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Pinoresinol rescues developmental phenotypes of Arabidopsis phenylpropanoid mutants overexpressing FERULATE 5-HYDROXYLASE

Most phenylpropanoid pathway flux is directed toward the production of monolignols, but this pathway also generates multiple bioactive metabolites. The monolignols coniferyl and sinapyl alcohol polymerize to form guaiacyl (G) and syringyl (S) units in lignin, components that are characteristic of plant secondary cell walls. Lignin negatively impacts the saccharification potential of lignocellulosic biomass. Although manipulation of its content and composition through genetic engineering has reduced biomass recalcitrance, in some cases, these genetic manipulations lead to impaired growth. Here, the reduced-growth phenotype is often attributed to poor water transport due to xylem collapse in low-lignin mutants, but alternative models suggest that it could be caused by the hyper- or hypoaccumulation of phenylpropanoid intermediates. In Arabidopsis thaliana, overexpression of FERULATE 5-HYDROXYLASE (F5H) shifts the normal G/S lignin ratio to nearly pure S lignin and does not result in substantial changes to plant growth. In contrast, when we overexpressed F5H in the low-lignin mutants cinnamyl dehydrogenase c and d (cadc cadd), cinnamoyl-CoA reductase 1, and reduced epidermal fluorescence 3, plant growth was severely compromised. In addition, cadc cadd plants overexpressing F5H exhibited defects in lateral root development. Exogenous coniferyl alcohol (CA) and its dimeric coupling product, pinoresinol, rescue these phenotypes. These data suggest that mutations in the phenylpropanoid pathway limit the biosynthesis of pinoresinol, and this effect is exacerbated by overexpression of F5H, which further draws down cellular pools of its precursor, CA. Overall, these genetic manipulations appear to restrict the synthesis of pinoresinol or a downstream metabolite that is necessary for plant growth.

59 BASIC BIOLOGICAL SCIENCES↗

In-Silico Design of Next Generation Cellulose-Derived Packaging Materials (CRADA Final Report)

Developing sustainable solutions for single-use packaging is an important objective to combat the environmental crisis of plastics pollution. Most embodiments of cellulose-based packaging materials, including CellophaneTM, are completely biodegradable in both terrestrial and marine environments. However, petroleum-derived alternatives offer some performance advantages for metrics such as moisture barriers and mechanical properties. This project leverages molecular dynamics simulation to investigate how molecular modifications to cellulose-based polymer assemblies impact their material properties. An important performance criterion for the modified materials was to retain biodegradability; thus, modifications by naturally occurring, biodegradable additives were the focus of this study. Specifically, we developed models with xylan and lignin of varying monomeric compositions into the cellulose matrix. The mechanical properties were investigated by performing stress-strain simulations, and the water barrier and hydrophobicity were investigated by simulating the water contact angle. Our findings indicate that the incorporation of xylan into the cellulose matrix tends to increase the mechanical properties with an optimal loading of ~27 wt%. We also predict that orienting the nanoscale directionality of the xylan chains such that they are perpendicular to the cellulose fibrils will dramatically increase mechanical strength. In contrast, the incorporation of lignin tends to weaken the composite at all loadings investigated. Simulations of water contact angle predicted that coating polymers on the surface of the cellulose assembly creates a more hydrophobic surface than incorporating them throughout the matrix. Of the coatings investigated, lignin resulted in the most hydrophobic surface, followed by pectin and keratin, which both imparted modest increases in hydrophobicity. Future experimental work done by Futamura will focus on designing material prototypes to capitalize on the predictions of performance enhancement obtained from molecular modeling. While substantial progress was made by the simulations performed in this project, there still exists a vast parameter space that we were unable to investigate, including branching, functional group decoration, and degree of polymerization of polymer additives. However, the methods developed in this initial investigation will facilitate more rapid evaluation of the impact of molecular characteristics on the performance of biopolymer composite materials and thereby accelerate future materials discovery efforts in this area.

36 MATERIALS SCIENCE↗

Modeling and Manipulating Phenylpropanoid Pathway Flux for Bioenergy

We have made important strides toward our project goals over the past five years. First, we developed and published a novel isotopic feeding system to investigate metabolic fluxes of the lignin biosynthesis. Next, we have developed and published a kinetic model of the phenylpropanoid pathway. As an extension of that work, we developed a multilayer kinetic model of lignin biosynthesis. Next we conducted a systematic transcriptome and metabolome analysis for phenylpropanoid metabolism. Finally, we have identified three strategies that enhance the accumulation of 2-phenylethanol in plants.

09 BIOMASS FUELS↗

Compositional analysis of organosolv poplar lignin by using high-performance liquid chromatography/high-resolution multi-stage tandem mass spectrometry

Organosolv treatment is an efficient and environmentally friendly process to degrade lignin into small compounds. The capability of characterizing the individual compounds in the complex mixtures formed upon organosolv treatment is essential for the optimization of the further lignin conversion processes and for the rational genetic engineering of plants used to produce lignin in order to improve lignin properties. In this study, an organosolv poplar lignin sample was initially analyzed by high-resolution mass spectrometry coupled with negative-ion mode electrospray ionization ((-)ESI HRMS). Lignin monomers and dimers were found to constitute the majority of the compounds in the organosolv lignin sample. Larger lignin oligomers, such as trimers and tetramers, and some not lignin-related compounds, were also detected. A high-performance liquid chromatograph/linear quadrupole ion trap/orbitrap mass spectrometer capable of multi-stage high-resolution tandem mass spectrometry experiments (HRMS n ), equipped with an (-)ESI source (HPLC/(-)ESI HRMS n ), was employed to separate the unknown compounds in the organosolv mixture and to obtain structural information for the deprotonated compounds via collision-activated dissociation (CAD) HRMS n experiments. To improve the understanding of the CAD behavior of deprotonated lignin-related compounds, 16 deprotonated model compounds with different functionalities and linkage types were examined. This approach enabled the assignment of likely structures for several lignin monomers, dimers, trimers, and tetramers, and some not lignin-related compounds, most likely fatty acids. Based on the proposed structures, compounds in the organosolv lignin sample contain β-O-4, 5–5, β-5, and possibly also 4-O-5 linkages. Most compounds contain G- and S-monomeric units although a small amount of H-units were also detected.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Lignin alkaline oxidation using reversibly-soluble bases

When excess base is required to drive desired reactions, such as in lignin alkaline oxidation, Sr(OH) 2 can offer a reversibly-soluble alternative to NaOH that allows simple recycle of the excess base with concomitant cost and environmental benefits.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enhancing the multi-functional properties of renewable lignin carbon fibers via defining the structure–property relationship using different biomass feedstocks

Lignin has been explored extensively as a renewable precursor for carbon materials, considering its abundance as a major component of plant cell walls and its sustainability as a byproduct of both lignocellulosic biorefinery and the paper-making industry. Despite the extensive efforts to define the process–property relationship, it remains largely unknown how lignin biosynthesis and its chemistry would impact the resultant carbon fiber properties, for both mechanical and electroconductive performances. Such inadequate understanding fundamentally limits feedstock design and selection to improve carbon fiber properties toward broader commercial applications. Using lignin from a broad range of biomass feedstocks for carbon fiber manufacturing, we have fundamentally explored the structure–function relationship between lignin chemistry and carbon fiber performance. Specifically, lignin extracted from hardwood (sugar maple), softwood (loblolly pine and red cedar), and herbaceous plants (corn stover and switchgrass) was used for carbon fiber manufacturing, considering the very different lignin structures from these feedstocks. Linear regression models were established to define the relationship between carbon fiber mechanical properties and lignin structural characteristics. The results highlighted that the content of β-O-4 linkages correlates significantly with the tensile strength and elastic modulus of lignin carbon fibers, indicating that more linear β-O-4 linkages would promote the carbon fiber mechanical performance. Moreover, electroconductive properties are essential for broader energy device application of lignin-based carbon fibers, yet the mechanisms controlling their electroconductivity are largely unknown. Furthermore, we hereby demonstrated that a higher β-O-4 content also promotes the electroconductivity of lignin carbon fibers. Microstructure analysis further revealed that the crystallite size and content of the pre-graphitic turbostratic carbon structure in lignin-based carbon fibers were enhanced as the β-O-4 linkages increased. The content of β-O-4 linkages has shown a strong correlation with the crystallite content in a linear regression model. This study thus revealed the underlying mechanisms regarding how the lignin structure in planta defines the resultant carbon fiber properties. Moreover, the study also highlighted the correlation between the mechanical and electroconductive properties of lignin-based carbon fibers, both of which were defined by the lignin structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes

Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding the influence of solvents on the Pt-catalyzed hydrodeoxygenation of guaiacol

Bio-oil derived from fast pyrolysis of lignocellulosic biomass needs to be deoxygenated to become a substitute for petroleum fuels. Here, we study the hydrodeoxygenation mechanism of guaiacol, a bio-oil model compound derived from the lignin fraction of biomass, on Pt(1 1 1) terrace sites in the presence of water, diethyl ether, 1-butanol, and n-hexane as solvent. Using first-principles periodic density functional theory (DFT) calculations and mean-field microkinetic reactor modeling, a detailed reaction mechanism is investigated targeting various products such as catechol, phenol, anisole, benzene, cyclohexanone, and cyclohexanol. Solvent phase DFT outcomes are mostly similar to that of the vapor phase; however, microkinetic modeling results suggest that rate controlling species and transition states differ somewhat in the various reaction environments. Catechol was found to be the major aromatic product across all reaction environments. Over Pt(1 1 1), unsaturated monooxygenate production from catechol is unlikely.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity

The factors controlling lignin composition remain unclear. Catechyl (C)–lignin is a homopolymer of caffeyl alcohol with unique properties as a biomaterial and precursor of industrial chemicals. The lignin synthesized in the seed coat of Cleome hassleriana switches from guaiacyl (G)– to C-lignin at around 12 to 14 days after pollination (DAP), associated with a rerouting of the monolignol pathway. Lack of synthesis of caffeyl alcohol limits C-lignin formation before around 12 DAP, but coniferyl alcohol is still synthesized and highly accumulated after 14 DAP. We propose a model in which, during C-lignin biosynthesis, caffeyl alcohol noncompetitively inhibits oxidation of coniferyl alcohol by cell wall laccases, a process that might limit movement of coniferyl alcohol to the apoplast. Developmental changes in both substrate availability and laccase specificity together account for the metabolic fates of G- and C-monolignols in the Cleome seed coat.

09 BIOMASS FUELS↗

Influence of particle size on NIR spectroscopic characterization of sorghum biomass for the biofuel industry

NIR spectroscopy is a rapid and accurate green technology for high-throughput biomass characterization, including sorghum (Sorghum bicolor), a promising energy crop for the biofuel industry. This study assessed the influence of particle size on NIR spectroscopic analysis (wavelength range: 867–2535 nm) of sorghum biomass composition. Grown under field conditions, a total of 113 types of genetically diverse sorghum accessions were dried, ground, and sieved (<250, 250–600, 600–850, and > 850 µm particle size) for developing partial least square regression (PLSR) prediction models for moisture, ash, extractive, glucan, xylan, acid-soluble lignin (ASL), acid-insoluble lignin (AIL), and total lignin (ASL + AIL). Overall, smaller particle sizes provided better model performance, while no single particle size provided the best performance for all the selected components. With only 9 selected bands and 4 latent variables (LVs), the best PLSR model was obtained for moisture with particle size of 600–850 µm with the square root of the coefficient of determination (R) of 0.85, the ratio of prediction to deviation (RPD) of 2.2, and the root mean square error (RMSE) of 0.46 % in external validation. Similar model performances were also obtained for ash, extractive, glucan, and xylan. This study showed that size reduction could effectively improve NIR spectroscopic analysis for lipid-producing sorghum biomass for the biofuel industry.

09 BIOMASS FUELS↗

Data for Influence of Particle Size on NIR Spectroscopic Characterization of Sorghum Biomass for the Biofuel Industry

NIR spectroscopy is a rapid and accurate green technology for high-throughput biomass characterization, including sorghum ( Sorghum bicolor ), a promising energy crop for the biofuel industry. This study assessed the influence of particle size on NIR spectroscopic analysis (wavelength range: 867–2535 nm) of sorghum biomass composition. Grown under field conditions, a total of 113 types of genetically diverse sorghum accessions were dried, ground, and sieved (<250, 250–600, 600–850, and > 850 µm particle size) for developing partial least square regression (PLSR) prediction models for moisture, ash, extractive, glucan, xylan, acid-soluble lignin (ASL), acid-insoluble lignin (AIL), and total lignin (ASL + AIL). Overall, smaller particle sizes provided better model performance, while no single particle size provided the best performance for all the selected components. With only 9 selected bands and 4 latent variables (LVs), the best PLSR model was obtained for moisture with particle size of 600–850 µm with the square root of the coefficient of determination (R) of 0.85, the ratio of prediction to deviation (RPD) of 2.2, and the root mean square error (RMSE) of 0.46 % in external validation. Similar model performances were also obtained for ash, extractive, glucan, and xylan. This study showed that size reduction could effectively improve NIR spectroscopic analysis for lipid-producing sorghum biomass for the biofuel industry.

Biomass Analytics↗

Pd/C promotes C–H bond activation and oxidation of p -hydroxybenzoate during hydrogenolysis of poplar

Hydrogenolysis of lignin generates a portfolio of products, the yields of which are generally calculated using a subset of phenolic monomers that are dependent on the lignin composition, product distribution, and analytical technique. Some lignins are naturally γ-acylated; poplar lignins, for example, have p-hydroxybenzoate groups on 1–15% of their syringyl subunits. Upon hydrogenolysis, it is generally assumed that the p-hydroxybenzoate is cleaved before the deacylated lignin is depolymerized. Hydrogenolysis of model γ-p-hydroxybenzoylated β-aryl ethers do not, however, produce the deacylated β-aryl ether intermediates, as was previously conjectured; products instead derive from palladium-assisted reactions on the cinnamyl p-hydroxybenzoates resulting in initial β-ether cleavage. The p-hydroxybenzoate moiety itself also undergoes carboxylate-assisted palladium-catalyzed C–H bond activation to form the 2,4-dihydroxybenzoate, that subsequently converts to the 2,4-dihydroxycyclohex-1-enoate. Furthermore, these details underscore previously unrecognized pathways and products that are key to understanding the different hydrogenolysis product distributions from naturally acylated lignins that are prevalent biomass-conversion feedstocks.

09 BIOMASS FUELS↗

Sustainability Trait Modeling of Field-Grown Switchgrass ( Panicum virgatum ) Using UAV-Based Imagery

Unmanned aerial vehicles (UAVs) provide an intermediate scale of spatial and spectral data collection that yields increased accuracy and consistency in data collection for morphological and physiological traits than satellites and expanded flexibility and high-throughput compared to ground-based data collection. In this study, we used UAV-based remote sensing for automated phenotyping of field-grown switchgrass (Panicum virgatum), a leading bioenergy feedstock. Using vegetation indices calculated from a UAV-based multispectral camera, statistical models were developed for rust disease caused by Puccinia novopanici, leaf chlorophyll, nitrogen, and lignin contents. For the first time, UAV remote sensing technology was used to explore the potentials for multiple traits associated with sustainable production of switchgrass, and one statistical model was developed for each individual trait based on the statistical correlation between vegetation indices and the corresponding trait. Also, for the first time, lignin content was estimated in switchgrass shoots via UAV-based multispectral image analysis and statistical analysis. The UAV-based models were verified by ground-truthing via correlation analysis between the traits measured manually on the ground-based with UAV-based data. The normalized difference red edge (NDRE) vegetation index outperformed the normalized difference vegetation index (NDVI) for rust disease and nitrogen content, while NDVI performed better than NDRE for chlorophyll and lignin content. Overall, linear models were sufficient for rust disease and chlorophyll analysis, but for nitrogen and lignin contents, nonlinear models achieved better results. As the first comprehensive study to model switchgrass sustainability traits from UAV-based remote sensing, these results suggest that this methodology can be utilized for switchgrass high-throughput phenotyping in the field.

60 APPLIED LIFE SCIENCES↗

Liquid–Liquid Equilibrium Prediction in Fast Pyrolysis Bio-Oil Systems: A Framework for Incorporating Bio-Oil Complexity

The study of mixtures of bio-oil, water and organic solvents in different proportions can serve as a cost-effective analysis of its content due to the formation of immiscible phases. This manuscript attempts to replicate experimentally determined partition coefficients (K OW ) of relevant species present in fast pyrolysis bio-oil (FPBO). A commercial flowsheeting simulator with surrogate bio-oil model representation is used. Concurrently, pyrolytic lignins in FPBO (‘pyrolignin’) do not have an agreed-upon structural representation, and the literature is ripe with wide variations of said representations. Thus, during the description of FPBO, this pyrolignin fraction was modeled using 20 possible structures (phenolic dimers to tetramers), with the goal of determining the structures for which the experimental data are best described. Two cases were considered: Case 1 normalized the reported experimental mass balance, while Case 2 included the unreported fraction in the mass balance to the total pyroligin. Please, add here a comment on the prediction of the Water oil equilibrium. The best KOW predictions for levoglucosan (LVG) were obtained when the system was modeled with no pyrolignin, presenting an MRE under 10% for both systems WO and BO. Among the possible structures, D2 (dimer), F1 (trimer) and I1, and I3 (tetramers) presented MRE ≤ 13% for both cases.

09 BIOMASS FUELS↗

Diffusion in intact secondary cell wall models of plants at different equilibrium moisture content

Secondary plant cell walls are composed of carbohydrate and lignin polymers, and collectively represent a significant renewable resource. Leveraging these resources depends in part on a mechanistic understanding for diffusive processes within plant cell walls. Common wood protection treatments and biomass conversion processes to create biorefinery feedstocks feature ion or solvent diffusion within the cell wall. X-ray fluorescence microscopy experiments have determined that ionic diffusion rates are dependent on cell wall hydration as well as the ionic species through non-linear relationships. In this work, we use classical molecular dynamics simulations to map the diffusion behavior of different plant cell wall components (cellulose, hemicellulose, lignin), ions (Na + , K + , Cu2 + , Cl - ) and water within a model for an intact plant cell wall at various hydration states (3-30 wt% water). From these simulations, we analyze the contacts between different plant cell wall components with each other and their interaction with the ions. Generally, diffusion increases with increasing hydration, with lignin and hemicellulose components increasing diffusion by an order of magnitude over the tested hydration range. Ion diffusion depends on charge. Positively charged cations preferentially interact with hemicellulose components, which include negatively charged carboxylates. As a result, positive ions diffuse more slowly than negatively charged ions. Measured diffusion coefficients are largely observed to best fit piecewise linear trends, with an inflection point between 10 and 15% hydration. These observations shed light onto the molecular mechanisms for diffusive processes within secondary plant cell walls at atomic resolution.

09 BIOMASS FUELS↗

An Improved CRISPR Interference Tool to Engineer Rhodococcus opacus

Rhodococcus opacus is a non-model bacterium that is well suited for valorizing lignin. Despite recent advances in our systems-level understanding of its versatile metabolism, studies of its gene functions at a single gene level are still lagging. Elucidating gene functions in non-model organisms is challenging due to limited genetic engineering tools that are convenient to use. To address this issue, we developed a simple gene repression system based on CRISPR interference (CRISPRi). This gene repression system uses a T 7 RNA polymerase system to express a small guide RNA, demonstrating improved repression compared to the previously demonstrated CRISPRi system (i.e., the maximum repression efficiency improved from 58% to 85%). Additionally, our cloning strategy allows for building multiple CRISPRi plasmids in parallel without any PCR step, facilitating the engineering of this GC-rich organism. Using the improved CRISPRi system, we confirmed the annotated roles of four metabolic pathway genes, which had been identified by our previous transcriptomic analysis to be related to the consumption of benzoate, vanillate, catechol, and acetate. Furthermore, we showed our tool’s utility by demonstrating the inducible accumulation of muconate that is a precursor of adipic acid, an important monomer for nylon production. While the maximum muconate yield obtained using our tool was 30% of the yield obtained using gene knockout, our tool showed its inducibility and partial repressibility. In conclusion, our CRISPRi tool will be useful to facilitate functional studies of this non-model organism and engineer this promising microbial chassis for lignin valorization.

09 BIOMASS FUELS↗

Systematic approaches to C-lignin engineering in Medicago truncatula

Abstract Background C-lignin is a homopolymer of caffeyl alcohol present in the seed coats of a variety of plant species including vanilla orchid, various cacti, and the ornamental plant Cleome hassleriana . Because of its unique chemical and physical properties, there is considerable interest in engineering C-lignin into the cell walls of bioenergy crops as a high-value co-product of bioprocessing. We have used information from a transcriptomic analysis of developing C. hassleriana seed coats to suggest strategies for engineering C-lignin in a heterologous system, using hairy roots of the model legume Medicago truncatula . Results We systematically tested strategies for C-lignin engineering using a combination of gene overexpression and RNAi-mediated knockdown in the caffeic acid/5-hydroxy coniferaldehyde 3/5-O-methyltransferase ( comt ) mutant background, monitoring the outcomes by analysis of lignin composition and profiling of monolignol pathway metabolites. In all cases, C-lignin accumulation required strong down-regulation of caffeoyl CoA 3- O -methyltransferase (CCoAOMT) paired with loss of function of COMT. Overexpression of the Selaginella moellendorffii ferulate 5-hydroxylase ( SmF5H ) gene in comt mutant hairy roots resulted in lines that unexpectedly accumulated high levels of S-lignin. Conclusion C-Lignin accumulation of up to 15% of total lignin in lines with the greatest reduction in CCoAOMT expression required the strong down-regulation of both COMT and CCoAOMT, but did not require expression of a heterologous laccase, cinnamyl alcohol dehydrogenase (CAD) or cinnamoyl CoA reductase (CCR) with preference for 3,4-dihydroxy-substituted substrates in M. truncatula hairy roots. Cell wall fractionation studies suggested that the engineered C-units are not present in a heteropolymer with the bulk of the G-lignin.

09 BIOMASS FUELS↗

Energy-resolved mass spectrometry as a tool for identification of lignin depolymerization products

Lignin is the largest source of bio-based aromatic compounds in nature, and its valorization is essential to the sustainability of lignocellulosic biorefining. Characterizing lignin-derived compounds remains challenging due to the heterogeneity of this biopolymer. Tandem mass spectrometry is a promising tool for lignin structural analytics, as fragmentation patterns of model compounds can be extrapolated to identify characteristic moieties in complex samples. This work extends previous resonance excitation type collision-induced dissociation (CID) methods that identified lignin oligomers containing β-Ο-4, β-5, and β-β bonds, to also identify characteristics of 5-5, β-1, and 4-Ο-5 dimers, enabled by quadrupole time-of-flight (QTOF) CID with energy-resolved mass spectrometry (ERMS). Overall, beam type ERMS offers in-depth structural information and could ultimately contribute to tools for high-throughput lignin dimer identification.

09 BIOMASS FUELS↗