Metabolic engineering of cyanobacteria for 1-butanol production from carbon dioxide

Enhancing the co-utilization of methanol and CO2 into 1-butanol by equipping synergistic reductive glycine pathway in Butyribacterium methylotrophicum

The biological fixation of CO2 and C1-feedstocks like methanol derived from CO2 are considered as an important technology combating in global warming issues. The microorganisms that can co-assimilate CO2 and methanol are highly desired. Here, we constructed a synergistic assimilation pathway in Butyribacterium methylotrophicum (B. methylotrophicum) for improved carbon utilization efficiency. Through a transcriptional analysis, the genes involving in the native methanol and CO2 assimilation pathway, oxidative phosphorylation and amino acid metabolism were significantly up-regulated, indicating the functional cooperation of the pathways in improving cell activity on methanol and CO2. Ultimately, by overexpressing exogenous genes of adhE2 in recombinant B. methylotrophicum, 1.4 g/L of 1-butanol was successfully synthesized from methanol and CO2, which was also the highest titer of 1-butanol synthesis using C1-feedstocks. Thus, the design of synergistic methanol assimilation pathway was an effective approach to improve the carbon assimilation capacity of strain for the establishment of C1-feedstock biotransformation platforms.

Facilitated Channeling of Fixed Carbon and Energy into Chemicals in Artificial Phototrophic Communities

Light-driven CO2 biovalorization offers a promising route for coupling carbon mitigation with petrochemical replacement. Synthetic phototrophic communities that mimic lichens can reduce the metabolic burden with improved CO2 utilization. However, inefficient channeling of carbon and energy between species seriously hinders the collaborative CO2-to-molecule route. Herein, we report a universal carbon sequestration (UCS) module based on photosynthetic microbes that provides a high-speed tunnel for channeling carbon and energy to heterotrophs. Compared to that of the traditional CO2-to-sucrose module, the UCS module sequestered 30% more carbon into glycerol, a generally available carbon source with high energy density. We demonstrated that the UCS module can be highly compatible with various industrial chassis and genetically recalcitrant microbes, enabling the rapid development of synthetic phototrophic communities without additional genetic manipulation. Notably, the accelerated electron transport and nutrient recycling systems may facilitate carbon and energy communications between cooperative partners. These UCS module-based communities efficiently channeled CO2 into a wide range of chemicals, with a negative carbon footprint of -25.04 to -440.74 kgCO2e/kg of products. This strategy widens the boundaries of artificial photosynthetic communities and may boost carbon-negative biomanufacturing.

Employment of light-inducible promoter in genetically engineered cyanobacteria for photosynthetic isobutanol production with simulated diurnal sunlight and CO2

Cyanobacteria are oxygen-evolving prokaryotes that can be engineered for biofuel production from solar energy, CO2, and water. Isobutanol (IB) has the potential to serve as an alternative fuel and important chemical feedstock. The research involves engineering Synechocystis sp. PCC 6803, for photosynthetic isobutanol production via the 2-keto-acid pathway and their cultivation in lab-scale photobioreactors. This synthetic pathway involves the heterologous expression of two enzymes, α-ketoisovalerate decarboxylase (Kivd) and alcohol dehydrogenase (Yqhd), under a strong light-inducible promotor, psbA2, known to show increased gene expression under high light. The use of psbA2 could be a valuable strategy for isobutanol production as economic scaling up demands the utilization of natural sunlight, which also provides very high light intensity at midday, facilitating increased production. The study reports isobutanol production from engineered strains containing both pathway genes and with only kivd. In shake flask studies, the highest isobutanol titre of 75 mg L-1 (12th day) was achieved from an engineered strain DM12 under optimized light intensity. DM12 was cultivated in a 2 L flat panel photobioreactor, resulting in a maximum isobutanol titre of 371.8 mg L-1 (10th day) with 2 % CO2 and 200 μmol photons m-2 s-1. Cultivation of DM12 in a photobioreactor under mimic diurnal sunlight demonstrated the highest productivity of 39 mg L-1 day-1 with the maximum titre of 308.5 mg L-1 (9th day). This work lays the foundation for sustainable, large-scale biobutanol production using solar energy.

Effects of n-butanol production on metabolism and the photosystem in Synecococcus elongatus PCC 7942 based on metabolic flux and target proteome analyses

Although n-butanol (BuOH) is an ideal fuel because of its superior physical properties, it has toxicity to microbes. Previously, a Synechococcus elongatus PCC 7942 derivative strain that produces BuOH from CO2 was developed by introducing six heterologous genes (BUOH-SE strain). To identify the bottleneck in BuOH production, the effects of BuOH production and its toxicity on central metabolism and the photosystem were investigated. Parental (WT) and BUOH-SE strains were cultured under autotrophic conditions. Consistent with the results of a previous study, BuOH production was observed only in the BUOH-SE strain. Isotopically non-stationary 13C-metabolic flux analysis revealed that the CO2 fixation rate was much larger than the BuOH production rate in the BUOH-SE strain (1.70 vs 0.03 mmol gDCW-1 h-1), implying that the carbon flow for BuOH biosynthesis was less affected by the entire flux distribution. No large difference was observed in the flux of metabolism between the WT and BUOH-SE strains. Contrastingly, in the photosystem, the chlorophyll content and maximum O2 evolution rate per dry cell weight of the BUOH-SE strain were decreased to 81% and 43% of the WT strain, respectively. Target proteome analysis revealed that the amounts of some proteins related to antennae (ApcA, ApcD, ApcE, and CpcC), photosystem II (PsbB, PsbU, and Psb28-2), and cytochrome b6f complex (PetB and PetC) in photosystems decreased in the BUOH-SE strain. The activation of photosynthesis would be a novel approach for further enhancing BuOH production in S. elongatus PCC 7942.

Arsenite S-Adenosylmethionine Methyltransferase Is Responsible for Antimony Biomethylation in Nostoc sp. PCC7120

Antimony (Sb) biomethylation is an important but uninformed process in Sb biogeochemical cycling. Methylated Sb species have been widely detected in the environment, but the gene and enzyme for Sb methylation remain unknown. Here, we found that arsenite S-adenosylmethionine methyltransferase (ArsM) is able to catalyze Sb(III) methylation. The stepwise methylation by ArsM forms mono-, di-, and trimethylated Sb species. Sb(III) is readily coordinated with glutathione, forming the preferred ArsM substrate which is anchored on three conserved cysteines. Overexpressing arsM in Escherichia coli AW3110 conferred resistance to Sb(III) by converting intracellular Sb(III) into gaseous methylated species, serving as a detoxification process. Methylated Sb species were detected in paddy soil cultures, and phylogenetic analysis of ArsM showed its great diversity in ecosystems, suggesting a high metabolic potential for Sb(III) methylation in the environment. This study shows an undiscovered microbial process methylating aqueous Sb(III) into the gaseous phase, mobilizing Sb on a regional and even global scale as a re-emerging contaminant.

Metabolic Engineering of Microorganisms to Produce Pyruvate and Derived Compounds

Pyruvate is a hub of various endogenous metabolic pathways, including glycolysis, TCA cycle, amino acid, and fatty acid biosynthesis. It has also been used as a precursor for pyruvate-derived compounds such as acetoin, 2,3-butanediol (2,3-BD), butanol, butyrate, and L-alanine biosynthesis. Pyruvate and derivatives are widely utilized in food, pharmaceuticals, pesticides, feed additives, and bioenergy industries. However, compounds such as pyruvate, acetoin, and butanol are often chemically synthesized from fossil feedstocks, resulting in declining fossil fuels and increasing environmental pollution. Metabolic engineering is a powerful tool for producing eco-friendly chemicals from renewable biomass resources through microbial fermentation. Here, we review and systematically summarize recent advances in the biosynthesis pathways, regulatory mechanisms, and metabolic engineering strategies for pyruvate and derivatives. Furthermore, the establishment of sustainable industrial synthesis platforms based on alternative substrates and new tools to produce these compounds is elaborated. Finally, we discuss the potential difficulties in the current metabolic engineering of pyruvate and derivatives and promising strategies for constructing efficient producers.

Characterization of a cyanobacterial rep protein with broad-host range and its utilization for expression vectors

Owing to their photosynthetic capabilities, cyanobacteria are regarded as ecologically friendly hosts for production of biomaterials. However, compared to other bacteria, tools for genetic engineering, especially expression vector systems, are limited. In this study, we characterized a Rep protein, exhibiting replication activity in multiple cyanobacteria and established an expression vector using this protein. Our comprehensive screening using a genomic library of Synechocystis sp. PCC 6803 revealed that a certain region encoding a Rep-related protein (here named Cyanobacterial Rep protein A2: CyRepA2) exhibits high autonomous replication activity in a heterologous host cyanobacterium, Synechococcus elongatus PCC 7942. A reporter assay using GFP showed that the expression vector pYS carrying CyRepA2 can be maintained in not only S. 6803 and S. 7942, but also Synechococcus sp. PCC 7002 and Anabaena sp. PCC 7120. In S. 7942, GFP expression in the pYS-based system was tightly regulated by IPTG, achieving 10-fold higher levels than in the chromosome-based system. Furthermore, pYS could be used together with the conventional vector pEX, which was constructed from an endogenous plasmid in S. 7942. The combination of pYS with other vectors is useful for genetic engineering, such as modifying metabolic pathways, and is expected to improve the performance of cyanobacteria as bioproduction chassis.

Metabolic Engineering Design Strategies for Increasing Carbon Fluxes Relevant for Biosynthesis in Cyanobacteria

Cyanobacteria are promising microbial cell factories for the direct production of biochemicals and biofuels from CO2. Through genetic and metabolic engineering, they can be modified to produce a variety of both natural and non-natural compounds. To enhance the yield of these products, various design strategies have been developed. In this chapter, strategies used to enhance metabolic fluxes towards common precursors used in biosynthesis, including pyruvate, acetyl-CoA, malonyl-CoA, TCA cycle intermediates, and aromatics, are discussed. Additionally, strategies related to cofactor availability and mixotrophic conditions for bioproduction are also summarize.

Introduction to Cyanobacteria

Cyanobacteria are highly interesting microbes with the capacity for oxygenic photosynthesis. They fulfill an important purpose in nature but are also potent biocatalysts. This chapter gives a brief overview of this diverse phylum and shortly addresses the functions these organisms have in the natural ecosystems. Further, it introduces the main topics covered in this volume, which is dealing with the development and application of cyanobacteria as solar cell factories for the production of chemicals including potential fuels. We discuss cyanobacteria as industrial workhorses, present established chassis strains, and give an overview of the current target products. Genetic engineering strategies aiming at the photosynthetic efficiency as well as approaches to optimize carbon fluxes are summarized. Finally, main cultivation strategies are sketched.

Biofuels from Renewable Sources, a Potential Option for Biodiesel Production

Ever-increasing population growth that demands more energy produces tremendous pressure on natural energy reserves such as coal and petroleum, causing their depletion. Climate prediction models predict that drought events will be more intense during the 21st century affecting agricultural productivity. The renewable energy needs in the global energy supply must stabilize surface temperature rise to 1.5 °C compared to pre-industrial values. To address the global climate issue and higher energy demand without depleting fossil reserves, growing bioenergy feedstock as the potential resource for biodiesel production could be a viable alternative. The interest in growing biofuels for biodiesel production has increased due to its potential benefits over fossil fuels and the flexibility of feedstocks. Therefore, this review article focuses on different biofuels and biomass resources for biodiesel production, their properties, procedure, factors affecting biodiesel production, different catalysts used, and greenhouse gas emissions from biodiesel production.

Emerging Trends of Nanotechnology and Genetic Engineering in Cyanobacteria to Optimize Production for Future Applications

Nanotechnology has the potential to revolutionize various fields of research and development. Multiple nanoparticles employed in a nanotechnology process are the magic elixir that provides unique features that are not present in the component's natural form. In the framework of contemporary research, it is inappropriate to synthesize microparticles employing procedures that include noxious elements. For this reason, scientists are investigating safer ways to produce genetically improved Cyanobacteria, which has many novel features and acts as a potential candidate for nanoparticle synthesis. In recent decades, cyanobacteria have garnered significant interest due to their prospective nanotechnological uses. This review will outline the applications of genetically engineered cyanobacteria in the field of nanotechnology and discuss its challenges and future potential. The evolution of cyanobacterial strains by genetic engineering is subsequently outlined. Furthermore, the recombination approaches that may be used to increase the industrial potential of cyanobacteria are discussed. This review provides an overview of the research undertaken to increase the commercial avenues of cyanobacteria and attempts to explain prospective topics for future research.

Recent Advances, Challenges and Metabolic Engineering Strategies in the Biosynthesis of 3-Hydroxypropionic Acid

As an attractive and valuable platform chemical, 3-hydroxypropionic acid (3-HP) can be used to produce a variety of industrially important commodity chemicals and biodegradable polymers. Moreover, the biosynthesis of 3-HP has drawn much attention in recent years due to its sustainability and environmental friendliness. Here, we focus on recent advances, challenges and metabolic engineering strategies in the biosynthesis of 3-HP. While glucose and glycerol are major carbon sources for its production of 3-HP via microbial fermentation, other carbon sources have also been explored. To increase yield and titer, synthetic biology and metabolic engineering strategies have been explored, including modifying pathway enzymes, eliminating flux blockages due to byproduct synthesis, eliminating toxic byproducts, and optimizing via genome-scale models. This review also provides insights on future directions for 3-HP biosynthesis. This article is protected by copyright. All rights reserved.

Metabolic transformation of cyanobacteria for biofuel production

World-wide, an emerging demand is moving towards the biofuels to replace the fossil fuels. In alternative biofuel production strategies, cyanobacteria have unique characteristic of accumulating glycogen, lipid, and fuel molecules through natural mechanisms. Moreover, the cyanobacteria can be easily engineered to synthesis a plenty of fuel molecules from CO₂. To obtain the fuel molecule from cyanobacteria, various techniques were invented in which the metabolic engineering is found to be a prerequisite to develop an economically feasible process. The expression of indigenous or heterologous pathways plays an important role in developing successful production process. In addition, the engineering of photosynthetic apparatus, destruction of competitive pathways and improvement of tolerance were also proven to improve the product specific synthesis. Although various metabolic engineering approaches have been developed, there are certain obstacles when it comes to implementation for the production. In this review, the important biosynthetic pathways for biofuels, alteration of other genes to improve the actual pathway and possibilities of developing cyanobacterial fuel production have been elaborated.

An updated review on advancement in fermentative production strategies for biobutanol using Clostridium spp

A significant concern of our fuel-dependent era is the unceasing exhaustion of petroleum fuel supplies. In parallel to this, environmental issues such as the greenhouse effect, change in global climate, and increasing global temperature must be addressed on a priority basis. Biobutanol, which has fuel characteristics comparable to gasoline, has attracted global attention as a viable green fuel alternative among the many biofuel alternatives. Renewable biomass could be used for the sustainable production of biobutanol by the acetone-butanol-ethanol (ABE) pathway. Non-extinguishable resources, such as algal and lignocellulosic biomass, and starch are some of the most commonly used feedstock for fermentative production of biobutanol, and each has its particular set of advantages. Clostridium, a gram-positive endospore-forming bacterium that can produce a range of compounds, along with n-butanol is traditionally known for its biobutanol production capabilities. Clostridium fermentation produces biobased n-butanol through ABE fermentation. However, low butanol titer, a lack of suitable feedstock, and product inhibition are the primary difficulties in biobutanol synthesis. Critical issues that are essential for sustainable production of biobutanol include (i) developing high butanol titer producing strains utilizing genetic and metabolic engineering approaches, (ii) renewable biomass that could be used for biobutanol production at a larger scale, and (iii) addressing the limits of traditional batch fermentation by integrated bioprocessing technologies with effective product recovery procedures that have increased the efficiency of biobutanol synthesis. Our paper reviews the current progress in all three aspects of butanol production and presents recent data on current practices in fermentative biobutanol production technology.

Recent advances in biofuel production through metabolic engineering

Rising global energy demands and climate crisis has created an unprecedented need for the bio-based circular economy to ensure sustainable development with the minimized carbon footprint. Along with conventional biofuels such as ethanol, microbes can be used to produce advanced biofuels which are equivalent to traditional fuels in their energy efficiencies and are compatible with already established infrastructure and hence can be directly blended in higher proportions without overhauling of the pre-existing setup. Metabolic engineering is at the frontiers to develop microbial chassis for biofuel bio-foundries to meet the industrial needs for clean energy. This review does a thorough inquiry of recent developments in metabolic engineering for increasing titers, rates, and yields (TRY) of biofuel production by engineered microorganisms.

Light-induced production of isobutanol and 3-methyl-1-butanol by metabolically engineered cyanobacteria

Background

Cyanobacteria are engineered via heterologous biosynthetic pathways to produce value-added chemicals via photosynthesis. Various chemicals have been successfully produced in engineered cyanobacteria. Chemical inducer-dependent promoters are used to induce the expression of target biosynthetic pathway genes. A chemical inducer is not ideal for large-scale reactions owing to its high cost; therefore, it is important to develop scaling-up methods to avoid their use. In this study, we designed a green light-inducible alcohol production system using the CcaS/CcaR green light gene expression system in the cyanobacterium Synechocystis sp. PCC 6803 (PCC 6803).

Results

To establish the green light-inducible production of isobutanol and 3-methyl-1-butanol (3MB) in PCC 6803, keto-acid decarboxylase (kdc) and alcohol dehydrogenase (adh) were expressed under the control of the CcaS/CcaR system. Increases in the transcription level were induced by irradiation with red and green light without severe effects on host cell growth. We found that the production of isobutanol and 3MB from carbon dioxide (CO₂) was induced under red and green light illumination and was substantially repressed under red light illumination alone. Finally, production titers of isobutanol and 3MB reached 238 mg L⁻¹ and 75 mg L⁻¹, respectively, in 5 days under red and green light illumination, and these values are comparable to those reported in previous studies using chemical inducers.

Conclusion

A green light-induced alcohol production system was successfully integrated into cyanobacteria to produce value-added chemicals without using expensive chemical inducers. The green light-regulated production of isobutanol and 3MB from CO₂ is eco-friendly and cost-effective. This study demonstrates that light regulation is a potential tool for producing chemicals and increases the feasibility of cyanobacterial bioprocesses.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01732-x.

Introduction of NADH-dependent nitrate assimilation in Synechococcus sp. PCC 7002 improves photosynthetic production of 2-methyl-1-butanol and isobutanol

Cyanobacteria hold promise for renewable chemical production due to their photosynthetic nature, but engineered strains frequently display poor production characteristics. These difficulties likely arise in part due to the distinctive photoautotrophic metabolism of cyanobacteria. In this work, we apply a genome-scale metabolic model of the cyanobacteria Synechococus sp. PCC 7002 to identify strain designs accounting for this unique metabolism that are predicted to improve the production of various biofuel alcohols (e.g. 2-methyl-1-butanol, isobutanol, and 1-butanol) synthesized via an engineered biosynthesis pathway. Using the model, we identify that the introduction of a large, non-native NADH-demand into PCC 7002's metabolic network is predicted to enhance production of these alcohols by promoting NADH-generating reactions upstream of the production pathways. To test this, we construct strains of PCC 7002 that utilize a heterologous, NADH-dependent nitrite reductase in place of the native, ferredoxin-dependent enzyme to create an NADH-demand in the cells when grown on nitrate-containing media. We find that photosynthetic production of both isobutanol and 2-methyl-1-butanol is significantly improved in the engineered strain background relative to that in a wild-type background. We additionally identify that the use of high-nutrient media leads to a substantial prolongment of the production curve in our alcohol production strains. The metabolic engineering strategy identified and tested in this work presents a novel approach to engineer cyanobacterial production strains that takes advantage of a unique aspect of their metabolism and serves as a basis on which to further develop strains with improved production of these alcohols and related products.

A review on cyanobacteria cultivation for carbohydrate-based biofuels: Cultivation aspects, polysaccharides accumulation strategies, and biofuels production scenarios

Cyanobacterial biomass has constituted a crucial third and fourth-generation biofuel material, with great potential to synthesize a wide range of metabolites, mainly carbohydrates. Lately, carbohydrate-based biofuels from cyanobacteria, such as bioethanol, biohydrogen, and biobutanol, have attracted attention as a sustainable alternative to petroleum-based products. Cyanobacteria can perform a simple process of saccharification, and extracted carbohydrates can be converted into biofuels with two alternatives; the first one consists of a fermentative process based on bacteria or yeasts, while the second alternative consists of an internal metabolic process of their own in intracellular carbohydrate content, either by the natural or genetic engineered process. This study reviewed carbohydrate-enriched cyanobacterial biomass as feedstock for biofuels. Detailed insights on technical strategies and limitations of cultivation, polysaccharide accumulation strategies for further fermentation process were provided. Advances and challenges in bioethanol, biohydrogen, and biobutanol production by cyanobacteria synthesis and an independent fermentative process are presented. Critical outlook on life-cycle assessment and techno-economical aspects for large-scale application of these technologies were discussed.

n-Butanol production by Rhodopseudomonas palustris TIE-1

Anthropogenic carbon dioxide (CO₂) release in the atmosphere from fossil fuel combustion has inspired scientists to study CO₂ to biofuel conversion. Oxygenic phototrophs such as cyanobacteria have been used to produce biofuels using CO₂. However, oxygen generation during oxygenic photosynthesis adversely affects biofuel production efficiency. To produce n-butanol (biofuel) from CO₂, here we introduce an n-butanol biosynthesis pathway into an anoxygenic (non-oxygen evolving) photoautotroph, Rhodopseudomonas palustris TIE-1 (TIE-1). Using different carbon, nitrogen, and electron sources, we achieve n-butanol production in wild-type TIE-1 and mutants lacking electron-consuming (nitrogen-fixing) or acetyl-CoA-consuming (polyhydroxybutyrate and glycogen synthesis) pathways. The mutant lacking the nitrogen-fixing pathway produce the highest n-butanol. Coupled with novel hybrid bioelectrochemical platforms, this mutant produces n-butanol using CO₂, solar panel-generated electricity, and light with high electrical energy conversion efficiency. Overall, this approach showcases TIE-1 as an attractive microbial chassis for carbon-neutral n-butanol bioproduction using sustainable, renewable, and abundant resources.

Approaches in the photosynthetic production of sustainable fuels by cyanobacteria using tools of synthetic biology

Cyanobacteria, photosynthetic prokaryotic microorganisms having a simple genetic composition are the prospective photoautotrophic cell factories for the production of a wide range of biofuel molecules. The simple genetic composition of cyanobacteria allows effortless genetic manipulation which leads to increased research endeavors from the synthetic biology approach. Various unicellular model cyanobacterial strains like Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 have been successfully engineered for biofuels generation. Improved development of synthetic biology tools, genetic modification methods and advancement in transformation techniques to construct a strain that can contain multiple foreign genes in a single operon have vastly expanded the functions that can be used for engineering photosynthetic cyanobacteria for the generation of various biofuel molecules. In this review, recent advancements and approaches in synthetic biology tools used for cyanobacterial genome editing have been discussed. Apart from this, cyanobacterial productions of various fuel molecules like isoprene, limonene, α-farnesene, squalene, alkanes, butanol, and fatty acids, which can be a substitute for petroleum and fossil fuels in the future, have been elaborated.

Management of microbial enzymes for biofuels and biogas production by using metagenomic and genome editing approaches

Non-renewable fossil fuels such as bitumen, coal, natural gas, oil shale, and petroleum are depleting over the world owing to unrestricted consumption. Biofuels such as biodiesel, biobutanol, bioethanol, and biogas are considered an eco-friendly and cost-effective alternatives of fossil fuels. For energy sustainability, the production of advanced biofuels is required. The advancement of genetic and metabolic engineering in microbial cells played a significant contribution to biofuels overproduction. Essential approaches such as next-generation sequencing technologies and CRISPR/Cas9-mediated genome editing of microbial cells are required for the mass manufacture of biofuels globally. Advanced "omics" approaches are used to construct effective microorganisms for biofuels manufacturing. A new investigation is required to augment the production of lignocellulosic-based biofuels with minimal use of energy. Advanced areas of metabolic engineering are introduced in the manufacture of biofuels by the use of engineered microbial strains. Genetically modified microorganisms are used for the production of biofuels in large quantities at a low-cost.

Establishment of a resource recycling strategy by optimizing isobutanol production in engineered cyanobacteria using high salinity stress

BACKGROUND

Isobutanol is an attractive biofuel with many advantages. Third-generation biorefineries that convert CO₂ into bio-based fuels have drawn considerable attention due to their lower feedstock cost and more ecofriendly refining process. Although autotrophic cyanobacteria have been genetically modified for isobutanol biosynthesis, there is a lack of stable and convenient strategies to improve their production.

RESULTS

In this study, we first engineered Synechococcus elongatus for isobutanol biosynthesis by introducing five exogenous enzymes, reaching a production titer of 0.126 g/L at day 20. It was then discovered that high salinity stress could result in a whopping fivefold increase in isobutanol production, with a maximal in-flask titer of 0.637 g/L at day 20. Metabolomics analysis revealed that high salinity stress substantially altered the metabolic profiles of the engineered S. elongatus. A major reason for the enhanced isobutanol production is the acceleration of lipid degradation under high salinity stress, which increases NADH. The NADH then participates in the engineered isobutanol-producing pathway. In addition, increased membrane permeability also contributed to the isobutanol production titer. A cultivation system was subsequently developed by mixing synthetic wastewater with seawater to grow the engineered cyanobacteria, reaching a similar isobutanol production titer as cultivation in the medium.

CONCLUSIONS

High salinity stress on engineered cyanobacteria is a practical and feasible biotechnology to optimize isobutanol production. This biotechnology provides a cost-effective approach to biofuel production, and simultaneously recycles chemical nutrients from wastewater and seawater.

Metabolic engineering for the production of butanol, a potential advanced biofuel, from renewable resources

Butanol is an important chemical and potential fuel. For more than 100 years, acetone-butanol-ethanol (ABE) fermentation of Clostridium strains has been the most successful process for biological butanol production. In recent years, other microbes have been engineered to produce butanol as well, among which Escherichia coli was the best one. Considering the crude oil price fluctuation, minimizing the cost of butanol production is of highest priority for its industrial application. Therefore, using cheaper feedstocks instead of pure sugars is an important project. In this review, we summarized butanol production from different renewable resources, such as industrial and food waste, lignocellulosic biomass, syngas and other renewable resources. This review will present the current progress in this field and provide insights for further engineering efforts on renewable butanol production.

Overview of Current Developments in Biobutanol Production Methods and Future Perspectives

Renewable biobutanol production is receiving more attention toward substituting fossil-based nonrenewable fuels. Biobutanol is recognized as the top most biofuel with extraordinary properties as compared with gasoline. The demand for biobutanol production is increasing enormously due to application in various industries as chemical substituent. Biobutanol production technology has attracted many researchers toward implementation of replacing cost-effective substrate and easy method to recover from the fermentation broth. Sugarcane bagasse, algal biomass, crude glycerol, and lignocellulosic biomass are potential cost-effective substrates which could replace consistent glucose-based substrates. The advantages and limitations of these substrates have been discussed in this chapter. Moreover, finding the integrated biobutanol recovery methods is an important factor parameter in production of biobutanol. This chapter also concentrated on possibilities and drawbacks of obtainable integrated biobutanol recovery methods. Thus, successful process involving cost-effective substrate and biobutanol recovery methods could help to implementation of biobutanol production industry. Overall, this chapter has endeavored to increase the viability of industrial production of biobutanol.

Multi-Omic Analyses Reveal Habitat Adaptation of Marine Cyanobacterium Synechocystis sp. PCC 7338

Cyanobacteria are considered as promising microbial cell factories producing a wide array of bio-products. Among them, Synechocystis sp. PCC 7338 has the advantage of growing in seawater, rather than requiring arable land or freshwater. Nonetheless, how this marine cyanobacterium grows under the high salt stress condition remains unknown. Here, we determined its complete genome sequence with the embedded regulatory elements and analyzed the transcriptional changes in response to a high-salt environment. Complete genome sequencing revealed a 3.70 mega base pair genome and three plasmids with a total of 3,589 genes annotated. Differential RNA-seq and Term-seq data aligned to the complete genome provided genome-wide information on genetic regulatory elements, including promoters, ribosome-binding sites, 5'- and 3'-untranslated regions, and terminators. Comparison with freshwater Synechocystis species revealed Synechocystis sp. PCC 7338 genome encodes additional genes, whose functions are related to ion channels to facilitate the adaptation to high salt and high osmotic pressure. Furthermore, a ferric uptake regulator binding motif was found in regulatory regions of various genes including SigF and the genes involved in energy metabolism, suggesting the iron-regulatory network is connected to not only the iron acquisition, but also response to high salt stress and photosynthesis. In addition, the transcriptomics analysis demonstrated a cyclic electron transport through photosystem I was actively used by the strain to satisfy the demand for ATP under high-salt environment. Our comprehensive analyses provide pivotal information to elucidate the genomic functions and regulations in Synechocystis sp. PCC 7338.

Rapidly Improving High Light and High Temperature Tolerances of Cyanobacterial Cell Factories Through the Convenient Introduction of an AtpA-C252F Mutation

Photosynthetic biomanufacturing is a promising route for green production of biofuels and biochemicals utilizing carbon dioxide and solar energy. Cyanobacteria are important microbial platforms for constructing photosynthetic cell factories. Toward scaled outdoor cultivations in the future, high light and high temperature tolerances of cyanobacterial chassis strains and cell factories would be determinant properties to be optimized. We proposed a convenient strategy for rapidly improving high light and high temperature tolerances of an important cyanobacterial chassis Synechococcus elongatus PCC 7942 and the derived cell factories. Through introduction and isolation of an AtpA-C252F mutation, PCC 7942 mutants with improved high light and high temperature tolerances could be obtained in only 4 days with an antibiotics-free mode. Adopting this strategy, cellular robustness and sucrose synthesizing capacities of a PCC 7942 cell factory were successfully improved.

Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications

Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.

Engineering Photosynthetic Bioprocesses for Sustainable Chemical Production: A Review

Microbial production of chemicals using renewable feedstocks such as glucose has emerged as a green alternative to conventional chemical production processes that rely primarily on petroleum-based feedstocks. The carbon footprint of such processes can further be reduced by using engineered cells that harness solar energy to consume feedstocks traditionally considered to be wastes as their carbon sources. Photosynthetic bacteria utilize sophisticated photosystems to capture the energy from photons to generate reduction potential with such rapidity and abundance that cells often cannot use it fast enough and much of it is lost as heat and light. Engineering photosynthetic organisms could enable us to take advantage of this energy surplus by redirecting it toward the synthesis of commercially important products such as biofuels, bioplastics, commodity chemicals, and terpenoids. In this work, we review photosynthetic pathways in aerobic and anaerobic bacteria to better understand how these organisms have naturally evolved to harness solar energy. We also discuss more recent attempts at engineering both the photosystems and downstream reactions that transfer reducing power to improve target chemical production. Further, we discuss different methods for the optimization of photosynthetic bioprocess including the immobilization of cells and the optimization of light delivery. We anticipate this review will serve as an important resource for future efforts to engineer and harness photosynthetic bacteria for chemical production.

Structural-Genetic Characterization Of Novel Butaryl co-A Dehydrogenase and Proposition of Butanol Biosynthesis Pathway in Pusillimonas ginsengisoli SBSA

Despite extensive use in the biofuel industry, only butyryl co-A dehydrogenase enzymes from the Clostridia group have undergone extensive structural and genetic characterization. The present study, portrays the characterization of structural, functional and phylogenetic properties of butyryl co-A dehydrogenase identified within the genome of Pusillimonas ginsengisoli SBSA. In silico characterization, homology modelling and docking data indicates that this protein is a homo-tetramer and 388 amino acid residue long, rich in alanine and leucine residue; having molecular weight of 42347.69 dalton. Its isoelectric point value is 5.78; indicate its neutral nature while 38.38 instability index value indicate its stable nature. Its thermostable nature evidenced by its high aliphatic index (93.14); makes its suitable for industry-based use. The secondary structure prediction analysis of butyryl co-A dehydrogenase unveiled that the proteins has secondary arrangements of 54% α-helix, 13% β-stand and 5% disordered conformation. However, phylogenetic analysis clearly indicates that probably horizontal gene transfer is the primary mechanism of spreading of this gene in this organism. Notably, multiple sequence alignment study of phylogenetically diverse butyryl co-A dehydrogenase sequence highlighted the presence of conserved amino acid residues i.e. YXV/LGXKXWXS/T. Physicochemical characterization of other relevant proteins involved in butanol metabolism of SBSA also has been carried out. However, metabolic construction of functional butanol biosynthesis pathway in SBSA, enlightened its cost-effective potential use in biofuel industry as an alternate to Clostridia system.

Trans-4-hydroxy-L-proline production by the cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria play an important role in photobiotechnology. Yet, one of their key central metabolic pathways, the tricarboxylic acid (TCA) cycle, has a unique architecture compared to most heterotrophs and still remains largely unexploited. The conversion of 2-oxoglutarate to succinate via succinyl-CoA is absent but is by-passed by several other reactions. Overall, fluxes under photoautotrophic growth conditions through the TCA cycle are low, which has implications for the production of chemicals. In this study, we investigate the capacity of the TCA cycle of Synechocystis sp PCC 6803 for the production of trans-4-hydroxy-L-proline (Hyp), a valuable chiral building block for the pharmaceutical and cosmetic industries. For the first time, photoautotrophic Hyp production was achieved in a cyanobacterium expressing the gene for the L-proline-4-hydroxylase (P4H) from Dactylosporangium sp. strain RH1. Interestingly, while elevated intracellular Hyp concentrations could be detected in the recombinant Synechocystis strains under all tested conditions, detectable Hyp secretion into the medium was only observed when the pH of the medium exceeded 9.5 and mostly in the late phases of the cultivation. We compared the rates obtained for autotrophic Hyp production with published sugar-based production rates in E. coli. The land-use efficiency (space-time yield) of the phototrophic process is already in the same order of magnitude as the heterotrophic process considering sugar farming as well. But, the remarkable plasticity of the cyanobacterial TCA cycle promises the potential for a 23–55 fold increase in space-time yield when using Synechocystis. Altogether, these findings contribute to a better understanding of bioproduction from the TCA cycle in photoautotrophs and broaden the spectrum of chemicals produced in metabolically engineered cyanobacteria.

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Phototrophic production of trans-4-hydroxy-L-prolin.

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pH dependency of product accumulation in Synechocystis PCC6803.

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Comparative analysis of land use efficiency in phototrophs & heterotrophs.

Post-translational Modifications of Serine/Threonine and Histidine Kinases and Their Roles in Signal Transductions in Synechocystis Sp. PCC 6803

Cyanobacterium Synechocystis sp. PCC 6803, a popular model organism for researches in photosynthesis and biofuel production, contains plant-like photosynthetic machineries which significantly contribute to global carbon fixation. There are 12 eukaryotic-type Ser/Thr kinases (SpkA-L) and 49 His kinases (Hik1-49) of two-component systems in the genome of Synechocystis sp. PCC 6803. They are the key regulators in sensing and transmitting stimuli including light- and glucose-mediate signal transduction. Proteomic studies were able to identify all the kinases. The majority of kinases no matter whether they have a predicted transmembrane domain were identified in the membrane fractions. Six Ser/Thr kinases (SpkA-D, F and G) and ten His kinases (Hik4, 12, 14, 21, 26-27, 29, 36, 43, and 46) were identified to have one or more of the three types of post-translational modifications: phosphorylation, acetylation, and thiol oxidation. Interestingly, SpkG has the phosphorylatable threonine residue that was aligned with the phosphorylated threonine residue in the activation loop of human CDK7, demonstrating conserved phosphorylation between cyanobacterial and human kinases. Transcriptomics and proteomics revealed differential expression of the kinases in heterotrophic and photoheterotrophic compared with photoautotrophic conditions, indicating their roles in regulating the growth modes of cyanobacteria. In summary, this review focuses on the discussions on post-transcriptional modifications, transcriptomic, and proteomic studies of Ser/Thr and His kinases. This together with our published review in 2019 present a complete story of an overview of sequences, domain architectures, and biochemical and physiological functions of cyanobacterial kinases with adequate details in the context of high throughput systems. We also emphasize the importance of discovering upstream molecules and substrates to understand the exact functions of the kinases in vivo. As an attempt, a model is proposed in which Hik31, His33, Sll1334, and IcfG are hypothesized to be critical for switching between autotrophic and heterotrophic modes based on the results from the phenotypes of the gene knockout strains combined with their post-translational modifications, and gene expression profiles.

Recent advances in synthetic biology of cyanobacteria for improved chemicals production

Cyanobacteria are Gram-negative photoautotrophic prokaryotes and have shown great importance to the Earth’s ecology. Based on their capability in oxygenic photosynthesis and genetic merits, they can be engineered as microbial chassis for direct conversion of carbon dioxide to value-added biofuels and chemicals. In the last decades, attempts have given to the application of synthetic biology tools and approaches in the development of cyanobacterial cell factories. Despite the successful proof-of-principle studies, large-scale application is still a technical challenge due to low yields of bioproducts. Therefore, recent efforts are underway to characterize and develop genetic regulatory parts and strategies for the synthetic biology applications in cyanobacteria. In this review, we present the recent advancements and application in cyanobacterial synthetic biology toolboxes. We also discuss the limitations and future perspectives for using such novel tools in cyanobacterial biotechnology.

Alcohol stress on cyanobacterial membranes: New insights revealed by transcriptomics

Cyanobacteria are model photosynthetic prokaryotic organisms often used in biotechnology to produce biofuels including alcohols. The effect of alcohols on cyanobacterial cell physiology and specifically on membrane fluidity is poorly understood. Previous research on various primary aliphatic alcohols found that alcohols with a short hydrocarbon chain (C₁-C₃) do not affect expression of genes related to membrane physical state. In addition, less water-soluble alcohols with a hydrocarbon chain longer than C₈ are found to have a reduced ability to reach cellular membranes hence do not drastically change membrane physical state or induce expression of stress-responsive genes. Therefore, hexan-1-ol (C₆) is suggested to have the most profound effect on cyanobacterial membrane physical state. Here, we studied the effects of hexan-1-ol on the cyanobacterium Synechocystis sp. PCC 6803 transcriptome. The transcriptome data obtained is compared to the previously reported analysis of gene expression induced by benzyl alcohol and butan-1-ol. The set of genes whose expression is induced after exposure to all three studied alcohols is identified. The expression under alcohol stress for several general stress response operons is analyzed, and examples of antisense interactions of RNA are investigated.

Metabolic pathway engineering: Perspectives and applications

BACKGROUND

Metabolic engineering aims at contriving microbes as biocatalysts for enhanced and cost-effective production of countless secondary metabolites. These secondary metabolites can be treated as the resources of industrial chemicals, pharmaceuticals and fuels. Plants are also crucial targets for metabolic engineers to produce necessary secondary metabolites. Metabolic engineering of both microorganism and plants also contributes towards drug discovery. In order to implement advanced metabolic engineering techniques efficiently, metabolic engineers should have detailed knowledge about cell physiology and metabolism. Principle behind methodologies: Genome-scale mathematical models of integrated metabolic, signal transduction, gene regulatory and protein-protein interaction networks along with experimental validation can provide such knowledge in this context. Incorporation of omics data into these models is crucial in the case of drug discovery. Inverse metabolic engineering and metabolic control analysis (MCA) can help in developing such models. Artificial intelligence methodology can also be applied for efficient and accurate metabolic engineering.

CONCLUSION

In this review, we discuss, at the beginning, the perspectives of metabolic engineering and its application on microorganism and plant leading to drug discovery. At the end, we elaborate why inverse metabolic engineering and MCA are closely related to modern metabolic engineering. In addition, some crucial steps ensuring efficient and optimal metabolic engineering strategies have been discussed. Moreover, we explore the use of genomics data for the activation of silent metabolic clusters and how it can be integrated with metabolic engineering. Finally, we exhibit a few applications of artificial intelligence to metabolic engineering.

Photosynthetic Reduction of Xylose to Xylitol Using Cyanobacteria

Photosynthetic generation of reducing power makes cyanobacteria an attractive host for biochemical reduction compared to cell-free and heterotrophic systems, which require burning of additional resources for the supply of reducing equivalent. Here, using xylitol synthesis as an example, efficient uptake and reduction of xylose photoautotrophically in Synechococcus elongatus PCC7942 are demonstrated upon introduction of an effective xylose transporter from Escherichia coli (Ec-XylE) and the NADPH-dependent xylose reductase from Candida boidinii (Cb-XR). Simultaneous activation of xylose uptake and matching of cofactor specificity enabled an average xylitol yield of 0.9 g g^-1 xylose and a maximum productivity of about 0.15 g L^-1 day^-1 OD^-1 with increased level of xylose supply. While long-term cellular maintenance still appears challenging, high-density conversion of xylose to xylitol using concentrated resting cell further pushes the titer of xylitol formation to 33 g L^-1 in six days with 85% of maximum theoretical yield. While the results show that the unknown dissipation of xylose can be minimized when coupled to a strong reaction outlet, it remains to be the major hurdle hampering the yield despite the reported inability of cyanobacteria to metabolize xylose.

Genetic engineering of non-native hosts for 1-butanol production and its challenges: a review

BACKGROUND

Owing to the increase in energy consumption, fossil fuel resources are gradually depleting which has led to the growing environmental concerns; therefore, scientists are being urged to produce sustainable and ecofriendly fuels. Thus, there is a growing interest in the generation of biofuels from renewable energy resources using microbial fermentation.

MAIN TEXT

Butanol is a promising biofuel that can substitute for gasoline; unfortunately, natural microorganisms pose challenges for the economical production of 1-butanol at an industrial scale. The availability of genetic and molecular tools to engineer existing native pathways or create synthetic pathways have made non-native hosts a good choice for the production of 1-butanol from renewable resources. Non-native hosts have several distinct advantages, including using of cost-efficient feedstock, solvent tolerant and reduction of contamination risk. Therefore, engineering non-native hosts to produce biofuels is a promising approach towards achieving sustainability. This paper reviews the currently employed strategies and synthetic biology approaches used to produce 1-butanol in non-native hosts over the past few years. In addition, current challenges faced in using non-native hosts and the possible solutions that can help improve 1-butanol production are also discussed.

CONCLUSION

Non-native organisms have the potential to realize commercial production of 1- butanol from renewable resources. Future research should focus on substrate utilization, cofactor imbalance, and promoter selection to boost 1-butanol production in non-native hosts. Moreover, the application of robust genetic engineering approaches is required for metabolic engineering of microorganisms to make them industrially feasible for 1-butanol production.

Regulatory Diversity and Functional Analysis of Two-Component Systems in Cyanobacterium Synechocystis sp. PCC 6803 by GC-MS Based Metabolomics

Two-component signal transduction systems are still poorly functionally characterized in the model cyanobacterium Synechocystis sp. PCC 6803. To address the issue, a GC-MS based comparative metabolomic analysis was conducted on a library of 44 knockout mutants for the response regulators (RRs) in Synechocystis. The metabolomic profiling analysis showed that 7 RRs mutants, namely Δslr1909, Δsll1291, Δslr6040, Δsll1330, Δslr2024, Δslr1584, and Δslr1693, were significantly different at metabolomic level, although their growth patterns are similar to the wild type under the normal autotrophic growth condition, suggesting regulatory diversity of RRs at metabolite level in Synechocystis. Additionally, a detailed metabolomic analysis coupled with RT-PCR verification led to useful clues for possible function of these 7 RRs, which were found involved in regulation of multiple aspects of cellular metabolisms in Synechocystis. Moreover, an integrative metabolomic and evolutionary analysis of all RR showed that four groups of RR genes clustered together in both metabolomic and evolutionary trees, suggesting of possible functional conservation of these RRs during the evolutionary process. Meanwhile, six groups of RRs with close evolutionary origin were found with different metabolomic profiles, suggesting possible functional changes during evolution. In contrast, more than 10 groups of RR genes with different clustering patterns in the evolutionary tree were found clustered together in metabolomics-based tree, suggesting possible functional convergences during the evolution. This study provided a metabolomic view of RR function, and the most needed functional clues for further characterization of these regulatory proteins in Synechocystis.

Comparison of Three Xylose Pathways in Pseudomonas putida KT2440 for the Synthesis of Valuable Products

Pseudomonas putida KT2440 is a well-established chassis in industrial biotechnology. To increase the substrate spectrum, we implemented three alternative xylose utilization pathways, namely the Isomerase, Weimberg, and Dahms pathways. The synthetic operons contain genes from Escherichia coli and Pseudomonas taiwanensis. For isolating the Dahms pathway in P. putida KT2440 two genes (PP_2836 and PP_4283), encoding an endogenous enzyme of the Weimberg pathway and a regulator for glycolaldehyde degradation, were deleted. Before and after adaptive laboratory evolution, these strains were characterized in terms of growth and synthesis of mono-rhamnolipids and pyocyanin. The engineered strain using the Weimberg pathway reached the highest maximal growth rate of 0.30 h-1. After adaptive laboratory evolution the lag phase was reduced significantly. The highest titers of 720 mg L-1 mono-rhamnolipids and 30 mg L-1 pyocyanin were reached by the evolved strain using the Weimberg or an engineered strain using the Isomerase pathway, respectively. The different stoichiometries of the three xylose utilization pathways may allow engineering of tailored chassis for valuable bioproduct synthesis.

Accumulation of sugars and nucleosides in response to high salt and butanol stress in 1-butanol producing Synechococcus elongatus

1-Butanol production using photosynthetic organisms such as cyanobacteria has garnered interest among researchers due to its high potential as a sustainable biofuel. Previously, the cyanobacterium Synechococcus elongatus PCC 7942 was engineered to produce 1-butanol through the introduction of a modified CoA-dependent pathway. S. elongatus strain DC11, a high producer of 1-butanol, was constructed based on metabolomics-assisted strain engineering. DC11 can reach a production titer of 418.7 mg/L in 6 days, cutting the production time in half compared to the previously constructed DC7. Regardless, the final 1-butanol titer of DC11 was still low compared to other microbial hosts. Sensitivity towards 1-butanol of the producing strain has been known as one of main hurdles for improving cyanobacterial production system. Thus, to improve cyanobacterial-based 1-butanol production in the future, we employed the metabolomics approach to study the intrinsic effect of improved 1-butanol productivity in DC11. This study focused on metabolite profiling of DC11 using LC/MS/MS. Results showed that there is an accumulation of disaccharide-P and sucrose/trehalose in DC11 compared to the DC7. These metabolites were previously reported to have a role in salt and alcohol stress response in cyanobacteria and therefore, DC11 was subjected to 0.2 M of NaCl and 1000 mg/L of 1-butanol for further investigation. DC11 with stress treatment showed a more prominent accumulation of sugars and nucleosides compared to control. The results obtained from this study may be beneficial for future strain improvement strategies in S. elongatus, particularly addressing the metabolic response of this strain upon 1-butanol stress.

To beat the heat - engineering of the most thermostable pyruvate decarboxylase to date

Pyruvate decarboxylase (PDC) is a key enzyme for the production of ethanol at high temperatures and for cell-free butanol synthesis. Thermostable, organic solvent stable PDC was evolved from bacterial PDCs. The new variant shows >1500-fold-improved half-life at 75 °C and >5000-fold-increased half-life in the presence of 9 vol% butanol at 50 °C.