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DOE OSTI2022

Hierarchical triply periodic minimal surface structures as heat exchangers and reactors

The present disclosure relates to a transport mechanism apparatus for transporting at least one of a gas or a fluid. The transport mechanism may have an inlet, an outlet and a triply periodic minimal surface (TPMS) structure. The TPMS structure is formed in a layer-by-layer three dimensional (3D) printing operation to include cells propagating in three dimensions, where the cells include wall portions having openings, and where the cells form a plurality of flow paths throughout the transport mechanism from the inlet to the outlet, and where the cells form the inlet and the outlet.

Roy, Pratanu↗

DOE OSTI2020

Development of Low-Cost, Crack-Tolerant Metallization Using Screen Printing

One of the ways to reduce the cost of solar electricity to 3/kWh, thus reaching parity with fossil-fuel-based generation, is to reduce the degradation rate of solar modules and extend their lifetime well beyond 30 years. The extended module lifetime in turn can positively influence the financial model and the bankability of utility-scale PV projects. Today, the highest-riskpriority solar module degradation mechanism is what is known as hot spots, often induced by cell cracks. In order to address this degradation mechanism, we make use of low-cost, multi-walled carbon nanotubes embedded in commercial screen-printable silver pastes. When the carbon nanotubes are properly functionalized and appropriately incorporated into commercial silver pastes, the resulting metal contacts on solar cells, after screen-printing and firing, show exceptional fracture toughness. These composite metal contacts possess increased ductility, electrical gap-bridging capability up to 50 um, and 'self-healing' to regain electrical continuity even after cycles of complete electrical failure under extreme strain.

14 SOLAR ENERGY↗

DOE OSTI2022

Editorial: Wood Development and Physiology in a Changing Climate

Wood of forest trees is a renewable, sustainable and easily workable material and has been widely used in construction, paper making, furniture, and as a feedstock for biofuels. Wood formation is the result of a highly ordered and finely regulated process. Secondary xylem (wood) and phloem are the inner and outer derivative products of the vascular cambium, respectively. Xylem is mainly composed of dead cells with thickened cell walls rich in cellulose, hemicelluloses, and lignin, which are responsible for providing mechanical support and conducting water and minerals for the trees. Phloem transports photoassimilates and signaling molecules, including phytohormones and peptides. Wood structure varies greatly between, and within, tree species. A thorough understanding of developmental processes and metabolic pathways during wood formation would provide a basis for improving wood biomass and modifying properties in forest trees.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides

The cell wall of the human bacterial pathogen Group A Streptococcus (GAS) consists of peptidoglycan decorated with the Lancefield group A carbohydrate (GAC). GAC is a promising target for the development of GAS vaccines. In this study, employing chemical, compositional, and NMR methods, we show that GAC is attached to peptidoglycan via glucosamine 1-phosphate. This structural feature makes the GAC-peptidoglycan linkage highly sensitive to cleavage by nitrous acid and resistant to mild acid conditions. Using this characteristic of the GAS cell wall, we identify PplD as a protein required for deacetylation of linkage N-acetylglucosamine (GlcNAc). X-ray structural analysis indicates that PplD performs catalysis via a modified acid/base mechanism. Genetic surveys in silico together with functional analysis indicate that PplD homologs deacetylate the polysaccharide linkage in many streptococcal species. We further demonstrate that introduction of positive charges to the cell wall by GlcNAc deacetylation protects GAS against host cationic antimicrobial proteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

A Group of O-Acetyltransferases Catalyze Xyloglucan Backbone Acetylation and Can Alter Xyloglucan Xylosylation Pattern and Plant Growth When Expressed in Arabidopsis

Abstract Xyloglucan is a major hemicellulose in plant cell walls and exists in two distinct types, XXXG and XXGG. While the XXXG-type xyloglucan from dicot species only contains O-acetyl groups on side-chain galactose (Gal) residues, the XXGG-type xyloglucan from Poaceae (grasses) and Solanaceae bears O-acetyl groups on backbone glucosyl (Glc) residues. Although O-acetyltransferases responsible for xyloglucan Gal acetylation have been characterized, the biochemical mechanism underlying xyloglucan backbone acetylation remains to be elucidated. In this study, we showed that recombinant proteins of a group of DUF231 members from rice and tomato were capable of transferring acetyl groups onto O-6 of Glc residues in cello-oligomer acceptors, indicating that they are xyloglucan backbone 6-O-acetyltransferases (XyBATs). We further demonstrated that XyBAT-acetylated cellohexaose oligomers could be readily xylosylated by AtXXT1 (Arabidopsis xyloglucan xylosyltransferase 1) to generate acetylated, xylosylated cello-oligomers, whereas AtXXT1-xylosylated cellohexaose oligomers were much less effectively acetylated by XyBATs. Heterologous expression of a rice XyBAT in Arabidopsis led to a severe reduction in cell expansion and plant growth and a drastic alteration in xyloglucan xylosylation pattern with the formation of acetylated XXGG-type units, including XGG, XGGG, XXGG, XXGG,XXGGG and XXGGG (G denotes acetylated Glc). In addition, recombinant proteins of two Arabidopsis XyBAT homologs also exhibited O-acetyltransferase activity toward cellohexaose, suggesting their possible role in mediating xyloglucan backbone acetylation in vivo. Our findings provide new insights into the biochemical mechanism underlying xyloglucan backbone acetylation and indicate the importance of maintaining the regular xyloglucan xylosylation pattern in cell wall function.

Cell Biology↗

DOE OSTI2023

Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products

Intracellular biomacromolecules, such as industrial enzymes and biopolymers, represent an important class of bio-derived products obtained from bacterial hosts. A common key step in the downstream separation of these biomolecules is lysis of the bacterial cell wall to effect release of cytoplasmic contents. Cell lysis is typically achieved either through mechanical disruption or reagent-based methods, which introduce issues of energy demand, material needs, high costs, and scaling problems. Osmolysis, a cell lysis method that relies on hypoosmotic downshock upon resuspension of cells in distilled water, has been applied for bioseparation of intracellular products from extreme halophiles and mammalian cells. However, most industrial bacterial strains are non-halotolerant and relatively resistant to hypoosmotic cell lysis. To overcome this limitation, we developed two strategies to increase the susceptibility of non-halotolerant hosts to osmolysis using Cupriavidus necator, a strain often used in electromicrobial production, as a prototypical strain. In one strategy, C. necator was evolved to increase its halotolerance from 1.5% to 3.25% (w/v) NaCl through adaptive laboratory evolution, and genes potentially responsible for this phenotypic change were identified by whole genome sequencing. The evolved halotolerant strain experienced an osmolytic efficiency of 47% in distilled water following growth in 3% (w/v) NaCl. In a second strategy, the cells were made susceptible to osmolysis by knocking out the large-conductance mechanosensitive channel (mscL) gene in C. necator. When these strategies were combined by knocking out the mscL gene from the evolved halotolerant strain, greater than 90% osmolytic efficiency was observed upon osmotic downshock. A modified version of this strategy was applied to E. coli BL21 by deleting the mscL and mscS (small-conductance mechanosensitive channel) genes. When grown in medium with 4% NaCl and subsequently resuspended in distilled water, this engineered strain experienced 75% cell lysis, although decreases in cell growth rate due to higher salt concentrations were observed. Our strategy is shown to be a simple and effective way to lyse cells for the purification of intracellular biomacromolecules and may be applicable in many bacteria used for bioproduction.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Chemical and Structural Changes in Corn Stover After Ensiling: Influence on Bioconversion

Production of biofuels, bioproducts, and bioenergy requires a well-characterized, stable, and reasonably uniform biomass supply and well-established supply chains for shipping biomass from farm fields to biorefineries, while achieving year-round production targets. Preserving and stabilizing biomass feedstock during storage is a necessity for cost-effective and sustainable biofuel production. Ensiling is a common storage method used to preserve and even improve forage quality; however, the impact of ensiling on biomass physical and chemical properties that influence bioconversion processes has been variable. Our objective in this work was to determine the effects of ensiling on lignocellulosic feedstock physicochemical properties and how that influences bioconversion requirements. We observed statistically significant decreases (p < 0.05) in the content of two major structural carbohydrates (glucan and xylan) of 5 and 8%, respectively, between the ensiled and non-ensiled materials. We were unable to detect differences in sugar yields from structural carbohydrates after pretreatment and enzymatic hydrolysis of the ensiled materials compared to non-ensiled controls. Based on this work, we conclude that ensiling the corn stover did not change the bioconversion requirements compared to the control samples and incurred losses of structural carbohydrates. At the light microscopy level, ensiled corn stover exhibited little structural change or relocation of cell wall components as detected by immunocytochemistry. However, more subtle structural changes were revealed by electron microscopy, as ensiled cell walls exhibit ultrastructural characteristics such as wall delimitation intermediate between non-ensiled and dilute-acid-pretreated cell walls. These findings suggest that alternative methods of conversion, such as deacetylation and mechanical refining, could take advantage of lamellar defects and may be more effective than dilute acid or hot water pretreatment for biomass conversion of ensiled materials.

09 BIOMASS FUELS↗

DOE OSTI2023

Novel candidate genes for lignin structure identified through genome-wide association study of naturally varying Populus trichocarpa

Populus is a promising lignocellulosic feedstock for biofuels and bioproducts. However, the cell wall biopolymer lignin is a major barrier in conversion of biomass to biofuels. To investigate the variability and underlying genetic basis of the complex structure of lignin, a population of 409 three-year-old, naturally varying Populus trichocarpa genotypes were characterized by heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR). A subsequent genome-wide association study (GWAS) was conducted using approximately 8.3 million single nucleotide polymorphisms (SNPs), which identified 756 genes that were significantly associated (−log 10 ( p -value)>6) with at least one lignin phenotype. Several promising candidate genes were identified, many of which have not previously been reported to be associated with lignin or cell wall biosynthesis. These results provide a resource for gaining insights into the molecular mechanisms of lignin biosynthesis and new targets for future genetic improvement in poplar.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism

Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem cells which imparts the strength to the wood. Identification of the genes involved in the secondary cell wall biosynthesis as well as their cognate regulators is crucial to understand how the production of wood occurs and serves as a starting point for developing breeding strategies to produce varieties with improved wood quality, better paper pulping or new potential uses such as biofuel production. In order to gain knowledge on the molecular mechanisms and gene regulation related with wood development in white teak, a de novo sequencing and transcriptome assembly approach was used employing secondary cell wall synthesizing cells from young white teak trees. For generation of transcriptome, RNA-seq reads were assembled into 110,992 transcripts and 49,364 genes were functionally annotated using plant databases; 5071 GO terms and 25,460 SSR markers were identified within xylem transcripts and 10,256 unigenes were assigned to KEGG database in 130 pathways. Among transcription factor families, C2H2, C3H, bLHLH and MYB were the most represented in xylem. Differential gene expression analysis using leaves as a reference was carried out and a total of 20,954 differentially expressed genes were identified including monolignol biosynthetic pathway genes. The differential expression of selected genes (4CL, COMT, CCoAOMT, CCR and NST1) was validated using qPCR. We report the very first de novo transcriptome of xylem-related genes in this tropical timber species of commercial importance and constitutes a valuable extension of the publicly available transcriptomic resource aimed at fostering both basic and breeding studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440

Lignin is an abundant and recalcitrant component of plant cell walls. While lignin degradation in nature is typically attributed to fungi, growing evidence suggests that bacteria also catabolize this complex biopolymer. However, the spatiotemporal mechanisms for lignin catabolism remain unclear. Improved understanding of this biological process would aid in our collective knowledge of both carbon cycling and microbial strategies to valorize lignin to value-added compounds. Here, we examine lignin modifications and the exoproteome of three aromatic–catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. P. putida cultivation in lignin-rich media is characterized by an abundant exoproteome that is dynamically and selectively packaged into outer membrane vesicles (OMVs). Interestingly, many enzymes known to exhibit activity toward lignin-derived aromatic compounds are enriched in OMVs from early to late stationary phase, corresponding to the shift from bioavailable carbon to oligomeric lignin as a carbon source. In vivo and in vitro experiments demonstrate that enzymes contained in the OMVs are active and catabolize aromatic compounds. Taken together, this work supports OMV-mediated catabolism of lignin-derived aromatic compounds as an extracellular strategy for nutrient acquisition by soil bacteria and suggests that OMVs could pote

biological funneling↗

DOE OSTI2024

Systems and methods for periodic nodal surface based reactors, distributors, contactors and heat exchangers

The present disclosure relates to a transport mechanism apparatus for transporting at least one of a gas or a fluid. The transport mechanism may have an inlet, an outlet and an engineered cellular structure forming a periodic nodal surface, which may include a triply periodic minimal surface (TPMS) structure. The structure is formed in a layer-by-layer three dimensional (3D) printing operation to include cells propagating in three dimensions, where the cells include non-intersecting, continuously curving wall portions having openings, and where the opening in the cells form a plurality of flow paths throughout the transport mechanism from the inlet to the outlet, and where portions of the cells form the inlet and the outlet.

Iyer, Jaisree Kannan↗

DOE OSTI2022

Lack of xyloglucan in the cell walls of the Arabidopsis xxt1/xxt2 mutant results in specific increases in homogalacturonan and glucomannan

Mutations in both ArabidopsisXyloglucan Xylosyltransferase1 (XXT1) and Xyloglucan Xylosyltransferase2 (XXT2) result in the absence of the major hemicellulose, xyloglucan (XyG). The growth physiology, tensile strength, and cell wall compositions of etiolated hypocotyls of xxt1/xxt2 double and xxt1/xxt2/xxt5 triple mutants were characterized and compared with those of mur2 and mur3 mutations that alter the side group composition of XyG. Wild type and mur2 demonstrated normal elongation growth, whereas the xxt double and triple mutants and mur3 showed reduced elongation and cell swelling at the base of the hypocotyl at the later stages of elongation. Whereas mur3 hypocotyls had reduced tensile strength, the xxt double and triple mutants had similar tensile strengths as wild type, but reached breaking points at lower strains. Loss of XyG in hypocotyls and rosette leaf cell walls was associated with specific increases in the relative abundance of homogalacturonan and the hemicellulose glucomannan, but not arabinoxylan. The increased homogalacturonan and glucomannan abundance did not result from enhanced expression of their polymer synthases. An analysis of published transcriptomic data indicated that genes encoding some members of the expansin, xyloglucan endotransglucosylase/hydrolase, arabinogalactan-protein, and structural protein families were upregulated in the xxt mutants. We hypothesize that an as yet unknown mechanism exists by which pectin and hemicellulose abundance can be altered other than by increased rates of biosynthesis to maintain a structurally sound cell wall.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Mechanism and Reaction Energy Landscape for Apiose Cross-Linking by Boric Acid in Rhamnogalacturonan II

Rhamnogalacturonan II (RG-II)—the most complex polysaccharide known in nature—exists as a borate cross-linked dimer in the plant primary cell wall. Boric acid facilitates the formation of this cross-link on the apiosyl residues of RG-II’s side chain A. Here, we detail the reaction mechanism for the cross-linking process with ab initio calculations coupled with transition state theory. We determine the formation of the first ester linkage to be the rate-limiting step of the mechanism. Our findings demonstrate that the regio- and stereospecific nature of subsequent steps in the reaction itinerary presents four distinct energetically plausible reaction pathways. This has significant implications for the overall structure of the cross-linked RG-II dimer assembly. Finally, our transition state and reaction path analyses reveal key geometric insights that corroborate previous experimental hypotheses on borate ester formation reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular “reactors.” In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Staphylococcus aureus vWF-binding protein triggers a strong interaction between clumping factor A and host vWF

The Staphylococcus aureus cell wall-anchored adhesin ClfA binds to the very large blood circulating protein, von Willebrand factor (vWF) via vWF-binding protein (vWbp), a secreted protein that does not bind the cell wall covalently. Here we perform force spectroscopy studies on living bacteria to unravel the molecular mechanism of this interaction. We discover that the presence of all three binding partners leads to very high binding forces (2000 pN), largely outperforming other known ternary complexes involving adhesins. Strikingly, our experiments indicate that a direct interaction involving features of the dock, lock and latch mechanism must occur between ClfA and vWF to sustain the extreme tensile strength of the ternary complex. Our results support a previously undescribed mechanism whereby vWbp activates a direct, ultra-strong interaction between ClfA and vWF. This intriguing interaction represents a potential target for therapeutic interventions, including synthetic peptides inhibiting the ultra-strong interactions between ClfA and its ligands.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Analysis of the Innovation Trend in Cell-Free Synthetic Biology

Cell-free synthetic biology is a maturing field that aims to assemble biomolecular reactions outside cells for compelling applications in drug discovery, metabolic engineering, biomanufacturing, diagnostics, and education. Cell-free systems have several key features. They circumvent mechanisms that have evolved to facilitate species survival, bypass limitations on molecular transport across the cell wall, enable high-yielding and rapid synthesis of proteins without creating recombinant cells, and provide high tolerance towards toxic substrates or products. Here, we analyze ~750 published patents and ~2000 peer-reviewed manuscripts in the field of cell-free systems. Three hallmarks emerged. First, we found that both patent filings and manuscript publications per year are significantly increasing (five-fold and 1.5-fold over the last decade, respectively). Second, we observed that the innovation landscape has changed. Patent applications were dominated by Japan in the early 2000s before shifting to China and the USA in recent years. Finally, we discovered an increasing prevalence of biotechnology companies using cell-free systems. Our analysis has broad implications on the future development of cell-free synthetic biology for commercial and industrial applications.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Electron tomography unravels new insights into fiber cell wall nanostructure; exploring 3D macromolecular biopolymeric nano-architecture of spruce fiber secondary walls

Lignocellulose biomass has a tremendous potential as renewable biomaterials for fostering the “bio-based society” and circular bioeconomy paradigm. It requires efficient use and breakdown of fiber cell walls containing mainly cellulose, hemicellulose and lignin biopolymers. Despite their great importance, there is an extensive debate on the true structure of fiber walls and knowledge on the macromolecular nano-organization is limited and remains elusive in 3D. We employed dual-axis electron tomography that allows visualization of previously unseen 3D macromolecular organization/biopolymeric nano-architecture of the secondary S2 layer of Norway spruce fiber wall. Unprecedented 3D nano-structural details with novel insights into cellulose microfibrils (~2 nm diameter), macrofibrils, nano-pore network and cell wall chemistry (volume %) across the S2 were explored and quantified including simulation of structure related permeability. Matrix polymer association with cellulose varied between microfibrils and macrofibrils with lignin directly associated with MFs. Simulated bio-nano-mechanical properties revealed stress distribution within the S2 and showed similar properties between the idealized 3D model and the native S2 (actual tomogram). Present work has great potential for significant advancements in lignocellulose research on nano-scale understanding of cell wall assembly/disassembly processes leading to more efficient industrial processes of functionalization, valorization and target modification technologies.

3-D reconstruction↗

DOE OSTI2020

Molecular Mechanism of Polysaccharide Acetylation by the Arabidopsis Xylan O-acetyltransferase XOAT1

Xylans are a major component of plant cell walls. O-Acetyl moieties are the dominant backbone substituents of glucuronoxylan in dicots and play a major role in the polymer-polymer interactions that are crucial for wall architecture and normal plant development. Here, we describe the biochemical, structural, and mechanistic characterization of Arabidopsis (Arabidopsis thaliana) xylan O-acetyltransferase 1 (XOAT1), a member of the plant-specific Trichome Birefringence Like (TBL) family. Detailed characterization of XOAT1-catalyzed reactions by real-time NMR confirms that it exclusively catalyzes the 2-O-acetylation of xylan, followed by nonenzymatic acetyl migration to the O-3 position, resulting in products that are monoacetylated at both O-2 and O-3 positions. In addition, we report the crystal structure of the catalytic domain of XOAT1, which adopts a unique conformation that bears some similarities to the a/ß/a topology of members of the GDSL-like lipase/acylhydrolase family. Finally, we use a combination of biochemical analyses, mutagenesis, and molecular simulations to show that XOAT1 catalyzes xylan acetylation through formation of an acyl-enzyme intermediate, Ac–Ser-216, by a double displacement bi-bi mechanism involving a Ser-His-Asp catalytic triad and unconventionally uses an Arg residue in the formation of an oxyanion hole.

acetylation↗