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Whole-Cell System and Synthetic Biology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 20 January 2025 | Viewed by 17931

Special Issue Editors

Prof. Dr. Zhihong Xin

E-Mail Website
Guest Editor
Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
Interests: food nutrition and safety; biodegradation; enzyme and enzyme engineering; synthetic biology; microbial secondary metabolites
Dr. Jingjing Tian

E-Mail Website
Guest Editor
Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
Interests: synthesis biology; molecular biology; functional nucleic acids; biosensor
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The whole-cell system has been of great interest recently and has advanced the analysis and manufacturing techniques in the past decade, benefitted by the development of molecular biology and synthetic biology. The understanding of cell metabolism and gene regulation at the molecular level is of particular significance. The understanding of how the whole-cell system is applied in analysis or manufacturing has progressed, but there is still a great deal to be learnt. Key issues gaps in the area are as follows: (1) Gene interactions and regulatory networks still need to be explored. (2) Technical approaches need to be upgraded to edit the whole cell system. (3) The performance of the whole-cell system needs to be improved. (4) How to effectively apply the whole cell system in food, environment and other fields needs to be understood. Therefore, the aim of this Special Issue is to summarize and broaden the knowledge in new gene circuits, innovative molecular modification methods and the application of whole cell systems.

Authors are invited to submit original research and review articles which address the areas discussed above. Topics include but are not limited to:

  • Identification and mining of new molecular networks in whole-cell systems;
  • Methods for upgrading and the modification of whole-cell systems;
  • Application of whole-cell systems in food, environment and other fields.

Prof. Dr. Zhihong Xin
Dr. Jingjing Tian
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • synthesis biology
  • molecular biology
  • functional nucleic acids
  • biosensor
  • CRISPR-Cas
  • directed evolution
  • whole-cell system

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Related Special Issue

Published Papers (8 papers)

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Research

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15 pages, 5275 KiB  
Article
Flower-Shaped PCR Scaffold-Based Lateral Flow Bioassay for Bacillus cereus Endospores Detection
by Jingjing Tian, Zhuyi Zhang, Yaning Shi, Zichao Wu, Yuting Shao, Limin Wang, Xinglian Xu and Zhihong Xin
Int. J. Mol. Sci. 2024, 25(20), 11286; https://doi.org/10.3390/ijms252011286 - 20 Oct 2024
Viewed by 756
Abstract
Bacillus cereus, a foodborne pathogen, produces resilient endospores that are challenging to detect with conventional methods. This study presents a novel Flower-Shaped PCR Scaffold-based Lateral Flow Biosensor (FSPCRS-LFB), which employs an aptamer-integrated PCR scaffold as capture probes, replacing the traditional streptavidin-biotin (SA-Bio) [...] Read more.
Bacillus cereus, a foodborne pathogen, produces resilient endospores that are challenging to detect with conventional methods. This study presents a novel Flower-Shaped PCR Scaffold-based Lateral Flow Biosensor (FSPCRS-LFB), which employs an aptamer-integrated PCR scaffold as capture probes, replacing the traditional streptavidin-biotin (SA-Bio) approach. The FSPCRS-LFB demonstrates high sensitivity and cost-efficiency in detecting B. cereus endospores, with a limit of detection (LOD) of 4.57 endospores/mL a visual LOD of 102 endospores/mL, and a LOD of 6.78 CFU/mL for endospore-cell mixtures. In chicken and tea samples, the platform achieved LODs of 74.5 and 52.8 endospores/mL, respectively, with recovery rates of 82.19% to 97.88%. Compared to existing methods, the FSPCRS-LFB offers a 3.7-fold increase in sensitivity while reducing costs by 26% over the SA-Bio strategy and 87.5% over rolling circle amplification (RCA). This biosensor provides a rapid, sensitive and cost-effective solution for point-of-care testing (POCT) of B. cereus endospores, expanding detection capabilities and offering novel approaches for pathogen detection. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology)
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14 pages, 2548 KiB  
Article
Development of a Whole-Cell System Based on the Use of Genetically Modified Protoplasts to Detect Nickel Ions in Food Matrices
by Monica De Caroli, Carla Perrotta and Patrizia Rampino
Int. J. Mol. Sci. 2024, 25(11), 6090; https://doi.org/10.3390/ijms25116090 - 31 May 2024
Viewed by 598
Abstract
Heavy metals are dangerous contaminants that constitute a threat to human health because they persist in soils and are easily transferred into the food chain, causing damage to human health. Among heavy metals, nickel appears to be one of the most dangerous, being [...] Read more.
Heavy metals are dangerous contaminants that constitute a threat to human health because they persist in soils and are easily transferred into the food chain, causing damage to human health. Among heavy metals, nickel appears to be one of the most dangerous, being responsible for different disorders. Public health protection requires nickel detection in the environment and food chains. Biosensors represent simple, rapid, and sensitive methods for detecting nickel contamination. In this paper, we report on the setting up a whole-cell-based system, in which protoplasts, obtained from Nicotiana tabacum leaves, were used as transducers to detect the presence of heavy metal ions and, in particular, nickel ions. Protoplasts were genetically modified with a plasmid containing the Green Fluorescent Protein reporter gene (GFP) under control of the promoter region of a sunflower gene coding for a small Heat Shock Protein (HSP). Using this device, the presence of heavy metal ions was detected. Thus, the possibility of using this whole-cell system as a novel tool to detect the presence of nickel ions in food matrices was assessed. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology)
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16 pages, 2982 KiB  
Article
Directed Evolution of 4-Hydroxyphenylpyruvate Biosensors Based on a Dual Selection System
by Hongxuan Du, Yaoyao Liang, Jianing Li, Xinyao Yuan, Fenglin Tao, Chengjie Dong, Zekai Shen, Guangchao Sui and Pengchao Wang
Int. J. Mol. Sci. 2024, 25(3), 1533; https://doi.org/10.3390/ijms25031533 - 26 Jan 2024
Cited by 2 | Viewed by 1563
Abstract
Biosensors based on allosteric transcription factors have been widely used in synthetic biology. In this study, we utilized the Acinetobacter ADP1 transcription factor PobR to develop a biosensor activating the PpobA promoter when bound to its natural ligand, 4-hydroxybenzoic acid (4HB). To [...] Read more.
Biosensors based on allosteric transcription factors have been widely used in synthetic biology. In this study, we utilized the Acinetobacter ADP1 transcription factor PobR to develop a biosensor activating the PpobA promoter when bound to its natural ligand, 4-hydroxybenzoic acid (4HB). To screen for PobR mutants responsive to 4-hydroxyphenylpyruvate(HPP), we developed a dual selection system in E. coli. The positive selection of this system was used to enrich PobR mutants that identified the required ligands. The following negative selection eliminated or weakened PobR mutants that still responded to 4HB. Directed evolution of the PobR library resulted in a variant where PobRW177R was 5.1 times more reactive to 4-hydroxyphenylpyruvate than PobRWT. Overall, we developed an efficient dual selection system for directed evolution of biosensors. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology)
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18 pages, 4541 KiB  
Article
CsCuAO1 Associated with CsAMADH1 Confers Drought Tolerance by Modulating GABA Levels in Tea Plants
by Yu Cao, Yiwen Chen, Nuo Cheng, Kexin Zhang, Yu Duan, Shimao Fang, Qiang Shen, Xiaowei Yang, Wanping Fang and Xujun Zhu
Int. J. Mol. Sci. 2024, 25(2), 992; https://doi.org/10.3390/ijms25020992 - 12 Jan 2024
Cited by 3 | Viewed by 1266
Abstract
Our previous study showed that COPPER-CONTAINING AMINE OXIDASE (CuAO) and AMINOALDEHYDE DEHYDROGENASE (AMADH) could regulate the accumulation of γ-aminobutyric acid (GABA) in tea through the polyamine degradation pathway. However, their biological function in drought tolerance has not been determined. In this study, Camellia [...] Read more.
Our previous study showed that COPPER-CONTAINING AMINE OXIDASE (CuAO) and AMINOALDEHYDE DEHYDROGENASE (AMADH) could regulate the accumulation of γ-aminobutyric acid (GABA) in tea through the polyamine degradation pathway. However, their biological function in drought tolerance has not been determined. In this study, Camellia sinensis (Cs) CsCuAO1 associated with CsAMADH1 conferred drought tolerance, which modulated GABA levels in tea plants. The results showed that exogenous GABA spraying effectively alleviated the drought-induced physical damage. Arabidopsis lines overexpressing CsCuAO1 and CsAMADH1 exhibited enhanced resistance to drought, which promoted the synthesis of GABA and putrescine by stimulating reactive oxygen species’ scavenging capacity and stomatal movement. However, the suppression of CsCuAO1 or CsAMADH1 in tea plants resulted in increased sensitivity to drought treatment. Moreover, co-overexpressing plants increased GABA accumulation both in an Agrobacterium-mediated Nicotiana benthamiana transient assay and transgenic Arabidopsis plants. In addition, a GABA transporter gene, CsGAT1, was identified, whose expression was strongly correlated with GABA accumulation levels in different tissues under drought stress. Taken together, CsCuAO1 and CsAMADH1 were involved in the response to drought stress through a dynamic GABA-putrescine balance. Our data will contribute to the characterization of GABA’s biological functions in response to environmental stresses in plants. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology)
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12 pages, 7188 KiB  
Article
Biodegradation of Poly(ethylene terephthalate) by Bacillus safensis YX8
by Caiting Zeng, Fanghui Ding, Jie Zhou, Weiliang Dong, Zhongli Cui and Xin Yan
Int. J. Mol. Sci. 2023, 24(22), 16434; https://doi.org/10.3390/ijms242216434 - 17 Nov 2023
Cited by 1 | Viewed by 1981
Abstract
Due to the extensive utilization of poly (ethylene terephthalate) (PET), a significant amount of PET waste has been discharged into the environment, endangering both human health and the ecology. As an eco-friendly approach to PET waste treatment, biodegradation is dependent on efficient strains [...] Read more.
Due to the extensive utilization of poly (ethylene terephthalate) (PET), a significant amount of PET waste has been discharged into the environment, endangering both human health and the ecology. As an eco-friendly approach to PET waste treatment, biodegradation is dependent on efficient strains and enzymes. In this study, a screening method was first established using polycaprolactone (PCL) and PET nanoparticles as substrates. A PET-degrading strain YX8 was isolated from the surface of PET waste. Based on the phylogenetic analysis of 16S rRNA and gyrA genes, this strain was identified as Bacillus safensis. Strain YX8 demonstrated the capability to degrade PET nanoparticles, resulting in the production of terephthalic acid (TPA), mono (2-hydroxyethyl) terephthalic acid (MHET), and bis (2-hydroxyethyl) terephthalic acid (BHET). Erosion spots on the PET film were observed after incubation with strain YX8. Furthermore, the extracellular enzymes produced by strain YX8 exhibited the ability to form a clear zone on the PCL plate and to hydrolyze PET nanoparticles to generate TPA, MHET, and BHET. This work developed a method for the isolation of PET-degrading microorganisms and provides new strain resources for PET degradation and for the mining of functional enzymes. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology)
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12 pages, 4045 KiB  
Article
A Novel Microbial Consortia Catalysis Strategy for the Production of Hydroxytyrosol from Tyrosine
by Pengfei Gong, Jiali Tang, Jiaying Wang, Chengtao Wang and Wei Chen
Int. J. Mol. Sci. 2023, 24(8), 6944; https://doi.org/10.3390/ijms24086944 - 8 Apr 2023
Cited by 5 | Viewed by 2143
Abstract
Hydroxytyrosol, a valuable plant-derived phenolic compound, is increasingly produced from microbial fermentation. However, the promiscuity of the key enzyme HpaBC, the two-component flavin-dependent monooxygenase from Escherichia coli, often leads to low yields. To address this limitation, we developed a novel strategy utilizing microbial [...] Read more.
Hydroxytyrosol, a valuable plant-derived phenolic compound, is increasingly produced from microbial fermentation. However, the promiscuity of the key enzyme HpaBC, the two-component flavin-dependent monooxygenase from Escherichia coli, often leads to low yields. To address this limitation, we developed a novel strategy utilizing microbial consortia catalysis for hydroxytyrosol production. We designed a biosynthetic pathway using tyrosine as the substrate and selected enzymes and overexpressing glutamate dehydrogenase GdhA to realize the cofactor cycling by coupling reactions catalyzed by the transaminase and the reductase. Additionally, the biosynthetic pathway was divided into two parts and performed by separate E. coli strains. Furthermore, we optimized the inoculation time, strain ratio, and pH to maximize the hydroxytyrosol yield. Glycerol and ascorbic acid were added to the co-culture, resulting in a 92% increase in hydroxytyrosol yield. Using this approach, the production of 9.2 mM hydroxytyrosol was achieved from 10 mM tyrosine. This study presents a practical approach for the microbial production of hydroxytyrosol that can be promoted to produce other value-added compounds. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology)
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Review

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23 pages, 2403 KiB  
Review
Applications of the Whole-Cell System in the Efficient Biosynthesis of Heme
by Hongfei Su, Xiaolin Chen, Shijing Chen, Mingzhang Guo and Huilin Liu
Int. J. Mol. Sci. 2023, 24(9), 8384; https://doi.org/10.3390/ijms24098384 - 7 May 2023
Cited by 4 | Viewed by 3321
Abstract
Heme has a variety of functions, from electronic reactions to binding gases, which makes it useful in medical treatments, dietary supplements, and food processing. In recent years, whole-cell system-based heme biosynthesis methods have been continuously explored and optimized as an alternative to the [...] Read more.
Heme has a variety of functions, from electronic reactions to binding gases, which makes it useful in medical treatments, dietary supplements, and food processing. In recent years, whole-cell system-based heme biosynthesis methods have been continuously explored and optimized as an alternative to the low-yield, lasting, and adverse ecological environment of chemical synthesis methods. This method relies on two biosynthetic pathways of microbial precursor 5-aminolevulinic acid (C4, C5) and three known downstream biosynthetic pathways of heme. This paper reviews the genetic and metabolic engineering strategies for heme production in recent years by optimizing culture conditions and techniques from different microorganisms. Specifically, we summarized and analyzed the possibility of using biosensors to explore new strategies for the biosynthesis of heme from the perspective of synthetic biology, providing a new direction for future exploration. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology)
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21 pages, 2059 KiB  
Review
Advances in Synthetic-Biology-Based Whole-Cell Biosensors: Principles, Genetic Modules, and Applications in Food Safety
by Shijing Chen, Xiaolin Chen, Hongfei Su, Mingzhang Guo and Huilin Liu
Int. J. Mol. Sci. 2023, 24(9), 7989; https://doi.org/10.3390/ijms24097989 - 28 Apr 2023
Cited by 15 | Viewed by 5134
Abstract
A whole-cell biosensor based on synthetic biology provides a promising new method for the on-site detection of food contaminants. The basic components of whole-cell biosensors include the sensing elements, such as transcription factors and riboswitches, and reporting elements, such as fluorescence, gas, etc. [...] Read more.
A whole-cell biosensor based on synthetic biology provides a promising new method for the on-site detection of food contaminants. The basic components of whole-cell biosensors include the sensing elements, such as transcription factors and riboswitches, and reporting elements, such as fluorescence, gas, etc. The sensing and reporting elements are coupled through gene expression regulation to form a simple gene circuit for the detection of target substances. Additionally, a more complex gene circuit can involve other functional elements or modules such as signal amplification, multiple detection, and delay reporting. With the help of synthetic biology, whole-cell biosensors are becoming more versatile and integrated, that is, integrating pre-detection sample processing, detection processes, and post-detection signal calculation and storage processes into cells. Due to the relative stability of the intracellular environment, whole-cell biosensors are highly resistant to interference without the need of complex sample preprocessing. Due to the reproduction of chassis cells, whole-cell biosensors replicate all elements automatically without the need for purification processing. Therefore, whole-cell biosensors are easy to operate and simple to produce. Based on the above advantages, whole-cell biosensors are more suitable for on-site detection than other rapid detection methods. Whole-cell biosensors have been applied in various forms such as test strips and kits, with the latest reported forms being wearable devices such as masks, hand rings, and clothing. This paper examines the composition, construction methods, and types of the fundamental components of synthetic biological whole-cell biosensors. We also introduce the prospect and development trend of whole-cell biosensors in commercial applications. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology)
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