Codon optimization improves the prediction of xylose metabolism from gene content in budding yeasts
Data accompanying Nalabothu et al. 2023 Molecular Biology and Evolution
genome evolution↗
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Effect of biomass liquefaction on glucose and xylose prices predicted by National Renewable Energy Laboratory biochemical sugar model
Abstract The National Renewable Energy Laboratory (NREL) published a model in 2017 that enables the minimum selling price of lignocellulosic sugar to be calculated. The model can be modified to suit any biomass feedstock and operational design. In the present case, the model is used to understand the economics of a process configuration that incorporates liquefaction as a preprocessing step in corn‐stover‐fed biorefinery. This study demonstrates a quantitative approach utilizing an existing biorefinery setup to simulate the biomass liquefaction technique while estimating the price of the resulting sugar product. The objective is to understand whether the addition of liquefaction methodology – and the substitution of acid pretreatment – can reduce the cost of lignocellulosic sugars. The reason for setting up a liquefaction unit at the start is to reduce the yield stress of biomass slurry so that the flow remains unrestricted downstream. The liquefaction process is also unique because it uses no chemicals and saves the cost of pretreatment. The pretreatment step is bypassed because the output of liquefaction can be fed into enzyme hydrolysis just after simple cooking. The liquefaction process can be performed in three modes: enzyme, enzyme mimetic, and a combination of enzyme and enzyme mimetic. The results from the BC1707 model indicate the minimum cost for the enzyme liquefaction route. © 2022 The Authors. Biofuels, Bioproducts and Biorefining published by Society of Industrial Chemistry and John Wiley & Sons Ltd.
09 BIOMASS FUELS↗
Arabinose- and xylose-modified analogs of 2′,3′-cGAMP act as STING agonists
Not provided.
Biochemistry & Molecular Biology↗
Bioprocess development and scale-up for cis , cis -muconic acid production from glucose and xylose by Pseudomonas putida
Bioprocess development enhanced muconate titers and productivities from mixed sugars, leading to reduced production costs and a significant decrease in GHG emissions compared to fossil carbon-based adipic acid production. Created with BioRender.com.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Over-expression of AZF1 improves the rate of anaerobic xylose fermentation in engineered yeast strains
The present invention provides an isolated AZF1 gene sequence, recombinant vectors, and recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast with isolated AZF1 gene sequence useful for biofuel production are also provided.
Gasch, Audrey P.↗
Data for Engineering and Evolution of Yarrowia lipolytica for Producing Lipids from Lignocellulosic Hydrolysates
Yarrowia lipolytica , an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.
Hydrolysate↗
Expanded genome and proteome reallocation in a novel, robust Bacillus coagulans strain capable of utilizing pentose and hexose sugars
Bacillus coagulans, a Gram-positive thermophilic bacterium, is recognized for its probiotic properties and recent development as a microbial cell factory. Despite its importance for biotechnological applications, the current understanding of B. coagulans’ robustness is limited, especially for undomesticated strains. To fill this knowledge gap, we characterized the metabolic capability and performed functional genomics and systems analysis of a novel, robust strain, B. coagulans B-768. Genome sequencing revealed that B-768 has the largest B. coagulans genome known to date (3.94 Mbp), about 0.63 Mbp larger than the average genome of sequenced B. coagulans strains, with expanded carbohydrate metabolism and mobilome. Functional genomics identified a well-equipped genetic portfolio for utilizing a wide range of C5 (xylose, arabinose), C6 (glucose, mannose, galactose), and C12 (cellobiose) sugars present in biomass hydrolysates, which was validated experimentally. For growth on individual xylose and glucose, the dominant sugars in biomass hydrolysates, B-768 exhibited distinct phenotypes and proteome profiles. Faster growth and glucose uptake rates resulted in lactate overflow metabolism, which makes B. coagulans a lactate overproducer; however, slower growth and xylose uptake diminished overflow metabolism due to the high energy demand for sugar assimilation. Carbohydrate Transport and Metabolism (COG-G), Translation (COG-J), and Energy Conversion and Production (COG-C) made up 60%–65% of the measured proteomes but were allocated differently when growing on xylose and glucose. The trade-off in proteome reallocation, with high investment in COG-C over COG-G, explains the xylose growth phenotype with significant upregulation of xylose metabolism, pyruvate metabolism, and tricarboxylic acid (TCA) cycle. Strain B-768 tolerates and effectively utilizes inhibitory biomass hydrolysates containing mixed sugars and exhibits hierarchical sugar utilization with glucose as the preferential substrate.
carbohydrate metabolism↗
Abundance of Major Cell Wall Components in Natural Variants and Pedigrees of Populus trichocarpa
The rapid analysis of biopolymers including lignin and sugars in lignocellulosic biomass cell walls is essential for the analysis of the large sample populations needed for identifying heritable genetic variation in biomass feedstocks for biofuels and bioproducts. In this study, we reported the analysis of cell wall lignin content, syringyl/guaiacyl (S/G) ratio, as well as glucose and xylose content by high-throughput pyrolysis-molecular beam mass spectrometry (py-MBMS) for >3,600 samples derived from hundreds of accessions of Populus trichocarpa from natural populations, as well as pedigrees constructed from 14 parents (7 × 7). Partial Least Squares (PLS) regression models were built from the samples of known sugar composition previously determined by hydrolysis followed by nuclear magnetic resonance (NMR) analysis. Key spectral features positively correlated with glucose content consisted of m/z 126, 98, and 69, among others, deriving from pyrolyzates such as hydroxymethylfurfural, maltol, and other sugar-derived species. Xylose content positively correlated primarily with many lignin-derived ions and to a lesser degree with m/z 114, deriving from a lactone produced from xylose pyrolysis. Models were capable of predicting glucose and xylose contents with an average error of less than 4%, and accuracy was significantly improved over previously used methods. The differences in the models constructed from the two sample sets varied in training sample number, but the genetic and compositional uniformity of the pedigree set could be a potential driver in the slightly better performance of that model in comparison with the natural variants. Broad-sense heritability of glucose and xylose composition using these data was 0.32 and 0.34, respectively. In summary, we have demonstrated the use of a single high-throughput method to predict sugar and lignin composition in thousands of poplar samples to estimate the heritability and phenotypic plasticity of traits necessary to develop optimized feedstocks for bioenergy applications.
09 BIOMASS FUELS↗
Engineering and evolution of Yarrowia lipolytica for producing lipids from lignocellulosic hydrolysates
Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.
60 APPLIED LIFE SCIENCES↗
Engineering the cellulolytic bacterium, Clostridium thermocellum, to co-utilize hemicellulose
Not Available
Chou, Katherine J. (ORCID:0000000203187857)↗
Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2
ABSTRACT Pseudomonas putida have emerged as promising biocatalysts for the conversion of sugars and aromatic compounds obtained from lignocellulosic biomass. Understanding the role of carbon catabolite repression (CCR) in these strains is critical to optimize biomass conversion to fuels and chemicals. The CCR functioning in P. putida M2, a strain capable of consuming both hexose and pentose sugars as well as aromatic compounds, was investigated by cultivation experiments, proteomics, and CRISPRi-based gene repression. Strain M2 co-utilized sugars and aromatic compounds simultaneously; however, during cultivation with glucose and aromatic compounds ( p- coumarate and ferulate) mixture, intermediates (4-hydroxybenzoate and vanillate) accumulated, and substrate consumption was incomplete. In contrast, xylose-aromatic consumption resulted in transient intermediate accumulation and complete aromatic consumption, while xylose was incompletely consumed. Proteomics analysis revealed that glucose exerted stronger repression than xylose on the aromatic catabolic proteins. Key glucose (Eda) and xylose (XylX) catabolic proteins were also identified at lower abundance during cultivation with aromatic compounds implying simultaneous catabolite repression by sugars and aromatic compounds. Reduction of crc expression via CRISPRi led to faster growth and glucose and p -coumarate uptake in the CRISPRi strains compared to the control, while no difference was observed on xylose+ p -coumarate. The increased abundances of Eda and amino acid biosynthesis proteins in the CRISPRi strain further supported these observations. Lastly, small RNAs (sRNAs) sequencing results showed that CrcY and CrcZ homologues levels in M2, previously identified in P. putida strains, were lower under strong CCR (glucose+ p -coumarate) condition compared to when repression was absent ( p -coumarate or glucose only). IMPORTANCE A newly isolated Pseudomonas putida strain, P. putida M2, can utilize both hexose and pentose sugars as well as aromatic compounds making it a promising host for the valorization of lignocellulosic biomass. Pseudomonads have developed a regulatory strategy, carbon catabolite repression, to control the assimilation of carbon sources in the environment. Carbon catabolite repression may impede the simultaneous and complete metabolism of sugars and aromatic compounds present in lignocellulosic biomass and hinder the development of an efficient industrial biocatalyst. This study provides insight into the cellular physiology and proteome during mixed-substrate utilization in P. putida M2. The phenotypic and proteomics results demonstrated simultaneous catabolite repression in the sugar-aromatic mixtures, while the CRISPRi and sRNA sequencing demonstrated the potential role of the crc gene and small RNAs in carbon catabolite repression.
59 BASIC BIOLOGICAL SCIENCES↗
raogroupuiuc/yl_variantcalling
NGS analysis for mutation analysis in Yarrowia lipolytica evolved strains. Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.
Deewan, Anshu↗
Cost impact of hexose-to-pentose sugar ratios for biomanufacturing
Central to the long-term vision for biomanufacturing is the ability to deconstruct plant cell walls to sugars that microbes can convert to products. Aside from glucose, the most abundant sugar in biomass is xylose, a pentose sugar. Industrially relevant microbes have been engineered to co-ferment xylose and glucose. Most nth plant technoeconomic analyses (TEAs) assume similar consumption rates and product yields for both sugars, but in reality, xylose is consumed more slowly. Feedstocks can be selected, or engineered, to alter the glucan-to-xylan ratio (GXR) but no TEAs have quantified the impact of this strategy systematically. This study explores the cost impacts of varying the glucan-to-xylan ratio (GXR) from 1.9 to 6.7 for co-fermenting glucose and xylose to ethanol and bisabolene. The minimum selling prices (MSPs) for both products decrease as the GXR increases, with the largest reductions at shorter residence times. For instance, with an increase in GXR from 1.9 to 6.7, ethanol’s MSP drops by 16 %, 5 %, and 3 % at 24, 72, and 144 h, respectively, while bisabolene’s MSP declines by 23 %, 20 %, and 15 % at 24, 72, and 120 h. Particularly for early-stage commercialization, the results suggest that altering or selecting for feedstocks with higher GXR can minimize capital costs by reducing optimal residence times. Capital-constrained biorefineries operating with shorter residence times can justify paying up to 1.5X to 2X the price for feedstocks with a higher GXR, based on the expected improvements in their product yield and overall process economics.
Delayed xylose utilization↗
A New Subfamily of Glycoside Hydrolase Family 30 with Strict Xylobiohydrolase Function
The Acetivibrioclariflavus (basonym: Clostridium clariflavum) glycoside hydrolase family 30 cellulosomal protein encoded by the Clocl_1795 gene was highly represented during growth on cellulosic substrates. In this report, the recombinantly expressed protein has been characterized and shown to be a non-reducing terminal (NRT)-specific xylobiohydrolase (AcXbh30A). Biochemical function, optimal biophysical parameters, and phylogeny were investigated. The findings indicate that AcXbh30A strictly cleaves xylobiose from the NRT up until an α-1,2-linked glucuronic acid (GA)-decorated xylose if the number of xyloses is even or otherwise a single xylose will remain resulting in a penultimate GA-substituted xylose. Unlike recently reported xylobiohydrolases, AcXbh30A has no other detectable hydrolysis products under our optimized reaction conditions. Sequence analysis indicates that AcXbh30A represents a new GH30 subfamily. This new xylobiohydrolase may be useful for commercial production of industrial quantities of xylobiose.
59 BASIC BIOLOGICAL SCIENCES↗
UDP-glucuronic acid decarboxylase in alfalfa: a target to improve ruminal digestibility of stems
Alfalfa (Medicago sativa) has a high nutritional value, but poor digestibility of the stems limits its value as an energy source in ruminant diets. Xylan and lignin negatively affect cell wall digestibility, whereas pectins have high digestibility in the rumen. In plants, UDP-xylose synthase (UXS) catalyses the decarboxylation of UDP-glucuronic acid to form UDP-xylose in an irreversible step that is key for xylan synthesis. Here, we functionally characterized two UXS genes in alfalfa, namely MsaUXS2 and MsaUXS4, and investigated their impact on ruminal digestibility. Both genes are more highly expressed in stems than leaves, and the enzymes have UDP-glucuronic acid decarboxylase activity in vitro. Silencing of MsaUXS2 and MsaUXS4 via RNAi altered plant growth and resulted in a 40% decrease in xylose, a 115% increase in arabinose, and a 60% increase in galacturonic acid in the polysaccharide matrix as well as a 20% decrease in lignin in the cell wall. Together, our results show a major role for UXS2 and UXS4 in xylan synthesis and secondary cell wall deposition in alfalfa. Additionally, in vitro rumen digestibility assays for the silenced lines had on average 30% increased gas production at 24 h, demonstrating the potential of targeting UXS genes to increase stem digestibility.
UDP-xylose synthase↗
Development of sulfonated carbon-based solid-acid catalysts derived from biorefinery residues and biomass ash for xylan hydrolysis
In this study, biorefinery residues and biomass ash were used to develop sulfonated carbon-based solid-acid catalysts to enhance xylan hydrolysis. Here, metals extracted from the biomass ash were impregnated into a carbon support prepared from biorefinery residues to synthesize sulfonated ash-impregnated carbon-based catalyst. Metals present in the ash most probably are responsible for the increased acid density in the catalyst. Using this catalyst, 11.4 % xylose yield was produced, an increase of 171 % over the yield obtained from a catalyst without ash impregnation. Using a xylan-to-catalyst ratio of 1:2, 72.9 % xylose yield was obtained, comparable to using 0.5 wt% sulfuric acid under the same reaction condition. Moreover, this catalyst significantly inhibited xylose dehydration, only forming 11.3 % furfural compared to that generated using dilute acid. Hence, these results show the potential for using biomass ash as a metal source to increase the number of acid sites in solid-acid catalysts used for biomass pretreatment.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Deconstruction of Woody Biomass via Protic and Aprotic Ionic Liquid Pretreatment for Ethanol Production
Ionic liquids (ILs) have emerged as important solvents for conversion of lignocellulosic feedstocks to fuels and chemicals due to their ability to enable efficient biomass deconstruction and fractionation. Woody biomass derived from forest and agricultural residues has the potential to be used for production of biofuels and its removal from forests can help mitigate disastrous wildfires in fire-prone states like California. This study evaluated woody biomass types (pine, almond, walnut, and fir) from California as potential biofuel feedstocks. The feedstocks were pretreated with the ILs cholinium lysinate ([Ch][Lys]) and ethanolamine acetate ([EOA][OAc]), followed by enzymatic hydrolysis and fermentation of lignocellulosic sugars to produce ethanol. Under optimal conditions, [EOA][OAc] pretreatment and enzymatic hydrolysis generated glucose and xylose yields in the range of 24-82 and 14-80%, respectively, while glucose and xylose yields for the [Ch][Lys] ranged between 28-83 and 23-80%, respectively. Maximum fermentable sugar was released from almond wood, and the lowest amount was from pine and fir. Further, blends of feedstocks were also explored, and a blend with a mass ratio of 2/2/1 (almond/walnut/pine) resulted in maximum glucose and xylose (>90%) yields using [Ch][Lys]. Fermentation of this hydrolysate using a C5-utilizing strain of Saccharomyces cerevisiae resulted in a maximum ethanol concentration of 17.9 g/L for mixture biomass hydrolysate, corresponding to 60.8% fermentation efficiency. This study represents the first demonstration of the use of these ILs for pretreatment of woody biomass blends that resulted in a high overall conversion efficiency for ethanol production.
09 BIOMASS FUELS↗
Selective designer hydrolysates from Miscanthus bioenergy crop for sustainable utilization
Designer enzymatic hydrolysates deliver targeted, optimized fermentable sugars while reducing the formation of inhibitory by-products. Herein, five distinct enzymatic hydrolysates (EH) were generated from Miscanthus biomass using alkaline-ethanol fractionation and hydrothermal-mechanical refining (HMR) pretreatment approaches. Noticeably, alkali-ethanol fractionated hemicellulose A (HMA) and hemicellulose B (HMB) hydrolysis resulted in xylose-rich enzymatic hydrolysates with 104.8 ± 5.6 g L −1 and 173.4 ± 4.6 g L −1 xylose, respectively. All five hydrolysates encompassing varied carbon to nitrogen ratios were evaluated for lipid production using an engineered oleaginous yeast, R. toruloides 880-ADS. Microbial fermentation of xylose-rich hydrolysates, viz. HMR-EH2, HMA-EH, and HMB-EH, resulted in lipid yields ranging from 0.05 to 0.12 g g −1 sugar. Compositional and 2D NMR analyses revealed that HMA-EH residues are highly lignin-enriched while preserving the non-condensed structure conducive to valorization. Overall, the findings highlighted a novel, selective trade-off approach for maximizing lipid titers from designer hydrolysates, corroborating complete resource recovery for establishing integrated biorefineries.
Singh, Shuchi [University of Illinois at Urbana-Ch↗