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Title: BglBricks: A flexible standard for biological part assembly

Abstract

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 amore » 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.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [1];  [3]
+ Show Author Affiliations
  1. 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
  2. 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)
  3. 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)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Science Foundation (NSF)
OSTI Identifier:
1629615
Grant/Contract Number:  
AC02-05CH11231; CBET-0756801; BES-0439124
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Engineering
Additional Journal Information:
Journal Volume: 4; Journal Issue: 1; Journal ID: ISSN 1754-1611
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Anderson, J. Christopher, Dueber, John E., Leguia, Mariana, Wu, Gabriel C., Goler, Jonathan A., Arkin, Adam P., and Keasling, Jay D. BglBricks: A flexible standard for biological part assembly. United States: N. p., 2010. Web. doi:10.1186/1754-1611-4-1.
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Anderson, J. Christopher, Dueber, John E., Leguia, Mariana, Wu, Gabriel C., Goler, Jonathan A., Arkin, Adam P., & Keasling, Jay D. BglBricks: A flexible standard for biological part assembly. United States. https://doi.org/10.1186/1754-1611-4-1
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Anderson, J. Christopher, Dueber, John E., Leguia, Mariana, Wu, Gabriel C., Goler, Jonathan A., Arkin, Adam P., and Keasling, Jay D. Wed . "BglBricks: A flexible standard for biological part assembly". United States. https://doi.org/10.1186/1754-1611-4-1. https://www.osti.gov/servlets/purl/1629615.
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@article{osti_1629615,
title = {BglBricks: A flexible standard for biological part assembly},
author = {Anderson, J. Christopher and Dueber, John E. and Leguia, Mariana and Wu, Gabriel C. and Goler, Jonathan A. and Arkin, Adam P. and Keasling, Jay D.},
abstractNote = {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.},
doi = {10.1186/1754-1611-4-1},
journal = {Journal of Biological Engineering},
number = 1,
volume = 4,
place = {United States},
year = {Wed Jan 20 00:00:00 EST 2010},
month = {Wed Jan 20 00:00:00 EST 2010}
}
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    journal, April 2010

    • Sleight, Sean C.; Bartley, Bryan A.; Lieviant, Jane A.
    • Nucleic Acids Research, Vol. 38, Issue 8
    • DOI: 10.1093/nar/gkq179

    The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes
    journal, November 2012

    • Silva-Rocha, Rafael; Martínez-García, Esteban; Calles, Belén
    • Nucleic Acids Research, Vol. 41, Issue D1
    • DOI: 10.1093/nar/gks1119

    High-throughput, cost-effective verification of structural DNA assembly
    journal, November 2013

    • Dharmadi, Yandi; Patel, Kedar; Shapland, Elaine
    • Nucleic Acids Research, Vol. 42, Issue 4
    • DOI: 10.1093/nar/gkt1088

    Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination
    journal, November 2013

    • Colloms, Sean D.; Merrick, Christine A.; Olorunniji, Femi J.
    • Nucleic Acids Research, Vol. 42, Issue 4
    • DOI: 10.1093/nar/gkt1101

    Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay
    journal, September 2013

    • Lee, Michael E.; Aswani, Anil; Han, Audrey S.
    • Nucleic Acids Research, Vol. 41, Issue 22
    • DOI: 10.1093/nar/gkt809

    Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly
    journal, September 2013

    • Torella, Joseph P.; Boehm, Christian R.; Lienert, Florian
    • Nucleic Acids Research, Vol. 42, Issue 1
    • DOI: 10.1093/nar/gkt860

    Broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria
    journal, July 2014

    • Taton, Arnaud; Unglaub, Federico; Wright, Nicole E.
    • Nucleic Acids Research, Vol. 42, Issue 17
    • DOI: 10.1093/nar/gku673

    GenoLIB: a database of biological parts derived from a library of common plasmid features
    journal, April 2015

    • Adames, Neil R.; Wilson, Mandy L.; Fang, Gang
    • Nucleic Acids Research, Vol. 43, Issue 10
    • DOI: 10.1093/nar/gkv272

    CasHRA (Cas9-facilitated Homologous Recombination Assembly) method of constructing megabase-sized DNA
    journal, May 2016

    • Zhou, Jianting; Wu, Ronghai; Xue, Xiaoli
    • Nucleic Acids Research, Vol. 44, Issue 14
    • DOI: 10.1093/nar/gkw475

    The art of vector engineering: towards the construction of next-generation genetic tools
    journal, September 2018

    • Nora, Luísa Czamanski; Westmann, Cauã Antunes; Martins-Santana, Leonardo
    • Microbial Biotechnology, Vol. 12, Issue 1
    • DOI: 10.1111/1751-7915.13318

    Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast
    journal, January 2012

    Standards for plant synthetic biology: a common syntax for exchange of DNA parts
    journal, July 2015

    • Patron, Nicola J.; Orzaez, Diego; Marillonnet, Sylvestre
    • New Phytologist, Vol. 208, Issue 1
    • DOI: 10.1111/nph.13532

    Characterization of an inducible promoter in different DNA copy number conditions
    journal, March 2012

    Construction of a genetic AND gate under a new standard for assembly of genetic parts
    journal, December 2010

    Engineering Escherichia coli for succinate production from hemicellulose via consolidated bioprocessing
    journal, January 2012

    Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli
    journal, January 2013

    • Eudes, Aymerick; Juminaga, Darmawi; Baidoo, Edward E. K.
    • Microbial Cell Factories, Vol. 12, Issue 1
    • DOI: 10.1186/1475-2859-12-62

    Systematic design methodology for robust genetic transistors based on I/O specifications via promoter-RBS libraries
    journal, October 2013

    Designing and engineering evolutionary robust genetic circuits
    journal, January 2010

    • Sleight, Sean C.; Bartley, Bryan A.; Lieviant, Jane A.
    • Journal of Biological Engineering, Vol. 4, Issue 1
    • DOI: 10.1186/1754-1611-4-12

    Rapid optimization of gene dosage in E. coli using DIAL strains
    journal, January 2011

    • Kittleson, Joshua T.; Cheung, Sherine; Anderson, J. Christopher
    • Journal of Biological Engineering, Vol. 5, Issue 1
    • DOI: 10.1186/1754-1611-5-10

    A genetic bistable switch utilizing nonlinear protein degradation
    journal, December 2012

    • Huang, Daniel; Holtz, William J.; Maharbiz, Michel M.
    • Journal of Biological Engineering, Vol. 6, Issue 1
    • DOI: 10.1186/1754-1611-6-9

    A survey of enabling technologies in synthetic biology
    journal, January 2013

    2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts
    journal, January 2013

    • Leguia, Mariana; Brophy, Jennifer AN; Densmore, Douglas
    • Journal of Biological Engineering, Vol. 7, Issue 1
    • DOI: 10.1186/1754-1611-7-2

    Targeting a heterologous protein to multiple plant organelles via rationally designed 5[prime] mRNA tags
    journal, January 2013

    • Voges, Mathias J.; Silver, Pamela A.; Way, Jeffrey C.
    • Journal of Biological Engineering, Vol. 7, Issue 1
    • DOI: 10.1186/1754-1611-7-20

    Secretion of polyhydroxybutyrate in Escherichia coli using a synthetic biological engineering approach
    journal, January 2013

    • Rahman, Asif; Linton, Elisabeth; Hatch, Alex D.
    • Journal of Biological Engineering, Vol. 7, Issue 1
    • DOI: 10.1186/1754-1611-7-24

    A strategy for enhanced circular DNA construction efficiency based on DNA cyclization after microbial transformation
    journal, February 2015

    Enhanced production of styrene by engineered Escherichia coli and in situ product recovery (ISPR) with an organic solvent
    journal, May 2019

    A seamless and iterative DNA assembly method named PS-Brick and its assisted metabolic engineering for threonine and 1-propanol production
    journal, July 2019

    A Modular Cloning System for Standardized Assembly of Multigene Constructs
    journal, February 2011

    A Biobrick Library for Cloning Custom Eukaryotic Plasmids
    journal, August 2011

    Automated Solid-Phase Subcloning Based on Beads Brought into Proximity by Magnetic Force
    journal, May 2012

    Bottom-Up Engineering of Biological Systems through Standard Bricks: A Modularity Study on Basic Parts and Devices
    journal, July 2012

    Parallel In Vivo DNA Assembly by Recombination: Experimental Demonstration and Theoretical Approaches
    journal, February 2013

    Secreted Gaussia princeps Luciferase as a Reporter of Escherichia coli Replication in a Mouse Tissue Cage Model of Infection
    journal, March 2014

    Artificially Constructed Quorum-Sensing Circuits Are Used for Subtle Control of Bacterial Population Density
    journal, August 2014

    Single Cell FRET Analysis for the Identification of Optimal FRET-Pairs in Bacillus subtilis Using a Prototype MEM-FLIM System
    journal, April 2015

    MXS-Chaining: A Highly Efficient Cloning Platform for Imaging and Flow Cytometry Approaches in Mammalian Systems
    journal, April 2015

    Beyond Escherichia coli: Synthetic Biology-Focused Platforms and Toolboxes for Engineering other Bacteria
    journal, July 2016

    Multi‐input CRISPR / C as genetic circuits that interface host regulatory networks
    journal, November 2014

    • Nielsen, Alec AK; Voigt, Christopher A.
    • Molecular Systems Biology, Vol. 10, Issue 11
    • DOI: 10.15252/msb.20145735

    An algal enzyme required for biosynthesis of the most abundant marine carotenoids
    text, January 2020

    Developments in the Tools and Methodologies of Synthetic Biology
    journal, November 2014

    • Kelwick, Richard; MacDonald, James T.; Webb, Alexander J.
    • Frontiers in Bioengineering and Biotechnology, Vol. 2
    • DOI: 10.3389/fbioe.2014.00060

    Production of Fatty Acid-Derived Valuable Chemicals in Synthetic Microbes
    journal, December 2014

    • Yu, Ai-Qun; Pratomo Juwono, Nina Kurniasih; Leong, Susanna Su Jan
    • Frontiers in Bioengineering and Biotechnology, Vol. 2
    • DOI: 10.3389/fbioe.2014.00078

    Analytics for Metabolic Engineering
    journal, September 2015

    • Petzold, Christopher J.; Chan, Leanne Jade G.; Nhan, Melissa
    • Frontiers in Bioengineering and Biotechnology, Vol. 3
    • DOI: 10.3389/fbioe.2015.00135

    Brighter Fluorescent Derivatives of UTI89 Utilizing a Monomeric vGFP
    journal, January 2016

    The Encapsulation of Cell-free Transcription and Translation Machinery in Vesicles for the Construction of Cellular Mimics
    journal, October 2013

    • Spencer, Amy C.; Torre, Paola; Mansy, Sheref S.
    • Journal of Visualized Experiments, Issue 80
    • DOI: 10.3791/51304-v
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