biosynthesis, and this inhibition was relieved by single amino acid mutations to IMP dehydrogenase. A strain that natively contains this coumarate catabolism pathway, Acinetobacter baumannii, is already resistant to inhibition by the relevant intermediate, suggesting that natural pathway transfers have faced and overcome similar challenges. These discoveries will aid in our understanding of HGT and ability to predictably engineer metabolism.\n\nThis manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).

microbiology↗