SBOL Visual: A Graphical Language for Genetic Designs

Quinn, Jacqueline; Cox, Robert Sidney; Adler, Aaron; Beal, Jacob; Bhatia, Swapnil; Cai, Yizhi; Chen, Joanna; Clancy, Kevin; Galdzicki, Michal; Hillson, Nathan J.; Novère, Nicolas Le; Maheshwari, Akshay J.; McLaughlin, James Alastair; Myers, Chris J.; Umesh, P; Pocock, Matthew; Rodriguez, Cesar; Soldatova, Larisa; Stan, Guy-Bart; Swainston, Neil; Wipat, Anil; Sauro, Herbert M.

doi:10.1371/journal.pbio.1002310

Cited by 89 publications

(91 citation statements)

References 32 publications

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“…The cut site is cleaved by the sgRNA–Cas9 complex, then repaired by donor DNA via HR. ( D ) The choice of parts can confer different biological activities, here represented using Synthetic Biology Open Language (SBOL) Visual glyphs (triangles, HR regions; half-circle, ribosome binding site; pentagons pointing to the right, protein-coding sequences; T, terminator; arrow, promoter; circle connected by dashed line, RNA stability element; circle connected by solid line, protein stability element) following established conventions (52). ( E ) By the choice of genetic parts, a gene of interest can be expressed under various expression programs (level, timing, subcellular localization).…”

Section: Resultsmentioning

confidence: 99%

A Cas9-based toolkit to program gene expression inSaccharomyces cerevisiae

et al. 2016

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Despite the extensive use of Saccharomyces cerevisiae as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locus and promoter selection, as well as protein localization and solubility. The toolkit includes 23 Cas9-sgRNA plasmids, 37 promoters of various strengths and temporal expression profiles, and 10 protein-localization, degradation and solubility tags. We facilitated the use of these parts via a web-based tool, that automates the generation of DNA fragments for integration. Our system builds upon existing gene editing methods in the thoroughness with which the parts are standardized and characterized, the types and number of parts available and the ease with which our methodology can be used to perform genetic edits in yeast. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important enzyme, taxadiene synthase (TXS). This approach enabled us to diagnose an issue with TXS solubility, the resolution of which yielded a 25-fold improvement in taxadiene production.

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Section: Resultsmentioning

confidence: 99%

A Cas9-based toolkit to program gene expression inSaccharomyces cerevisiae

et al. 2016

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“…In order to ensure an accurate description of the circuit and the construct as a whole, the digitalizer was formatted using the Synthetic Biology Open Language (Quinn et al , ; Madsen et al, ), an open standard for precise description of in silico biological designs and uploaded to the SynBioHub repository (McLaughlin et al , ). SBOL improves existing formats by allowing researchers to record more information on genetic circuits and share all its features in a machine‐readable form (Roehner et al , ).…”

Section: Resultsmentioning

confidence: 99%

Digitalizing heterologous gene expression in Gram‐negative bacteria with a portable ON/OFF module

Calles

Goñi-Moreno

Lorenzo

2019

Molecular Systems Biology

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While prokaryotic promoters controlled by signal‐responding regulators typically display a range of input/output ratios when exposed to cognate inducers, virtually no naturally occurring cases are known to have an OFF state of zero transcription—as ideally needed for synthetic circuits. To overcome this problem, we have modelled and implemented a simple digitalizer module that completely suppresses the basal level of otherwise strong promoters in such a way that expression in the absence of induction is entirely impeded. The circuit involves the interplay of a translation‐inhibitory sRNA with the translational coupling of the gene of interest to a repressor such as LacI. The digitalizer module was validated with the strong inducible promoters Pm (induced by XylS in the presence of benzoate) and PalkB (induced by AlkS/dicyclopropyl ketone) and shown to perform effectively in both Escherichia coli and the soil bacterium Pseudomonas putida. The distinct expression architecture allowed cloning and conditional expression of, e.g. colicin E3, one molecule of which per cell suffices to kill the host bacterium. Revertants that escaped ColE3 killing were not found in hosts devoid of insertion sequences, suggesting that mobile elements are a major source of circuit inactivation in vivo.

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“…Measurement tools included Polymerase Per Second (PoPS) [77], relative promoter unit (RPU) [47], relative mammalian promoter unit (RMPU) [78], functional composition tools included the expression operating unit (EOU) [45], and data exchange tools included Synthetic Biology Open Language (SBOL) [79], SBOL Visual (SBOLv) [80,81], and visual or electronic data sheets for biological parts and devices [82,83]. …”

Section: Methodsmentioning

confidence: 99%

A survey of enabling technologies in synthetic biology

Kahl

Endy

2013

J Biol Eng

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BackgroundRealizing constructive applications of synthetic biology requires continued development of enabling technologies as well as policies and practices to ensure these technologies remain accessible for research. Broadly defined, enabling technologies for synthetic biology include any reagent or method that, alone or in combination with associated technologies, provides the means to generate any new research tool or application. Because applications of synthetic biology likely will embody multiple patented inventions, it will be important to create structures for managing intellectual property rights that best promote continued innovation. Monitoring the enabling technologies of synthetic biology will facilitate the systematic investigation of property rights coupled to these technologies and help shape policies and practices that impact the use, regulation, patenting, and licensing of these technologies.ResultsWe conducted a survey among a self-identifying community of practitioners engaged in synthetic biology research to obtain their opinions and experiences with technologies that support the engineering of biological systems. Technologies widely used and considered enabling by survey participants included public and private registries of biological parts, standard methods for physical assembly of DNA constructs, genomic databases, software tools for search, alignment, analysis, and editing of DNA sequences, and commercial services for DNA synthesis and sequencing. Standards and methods supporting measurement, functional composition, and data exchange were less widely used though still considered enabling by a subset of survey participants.ConclusionsThe set of enabling technologies compiled from this survey provide insight into the many and varied technologies that support innovation in synthetic biology. Many of these technologies are widely accessible for use, either by virtue of being in the public domain or through legal tools such as non-exclusive licensing. Access to some patent protected technologies is less clear and use of these technologies may be subject to restrictions imposed by material transfer agreements or other contract terms. We expect the technologies considered enabling for synthetic biology to change as the field advances. By monitoring the enabling technologies of synthetic biology and addressing the policies and practices that impact their development and use, our hope is that the field will be better able to realize its full potential.

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SBOL Visual: A Graphical Language for Genetic Designs

Cited by 89 publications

References 32 publications

A Cas9-based toolkit to program gene expression inSaccharomyces cerevisiae

A Cas9-based toolkit to program gene expression inSaccharomyces cerevisiae

Digitalizing heterologous gene expression in Gram‐negative bacteria with a portable ON/OFF module

A survey of enabling technologies in synthetic biology

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