Development of Next Generation Synthetic Biology Tools for Use in Streptomyces venezuelae

2016 ◽  
Vol 6 (1) ◽  
pp. 159-166 ◽  
Author(s):  
Ryan M. Phelan ◽  
Daniel Sachs ◽  
Shayne J. Petkiewicz ◽  
Jesus F. Barajas ◽  
Jacquelyn M. Blake-Hedges ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Next Generation ◽  
Streptomyces Venezuelae

scholarly journals Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology

2010 ◽  
Vol 2010 ◽  
pp. 1-18 ◽  
Author(s):  
Laura R. Jarboe ◽  
Xueli Zhang ◽  
Xuan Wang ◽  
Jonathan C. Moore ◽  
K. T. Shanmugam ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Synthetic Biology ◽  
Plant Material ◽  
Microbial Fermentation ◽  
Next Generation ◽  
Fermentation Conditions ◽  
Fermentative Production ◽  
Chemical Inhibitors ◽  
Fuels And Chemicals

Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.

Peptide–membrane interactions and biotechnology; enabling next-generation synthetic biology: general discussion

2021 ◽  
Author(s):  
Mibel Aguilar ◽  
Patricia Bassereau ◽  
Margarida Bastos ◽  
Paul Beales ◽  
Burkhard Bechinger ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Next Generation ◽  
Membrane Interactions

scholarly journals Computational Methods Enabling Next-Generation Bioprocesses

Processes ◽  
2019 ◽  
Vol 7 (4) ◽  
pp. 214 ◽  
Author(s):  
Julio R. Banga ◽  
Filippo Menolascina
Keyword(s):  
Synthetic Biology ◽  
Computational Methods ◽  
Next Generation ◽  
Biomolecular Networks

Synthetic biology—the engineering of cells to rewire the biomolecular networks inside them—has witnessed phenomenal progress [...]

scholarly journals Building biological foundries for next-generation synthetic biology

2015 ◽  
Vol 58 (7) ◽  
pp. 658-665 ◽  
Author(s):  
Ran Chao ◽  
YongBo Yuan ◽  
HuiMin Zhao
Keyword(s):  
Synthetic Biology ◽  
Next Generation

scholarly journals A modular, dynamic, DNA-based platform for regulating cargo distribution and transport between lipid domains

2021 ◽  
Author(s):  
Roger Rubio-Sánchez ◽  
Simone Eizagirre Barker ◽  
Michal Walczak ◽  
Pietro Cicuta ◽  
Lorenzo Di Michele
Keyword(s):  
Synthetic Biology ◽  
Cell Membranes ◽  
Cellular Systems ◽  
Lateral Distribution ◽  
Modular Approach ◽  
Lipid Domains ◽  
Dna Nanostructures ◽  
Next Generation ◽  
Cargo Transport ◽  
Program Partitioning

AbstractCell membranes regulate the distribution of biological machinery between phase-separated lipid domains to facilitate key processes including signalling and transport, which are among the life-like functionalities that bottom-up synthetic biology aims to replicate in artificial-cellular systems. Here, we introduce a modular approach to program partitioning of amphiphilic DNA nanostructures in co-existing lipid domains. Exploiting the tendency of different hydrophobic “anchors” to enrich different phases, we modulate the lateral distribution of our devices by rationally combining hydrophobes, and by changing nanostructure size and its topology. We demonstrate the functionality of our strategy with a bio-inspired DNA architecture, which dynamically undergoes ligand-induced reconfiguration to mediate cargo transport between domains via lateral re-distribution. Our findings pave the way to next-generation biomimetic platforms for sensing, transduction, and communication in synthetic cellular systems.

scholarly journals Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe

2016 ◽  
Vol 83 (5) ◽  
Author(s):  
Paul C. M. Fogg ◽  
Joshua A. Haley ◽  
W. Marshall Stark ◽  
Margaret C. M. Smith
Keyword(s):  
Synthetic Biology ◽  
High Efficiency ◽  
Dna Recombination ◽  
Streptomyces Venezuelae ◽  
Site Specific ◽  
Content Type ◽  
Wide Range ◽  
Serine Integrase

ABSTRACT Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In Streptomyces, most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for diverse synthetic biology applications. Here, we present the genome of a new Streptomyces phage, ϕJoe, and investigate the conditions for integration and excision of the ϕJoe genome. ϕJoe belongs to the largest Streptomyces phage cluster (R4-like) and encodes a serine integrase. The attB site from Streptomyces venezuelae was used efficiently by an integrating plasmid, pCMF92, constructed using the ϕJoe int-attP locus. The attB site for ϕJoe integrase was occupied in several Streptomyces genomes, including that of S. coelicolor, by a mobile element that varies in gene content and size between host species. Serine integrases require a phage-encoded recombination directionality factor (RDF) to activate the excision reaction. The ϕJoe RDF was identified, and its function was confirmed in vivo. Both the integrase and RDF were active in in vitro recombination assays. The ϕJoe site-specific recombination system is likely to be an important addition to the synthetic biology and genome engineering toolbox. IMPORTANCE Streptomyces spp. are prolific producers of secondary metabolites, including many clinically useful antibiotics. Bacteriophage-derived integrases are important tools for genetic engineering, as they enable integration of heterologous DNA into the Streptomyces chromosome with ease and high efficiency. Recently, researchers have been applying phage integrases for a variety of applications in synthetic biology, including rapid assembly of novel combinations of genes, biosensors, and biocomputing. An important requirement for optimal experimental design and predictability when using integrases, however, is the need for multiple enzymes with different specificities for their integration sites. In order to provide a broad platform of integrases, we identified and validated the integrase from a newly isolated Streptomyces phage, ϕJoe. ϕJoe integrase is active in vitro and in vivo. The specific recognition site for integration is present in a wide range of different actinobacteria, including Streptomyces venezuelae, an emerging model bacterium in Streptomyces research.

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