scholarly journals Corynebacterium glutamicum Chassis C1*: Building and Testing a Novel Platform Host for Synthetic Biology and Industrial Biotechnology

2017 ◽  
Vol 7 (1) ◽  
pp. 132-144 ◽  
Author(s):  
Meike Baumgart ◽  
Simon Unthan ◽  
Ramona Kloß ◽  
Andreas Radek ◽  
Tino Polen ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Corynebacterium Glutamicum ◽  
Industrial Biotechnology

Synthetic biology platform of CoryneBrick vectors for gene expression in Corynebacterium glutamicum and its application to xylose utilization

2014 ◽  
Vol 98 (13) ◽  
pp. 5991-6002 ◽  
Author(s):  
Min-Kyoung Kang ◽  
Jungseok Lee ◽  
Youngsoon Um ◽  
Taek Soon Lee ◽  
Michael Bott ◽  
...  
Keyword(s):  
Gene Expression ◽  
Synthetic Biology ◽  
Corynebacterium Glutamicum ◽  
Xylose Utilization

scholarly journals Construction of a Prophage-Free Variant of Corynebacterium glutamicum ATCC 13032 for Use as a Platform Strain for Basic Research and Industrial Biotechnology

2013 ◽  
Vol 79 (19) ◽  
pp. 6006-6015 ◽  
Author(s):  
Meike Baumgart ◽  
Simon Unthan ◽  
Christian Rückert ◽  
Jasintha Sivalingam ◽  
Alexander Grünberger ◽  
...  
Keyword(s):  
Corynebacterium Glutamicum ◽  
Fluorescent Protein ◽  
Yellow Fluorescent Protein ◽  
Stress Conditions ◽  
Phenotypic Characterization ◽  
Industrial Biotechnology ◽  
Plasmid Copy ◽  
Enhanced Yellow Fluorescent Protein ◽  
Modification System ◽  
Content Type

ABSTRACTThe activity of bacteriophages and phage-related mobile elements is a major source for genome rearrangements and genetic instability of their bacterial hosts. The genome of the industrial amino acid producerCorynebacterium glutamicumATCC 13032 contains three prophages (CGP1, CGP2, and CGP3) of so far unknown functionality. Several phage genes are regularly expressed, and the large prophage CGP3 (∼190 kbp) has recently been shown to be induced under certain stress conditions. Here, we present the construction of MB001, a prophage-free variant ofC. glutamicumATCC 13032 with a 6% reduced genome. This strain does not show any unfavorable properties during extensive phenotypic characterization under various standard and stress conditions. As expected, we observed improved growth and fitness of MB001 under SOS-response-inducing conditions that trigger CGP3 induction in the wild-type strain. Further studies revealed that MB001 has a significantly increased transformation efficiency and produced about 30% more of the heterologous model protein enhanced yellow fluorescent protein (eYFP), presumably as a consequence of an increased plasmid copy number. These effects were attributed to the loss of the restriction-modification system (cg1996-cg1998) located within CGP3. The deletion of the prophages without any negative effect results in a novel platform strain for metabolic engineering and represents a useful step toward the construction of aC. glutamicumchassis genome of strain ATCC 13032 for biotechnological applications and synthetic biology.

scholarly journals Halomonas as a chassis

2021 ◽  
Author(s):  
Jian-Wen Ye ◽  
Guo-Qiang Chen
Keyword(s):  
Synthetic Biology ◽  
Rapid Development ◽  
High Energy ◽  
Strain Engineering ◽  
Current Status ◽  
Industrial Biotechnology ◽  
Cell Factories ◽  
Energy Consuming ◽  
Significant Cost Reduction ◽  
Process Complexity

Abstract With the rapid development of systems and synthetic biology, the non-model bacteria, Halomonas spp., have been developed recently to become a cost-competitive platform for producing a variety of products including polyesters, chemicals and proteins owing to their contamination resistance and ability of high cell density growth at alkaline pH and high salt concentration. These salt-loving microbes can partially solve the challenges of current industrial biotechnology (CIB) which requires high energy-consuming sterilization to prevent contamination as CIB is based on traditional chassis, typically, Escherichia coli, Bacillus subtilis, Pseudomonas putida and Corynebacterium glutamicum. The advantages and current status of Halomonas spp. including their molecular biology and metabolic engineering approaches as well as their applications are reviewed here. Moreover, a systematic strain engineering streamline, including product-based host development, genetic parts mining, static and dynamic optimization of modularized pathways and bioprocess-inspired cell engineering are summarized. All of these developments result in the term called next-generation industrial biotechnology (NGIB). Increasing efforts are made to develop their versatile cell factories powered by synthetic biology to demonstrate a new biomanufacturing strategy under open and continuous processes with significant cost-reduction on process complexity, energy, substrates and fresh water consumption.

scholarly journals RetroPath2.0: a retrosynthesis workflow for metabolic engineers

2017 ◽  
Author(s):  
Baudoin Delépine ◽  
Thomas Duigou ◽  
Pablo Carbonell ◽  
Jean-Loup Faulon
Keyword(s):  
Synthetic Biology ◽  
Open Source ◽  
Computer Aided Design ◽  
Reaction Network ◽  
Ease Of Use ◽  
Chemical Diversity ◽  
Industrial Biotechnology ◽  
List Type ◽  
Enzyme Promiscuity ◽  
Main Challenge

AbstractSynthetic biology applied to industrial biotechnology is transforming the way we produce chemicals. However, despite advances in the scale and scope of metabolic engineering, the bioproduction process still remains costly. In order to expand the chemical repertoire for the production of next generation compounds, a major engineering biology effort is required in the development of novel design tools that target chemical diversity through rapid and predictable protocols. Addressing that goal involves retrosynthesis approaches that explore the chemical biosynthetic space. However, the complexity associated with the large combinatorial retrosynthesis design space has often been recognized as the main challenge hindering the approach. Here, we provide RetroPath2.0, an automated open source workflow for retrosynthesis based on generalized reaction rules that perform the retrosynthesis search from chassis to target through an efficient and well-controlled protocol. Its easiness of use and the versatility of its applications make of this tool a valuable addition into the biological engineer bench desk. We show through several examples the application of the workflow to biotechnological relevant problems, including the identification of alternative biosynthetic routes through enzyme promiscuity; or the development of biosensors. We demonstrate in that way the ability of the workflow to streamline retrosynthesis pathway design and its major role in reshaping the design, build, test and learn pipeline by driving the process toward the objective of optimizing bioproduction. The RetroPath2.0 workflow is built using tools developed by the bioinformatics and cheminformatics community, because it is open source we anticipate community contributions will likely expand further the features of the workflow.HighlightsState-of-the-art Computer-Aided Design retrosynthesis solutions lack open source and ease of useWe propose RetroPath2.0 a modular and open-source workflow to perform retrosynthesisRetroPath2.0 computes reaction network between Source and Sink sets of compoundsRetroPath2.0 is distributed as a KNIME workflow for desktop computersRetroPath2.0 is ready-for-use and distributed with reaction rulesFundingThis work was supported by the French National Research Agency [ANR-15-CE1-0008], the Biotechnology and Biological Sciences Research Council, Centre for synthetic biology of fine and speciality chemicals [BB/M017702/1]; Synthetic Biology Applications for Protective Materials [EP/N025504/1], and GIP Genopole.

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