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Abstract
Traditional enzyme characterization methods are low-throughput and therefore limit engineering efforts in synthetic biology and biotechnology. Here, we propose a DNA-linked enzyme-coupled assay (DLEnCA) to monitor enzyme reactions in a high-throughput manner. Throughput is improved by removing the need for protein purification and by limiting the need for liquid chromatography mass spectrometry (LCMS) product detection by linking enzymatic function to DNA modification. We demonstrate the DLEnCA methodology using glucosyltransferases as an illustration. The assay utilizes cell free transcription/translation systems to produce enzymes of interest, while UDP-glucose and T4-β-glucosyltransferase are used to modify DNA, which is detected postreaction using qPCR or a similar means of DNA analysis. OleD and two glucosyltransferases from Arabidopsis were used to verify the assay's generality toward glucosyltransferases. We further show DLEnCA's utility by mapping out the substrate specificity for these enzymes.
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Affiliation(s)
- David J. Sukovich
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Cyrus Modavi
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Markus de Raad
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Robin N. Prince
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - J. Christopher Anderson
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
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Hsiau THC, Sukovich D, Elms P, Prince RN, Strittmatter T, Ruan P, Curry B, Anderson P, Sampson J, Anderson JC. Correction: A method for multiplex gene synthesis employing error correction based on expression. PLoS One 2015; 10:e0126078. [PMID: 25945930 PMCID: PMC4422662 DOI: 10.1371/journal.pone.0126078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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Hsiau THC, Sukovich D, Elms P, Prince RN, Stritmatter T, Ruan P, Curry B, Anderson P, Sampson J, Anderson JC. A method for multiplex gene synthesis employing error correction based on expression. PLoS One 2015; 10:e0119927. [PMID: 25790188 PMCID: PMC4366238 DOI: 10.1371/journal.pone.0119927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/17/2015] [Indexed: 11/18/2022] Open
Abstract
Our ability to engineer organisms with new biosynthetic pathways and genetic circuits is limited by the availability of protein characterization data and the cost of synthetic DNA. With new tools for reading and writing DNA, there are opportunities for scalable assays that more efficiently and cost effectively mine for biochemical protein characteristics. To that end, we have developed the Multiplex Library Synthesis and Expression Correction (MuLSEC) method for rapid assembly, error correction, and expression characterization of many genes as a pooled library. This methodology enables gene synthesis from microarray-synthesized oligonucleotide pools with a one-pot technique, eliminating the need for robotic liquid handling. Post assembly, the gene library is subjected to an ampicillin based quality control selection, which serves as both an error correction step and a selection for proteins that are properly expressed and folded in E. coli. Next generation sequencing of post selection DNA enables quantitative analysis of gene expression characteristics. We demonstrate the feasibility of this approach by building and testing over 90 genes for empirical evidence of soluble expression. This technique reduces the problem of part characterization to multiplex oligonucleotide synthesis and deep sequencing, two technologies under extensive development with projected cost reduction.
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Affiliation(s)
- Timothy H.-C. Hsiau
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - David Sukovich
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - Phillip Elms
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - Robin N. Prince
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - Tobias Stritmatter
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - Paul Ruan
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, United States of America
| | - Bo Curry
- Agilent Technologies, Santa Clara, CA, United States of America
| | - Paige Anderson
- Agilent Technologies, Santa Clara, CA, United States of America
| | - Jeff Sampson
- Agilent Technologies, Santa Clara, CA, United States of America
| | - J. Christopher Anderson
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
- Synthetic Biology Institute, University of California, Berkeley, CA, United States of America
- * E-mail:
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Jay SM, Kurtagic E, Alvarez LM, de Picciotto S, Sanchez E, Hawkins JF, Prince RN, Guerrero Y, Treasure CL, Lee RT, Griffith LG. Engineered bivalent ligands to bias ErbB receptor-mediated signaling and phenotypes. J Biol Chem 2011; 286:27729-40. [PMID: 21622572 PMCID: PMC3149363 DOI: 10.1074/jbc.m111.221093] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ErbB receptor family is dysregulated in many cancers, and its therapeutic manipulation by targeted antibodies and kinase inhibitors has resulted in effective chemotherapies. However, many malignancies remain refractory to current interventions. We describe a new approach that directs ErbB receptor interactions, resulting in biased signaling and phenotypes. Due to known receptor-ligand affinities and the necessity of ErbB receptors to dimerize to signal, bivalent ligands, formed by the synthetic linkage of two neuregulin-1β (NRG) moieties, two epidermal growth factor (EGF) moieties, or an EGF and a NRG moiety, can potentially drive homotypic receptor interactions and diminish formation of HER2-containing heterodimers, which are implicated in many malignancies and are a prevalent outcome of stimulation by native, monovalent EGF, or NRG. We demonstrate the therapeutic potential of this approach by showing that bivalent NRG (NN) can bias signaling in HER3-expressing cancer cells, resulting in some cases in decreased migration, inhibited proliferation, and increased apoptosis, whereas native NRG stimulation increased the malignant potential of the same cells. Hence, this new approach may have therapeutic relevance in ovarian, breast, lung, and other cancers in which HER3 has been implicated.
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Affiliation(s)
- Steven M Jay
- From the Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Prince RN, Schreiter ER, Zou P, Wiley HS, Ting AY, Lee RT, Lauffenburger DA. The heparin-binding domain of HB-EGF mediates localization to sites of cell-cell contact and prevents HB-EGF proteolytic release. J Cell Sci 2010; 123:2308-18. [PMID: 20530570 DOI: 10.1242/jcs.058321] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Heparin-binding EGF-like growth factor (HB-EGF) is a ligand for EGF receptor (EGFR) and possesses the ability to signal in juxtacrine, autocrine and/or paracrine mode, with these alternatives being governed by the degree of proteolytic release of the ligand. Although the spatial range of diffusion of released HB-EGF is restricted by binding heparan-sulfate proteoglycans (HSPGs) in the extracellular matrix and/or cellular glycocalyx, ascertaining mechanisms governing non-released HB-EGF localization is also important for understanding its effects. We have employed a new method for independently tracking the localization of the extracellular EGF-like domain of HB-EGF and the cytoplasmic C-terminus. A striking observation was the absence of the HB-EGF transmembrane pro-form from the leading edge of COS-7 cells in a wound-closure assay; instead, this protein localized in regions of cell-cell contact. A battery of detailed experiments found that this localization derives from a trans interaction between extracellular HSPGs and the HB-EGF heparin-binding domain, and that disruption of this interaction leads to increased release of soluble ligand and a switch in cell phenotype from juxtacrine-induced growth inhibition to autocrine-induced proliferation. Our results indicate that extracellular HSPGs serve to sequester the transmembrane pro-form of HB-EGF at the point of cell-cell contact, and that this plays a role in governing the balance between juxtacrine versus autocrine and paracrine signaling.
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Affiliation(s)
- Robin N Prince
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Yoshioka J, Prince RN, Huang H, Perkins SB, Cruz FU, MacGillivray C, Lauffenburger DA, Lee RT. Cardiomyocyte hypertrophy and degradation of connexin43 through spatially restricted autocrine/paracrine heparin-binding EGF. Proc Natl Acad Sci U S A 2005; 102:10622-7. [PMID: 16020536 PMCID: PMC1180761 DOI: 10.1073/pnas.0501198102] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Growth factor signaling can affect tissue remodeling through autocrine/paracrine mechanisms. Recent evidence indicates that EGF receptor transactivation by heparin-binding EGF (HB-EGF) contributes to hypertrophic signaling in cardiomyocytes. Here, we show that HB-EGF operates in a spatially restricted circuit in the extracellular space within the myocardium, revealing the critical nature of the local microenvironment in intercellular signaling. This highly localized microenvironment of HB-EGF signaling was demonstrated with 3D morphology, consistent with predictions from a computational model of EGF signaling. HB-EGF secretion by a given cardiomyocyte in mouse left ventricles led to cellular hypertrophy and reduced expression of connexin43 in the overexpressing cell and in immediately adjacent cells but not in cells farther away. Thus, HB-EGF acts as an autocrine and local paracrine cardiac growth factor that leads to loss of gap junction proteins within a spatially confined microenvironment. These findings demonstrate how cells can coordinate remodeling with their immediate neighboring cells with highly localized extracellular EGF signaling.
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Affiliation(s)
- Jun Yoshioka
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02139, USA
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Cushing D, Prince RN, Seiberlich J. Chloride-free Filter Paper. Science 1946; 103:568-9. [PMID: 17800119 DOI: 10.1126/science.103.2679.568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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