Engineering and modification of microbial chassis for systems and synthetic biology

Abstract

Engineering and modifying synthetic microbial chassis is one of the best ways not only to unravel the fundamental principles of life but also to enhance applications in the health, medicine, agricultural, veterinary, and food industries. The two primary strategies for constructing a microbial chassis are the top-down approach (genome reduction) and the bottom-up approach (genome synthesis). Research programs on this topic have been funded in several countries. The ‘Minimum genome factory’ (MGF) project was launched in 2001 in Japan with the goal of constructing microorganisms with smaller genomes for industrial use. One of the best examples of the results of this project is E. coli MGF-01, which has a reduced-genome size and exhibits better growth and higher threonine production characteristics than the parental strain [1]. The ‘cell factory’ project was carried out from 1998 to 2002 in the Fifth Framework Program of the EU (European Union), which tried to comprehensively understand microorganisms used in the application field. One of the outstanding results of this project was the elucidation of proteins secreted by Bacillus subtilis, which was summarized as the ‘secretome’ [2]. The GTL (Genomes to Life) program began in 2002 in the United States. In this program, researchers aimed to create artificial cells both in silico and in vitro, such as the successful design and synthesis of a minimal bacterial genome by John Craig Venter's group [3]. This review provides an update on recent advances in engineering, modification and application of synthetic microbial chassis, with particular emphasis on the value of learning about chassis as a way to better understand life and improve applications.

Engineering Biology to Construct Microbial Chassis for the Production of Difficult-to-Express Proteins

“…In addition, the design and synthesis of minimal genomes can be paralleled with re-engineering efforts to repurpose a cell to execute certain functions, including genome recoding to expedite production of unnatural polypeptides [29], and refactoring genes to make transcriptional and translational regulation more controllable [30]. Hosts of different microbial synthetic minimal genomes have been published to date (reviewed in [31]), with many harboring genetic and phenotypic traits to better house and support biosynthesis of heterologous proteins and commodity biomolecules.…”

Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals

“…Eventually, these efforts will build various genetic circuits capable of producing predictable outputs in response to various input signals through standardized components and modularization [ 11 , 12 , 13 , 14 , 15 ]. In recent years, various microorganisms have been engineered to maximize their productivity by establishing predictable systems through the development of synthetic promoters, untranslated regions (UTRs), evolved metabolic enzymes, genome-editing tools, regulatory circuits, and chassis platforms [ 11 , 12 , 16 , 17 , 18 , 19 , 20 , 21 , 22 ]. If these synthetic biology approaches are fully applied to acetogens, many of their limitations, such as the ones mentioned above, could be resolved.…”

Lox’d in translation: Contradictions in the nomenclature surrounding common lox site mutants and their implications in experiments

“…Live biotherapeutics have the potential to become key players in healthcare over the coming years. Engineered bacteria can be used as drug delivery systems, acting as a chassis from which therapeutic platforms can be plugged into to activate new functions (Ausländer et al, 2012;Chi et al, 2019;Claesen and Fischbach, 2015;Hörner et al, 2012;Vickers et al, 2010). A chassis will need to display growth characteristics and phenotypes that fulfil biosafety requirements, yet which may be foreign or counterproductive to wild-type cells.…”

“…As more and more advanced engineering tools become available to researchers, the scope for genome engineering has similarly increased in scale (Annaluru et al, 2015;Cameron et al, 2014;Hsu et al, 2014). One of the grand long-term goals in systems and synthetic biology is the generation of a minimal chassis cell (Chi et al, 2019;Sung et al, 2016). While the definition of a true 'minimal cell' is almost impossible to define (Choe et al, 2016;Glass et al, 2017;Koonin, 2000), a general consensus has emerged around a cell with a reduced genome, capable of completing a specific task with as few superfluous functions as possible (Hutchison et al, 2016;Juhas et al, 2011;Zhang, 2010).…”