Synthetic Biology and Engineering Open Access

ISSN: 2958-9053 (Online)

2958-9045 (Print)

An Official Journal of Center of Synthetic Biology and Integrated Bioengineering, Westlake University

Synthetic Biology and Engineering (SBE) is an international, peer-reviewed, open access journal dealing with interdisciplinary research of synthetic biology, from living systems to industry translation. It is published quarterly online by SCIEPublish. View full Aims&Scope

Editors-in-Chief Editorial Board

Articles (45) All Articles

Open Access

Article

19 May 2025

Quorum Sensing Systems Engineering for Enhanced iso-Butylamine Production in Escherichia coli

Quorum sensing (QS), characterized by pathway-independence and autonomous control, has been applied in bio-manufacturing, while the lack of versatile and functional regulatory components limits its broader applications. To address this issue, a series of efficient QS systems with diverse properties were established in Escherichia coli. Firstly, combinatorial optimization, including element selection and promoter replacement, led to an improvement of 8.82- and 3.03-fold in output range and response threshold, respectively. Then, a library of LuxR mutants was constructed for screening novel variants with decreased sensitivity to acyl-homoserine lactone through the high-throughput screening technique. Notably, the optimal variant V36E/H89L/P97L exhibited a decrease of 266-fold in the sensitivity. As a proof-of-concept, iso-butylamine biosynthesis was tested by re-directing pyruvate catabolism using QS circuits, and in particular, a total of 15.4 g/L iso-butylamine was generated in strain IB21 during the fed-batch culture, marking a 2.96-fold increase over the static control. Finally, the generated bioproduct reached 44.23 g/L in a bioreactor, representing the highest reported titer so far. In summary, this study not only enriches the genetic toolbox of QS systems, but also facilitates industrial applications in value-added chemical production.

Open Access

Review

14 May 2025

Current Status of Biological Production Using C2 Feedstocks

C2 feedstocks have emerged as promising carbon sources for the biological production of various value-added chemicals. Compared to the traditional C6/C5 sugars-contained/constituted feedstocks, C2 feedstocks have diverse and abundant sources, including non-food biomass, industrial by-products, and C1 gases. This diversification not only eliminates competition with human food demands but also aligns with environmental sustainability goals. Moreover, the metabolic route for C2 compounds to enter central carbon metabolism is more direct, which minimizes the carbon loss and enhances the efficiency of bio-based production processes. This review extensively analyzes three prominent C2 chemicals: ethylene glycol, ethanol, and acetate. After introducing the sources of those compounds, it details the metabolic pathways through which they are converted into acetyl-CoA in vivo. Several chemicals produced from these C2 feedstocks in fermentation are also exemplified. Furthermore, different perspectives are proposed to promote the efficient utilization of C2 feedstocks.

Open Access

Article

14 April 2025

Efficient Extracellular Production of Phospholipase D in Escherichia coli via Genetic and Process Engineering Modification

Phospholipase D (PLD) is the key enzyme in the catalytic production of rare phospholipids including phosphatidylserine. It was considered a promising method via genetic manipulation for the heterologous production of PLD in the model chassis. Few works focused on the extracellular production of PLD in engineered microbes. Herein, genetic and process engineering modification strategies were developed to achieve secretory production of PLD in Escherichia coli. The N-terminal fusion secretion signal peptide OmpA and the plasmid pBAD-gⅢC with pBAD promoter were proven to be the most effective in promoting the secretory production of PLD. Given the limitation of the cell membrane, the regulation of the key protein expression in the cell membrane as well as the addition of surfactants, were explored to accelerate the secretory production of PLD further. It was indicated that adding 0.5% (w/v) Triton X-100 was more conducive to producing PLD. Finally, fed-batch fermentation was conducted, and the maximum extracellular PLD activity achieved was 33.25 U/mL, which was the highest level reported so far. Our work demonstrated the effectiveness of genetic and process engineering strategies for the secretory production of PLD in E. coli, which provided an alternative platform for the industrial production of PLD.

Open Access

Review

24 March 2025

Recent Advances and Challenges in Engineering Metabolic Pathways and Cofactor Regeneration for Enhanced n-Butanol Biosynthesis

The biological production of n-butanol has seen renewed interest due to the need for the production of sustainable aviation fuel, for which n-butanol serves as a direct precursor. However, biological production of this alcohol is still limited by the fermentation’s low titers and low yields. Many approaches have been taken to increase n-butanol production, such as using alternative host organisms, utilizing heterologous enzymes for acid reduction and cofactor regeneration, and protein engineering of critical enzymes in the n-butanol production metabolic pathway. This review highlights key achievements made in each of these areas and shows the potential for these approaches in increasing n-butanol production. The review closes by pinpointing the challenges and limitations in these approaches and recommends that the ultimate approach to n-butanol production should inevitably utilize noncanonical redox cofactors to drive metabolic flux for butanol biosynthesis from glucose.

Open Access

Article

20 March 2025

Metabolic Engineering and Genome-Wide Adaptive Evolution for Efficient Reduction of Glycerol in Industrial Saccharomyces cerevisiae

The production of glycerol as a major by-product during yeast-based bioethanol fermentation arises directly from the need to re-oxidize excess NADH, which reduces conversion efficiency. In this study, an optimized Cas9-based genome editing method was performed to develop a mixotrophic CO2-fixing industrial Saccharomyces cerevisiae by heterologous expression of ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO form Pseudomonas sp.) and phosphoribulokinase (PRK form Spinach). Additionally, the gene encoding alcohol dehydrogenase (ADH2) responsible for converting ethanol to acetaldehyde was deleted, while the great wall-family protein kinase Rim15 gene was overexpressed to facilitate the reduction in glycerol content. The resulting CO2-fixing yeast M-2 led to a 21.5% reduction of the by-product glycerol in corn mash fermentation cultures at 39 ℃. Moreover, we established a novel gene mutators mediated genome-wide mutations system that accumulates distinct mutations in the industrial S. cerevisiae strains under the stress conditions to improve the robustness in the S. cerevisiae strains efficiently.

Open Access

Perspective

17 March 2025

Navigable Genome Engineering: Stepwise Correlation for Precision-Guided Optimization of Microbial Cell Factory Phenotypes

Microbial cell factories, akin to “chips” in biomanufacturing, concentrate the most intricate scientific challenges, technical bottlenecks, and densest intellectual property. However, despite extensive efforts in rational engineering, the inherent complexity of biological systems and the limited knowledge of their underlying mechanisms still incur substantial trial-and-error costs. This Perspective seeks to explore the potential of a prior-knowledge-independent approach for optimizing microbial cell factory phenotypes. We discuss the feasibility of stepwise genotypic navigation in genome engineering and emphasize its ability to generate high-quality genotype–phenotype association data, thereby advancing AI-assisted genome modeling and further enabling precision-guided optimization.

Open Access

Review

28 February 2025

Synthetic Biology Boosts the Biological Depolymerization and Upcycling of Waste Plastic Resources

The high molecular weight, hydrophobicity, and strong chemical bonds of petroleum-based synthetic plastics make them highly resistant to both abiotic and microbial degradation. This resistance plays a significant role in the growing problem of “white pollution” where the accumulation of plastic waste has become a major environmental issue worldwide. Currently, plastic waste management relies largely on landfill disposal and incineration, with only about 20% of plastic waste being recycled. However, both methods create secondary environmental risks, such as contamination of groundwater, soil, air, and oceans. Therefore, developing a sustainable and efficient approach for recycling and reusing plastic waste is essential for tackling plastic pollution and promoting a circular plastic economy. One promising solution involves utilizing microorganisms and enzymes to break down plastics into oligomers or monomers, which can then be transformed into valuable chemicals. This method provides a more environmentally friendly and milder alternative to conventional waste management techniques. This review explores recent progress in biodepolymerization and biotransformation processes for plastic waste, including the identification of plastic-degrading microorganisms and enzymes, the creation of microbial consortia and enzyme mixtures, an investigation into the mechanisms of plastic depolymerization, and the conversion of degradation products into useful materials such as chemicals, energy, and other resources. Despite these advancements, several challenges remain, such as the limited availability of effective degradation enzymes, low degradation efficiency, and difficulties in utilizing the breakdown products. However, emerging technologies in synthetic biology, such as high-throughput screening, evolutionary metabolic engineering, and bioinformatics to study catalytic mechanisms of degradation enzymes, offer promising solutions to address these issues. By improving enzyme design, optimizing microbial consortia interactions, and developing efficient metabolic pathways for plastic degradation products, these innovations could greatly enhance plastic biodegradation. These advancements hold the potential to provide environmentally sustainable, economically feasible, and technically viable solutions for promoting a circular plastic economy, particularly in countries like China.

Open Access

Review

13 February 2025

High-Temperature Catalytic Platform Powered by Thermophilic Microorganisms and Thermozymes

Thermophilic microorganisms, capable of thriving under high temperatures, are emerging as key platforms for next-generation industrial biotechnology (NGIB), driving innovations in lignin biorefining, bioplastics synthesis, biodiesel production, and environmental remediation. Enzymes derived from thermophilic microorganisms, thermozymes, exhibit remarkable stability and efficiency under extreme conditions, making them highly suitable for diverse industrial applications. This review highlights recent advances in leveraging thermophilic microorganisms and thermozymes for high-temperature catalysis, focusing on their economic and environmental benefits. It also emphasizes progress in high-throughput screening and artificial intelligence (AI), which have revolutionized the bioprospecting, engineering, and application potential of thermozymes. Challenges and potential solutions for industrial implementation of high-temperature catalytic platforms are also discussed, highlighting their transformative impact on sustainable biotechnology.

Synth. Biol. Eng.
2025,
3
(1), 10001; 
Open Access

Article

03 December 2024

Pathway Engineering of E. coli for Production of Fritschiellaxanthin and Other Carotenoids with α-Carotene Backbone and Their Singlet Oxygen-Quenching Activities

Some photosynthetic organisms are capable of biosynthesizing carotenoids (xanthophylls) with α-carotene backbone, that is, α-carotene-derived carotenoids, such as (3R,3′R,6′R)-3,3′-dihydroxy α-carotene (lutein). Except for lutein, such carotenoids are minor compounds in nature. In this study, α-carotene-derived carotenoids were produced with E. coli. To achieve this, carotenoid biosynthesis genes from the bacterium Pantoea ananatis containing the 4-β-ketolase (crtW) gene with/without the 3-β-hydroxylase (crtZ) gene, in addition to crtEBI genes, and biosynthesis genes (MpLCYb, MpLCYe, and MpCYP97C) from liverwort Marchantia polymorpha, along with the HpIDI gene, were cloned into plasmids. The transformed E. coli cells biosynthesized (3S,3′R,6′R)-3,3′-dihydroxy-4-keto-α-carotene (fritschiellaxanthin (4-ketolutein)), (3′R,6′R)-3′-hydroxy-4-keto-α-carotene (4-keto-α-cryptoxanthin), and (3′R,6′R)-3′-hydroxy-α-carotene (α-cryptoxanthin), as carotenoids that have not been produced by a heterologous microbial system so far. These carotenoids show potent singlet oxygen-quenching activity.

Open Access

Article

14 November 2024

Sortase A-Mediated Enzyme Assembly on Multimeric Protein for Improving Mevalonate Production

Microorganisms have been extensively studied for their production of valuable chemicals. However, conventional gene fusion approaches often lack versatility and can result in enzyme inactivation. This study explored an alternative strategy for inducing metabolic channeling through sortase A-mediated ligation of metabolic enzymes. Sortase A recognizes specific amino acid sequences and selectively conjugates proteins at these sites. We focused on mevalonate production as a proof-of-concept to enhance the yield by assembling metabolic enzymes on a protein scaffold using sortase A. Although metabolic enzyme complexes were successfully formed using streptavidin as a scaffold, production did not improve. The use of CutA as a scaffold led to a 1.32-fold increase in production compared with that of the strain without the scaffold, demonstrating the efficacy of CutA in mevalonate production. These findings suggest that using sortase A to assemble metabolic enzymes onto a scaffold can effectively enhance microbial bioproduction.

Open Access

Commentary

14 September 2023

Synthetic Biology Industry in China: Current State and Future Prospects

In this article, we provided an overview of the current state of the SynBio industry in China with a focus on its research and technology, its main applications, and major players. We also discussed future prospects including the challenges and advantages of the SynBio industry in China.

WeiLuo
YangZhang
JunPeng
LishanZhao
Synth. Biol. Eng.
2023,
1
(2), 10014; 
Open Access

Review

31 October 2023

Metabolic Engineering of Microorganisms Towards the Biomanufacturing of Non-Natural C5 and C6 Chemicals

Five-carbon (C5) and six-carbon (C6) chemicals are essential components in the manufacturing of a variety of pharmaceuticals, fuels, polymers, and other materials. However, the predominant reliance on chemical synthesis methods and unsustainable feedstock sources has placed significant strain on Earth’s finite fossil resources and the environment. To address this challenge and promote sustainability, significant efforts have been undertaken to re-program microorganisms through metabolic engineering and synthetic biology approaches allowing for bio-based manufacturing of these compounds. This review provides a comprehensive overview of the advancements in microbial production of commercially significant non-natural C5 chemicals, including 1-pentanol, 1,5-pentanediol, cadaverine, δ-valerolactam, glutaric acid, glutaconic acid, and 5-hydroxyvaleric acid, as well as C6 chemicals, including cis, cis-muconic acid, adipic acid, 1,6-hexamethylenediamine, 6-aminocaproic acid, β-methyl-δ-valerolactone, 1-hexanol, ε-caprolactone, 6-hydroxyhexanoic acid, and 1,6-hexanediol.

Ashley Tseng
VannaNguyen
YuhengLin
Synth. Biol. Eng.
2023,
1
(3), 10015; 
Open Access

Perspective

29 December 2023
Open Access

Review

14 August 2024

Application of Synthetic Biology to the Biosynthesis of Polyketides

Polyketides (PKs) are a large class of secondary metabolites produced by microorganisms and plants, characterized by highly diverse structures and broad biological activities. They have wide market and application prospects in medicine, agriculture, and the food industry. The complex chemical structures and multiple steps of natural polyketides result in yield that cannot be met by purely synthetic methods. With the development of synthetic biology, a number of novel technologies and synthetic strategies have been developed for the efficient synthesis of polyketides. This paper first introduces polyketides from different sources and classifications, then the reconstruction of biosynthetic pathways is described using a “bottom-up” synthetic biology approach. Through methods such as enhancing precursors, relieving feedback inhibition, and dynamic regulation, the efficient production of polyketides is achieved. Finally, the challenges faced by polyketides research and future development directions are discussed.

XiaChen
XinyingLi
GenlinZhang
ChaoWang
ChunLi
Synth. Biol. Eng.
2024,
2
(3), 10012; 
Open Access

Review

01 September 2023

In Vitro BioTransformation (ivBT): Definitions, Opportunities, and Challenges

Great needs always motivate the birth and development of new disciplines and tools. Here we propose in vitro BioTransformation (ivBT) as a new biomanufacturing platform, between the two dominant platforms—microbial fermentation and enzymatic biocatalysis. ivBT mediated by in vitro synthetic enzymatic biosystems (ivSEBs) is an emerging biomanufacturing platform for the production of biocommodities (i.e., low-value and bulk biochemicals). ivSEB is the in vitro reconstruction of artificial (non-natural) enzymatic pathways with numerous natural enzymes, artificial enzymes, and/or (biomimetic or natural) coenzymes without living cell’s constraints, such as cell duplication, basic metabolisms, complicated regulation, bioenergetics, and so on. The two great needs (i.e., food security and the carbon-neutral renewable energy system) have motivated the birth and development of ivBT. Food security could be addressed by making artificial food from nonfood lignocellulose and artificial photosynthesis for starch synthesis from CO2. The carbon-neutral renewable energy system could be addressed by the construction of the electricity-hydrogen-carbohydrate cycle, where starch could be a high density of hydrogen carrier (up to 14.8% H2 wt/wt) and an electricity storage compound (greater than 3000 Wh/kg). Also, ivBT can make a number of biocommodities, such as inositol, healthy sweeteners (e.g., D-allulose, D-tagatose, D-mannose), advanced biofuels, polymer precursors, organic acids, and so on. The industrial biomanufacturing of the first several biocommodities (e.g., myo-inositol, D-tagatose, D-mannose, and cellulosic starch) would wipe off any prejudice and doubt on ivBT. Huge potential markets of biocommodities with more than tens of trillions of Chinese Yuan would motivate scientists and engineers to address the remaining technical challenges and develop new tools within the next decade.

Yi-HengP. JobZhang
Zhiguang Zhu
ChunYou
Lingling Zhang
KuanqingLiu
Synth. Biol. Eng.
2023,
1
(2), 10013; 
Open Access

Article

13 March 2023

Design of Oscillatory Networks through Post-Translational Control of Network Components

Many essential functions in biological systems, including cell cycle progression and circadian rhythm regulation, are governed by the periodic behaviors of specific molecules. These periodic behaviors arise from the precise arrangement of components in biomolecular networks that generate oscillatory output signals. The dynamic properties of individual components of these networks, such as maturation delays and degradation rates, often play a key role in determining the network's oscillatory behavior. In this study, we explored the post-translational modulation of network components as a means to generate genetic circuits with oscillatory behaviors and perturb the oscillation features. Specifically, we used the NanoDeg platform—A bifunctional molecule consisting of a target-specific nanobody and a degron tag—to control the degradation rates of the circuit’s components and predicted the effect of NanoDeg-mediated post-translational depletion of a key circuit component on the behavior of a series of proto-oscillating network topologies. We modeled the behavior of two main classes of oscillators, namely relaxation oscillator topologies (the activator-repressor and the Goodwin oscillator) and ring oscillator topologies (repressilators). We identified two main mechanisms by which non-oscillating networks could be induced to oscillate through post-translational modulation of network components: an increase in the separation of timescales of network components and mitigation of the leaky expression of network components. These results are in agreement with previous findings describing the effect of timescale separation and mitigation of leaky expression on oscillatory behaviors. This work thus validates the use of tools to control protein degradation rates as a strategy to modulate existing oscillatory signals and construct oscillatory networks. In addition, this study provides the design rules to implement such an approach based on the control of protein degradation rates using the NanoDeg platform, which does not require genetic manipulation of the network components and can be adapted to virtually any cellular protein. This work also establishes a framework to explore the use of tools for post-translational perturbations of biomolecular networks and generates desired behaviors of the network output.

Brianna E.K. Jayanthi
Shridhar Jayanthi
Laura Segatori
Synth. Biol. Eng.
2023,
1
(1), 10004; 
Open Access

Editorial

13 December 2022
Open Access

Article

10 May 2023

Development of a New 1,2,4-butanetriol Biosynthesis Pathway in an Engineered Homoserine-producing Strain of Escherichia coli

1,2,4-butanetriol (BT) is a compound of high interest with applications in pharmaceutical and materials. In this work, we designed a novel biosynthetic pathway for BT from glucose via a nonessential amino acid homoserine. This non-natural pathway used an engineered phosphoserine transaminase (SerCR42W/R77W) to achieve the deamination of homoserine to 4-hydroxy-2-oxobutanoic acid (HOBA). Three consecutive enzymes including a lactate dehydrogenase, a 4-hydroxybutyrate CoA-transferase and a bifunctional aldehyde/alcohol dehydrogenase are used to catalyze HOBA to BT. To enhance the carbon flux to homoserine, a homoserine-producing Escherichia coli was developed by improving the overexpression of two relevant key genes metL and lysC (V339A). The simultaneous overexpression of the genes encoding these enzymes for the homoserine-derived BT pathway enabled production of 19.6 mg/L BT from glucose in the homoserine-producing E. coli.

Yujun Zhang
Lin Chen
Antu Thomas
An-Ping Zeng
Synth. Biol. Eng.
2023,
1
(1), 10007; 
Open Access

Review

16 February 2023

Increasing Nutritional Value of Cyanobacteria by Engineering Valine, Phenylalanine, and Fatty Acid Production

In 2020, the United Nations estimated that 2.37 billion people globally were without food or unable to eat a healthy balanced diet. The number of people with insufficient nutrition has increased in the short term due to COVID-19 pandemic and longer-term climate change is leading to shifts in arable land and water availability leading to a continued need to develop scalable sources of nutrition. One of the options that can yield high food mass per square foot of land use is the high-density culture of microalgae or other photosynthetic microorganisms. While photosynthetic microorganisms may provide high amounts of biomass with a small land footprint, the nutritional value of unmodified microorganisms may be limited. This mini-review presents the base nutritional value in terms of macro- and micronutrients of several cyanobacteria (Nostoc, Anabaena, Spirulina) in relation to established human nutritional requirements as a starting point for better utilization of cyanobacteria as nutritional supplements. It also discusses synthetic biology approaches that have been implemented in different organisms to increase the production of L-valine, L-phenylalanine, and fatty acids demonstrating some common genetic engineering design approaches and some approaches that are organism-specific.

NickLopez-Riveira
StephenS.Fong
Synth. Biol. Eng.
2023,
1
(1), 10003; 
Open Access

Review

15 March 2023

Thermoanaerobacter Species: The Promising Candidates for Lignocellulosic Biofuel Production

Thermoanaerobacter species, which have broad substrate range and high operating temperature, can directly utilize lignocellulosic materials for biofuels production. Compared with the mesophilic process, thermophilic process shows greater prospects in consolidated bioprocessing (CBP) due to its relatively higher efficiency of lignocellulose degradation and lower risk of microbial contamination. Additionally, thermophilic conditions can reduce cooling costs, and further facilitate downstream product recovery. This review comprehensively summarizes the advances of Thermoanaerobacter species in lignocellulosic biorefinery, including their performance on substrates utilization, and genetic modification or other strategies for enhanced biofuels production. Furthermore, bottlenecks of sugar co-fermentation, metabolic engineering, and bioprocessing are also discussed.

KaiqunDai
ChunyunQu
HongxinFu
JufangWang
Synth. Biol. Eng.
2023,
1
(1), 10005; 
Open Access

Review

01 September 2023

In Vitro BioTransformation (ivBT): Definitions, Opportunities, and Challenges

Great needs always motivate the birth and development of new disciplines and tools. Here we propose in vitro BioTransformation (ivBT) as a new biomanufacturing platform, between the two dominant platforms—microbial fermentation and enzymatic biocatalysis. ivBT mediated by in vitro synthetic enzymatic biosystems (ivSEBs) is an emerging biomanufacturing platform for the production of biocommodities (i.e., low-value and bulk biochemicals). ivSEB is the in vitro reconstruction of artificial (non-natural) enzymatic pathways with numerous natural enzymes, artificial enzymes, and/or (biomimetic or natural) coenzymes without living cell’s constraints, such as cell duplication, basic metabolisms, complicated regulation, bioenergetics, and so on. The two great needs (i.e., food security and the carbon-neutral renewable energy system) have motivated the birth and development of ivBT. Food security could be addressed by making artificial food from nonfood lignocellulose and artificial photosynthesis for starch synthesis from CO2. The carbon-neutral renewable energy system could be addressed by the construction of the electricity-hydrogen-carbohydrate cycle, where starch could be a high density of hydrogen carrier (up to 14.8% H2 wt/wt) and an electricity storage compound (greater than 3000 Wh/kg). Also, ivBT can make a number of biocommodities, such as inositol, healthy sweeteners (e.g., D-allulose, D-tagatose, D-mannose), advanced biofuels, polymer precursors, organic acids, and so on. The industrial biomanufacturing of the first several biocommodities (e.g., myo-inositol, D-tagatose, D-mannose, and cellulosic starch) would wipe off any prejudice and doubt on ivBT. Huge potential markets of biocommodities with more than tens of trillions of Chinese Yuan would motivate scientists and engineers to address the remaining technical challenges and develop new tools within the next decade.utf-8

Yi-HengP. JobZhang
Zhiguang Zhu
ChunYou
Lingling Zhang
KuanqingLiu
Synth. Biol. Eng.
2023,
1
(2), 10013; 
Open Access

Article

31 May 2023

Nitrogen-controlled Valorization of Xylose-derived Compounds by Metabolically Engineered Corynebacterium glutamicum

The implementation of bioprocesses in an economically feasible and industrial competitive manner requires the optimal allocation of resources for a balanced distribution between biomass formation and product synthesis. The decoupling of growth and production in two-stage bioprocesses, aiming to ensure sufficient growth before the onset of production, is particularly relevant when target products inhibit growth. In order to avoid expensive inducer molecules, continuing process monitoring, elaborate individual process optimization, and strain engineering, we developed and applied nitrogen deprivation-induced expression of genes for product biosynthesis. Two native nitrogen deprivation-inducible promoters were identified and shown to function for dynamic growth-decoupled gene expression or CRISPRi-mediated gene knockdown in C. glutamicum with superior induction factors than the standard IPTG-inducible Ptrc promoter. Valorization of xylose to produce either the sugar acid xylonic acid or the sugar alcohol xylitol from xylose as sole source of carbon and energy was demonstrated. Competitive titers of up to 34 g·L−1 xylonate and 13 g·L−1 xylitol were achieved in two-stage processes. We discussed that the transfer to bioprocesses with C. glutamicum using carbon sources other than xylose appears straightforward in particular regarding production of growth-inhibitory compounds by their growth-decoupled fermentative production.utf-8

LynnS.Schwardmann
Marielle Rieks
Volker F.Wendisch
Synth. Biol. Eng.
2023,
1
(2), 10009; 
Open Access

Article

06 February 2024

Bio-Based Production of Uroporphyrin in Escherichia coli

Uroporphyrin (UP) is a porphyrin compound with medical applications and a key precursor for heme biosynthesis. However, there is no biosynthetic strategy for UP production. In this study, we present a novel bioprocess for enhanced production of UP in engineered Escherichia coli. We first implemented the Shemin/C4 pathway heterologously in an E. coli strain with an enlarged intracellular pool of succinyl-CoA. Using a plasmid with the trc promoter regulating the expression of a synthesized gene operon, the effects of key pathway genes, including hemA, hemB, hemC, and hemD, on UP biosynthesis were characterized. By cultivating the resulting engineered E. coli strains in a batch bioreactor with 30 g/L glycerol under aerobic conditions, up to 901.9 mg/L UP was produced. Most of the synthesized UP was extracellularly secreted with a high purity more than 80 wt%, facilitating its downstream purification. The study paves the way for large-scale bio-based production of UP using synthetic biology and metabolic engineering strategies.utf-8

Bahareh Arab
Adam W. Westbrook
Murray Moo-Young
Yilan Liu
C. Perry Chou
Synth. Biol. Eng.
2024,
2
(1), 10002; 
Open Access

Review

13 February 2024

Development and Perspective of Production of Terpenoids in Yeast

Terpenoids are a large class of secondary metabolites known for their remarkable diverse biological activities, making them widely utilized in the pharmaceutical, food, cosmetic, biofuel and agricultural fields. However, the current production of terpenoids heavily relies on plant extraction and chemical synthesis, which brings about concerns regarding infield, environmental and ecological issues. With the advancements in metabolic engineering and emerging synthetic biology tools, it is now possible to sustainably produce these high value-added terpenoids using microbial chassis. Among them, yeast has emerged as a promising candidate for the heterologous biosynthesis of terpenoids due to its inherent advantages, including robustness, safety, and the availability of sufficient precursor. This review focuses on the diverse strategies employed to enable terpenoids production in yeasts. These strategies encompass metabolic engineering approaches to optimize the mevalonate pathway, protein engineering techniques to improve terpenoid biosynthesis, the applications of organelles compartmentalization, high throughput screening and global approaches for the development of efficient cell factories. Furthermore, this review discusses the future prospects and challenges associated with yeast-based terpenoid production, while also emphasizing guidelines for future studies in this field.utf-8

YayingXia
CongnaLi
RuidiCao
LuQin
ShuoboShi
Synth. Biol. Eng.
2024,
2
(1), 10003; 
Open Access

Review

15 March 2023

Thermoanaerobacter Species: The Promising Candidates for Lignocellulosic Biofuel Production

Thermoanaerobacter species, which have broad substrate range and high operating temperature, can directly utilize lignocellulosic materials for biofuels production. Compared with the mesophilic process, thermophilic process shows greater prospects in consolidated bioprocessing (CBP) due to its relatively higher efficiency of lignocellulose degradation and lower risk of microbial contamination. Additionally, thermophilic conditions can reduce cooling costs, and further facilitate downstream product recovery. This review comprehensively summarizes the advances of Thermoanaerobacter species in lignocellulosic biorefinery, including their performance on substrates utilization, and genetic modification or other strategies for enhanced biofuels production. Furthermore, bottlenecks of sugar co-fermentation, metabolic engineering, and bioprocessing are also discussed.utf-8

KaiqunDai
ChunyunQu
HongxinFu
JufangWang
Synth. Biol. Eng.
2023,
1
(1), 10005; 
Open Access

Review

28 August 2023

Dynamic Metabolic Control: From the Perspective of Regulation Logic

Establishing microbial cell factories has become a sustainable and increasingly promising approach for the synthesis of valuable chemicals. However, introducing heterologous pathways into these cell factories can disrupt the endogenous cellular metabolism, leading to suboptimal production performance. To address this challenge, dynamic pathway regulation has been developed and proven effective in improving microbial biosynthesis. In this review, we summarized typical dynamic regulation strategies based on their control logic. The applicable scenarios for each control logic were highlighted and perspectives for future research direction in this area were discussed.utf-8

Tian Jiang
Chenyi Li
Yuxi Teng
Jianli Zhang
Diana Alexis Logan
YajunYan
Synth. Biol. Eng.
2023,
1
(2), 10012; 
Open Access

Article

20 December 2023

Serine Integrase-based Recombination Enables Direct Plasmid Assembly In Vivo

Serine integrases are emerging as one of the powerful tools for synthetic biology. They have been widely developed across genome engineering, biological part construction, genetic circuit design, and in vitro DNA assembly. However, the strategy of in vivo DNA assembly by serine integrases has not yet been reported. To address this opportunity, here we developed a serine integrase-based in vivo DNA (plasmid) assembly approach. First, we demonstrated that the engineered “Acceptor” plasmids could be assembled with diverse “Donor” plasmids by serine integrases (Bxb1 and phiC31) in Escherichia coli (E. coli). Then, by programming the “Donor” plasmids and the host E. coli cells, we established an assembly cascade procedure and finally constructed plasmids that could constitutively express three different fluorescent proteins. Moreover, we used this approach to assemble different chromoprotein genes and generated colored E. coli cells. We anticipate that this approach will enrich the serine integrase-based biotechnology toolbox, and accelerate multiple plasmid assembly for synthetic biology with broad applications.utf-8

LuyaoWang
YufeiZhang
Wan-QiuLiu
FangBa
JianLi
Synth. Biol. Eng.
2023,
1
(3), 10017; 
Open Access

Review

08 April 2024

Tolerance in Solventogenic Clostridia for Enhanced Butanol Production: Genetic Mechanisms and Recent Strain Engineering Advances

Biobutanol is a promising candidate for replacing fossil fuels due to its superior properties compared to ethanol. Solventogenic clostridia can naturally produce biobutanol among other valuable chemicals. Lignocellulosic material stands out as a promising source for biobutanol production, avoiding competition with food production and making use of residues from both agroindustry and forestry activities. However, Clostridium strains are subject to different chemical stressors, including oxygen, self-product inhibition, inhibitors generated during biomass pretreatment and hydrolysis, and others. Recent advances in genetic engineering tools have enabled the metabolic engineering of Clostridium strains to increase their robustness and tolerance to these stressors. This review provides a summary of the various types of inhibitors, the genetic mechanisms related to tolerance, and recent strain engineering efforts for tolerance enhancement. In addition, we offer a valuable perspective on the future research directions in this area.utf-8

Pablo Jiménez-Bonilla
Shangjun Wang
Tyler Whitfield
David Blersch
Yifen Wang
Luz-Estela Gonzalez-de-Bashan
Wei Luo
Yi Wang
Synth. Biol. Eng.
2024,
2
(2), 10007; 
Open Access

Review

31 October 2023

Metabolic Engineering of Microorganisms Towards the Biomanufacturing of Non-Natural C5 and C6 Chemicals

Five-carbon (C5) and six-carbon (C6) chemicals are essential components in the manufacturing of a variety of pharmaceuticals, fuels, polymers, and other materials. However, the predominant reliance on chemical synthesis methods and unsustainable feedstock sources has placed significant strain on Earth’s finite fossil resources and the environment. To address this challenge and promote sustainability, significant efforts have been undertaken to re-program microorganisms through metabolic engineering and synthetic biology approaches allowing for bio-based manufacturing of these compounds. This review provides a comprehensive overview of the advancements in microbial production of commercially significant non-natural C5 chemicals, including 1-pentanol, 1,5-pentanediol, cadaverine, δ-valerolactam, glutaric acid, glutaconic acid, and 5-hydroxyvaleric acid, as well as C6 chemicals, including cis, cis-muconic acid, adipic acid, 1,6-hexamethylenediamine, 6-aminocaproic acid, β-methyl-δ-valerolactone, 1-hexanol, ε-caprolactone, 6-hydroxyhexanoic acid, and 1,6-hexanediol.utf-8

Ashley Tseng
VannaNguyen
YuhengLin
Synth. Biol. Eng.
2023,
1
(3), 10015; 
Open Access

Editorial

13 December 2022

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