Bryon Donohoe

Additional file 5: Table S4. Differentially expressed genes involved in the different pathway including EMP, PPP, FA biosynthesis, TAG biosynthesis, phospholipid biosynthesis, TCA cycle, N and AA metabolism in two strains, and two nitrogen concentrations at different time points (T1, T2, and T3). The ratio is a log2-based value. All transcriptional differences are shown as the mean of duplicate log2-based values.

Additional file 4: Table S3. Differentially expressed genes in the two strains and two nitrogen concentrations at the different time points (T1, T2, and T3). The ratio is a log2-based value. All transcriptional differences are shown as the mean of duplicate log2-based values.

Additional file 3: Table S2. Transcriptomics profiling difference in D5A and BY4741 at different time points and nitrogen concentrations. The ratio is a log2-based value. All transcriptional differences are shown as the mean of duplicate log2-based values.

Feedstock recalcitrance is the most important barrier impeding cost-effective production of cellulosic biofuels. Pioneer commercial cellulosic ethanol facilities employ thermochemical pretreatment and addition of fungal cellulase, reflecting the main research emphasis in the field. However, it has been suggested that it may be possible to process cellulosic biomass without thermochemical pretreatment using thermophilic, cellulolytic bacteria. To further explore this idea, we examine the ability of various biocatalysts to solubilize autoclaved but otherwise unpretreated cellulosic biomass under controlled but not industrial conditions. Carbohydrate solubilization of mid-season harvested switchgrass after 5 days ranged from 24 % for Caldicellulosiruptor bescii to 65 % for Clostridium thermocellum, with intermediate values for a thermophilic horse manure enrichment, Clostridium clariflavum, Clostridium cellulolyticum, and simultaneous saccharification and fermentation (SSF) featuring a...

To improve the deconstruction of biomass, the most abundant terrestrial source of carbon polymers, en route to renewable fuels, chemicals, and materials more knowledge is needed into the mechanistic interplay between thermochemical pretreatment and enzymatic hydrolysis. In this review we highlight recent progress in advanced imaging techniques that have been used to elucidate the effects of thermochemical pretreatment on plant cell walls across a range of spatial scales and the relationship between the substrate structure and the function of various glycoside hydrolase components. The details of substrate and enzyme interactions are not yet fully understood and the challenges of characterizing plant cell wall architecture, how it dictates recalcitrance, and how it relates to enzyme-substrate interactions is the focus for many research groups in the field. Better understanding of how to match pretreatments with improved enzyme mixtures will lead to lower costs for industrial biorefin...

An Enzyme Drill Cellulase enzymes degrade the cell walls of plants by breaking down cellulose into its constituent sugar fragments and thus have attracted interest for biofuels production. Using transmission electron microscopy Brunecky et al. (p. 1513 ; see the Perspective by Berlin ) discovered that an especially active cellulase, CelA, from Caldicellulosiruptor bescii bacteria does not move along the surface of the substrate, but drills into the cellulose to form cavities.

Background Recently developed iron cocatalyst enhancement of dilute acid pretreatment of biomass is a promising approach for enhancing sugar release from recalcitrant lignocellulosic biomass. However, very little is known about the underlying mechanisms of this enhancement. In the current study, our aim was to identify several essential factors that contribute to ferrous ion-enhanced efficiency during dilute acid pretreatment of biomass and to initiate the investigation of the mechanisms that result in this enhancement. Results During dilute acid and ferrous ion cocatalyst pretreatments, we observed concomitant increases in solubilized sugars in the hydrolysate and reducing sugars in the (insoluble) biomass residues. We also observed enhancements in sugar release during subsequent enzymatic saccharification of iron cocatalyst-pretreated biomass. Fourier transform Raman spectroscopy showed that major peaks representing the C-O-C and C-H bonds in cellulose are significantly attenuated...

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 t...

Ferrous ion co-catalyst enhancement of dilute-acid (DA) pretreatment of biomass is a promising technology for increasing the release of sugars from recalcitrant lignocellulosic biomass. However, due to the reductive status of ferrous ion and its susceptibility to oxidation with exposure to atmosphere, its effective application presumably requires anaerobic aqueous conditions created by nitrogen gas-purging, which adds extra costs. The objective of this study was to assess the effectiveness of oxidative iron ion, (i.e., ferric ion) as a co-catalyst in DA pretreatment of biomass, using an anaerobic chamber to strictly control exposure to oxygen during setup and post-pretreatment analyses. Remarkably, the ferric ions were found to be as efficient as ferrous ions in enhancing sugar release during DA pretreatment of biomass, which may be attributed to the observation that a major portion of the initial ferric ions were converted to ferrous during pretreatment. Furthermore, the detection ...

Mechanical refining is a low-capital and well-established technology used in pulp and paper industry to improve fiber bonding for product strength. Refining can also be applied in a biorefinery context to overcome the recalcitrance of pretreated biomass by opening up the biomass structure and modifying substrate properties (e.g., morphology, particle size, porosity, crystallinity), which increases enzyme accessibility to substrate and improves carbohydrate conversion. Although several characterization methods have been used to identify the changes in substrate properties, there is no systematic approach to evaluate the extent of fiber cell wall disruption and what physical properties can explain the improvement in enzymatic digestibility when pretreated lignocellulosic biomass is mechanically refined. This is because the fiber cell wall is complex across multiple scales, including the molecular scale, nano- and meso-scale (microfibril), and microscale (tissue level). A combination o...

The model yeast, is not known to be oleaginous. However, an industrial wild-type strain, D5A, was shown to accumulate over 20% storage lipids from glucose when growth is nitrogen-limited compared to no more than 7% lipid accumulation without nitrogen stress. To elucidate the mechanisms of D5A oleaginicity, we compared physiological and metabolic changes; as well as the transcriptional profiles of the oleaginous industrial strain, D5A, and a non-oleaginous laboratory strain, BY4741, under normal and nitrogen-limited conditions using analytic techniques and next-generation sequencing-based RNA-Seq transcriptomics. Transcriptional levels for genes associated with fatty acid biosynthesis, nitrogen metabolism, amino acid catabolism, as well as the pentose phosphate pathway and ethanol oxidation in central carbon (C) metabolism, were up-regulated in D5A during nitrogen deprivation. Despite increased carbon flux to lipids, most gene-encoding enzymes involved in triacylglycerol (TAG) assemb...

Strategies for maximizing the microbial production of bio-based chemicals and fuels include eliminating branched points to streamline metabolic pathways. While this is often achieved by removing key enzymes, the introduction of nonnative enzymes can provide metabolic shortcuts, bypassing branched points to decrease the production of undesired side-products. Pyruvate decarboxylase (PDC) can provide such a shortcut in industrially promising thermophilic organisms; yet to date, this enzyme has not been found in any thermophilic organism. Incorporating nonnative enzymes into host organisms can be challenging in cases such as this, where the enzyme has evolved in a very different environment from that of the host. In this study, we use computational protein design to engineer the PDC to resist thermal denaturation at the growth temperature of a thermophilic host. We generate thirteen PDC variants using the Rosetta protein design software. We measure thermal stability of the wild-type PDC...

Microorganisms have evolved different and yet complementary mechanisms to degrade biomass in the biosphere. The chemical biology of lignocellulose deconstruction is a complex and intricate process that appears to vary in response to specific ecosystems. These microorganisms rely on simple to complex arrangements of glycoside hydrolases to conduct most of these polysaccharide depolymerization reactions and also, as discovered more recently, oxidative mechanisms via lytic polysaccharide monooxygenases or non-enzymatic Fenton reactions which are used to enhance deconstruction. It is now clear that these deconstruction mechanisms are often more efficient in the presence of the microorganisms. In general, a major fraction of the total plant biomass deconstruction in the biosphere results from the action of various microorganisms, primarily aerobic bacteria and fungi, as well as a variety of anaerobic bacteria. Beyond carbon recycling, specialized microorganisms interact with plants to ma...

Switchgrass (), a robust perennial C4-type grass, has been evaluated and designated as a model bioenergy crop by the U.S. DOE and USDA. Conventional breeding of switchgrass biomass is difficult because it displays self-incompatible hindrance. Therefore, direct genetic modifications of switchgrass have been considered the more effective approach to tailor switchgrass with traits of interest. Successful transformations have demonstrated increased biomass yields, reduction in the recalcitrance of cell walls and enhanced saccharification efficiency. Several tissue culture protocols have been previously described to produce transgenic switchgrass lines using different nutrient-based media, co-cultivation approaches, and antibiotic strengths for selection. After evaluating the published protocols, we consolidated these approaches and optimized the process to develop a more efficient protocol for producing transgenic switchgrass. First, seed sterilization was optimized, which led to a 20% ...

Poly(ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers and is accumulating in the environment at a staggering rate as discarded packaging and textiles. The properties that make PET so useful also endow it with an alarming resistance to biodegradation, likely lasting centuries in the environment. Our collective reliance on PET and other plastics means that this buildup will continue unless solutions are found. Recently, a newly discovered bacterium, 201-F6, was shown to exhibit the rare ability to grow on PET as a major carbon and energy source. Central to its PET biodegradation capability is a secreted PETase (PET-digesting enzyme). Here, we present a 0.92 Å resolution X-ray crystal structure of PETase, which reveals features common to both cutinases and lipases. PETase retains the ancestral α/β-hydrolase fold but exhibits a more open active-site cleft than homologous cutinases. By narrowing the binding cleft via mutation of two active-site resi...

Consolidated bioprocessing (CBP) by anaerobes, such as Clostridium thermocellum, which combine enzyme production, hydrolysis, and fermentation are promising alternatives to historical economic challenges of using fungal enzymes for biological conversion of lignocellulosic biomass. However, limited research has integrated CBP with real pretreated biomass, and understanding how pretreatment impacts subsequent deconstruction by CBP vs. fungal enzymes can provide valuable insights into CBP and suggest other novel biomass deconstruction strategies. This study focused on determining the effect of pretreatment by dilute sulfuric acid alone (DA) and with tetrahydrofuran (THF) addition via co-solvent-enhanced lignocellulosic fractionation (CELF) on deconstruction of corn stover and Populus with much different recalcitrance by C. thermocellum vs. fungal enzymes and changes in pretreated biomass related to these differences. Coupling CELF fractionation of corn stover and Populus with subsequen...

In planta expression of a thermophilic endoglucanase (AcCel5A) reduces recalcitrance by creating voids and other irregularities in cell walls of Arabidopsis thaliana that increase enzyme accessibility without negative impacts on plant growth or cell wall composition. Our results suggest that cellulose β-1-4 linkages can be cut sparingly in the assembling wall and that these minimal changes, made at the proper time, have an impact on plant cell wall recalcitrance without negative effects on overall plant development.

... Mark W. Jarvis†, Thomas J. Haas‡, Bryon S. Donohoe‡, John W. Daily§, Katherine R. Gaston†, W ... This analysis revealed that micropores develop in the cell wall around 550 °C and increase in size and coalesce into a cenosphere morphology with increasing temperature. ...

ABSTRACT Research conducted at NREL has shown that lignin undergoes a phase transition during thermochemical pretreatments conducted above its glass transition temperature. The lignin coalesces within the plant cell wall and appears as microscopic droplets on cell surfaces. It is clear that pretreatment causes significant changes in lignin distribution in pretreatments at all scales from small laboratory reactors to pilot scale reactors. A method for selectively extracting lignin droplets from the surfaces of pretreated cell walls has allowed us to characterize the chemical nature and molecular weight distribution of this fraction. The effect of lignin redistribution on the digestibility of pretreated solids has also been tested. It is clear that removal of the droplets increases the digestibility of pretreated corn stover. The improved digestibility could be due to decreased non-specific binding of enzymes to lignin in the droplets, or because the droplets no longer block access to cellulose.

ABSTRACT The purpose of this research was to advance our understanding of the effect of pretreatment on the lignin component in biomass so that engineering research can be directed more efficiently. Research conducted at NREL over the past few years has shown that lignin undergoes a phase transition during thermochemical pretreatments conducted above its glass transition temperature. The lignin coalesces within the plant cell wall and appears as microscopic droplets on the surfaces of cells. In recent years, we have studied the redistribution of lignin that occurs during dilute acid pretreatment using small lab scale reactors operated under conditions that were not strictly process relevant. Typically, samples were pretreated in flow reactors with high liquid to solid ratios, with no acid, and for relatively long periods of time. However, microscopic analysis showed that changes were occurring both within the cell wall and on cell surfaces. It was clear that pretreatment could cause significant changes in the distribution of lignin. More recently we have studied the changes in lignin distribution that could occur under more process relevant conditions. Dilute acid pretreatments have been performed in a steam gun reactor at high solids loadings (43%), although at somewhat lower temperatures (150 and 170oC) and longer times (5-60 min) than normally used in our pilot scale reactors. Our studies have shown that lignin still undergoes a significant change in distribution and that coalescence and droplet formation still occur under these conditions. A method for selectively isolating these lignin droplets from the surface of pretreated cell walls using extraction with aqueous dioxane has been successfully employed. Characterization of the extracts by 2D NMR (HSQC) showed they contained carbohydrates and that the carbohydrates were covalently bound to the lignin in at least 2 types of lignin-carbohydrate complexes. Chemical analysis of the extracts showed the extracts contained only low levels of carbohydrates (2-6%) with the highest levels observed in the extracts from pretreatments performed at the lowest severity conditions. There was also evidence that the carbohydrates were at least oligomeric in size (i.e., not monomers or dimers). Based on this evidence, it appears likely that the frequency of the lignin-carbohydrate linkages found in the lignin extracts were low at about one cross-linkage per 80 to 100 lignin units. The effect of lignin redistribution on the digestibility of the pretreated solids was also tested, using the solids remaining after extracting the lignin droplets from the cell wall surfaces It was clear that removal of the droplets produced an increase in the digestibility of the pretreated corn stover. Whereas the digestibility of the cellulose was strongly correlated with the level of xylan removal, droplet removal increased cellulose conversion by about 15%. The improved digestibility could be due to a decrease in non-specific binding of the enzymes to the lignin in the droplets, or it could be because the droplets no longer blocked access to cellulose in the pretreated solids.