Synthetic Biology and Engineering

Guide for Authors Submit to SBE

Molecular Tools in Synthetic Biology

Deadline for manuscript submissions: 30 September 2024.

Guest Editors (2)

Bernd Mueller-Roeber
Prof. Dr. Bernd Mueller-Roeber 
University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, Potsdam, 14476, Germany
Interests: Biotechnology; Transcription Factors; Gene Regulatory Networks; Synthetic Biology; Plant Molecular Biology
Website: https://www.uni-potsdam.de/en/ibb-molecularbiology/research-overview
Daniel Schindler
Dr. Daniel Schindler 
Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
Interests: Synthetic Biology; Synthetic Genomics; Genome Engineering; Molecular Biology; Genome Architecture
Website: https://www.mpi-marburg.mpg.de/person/107383/2511

Topic Collection Information

Topic Introduction

Synthetic biology (SynBio) is a scientific discipline utilizing molecular-biological technologies for the intentional generation of new genetic networks, metabolic traits, signaling pathways, cellular entities, organisms, and even consortia of diverse species. Typically, the molecular parts assembled in genetic constructs for SynBio originate from diverse biological sources, such as viruses, microbes, fungi, plants or animals, leading to newly engineered organisms that do not occur naturally. SynBio also embarks on the development of molecular, chemical and physical frameworks for the creation of artificial life forms that go beyond the limits of Nature and may hold promising capacity for future applications on Earth or even extraterrestrial environments such as during space missions. 

The Topic Collection expects contributions from a wide range of SynBio areas, including those that explore and implement novel molecular tools for demonstrating functionalities in specific microbial or non-microbial species, and across a wider range of taxonomic boundaries. We seek articles that demonstrate a successful employment of new tools in either basic SynBio research and/or in real-world technical applications. Original research and review articles are welcome alike. We also warmly welcome opinion and vision papers. 

Keywords

  • Synthetic transcription factors and gene regulatory networks
  • Synthetic protein-based control elements
  • Optogenetics
  • DNA assembly, alternative nucleotides, codon expansion
  • Genome editing at multigene level
  • Genome minimization
  • Synthetic chromosomes, neochromosomes
  • Synthetic organelles
  • Synthetic multicellularity
  • Orthologous systems
  • Synthetic biology for non-canonical chassis organisms
  • Cell-free technologies
  • Tools for bottom-up creation of artificial life forms
  • Software tools for synthetic biology
  • Use of artificial intelligence in synthetic biology

Published Papers (2 papers)

Article

17 June 2024

Cytosine Deaminase-Assisted Mutator for Genome Evolution in Cupriavidus necator

Cupriavidus necator H16 has been intensively explored for its potential as a versatile microbial cell factory, especially for its CO2 fixation capability over the past few decades. However, rational metabolic engineering remains challenging in the construction of microbial cell factories with complex phenotypes due to the limited understanding of its metabolic regulatory network. To overcome this obstacle, laboratory adaptive evolution emerges as an alternative. In the present study, CAM (cytosine deaminase-assisted mutator) was established for the genome evolution of C. necator, addressing the issue of low mutation rates. By fusing cytosine deaminase with single-stranded binding proteins, CAM introduced genome-wide C-to-T mutations during DNA replication. This innovative approach could boost mutation rates, thereby expediting laboratory adaptive evolution. The applications of CAM were demonstrated in improving cell factory robustness and substrate utilization, with H2O2 resistance and ethylene glycol utilization as illustrative case studies. This genetic tool not only facilitates the development of efficient cell factories but also opens avenues for exploring the intricate phenotype-genotype relationships in C. necator.

Haojie Pan
Zhijiao Wang
Jiazhang Lian*

Article

26 August 2024

Delivery of Novel Replicating Vectors to Synechococcus sp. PCC 7002 Via Natural Transformation of Plasmid Multimers

In most cyanobacteria, genetic engineering efforts currently rely upon chromosomal integration; a time-consuming process due to their polyploid nature. To enhance strain construction, here we develop and characterize two novel replicating plasmids for use in Synechococcus sp. PCC 7002. Following an initial screen of plasmids comprising seven different origins of replication, two were found capable of replication: one based on the WVO1 broad host range plasmid and the other a shuttle vector derived from pCB2.4 from Synechocystis sp. PCC 6803. These were then used to construct a set of new replicating plasmids, which were shown to be both co-transformable and stably maintained in PCC 7002 at copy numbers between 7–16 and 0.6–1.4, respectively. Lastly, we demonstrate the importance of using multimeric plasmids during natural transformation of PCC 7002, with higher order multimers providing a 30-fold increase in transformation efficiency relative to monomeric plasmids. Useful considerations and methods for enhancing multimer content in plasmid samples are also presented.

Cody Kamoku
Cheyanna Cooper
Ashley Straub
Nathan Miller
David R.Nielsen*
TOP