Industrial systems biology and its impact on synthetic biology of yeast cell factories

2015 ◽  
Vol 113 (6) ◽  
pp. 1164-1170 ◽  
Author(s):  
Eugene Fletcher ◽  
Anastasia Krivoruchko ◽  
Jens Nielsen
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Yeast Cell ◽  
Industrial Systems ◽  
Cell Factories

scholarly journals A standard-enabled workflow for synthetic biology

2017 ◽  
Vol 45 (3) ◽  
pp. 793-803 ◽  
Author(s):  
Chris J. Myers ◽  
Jacob Beal ◽  
Thomas E. Gorochowski ◽  
Hiroyuki Kuwahara ◽  
Curtis Madsen ◽  
...  
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Markup Language ◽  
Design Tools ◽  
Data Standards ◽  
Data Repositories ◽  
Simulation Tools ◽  
Systems Biology Markup Language ◽  
Visualization Tools ◽  
Synthetic Biology Open Language

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

scholarly journals Development of oriC-Based Plasmids for Mesoplasma florum

2017 ◽  
Vol 83 (7) ◽  
Author(s):  
Dominick Matteau ◽  
Marie-Eve Pepin ◽  
Vincent Baby ◽  
Samuel Gauthier ◽  
Mélissa Arango Giraldo ◽  
...  
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Genetic Engineering ◽  
Genome Engineering ◽  
Antibiotic Resistance Genes ◽  
Viable Cell ◽  
Pathogenic Potential ◽  
Strong Basis ◽  
Content Type ◽  
Basic Biology

ABSTRACT The near-minimal bacterium Mesoplasma florum constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. However, the lack of genetic engineering tools for this microorganism has limited our capacity to understand its basic biology and modify its genome. To address this issue, we have evaluated the susceptibility of M. florum to common antibiotics and developed the first generation of artificial plasmids able to replicate in this bacterium. Selected regions of the predicted M. florum chromosomal origin of replication (oriC) were used to create different plasmid versions that were tested for their transformation frequency and stability. Using polyethylene glycol-mediated transformation, we observed that plasmids harboring both rpmH-dnaA and dnaA-dnaN intergenic regions, interspaced or not with a copy of the dnaA gene, resulted in a frequency of ∼4.1 × 10−6 transformants per viable cell and were stably maintained throughout multiple generations. In contrast, plasmids containing only one M. florum oriC intergenic region or the heterologous oriC region of Mycoplasma capricolum, Mycoplasma mycoides, or Spiroplasma citri failed to produce any detectable transformants. We also developed alternative transformation procedures based on electroporation and conjugation from Escherichia coli, reaching frequencies up to 7.87 × 10−6 and 8.44 × 10−7 transformants per viable cell, respectively. Finally, we demonstrated the functionality of antibiotic resistance genes active against tetracycline, puromycin, and spectinomycin/streptomycin in M. florum. Taken together, these valuable genetic tools will facilitate efforts toward building an M. florum-based near-minimal cellular chassis for synthetic biology. IMPORTANCE Mesoplasma florum constitutes an attractive model for systems biology and for the development of a simplified cell chassis in synthetic biology. M. florum is closely related to the mycoides cluster of mycoplasmas, which has become a model for whole-genome cloning, genome transplantation, and genome minimization. However, M. florum shows higher growth rates than other Mollicutes, has no known pathogenic potential, and possesses a significantly smaller genome that positions this species among some of the simplest free-living organisms. So far, the lack of genetic engineering tools has limited our capacity to understand the basic biology of M. florum in order to modify its genome. To address this issue, we have evaluated the susceptibility of M. florum to common antibiotics and developed the first artificial plasmids and transformation methods for this bacterium. This represents a strong basis for ongoing genome engineering efforts using this near-minimal microorganism.

scholarly journals Optimizing Oleaginous Yeast Cell Factories for Flavonoids and Hydroxylated Flavonoids Biosynthesis

2019 ◽  
Vol 8 (11) ◽  
pp. 2514-2523 ◽  
Author(s):  
Yongkun Lv ◽  
Monireh Marsafari ◽  
Mattheos Koffas ◽  
Jingwen Zhou ◽  
Peng Xu
Keyword(s):  
Yeast Cell ◽  
Oleaginous Yeast ◽  
Cell Factories ◽  
Flavonoids Biosynthesis

scholarly journals Metabolic engineering and synthetic biology employing Lactococcus lactis and Bacillus subtilis cell factories

2019 ◽  
Vol 59 ◽  
pp. 1-7 ◽  
Author(s):  
Amanda Y van Tilburg ◽  
Haojie Cao ◽  
Sjoerd B van der Meulen ◽  
Ana Solopova ◽  
Oscar P Kuipers
Keyword(s):  
Bacillus Subtilis ◽  
Metabolic Engineering ◽  
Synthetic Biology ◽  
Lactococcus Lactis ◽  
Subtilis Cell ◽  
Cell Factories

Systems Biology and Synthetic Biology

Crop Science ◽  
2010 ◽  
Vol 50 (2) ◽  
pp. 751-752
Author(s):  
S. K. Basu ◽  
A. Goyal
Keyword(s):  
Systems Biology ◽  
Synthetic Biology

Systems biology of the yeast cell cycle engine

2005 ◽  
pp. 305-324 ◽  
Author(s):  
Béla Novák ◽  
Katherine C. Chen ◽  
John J. Tyson
Keyword(s):  
Cell Cycle ◽  
Systems Biology ◽  
Yeast Cell ◽  
Yeast Cell Cycle
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