Synthetic Biology and Engineering

Guide for Authors Submit to SBE

Synthetic Biology in the Manufacturing of Chemicals and Fuels

Deadline for manuscript submissions: 31 October 2025.

Guest Editors (6)

George N. Bennett
Prof. George N. Bennett 
Department of BioSciences, Rice University, Houston, 77005, TX, USA
Interests: Molecular Biology of Prokaryotes; Metabolic Engineering; Biosensors
Website: https://profiles.rice.edu/faculty/george-n-bennett
Pablo Carbonell
Prof. Pablo Carbonell 
Institute of Industrial Control Systems and Computing (AI2), Polytechnic University of Valencia, Valencia, Spain
Interests: Synthetic Biology; Systems Biology; Computational Biology; Control Engineering; Biological Engineering
Website: http://www.upv.es/ficha-personal/pjcarbon
Weiliang Dong
Prof. Weiliang Dong 
State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
Interests: Microbial Strains and Enzymes; Combinin Gadaptive Evolution; High Throughput Screening; Synthetic Biotechnology; Protein Structure Design and Scale-up Process
Website: https://www.mix-up.eu/partner/ntu
Min Jiang
Prof. Min Jiang 
State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
Interests: Synthetic Biology; Fermentation Engineering; Organic Wastes Bioconversion; Microbial Consortia
Website: https://www.mix-up.eu/partner/ntu
Yi Wang
Prof. Yi Wang 
Department of Biosystems Engineering, Auburn University, Auburn, AL, USA; Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL, USA
Interests: Metabolic Engineering; Synthetic Biology; Bioprocess Engineering; Biomanufacturing; Biofuels and Biochemicals; Applied Microbiology; Environmental Microbiology
Website: https://eng.auburn.edu/directory/yzw0066
Jufang Wang
Prof. Jufang Wang 
School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
Interests: Synthetic Biology; Fermentation Engineering; Biochemistry and Molecular Biology; Biosafety and Detection; Microbiology
Website: https://www2.scut.edu.cn/biology/2018/1108/c15457a294052/page.htm

Topic Collection Information

Topic Introduction

Synthetic biology, an interdisciplinary field that combines engineering, biology, and computational approaches, offers a powerful tool for the sustainable production of biochemicals and biofuels from renewable resources. By manipulating and engineering genetic circuits, synthetic biology enables the optimization of metabolic pathways in microorganisms or with cell free systems for the synthesis of desired chemical compounds. This has led to the creation of novel and valuable biochemicals, such as pharmaceuticals and flavors, as well as the development of cost-effective and environmentally friendly biofuels. This special topic collection will highlight the latest advancements in synthetic biology for biochemicals and biofuels production, covering a broad range of topics, including the development of non-conventional microbial chassis, the engineering of novel carbon metabolisms (C1 substrate, lignin, etc.), the design of innovative pathways, the development of high-value chemicals, the enhanced production of biofuels, and the integration or hybridization of synthetic biology with other emerging technologies and innovative processes. Additionally, this special issue welcomes reviews and perspectives on the challenges and opportunities for the future of this exciting research field. 

Keywords

  • Synthetic Biology
  • Genome Editing
  • CRISPR
  • Biofuels
  • Biochemicals
  • Non-conventional Microorganisms
  • Cell Free System
  • Carbon Metabolism
  • Metabolic Pathways
  • Carbon Sequestration
  • Environmental Sustainability

Published Papers (5 papers)

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.

Tian  Jiang
Chenyi  Li
Yuxi  Teng
Jianli  Zhang
Diana  Alexis Logan
Yajun Yan*

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.

Mian Wu
Junwei Zhuang
Xijing He
Feihong Zhu
Qinwen Lai
Xiujuan Qian*
Weiliang Dong*
Min Jiang

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.

Xinyu Yu
Jia Guo
Jiacheng Sun
Chong Zhang*

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.

Na  Xu
Hui  Chen
Yan  Zhang
Yuxian Yang
Yasi Wang
Bei  Liao
Nan  Peng
Xiaosong  Gu *

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.

Curtis D.Moore
Qingke Wang
Geng Wang
Shang-Tian Yang*
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