The Joint BioEnergy Institute (JBEI) is a research institute funded by the United States Department of Energy. JBEI is led by the Lawrence Berkeley National Laboratory, and includes participation from the Sandia National Laboratory, Lawrence Livermore National Laboratory, as well as UC Berkeley, UC Davis, Iowa State University, and the Carnegie Institute. JBEI is located in Emeryville, California.The goal of The Joint BioEnergy Institute is to develop biofuels, bio-synthesized from lignin derived from corn stover, sorghum and other plant feedstocks (see second generation biofuels) as an alternative to fossil fuels. Additionally, there are efforts to produce bio-based chemicals derived from the deconstruction of lignocellulosic biomass to create bio-based polymers and other commodities such as perfumes, dietary supplements as well as other high-end products. The goal is to use these bio-based chemicals to help finance the change in infrastructure from petroleum fuels to biofuels.JBEI functions as an incubator for scientific discovery bringing together the best and brightest researchers from around the country and the globe.Inside JBEI's Emeryville laboratories, five interlocking scientific divisions–Life-cycle, Economics and Agronomy; Feedstocks; Deconstruction; Biofuels and Bioproducts; and Technology–bring the sunlight-to-biofuels/bioproducts pipeline under one roof.JBEI represents a departure from traditional research institutions that specialize in a single field. Here, an inter-disciplinary team of some 160-plus scientists, post doctoral researchers and graduate students combine their expertise and collaborate to develop genetic, biological, computational and robotic technologies to accelerate the process of discovery.JBEI researchers are developing scientific breakthroughs to produce clean, sustainable, carbon-neutral biofuels and bioproducts.An inter-disciplinary team of scientists is using the latest techniques in molecular biology, chemical and genetic engineering to develop new biological systems, processes and technologies to convert biomass to biofuels and bioproducts.In the lab, JBEI researchers are engineering microbes to transform sugars into energy-rich fuels that can directly replace petroleum-derived gasoline, diesel and jet fuel. Advanced biofuels can also be dropped into today's engines and infrastructures with no loss of performance.Harnessing the solar energy in biomass from grasses and other non-edible plants could meet much of the nation's annual transportation energy needs without contributing to global climate change..
Infiltration of Agrobacterium tumefaciens into Nicotiana benthamiana has become a foundational technique in plant biology, enabling efficient delivery of transgenes in planta with technical ease, robust signal, and relatively high throughput. Despite transient expression's prevalence in disciplines such as synthetic biology, little work has been done to describe and address the variability inherent in this system, a concern for experiments that rely on highly quantitative readouts. In a comprehensive analysis of N. benthamiana agroinfiltration experiments, we model sources of variability that affect transient expression. Our findings emphasize the need to validate normalization methods under the specific conditions of each study, as distinct normalization schemes do not always reduce variation either within or between experiments. Using a dataset of 1915 plants collected over three years, we develop a model of variation in N. benthamiana transient expression, using power analysis to determine the number of individual plants required for a given effect size. Drawing on our longitudinal data, these findings inform practical guidelines for minimizing variability through strategic experimental design and power analysis, providing a foundation for more robust and reproducible use of N. benthamiana in quantitative plant biology and synthetic biology applications.
Lignin is the largest renewable source of aromatic carbon, yet its heterogeneity and recalcitrance limit its use in higher-value bioconversion processes. In this study, Aspergillus niger was engineered to enable the bioconversion of lignin-derived aromatics and base-catalyzed depolymerized (BCD) lignin streams into malic acid, a value-added C4 dicarboxylic acid with broad industrial relevance. Overexpression of the C4 dicarboxylate transporter C4T318 from Aspergillus oryzae enhanced malic acid secretion, while medium optimization under buffered conditions further improved the production. The engineered strain efficiently assimilated representative lignin-derived aromatics, including 4-hydroxybenzoic acid and p-coumaric acid, producing up to 3.9 g/L malic acid. Conversion of BCD lignin liquors from poplar and sorghum demonstrated effective utilization of heterogeneous aromatic mixtures, generating up to 0.82 g/L malic acid. This work demonstrates direct fungal conversion of real lignin streams into malic acid and establishes A. niger as a promising platform for sustainable lignin valorization.
Achieving cost-competitiveness in bio-based products will require efficient use of all biomass components, including the underutilized protein fraction. Proteinaceous biomass sources (such as food waste, distillers grain, and agricultural residues) offer significant potential as feedstocks for integrated biorefineries that can convert all components into fuels, chemicals, and high-value products. This perspective evaluates protein valorization strategies alongside carbohydrate processing, emphasizing the trade-offs between efficient sugar release and maintaining protein functionality. Challenges, including biomass component interactions, pretreatment effects, and nutritional factors, are discussed along with the trade-offs between protein-first and carbohydrate-first processing methods. Critical gaps remain in linking pretreatment conditions to protein yield and quality, standardizing metrics, and assessing techno-economic feasibility. Integrating protein recovery can improve energy efficiency, strengthen supply chains, and enhance overall cost-competitiveness, supporting the advancement of biorefineries as sustainable and viable contributors to the bioeconomy.
Abstract Agrobacterium -mediated transformation (AMT) is a critical method for genetic manipulation of non-model fungi, yet it remains a laborious and inefficient technique. When cocultured in acetosyringone-supplemented induction medium, Agrobacterium transfers DNA directly into yeast cells using its virulence machinery. Membrane filters are commonly used to support the co-culture of yeast and Agrobacterium on agar plates, however some reports demonstrate that these filters are unnecessary for specific yeast species. Here we confirm across diverse budding yeasts that membrane filters are not necessary for effective AMT. Concentrating the cells via centrifugation and “spotting” the cell pellet directly onto the induction medium proved effective. This reduces hands-on time to 15 minutes and eliminates filter cost. In the oleaginous yeast, Rhodotorula toruloides, this simplified method increases transformation efficiency by 66% to 2,500 transformants per 10 6 recipient cells. We further optimized the Agrobacterium : Rhodotorula cell ratio and culture resuspension volume to achieve more than 200,000 CFU per transformation representing a 2-3 fold improvement over previously implemented protocols. This spot-plating method was successfully applied to seven yeast species, including one for which genetic transformation has not previously been reported, Botryozyma nematodophila . This approach highlights the broad applicability of the spot-plating method across diverse yeast systems. Furthermore, this method could facilitate high-throughput transformation workflows that are critical for genome-scale functional studies.
Polyketide synthases (PKSs) are modular enzymes with exceptional potential as biocatalysts for producing non-native compounds. Here, we report the first PKS-based pathway for adipic acid (AA), an industrial monomer for nylon production, by engineering one of the most extensively hybridized PKS systems to date. Using a retrobiosynthetic approach, we identified EtnB, a succinyl-CoA-loading module that uniquely retains the terminal carboxyl group, enabling access to dicarboxylic polyketide products, rarely produced by canonical PKSs. EtnB was coupled to a fully reducing extension module through an engineered communication linker, which improved ACP-KS interactions, enhanced titers, and demonstrated selective succinyl-CoA loading in vivo. This construct integrates genes from five organisms─with domains from seven PKS modules joined across six non-natural junctions─and functions in both Escherichia coli and Pseudomonas putida. Additional engineering that included AT domain exchanges, optimization of extender unit supply, and host strain metabolic rewiring further increased AA production. Together, this work demonstrates that highly chimeric PKSs can be rendered functional through rational design, expands the PKS toolkit with a carboxyl-retaining loading module, and establishes a versatile platform for engineering diacids and other noncanonical products through PKS pathways.
