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Synthetic Genetic Elements, Devices, and Systems: 2nd Edition
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Synthetic Genetic Elements, Devices, and Systems: 2nd Edition

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Synthetic Biology and Systems Biology".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 1725

Special Issue Editors

Prof. Dr. Chunbo Lou

E-Mail Website
Guest Editor
CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, University Town, Nanshan, Shenzhen 518055, China
Interests: genetic circuits; modular design; promoter design; insulators
Special Issues, Collections and Topics in MDPI journals
Dr. Yusuke Kato

E-Mail Website
Guest Editor
Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Oowashi 1-2, Tsukuba, Ibaraki 305-8634, Japan
Interests: biological containment; synthetic biology; development of novel genetic parts; unnatural amino acids; heterologous protein production
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue’s first edition was a great achievement. We are now inviting you to contribute to the second edition (https://www.mdpi.com/journal/life/special_issues/Synth_Genet).

Since the beginning of life on Earth, over the course of 3–4 billion years, nature has created vast numbers of genetic elements, subsequently submitting them to natural selection, where winners survived and losers disappeared. Only genetically stable elements that contributed to the maintenance of life were permitted to persevere. Contrarily, natural selection restricted the diversity of genetic elements. In the last 20 years, i.e., 2 × 10−8 billion years, synthetic biologists have tried to create novel genetic elements that “nature has not invented or cannot invent”. The objective of this research is to go beyond the restriction of natural selection and obtain novel genetic elements that are “useful for human use”. From the limited modification of characteristics of natural elements to originally designed elements, various synthetic genetic elements have been reported. “Genetic devices”, such as logic gates and memory elements, and higher order “genetic systems”, such as metabolite factories and biological containment systems, can be constructed using these synthetic genetic elements in combination with other genetic elements. Through this approach, the incorporation of synthetic genetic elements is dramatically expanding biological functions.

This Special Issue, “Synthetic Genetic Elements, Devices, and Systems: 2nd Edition”, will explore the current state of the art in this growing field. We hereby invite articles (full articles, short communications, and reviews) covering a broad range of topics.

Topics for this Special Issue include, but are not limited to, the following:

  1. Synthetic genetic elements in prokaryotes and eukaryotes (promoters, transcription factors, RBS, degradation tags, transcriptional terminators, sensors, indicators, ribozymes and riboswitches, enzymes such as recombinases and proteases as regulatory elements, etc.).
  2. Synthetic genetic circuits as devices and systems (either involving or not involving synthetic genetic elements, but with the purpose of eliciting designed behavior).
  3. Methods to develop synthetic genetic elements, devices, and systems.
  4. Applications for laboratory and industrial use.
  5. History and future perspectives.

Prof. Dr. Chunbo Lou
Dr. Yusuke Kato
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. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • synthetic biology
  • synthetic genetic elements/parts
  • biobricks
  • artificial gene synthesis
  • biocomputing
  • directed evolution
  • metabolic engineering/cell factory
  • optogenetics
  • genetic code expansion
  • xenobiology

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Published Papers (2 papers)

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Research

15 pages, 2988 KB  
Article
Prophage Activation: An In Silico Platform for Identifying Prophage Regulatory Elements to Inform Phage Engineering Against Drug-Resistant Bacteria
by Saher Musrrat, Zequan Han, Kai Wang, Yunhai Huang, Yanhui Xiang, Sen Liu and Wen Yin
Life 2025, 15(9), 1417; https://doi.org/10.3390/life15091417 - 9 Sep 2025
Viewed by 585
Abstract
Multidrug-resistant bacterial infections pose a severe global health threat, highlighting the urgent need for innovative therapeutic options beyond traditional antibiotics. Phage therapy, which employs bacteriophages to infect and eradicate pathogenic bacteria, specifically offers a promising solution. However, the lack of well-characterized therapeutic phages [...] Read more.
Multidrug-resistant bacterial infections pose a severe global health threat, highlighting the urgent need for innovative therapeutic options beyond traditional antibiotics. Phage therapy, which employs bacteriophages to infect and eradicate pathogenic bacteria, specifically offers a promising solution. However, the lack of well-characterized therapeutic phages has limited their broader clinical use. A critical aspect of activating the lytic potential of dormant prophages involves the strategic manipulation of transcription factor binding sites (TFBS), which function as pivotal regulatory nodes governing the transition between lysogenic dormancy and lytic activation. Our platform utilizes advanced bioinformatics tools to accurately identify and analyze TFBS, facilitating the targeted redesign or replacement of these sites to disrupt host-mediated repression. By systematically simulating modifications of these regulatory ‘switches,’ our platform computationally predicts reduced repressor activity, suggesting the potential for prophage activation and bacterial cell lysis. This novel methodology not only broadens the spectrum of therapeutic bacteriophages but also establishes a basis for individualized phage-based therapies, presenting a robust strategy to address the escalating challenge of antibiotic-resistant infections. By enabling the precise identification and engineering of TFBS, our platform signifies a transformative advancement in phage biology, effectively bridging the divide between computational analysis and therapeutic application. Full article
(This article belongs to the Special Issue Synthetic Genetic Elements, Devices, and Systems: 2nd Edition)
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16 pages, 5499 KB  
Article
A Programmable Finite-Replicated Organism Framework for Balanced Safety and Functionality
by Mengyuan Wang, Pei Du, Fankang Meng, Wenhui Zhang, Yanhui Xiang, Qiong Wu and Chunbo Lou
Life 2025, 15(9), 1381; https://doi.org/10.3390/life15091381 - 1 Sep 2025
Viewed by 565
Abstract
Live-attenuated vaccines face a critical challenge in balancing immunogenicity with safety. To address this, we engineered programmable finite-replicated organisms (FROs) by depositing a limited number of indispensable components (such as noncanonical amino acids, ncAAs) within the cell, consuming the coenabling precise control of [...] Read more.
Live-attenuated vaccines face a critical challenge in balancing immunogenicity with safety. To address this, we engineered programmable finite-replicated organisms (FROs) by depositing a limited number of indispensable components (such as noncanonical amino acids, ncAAs) within the cell, consuming the coenabling precise control of bacterial replication capability while preserving antigenic breadth. Two strategies were adopted to achieve the following purposes: (1) encoding ncAA in essential genes; (2) encoding ncAA in antitoxin of toxin–antitoxin (TA) systems. As noncanonical amino acids, 3,5-dichlorotyrosine (Cl2Y) was encoded by the amber codon (TAG) and inserted into the essential genes (e.g., serS, murG, and dnaA) or antitoxin genes. After optimizing expression and the number of amber codons in the storage genes, the FRO cells can grow up to six generations, achieving amplification approaching 100 times after depletion of the ncAA in the growth medium. The escape frequencies are 10−5 to 10−7, which need to be optimized by combining multiple storage genes in the same genome in the future. This work holds the potential to amplify the amounts of antigens for vaccines, potentially accelerating the development of next-generation vaccines against antibiotic-resistant threats. Full article
(This article belongs to the Special Issue Synthetic Genetic Elements, Devices, and Systems: 2nd Edition)
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