Converting Sugars to Biofuels: Ethanol and Beyond

Comprehensive genomic and phenotypic characterization of thermophilic bacterium Sinimarinibacterium thermocellulolyticum sp. nov. HSW-8T, a cellulase-producing bacterium isolated from hot spring water in South Korea

A thermophilic cellulase-producing bacterium, strain HSW-8T, isolated from hot spring waters in South Korea, was subjected to a taxonomic analysis. Cells of strain HSW-8T were gram-stain-negative, facultatively anaerobic, rod-shaped, with optimum growth at 45 °C, pH 7.0, in the presence of 0% (w/v) NaCl. Strain HSW-8T showed the highest 16S rRNA gene sequence similarity to Sinimarinibacterium flocculans NH6-24T (97.52%), followed by Fontimonas thermophila DSM 23609T (96.97%), Solimonas flava CW-KD 4T (95.24%), and Solimonas variicoloris DSM 15731T (95.18%). Based on 16S rRNA phylogeny, strain HSW-8T is phylogenetically closely related to Fontimonas thermophila DSM 23609T and Sinimarinibacterium flocculans DSM 104150T and could be distinguished from the type species based on their phenotypic properties. The genome length of strain HSW-8T was 3.32 Mbp with a 67.33% G + C content. The average nucleotide identity and digital DNA-DNA hybridization values between strain HSW-8T and its closely related type strains were 75.4-83.2 and 20.2-26.2%, respectively. Summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, and iso-C16:0 identified the major fatty acids (> 10%). Phosphatidylglycerol and phosphatidylethanolamine were demonstrated as the major polar lipids while the respiratory quinone is ubiquinone-8. Strain HSW-8T exhibited multiple adaptations for survival at high temperatures, including diverse potential motility mechanisms and toxin-antitoxin systems, as evidenced by both phenotypic characteristics and genomic analysis. Based on genotypic and phenotypic features, strain HSW-8T (= KCTC 92765T = GDMCC 1.4313T) represents a novel Sinimarinibacterium species, in which the name Sinimarinibacterium thermocellulolyticum sp. nov. is proposed.

Ethanol-mediated Anaerobic Digestion: Functional Bacteria and Metabolic Pathways

Ethanol-mediated Anaerobic digestion (Ethanol-AD) is a biological process that converts organic waste into biogas, predominantly composed of methane (CH₄), hydrogen (H₂), and carbon dioxide (CO₂), through the breakdown of complex organic materials while ethanol is an intermediate metabolite. Ethanol improves the digestion of complex organic waste by serving as an electron precursor for interspecies electron transfer, leading to enhanced biogas production. It further serves as a substrate for acetogens or syntrophic bacteria, while mean its oxidation leads to acetate formation, which methanogens can then consume to generate methane. Methanogenesis, the final and crucial step in the anaerobic digestion in which methanogens produce methane through various metabolic routes, most notably via the hydrogenotrophic and syntrophic pathways. In hydrogenotrophic methanogenesis, methanogens consume hydrogen as an electron precursor and carbon dioxide as an electron acceptor, leading to methane generation. Alternatively, syntrophic methanogenesis, which is increasingly recognized for its efficiency, is dominated by DIET between syntrophic partners, bypassing the need for hydrogen as a mediator. This mode of electron transfer enhances the metabolic cooperation between microbes, facilitating a more efficient methanogenesis process. As research continues to explore the mechanisms underlying DIET and the role of (semi) conductive materials, there is potential for optimizing AD systems for renewable energy production by advancing the methanogenesis process, and enhancing biogas quality. The novelty of this review lies in its dual exploration of direct and indirect interspecies electron transfer (DIET and IIET) within ethanol-mediated anaerobic digestion. While DIET in ethanol-driven systems has been previously discussed, this review is the first to comprehensively examine the interplay between both direct and indirect electron transfer mechanisms, offering new insights into optimizing microbial interactions and improving methane production efficiency.

Synthesis of an Ethylenediaminetetraacetic Acid-like Ligand Based on Sucrose Scaffold and Complexation and Proton Relaxivity Studies of Its Gadolinium(III) Complex in Solution

Sucrose constitutes a non-toxic, biodegradable, low-cost and readily available natural product. To expand its utility, we developed total synthesis for a ligand based on a sucrose scaffold for potential use as a metal chelation agent. The designed target (compound 2) has a metal-chelating functionality at both the C-6 and C-6' positions, which can provide a first coordination sphere of eight valencies. The designed total synthesis was highly efficient. To demonstrate the utility of the ligand, we studied its complexation with Gd(III). Using potentiometric titration and high-resolution mass spectrometry, we confirmed the formation of a 1:1 complex with Gd(III), which has a respectable formation constant of ~1013.4. Further NMR relaxivity studies show that the Gd(III) complex has a relaxivity (r1) of 7.6958 mmol-1 s-1.

Catalytic Transformation of Carbohydrates into Renewable Organic Chemicals by Revering the Principles of Green Chemistry

Adherence to the principles of green chemistry in a biorefinery setting ensures energy efficiency, reduces the consumption of materials, simplifies reactor design, and rationalizes the process parameters for synthesizing affordable organic chemicals of desired functional efficacy and ingrained sustainability. The green chemistry metrics facilitate assessing the relative merits and demerits of alternative synthetic pathways for the targeted product(s). This work elaborates on how green chemistry has emerged as a transformative framework and inspired innovations toward the catalytic conversion of biomass-derived carbohydrates into fuels, chemicals, and synthetic polymers. Specific discussions have been incorporated on the judicious selection of feedstock, reaction parameters, reagents (stoichiometric or catalytic), and other synthetic auxiliaries to obtain the targeted product(s) in desired selectivity and yield. The prospects of a carbohydrate-centric biorefinery have been emphasized and research avenues have been proposed to eliminate the remaining roadblocks. The analyses presented in this review will steer to developing superior synthetic strategies and processes for envisaging a sustainable bioeconomy centered on biomass-derived carbohydrates.

Cellulolytic and Ethanologenic Evaluation of Heterotermes indicola's Gut-Associated Bacterial Isolates

Cellulose is the basic component of lignocellulosic biomass (LCB) making it a suitable substrate for bioethanol fermentation. Cellulolytic and ethanologenic bacteria possess cellulases that convert cellulose to glucose, which in turn yields ethanol subsequently. Heterotermes indicola is a subterranean termite that causes destructive damage by consuming wooden structures of infrastructure, LCB products, etc. Prospectively, the study envisioned the screening of cellulolytic and ethanologenic bacteria from the termite gut. Twenty six bacterial strains (H1-H26) based on varied colonial morphologies were isolated. Bacterial cellulolytic activity was tested biochemically. Marked gas production in the form of bubbles (0.1-4 cm) in Durham tubes was observed in H3, H7, H13, H15, H17, H21, and H22. Sugar degradation of all isolates was indicated by pink to maroon color development with the tetrazolium salt. Hallow zones (0.42-11 mm) by Congo red staining was exhibited by all strains except H2, H7, H8, and H19. Among the 26 bacterial isolates, 12 strains were identified as efficient cellulolytic bacteria. CMCase activity and ethanol titer of all isolates varied from 1.30 ± 0.03 (H13) to 1.83 ± 0.01 (H21) umol/mL/min and 2.36 ± 0.01 (H25) to 7.00 ± 0.01 (H21) g/L, respectively. Likewise, isolate H21 exhibited an ethanol yield of 0.40 ± 0.10 g/g with 78.38 ± 2.05% fermentation efficiency. Molecular characterization of four strains, Staphylococcus sp. H13, Acinetobacter baumanni H17, Acinetobacter sp. H21, and Acinetobacter nosocomialis H22, were based on the maximum cellulolytic index and the ethanol yield. H. indicola harbor promising and novel bacteria with a natural cellulolytic tendency for efficient bioconversion of LCB to value-added products. Hence, the selected cellulolytic bacteria can become an excellent addition for use in enzyme purification, composting, and production of biofuel at large.

Isolation and Characterization of Bacteria from Natural Hot Spring and Insights into the Thermophilic Cellulase Production

A thermophilic cellulase-producing bacterium, Bacillus velezensis strain MRC 5958, from Bakra natural hot Springs, India was characterized through genome sequencing. It has a genome size of 4,467,129 bp and a GC content of 45.7%. A cellulase purified from its fermentation broth has a molecular weight of about 18 kDa. The optimum temperature and pH for carboxymethyl cellulase activity were at 55 °C and pH ~ 7.0. The enzyme is stable over a wide range of temperatures from 30 °C to 70 °C with maximum activity observed at 48 h of incubation. The strain produces cellulase on alkali-treated sugarcane bagasse, rice straw, rice husk, rice bran, and sawdust. The sugarcane bagasse exhibited the most effective carbon source for cellulase production at (85 U/ml) followed by rice bran (68 U/ml), rice husk (60 U/ml), rice straw (48 U/ml), and sawdust (39 U/ml). Therefore, this strain can be a potential thermostable cellulase-producing candidate for converting the waste biomass into biofuel and other industrial enzymes.

Sustainable Feedstocks and Challenges in Biodiesel Production: An Advanced Bibliometric Analysis

Biodiesel can be produced from vegetable oils, animal fats, frying oils, and from microorganism-synthesized oils. These sources render biodiesel an easily biodegradable fuel. The aim of this work was to perform an advanced bibliometric analysis of primary studies relating to biodiesel production worldwide by identifying the key countries and regions that have shown a strong engagement in this area, and by understanding the dynamics of their collaboration and research outputs. Additionally, an assessment of the main primary feedstocks employed in this research was carried out, along with an analysis of the current and future trends that are expected to define new paths and methodologies to be used in the manufacture of biodegradable and renewable fuels. A total of 4586 academic outputs were selected, including peer-reviewed research articles, conference papers, and literature reviews related to biodiesel production, in the time period spanning from 2010 to 2021. Articles that focused on feedstocks for the production of biodiesel were also included, with a search that returned 330 papers. Lastly, 60 articles relating to biodiesel production via sewage were specifically included to allow for an analysis of this source as a promising feedstock in the future of the biofuel market. Via the geocoding and the document analyses performed, we concluded that China, Malaysia, and India are the largest writers of articles in this area, revealing a great interest in biofuels in Asia. Additionally, it was noted that environmental concerns have caused authors to conduct research on feedstocks that can address the sustainability challenges in the production of biodiesel.

Bioengineered microbial platforms for biomass-derived biofuel production - A review

Global warming issues, rapid fossil fuel diminution, and increasing worldwide energy demands have diverted accelerated attention in finding alternate sources of biofuels and energy to combat the energy crisis. Bioconversion of lignocellulosic biomass has emerged as a prodigious way to produce various renewable biofuels such as biodiesel, bioethanol, biogas, and biohydrogen. Ideal microbial hosts for biofuel synthesis should be capable of using high substrate quantity, tolerance to inhibiting substances and end-products, fast sugar transportation, and amplified metabolic fluxes to yielding enhanced fermentative bioproduct. Genetic manipulation and microbes' metabolic engineering are fascinating strategies for the economical production of next-generation biofuel from lignocellulosic feedstocks. Metabolic engineering is a rapidly developing approach to construct robust biofuel-producing microbial hosts and an important component for future bioeconomy. This approach has been widely adopted in the last decade for redirecting and revamping the biosynthetic pathways to obtain a high titer of target products. Biotechnologists and metabolic scientists have produced a wide variety of new products with industrial relevance through metabolic pathway engineering or optimizing native metabolic pathways. This review focuses on exploiting metabolically engineered microbes as promising cell factories for the enhanced production of advanced biofuels.

Bioconversion of organic wastes into value-added products: A review

Rapid urbanization has increased the demand for food, feed, and chemicals that have in turn augmented the use of fossil-based resources and generation of organic waste. Owning to the characteristics like high abundance, renewability, and ease of accessibility, valorization of organic wastes serves as a potential solution for waste management issues. Several industrial wastes, due to their organic and nutrient-rich composition, have been utilized as a resource for the production of value-added products such as biofuels, biopesticides, biohydrogen, enzymes, and bioplastics via microbial fermentation processes. The process consists of pre-treatment of the waste biomass, production of value-added product in reactors and downstream processing for product's recovery. The integration of new comprehensive technologies for organic waste utilization will also stimulate the transition towards a circular economy. Therefore, the feasibility and sustainability of the production of various value-added products from biowastes and byproduct streams will be discussed in the present review.

Preparation, Characterization and Application of Amorphized Cellulose-A Review

This review describes the methods of cellulose amorphization, such as dry grinding, mercerization, treatment with liquid ammonia, swelling in solvents, regeneration from solutions, etc. In addition, the main characteristics and applications of amorphized celluloses are discussed. An optimal method for preparing completely amorphous cellulose (CAC) via the treatment of original cellulose material with a cold NaOH/Urea-solvent at the solvent to cellulose ratio R ≥ 5 is proposed. Structural studies show that amorphous cellulose contains mesomorphous clusters with a size of 1.85 nm and specific gravity of 1.49 g/cm³. Furthermore, each such cluster consists of about five glucopyranose layers with an average interlayer spacing of 0.45 nm. Amorphous cellulose is characterized by increased hydrophilicity, reactivity, and enzymatic digestibility. Due to its amorphous structure, the CAC can be used as a promising substrate for enzymatic hydrolysis to produce glucose, which can be applied in biotechnology for growing various microorganisms. In addition, the application of CAC in agriculture is described. A waste-free method for producing amorphous nanocellulose is considered, and the main applications of nanosized amorphous cellulose are discussed.

Membrane-Based Harvesting Processes for Microalgae and Their Valuable-Related Molecules: A Review

The interest in microalgae production deals with its role as the third generation of feedstock to recover renewable energy. Today, there is a need to analyze the ultimate research and advances in recovering the microalgae biomass from the culture medium. Therefore, this review brings the current research developments (over the last three years) in the field of harvesting microalgae using membrane-based technologies (including microfiltration, ultrafiltration and forward osmosis). Initially, the principles of membrane technologies are given to outline the main parameters influencing their operation. The main strategies adopted by the research community for the harvesting of microalgae using membranes are subsequently addressed, paying particular attention to the novel achievements made for improving filtration performance and alleviating fouling. Moreover, this contribution also gives an overview of the advantages of applying membrane technologies for the efficient extraction of the high added-value compounds in microalgae cells, such as lipids, proteins and carbohydrates, which together with the production of renewable biofuels could boost the development of more sustainable and cost-effective microalgae biorefineries.

Product Distributions of Cytochrome P450 OleTJE with Phenyl-Substituted Fatty Acids: A Computational Study

There are two types of cytochrome P450 enzymes in nature, namely, the monooxygenases and the peroxygenases. Both enzyme classes participate in substrate biodegradation or biosynthesis reactions in nature, but the P450 monooxygenases use dioxygen, while the peroxygenases take H2O2 in their catalytic cycle instead. By contrast to the P450 monooxygenases, the P450 peroxygenases do not require an external redox partner to deliver electrons during the catalytic cycle, and also no external proton source is needed. Therefore, they are fully self-sufficient, which affords them opportunities in biotechnological applications. One specific P450 peroxygenase, namely, P450 OleTJE, reacts with long-chain linear fatty acids through oxidative decarboxylation to form hydrocarbons and, as such, has been implicated as a suitable source for the biosynthesis of biofuels. Unfortunately, the reactions were shown to produce a considerable amount of side products originating from Cα and Cβ hydroxylation and desaturation. These product distributions were found to be strongly dependent on whether the substrate had substituents on the Cα and/or Cβ atoms. To understand the bifurcation pathways of substrate activation by P450 OleTJE leading to decarboxylation, Cα hydroxylation, Cβ hydroxylation and Cα-Cβ desaturation, we performed a computational study using 3-phenylpropionate and 2-phenylbutyrate as substrates. We set up large cluster models containing the heme, the substrate and the key features of the substrate binding pocket and calculated (using density functional theory) the pathways leading to the four possible products. This work predicts that the two substrates will react with different reaction rates due to accessibility differences of the substrates to the active oxidant, and, as a consequence, these two substrates will also generate different products. This work explains how the substrate binding pocket of P450 OleTJE guides a reaction to a chemoselectivity.

Non-Conventional Yeasts as Alternatives in Modern Baking for Improved Performance and Aroma Enhancement

Saccharomyces cerevisiae remains the baker’s yeast of choice in the baking industry. However, its ability to ferment cereal flour sugars and accumulate CO2 as a principal role of yeast in baking is not as unique as previously thought decades ago. The widely conserved fermentative lifestyle among the Saccharomycotina has increased our interest in the search for non-conventional yeast strains to either augment conventional baker’s yeast or develop robust strains to cater for the now diverse consumer-driven markets. A decade of research on alternative baker’s yeasts has shown that non-conventional yeasts are increasingly becoming important due to their wide carbon fermentation ranges, their novel aromatic flavour generation, and their robust stress tolerance. This review presents the credentials of non-conventional yeasts as attractive yeasts for modern baking. The evolution of the fermentative trait and tolerance to baking-associated stresses as two important attributes of baker’s yeast are discussed besides their contribution to aroma enhancement. The review further discusses the approaches to obtain new strains suitable for baking applications.

Bioethanolic yeasts from dung beetles: tapping the potential of extremophilic yeasts for improvement of lignocellulolytic feedstock fermentation

Bioethanol from abundant and inexpensive agricultural and industrial wastes possesses the potential to reduce greenhouse gas emissions. Bioethanol as renewable fuel addresses elevated production costs, as well as food security concerns. Although technical advancements in simultaneous saccharification and fermentation have reduced the cost of production, one major drawback of this technology is that the pre-treatment process creates environmental stressors inhibitory to fermentative yeasts subsequently reducing bioethanol productivity. Robust fermentative yeasts with extreme stress tolerance remain limited. This review presents the potential of dung beetles from pristine and unexplored environments as an attractive source of extremophilic bioethanolic yeasts. Dung beetles survive on a recalcitrant lignocellulose-rich diet suggesting the presence of symbiotic yeasts with a cellulolytic potential. Dung beetles inhabiting extreme stress environments have the potential to harbour yeasts with the ability to withstand inhibitory environmental stresses typically associated with bioethanol production. The review further discusses established methods used to isolate bioethanolic yeasts, from dung beetles.

Principles and practice of designing microbial biocatalysts for fuel and chemical production

The finite nature of fossil fuels and the environmental impact of its use have raised interest in alternate renewable energy sources. Specifically, non-food carbohydrates, such as lignocellulosic biomass, can be used to produce next generation biofuels, including cellulosic ethanol and other non-ethanol fuels like butanol. However, currently there is no native microorganism that can ferment all lignocellulosic sugars to fuel molecules. Thus, research is focused on engineering improved microbial biocatalysts for production of liquid fuels at high productivity, titer and yield. A clear understanding and application of the basic principles of microbial physiology and biochemistry are crucial to achieve this goal. In this review, we present and discuss the construction of microbial biocatalysts that integrate these principles with ethanol-producing Escherichia coli as an example of metabolic engineering. These principles also apply to fermentation of lignocellulosic sugars to other chemicals that are currently produced from petroleum.

Bioprospecting of microbial strains for biofuel production: metabolic engineering, applications, and challenges

The issues of global warming, coupled with fossil fuel depletion, have undoubtedly led to renewed interest in other sources of commercial fuels. The search for renewable fuels has motivated research into the biological degradation of lignocellulosic biomass feedstock to produce biofuels such as bioethanol, biodiesel, and biohydrogen. The model strain for biofuel production needs the capability to utilize a high amount of substrate, transportation of sugar through fast and deregulated pathways, ability to tolerate inhibitory compounds and end products, and increased metabolic fluxes to produce an improved fermentation product. Engineering microbes might be a great approach to produce biofuel from lignocellulosic biomass by exploiting metabolic pathways economically. Metabolic engineering is an advanced technology for the construction of highly effective microbial cell factories and a key component for the next-generation bioeconomy. It has been extensively used to redirect the biosynthetic pathway to produce desired products in several native or engineered hosts. A wide range of novel compounds has been manufactured through engineering metabolic pathways or endogenous metabolism optimizations by metabolic engineers. This review is focused on the potential utilization of engineered strains to produce biofuel and gives prospects for improvement in metabolic engineering for new strain development using advanced technologies.

Toward Replacing Ethylene Oxide in a Sustainable World: Glycolaldehyde as a Bio-Based C2 Platform Molecule

Fossil-based platform molecules such as ethylene and ethylene oxide currently serve as the primary feedstock for the C₂ -based chemical industry. However, in the search for a more sustainable chemical industry, fossil-based resources may preferentially be replaced by renewable alternatives, provided there is realistic economic feasibility. This Review compares and critically discusses several production routes toward bio-based structural analogues of ethylene oxide and the required adaptations for their implementation in state-of-the-art C₂ -based chemical processes. For example, glycolaldehyde, a structural analogue obtainable from carbohydrates by atom-economic retro-aldol reactions, may replace ethylene oxide's leading role. This alternative chemical route may not only allow the carbon footprint of conventional chemicals production to be lowered, but the introduction of a bio-based pathway may also contribute to safer production processes. Where possible, challenges, drawbacks, and prospects are highlighted.

A common approach for absolute quantification of short chain CoA thioesters in prokaryotic and eukaryotic microbes

BACKGROUND

Thioesters of coenzyme A participate in 5% of all enzymatic reactions. In microbial cell factories, they function as building blocks for products of recognized commercial value, including natural products such as polyketides, polyunsaturated fatty acids, biofuels, and biopolymers. A core spectrum of approximately 5-10 short chain thioesters is present in many microbes, as inferred from their genomic repertoire. The relevance of these metabolites explains the high interest to trace and quantify them in microbial cells.

RESULTS

Here, we describe a common workflow for extraction and absolute quantification of short chain CoA thioesters in different gram-positive and gram-negative bacteria and eukaryotic yeast, i.e. Corynebacterium glutamicum, Streptomyces albus, Pseudomonas putida, and Yarrowia lipolytica. The approach assessed intracellular CoA thioesters down to the picomolar level and exhibited high precision and reproducibility for all microbes, as shown by principal component analysis. Furthermore, it provided interesting insights into microbial CoA metabolism. A succinyl-CoA synthase defective mutant of C. glutamicum exhibited an unaffected level of succinyl-CoA that indicated a complete compensation by the L-lysine pathway to bypass the disrupted TCA cycle. Methylmalonyl-CoA, an important building block of high-value polyketides, was identified as dominant CoA thioester in the actinomycete S. albus. The microbe revealed a more than 10,000-fold difference in the abundance of intracellular CoA thioesters. A recombinant strain of S. albus, which produced different derivatives of the antituberculosis polyketide pamamycin, revealed a significant depletion of CoA thioesters of the ethylmalonyl CoA pathway, influencing product level and spectrum.

CONCLUSIONS

The high relevance of short chain CoA thioesters to synthetize industrial products and the interesting insights gained from the examples shown in this work, suggest analyzing these metabolites in microbial cell factories more routinely than done so far. Due to its broad application range, the developed approach appears useful to be applied this purpose. Hereby, the possibility to use one single protocol promises to facilitate automatized efforts, which rely on standardized workflows.

Progress Toward Sustainable Reversible Deactivation Radical Polymerization

The recent focus of media and governments on renewability, green chemistry, and circular economy has led to a surge in the synthesis of renewable monomers and polymers. In this review, focussing on renewable monomers for reversible deactivation radical polymerizations (RDRP), it is highlighted that for the majority of the monomers and polymers reported, the claim to renewability is not always accurate. By closely examining the sustainability of synthetic routes and the renewability of starting materials, fully renewable monomers are identified and discussed in terms of sustainability, polymerization behavior, and properties obtained after polymerization. The holistic discussion considering the overall preparation process of polymers, that is, monomer syntheses, origin of starting materials, solvents used, the type of RDRP technique utilized, and the purification method, allows to highlight certain topics which need to be addressed in order to progress toward not only (partially) renewable, but sustainable monomers and polymers using RDRPs.

A Case of Auto-brewery Syndrome Treated with Micafungin

Auto-brewery syndrome is caused by alcohol brewing inside the human body; it is a rare clinical condition where the patient becomes inebriated without exogenous alcohol use. Yeast is responsible, and treatment requires an appropriate antifungal agent. If undiagnosed, the patient's life becomes a misery. We present a case of a 45-year-old male who suffered from this condition for over three years with two arrests for driving under the influence prior to being diagnosed. The patient stated that he felt the episodes were related to his meal intakes; therefore, he would skip most meals of the day. The patient visited several centers where he was told there was not much they could offer him and he was left without a diagnosis. A carbohydrate challenge test in a monitored setting showed elevated blood alcohol levels. He was treated with antifungals and a low carbohydrate diet which resulted in the resolution of his symptoms. Hence the importance of awareness among physicians is necessary along with a high index of suspicion.

Redirecting Metabolic Flux via Combinatorial Multiplex CRISPRi-Mediated Repression for Isopentenol Production in Escherichia coli

CRISPR interference (CRISPRi) via target guide RNA (gRNA) arrays and a deactivated Cas9 (dCas9) protein has been shown to simultaneously repress expression of multiple genomic DNA loci. By knocking down endogenous genes in competing pathways, CRISPRi technology can be utilized to redirect metabolic flux toward target metabolite. In this study, we constructed a CRISPRi-mediated multiplex repression system to silence transcription of several endogenous genes to increase precursor availability in a heterologous isopentenol biosynthesis pathway. To identify genomic knockdown targets in competing pathways, we first designed a single-gRNA library with 15 individual targets, where 3 gRNA cassettes targeting gene asnA, prpE, and gldA increased isopentenol titer by 18-24%. We then combined the 3 single-gRNA cassettes into a two- or three-gRNA array and observed up to 98% enhancement in production by fine-tuning the repression level through titrating dCas9 expression. Our strategy shows that multiplex combinatorial knockdown of competing genes using CRISPRi can increase production of the target metabolite, while the repression level needs to be adjusted to balance the metabolic network and achieve the maximum titer improvement.

Feasibility of advancing the development of compact energy systems

It is necessary to advance the development of compact energy systems for making energy from biomass like wood or switchgrass, as an alternative to the construction of highly capital-intensive large scale biorefineries.

Integrating Cellular and Bioprocess Engineering in the Non-Conventional Yeast Yarrowia lipolytica for Biodiesel Production: A Review

As one of the major biofuels to replace fossil fuel, biodiesel has now attracted more and more attention due to its advantages in higher energy density and overall less greenhouse gas generation. Biodiesel (fatty acid alkyl esters) is produced by chemically or enzymatically catalyzed transesterification of lipids from microbial cells, microalgae, oil crops, or animal fats. Currently, plant oils or waste cooking oils/fats remain the major source for biodiesel production via enzymatic route, but the production capacity is limited either by the uncertain supplement of plant oils or by the low or inconsistent quality of waste oils/fats. In the past decades, significant progresses have been made on synthesis of microalgae oils directly from CO₂via a photosynthesis process, but the production cost from any current technologies is still too high to be commercialized due to microalgae’s slow growth rate on CO₂, inefficiency in photo-bioreactors, lack of efficient contamination control methods, and high cost in downstream recovery. At the same time, many oleaginous microorganisms have been studied to produce lipids via the fatty acid synthesis pathway under aerobic fermentation conditions, among them one of the most studied is the non-conventional yeast, Yarrowia lipolytica, which is able to produce fatty acids at very high titer, rate, and yield from various economical substrates. This review summarizes the recent research progresses in both cellular and bioprocess engineering in Y. lipolytica to produce lipids at a low cost that may lead to commercial-scale biodiesel production. Specific technologies include the strain engineering for using various substrates, metabolic engineering in high-yield lipid synthesis, cell morphology study for efficient substrate uptake and product formation, free fatty acid formation and secretion for improved downstream recovery, and fermentation engineering for higher productivities and less operating cost. To further improve the economics of the microbial oil-based biodiesel, production of lipid-related or -derived high-value products are also discussed.

Ethanol production in Brazil: a bridge between science and industry

In the last 40 years, several scientific and technological advances in microbiology of the fermentation have greatly contributed to evolution of the ethanol industry in Brazil. These contributions have increased our view and comprehension about fermentations in the first and, more recently, second-generation ethanol. Nowadays, new technologies are available to produce ethanol from sugarcane, corn and other feedstocks, reducing the off-season period. Better control of fermentation conditions can reduce the stress conditions for yeast cells and contamination by bacteria and wild yeasts. There are great research opportunities in production processes of the first-generation ethanol regarding high-value added products, cost reduction and selection of new industrial yeast strains that are more robust and customized for each distillery. New technologies have also focused on the reduction of vinasse volumes by increasing the ethanol concentrations in wine during fermentation. Moreover, conversion of sugarcane biomass into fermentable sugars for second-generation ethanol production is a promising alternative to meet future demands of biofuel production in the country. However, building a bridge between science and industry requires investments in research, development and transfer of new technologies to the industry as well as specialized personnel to deal with new technological challenges.