Engineering BioBrick vectors from BioBrick parts

By Reshma P. Shetty, Drew Endy, Thomas F. Knight. Journal of Biological Engineering, 2008

797 citations recorded by the source corpus.

BackgroundThe underlying goal of synthetic biology is to make the process of engineering biological systems easier. Recent work has focused on defining and developing standard biological parts. The technical standard that has gained the most traction in the synthetic biology community is the BioBrick standard for physical composition of genetic parts. Parts that conform to the BioBrick assembly standard are BioBrick standard biological parts. To date, over 2,000 BioBrick parts have been contributed to, and are available from, the Registry of Standard Biological Parts.ResultsHere we extended the same advantages of BioBrick standard biological parts to the plasmid-based vectors that are used to provide and propagate BioBrick parts. We developed a process for engineering BioBrick vectors from BioBrick parts. We designed a new set of BioBrick parts that encode many useful vector functions. We combined the new parts to make a BioBrick base vector that facilitates BioBrick vector construction. We demonstrated the utility of the process by constructing seven new BioBrick vectors. We also successfully used the resulting vectors to assemble and propagate other BioBrick standard biological parts.ConclusionWe extended the principles of part reuse and standardization to BioBrick vectors. As a result, myriad new BioBrick vectors can be readily produced from all existing and newly designed BioBrick parts. We invite the synthetic biology community to (1) use the process to make and share new BioBrick vectors; (2) expand the current collection of BioBrick vector parts; and (3) characterize and improve the available collection of BioBrick vector parts.

Subfields: Astronomy and Astrophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9095e263ff04548cac9417797747ca1402a2d96a

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Citations in the corpus

A Synthetic Genetic Edge Detection Program (2009, background): “All of the circuit plasmids are based on the pSB4A3 BioBrick vector backbone (Shetty et al., 2008), which contains the pSC101* origin of replication and Amp.”
BglBricks: A flexible standard for biological part assembly (2010, background): “Over 2,000 basic parts that conform to this standard have been described, and they have been used in the construction of a wide range of genetic circuits and biosynthetic devices [5-8].”
Measuring the activity of BioBrick promoters using an in vivo reference standard (2009, methodology): “The process for inserting a promoter upstream of the GFP reporter device is based on three-antibiotic BioBrick standard assembly [25], and is outlined in the instructions included with the kit (Additional file 1 [Supplementary Box 1]).”
Synthetic protein scaffolds provide modular control over metabolic flux (2009, methodology): “Scaffolds were built by tethering multiple protein-protein interaction domains via nine-amino acid poly-GLY-SER linkers using the BioBrick b (BBb) strateg”
Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System (2015, methodology): “pTargetF-kefB-yjcS consisting of double sgRNAs was achieved by BioBrick cloning with BamHI and BglII (39).”
CRISPR interference (CRISPRi) for sequence-specific control of gene expression (2013, methodology): “1b,c and 5) 42 .”
The second wave of synthetic biology: from modules to systems (2009, background): “Efforts are underway to characterize and standardize parts and small modules by measuring, manipulating and matching their input–output threshold”
j5 DNA assembly design automation software. (2012, methodology): “These methods can offer benefits over BioBrick-style assembly, 16,17 for which 6 base pair scars result at every assembly junction and only two fragments can be assembled per step.”
The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes (2012, background): “One example is the proposition of the BioBrick standard (22), which allows for the successive incorporation of DNA parts that are retrieved from a formatted repository of functional sequences to a cognate plasmid scaffold.”
Computational protein design enables a novel one-carbon assimilation pathway (2015, methodology): “0 and subcloned by digestion with EcoRI and PstI (NEB) and ligation with T4 DNA ligase (Promega) into Biobrick vectors to give pSB1A3 Des1-yDHAK (constitutive promoter) and pSB3K3 ecACS_ecACDH (lac inducible promoter)(2).”
Design, construction and characterization of a set of insulated bacterial promoters (2010, methodology): “With the exception of assays for promoter function on the chromosome, all experiments utilized plasmid pSB3C5 and the construct of interest was cloned via standard procedures between the BioBrick cloning sites (35).”
Advancing Crop Transformation in the Era of Genome Editing[OPEN] (2016, background): “For example, “Phytobricks,” similar to the Biobricks used in bacterial synthetic biology (Shetty et al., 2008), might be designed to carry swappable selectable markers, promoters, 39 untranslated regions, and insulators.”