Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
10.0
5.6
Journals
IJMS
Special Issues
Whole-Cell System and Synthetic Biology, 2nd Edition
ijms-logo
Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Whole-Cell System and Synthetic Biology, 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (20 May 2026) | Viewed by 7096

Editor

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, benefitting from 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, the environment and other fields needs to be understood. Therefore, the aim of this Special Issue is to summarize and broaden the knowledge of new gene circuits, innovative molecular modification methods and the application of whole cell systems.

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

  • 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.

Dr. Jingjing Tian
Guest Editor

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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized 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.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Related Special Issue

Published Papers (4 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

15 pages, 634 KB  
Article
A Clozapine-Responsive GPCR-Based Gene Switch for Pharmacological Control of Gene Expression in Mammalian Cells and In Vivo
by Guanyang Chen, Shiting Li and Peng Bai
Int. J. Mol. Sci. 2026, 27(8), 3381; https://doi.org/10.3390/ijms27083381 - 9 Apr 2026
Viewed by 608
Abstract
The safe and precise regulation of therapeutic gene expression remains a major challenge for mammalian synthetic biology and cell-based therapies. Many existing inducible systems rely on non-mammalian regulatory components or ligands with limited clinical compatibility. Designer receptors exclusively activated by designer drugs (DREADDs) [...] Read more.
The safe and precise regulation of therapeutic gene expression remains a major challenge for mammalian synthetic biology and cell-based therapies. Many existing inducible systems rely on non-mammalian regulatory components or ligands with limited clinical compatibility. Designer receptors exclusively activated by designer drugs (DREADDs) offer a human G protein-coupled receptor (GPCR)-based framework for pharmacological control of intracellular signaling, yet their application as clinically relevant gene-regulation platforms remains underexplored. Here, we report a clozapine-responsive gene switch that couples a designer GPCR to signaling-dependent transcriptional control. By linking clozapine-activated receptors to cyclic adenosine monophosphate (cAMP)- or calcium-responsive synthetic promoters, receptor activation is converted into robust transgene expression across a broad dynamic range, with sensitivity to sub-nanomolar to low-nanomolar clozapine concentrations. In vivo, alginate-encapsulated reporter cells implanted in C57BL/6J mice responded to systemic or local clozapine administration with efficient secretion of a reporter protein, achieving robust induction at low daily doses (0.3 mg/kg) following either oral administration or local delivery. Together, these results establish a human GPCR-based clozapine-responsive gene switch that integrates regulation by a clinically used small molecule with modular transcriptional outputs, providing an additional approach for pharmacologically controllable gene expression in mammalian cells and in vivo. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology, 2nd Edition)
►▼ Show Figures

Figure 1

14 pages, 4166 KB  
Article
Development and Characterization of a Novel α-Synuclein-PEST H4 Cell Line for Enhanced Drug Screening in α-Synucleinopathies
by Nancy Carullo, Viktor Haellman, Simon Gutbier, Sonja Schlicht, Thien Thuong Nguyen, Rita Blum Marti, Philippe Hartz, Lothar Lindemann and Lina Schukur
Int. J. Mol. Sci. 2025, 26(15), 7205; https://doi.org/10.3390/ijms26157205 - 25 Jul 2025
Viewed by 1521
Abstract
Alpha-Synuclein (α-Syn) is a presynaptic neuronal protein implicated in the pathogenesis of Parkinson’s disease (PD) and other synucleinopathies, primarily through its aggregation into insoluble fibrils. The extended α-Syn half-life necessitates treatment durations that are incompatible with efficient high-throughput drug screening, can risk compound [...] Read more.
Alpha-Synuclein (α-Syn) is a presynaptic neuronal protein implicated in the pathogenesis of Parkinson’s disease (PD) and other synucleinopathies, primarily through its aggregation into insoluble fibrils. The extended α-Syn half-life necessitates treatment durations that are incompatible with efficient high-throughput drug screening, can risk compound stability or cause cellular toxicity. To address this, we inserted a PEST sequence, a motif known to promote rapid protein degradation, at the C-terminus of the SNCA gene using CRISPR/Cas9 to create a novel cell line with reduced α-Syn half-life. This modification accelerates α-Syn turnover, providing a robust model for studying α-Syn dynamics and offering a platform that is applicable to other long-lived proteins. Our results demonstrate a six-fold reduction in α-Syn half-life, enabling the rapid detection of changes in protein levels and facilitating the identification of molecules that modulate α-Syn production and degradation pathways. Using inhibitors of the proteasome, transcription, and translation further validated the model’s utility in examining various mechanisms that impact protein levels. This novel cell line represents a significant advancement for studying α-Syn dynamics and offers promising avenues to develop therapeutics for α-synucleinopathies. Future research should focus on validating this model in diverse experimental settings and exploring its potential in high-throughput screening applications. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology, 2nd Edition)
►▼ Show Figures

Figure 1

16 pages, 1717 KB  
Article
Utilization of Crab Shell Waste for Value-Added Bioplastics by Pseudomonas-Based Microbial Cell Factories
by Xiaofen Song, Hansheng Wei, Yueyue Zhou, Weiwei Song, Ce Shi, Changkao Mu, Chunlin Wang and Xiaopeng Wang
Int. J. Mol. Sci. 2025, 26(6), 2543; https://doi.org/10.3390/ijms26062543 - 12 Mar 2025
Cited by 4 | Viewed by 2831
Abstract
With the development of the aquatic products processing industry, 6–8 million tons of shrimp and crab shell waste are produced globally annually, but, due to the lack of high-value conversion technology, crab shells are often discarded in large quantities as a by-product of [...] Read more.
With the development of the aquatic products processing industry, 6–8 million tons of shrimp and crab shell waste are produced globally annually, but, due to the lack of high-value conversion technology, crab shells are often discarded in large quantities as a by-product of processing. Pseudomonas-based microbial cell factories are capable of biosynthesis of high-value products using a wide range of substrates; however, there is currently no reliable fermentation model for producing high-value chemicals using crab shell waste by Pseudomonas strains. In this study, we first explored the culture conditions of shell fermentation using KT2440 through single-factor and orthogonal experiments, and the optimized fermentation parameters obtained are given as follows: a temperature of 30 °C, fermentation time of 42 h, substrate solid–liquid ratio of 7%, and rotational speed of 200 rpm. After optimization, the maximum cell growth was increased by 64.39% from 350.67 × 108 CFU/mL to 576.44 × 108 CFU/mL. Combined with engineering modification, two engineered strains, KT+IV and KT+lasBT, expressing exogenous proteases, were obtained, and the maximum growth was increased from 316.44 × 108 CFU/mL to 1268.44 × 108 CFU/mL and 616.89 × 108 CFU/mL, which were 300.84% and 94.94% higher, respectively. In addition, the engineered strain KT+NtrcT-D55E, which regulates nitrogen metabolism, was obtained, and the accumulation of intracellular polyhydroxy fatty acid esters (PHA) was increased from 20.00 mg/L to 78.58 mg/L, which was a significant increase of 292.93% relative to the control group. This study provides a theoretical basis and technical support for the high-value utilization of shrimp and crab shell resources and the development of environmentally friendly bioproducts. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology, 2nd Edition)
►▼ Show Figures

Figure 1

Review

Jump to: Research

34 pages, 9510 KB  
Review
Advances in DNAzyme Selection, Molecular Engineering and Biomedical Applications
by Li Yan, Jingjing Tian, Hongyu Yang, Shuai Liu, Zaihui Du, Chen Li and Hongtao Tian
Int. J. Mol. Sci. 2026, 27(4), 1833; https://doi.org/10.3390/ijms27041833 - 14 Feb 2026
Cited by 1 | Viewed by 1350
Abstract
DNAzymes are catalytically active single-stranded DNAs that fold into metal-ion-assisted architectures to mediate diverse reactions. Addressing the performance gap in biological settings, we establish a novel conceptual framework based on a continuous iteration workflow of selection, enhancement, and application. This paradigm integrates selection [...] Read more.
DNAzymes are catalytically active single-stranded DNAs that fold into metal-ion-assisted architectures to mediate diverse reactions. Addressing the performance gap in biological settings, we establish a novel conceptual framework based on a continuous iteration workflow of selection, enhancement, and application. This paradigm integrates selection constraints, molecular engineering, and clinical context into a unified cycle. We summarize the evolution of SELEX toward application-driven selection incorporating functional/environmental constraints, deep-sequencing-enabled high-throughput activity readouts, droplet compartmentalization and structure- and computation-guided design. We further consolidate engineering strategies to improve stability, kinetics and controllability, including 2′-sugar modifications and XNA substitution, backbone and nucleobase functionalization, arm and secondary-structure engineering for switchable or split architectures and multivalent organization on nanocarriers or nucleic acid scaffolds to enhance local concentration, protection and targeted delivery. Finally, we survey applications in ultrasensitive biosensing and portable diagnostics, activatable and multimodal in vivo imaging, and therapies for cancer, inflammatory diseases and airway disorders, and outline translational priorities: data-driven design, next-generation delivery, standardized safety/PK-PD evaluation and scalable manufacturing, ultimately for clinical and point-of-care deployment. Full article
(This article belongs to the Special Issue Whole-Cell System and Synthetic Biology, 2nd Edition)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-4
Back to TopTop