More Like this

1. Advances and opportunities in gene editing and gene regulation technology for Yarrowia lipolytica

   https://doi.org/10.1186/s12934-019-1259-x  

   Ganesan, Vijaydev; Spagnuolo, Michael; Agrawal, Ayushi; Smith, Spencer; Gao, Difeng; Blenner, Mark (December 2019, Microbial Cell Factories)

   null (Ed.)

   Abstract Yarrowia lipolytica has emerged as a biomanufacturing platform for a variety of industrial applications. It has been demonstrated to be a robust cell factory for the production of renewable chemicals and enzymes for fuel, feed, oleochemical, nutraceutical and pharmaceutical applications. Metabolic engineering of this non-conventional yeast started through conventional molecular genetic engineering tools; however, recent advances in gene/genome editing systems, such as CRISPR–Cas9, transposons, and TALENs, has greatly expanded the applications of synthetic biology, metabolic engineering and functional genomics of Y. lipolytica . In this review we summarize the work to develop these tools and their demonstrated uses in engineering Y. lipolytica , discuss important subtleties and challenges to using these tools, and give our perspective on important gaps in gene/genome editing tools in Y. lipolytica . 

   more » « less
2. Perspectives for Using CO2 as a Feedstock for Biomanufacturing of Fuels and Chemicals

   https://doi.org/10.3390/bioengineering10121357  

   Kurt, Elif; Qin, Jiansong; Williams, Alexandria; Zhao, Youbo; Xie, Dongming (December 2023, Bioengineering)

   Microbial cell factories offer an eco-friendly alternative for transforming raw materials into commercially valuable products because of their reduced carbon impact compared to conventional industrial procedures. These systems often depend on lignocellulosic feedstocks, mainly pentose and hexose sugars. One major hurdle when utilizing these sugars, especially glucose, is balancing carbon allocation to satisfy energy, cofactor, and other essential component needs for cellular proliferation while maintaining a robust yield. Nearly half or more of this carbon is inevitably lost as CO2 during the biosynthesis of regular metabolic necessities. This loss lowers the production yield and compromises the benefit of reducing greenhouse gas emissions—a fundamental advantage of biomanufacturing. This review paper posits the perspectives of using CO2 from the atmosphere, industrial wastes, or the exhausted gases generated in microbial fermentation as a feedstock for biomanufacturing. Achieving the carbon-neutral or -negative goals is addressed under two main strategies. The one-step strategy uses novel metabolic pathway design and engineering approaches to directly fix the CO2 toward the synthesis of the desired products. Due to the limitation of the yield and efficiency in one-step fixation, the two-step strategy aims to integrate firstly the electrochemical conversion of the exhausted CO2 into C1/C2 products such as formate, methanol, acetate, and ethanol, and a second fermentation process to utilize the CO2-derived C1/C2 chemicals or co-utilize C5/C6 sugars and C1/C2 chemicals for product formation. The potential and challenges of using CO2 as a feedstock for future biomanufacturing of fuels and chemicals are also discussed. 

   more » « less
3. Synthetic Biology Tool Development Advances Predictable Gene Expression in the Metabolically Versatile Soil Bacterium Rhodopseudomonas palustris

   https://doi.org/10.3389/fbioe.2022.800734  

   Immethun, Cheryl M.; Kathol, Mark; Changa, Taity; Saha, Rajib (March 2022, Frontiers in Bioengineering and Biotechnology)

   Harnessing the unique biochemical capabilities of non-model microorganisms would expand the array of biomanufacturing substrates, process conditions, and products. There are non-model microorganisms that fix nitrogen and carbon dioxide, derive energy from light, catabolize methane and lignin-derived aromatics, are tolerant to physiochemical stresses and harsh environmental conditions, store lipids in large quantities, and produce hydrogen. Model microorganisms often only break down simple sugars and require low stress conditions, but they have been engineered for the sustainable manufacture of numerous products, such as fragrances, pharmaceuticals, cosmetics, surfactants, and specialty chemicals, often by using tools from synthetic biology. Transferring complex pathways has proven to be exceedingly difficult, as the cofactors, cellular conditions, and energy sources necessary for this pathway to function may not be present in the host organism. Utilization of unique biochemical capabilities could also be achieved by engineering the host; although, synthetic biology tools developed for model microbes often do not perform as designed in other microorganisms. The metabolically versatile Rhodopseudomonas palustris CGA009, a purple non-sulfur bacterium, catabolizes aromatic compounds derived from lignin in both aerobic and anaerobic conditions and can use light, inorganic, and organic compounds for its source of energy. R. palustris utilizes three nitrogenase isozymes to fulfill its nitrogen requirements while also generating hydrogen. Furthermore, the bacterium produces two forms of RuBisCo in response to carbon dioxide/bicarbonate availability. While this potential chassis harbors many beneficial traits, stable heterologous gene expression has been problematic due to its intrinsic resistance to many antibiotics and the lack of synthetic biology parts investigated in this microbe. To address these problems, we have characterized gene expression and plasmid maintenance for different selection markers, started a synthetic biology toolbox specifically for the photosynthetic R. palustris , including origins of replication, fluorescent reporters, terminators, and 5′ untranslated regions, and employed the microbe’s endogenous plasmid for exogenous protein production. This work provides essential synthetic biology tools for engineering R. palustris ’ many unique biochemical processes and has helped define the principles for expressing heterologous genes in this promising microbe through a methodology that could be applied to other non-model microorganisms. 

   more » « less
4. Integrated design for electrocatalytic carbon dioxide reduction

   https://doi.org/10.1039/D0CY00453G  

   Zhao, Xin; Du, Lijie; You, Bo; Sun, Yujie (May 2020, Catalysis Science & Technology)

   null (Ed.)

   The electrocatalytic carbon dioxide reduction reaction (CO 2 RR) to produce valuable fuels and chemicals with renewable energy inputs is an attractive route to convert intermittent green energy sources ( e.g. , solar and wind) to chemical energy, alleviate our dependence on fossil fuels, and simultaneously reduce net carbon dioxide emission. However, the generation of reduced multi-carbon products with high energy density and wide applicability from the CO 2 RR, such as oxygenates and hydrocarbons, suffers from high overpotential, slow reaction rate, and low selectivity due to its intrinsic multi-electron transfer nature. Moreover, the involved anodic oxygen evolution reaction (OER) also requires large overpotential and its product O 2 bears limited economic value. The potentially generated reactive oxygen species (ROS) during the OER may also degrade the membrane of a CO 2 reduction electrolyzer. Herein, we review the recent progress in novel integrated strategies to address the aforementioned challenges in the electrocatalytic CO 2 RR. These innovative strategies include (1) concurrent CO 2 electroreduction via co-feeding additional chemicals besides CO 2 gas, (2) tandem CO 2 electroreduction utilizing other catalysts for converting the in situ formed products from the CO 2 RR into more valuable chemicals, and (3) hybrid CO 2 electroreduction through integrating thermodynamically more favourable organic upgrading reactions to replace the anodic OER. We specifically highlight these novel integrated electrolyzer designs instead of focusing on nanostructured engineering of various electrocatalysts, in the hope of inspiring others to approach CO 2 electroreduction from a holistic perspective. The current challenges and future opportunities of electrocatalytic CO 2 reduction will also be discussed at the end. 

   more » « less
5. Increasing the revenue from lignocellulosic biomass: Maximizing feedstock utilization

   https://doi.org/DOI: 10.1126/sciadv.1603301  

   Martin Alonso, David; Hakim, Sikander H; Zhou, Shengfei; Won, Wangyun; Hosseinaei, Omid; Tao, Jingming; Garcia-Negron, Valerie; Motagamwala, Ali Hussain; Mellmer, Max A.; Huang, Kefeng; et al (May 2017, Science advances)

   The production of renewable chemicals and biofuels must be cost- and performance- competitive with petroleum-derived equivalents to be widely accepted by markets and society. We propose a biomass conversion strategy that maximizes the conversion of lignocellulosic biomass (up to 80% of the biomass to useful products) into high-value products that can be commercialized, providing the opportunity for successful translation to an economically viable commercial process. Our fractionation method preserves the value of all three primary components: (i) cellulose, which is converted into dissolving pulp for fibers and chemicals production; (ii) hemicellulose, which is converted into furfural (a building block chemical); and (iii) lignin, which is converted into carbon products (carbon foam, fibers, or battery anodes), together producing revenues of more than $500 per dry metric ton of biomass. Once de-risked, our technology can be extended to produce other renewable chemicals and biofuels. 

   more » « less