Selection and optimization of microbial hosts for biofuels production

A comparative assessment of microbial biodiesel and its life cycle analysis

Biodiesel is a type of sustainable, biodegradable energy made from natural sources like vegetable oils, animal fat, and from microbes. Unlike traditional diesel, it has a lower carbon footprint and produces fewer harmful emissions when burned. Biodiesel has gained popularity as a more sustainable substitute for hydrocarbon-based diesel and may be utilized in diesel engines without any modification. In this review, biodiesel from microorganisms such as algae, yeast, and fungi and advantages over another feedstock were discussed. The life cycle evaluation of biodiesel is a thorough assessment of the ecological and economic effects of biodiesel production and use, from the extraction of raw ingredients to the waste disposal process. The life cycle analysis considers the entire process, including the production of feedstocks, the production of biodiesel, and the use of biodiesel in vehicles and other applications. Life cycle analysis of biodiesel produced from microorganisms takes into consideration the environmental impact and sustainability of each step in the production process, including the impact on land use, water use, greenhouse gas emissions, and the availability of resources. In this section, biodiesel produced from microorganisms and other raw materials, its comparisons, and also steps involved in the life cycle such as the cultivation of microorganisms, harvesting of biomass, and conversion to biodiesel were discussed. The processes like extraction and purification, hydrothermal liquefaction, and their environmental impacts were examined by using various LCA software from the previously mentioned process.

Global regulator IrrE on stress tolerance: a review

Stress tolerance is a vital attribute for all living beings to cope with environmental adversities. IrrE (also named PprI) from Deinococcus radiodurans enhances resistance to extreme radiation stress by functioning as a global regulator, mediating the transcription of genes involved in deoxyribonucleic acid (DNA) damage response (DDR). The expression of IrrE augmented the resilience of various species to heat, radiation, oxidation, osmotic stresses and inhibitors, encompassing bacterial, fungal, plant, and mammalian cells. Moreover, IrrE was employed in a global regulator engineering strategy to broaden its applications in stress tolerance. The regulatory impacts of heterologously expressed IrrE have been investigated at the molecular and systems level, including the regulation of genes, proteins, modules, or pathways involved in DNA repair, detoxification proteins, protective molecules, native regulators and other aspects. In this review, we discuss the regulatory role and mechanism of IrrE in the antiradiation response of D. radiodurans. Furthermore, the applications and regulatory effects of heterologous expression of IrrE to enhance abiotic stress tolerance are summarized in particular.

Identification of membrane engineering targets for increased butanol tolerance in Clostridium saccharoperbutylacetonicum

There is a growing interest in the use of microbial cell factories to produce butanol, an industrial solvent and platform chemical. Biobutanol can also be used as a biofuel and represents a cleaner and more sustainable alternative to the use of conventional fossil fuels. Solventogenic Clostridia are the most popular microorganisms used due to the native expression of butanol synthesis pathways. A major drawback to the wide scale implementation and development of these technologies is the toxicity of butanol. Various membrane properties and related functions are perturbed by the interaction of butanol with the cell membrane, causing lower yields and higher purification costs. This is ultimately why the technology remains underemployed. This study aimed to develop a deeper understanding of butanol toxicity at the membrane to determine future targets for membrane engineering. Changes to the lipidome in Clostridium saccharoperbutylacetonicum N1-4 (HMT) throughout butanol fermentation were investigated with thin layer chromatography and mass spectrometry. By the end of fermentation, levels of phosphatidylglycerol lipids had increased significantly, suggesting an important role of these lipid species in tolerance to butanol. Using membrane models and in vitro assays to investigate characteristics such as permeability, fluidity, and swelling, it was found that altering the composition of membrane models can convey tolerance to butanol, and that modulating membrane fluidity appears to be a key factor. Data presented here will ultimately help to inform rational strain engineering efforts to produce more robust strains capable of producing higher butanol titres.

Cyanobacteria-Mediated Light-Driven Biotransformation: The Current Status and Perspectives

Most chemicals are manufactured by traditional chemical processes but at the expense of toxic catalyst use, high energy consumption, and waste generation. Biotransformation is a green, sustainable, and cost-effective process. As cyanobacteria can use light as the energy source to power the synthesis of NADPH and ATP, using cyanobacteria as the chassis organisms to design and develop light-driven biotransformation platforms for chemical synthesis has been gaining attention, since it can provide a theoretical and practical basis for the sustainable and green production of chemicals. Meanwhile, metabolic engineering and genome editing techniques have tremendous prospects for further engineering and optimizing chassis cells to achieve efficient light-driven systems for synthesizing various chemicals. Here, we display the potential of cyanobacteria as a promising light-driven biotransformation platform for the efficient synthesis of green chemicals and current achievements of light-driven biotransformation processes in wild-type or genetically modified cyanobacteria. Meanwhile, future perspectives of one-pot enzymatic cascade biotransformation from biobased materials in cyanobacteria have been proposed, which could provide additional research insights for green biotransformation and accelerate the advancement of biomanufacturing industries.

Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion

Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use.

Engineering Corynebacterium glutamicum for de novo production of 2-phenylethanol from lignocellulosic biomass hydrolysate

BACKGROUND

2-Phenylethanol is a specific aromatic alcohol with a rose-like smell, which has been widely used in the cosmetic and food industries. At present, 2-phenylethanol is mainly produced by chemical synthesis. The preference of consumers for "natural" products and the demand for environmental-friendly processes have promoted biotechnological processes for 2-phenylethanol production. Yet, high 2-phenylethanol cytotoxicity remains an issue during the bioproduction process.

RESULTS

Corynebacterium glutamicum with inherent tolerance to aromatic compounds was modified for the production of 2-phenylethanol from glucose and xylose. The sensitivity of C. glutamicum to 2-phenylethanol toxicity revealed that this host was more tolerant than Escherichia coli. Introduction of a heterologous Ehrlich pathway into the evolved phenylalanine-producing C. glutamicum CALE1 achieved 2-phenylethanol production, while combined expression of the aro10. Encoding 2-ketoisovalerate decarboxylase originating from Saccharomyces cerevisiae and the yahK encoding alcohol dehydrogenase originating from E. coli was shown to be the most efficient. Furthermore, overexpression of key genes (aroG^fbr, pheA^fbr, aroA, ppsA and tkt) involved in the phenylpyruvate pathway increased 2-phenylethanol titer to 3.23 g/L with a yield of 0.05 g/g glucose. After introducing a xylose assimilation pathway from Xanthomonas campestris and a xylose transporter from E. coli, 3.55 g/L 2-phenylethanol was produced by the engineered strain CGPE15 with a yield of 0.06 g/g xylose, which was 10% higher than that with glucose. This engineered strain CGPE15 also accumulated 3.28 g/L 2-phenylethanol from stalk hydrolysate.

CONCLUSIONS

In this study, we established and validated an efficient C. glutamicum strain for the de novo production of 2-phenylethanol from corn stalk hydrolysate. This work supplied a promising route for commodity 2-phenylethanol bioproduction from nonfood lignocellulosic feedstock.

Parallel engineering of environmental bacteria and performance over years under jungle-simulated conditions

Engineered bacteria could perform many functions in the environment, for example, to remediate pollutants, deliver nutrients to crops or act as in-field biosensors. Model organisms can be unreliable in the field, but selecting an isolate from the thousands that naturally live there and genetically manipulating them to carry the desired function is a slow and uninformed process. Here, we demonstrate the parallel engineering of isolates from environmental samples by using the broad-host-range XPORT conjugation system (Bacillus subtilis mini-ICEBs1) to transfer a genetic payload to many isolates in parallel. Bacillus and Lysinibacillus species were obtained from seven soil and water samples from different locations in Israel. XPORT successfully transferred a genetic function (reporter expression) into 25 of these isolates. They were then screened to identify the best-performing chassis based on the expression level, doubling time, functional stability in soil, and environmentally-relevant traits of its closest annotated reference species, such as the ability to sporulate and temperature tolerance. From this library, we selected Bacillus frigoritolerans A3E1, re-introduced it to soil, and measured function and genetic stability in a contained environment that replicates jungle conditions. After 21 months of storage, the engineered bacteria were viable, could perform their function, and did not accumulate disruptive mutations.

Development of shuttle vectors for rapid prototyping of engineered Synechococcus sp. PCC7002

Cyanobacteria are of particular interest for chemical production as they can assimilate CO₂ and use solar energy to power chemical synthesis. However, unlike the model microorganism of Escherichia coli, the availability of genetic toolboxes for rapid proof-of-concept studies in cyanobacteria is generally lacking. In this study, we first characterized a set of promoters to efficiently drive gene expressions in the marine cyanobacterium Synechococcus sp. PCC7002. We identified that the endogenous cpcBA promoter represented one of the strongest promoters in PCC7002. Next, a set of shuttle vectors was constructed based on the endogenous pAQ1 plasmid to facilitate the rapid pathway assembly. Moreover, we used the shuttle vectors to modularly optimize the amorpha-4,11-diene synthesis in PCC7002. By modularly optimizing the metabolic pathway, we managed to redistribute the central metabolism toward the amorpha-4,11-diene production in PCC7002 with enhanced product titer. Taken together, the plasmid toolbox developed in this study will greatly accelerate the generation of genetically engineered PCC7002. KEY POINTS: • Promoter characterization revealed that the endogenous cpcBA promoter represented one of the strongest promoters in PCC7002 • A set of shuttle vectors with different antibiotic selection markers was constructed based on endogenous pAQ1 plasmid • By modularly optimizing the metabolic pathway, amorpha-4,11-diene production in PCC7002 was improved.

Analysis of the Propionate Metabolism in Bacillus subtilis during 3-Indolacetic Production

The genera Bacillus belongs to the group of microorganisms that are known as plant growth-promoting bacteria, their metabolism has evolved to produce molecules that benefit the growth of the plant, and the production of 3-indole acetic acid (IAA) is part of its secondary metabolism. In this work, Bacillus subtilis was cultivated in a bioreactor to produce IAA using propionate and glucose as carbon sources in an M9-modified media; in both cases, tryptophan was added as a co-substrate. The yield of IAA using propionate is 17% higher compared to glucose. After 48 h of cultivation, the final concentration was 310 mg IAA/L using propionate and 230 mg IAA/L using glucose, with a concentration of 500 mg Trp/L. To gain more insight into propionate metabolism and its advantages, the genome-scale metabolic model of B. subtilis (iBSU 1147) and computational analysis were used to calculate flux distribution and evaluate the metabolic capabilities to produce IAA using propionate. The metabolic fluxes demonstrate that propionate uptake favors the production of precursors needed for the synthesis of the hormone, and the sensitivity analysis shows that the control of a specific growth rate has a positive impact on the production of IAA.

Efficient Large-Scale and Scarless Genome Engineering Enables the Construction and Screening of Bacillus subtilis Biofuel Overproducers

Bacillus subtilis is a versatile microbial cell factory that can produce valuable proteins and value-added chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable host strains. Herein, we develop an efficient CRISPR-Cas9 method for large-scale and scarless genome engineering in the Bacillus subtilis genome, which can delete up to 134.3 kb DNA fragments, 3.5 times as long as the previous report, with a positivity rate of 100%. The effects of using a heterologous NHEJ system, linear donor DNA, and various donor DNA length on the engineering efficiencies were also investigated. The CRISPR-Cas9 method was then utilized for Bacillus subtilis genome simplification and construction of a series of individual and cumulative deletion mutants, which are further screened for overproducer of isobutanol, a new generation biofuel. These results suggest that the method is a powerful genome engineering tool for constructing and screening engineered host strains with enhanced capabilities, highlighting the potential for synthetic biology and metabolic engineering.

Anaerobic Acidogenic Fermentation of Cellobiose by Immobilized Cells: Prediction of Organic Acids Production by Response Surface Methodology

Response surface methodology was used to derive a prediction model for organic acids production by anaerobic acidogenic fermentation of cellobiose, using a mixed culture immobilized on γ-alumina. Three parameters (substrate concentration, temperature, and initial pH) were evaluated. In order to determine the limits of the parameters, preliminary experiments at 37 °C were conducted using substrates of various cellobiose concentrations and pH values. Cellobiose was used as a model sugar for subsequent experiments with lignocellulosic biomass. The culture was well adapted to cellobiose by successive subculturing at 37 °C in synthetic media (with 100:5:1 COD:N:P ratio). The experimental data of successive batch fermentations were fitted into a polynomial model for the total organic acids concentration in order to derive a predictive model that could be utilized as a tool to predict fermentation results when lignocellulosic biomass is used as a substrate. The quadratic effect of temperature was the most significant, followed by the quadratic effect of initial pH and the linear effect of cellobiose concentration. The results corroborated the validity and effectiveness of the model.

Adaptive laboratory evolution principles and applications in industrial biotechnology

Adaptive laboratory evolution (ALE) is an innovative approach for the generation of evolved microbial strains with desired characteristics, by implementing the rules of natural selection as presented in the Darwinian Theory, on the laboratory bench. New as it might be, it has already been used by several researchers for the amelioration of a variety of characteristics of widely used microorganisms in biotechnology. ALE is used as a tool for the deeper understanding of the genetic and/or metabolic pathways of evolution. Another important field targeted by ALE is the manufacturing of products of (high) added value, such as ethanol, butanol and lipids. In the current review, we discuss the basic principles and techniques of ALE, and then we focus on studies where it has been applied to bacteria, fungi and microalgae, aiming to improve their performance to biotechnological procedures and/or inspect the genetic background of evolution. We conclude that ALE is a promising and efficacious method that has already led to the acquisition of useful new microbiological strains in biotechnology and could possibly offer even more interesting results in the future.

Producing Energy-Rich Microalgae Biomass for Liquid Biofuels: Influence of Strain Selection and Culture Conditions

Energy-storage metabolites such as neutral lipids and carbohydrates are valuable compounds for liquid biofuel production. The aim of this work is to elucidate the main biological responses of two algae species known for their effective energy-rich compound accumulation in nitrogen limitation and day–night cycles: Nannochloropsis gaditana, a seawater species, and Parachlorella kessleri, a freshwater species. Lipid and carbohydrate production are investigated, as well as cell resistance to mechanical disruption for energy-rich compound release. Nitrogen-depleted N. gaditana showed only a low consumption of energy-storage molecules with a non-significant preference for neutral lipids (TAG) and carbohydrates in day–night cycles. However, it did accumulate significantly fewer carbohydrates than P. kessleri. Following this, the highest levels of productivity for N. gaditana in chemostat cultures at four levels of nitrogen limitation were found to be 3.4 and 2.2 × 10−3 kg/m2·d for carbohydrates and TAG, respectively, at 56%NO3 limitation. The cell disruption rate of N. gaditana decreased along with nitrogen limitation, from 75% (at 200%NO3) to 17% (at 13%NO3). In the context of potentially recoverable energy for biofuels, P. kessleri showed good potential for biodiesel and high potential for bioethanol; by contrast, N. gaditana was found to be more efficient for biodiesel production only.

Bedform characteristics and biofilm community development interact to modify hyporheic exchange

The physical and biological attributes of riverine ecosystems interact in a complex manner which can affect the hydrodynamic behaviour of the system. This can alter the mixing characteristics of a river at the sediment-water interface. Research on hyporheic exchange has increased in recent years driven by a greater appreciation for the importance of this dynamic ecotone in connecting and regulating river systems. An understanding of process-based interactions driving hyporheic exchange is still limited, specifically the feedbacks between the physical and biological controlling factors. The interplay between bed morphology and sediment size on biofilm community development and the impact on hyporheic exchange mechanisms, was experimentally considered. Purpose built recirculating flume systems were constructed and three profiles of bedform investigated: i) flat, ii) undulating λ = 1 m, ii) undulating λ = 0.2 m, across two different sized sediments (0.5 mm and 5 mm). The influence of biofilm growth and bedform interaction on hyporheic exchange was explored, over time, using discrete repeat injections of fluorescent dye into the flumes. Hyporheic exchange rates were greatest in systems with larger sediment sizes (5 mm) and with more bedforms (undulating λ = 0.2). Sediment size was a dominant control in governing biofilm growth and hyporheic exchange in systems with limited bedform. In systems where bedform was prevalent, sediment size and biofilm appeared to no longer be a control on exchange due to the physical influence of advective pumping. Here, exchange rates within these environments were more consistent overtime, despite greater microbial growth. As such, bedform has the potential to overcome the rate limiting effects of biotic factors on hyporheic exchange and sediment size on microbial penetration. This has implications for pollutant and nutrient penetration; bedforms increase hydrological connectivity, generating the opportunity to support microbial communities at depth and as such, improve the self-purification ability of river systems.

Synergy of municipal solid waste co-processing with lignocellulosic waste for improved biobutanol production

Co-processing of lignocellulosic wastes, e.g., garden and paper wastes, and the organic matters fraction of municipal solid waste (OMSW) in an integrated bioprocess is a possible approach to realize the potential of wastes for biobutanol production. Dilute acid pretreatment is a multi-functional stage for breaking the recalcitrant lignocellulose's structure, hydrolyzing hemicellulose, and hydrolyzing/solubilizing starch, leading to a pretreated solid and a rich hydrolysate. In this study, dilute-acid pretreatment of the combination of wastepaper and OMSW, composite I, as well as garden waste and OMSW, composite II, at severe conditions resulted in "pretreatment hydrolysates" containing 33.7 and 19.4 g/L sugar along with 18.9 and 33.2 g/L soluble starch, respectively. In addition, the hydrolysis of solid remained after the pretreatment of composite I and II resulted in "enzymatic hydrolysates" comprising 19.4 and 33 g/L sugar, respectively. The fermentation of the pretreatment hydrolysates and enzymatic hydrolysates resulted in 3.5 and 6.4 g/L ABE from composite I and 15 and 5.2 g/L ABE from composite II, respectively. In this process, 148 and 173 g ABE (60 and 100 g gasoline equivalent/kg) was obtained from each kg composite I and composite II, respectively, where co-processing of OMSW with lignocellulosic wastes resulted in 10 and 49% higher ABE than that produced from the individual substrates.

The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels

Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology.

Enhanced Thermostability and Enzymatic Activity of Cel6A Variants from Thermobifida fusca by Empirical Domain Engineering (Short Title: Domain Engineering of Cel6A)

Cellulases are a set of lignocellulolytic enzymes, capable of producing eco-friendly low-cost renewable bioethanol. However, low stability and hydrolytic activity limit their wide-scale applicability at the industrial scale. In this work, we report the domain engineering of endoglucanase (Cel6A) of Thermobifida fusca to improve their catalytic activity and thermal stability. Later, enzymatic activity and thermostability of the most efficient variant named as Cel6A.CBC was analyzed by molecular dynamics simulations. This variant demonstrated profound activity against soluble and insoluble cellulosic substrates like filter paper, alkali-treated bagasse, regenerated amorphous cellulose (RAC), and bacterial microcrystalline cellulose. The variant Cel6A.CBC showed the highest catalysis of carboxymethyl cellulose (CMC) and other related insoluble substrates at a pH of 6.0 and a temperature of 60 °C. Furthermore, a sound rationale was observed between experimental findings and molecular modeling of Cel6A.CBC which revealed thermostability of Cel6A.CBC at 26.85, 60.85, and 74.85 °C as well as structural flexibility at 126.85 °C. Therefore, a thermostable derivative of Cel6A engineered in the present work has enhanced biological performance and can be a useful construct for the mass production of bioethanol from plant biomass.

Effect of tungsten and selenium on C1 gas bioconversion by an enriched anaerobic sludge and microbial community analysis

The effect of trace metals, namely tungsten and selenium, on the production of acids and alcohols through gas fermentation by a CO-enriched anaerobic sludge in a continuous gas-fed bioreactor was investigated. The CO-enriched sludge was first supplied with a tungsten-deficient medium (containing selenium) and in a next assay, a selenium-deficient medium (containing tungsten) was fed to the bioreactor, at a CO gas flow rate of 10 mL/min. In the absence of tungsten (tungstate), an initial pH of 6.2 followed by a pH decrease to 4.9 yielded 7.34 g/L acetic acid as the major acid during the high pH period. Subsequently, bioconversion of the acids at a lower pH of 4.9 yielded only 1.85 g/L ethanol and 1.2 g/L butanol in the absence of tungsten (tungstate). A similar follow up assay in the same bioreactor with two consecutive periods at different pH values (i.e., 6.2 and 4.9) with a selenium deficient medium yielded 6.6 g/L acetic acid at pH 6.2 and 4 g/L ethanol as well as 1.88 g/L butanol at pH 4.9. The results from the microbial community analysis showed that the only known CO fixing microorganism able to produce alcohols detected in the bioreactor was Clostridium autoethanogenum, both in the tungsten and the selenium deprived media, although that species has so far not been reported to be able to produce butanol. No other solventogenic acetogen was detected.

Comparative Study of Extracellular Proteolytic, Cellulolytic, and Hemicellulolytic Enzyme Activities and Biotransformation of Palm Kernel Cake Biomass by Lactic Acid Bacteria Isolated from Malaysian Foods

Biotransformation via solid state fermentation (SSF) mediated by microorganisms is a promising approach to produce useful products from agricultural biomass. Lactic acid bacteria (LAB) that are commonly found in fermented foods have been shown to exhibit extracellular proteolytic, β-glucosidase, β-mannosidase, and β-mannanase activities. Therefore, extracellular proteolytic, cellulolytic, and hemicellulolytic enzyme activities of seven Lactobacillus plantarum strains (a prominent species of LAB) isolated from Malaysian foods were compared in this study. The biotransformation of palm kernel cake (PKC) biomass mediated by selected L. plantarum strains was subsequently conducted. The results obtained in this study exhibited the studied L. plantarum strains produced versatile multi extracellular hydrolytic enzyme activities that were active from acidic to alkaline pH conditions. The highest total score of extracellular hydrolytic enzyme activities were recorded by L. plantarum RI11, L. plantarum RG11, and L. plantarum RG14. Therefore, they were selected for the subsequent biotransformation of PKC biomass via SSF. The hydrolytic enzyme activities of treated PKC extract were compared for each sampling interval. The scanning electron microscopy analyses revealed the formation of extracellular matrices around L. plantarum strains attached to the surface of PKC biomass during SSF, inferring that the investigated L. plantarum strains have the capability to grow on PKC biomass and perform synergistic secretions of various extracellular proteolytic, cellulolytic, and hemicellulolytic enzymes that were essential for the effective biodegradation of PKC. The substantial growth of selected L. plamtraum strains on PKC during SSF revealed the promising application of selected L. plantarum strains as a biotransformation agent for cellulosic biomass.

Enhancing butanol tolerance of Escherichia coli reveals hydrophobic interaction of multi-tasking chaperone SecB

BACKGROUND

Escherichia coli has been proved to be one promising platform chassis for the production of various natural products, such as biofuels. Product toxicity is one of the main bottlenecks for achieving maximum production of biofuels. Host strain engineering is an effective approach to alleviate solvent toxicity issue in fermentation.

RESULTS

Thirty chaperones were overexpressed in E. coli JM109, and SecB recombinant strain was identified with the highest n-butanol tolerance. The tolerance (T) of E. coli overexpressing SecB, calculated by growth difference in the presence and absence of solvents, was determined to be 9.13% at 1.2% (v/v) butanol, which was 3.2-fold of the control strain. Random mutagenesis of SecB was implemented and homologously overexpressed in E. coli, and mutant SecB_T10A was identified from 2800 variants rendering E. coli the highest butanol tolerance. Saturation mutagenesis on T10 site revealed that hydrophobic residues were required for high butanol tolerance of E. coli. Compared with wild-type (WT) SecB, the T of SecB_T10A strain was further increased from 9.14 to 14.4% at 1.2% butanol, which was 5.3-fold of control strain. Remarkably, E. coli engineered with SecB_T10A could tolerate as high as 1.8% butanol (~ 14.58 g/L). The binding affinity of SecB_T10A toward model substrate unfolded maltose binding protein (preMBP) was 11.9-fold of that of WT SecB as determined by isothermal titration calorimetry. Residue T10 locates at the entrance of hydrophobic substrate binding groove of SecB, and might play an important role in recognition and binding of cargo proteins.

CONCLUSIONS

SecB chaperone was identified by chaperone mining to be effective in enhancing butanol tolerance of E. coli. Maximum butanol tolerance of E. coli could reach 1.6% and 1.8% butanol by engineering single gene of SecB or SecB_T10A. Hydrophobic interaction is vital for enhanced binding affinity between SecB and cargo proteins, and therefore improved butanol tolerance.

Engineering Robust Production Microbes for Large-Scale Cultivation

Systems biology and synthetic biology are increasingly used to examine and modulate complex biological systems. As such, many issues arising during scaling-up microbial production processes can be addressed using these approaches. We review differences between laboratory-scale cultures and larger-scale processes to provide a perspective on those strain characteristics that are especially important during scaling. Systems biology has been used to examine a range of microbial systems for their response in bioreactors to fluctuations in nutrients, dissolved gases, and other stresses. Synthetic biology has been used both to assess and modulate strain response, and to engineer strains to improve production. We discuss these approaches and tools in the context of their use in engineering robust microbes for applications in large-scale production.

New technologies provide more metabolic engineering strategies for bioethanol production in Zymomonas mobilis

Bioethanol has been considered as a potentially renewable energy source, and metabolic engineering plays an important role in the production of biofuels. As an efficient ethanol-producing bacterium, Zymomonas mobilis has garnered special attention due to its high sugar uptake, ethanol yield, and tolerance. Different metabolic engineering strategies have been used to establish new metabolic pathways for Z. mobilis to broaden its substrate range, remove competing pathways, and enhance its tolerance to ethanol and lignocellulosic hydrolysate inhibitors. Recent advances in omics technology, computational modeling and simulation, system biology, and synthetic biology contribute to the efficient re-design and manipulation of microbes via metabolic engineering at the whole-cell level. In this review, we summarize the progress of some new technologies used for metabolic engineering to improve bioethanol production and tolerance in Z. mobilis. Some successful examples of metabolic engineering used to develop strains for ethanol production are described in detail. Lastly, some important strategies for future metabolic engineering efforts are also highlighted.

Experimental evolution: its principles and applications in developing stress-tolerant yeasts

Stress tolerance and resistance in industrial yeast strains are important attributes for cost-effective bioprocessing. The source of stress-tolerant yeasts ranges from extremophilic environments to laboratory engineered strains. However, industrial stress-tolerant yeasts are very rare in nature as the natural environment forces them to evolve traits that optimize survival and reproduction and not the ability to withstand harsh habitat-irrelevant industrial conditions. Experimental evolution is a frequent method used to uncover the mechanisms of evolution and microbial adaption towards environmental stresses. It optimizes biological systems by means of adaptation to environmental stresses and thus has immense power of development of robust stress-tolerant yeasts. This mini-review briefly outlines the basics and implications of evolution experiments and their applications to industrial biotechnology. This work is meant to serve as an introduction to those new to the field of experimental evolution, and as a guide to biologists working in the field of yeast stress response. Future perspectives of experimental evolution for potential biotechnological applications have also been elucidated.

Tolerance against butanol stress by disrupting succinylglutamate desuccinylase inEscherichia coli

The four-carbon alcohol, butanol, is emerging as a promising biofuel and efforts have been undertaken to improve several microbial hosts for its production.

Genotype-by-Environment-by-Environment Interactions in the Saccharomyces cerevisiae Transcriptomic Response to Alcohols and Anaerobiosis

Next generation biofuels including longer-chain alcohols such as butanol are attractive as renewable, high-energy fuels. A barrier to microbial production of butanols is the increased toxicity compared to ethanol; however, the cellular targets and microbial defense mechanisms remain poorly understood, especially under anaerobic conditions used frequently in industry. Here we took a comparative approach to understand the response of Saccharomyces cerevisiae to 1-butanol, isobutanol, or ethanol, across three genetic backgrounds of varying tolerance in aerobic and anaerobic conditions. We find that strains have different growth properties and alcohol tolerances with and without oxygen availability, as well as unique and common responses to each of the three alcohols. Our results provide evidence for strain-by-alcohol-by-oxygen interactions that moderate how cells respond to alcohol stress.

Elimination of biosynthetic pathways for l-valine and l-isoleucine in mitochondria enhances isobutanol production in engineered Saccharomyces cerevisiae

Saccharomyces cerevisiae has a natural ability to produce higher alcohols, making it a promising candidate for production of isobutanol. However, the several pathways competing with isobutanol biosynthesis lead to production of substantial amounts of l-valine and l-isoleucine in mitochondria and isobutyrate, l-leucine, and ethanol in cytosol. To increase flux to isobutanol by removing by-product formation, the genes associated with formation of l-valine (BAT1), l-isoleucine (ILV1), isobutyrate (ALD6), l-leucine (LEU1), and ethanol (ADH1) were disrupted to construct the S. cerevisiae WΔGBIALA1_2vec strain. This strain showed 8.9 and 8.6 folds increases in isobutanol concentration and yield, respectively, relative the corresponding values of the background strain on glucose medium. In a bioreactor fermentation with a gas trapping system, the WΔGBIALA1_2vec strain produced 662 mg/L isobutanol concentration with a yield of 6.71 mg_isobutanol/g_glucose. With elimination of the competing pathways, the WΔGBIALA1_2vec strain would serve as a platform strain for isobutanol production.

A Mathematical Model for End-Product Toxicity

Alcohol based biofuels, such as bio-butanol, have considerable potential to reduce the demand for petrochemical fuels. However, one of the main obstacles to the commercial development of biological based production processes of biofuels is end-product toxicity to the biocatalyst. We investigate the effect of end-product toxicity upon the steady-state production of a biofuel produced through the growth of microorganisms in a continuous flow bioreactor. The novelty of the model formulation is that the product is assumed to be toxic to the biomass. The increase in the per-capita decay rate due to the presence of the product is assumed to be proportional to the the concentration of the product. The steady-state solutions for the model are obtained, and their stability determined as a function of the residence time. These solutions are used to investigate how the maximum yield and the reactor productivity depend upon system parameters. Unlike systems which do not exhibit toxicity there is a value of the feed concentration which maximises the product yield. The maximum reactor productivity is shown to be a sharply decreasing function of both the feed concentration and the toxicity parameter. In conclusion, alternative reactor configurations are required to reduce the effects of highly toxic products.

1-Butanol as a Solvent for Efficient Extraction of Polar Compounds from Aqueous Medium: Theoretical and Practical Aspects

The extraction of polar molecules from aqueous solution is a challenging task in organic synthesis. 1-Butanol has been used sporadically as an eluent for polar molecules, but it is unclear which molecular features drive its efficiency. Here, we employ free energy simulations to study the partitioning of 15 solutes between water and 1-butanol. The simulations demonstrate that the high affinity of polar molecules to the wet 1-butanol phase is associated with its nanostructure. Small inverse micelles of water are able to accommodate polar solutes and locally mimic an aqueous environment. We verify the simulations based on partition coefficients between water and 1-octanol, and include a blind prediction of the water/1-butanol partition coefficient of cyclohexane-1,2-diol. The calculations are in excellent agreement with experiment, reaching root-mean-square deviations below 0.7 kcal/mol. Actual extractions of cyclohexane-1,2-diol from buffer solutions that mimic cell lysates and suspensions in biocatalytic reactions further exemplify our findings. The yields highlight that extractions with 1-butanol can be significantly more efficient than the conventional protocol based on ethyl acetate.

A review on microbial lipids as a potential biofuel

Energy security, environmental concerns, and unstable oil prices have been the driving trifecta of demand for alternative fuels in the United States. The United States' dependence on energy resources, often from unstable oil-producing countries has created political insecurities and concerns. As we try to gain energy security, unconventional oil becomes more common, flooding the market, and causing the major downshift of the usual unstable oil prices. Meanwhile, consumption of fossil fuels and the consequent CO₂ emissions have driven disruptions in the Earth's atmosphere and are recognized to be responsible for global climate change. While the significance of each of these three factors may fluctuate with global politics or new technologies, transportation energy will remain the prominent focus of multi-disciplined research. Bioenergy future depends on the price of oil. Current energy policy of the United States heavily favors petroleum industry. In this review, the current trend in microbial lipids as a potential biofuel is discussed.

Incorporating comparative genomics into the design-test-learn cycle of microbial strain engineering

Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling and regulatory rewiring, has proven to significantly advance industrial strain engineering. This review highlights how comparative genomics can also facilitate strain engineering, by identifying novel genes and pathways, regulatory mechanisms and genetic background effects for engineering. We discuss how incorporating comparative genomics into the design-test-learn cycle of strain engineering can provide novel information that complements other engineering strategies.

Metabolic engineering of the 2-ketobutyrate biosynthetic pathway for 1-propanol production in Saccharomyces cerevisiae

Background

To produce 1-propanol as a potential biofuel, metabolic engineering of microorganisms, such as E. coli, has been studied. However, 1-propanol production using metabolically engineered Saccharomyces cerevisiae, which has an amazing ability to produce ethanol and is thus alcohol-tolerant, has infrequently been reported. Therefore, in this study, we aimed to engineer S. cerevisiae strains capable of producing 1-propanol at high levels.

Results

We found that the activity of endogenous 2-keto acid decarboxylase and alcohol/aldehyde dehydrogenase is sufficient to convert 2-ketobutyrate (2 KB) to 500 mg/L 1-propanol in yeast. Production of 1-propanol could be increased by: (i) the construction of an artificial 2 KB biosynthetic pathway from pyruvate via citramalate (cimA); (ii) overexpression of threonine dehydratase (tdcB); (iii) enhancement of threonine biosynthesis from aspartate (thrA, thrB and thrC); and (iv) deletion of the GLY1 gene that regulates a competing pathway converting threonine to glycine. With high-density anaerobic fermentation of the engineered S. cerevisiae strain YG5C4231, we succeeded in producing 180 mg/L 1-propanol from glucose.

Conclusion

These results indicate that the engineering of a citramalate-mediated pathway as a production method for 1-propanol in S. cerevisiae is effective. Although optimization of the carbon flux in S. cerevisiae is necessary to harness this pathway, it is a promising candidate for the large-scale production of 1-propanol.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0883-1) contains supplementary material, which is available to authorized users.

Beyond editing to writing large genomes

Recent exponential advances in genome sequencing and engineering technologies have enabled an unprecedented level of interrogation into the impact of DNA variation (genotype) on cellular function (phenotype). Furthermore, these advances have also prompted realistic discussion of writing and radically re-writing complex genomes. In this Perspective, we detail the motivation for large-scale engineering, discuss the progress made from such projects in bacteria and yeast and describe how various genome-engineering technologies will contribute to this effort. Finally, we describe the features of an ideal platform and provide a roadmap to facilitate the efficient writing of large genomes.

Expression of Heterologous Sigma Factor Expands the Searchable Space for Biofuel Tolerance Mechanisms

Microorganisms can produce hydrocarbons that can serve as replacements or additions to conventional liquid fuels for use in the transportation sector. However, a common problem in the microbial synthesis of biofuels is that these compounds often have toxic effects on the cell. In this study, we focused on mitigating the toxicity of the biojet fuel precursor pinene on Escherichia coli. We used genomic DNA from Pseudomonas putida KT2440, which has innate solvent-tolerance properties, to create transgenic libraries in an E. coli host. We exposed cells containing the library to pinene, selecting for genes that improved tolerance. Importantly, we found that expressing the sigma factor RpoD from P. putida greatly expanded the diversity of tolerance genes recovered. With low expression of rpoD_P.putida, we isolated a single pinene tolerance gene; with increased expression of the sigma factor our selection experiments returned multiple distinct tolerance mechanisms, including some that have been previously documented and also new mechanisms. Interestingly, high levels of rpoD_P.putida induction resulted in decreased diversity. We found that the tolerance levels provided by some genes are highly sensitive to the level of induction of rpoD_P.putida, while others provide tolerance across a wide range of rpoD_P.putida levels. This method for unlocking diversity in tolerance screening using heterologous sigma factor expression was applicable to both plasmid and fosmid-based transgenic libraries. These results suggest that by controlling the expression of appropriate heterologous sigma factors, we can greatly increase the searchable genomic space within transgenic libraries.

Generation and Characterization of Acid Tolerant Fibrobacter succinogenes S85

Microorganisms are key components for plant biomass breakdown within rumen environments. Fibrobacter succinogenes have been identified as being active and dominant cellulolytic members of the rumen. In this study, F. succinogenes type strain S85 was adapted for steady state growth in continuous culture at pH 5.75 and confirmed to grow in the range of pH 5.60–5.65, which is lower than has been reported previously. Wild type and acid tolerant strains digested corn stover with equal efficiency in batch culture at low pH. RNA-seq analysis revealed 268 and 829 genes were differentially expressed at pH 6.10 and 5.65 compared to pH 6.70, respectively. Resequencing analysis identified seven single nucleotide polymorphisms (SNPs) in the sufD, yidE, xylE, rlmM, mscL and dosC genes of acid tolerant strains. Due to the absence of a F. succinogenes genetic system, homologues in Escherichia coli were mutated and complemented and the resulting strains were assayed for acid survival. Complementation with wild-type or acid tolerant F. succinogenes sufD restored E. coli wild-type levels of acid tolerance, suggesting a possible role in acid homeostasis. Recent genetic engineering developments need to be adapted and applied in F. succinogenes to further our understanding of this bacterium.

The significance of proline and glutamate on butanol chaotropic stress in Bacillus subtilis 168

BACKGROUND

Butanol is an intensively used industrial solvent and an attractive alternative biofuel, but the bioproduction suffers from its high toxicity. Among the native butanol producers and heterologous butanol-producing hosts, Bacillus subtilis 168 exhibited relatively higher butanol tolerance. Nevertheless, organic solvent tolerance mechanisms in Bacilli and Gram-positive bacteria have relatively less information. Thus, this study aimed to elucidate butanol stress responses that may involve in unique tolerance of B. subtilis 168 to butanol and other alcohol biocommodities.

RESULTS

Using comparative proteomics approach and molecular analysis of butanol-challenged B. subtilis 168, 108 butanol-responsive proteins were revealed, and classified into seven groups according to their biological functions. While parts of them may be similar to the proteins reportedly involved in solvent stress response in other Gram-positive bacteria, significant role of proline in the proline-glutamate-arginine metabolism was substantiated. Detection of intracellular proline and glutamate accumulation, as well as glutamate transient conversion during butanol exposure confirmed their necessity, especially proline, for cellular butanol tolerance. Disruption of the particular genes in proline biosynthesis pathways clarified the essential role of the anabolic ProB-ProA-ProI system over the osmoadaptive ProH-ProA-ProJ system for cellular protection in response to butanol exposure. Molecular modifications to increase gene dosage for proline biosynthesis as well as for glutamate acquisition enhanced butanol tolerance of B. subtilis 168 up to 1.8% (vol/vol) under the conditions tested.

CONCLUSION

This work revealed the important role of proline as an effective compatible solute that is required to protect cells against butanol chaotropic effect and to maintain cellular functions in B. subtilis 168 during butanol exposure. Nevertheless, the accumulation of intracellular proline against butanol stress required a metabolic conversion of glutamate through the specific biosynthetic ProB-ProA-ProI route. Thus, exogenous addition of glutamate, but not proline, enhanced butanol tolerance. These findings serve as a practical knowledge to enhance B. subtilis 168 butanol tolerance, and demonstrate means to engineer the bacterial host to promote higher butanol/alcohol tolerance of B. subtilis 168 for the production of butanol and other alcohol biocommodities.

Synthesis and analysis of separation networks for the recovery of intracellular chemicals generated from microbial-based conversions

BACKGROUND

Bioseparations can contribute to more than 70% in the total production cost of a bio-based chemical, and if the desired chemical is localized intracellularly, there can be additional challenges associated with its recovery. Based on the properties of the desired chemical and other components in the stream, there can be multiple feasible options for product recovery. These options are composed of several alternative technologies, performing similar tasks. The suitability of a technology for a particular chemical depends on (1) its performance parameters, such as separation efficiency; (2) cost or amount of added separating agent; (3) properties of the bioreactor effluent (e.g., biomass titer, product content); and (4) final product specifications. Our goal is to first synthesize alternative separation options and then analyze how technology selection affects the overall process economics. To achieve this, we propose an optimization-based framework that helps in identifying the critical technologies and parameters.

RESULTS

We study the separation networks for two representative classes of chemicals based on their properties. The separation network is divided into three stages: cell and product isolation (stage I), product concentration (II), and product purification and refining (III). Each stage exploits differences in specific product properties for achieving the desired product quality. The cost contribution analysis for the two cases (intracellular insoluble and intracellular soluble) reveals that stage I is the key cost contributor (>70% of the overall cost). Further analysis suggests that changes in input conditions and technology performance parameters lead to new designs primarily in stage I.

CONCLUSIONS

The proposed framework provides significant insights for technology selection and assists in making informed decisions regarding technologies that should be used in combination for a given set of stream/product properties and final output specifications. Additionally, the parametric sensitivity provides an opportunity to make crucial design and selection decisions in a comprehensive and rational manner. This will prove valuable in the selection of chemicals to be produced using bioconversions (bioproducts) as well as in creating better bioseparation flow sheets for detailed economic assessment and process implementation on the commercial scale.