The Constructor: a web application optimizing cloning strategies based on modules from the registry of standard biological parts
- Matthijn C Hesselman†1,
- Jasper J Koehorst†1,
- Thijs Slijkhuis1,
- Dorett I Odoni1,
- Floor Hugenholtz1, 2 and
- MarkW J van Passel1, 3Email author
© Hesselman et al.; licensee BioMed Central Ltd. 2012
Received: 27 June 2012
Accepted: 2 September 2012
Published: 4 September 2012
Synthetic biology is an emerging field that combines molecular biology with engineering principles, which requires abstraction levels applied to a modular biological componentry. The Registry of Standard Biological Parts harbours such a repository of standardized parts, and thereby facilitates the combination of complex molecular modules to novel genetic circuits and devices. However, since finding the best parts for a pre-determined genetic design can be time consuming, we devised the Constructor, a web tool that recommends the smallest number of cloning steps for pre-designed circuits, and implements user-defined quality checks.
We present the Constructor (http://www.systemsbiology.nl/the_constructor) as a constructive web tool that simplifies the in silico assembly of pre-designed gene circuitries from standard parts, reducing both planning and subsequent cloning time.
KeywordsSynthetic Biology BioBrick parts Transcription units Genetic circuit
In recent years striking biological circuits have been fabricated, often resembling devices from electrical engineering. Examples include a genetic toggle switch, oscillators, a rewritable memory unit, but also more complex features such as a DNA-guided assembly line. These sorts of devices provide a starting ground for further engineering. However, next to the development of stable and streamlined microbial chassis[5–7], biological engineering requires accessible, modular, standard parts with reliable characteristics. Even though several repositories have been constructed, the most well-known library is the Registry of Standard Biological Parts (http://partsregistry.org). It is widely used in the international Genetically Engineered Machine (iGEM) competition aimed at teaching synthetic biology to undergraduate students,, but also outside of this competition. Users can design new devices from so-called BioBrick parts, the standard genetic parts, and are encouraged to submit new parts and devices to this Registry, which has grown to approximately 20,000 entries in 2012.
However, the vast number of entries in this Registry as well as the numerous parts with an unconfirmed status can frustrate the straightforward design of new genetic circuits. Furthermore, often several variants of parts and devices are available in the databases, which makes it difficult to find the shortest and most reliable strategy to clone new gene circuits. We found a need to automate querying the Registry in order to find the most straightforward cloning strategy for any pre-designed genetic circuit. This would simultaneously reduce time spent on finding appropriate parts in the Registry. We therefore set out to code the Constructor, a web-based application that recommends the smallest number of biological parts for a user-defined gene circuit, reducing both dry-lab and wet-lab time.
For each circuit arrangement, an SQL database containing information of ~20,000 parts (assembly standard 10 compatible) is queried. Since each circuit arrangement has a different sequence of genetic elements, each arrangement could collect a few arrangement-specific BioBrick parts. Through the combination of these specific BioBrick parts and the unique arrangement of genetic elements, some circuit arrangements could be constructed with fewer parts than others. An extra filter can be set if required on the availability, validity and quality of selected BioBrick parts by The Constructor.
Of all these possible combinations, the top three arrangements that could be assembled with the smallest number of BioBrick parts are shown as a recommendation to the user (Figure 1).
Validation of the Constructor by comparing five 2011 iGEM team cloning approaches to the recommendation by the Constructor
iGEM 2011 team
iGEM project title
# of TUs in the designed circuit
# of used Biobrick Parts
Processing time (min)
Used by team
Recommended by the Constructor
< 1 min
S.C.I.E.N.C.E. : Simple Code Interpretation Enabling Circuit in E. coli
i-ccdB: intelligent Control of Cell Density in Bacteria
< 1 min
Red Fluorescent Stress Sensor
< 1 min
The Synchroscillator: a Synchronized Oscillatory System
< 2 min
The Constructor facilitates the cloning strategy of complex pre-designed genetic circuits from elements of the Registry of Standard Biological Parts. Although the Constructor specifically focuses on this Registry, the same search algorithms for assembly optimization recommendations can be applied to other extensiveand well-defined parts libraries. Furthermore, theConstructor uses a straightforward transcriptional unit concept, which could be expanded by including different parts such as splicing signals. Finally, the web tool could be further optimised by suggesting alternatives for certain parts, like available reporter genes with another fluorescent ability, or different inducible promoters.
The Constructor is available athttp://www.systemsbiology.nl/the_Constructor. Help functions and a tutorial are provided with test cases of user defined gene circuits. All scripts are available from the authors upon request.
The authors gratefully acknowledge the input from both the 2011 and 2012 WageningenUR iGEM student teams, specifically Brendan Ryback for critically reading the manuscript. FH is funded by the Netherlands Consortium for Systems Biology (NCSB), which is part of the Netherlands Genomics Initiative and the Netherlands Organization for Scientific Research (NWO). MWJvP is funded by NWO via a VENI grant.
- Gardner TS, Cantor CR, Collins JJ: Construction of a genetic toggle switch in Escherichia coli. Nature 2000,403(6767):339-342. 10.1038/35002131View Article
- Elowitz MB, Leibler S: A synthetic oscillatory network of transcriptional regulators. Nature 2000,403(6767):335-338. 10.1038/35002125View Article
- Bonnet J, Subsoontorn P, Endy D: Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci USA 2012,109(23):8884-8889. 10.1073/pnas.1202344109View Article
- Conrado RJ, Wu GC, Boock JT, Xu H, Chen SY, Lebar T, Turnsek J, Tomsic N, Avbelj M, Gaber R, et al.: DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res 2011,40(4):1879-1889.View Article
- Leprince A, van Passel MW, Dos Santos VA: Streamlining genomes: toward the generation of simplified and stabilized microbial systems. Curr Opin Biotechnol 2012.
- Posfai G, Plunkett G, Feher T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, et al.: Emergent properties of reduced-genome Escherichia coli. Science 2006,312(5776):1044-1046. 10.1126/science.1126439View Article
- Leprince A, de Lorenzo V, Voller P, van Passel MW, Martins Dos Santos VA: Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida. Environ Microbiol 2012,14(6):1444-1453. 10.1111/j.1462-2920.2012.02730.xView Article
- Constante M, Grunberg R, Isalan M: A biobrick library for cloning custom eukaryotic plasmids. PLoS One 2011,6(8):e23685. 10.1371/journal.pone.0023685View Article
- Smolke CD: Building outside of the box: iGEM and the BioBricks Foundation. Nat Biotechnol 2009,27(12):1099-1102. 10.1038/nbt1209-1099View Article
- Hesselman MC, Odoni DI, Ryback BM, de Groot S, van Heck RG, Keijsers J, Kolkman P, Nieuwenhuijse D, van Nuland YM, Sebus E, et al.: A multi-platform flow device for microbial (co-) cultivation and microscopic analysis. PLoS One 2012,7(5):e36982. 10.1371/journal.pone.0036982View Article
- Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, Dewerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, et al.: A BioBrick compatible strategy for genetic modification of plants. J Biol Eng 2012,6(1):8. 10.1186/1754-1611-6-8View Article
- Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, Endy D: Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng 2009, 3: 4. 10.1186/1754-1611-3-4View Article
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.