1
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Goike J, Hsieh CL, Horton AP, Gardner EC, Zhou L, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Xie X, Xia H, Shi PY, Renberg R, Segall-Shapiro TH, Terrace CI, Wu W, Shroff R, Byrom M, Ellington AD, Marcotte EM, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Weaver SC, Dye JM, Boutz DR, McLellan JS, Gollihar JD. SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode. Commun Biol 2023; 6:1250. [PMID: 38082099 PMCID: PMC10713552 DOI: 10.1038/s42003-023-05649-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has provided unprecedented insight into mutations enabling immune escape. Understanding how these mutations affect the dynamics of antibody-antigen interactions is crucial to the development of broadly protective antibodies and vaccines. Here we report the characterization of a potent neutralizing antibody (N3-1) identified from a COVID-19 patient during the first disease wave. Cryogenic electron microscopy revealed a quaternary binding mode that enables direct interactions with all three receptor-binding domains of the spike protein trimer, resulting in extraordinary avidity and potent neutralization of all major variants of concern until the emergence of Omicron. Structure-based rational design of N3-1 mutants improved binding to all Omicron variants but only partially restored neutralization of the conformationally distinct Omicron BA.1. This study provides new insights into immune evasion through changes in spike protein dynamics and highlights considerations for future conformationally biased multivalent vaccine designs.
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Affiliation(s)
- Jule Goike
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew P Horton
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Elizabeth C Gardner
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Shawn Abbassi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rebecca Renberg
- DEVCOM Army Research Laboratory, Biotechnology Branch, Adelphi, MD, USA
| | - Thomas H Segall-Shapiro
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- DEVCOM Army Research Laboratory-South, Austin, TX, USA
| | | | - Wesley Wu
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Raghav Shroff
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- DEVCOM Army Research Laboratory-South, Austin, TX, USA
| | - Michelle Byrom
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - James M Musser
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Suresh V Kuchipudi
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, PA, USA
| | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - George Georgiou
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Scott C Weaver
- University of Texas Medical Branch, World Reference Center for Emerging Viruses and Arboviruses, Galveston, TX, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Daniel R Boutz
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA.
- DEVCOM Army Research Laboratory-South, Austin, TX, USA.
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Jimmy D Gollihar
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Antibody Discovery and Accelerated Protein Therapeutics, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA.
- DEVCOM Army Research Laboratory-South, Austin, TX, USA.
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2
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Javanmardi K, Segall-Shapiro TH, Chou CW, Boutz DR, Olsen RJ, Xie X, Xia H, Shi PY, Johnson CD, Annapareddy A, Weaver S, Musser JM, Ellington AD, Finkelstein IJ, Gollihar JD. Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein. Cell Host Microbe 2022; 30:1242-1254.e6. [PMID: 35988543 PMCID: PMC9350683 DOI: 10.1016/j.chom.2022.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/17/2022] [Accepted: 07/27/2022] [Indexed: 12/03/2022]
Abstract
The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the repeated emergence of variants of concern. For the Omicron variant, sub-lineages BA.1 and BA.2, respectively, contain 33 and 29 nonsynonymous and indel spike protein mutations. These amino acid substitutions and indels are implicated in increased transmissibility and enhanced immune evasion. By reverting individual spike mutations of BA.1 or BA.2, we characterize the molecular effects of the Omicron spike mutations on expression, ACE2 receptor affinity, and neutralizing antibody recognition. We identified key mutations enabling escape from neutralizing antibodies at a variety of epitopes. Stabilizing mutations in the N-terminal and S2 domains of the spike protein can compensate for destabilizing mutations in the receptor binding domain, enabling the record number of mutations in Omicron. Our results provide a comprehensive account of the mutational effects in the Omicron spike protein and illustrate previously uncharacterized mechanisms of host evasion.
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Affiliation(s)
- Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Thomas H Segall-Shapiro
- Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Daniel R Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Randall J Olsen
- Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA; Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, HMRI and Department of Pathology and Genomic Medicine, HMH, Houston, TX, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Charlie D Johnson
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Ankur Annapareddy
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Scott Weaver
- University of Texas Medical Branch, World Reference Center for Emerging Viruses and Arboviruses, Galveston, TX, USA
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, HMRI and Department of Pathology and Genomic Medicine, HMH, Houston, TX, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA.
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3
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King AM, Anderson DA, Glassey E, Segall-Shapiro TH, Zhang Z, Niquille DL, Embree AC, Pratt K, Williams TL, Gordon DB, Voigt CA. Selection for constrained peptides that bind to a single target protein. Nat Commun 2021; 12:6343. [PMID: 34732700 PMCID: PMC8566587 DOI: 10.1038/s41467-021-26350-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 09/27/2021] [Indexed: 12/16/2022] Open
Abstract
Peptide secondary metabolites are common in nature and have diverse pharmacologically-relevant functions, from antibiotics to cross-kingdom signaling. Here, we present a method to design large libraries of modified peptides in Escherichia coli and screen them in vivo to identify those that bind to a single target-of-interest. Constrained peptide scaffolds were produced using modified enzymes gleaned from microbial RiPP (ribosomally synthesized and post-translationally modified peptide) pathways and diversified to build large libraries. The binding of a RiPP to a protein target leads to the intein-catalyzed release of an RNA polymerase σ factor, which drives the expression of selectable markers. As a proof-of-concept, a selection was performed for binding to the SARS-CoV-2 Spike receptor binding domain. A 1625 Da constrained peptide (AMK-1057) was found that binds with similar affinity (990 ± 5 nM) as an ACE2-derived peptide. This demonstrates a generalizable method to identify constrained peptides that adhere to a single protein target, as a step towards "molecular glues" for therapeutics and diagnostics.
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Affiliation(s)
- Andrew M King
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel A Anderson
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emerson Glassey
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas H Segall-Shapiro
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhengan Zhang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David L Niquille
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Katelin Pratt
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - D Benjamin Gordon
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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4
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Meyer AJ, Segall-Shapiro TH, Glassey E, Zhang J, Voigt CA. Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. Nat Chem Biol 2018; 15:196-204. [DOI: 10.1038/s41589-018-0168-3] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/05/2018] [Indexed: 11/09/2022]
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5
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Jones AM, Mehta MM, Thomas EE, Atkinson JT, Segall-Shapiro TH, Liu S, Silberg JJ. The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation. ACS Synth Biol 2016; 5:415-25. [PMID: 26976658 DOI: 10.1021/acssynbio.5b00305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins can be engineered for synthetic biology through circular permutation, a sequence rearrangement in which native protein termini become linked and new termini are created elsewhere through backbone fission. However, it remains challenging to anticipate a protein's functional tolerance to circular permutation. Here, we describe new transposons for creating libraries of randomly circularly permuted proteins that minimize peptide additions at their termini, and we use transposase mutagenesis to study the tolerance of a thermophilic adenylate kinase (AK) to circular permutation. We find that libraries expressing permuted AKs with either short or long peptides amended to their N-terminus yield distinct sets of active variants and present evidence that this trend arises because permuted protein expression varies across libraries. Mapping all sites that tolerate backbone cleavage onto AK structure reveals that the largest contiguous regions of sequence that lack cleavage sites are proximal to the phosphotransfer site. A comparison of our results with a range of structure-derived parameters further showed that retention of function correlates to the strongest extent with the distance to the phosphotransfer site, amino acid variability in an AK family sequence alignment, and residue-level deviations in superimposed AK structures. Our work illustrates how permuted protein libraries can be created with minimal peptide additions using transposase mutagenesis, and it reveals a challenge of maintaining consistent expression across permuted variants in a library that minimizes peptide additions. Furthermore, these findings provide a basis for interpreting responses of thermophilic phosphotransferases to circular permutation by calibrating how different structure-derived parameters relate to retention of function in a cellular selection.
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Affiliation(s)
- Alicia M. Jones
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Manan M. Mehta
- Medical
Scientist Training Program, Northwestern University, 303 East
Chicago Avenue, Morton 1-670, Chicago, Illinois 60611, United States
| | - Emily E. Thomas
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Joshua T. Atkinson
- Systems,
Synthetic, and Physical Biology Graduate Program, Rice University, 6100
Main MS-180, Houston, Texas 77005, United States
| | - Thomas H. Segall-Shapiro
- Department
of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 500 Technology Square, NE47-257, Cambridge, Massachusetts 02139, United States
| | - Shirley Liu
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J. Silberg
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
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Chandran S, Noskov VN, Segall-Shapiro TH, Ma L, Whiteis C, Lartigue C, Jores J, Vashee S, Chuang RY. TREC-IN: gene knock-in genetic tool for genomes cloned in yeast. BMC Genomics 2014; 15:1180. [PMID: 25539750 PMCID: PMC4407568 DOI: 10.1186/1471-2164-15-1180] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [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] [Received: 10/18/2014] [Accepted: 12/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the development of several new technologies using synthetic biology, it is possible to engineer genetically intractable organisms including Mycoplasma mycoides subspecies capri (Mmc), by cloning the intact bacterial genome in yeast, using the host yeast's genetic tools to modify the cloned genome, and subsequently transplanting the modified genome into a recipient cell to obtain mutant cells encoded by the modified genome. The recently described tandem repeat coupled with endonuclease cleavage (TREC) method has been successfully used to generate seamless deletions and point mutations in the mycoplasma genome using the yeast DNA repair machinery. But, attempts to knock-in genes in some cases have encountered a high background of transformation due to maintenance of unwanted circularization of the transforming DNA, which contains possible autonomously replicating sequence (ARS) activity. To overcome this issue, we incorporated a split marker system into the TREC method, enabling seamless gene knock-in with high efficiency. The modified method is called TREC-assisted gene knock-in (TREC-IN). Since a gene to be knocked-in is delivered by a truncated non-functional marker, the background caused by an incomplete integration is essentially eliminated. RESULTS In this paper, we demonstrate applications of the TREC-IN method in gene complementation and genome minimization studies in Mmc. In the first example, the Mmc dnaA gene was seamlessly replaced by an orthologous gene, which shares a high degree of identity at the nucleotide level with the original Mmc gene, with high efficiency and low background. In the minimization example, we replaced an essential gene back into the genome that was present in the middle of a cluster of non-essential genes, while deleting the non-essential gene cluster, again with low backgrounds of transformation and high efficiency. CONCLUSION Although we have demonstrated the feasibility of TREC-IN in gene complementation and genome minimization studies in Mmc, the applicability of TREC-IN ranges widely. This method proves to be a valuable genetic tool that can be extended for genomic engineering in other genetically intractable organisms, where it may be implemented in elucidating specific metabolic pathways and in rationale vaccine design.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ray-Yuan Chuang
- The J, Craig Venter Institute, 9704 Medical Center Drive, Rockville 20850, MD, USA.
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7
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Abstract
Synthetic genetic systems share resources with the host, including machinery for transcription
and translation. Phage RNA polymerases (RNAPs) decouple transcription from the host and generate
high expression. However, they can exhibit toxicity and lack accessory proteins (σ factors
and activators) that enable switching between different promoters and modulation of activity. Here,
we show that T7 RNAP (883 amino acids) can be divided into four fragments that have to be
co-expressed to function. The DNA-binding loop is encoded in a C-terminal 285-aa ‘σ
fragment’, and fragments with different specificity can direct the remaining 601-aa
‘core fragment’ to different promoters. Using these parts, we have built a resource
allocator that sets the core fragment concentration, which is then shared by multiple σ
fragments. Adjusting the concentration of the core fragment sets the maximum transcriptional
capacity available to a synthetic system. Further, positive and negative regulation is implemented
using a 67-aa N-terminal ‘α fragment’ and a null (inactivated) σ
fragment, respectively. The α fragment can be fused to recombinant proteins to make promoters
responsive to their levels. These parts provide a toolbox to allocate transcriptional resources via
different schemes, which we demonstrate by building a system which adjusts promoter activity to
compensate for the difference in copy number of two plasmids.
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Affiliation(s)
- Thomas H Segall-Shapiro
- Department of Biological Engineering, Synthetic Biology Center Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam J Meyer
- Institute for Cellular and Molecular Biology University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology University of Texas at Austin, Austin, TX, USA
| | - Eduardo D Sontag
- Department of Mathematics, Rutgers University, Piscataway, NJ, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center Massachusetts Institute of Technology, Cambridge, MA, USA
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8
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Rhodius VA, Segall-Shapiro TH, Sharon BD, Ghodasara A, Orlova E, Tabakh H, Burkhardt DH, Clancy K, Peterson TC, Gross CA, Voigt CA. Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Mol Syst Biol 2013; 9:702. [PMID: 24169405 PMCID: PMC3817407 DOI: 10.1038/msb.2013.58] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 09/26/2013] [Indexed: 01/22/2023] Open
Abstract
Cells react to their environment through gene regulatory networks. Network integrity requires minimization of undesired crosstalk between their biomolecules. Similar constraints also limit the use of regulators when building synthetic circuits for engineering applications. Here, we mapped the promoter specificities of extracytoplasmic function (ECF) σs as well as the specificity of their interaction with anti-σs. DNA synthesis was used to build 86 ECF σs (two from every subgroup), their promoters, and 62 anti-σs identified from the genomes of diverse bacteria. A subset of 20 σs and promoters were found to be highly orthogonal to each other. This set can be increased by combining the -35 and -10 binding domains from different subgroups to build chimeras that target sequences unrepresented in any subgroup. The orthogonal σs, anti-σs, and promoters were used to build synthetic genetic switches in Escherichia coli. This represents a genome-scale resource of the properties of ECF σs and a resource for synthetic biology, where this set of well-characterized regulatory parts will enable the construction of sophisticated gene expression programs.
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Affiliation(s)
- Virgil A Rhodius
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Thomas H Segall-Shapiro
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian D Sharon
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Amar Ghodasara
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ekaterina Orlova
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Hannah Tabakh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - David H Burkhardt
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Clancy
- Synthetic Biology Research and Development, Life Technologies, Carlsbad, CA, USA
| | - Todd C Peterson
- Synthetic Biology Research and Development, Life Technologies, Carlsbad, CA, USA
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
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9
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Mahdavi A, Segall-Shapiro TH, Kou S, Jindal GA, Hoff KG, Liu S, Chitsaz M, Ismagilov RF, Silberg JJ, Tirrell DA. A genetically encoded and gate for cell-targeted metabolic labeling of proteins. J Am Chem Soc 2013; 135:2979-82. [PMID: 23406315 DOI: 10.1021/ja400448f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We describe a genetic AND gate for cell-targeted metabolic labeling and proteomic analysis in complex cellular systems. The centerpiece of the AND gate is a bisected methionyl-tRNA synthetase (MetRS) that charges the Met surrogate azidonorleucine (Anl) to tRNA(Met). Cellular protein labeling occurs only upon activation of two different promoters that drive expression of the N- and C-terminal fragments of the bisected MetRS. Anl-labeled proteins can be tagged with fluorescent dyes or affinity reagents via either copper-catalyzed or strain-promoted azide-alkyne cycloaddition. Protein labeling is apparent within 5 min after addition of Anl to bacterial cells in which the AND gate has been activated. This method allows spatial and temporal control of proteomic labeling and identification of proteins made in specific cellular subpopulations. The approach is demonstrated by selective labeling of proteins in bacterial cells immobilized in the center of a laminar-flow microfluidic channel, where they are exposed to overlapping, opposed gradients of inducers of the N- and C-terminal MetRS fragments. The observed labeling profile is predicted accurately from the strengths of the individual input signals.
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Affiliation(s)
- Alborz Mahdavi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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10
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Abstract
Synthetic genetic sensors and circuits enable programmable control over the timing and conditions of gene expression. They are being increasingly incorporated into the control of complex, multigene pathways and cellular functions. Here, we propose a design strategy to genetically separate the sensing/circuitry functions from the pathway to be controlled. This separation is achieved by having the output of the circuit drive the expression of a polymerase, which then activates the pathway from polymerase-specific promoters. The sensors, circuits and polymerase are encoded together on a 'controller' plasmid. Variants of T7 RNA polymerase that reduce toxicity were constructed and used as scaffolds for the construction of four orthogonal polymerases identified via part mining that bind to unique promoter sequences. This set is highly orthogonal and induces cognate promoters by 8- to 75-fold more than off-target promoters. These orthogonal polymerases enable four independent channels linking the outputs of circuits to the control of different cellular functions. As a demonstration, we constructed a controller plasmid that integrates two inducible systems, implements an AND logic operation and toggles between metabolic pathways that change Escherichia coli green (deoxychromoviridans) and red (lycopene). The advantages of this organization are that (i) the regulation of the pathway can be changed simply by introducing a different controller plasmid, (ii) transcription is orthogonal to host machinery and (iii) the pathway genes are not transcribed in the absence of a controller and are thus more easily carried without invoking evolutionary pressure.
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Affiliation(s)
- Karsten Temme
- UCB/UCSF Joint Graduate Group in Bioengineering, MC2540, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
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Segall-Shapiro TH, Nguyen PQ, Dos Santos ED, Subedi S, Judd J, Suh J, Silberg JJ. Mesophilic and hyperthermophilic adenylate kinases differ in their tolerance to random fragmentation. J Mol Biol 2010; 406:135-48. [PMID: 21145325 DOI: 10.1016/j.jmb.2010.11.057] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/15/2010] [Accepted: 11/30/2010] [Indexed: 02/03/2023]
Abstract
The extent to which thermostability influences the location of protein fragmentation sites that allow retention of function is not known. To evaluate this, we used a novel transposase-based approach to create libraries of vectors that express structurally-related fragments of Bacillus subtilis adenylate kinase (BsAK) and Thermotoga neapolitana adenylate kinase (TnAK) with identical modifications at their termini, and we selected for variants in each library that complement the growth of Escherichia coli with a temperature-sensitive adenylate kinase (AK). Mutants created using the hyperthermophilic TnAK were found to support growth with a higher frequency (44%) than those generated from the mesophilic BsAK (6%), and selected TnAK mutants complemented E. coli growth more strongly than homologous BsAK variants. Sequencing of functional clones from each library also identified a greater dispersion of fragmentation sites within TnAK. Nondisruptive fission sites were observed within the AMP binding and core domains of both AK homologs. However, only TnAK contained sites within the lid domain, which undergoes dynamic fluctuations that are critical for catalysis. These findings implicate the flexible lid domain as having an increased sensitivity to fission events at physiological temperatures. In addition, they provide evidence that comparisons of nondisruptive fission sites in homologous proteins could be useful for finding dynamic regions whose conformational fluctuations are important for function, and they show that the discovery of protein fragments that cooperatively function in mesophiles can be aided by the use of thermophilic enzymes as starting points for protein design.
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Affiliation(s)
- Thomas H Segall-Shapiro
- Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, MS 140, Houston, TX 77005, USA
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Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA, Smith HO, Venter JC. Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 2010; 329:52-6. [PMID: 20488990 DOI: 10.1126/science.1190719] [Citation(s) in RCA: 1312] [Impact Index Per Article: 93.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Daniel G Gibson
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
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Noskov VN, Segall-Shapiro TH, Chuang RY. Tandem repeat coupled with endonuclease cleavage (TREC): a seamless modification tool for genome engineering in yeast. Nucleic Acids Res 2010; 38:2570-6. [PMID: 20228123 PMCID: PMC2860121 DOI: 10.1093/nar/gkq099] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [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: 02/02/2023] Open
Abstract
The complete synthetic Mycoplasma genitalium genome (∼583 kb) has been assembled and cloned as a circular plasmid in the yeast Saccharomyces cerevisiae. Attempts to engineer the cloned genome by standard genetic methods involving the URA3/5-fluoroorotic acid (5-FOA) counter-selection have shown a high background of 5-FOA resistant clones derived from spontaneous deletions of the bacterial genome maintained in yeast. Here, we report a method that can seamlessly modify the bacterial genome in yeast with high efficiency. This method requires two sequential homologous recombination events. First, the target region is replaced with a mutagenesis cassette that consists of a knock-out CORE (an18-bp I-SceI recognition site, the SCEI gene under the control of the GAL1 promoter, and the URA3 marker) and a DNA fragment homologous to the sequence upstream of the target site. The replacement generates tandem repeat sequences flanking the CORE. Second, galactose induces the expression of I-SceI, which generates a double-strand break (DSB) at the recognition site. This DSB promotes intra-molecular homologous recombination between the repeat sequences, and leads to an excision of the CORE. As a result, a seamless modification is generated. This method can be adapted for a variety of genomic modifications and may provide an important tool to modify and design natural or synthetic genomes propagated in yeast.
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Affiliation(s)
- Vladimir N Noskov
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
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