BglBricks: A flexible standard for biological part assembly

Anderson, J. Christopher; Dueber, John E.; Leguia, Mariana; Wu, Gabriel C.; Goler, Jonathan A.; Arkin, Adam P.; Keasling, Jay D.

doi:10.1186/1754-1611-4-1

Title: BglBricks: A flexible standard for biological part assembly

Journal Article · 20 January 2010 · Journal of Biological Engineering

DOI: https://doi.org/10.1186/1754-1611-4-1 · OSTI ID:1629615

Anderson, J. Christopher ^[1]; Dueber, John E. ^[2]; Leguia, Mariana ^[2]; Wu, Gabriel C. ^[2]; Goler, Jonathan A. ^[3]; Arkin, Adam P. ^[2]; Keasling, Jay D. ^[4]

Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; Univ. of California, Berkeley, CA (United States). QB3: California Inst. for Quantitative Biological Research; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; Univ. of California, Berkeley, CA (United States). Synthetic Biology Engineering Research Center; DOE/OSTI
Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; Univ. of California, Berkeley, CA (United States). QB3: California Inst. for Quantitative Biological Research; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; Univ. of California, Berkeley, CA (United States). Synthetic Biology Engineering Research Center
Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; Univ. of California, Berkeley, CA (United States). Synthetic Biology Engineering Research Center; Joint BioEnergy Institute (JBEI), Emeryville, CA (United States)
Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; Univ. of California, Berkeley, CA (United States). QB3: California Inst. for Quantitative Biological Research; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; Univ. of California, Berkeley, CA (United States). Synthetic Biology Engineering Research Center. Dept. of Chemical Engineering; Joint BioEnergy Institute (JBEI), Emeryville, CA (United States)

Background: Standard biological parts, such as BioBricks™ parts, provide the foundation for a new engineering discipline that enables the design and construction of synthetic biological systems with a variety of applications in bioenergy, new materials, therapeutics, and environmental remediation. Although the original BioBricks™ assembly standard has found widespread use, it has several shortcomings that limit its range of potential applications. In particular, the system is not suitable for the construction of protein fusions due to an unfavorable scar sequence that encodes an in-frame stop codon. Results: Here, we present a similar but new composition standard, called BglBricks, that addresses the scar translation issue associated with the original standard. The new system employs BglII and BamHI restriction enzymes, robust cutters with an extensive history of use, and results in a 6-nucleotide scar sequence encoding glycine-serine, an innocuous peptide linker in most protein fusion applications. We demonstrate the utility of the new standard in three distinct applications, including the construction of constitutively active gene expression devices with a wide range of expression profiles, the construction of chimeric, multi-domain protein fusions, and the targeted integration of functional DNA sequences into specific loci of the E. coli genome. Conclusions: The BglBrick standard provides a new, more flexible platform from which to generate standard biological parts and automate DNA assembly. Work on BglBrick assembly reactions, as well as on the development of automation and bioinformatics tools, is currently underway. These tools will provide a foundation from which to transform genetic engineering from a technically intensive art into a purely design-based discipline.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Science Foundation (NSF)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1629615

Journal Information:: Journal of Biological Engineering, Journal Name: Journal of Biological Engineering Journal Issue: 1 Vol. 4; ISSN 1754-1611

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (19)

PCR-mediated recombination and mutagenesis: SOEing together tailor-made genes Horton, Robert M. Molecular Biotechnology, Vol. 3, Issue 2 https://doi.org/10.1007/bf02789105	journal	April 1995
A cell-based screening method for specifically detecting kinase activity Suda, Mikiya; Ishii, Tsuyoshi; Sootome, Hiroshi Analytical and Bioanalytical Chemistry, Vol. 390, Issue 1 https://doi.org/10.1007/s00216-007-1685-1	journal	November 2007
Quantitative Understanding of the Energy Transfer between Fluorescent Proteins Connected via Flexible Peptide Linkers Evers, Toon H.; van Dongen, Elisabeth M. W. M.; Faesen, Alex C. Biochemistry, Vol. 45, Issue 44 https://doi.org/10.1021/bi061288t	journal	November 2006
Foundations for engineering biology Endy, Drew Nature, Vol. 438, Issue 7067 https://doi.org/10.1038/nature04342	journal	November 2005
Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors Yeh, Brian J.; Rutigliano, Robert J.; Deb, Anrica Nature, Vol. 447, Issue 7144 https://doi.org/10.1038/nature05851	journal	May 2007
Refinement and standardization of synthetic biological parts and devices Canton, Barry; Labno, Anna; Endy, Drew Nature Biotechnology, Vol. 26, Issue 7, p. 787-793 https://doi.org/10.1038/nbt1413	journal	July 2008
Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC Li, Mamie Z.; Elledge, Stephen J. Nature Methods, Vol. 4, Issue 3 https://doi.org/10.1038/nmeth1010	journal	February 2007
Bottom-up genome assembly using the Bacillus subtilis genome vector Itaya, Mitsuhiro; Fujita, Kyoko; Kuroki, Azusa Nature Methods, Vol. 5, Issue 1 https://doi.org/10.1038/nmeth1143	journal	December 2007
Machine learning discovery of missing links that mediate alternative branches to plant alkaloids Vavricka, Christopher J.; Takahashi, Shunsuke; Watanabe, Naoki Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-28883-8	journal	March 2022
The iGEM competition: building with biology Brown, J. IET Synthetic Biology, Vol. 1, Issue 1 https://doi.org/10.1049/iet-stb:20079020	journal	June 2007
Assembly of Cell Regulatory Systems Through Protein Interaction Domains Pawson, T. Science, Vol. 300, Issue 5618 https://doi.org/10.1126/science.1083653	journal	April 2003
Reprogramming Control of an Allosteric Signaling Switch Through Modular Recombination Dueber, J. E. Science, Vol. 301, Issue 5641 https://doi.org/10.1126/science.1085945	journal	September 2003
Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics Bashor, C. J.; Helman, N. C.; Yan, S. Science, Vol. 319, Issue 5869 https://doi.org/10.1126/science.1151153	journal	March 2008
Chromosomal insertion sites for phages and plasmids Campbell, A. M. Journal of Bacteriology, Vol. 174, Issue 23 https://doi.org/10.1128/jb.174.23.7495-7499.1992	journal	December 1992
Conditional-Replication, Integration, Excision, and Retrieval Plasmid-Host Systems for Gene Structure-Function Studies of Bacteria Haldimann, A.; Wanner, B. L. Journal of Bacteriology, Vol. 183, Issue 21 https://doi.org/10.1128/jb.183.21.6384-6393.2001	journal	November 2001
Applications of the Saccharomyces cerevisiae Flp-FRT System in Bacterial Genetics Schweizer, Herbert P. Microbial Physiology, Vol. 5, Issue 2 https://doi.org/10.1159/000069976	journal	January 2003
Engineering BioBrick vectors from BioBrick parts Shetty, Reshma P.; Endy, Drew; Knight, Thomas F. Journal of Biological Engineering, Vol. 2, Article No. 5 https://doi.org/10.1186/1754-1611-2-5	journal	January 2008
Targeted Development of Registries of Biological Parts Peccoud, Jean; Blauvelt, Megan F.; Cai, Yizhi PLoS ONE, Vol. 3, Issue 7 https://doi.org/10.1371/journal.pone.0002671	journal	July 2008
Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes Engler, Carola; Gruetzner, Ramona; Kandzia, Romy PLoS ONE, Vol. 4, Issue 5 https://doi.org/10.1371/journal.pone.0005553	journal	May 2009

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Queueing up for enzymatic processing: correlated signaling through coupled degradation Cookson, Natalie A.; Mather, William H.; Danino, Tal Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.94	journal	January 2011
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Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro Yacoby, I.; Pochekailov, S.; Toporik, H. Proceedings of the National Academy of Sciences, Vol. 108, Issue 23 https://doi.org/10.1073/pnas.1103659108	journal	May 2011
Engineering robust control of two-component system phosphotransfer using modular scaffolds Whitaker, W. R.; Davis, S. A.; Arkin, A. P. Proceedings of the National Academy of Sciences, Vol. 109, Issue 44 https://doi.org/10.1073/pnas.1209230109	journal	October 2012
Review of Nanobiopolymers for Controlled Drug Delivery Saranya, S.; Radha, K. V. Polymer-Plastics Technology and Engineering, Vol. 53, Issue 15 https://doi.org/10.1080/03602559.2014.915035	journal	September 2014
Standardization in synthetic biology: an engineering discipline coming of age Decoene, Thomas; De Paepe, Brecht; Maertens, Jo Critical Reviews in Biotechnology, Vol. 38, Issue 5 https://doi.org/10.1080/07388551.2017.1380600	journal	September 2017
Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities DePaoli, Henrique C.; Borland, Anne M.; Tuskan, Gerald A. Journal of Experimental Botany, Vol. 65, Issue 13, p. 3381-3393 https://doi.org/10.1093/jxb/eru038	journal	February 2014
The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes Silva-Rocha, Rafael; Martínez-García, Esteban; Calles, Belén Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1119	journal	November 2012
High-throughput, cost-effective verification of structural DNA assembly Dharmadi, Yandi; Patel, Kedar; Shapland, Elaine Nucleic Acids Research, Vol. 42, Issue 4 https://doi.org/10.1093/nar/gkt1088	journal	November 2013
Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination Colloms, Sean D.; Merrick, Christine A.; Olorunniji, Femi J. Nucleic Acids Research, Vol. 42, Issue 4 https://doi.org/10.1093/nar/gkt1101	journal	November 2013
Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly Torella, Joseph P.; Boehm, Christian R.; Lienert, Florian Nucleic Acids Research, Vol. 42, Issue 1 https://doi.org/10.1093/nar/gkt860	journal	September 2013
One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy Casini, Arturo; MacDonald, James T.; Jonghe, Joachim De Nucleic Acids Research, Vol. 42, Issue 1 https://doi.org/10.1093/nar/gkt915	journal	October 2013
Broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria Taton, Arnaud; Unglaub, Federico; Wright, Nicole E. Nucleic Acids Research, Vol. 42, Issue 17 https://doi.org/10.1093/nar/gku673	journal	July 2014
CasHRA (Cas9-facilitated Homologous Recombination Assembly) method of constructing megabase-sized DNA Zhou, Jianting; Wu, Ronghai; Xue, Xiaoli Nucleic Acids Research, Vol. 44, Issue 14 https://doi.org/10.1093/nar/gkw475	journal	May 2016
De novo design and synthesis of a 30-cistron translation-factor module Shepherd, Tyson R.; Du, Liping; Liljeruhm, Josefine Nucleic Acids Research, Vol. 45, Issue 18 https://doi.org/10.1093/nar/gkx753	journal	September 2017
Start-Stop Assembly: a functionally scarless DNA assembly system optimized for metabolic engineering Taylor, George M.; Mordaka, Paweł M.; Heap, John T. Nucleic Acids Research, Vol. 47, Issue 3 https://doi.org/10.1093/nar/gky1182	journal	November 2018
Abstractions for DNA circuit design Lakin, Matthew R.; Youssef, Simon; Cardelli, Luca Journal of The Royal Society Interface, Vol. 9, Issue 68 https://doi.org/10.1098/rsif.2011.0343	journal	July 2011
Harnessing a Novel P450 Fatty Acid Decarboxylase from Macrococcus caseolyticus for Microbial Biosynthesis of Odd Chain Terminal Alkenes Lee, Jong-won; Niraula, Narayan P.; Trinh, Cong T. Metabolic Engineering Communications https://doi.org/10.1101/255539	posted_content	January 2018
CozEa and CozEb play overlapping and essential roles in controlling cell division in Staphylococcus aureus Stamsås, Gro Anita; Myrbråten, Ine Storaker; Straume, Daniel bioRxiv https://doi.org/10.1101/256560	posted_content	January 2018
Dual pathway for metabolic engineering of E. coli metabolism to produce the highly valuable hydroxytyrosol Trantas, Emmanouil; Navakoudis, Eleni; Pavlidis, Theofilos bioRxiv https://doi.org/10.1101/536458	posted_content	January 2019
Three new integration vectors and fluorescent proteins for use in the opportunistic human pathogen Streptococcus pneumoniae Keller, Lance E.; Rueff, Anne-Stéphanie; Kurushima, Jun bioRxiv https://doi.org/10.1101/594697	posted_content	January 2019
Synthetic gene regulatory networks in the opportunistic human pathogen Streptococcus pneumoniae Sorg, Robin A.; Gallay, Clement; Veening, Jan-Willem bioRxiv https://doi.org/10.1101/834689	posted_content	January 2019
The art of vector engineering: towards the construction of next-generation genetic tools Nora, Luísa Czamanski; Westmann, Cauã Antunes; Martins-Santana, Leonardo Microbial Biotechnology, Vol. 12, Issue 1 https://doi.org/10.1111/1751-7915.13318	journal	September 2018
Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast Oud, Bart; Maris, Antonius J. A.; Daran, Jean-Marc FEMS Yeast Research, Vol. 12, Issue 2 https://doi.org/10.1111/j.1567-1364.2011.00776.x	journal	January 2012
CozEa and CozEb play overlapping and essential roles in controlling cell division in Staphylococcus aureus Stamsås, Gro Anita; Myrbråten, Ine Storaker; Straume, Daniel Molecular Microbiology, Vol. 109, Issue 5 https://doi.org/10.1111/mmi.13999	journal	August 2018
Standards for plant synthetic biology: a common syntax for exchange of DNA parts Patron, Nicola J.; Orzaez, Diego; Marillonnet, Sylvestre New Phytologist, Vol. 208, Issue 1 https://doi.org/10.1111/nph.13532	journal	July 2015
Modular Engineering of l-Tyrosine Production in Escherichia coli Juminaga, Darmawi; Baidoo, Edward E. K.; Redding-Johanson, Alyssa M. Applied and Environmental Microbiology, Vol. 78, Issue 1, p. 89-98 https://doi.org/10.1128/aem.06017-11	journal	October 2011
CRISPR Interference for Rapid Knockdown of Essential Cell Cycle Genes in Lactobacillus plantarum Myrbråten, Ine Storaker; Wiull, Kamilla; Salehian, Zhian mSphere, Vol. 4, Issue 2 https://doi.org/10.1128/msphere.00007-19	journal	April 2019
Engineering Escherichia coli for succinate production from hemicellulose via consolidated bioprocessing Zheng, Zongbao; Chen, Tao; Zhao, Meina Microbial Cell Factories, Vol. 11, Issue 1 https://doi.org/10.1186/1475-2859-11-37	journal	January 2012
Introduction of customized inserts for streamlined assembly and optimization of BioBrick synthetic genetic circuits Norville, Julie E.; Derda, Ratmir; Gupta, Saurabh Journal of Biological Engineering, Vol. 4, Issue 1 https://doi.org/10.1186/1754-1611-4-17	journal	December 2010
Rapid optimization of gene dosage in E. coli using DIAL strains Kittleson, Joshua T.; Cheung, Sherine; Anderson, J. Christopher Journal of Biological Engineering, Vol. 5, Issue 1 https://doi.org/10.1186/1754-1611-5-10	journal	January 2011
BglBrick vectors and datasheets: A synthetic biology platform for gene expression Lee, Taek; Krupa, Rachel A.; Zhang, Fuzhong Journal of Biological Engineering, Vol. 5, Issue 1 https://doi.org/10.1186/1754-1611-5-12	journal	January 2011
A standard vector for the chromosomal integration and characterization of BioBrick™ parts in Escherichia coli Zucca, Susanna; Pasotti, Lorenzo; Politi, Nicolò Journal of Biological Engineering, Vol. 7, Issue 1 https://doi.org/10.1186/1754-1611-7-12	journal	January 2013
Secretion of polyhydroxybutyrate in Escherichia coli using a synthetic biological engineering approach Rahman, Asif; Linton, Elisabeth; Hatch, Alex D. Journal of Biological Engineering, Vol. 7, Issue 1 https://doi.org/10.1186/1754-1611-7-24	journal	January 2013
Combinatorial engineering of hybrid mevalonate pathways in Escherichia coli for protoilludene production Yang, Liyang; Wang, Chonglong; Zhou, Jia Microbial Cell Factories, Vol. 15, Issue 1 https://doi.org/10.1186/s12934-016-0409-7	journal	January 2016
Combinatorial approach for improved cyanidin 3-O-glucoside production in Escherichia coli Shrestha, Biplav; Pandey, Ramesh Prasad; Darsandhari, Sumangala Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1056-6	journal	January 2019
Enhanced production of styrene by engineered Escherichia coli and in situ product recovery (ISPR) with an organic solvent Lee, Kyungsoo; Bang, Hyun Bae; Lee, Yoon Hyeok Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1129-6	journal	May 2019
A seamless and iterative DNA assembly method named PS-Brick and its assisted metabolic engineering for threonine and 1-propanol production Liu, Shuwen; Xiao, Haihan; Zhang, Fangfang Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1520-x	journal	July 2019
A Modular Cloning System for Standardized Assembly of Multigene Constructs Weber, Ernst; Engler, Carola; Gruetzner, Ramona PLoS ONE, Vol. 6, Issue 2 https://doi.org/10.1371/journal.pone.0016765	journal	February 2011
GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules Sarrion-Perdigones, Alejandro; Falconi, Erica Elvira; Zandalinas, Sara I. PLoS ONE, Vol. 6, Issue 7, Article No. e21622 https://doi.org/10.1371/journal.pone.0021622	journal	July 2011
Bottom-Up Engineering of Biological Systems through Standard Bricks: A Modularity Study on Basic Parts and Devices Pasotti, Lorenzo; Politi, Nicolò; Zucca, Susanna PLoS ONE, Vol. 7, Issue 7 https://doi.org/10.1371/journal.pone.0039407	journal	July 2012
Parallel In Vivo DNA Assembly by Recombination: Experimental Demonstration and Theoretical Approaches Shi, Zhenyu; Wedd, Anthony G.; Gras, Sally L. PLoS ONE, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pone.0056854	journal	February 2013
MXS-Chaining: A Highly Efficient Cloning Platform for Imaging and Flow Cytometry Approaches in Mammalian Systems Sladitschek, Hanna L.; Neveu, Pierre A. PLOS ONE, Vol. 10, Issue 4 https://doi.org/10.1371/journal.pone.0124958	journal	April 2015
Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly Andreou, Andreas I.; Nakayama, Naomi PLOS ONE, Vol. 13, Issue 1 https://doi.org/10.1371/journal.pone.0189892	journal	January 2018
Standards for plant synthetic biology: a common syntax for exchange of DNA parts. Patron, Nicola J.; Orzaez, Diego; Marillonnet, Sylvestre Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.22831	text	January 2015
Peptide vectors for gene delivery: from single peptides to multifunctional peptide nanocarriers Raad, Markus de; Teunissen, Erik A.; Mastrobattista, Enrico Nanomedicine, Vol. 9, Issue 14 https://doi.org/10.2217/nnm.14.90	journal	July 2014
Developments in the Tools and Methodologies of Synthetic Biology Kelwick, Richard; MacDonald, James T.; Webb, Alexander J. Frontiers in Bioengineering and Biotechnology, Vol. 2 https://doi.org/10.3389/fbioe.2014.00060	journal	November 2014
Production of Fatty Acid-Derived Valuable Chemicals in Synthetic Microbes Yu, Ai-Qun; Pratomo Juwono, Nina Kurniasih; Leong, Susanna Su Jan Frontiers in Bioengineering and Biotechnology, Vol. 2 https://doi.org/10.3389/fbioe.2014.00078	journal	December 2014
Analytics for Metabolic Engineering Petzold, Christopher J.; Chan, Leanne Jade G.; Nhan, Melissa Frontiers in Bioengineering and Biotechnology, Vol. 3 https://doi.org/10.3389/fbioe.2015.00135	journal	September 2015
Three New Integration Vectors and Fluorescent Proteins for Use in the Opportunistic Human Pathogen Streptococcus pneumoniae Keller, Lance E.; Rueff, Anne-Stéphanie; Kurushima, Jun Genes, Vol. 10, Issue 5 https://doi.org/10.3390/genes10050394	journal	May 2019
Combinatorial engineering for heterologous gene expression Zwick, Friederike; Lale, Rahmi; Valla, Svein Bioengineered, Vol. 4, Issue 6 https://doi.org/10.4161/bioe.24703	journal	November 2013
Finding and defining the natural automata acting in living plants: Toward the synthetic biology for robotics and informatics in vivo Kawano, Tomonori; Bouteau, François; Mancuso, Stefano Communicative & Integrative Biology, Vol. 5, Issue 6 https://doi.org/10.4161/cib.21805	journal	November 2012
On the use of mathematical programs with complementarity constraints in combined topological and parametric design of biochemical enzyme networks Guo, Tinghao; Allison, James T. Taylor & Francis https://doi.org/10.6084/m9.figshare.3472202	text	January 2016
On the use of mathematical programs with complementarity constraints in combined topological and parametric design of biochemical enzyme networks Guo, Tinghao; Allison, James T. Taylor & Francis https://doi.org/10.6084/m9.figshare.3472202.v1	text	January 2016

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