Key Technologies of Synthetic Biology in Industrial Microbiology
Abstract
1. Introduction
1.1. Overall Synthetic Biology Market
1.2. The Importance of Industrial Microorganisms
1.3. Significance of Integrating Synthetic Biology with Industrial Microbiology
2. Key Technologies of Synthetic Biology in Industrial Microorganisms
2.1. Gene Editing Technologies
2.1.1. ZFNs
2.1.2. TALENs
2.1.3. CRISPR/Cas System
2.1.4. Examples of Gene Editing Applications in Industrial Microorganisms
2.2. Metabolic Engineering
2.2.1. Optimization and Reconstruction of Metabolic Pathways
Expression Regulation of Key Enzymes
Metabolic Flux Analysis
Exogenous Pathway Introduction
2.3. High-Throughput Screening and Automation Platform
2.4. Synthetic Genomics
2.4.1. Construction of Minimal Genomes
2.4.2. Design and Assembly of Synthetic Chromosomes
2.4.3. Synthetic Genomes in Industrial Microorganisms
3. Conclusions and Outlook
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
PLA | polylactic acid |
PHA | polyhydroxyalkanoates |
HR | homologous recombination |
ZFNs | zinc finger nucleases |
TALENs | transcription activator-like effector nucleases |
CRSISPR | clustered regularly interspaced short palindromic repeats |
HSCs | hematopoietic stem cells |
HbF | hemoglobin |
RVDs | repeat variable diresidues |
Cas9-PE | Cas9-mediated Prime Editing |
scFv | single-chain variable fragment |
eGFP | enhanced green fluorescent protein |
TRY | titers, rates, and yields |
DBTL | design-build-test-learn |
MFA | metabolic flux analysis |
GEMs | genome-scale metabolic models |
PTS | patchouli alcohol synthase |
SF | sodium fumarate |
HTS | high-throughput screening |
FACS | fluorescence-activated cell sorting |
NGS | next-generation sequencing |
WGS | whole-genome sequencing |
ALE | adaptive laboratory evolution |
QTL | quantitative trait locus |
FBA | flux balance analysis |
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Areas of Application | Examples of Industrial Microorganisms | Application | References |
---|---|---|---|
Chemicals and materials | Corynebacterium glutamicum | production of proteinogenic amino acids | [61] |
Kappaphycus alvarezii, Bacillus megaterium | production of bioplastic polyhydroxy fatty acid esters | [62] | |
Xanthomonas campestris | production of xanthan gum for oil extraction | [63] | |
Drugs and vaccines | Xanthomonas, Xanthomonas campestris | production of β-glucan for biopharmaceuticals | [64] |
Nannochloropsis, Saccharomyces cerevisiae, Sparassis crispa, Bacillus subtilis | production of cyclosporin A, for immunosuppression after organ transplantation | [65] | |
Streptomyces | production of Adriamycin for the treatment of various cancers | [66] | |
Food and beverage industry | Lactic acid bacteria | fermentation of plant-based dairy alternatives, vegetables, sweet rice wine, yogurt, cheese | [67,68,69,70,71] |
Acetic acid bacteria | fermented vinegar | [72] | |
Environmental remediation | Thermotolerant yeast, Oleaginous yeast, Lactic acid bacteria | production of ethanol, lipid and lactic acid from mixed agrowastes hydrolysate | [73] |
Stenotrophomonas, Achromobacter, | degradation of plastics | [74] | |
Proteobacteria, Actinobacteria | degradation of oil pollutants | [75] | |
Agricultural | Nitrogen-fixing bacteria | biofertiliser | [76] |
Filamentous fungi | bio-pesticides | [77] | |
Soil microalgae and Cyanobacteria | maintenance of soil fertility and health | [78] | |
Energy production | Betaproteobacteria | generation of oxygenated methane | [79] |
Cyanobacteria, Microalgae | biodiesel production | [80] | |
Chlorella vulgaris, Chlamydomonas reinhardtii, Chlorella fusca | biohydrogen production | [81,82,83] | |
Saccharomyces cerevisiae | bioethanol | [84,85] |
Technology Name | ZFN | TALEN | CRISPR/Cas9 |
---|---|---|---|
Recognition mode | Protein-DNA | Protein-DNA | RNA-DNA |
Targeting element | ZF array Protein | TALE array Protein | sgRNA Protein |
Cutting element | Fok1 Protein | Fok1 Protein | Cas9 Protein |
Advantages | Mature platform, higher efficiency than passive homologous recombination | Simpler design than ZFN, high specificity | Precise targeting, low off-target rate, low cytotoxicity, cheap |
Disadvantages | Design dependent on upstream and downstream sequences, high off-target rate, cytotoxic | Cytotoxic, cumbersome module assembly, requires extensive sequencing | Cannot be cleaved without a PAM in front of the target region, low specificity, NHEJ still produces on-target toxicity |
The Potential of RNA Editing | No | No | Yes |
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Jiang, X.; Ji, J.; Yang, Q.; Dou, Y.; Li, Y.; Yang, X.; Liu, C.; Dou, S.; Dong, L. Key Technologies of Synthetic Biology in Industrial Microbiology. Microorganisms 2025, 13, 2343. https://doi.org/10.3390/microorganisms13102343
Jiang X, Ji J, Yang Q, Dou Y, Li Y, Yang X, Liu C, Dou S, Dong L. Key Technologies of Synthetic Biology in Industrial Microbiology. Microorganisms. 2025; 13(10):2343. https://doi.org/10.3390/microorganisms13102343
Chicago/Turabian StyleJiang, Xinyue, Jiayi Ji, Qi Yang, Yao Dou, Yujue Li, Xiaoyu Yang, Chunying Liu, Shaohua Dou, and Liang Dong. 2025. "Key Technologies of Synthetic Biology in Industrial Microbiology" Microorganisms 13, no. 10: 2343. https://doi.org/10.3390/microorganisms13102343
APA StyleJiang, X., Ji, J., Yang, Q., Dou, Y., Li, Y., Yang, X., Liu, C., Dou, S., & Dong, L. (2025). Key Technologies of Synthetic Biology in Industrial Microbiology. Microorganisms, 13(10), 2343. https://doi.org/10.3390/microorganisms13102343