Bradley M. Holmes

Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli.

One approach to reducing the costs of advanced biofuel production from cellulosic biomass is to engineer a single microorganism to both digest plant biomass and produce hydrocarbons that have the properties of petrochemical fuels. Such an organism would require pathways for hydrocarbon production and the capacity to secrete sufficient enzymes to efficiently hydrolyze cellulose and hemicellulose. To demonstrate how one might engineer and coordinate all of the necessary components for a biomass-degrading, hydrocarbon-producing microorganism, we engineered a microorganism naïve to both processes, Escherichia coli, to grow using both the cellulose and hemicellulose fractions of several types of plant biomass pretreated with ionic liquids. Our engineered strains express cellulase, xylanase, beta-glucosidase, and xylobiosidase enzymes under control of native E. coli promoters selected to optimize growth on model cellulosic and hemicellulosic substrates. Furthermore, our strains grow using either the cellulose or hemicellulose components of ionic liquid-pretreated biomass or on both components when combined as a coculture. Both cellulolytic and hemicellulolytic strains were further engineered with three biofuel synthesis pathways to demonstrate the production of fuel substitutes or precursors suitable for gasoline, diesel, and jet engines directly from ionic liquid-treated switchgrass without externally supplied hydrolase enzymes. This demonstration represents a major advance toward realizing a consolidated bioprocess. With improvements in both biofuel synthesis pathways and biomass digestion capabilities, our approach could provide an economical route to production of advanced biofuels.

Understanding the interactions of cellulose with ionic liquids: a molecular dynamics study.

Ionic liquids (ILs) have recently been demonstrated to be highly effective solvents for the dissolution of cellulose and lignocellulosic biomass. To date, there is no definitive rationale for selecting ionic liquids that are capable of dissolving these biopolymers. In this work, an all-atom force field for the IL 1-ethyl-3-methylimidazolium acetate [C2mim][OAc] was developed and the behavior of cellulose in this IL was examined using molecular dynamics simulations of a series of (1-4) linked beta-d-glucose oligomers with a degree of polymerization n = 5, 6, 10, and 20. Molecular dynamics simulations were also carried out on cellulose oligomers in two common solvents, water and methanol, which are known to precipitate cellulose from IL solutions, to determine the extent and energetics of the interactions between these solvents and the cellulosic oligomers. Thermodynamic properties, such as density and solubility, as well as the two-body solute-solvent interaction energy terms, were calculated. The structural and dynamic behavior of solutions was analyzed and the conformations of cellulose oligomers were compared in ionic liquid and water mixtures. It was found that the interaction energy between the polysaccharide chain and the IL was stronger than that for either water or methanol. In addition to the anion acetate forming strong hydrogen bonds with hydroxyl groups of the cellulose, some of the cations were found to be in close contact with the polysaccharides through hydrophobic interactions. These results support the concept that the cation may play a significant role in the dissolution of cellulose by [C2mim][OAc]. It is also observed that the preferred beta-(1,4)-glycosidic linkage conformation of the cellulose was altered when dissolved in [C2mim][OAc] as compared to that found in crystalline cellulose dispersed in water. To our knowledge, this report is the first theoretical study that addresses the key factors in cellulose dissolution using an ionic liquid.

Understanding the impact of ionic liquid pretreatment on eucalyptus

Background: The development of cost-competitive biofuels necessitates the realization of advanced biomass pretreatment technologies. Ionic liquids provide a basis for one of the most promising pretreatment technologies and are known to allow effective processing of cellulose and some biomass species. Results & discussion: Here, we demonstrate that the ionic liquid 1-ethyl-3-methyl imidazolium acetate, [C2mim][OAc], induces structural changes at the molecular level in the cell wall of Eucalyptus globulus. Deacetylation of xylan, acetylation of the lignin units, selective removal of guaiacyl units (increasing the syringyl:guaiacyl ratio) and decreased β-ether content were the most prominent changes observed. Scanning electron microscopy images of the plant cell wall sections reveal extensive swelling during [C2mim][OAc] pretreatment. X-ray diffraction measurements indicate a change in cellulose crystal structure from cellulose I to cellulose II after [C2mim][OAc] pretreatment. Enzymatic saccharification of the pretreated material produced increased sugar yields and improved hydrolysis kinetics after [C2mim][OAc] pretreatment. Conclusion: These results provide new insight into the mechanism of ionic liquid pretreatment and reaffirm that this approach may be promising for the production of cellulosic biofuels from woody biomass.

Recovery of sugars from ionic liquid biomass liquor by solvent extraction

The dissolution of biomass into ionic liquids (ILs) has been shown to be a promising alternative biomass pretreatment technology, facilitating faster breakdown of cellulose through the disruption of lignin and the decrystallization of cellulose. Both biological and chemical catalysis have been employed to enhance the conversion of IL-treated biomass polysaccharides into monomeric sugars. However, biomass-dissolving ILs, sugar monomers, and smaller carbohydrate oligomers are all soluble in water. This reduces the overall sugar content in the recovered solid biomass and complicates the recovery and recycle of the IL. Near-complete recovery of the IL and the holocellulose is essential for an IL-based pretreatment technology to be economically feasible. To address this, a solvent extraction technique, based on the chemical affinity of boronates such as phenylboronic acid and naphthalene-2-boronic acid for sugars, was applied to the extraction of glucose, xylose, and cellobiose from aqueous mixtures of 1-ethyl-3-methylimidazolium acetate. It was shown that boronate complexes could extract up to 90% of mono- and disaccharides from aqueous IL solutions, 100% IL systems, and hydrolysates of corn stover containing IL. The use of boronate complexes shows significant potential as a way to recover sugars at several stages in ionic liquid biomass pretreatment processes, delivering a concentrated solution of fermentable sugars, minimizing toxic byproducts, and facilitating ionic liquid cleanup and recycle.

A facile method for the recovery of ionic liquid and lignin from biomass pretreatment

In the biochemical conversion of lignocellulosic biomass to biofuels, the process of pretreatment is currently one of the most difficult and expensive operations. The use of ionic liquids (ILs) in biomass pretreatment has received considerable attention recently because of their effectiveness at decreasing biomass recalcitrance to subsequent enzymatic hydrolysis. In addition, ILs have the potential for decreasing the need for corrosive or toxic chemicals and associated waste streams that can be generated by other pretreatment methods that utilize acids and/or bases. In this article, we address two significant challenges to the realization of a practical IL pretreatment process. First, we describe a mixture containing specific proportions of a ketone and an alcohol that precipitates cellulose and lignocellulosic biomass from solutions of the IL 1-ethyl-3-methylimidazolium acetate without the formation of intermediate gel phases. Second, an IL recovery process is described that removes lignin and most residual IL solutes and that minimizes energy and solvent use. These two techniques are demonstrated by the pretreatment of 100 g of corn stover with the recovery of 89% of the initial IL and separate corn stover fractions rich in glucans, xylans, lignin, and non-polar substances. These results highlight one potential approach towards the realization of a scalable ionic liquid pretreatment process technology that enables ionic liquid recovery and reuse.

Production and extraction of sugars from switchgrass hydrolyzed in ionic liquids

BackgroundThe use of Ionic liquids (ILs) as biomass solvents is considered to be an attractive alternative for the pretreatment of lignocellulosic biomass. Acid catalysts have been used previously to hydrolyze polysaccharides into fermentable sugars during IL pretreatment. This could potentially provide a means of liberating fermentable sugars from biomass without the use of costly enzymes. However, the separation of the sugars from the aqueous IL and recovery of IL is challenging and imperative to make this process viable.ResultsAqueous alkaline solutions are used to induce the formation of a biphasic system to recover sugars produced from the acid catalyzed hydrolysis of switchgrass in imidazolium-based ILs. The amount of sugar produced from this process was proportional to the extent of biomass solubilized. Pretreatment at high temperatures (e.g., 160°C, 1.5 h) was more effective in producing glucose. Sugar extraction into the alkali phase was dependent on both the amount of sugar produced by acidolysis and the alkali concentration in the aqueous extractant phase. Maximum yields of 53% glucose and 88% xylose are recovered in the alkali phase, based on the amounts present in the initial biomass. The partition coefficients of glucose and xylose between the IL and alkali phases can be accurately predicted using molecular dynamics simulations.ConclusionsThis biphasic system may enable the facile recycling of IL and rapid recovery of the sugars, and provides an alternative route to the production of monomeric sugars from biomass that eliminates the need for enzymatic saccharification and also reduces the amount of water required.

Biological Characterisation of Haliclona (?gellius) sp.: Sponge and Associated Microorganisms

We have characterised the northern Pacific undescribed sponge Haliclona (?gellius) sp. based on rDNA of the sponge and its associated microorganisms. The sponge is closely related to Amphimedon queenslandica from the Great Barrier Reef as the near-complete 18S rDNA sequences of both sponges were identical. The microbial fingerprint of three specimens harvested at different times and of a transplanted specimen was compared to identify stably associated microorganisms. Most bacterial phyla were detected in each sample, but only a few bacterial species were determined to be stably associated with the sponge. A sponge-specific β- and γ-Proteobacterium were abundant clones and both of them were present in three of the four specimens analysed. In addition, a Planctomycete and a Crenarchaea were detected in all sponge individuals. Both were closely related to operational taxonomic units that have been found in other sponges, but not exclusively in sponges. Interestingly, also a number of clones that are closely related to intracellular symbionts from insects and amoeba were detected.

High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration

The high cost of lignocellulolytic enzymes is one of the main barriers towards the development of economically competitive biorefineries. Enzyme engineering can be used to significantly increase the production rate as well as specific activity of enzymes. However, the success of enzyme optimization efforts is currently limited by a lack of robust high-throughput (HTP) cellulase screening platforms for insoluble pretreated lignocellulosic substrates. We have developed a cost-effective microplate based HTP enzyme-screening platform for ionic liquid (IL) pretreated lignocellulose. By performing in-situ biomass regeneration in micro-volumes, we can volumetrically meter biomass (sub-mg loading) and also precisely control the amount of residual IL for engineering novel IL-tolerant cellulases. Our platform only requires straightforward liquid-handling steps and allows the integration of biomass regeneration, washing, saccharification, and imaging steps in a single microtiter plate. The proposed method can be used to screen individual cellulases as well as to develop novel cellulase cocktails.

Enzymatic hydrolysis of cellulose by the cellobiohydrolase domain of CelB from the hyperthermophilic bacterium Caldicellulosiruptor saccharolyticus

The celB gene of Caldicellulosiruptor saccharolyticus was cloned and expressed in Escherichia coli to create a recombinant biocatalyst for hydrolyzing lignocellulosic biomass at high temperature. The GH5 domain of CelB hydrolyzed 4-nitrophenyl-β-D-cellobioside and carboxymethyl cellulose with optimum activity at pH 4.7-5.5 and 80°C. The recombinant GH5 and CBM3-GH5 constructs were both stable at 80°C with half-lives of 23 h and 39 h, respectively, and retained >94% activity after 48 h at 70°C. Enzymatic hydrolysis of corn stover and cellulose pretreated with the ionic liquid 1-ethyl-3-methylimidazolium acetate showed that GH5 and CBM3-GH5 primarily produce cellobiose, with product yields for CBM3-GH5 being 1.2- to 2-fold higher than those for GH5. Confocal microscopy of bound protein on cellulose confirmed tighter binding of CBM3-GH5 to cellulose than GH5, indicating that the enhancement of enzymatic activity on solid substrates may be due to the substrate binding activity of CBM3 domain.

Identification and Functional Analysis of a Delta-6 Desaturase from the Marine Microalga Glossomastix chrysoplasta

A delta-6 (Δ6) desaturase gene was isolated from the marine microalga Glossomastix chrysoplasta, a stramenopile that produces large amounts of eicosapentaenoic acid (EPA). A functional analysis of this gene was performed in Saccharomyces cerevisiae. Isolation of the Δ6 fatty acid desaturase was achieved via reverse transcriptase-polymerase chain reaction (RT-PCR) with degenerate primers designed from conserved histidine motifs and 5′ and 3′ RACE. Two almost identical copies of Δ6 desaturase were found, differing by nine silent mutations. The existence of two such genes may be a result of a recent gene duplication event, or may have arisen from the possible diploid nature of vegetative algae. This appears to be the first instance of two Δ6 desaturase mRNA sequences existing in the same organism. The isolated mRNA sequences and their corresponding hypothetical protein, GcDES6, were found to contain features characteristic of a membrane-bound Δ6 desaturase, including membrane-spanning regions separating conserved histidine boxes and N-terminal cytochrome b5 fusion. Heterologous expression in S. cerevisiae was used to confirm Δ6 regioselectivity and the function of GcDES6. Both ω3(18:3Δ9,12,15) and ω6(18:2Δ9,12) precursors can be used by GcDES6 in vivo with similar desaturase activity. One intron site was found in the cytochrome b5 fusion region of GcDES6. Although the conservation of intron-exon junctions has been found for several desaturases in humans and in Caenorhabditis elegans, a comparison of introns in GcDES6 and other Δ6 desaturases has not revealed any strong similarities.