1
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Zhao Y, Coelho C, Hughes AL, Lazar-Stefanita L, Yang S, Brooks AN, Walker RSK, Zhang W, Lauer S, Hernandez C, Cai J, Mitchell LA, Agmon N, Shen Y, Sall J, Fanfani V, Jalan A, Rivera J, Liang FX, Bader JS, Stracquadanio G, Steinmetz LM, Cai Y, Boeke JD. Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions. Cell 2023; 186:5220-5236.e16. [PMID: 37944511 DOI: 10.1016/j.cell.2023.09.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 01/03/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023]
Abstract
The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual Sc2.0 chromosomes assembled. Here, we describe the consolidation of multiple synthetic chromosomes using advanced endoreduplication intercrossing with tRNA expression cassettes to generate a strain with 6.5 synthetic chromosomes. The 3D chromosome organization and transcript isoform profiles were evaluated using Hi-C and long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or "CRISPR D-BUGS," to map phenotypic variants caused by specific designer modifications, known as "bugs." We first fine-mapped a bug in synthetic chromosome II (synII) and then discovered a combinatorial interaction associated with synIII and synX, revealing an unexpected genetic interaction that links transcriptional regulation, inositol metabolism, and tRNASerCGA abundance. Finally, to expedite consolidation, we employed chromosome substitution to incorporate the largest chromosome (synIV), thereby consolidating >50% of the Sc2.0 genome in one strain.
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Affiliation(s)
- Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Camila Coelho
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Amanda L Hughes
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Luciana Lazar-Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Sandy Yang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Aaron N Brooks
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Roy S K Walker
- School of Engineering, Institute for Bioengineering, the University of Edinburgh, Edinburgh EH9 3BF
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Stephanie Lauer
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Cindy Hernandez
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Jitong Cai
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Leslie A Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Yue Shen
- BGI, Shenzhen, Beishan, Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI, Shenzhen, Shenzhen 518120, China
| | - Joseph Sall
- Microscopy Laboratory, NYU Langone Health, New York, NY 10016, USA
| | - Viola Fanfani
- School of Biological Sciences, the University of Edinburgh, Edinburgh EH9 3BF
| | - Anavi Jalan
- Department of Biology, New York University, New York, NY, USA
| | - Jordan Rivera
- Department of Biology, New York University, New York, NY, USA
| | - Feng-Xia Liang
- Microscopy Laboratory, NYU Langone Health, New York, NY 10016, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics and Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | - Yizhi Cai
- Manchester Institute of Biotechnology, the University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York, NY 11201, USA.
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2
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Luo J, Vale-Silva LA, Raghavan AR, Mercy G, Heldrich J, Sun X, Li MK, Zhang W, Agmon N, Yang K, Cai J, Stracquadanio G, Thierry A, Zhao Y, Coelho C, McCulloch LH, Lauer S, Kaback DB, Bader JS, Mitchell LA, Mozziconacci J, Koszul R, Hochwagen A, Boeke JD. Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function. Cell Genom 2023; 3:100439. [PMID: 38020967 PMCID: PMC10667551 DOI: 10.1016/j.xgen.2023.100439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 08/23/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
We designed and synthesized synI, which is ∼21.6% shorter than native chrI, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns surrounding potential instability and karyotype imbalance and is now attached to synIII, yielding the first synthetic yeast fusion chromosome. Additional fusion chromosomes were constructed to study nuclear function. ChrIII-I and chrIX-III-I fusion chromosomes have twisted structures, which depend on silencing protein Sir3. As a smaller chromosome, chrI also faces special challenges in assuring meiotic crossovers required for efficient homolog disjunction. Centromere deletions into fusion chromosomes revealed opposing effects of core centromeres and pericentromeres in modulating deposition of the crossover-promoting protein Red1. These effects extend over 100 kb and promote disproportionate Red1 enrichment, and thus crossover potential, on small chromosomes like chrI. These findings reveal the power of synthetic genomics to uncover new biology and deconvolute complex biological systems.
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Affiliation(s)
- Jingchuan Luo
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Biochemistry, Cellular and Molecular Biology Graduate program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | - Guillaume Mercy
- Institut Pasteur, CNRS UMR3525, Université de Paris, Unité Régulation Spatiale des Génomes, 75015 Paris, France
- Collège Doctoral, Sorbonne Université, 75005 Paris, France
| | - Jonna Heldrich
- Department of Biology, New York University, New York, NY 10003, USA
| | - Xiaoji Sun
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Mingyu Kenneth Li
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Kun Yang
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA
| | - Jitong Cai
- Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA
| | - Giovanni Stracquadanio
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, JHU, Baltimore, MD 21218, USA
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR3525, Université de Paris, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Camila Coelho
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Laura H. McCulloch
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Stephanie Lauer
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - David B. Kaback
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, International Center for Public Health, Newark, NJ 07101-1709, USA
| | - Joel S. Bader
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Leslie A. Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Julien Mozziconacci
- Structure and instability of Genomes Lab, UMR 7196, Muséum National d'Histoire Naturelle (MNHN), 75005 Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR3525, Université de Paris, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | | | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, Tandon School of Engineering, Brooklyn, NY 11201, USA
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3
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Goldberg GW, Spencer JM, Giganti DO, Camellato BR, Agmon N, Ichikawa DM, Boeke JD, Noyes MB. Engineered dual selection for directed evolution of SpCas9 PAM specificity. Nat Commun 2021; 12:349. [PMID: 33441553 PMCID: PMC7807044 DOI: 10.1038/s41467-020-20650-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 03/27/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
The widely used Streptococcus pyogenes Cas9 (SpCas9) nuclease derives its DNA targeting specificity from protein-DNA contacts with protospacer adjacent motif (PAM) sequences, in addition to base-pairing interactions between its guide RNA and target DNA. Previous reports have established that the PAM specificity of SpCas9 can be altered via positive selection procedures for directed evolution or other protein engineering strategies. Here we exploit in vivo directed evolution systems that incorporate simultaneous positive and negative selection to evolve SpCas9 variants with commensurate or improved activity on NAG PAMs relative to wild type and reduced activity on NGG PAMs, particularly YGG PAMs. We also show that the PAM preferences of available evolutionary intermediates effectively determine whether similar counterselection PAMs elicit different selection stringencies, and demonstrate that negative selection can be specifically increased in a yeast selection system through the fusion of compensatory zinc fingers to SpCas9.
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Affiliation(s)
- Gregory W Goldberg
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA.
| | - Jeffrey M Spencer
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - David O Giganti
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - Brendan R Camellato
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - Neta Agmon
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
- Neochromosome, Inc., Alexandria Center for Life Science, New York, NY, 10016, USA
| | - David M Ichikawa
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
| | - Marcus B Noyes
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA.
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4
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Mita P, Sun X, Fenyö D, Kahler DJ, Li D, Agmon N, Wudzinska A, Keegan S, Bader JS, Yun C, Boeke JD. BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells. Nat Struct Mol Biol 2020; 27:179-191. [PMID: 32042152 PMCID: PMC7082080 DOI: 10.1038/s41594-020-0374-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 02/08/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022]
Abstract
Long interspersed element-1 (LINE-1 or L1) is the only autonomous retrotransposon active in human cells. Different host factors have been shown to influence L1 mobility however, systematic analyses of these factors are limited. Here, we developed a high-throughput microscopy-based retrotransposition assay that identified the Double-Stranded Break (DSB) repair and Fanconi Anemia factors active in the S/G2 phase as potent inhibitors and regulators of L1 activity. In particular BRCA1, an E3 ubiquitin ligase with a key role in several DNA repair pathways, directly affects L1 retrotransposition frequency and structure and also plays a distinct role in controlling L1 ORF2 protein translation through L1 mRNA binding. These results suggest the existence of a “battleground” at the DNA replication fork between HR factors and L1 retrotransposons, and revealing a potential role for L1 in the genotypic evolution of tumors characterized by BRCA1 and HR repair deficiencies.
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Affiliation(s)
- Paolo Mita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
| | - Xiaoji Sun
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.,Cellarity Inc., Cambridge, MA, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - David J Kahler
- High Throughput Biology Core, NYU Langone Health, New York, NY, USA.,Planet Pharma, Boston, MA, USA
| | - Donghui Li
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.,Flagship VL58, Inc., Cambridge, MA, USA
| | - Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Aleksandra Wudzinska
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Chi Yun
- High Throughput Biology Core, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
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5
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Agmon N, Temple J, Tang Z, Schraink T, Baron M, Chen J, Mita P, Martin JA, Tu BP, Yanai I, Fenyö D, Boeke JD. Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast. Nucleic Acids Res 2020; 48:486-499. [PMID: 31745563 PMCID: PMC7145547 DOI: 10.1093/nar/gkz1098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 08/26/2019] [Revised: 11/04/2019] [Accepted: 11/16/2019] [Indexed: 12/30/2022] Open
Abstract
Cross-species pathway transplantation enables insight into a biological process not possible through traditional approaches. We replaced the enzymes catalyzing the entire Saccharomyces cerevisiae adenine de novo biosynthesis pathway with the human pathway. While the 'humanized' yeast grew in the absence of adenine, it did so poorly. Dissection of the phenotype revealed that PPAT, the human ortholog of ADE4, showed only partial function whereas all other genes complemented fully. Suppressor analysis revealed other pathways that play a role in adenine de-novo pathway regulation. Phylogenetic analysis pointed to adaptations of enzyme regulation to endogenous metabolite level 'setpoints' in diverse organisms. Using DNA shuffling, we isolated specific amino acids combinations that stabilize the human protein in yeast. Thus, using adenine de novo biosynthesis as a proof of concept, we suggest that the engineering methods used in this study as well as the debugging strategies can be utilized to transplant metabolic pathway from any origin into yeast.
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Affiliation(s)
- Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jasmine Temple
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Zuojian Tang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobias Schraink
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Maayan Baron
- Institute for Computational Medicine and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jun Chen
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Paolo Mita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - James A Martin
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Benjamin P Tu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Itai Yanai
- Institute for Computational Medicine and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
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6
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Billerbeck S, Brisbois J, Agmon N, Jimenez M, Temple J, Shen M, Boeke JD, Cornish VW. Author Correction: A scalable peptide-GPCR language for engineering multicellular communication. Nat Commun 2019; 10:554. [PMID: 30696846 PMCID: PMC6351685 DOI: 10.1038/s41467-019-08545-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article omitted a declaration from the Competing Interests statement, which should have included the following: 'J.D.B. is a founder and Director of the following: Neochromosome, Inc., the Center of Excellence for Engineering Biology, and CDI Labs, Inc. and serves on the Scientific Advisory Board of the following: Modern Meadow, Inc., Recombinetics, Inc., and Sample6, Inc.'. This has now been corrected in both the PDF and HTML versions of the Article.
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Affiliation(s)
- Sonja Billerbeck
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - James Brisbois
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, NY, 10016, USA
| | - Miguel Jimenez
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.,The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jasmine Temple
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, NY, 10016, USA
| | - Michael Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, NY, 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, NY, 10016, USA
| | - Virginia W Cornish
- Department of Chemistry, Columbia University, New York, NY, 10027, USA. .,Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
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7
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Billerbeck S, Brisbois J, Agmon N, Jimenez M, Temple J, Shen M, Boeke JD, Cornish VW. A scalable peptide-GPCR language for engineering multicellular communication. Nat Commun 2018; 9:5057. [PMID: 30498215 PMCID: PMC6265332 DOI: 10.1038/s41467-018-07610-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 08/20/2018] [Accepted: 11/05/2018] [Indexed: 01/09/2023] Open
Abstract
Engineering multicellularity is one of the next breakthroughs for Synthetic Biology. A key bottleneck to building multicellular systems is the lack of a scalable signaling language with a large number of interfaces that can be used simultaneously. Here, we present a modular, scalable, intercellular signaling language in yeast based on fungal mating peptide/G-protein-coupled receptor (GPCR) pairs harnessed from nature. First, through genome-mining, we assemble 32 functional peptide-GPCR signaling interfaces with a range of dose-response characteristics. Next, we demonstrate that these interfaces can be combined into two-cell communication links, which serve as assembly units for higher-order communication topologies. Finally, we show 56 functional, two-cell links, which we use to assemble three- to six-member communication topologies and a three-member interdependent community. Importantly, our peptide-GPCR language is scalable and tunable by genetic encoding, requires minimal component engineering, and should be massively scalable by further application of our genome mining pipeline or directed evolution.
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Affiliation(s)
- Sonja Billerbeck
- Department of Chemistry, Columbia University, New York, New York, 10027, USA
| | - James Brisbois
- Department of Chemistry, Columbia University, New York, New York, 10027, USA
| | - Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Miguel Jimenez
- Department of Chemistry, Columbia University, New York, New York, 10027, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Jasmine Temple
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Michael Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Virginia W Cornish
- Department of Chemistry, Columbia University, New York, New York, 10027, USA.
- Department of Systems Biology, Columbia University, New York, New York, 10032, USA.
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8
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Xie ZX, Mitchell LA, Liu HM, Li BZ, Liu D, Agmon N, Wu Y, Li X, Zhou X, Li B, Xiao WH, Ding MZ, Wang Y, Yuan YJ, Boeke JD. Rapid and Efficient CRISPR/Cas9-Based Mating-Type Switching of Saccharomyces cerevisiae. G3 (Bethesda) 2018; 8:173-183. [PMID: 29150593 PMCID: PMC5765346 DOI: 10.1534/g3.117.300347] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/06/2017] [Indexed: 12/02/2022]
Abstract
Rapid and highly efficient mating-type switching of Saccharomyces cerevisiae enables a wide variety of genetic manipulations, such as the construction of strains, for instance, isogenic haploid pairs of both mating-types, diploids and polyploids. We used the CRISPR/Cas9 system to generate a double-strand break at the MAT locus and, in a single cotransformation, both haploid and diploid cells were switched to the specified mating-type at ∼80% efficiency. The mating-type of strains carrying either rod or ring chromosome III were switched, including those lacking HMLα and HMR a cryptic mating loci. Furthermore, we transplanted the synthetic yeast chromosome V to build a haploid polysynthetic chromosome strain by using this method together with an endoreduplication intercross strategy. The CRISPR/Cas9 mating-type switching method will be useful in building the complete synthetic yeast (Sc2.0) genome. Importantly, it is a generally useful method to build polyploids of a defined genotype and generally expedites strain construction, for example, in the construction of fully a/a/α/α isogenic tetraploids.
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MESH Headings
- CRISPR-Cas Systems
- Cell Engineering/methods
- Chromosomes, Artificial/chemistry
- DNA Breaks, Double-Stranded
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- Gene Editing/methods
- Genes, Mating Type, Fungal
- Genetic Loci
- Genome, Fungal
- Plasmids/chemistry
- Plasmids/metabolism
- Ploidies
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
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Affiliation(s)
- Ze-Xiong Xie
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
- Institute for Systems Genetics, NYU Langone Health, New York 10016
| | - Leslie A Mitchell
- Department of Biochemistry and Molecular Pharmacology NYU Langone Health, New York 10016
- Institute for Systems Genetics, NYU Langone Health, New York 10016
| | - Hui-Min Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
| | - Duo Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
| | - Neta Agmon
- Department of Biochemistry and Molecular Pharmacology NYU Langone Health, New York 10016
- Institute for Systems Genetics, NYU Langone Health, New York 10016
| | - Yi Wu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
- Institute for Systems Genetics, NYU Langone Health, New York 10016
| | - Xia Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
| | - Xiao Zhou
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
| | - Bo Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
| | - Wen-Hai Xiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
| | - Ming-Zhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
| | - Ying Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, China
| | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology NYU Langone Health, New York 10016
- Institute for Systems Genetics, NYU Langone Health, New York 10016
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10
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Agmon N, Mitchell LA, Cai Y, Ikushima S, Chuang J, Zheng A, Choi WJ, Martin JA, Caravelli K, Stracquadanio G, Boeke JD. Yeast Golden Gate (yGG) for the Efficient Assembly of S. cerevisiae Transcription Units. ACS Synth Biol 2015; 4:853-9. [PMID: 25756291 DOI: 10.1021/sb500372z] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have adapted the Golden Gate DNA assembly method to the assembly of transcription units (TUs) for the yeast Saccharomyces cerevisiae, in a method we call yeast Golden Gate (yGG). yGG allows for the easy assembly of TUs consisting of promoters (PRO), coding sequences (CDS), and terminators (TER). Carefully designed overhangs exposed by digestion with a type IIS restriction enzyme enable virtually seamless assembly of TUs that, in principle, contain all of the information necessary to express a gene of interest in yeast. We also describe a versatile set of yGG acceptor vectors to be used for TU assembly. These vectors can be used for low or high copy expression of assembled TUs or integration into carefully selected innocuous genomic loci. yGG provides synthetic biologists and yeast geneticists with an efficient new means by which to engineer S. cerevisiae.
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Affiliation(s)
- Neta Agmon
- Institute
for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, United States
| | - Leslie A. Mitchell
- Institute
for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, United States
| | - Yizhi Cai
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
- School
of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JR, United Kingdom
| | - Shigehito Ikushima
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - James Chuang
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - Allen Zheng
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - Woo-Jin Choi
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - J. Andrew Martin
- Institute
for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, United States
| | - Katrina Caravelli
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - Giovanni Stracquadanio
- High
Throughput Biology Center, School of Medicine, Johns Hopkins University, Edward D.
Miller Research Building, 733 North Broadway, Baltimore, Maryland 21205, United States
| | - Jef D. Boeke
- Institute
for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, United States
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11
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Mitchell LA, Chuang J, Agmon N, Khunsriraksakul C, Phillips NA, Cai Y, Truong DM, Veerakumar A, Wang Y, Mayorga M, Blomquist P, Sadda P, Trueheart J, Boeke JD. Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae. Nucleic Acids Res 2015; 43:6620-30. [PMID: 25956652 PMCID: PMC4513848 DOI: 10.1093/nar/gkv466] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [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: 03/16/2015] [Accepted: 04/27/2015] [Indexed: 11/14/2022] Open
Abstract
We have developed a method for assembling genetic pathways for expression in Saccharomyces cerevisiae. Our pathway assembly method, called VEGAS (Versatile genetic assembly system), exploits the native capacity of S. cerevisiae to perform homologous recombination and efficiently join sequences with terminal homology. In the VEGAS workflow, terminal homology between adjacent pathway genes and the assembly vector is encoded by 'VEGAS adapter' (VA) sequences, which are orthogonal in sequence with respect to the yeast genome. Prior to pathway assembly by VEGAS in S. cerevisiae, each gene is assigned an appropriate pair of VAs and assembled using a previously described technique called yeast Golden Gate (yGG). Here we describe the application of yGG specifically to building transcription units for VEGAS assembly as well as the VEGAS methodology. We demonstrate the assembly of four-, five- and six-gene pathways by VEGAS to generate S. cerevisiae cells synthesizing β-carotene and violacein. Moreover, we demonstrate the capacity of yGG coupled to VEGAS for combinatorial assembly.
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Affiliation(s)
- Leslie A Mitchell
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York City, NY 10016, USA Institute for Systems Genetics, New York University Langone School of Medicine, New York City, NY 10016, USA High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James Chuang
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Neta Agmon
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York City, NY 10016, USA Institute for Systems Genetics, New York University Langone School of Medicine, New York City, NY 10016, USA High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chachrit Khunsriraksakul
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nick A Phillips
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA Department of Biomedical Engineering and Institute of Genetic Medicine, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yizhi Cai
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David M Truong
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York City, NY 10016, USA Institute for Systems Genetics, New York University Langone School of Medicine, New York City, NY 10016, USA
| | - Ashan Veerakumar
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yuxuan Wang
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | | | - Praneeth Sadda
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York City, NY 10016, USA Institute for Systems Genetics, New York University Langone School of Medicine, New York City, NY 10016, USA High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CYL, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, Chandrasegaran S. Total synthesis of a functional designer eukaryotic chromosome. Science 2014; 344:55-8. [PMID: 24674868 DOI: 10.1126/science.1249252] [Citation(s) in RCA: 364] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair native Saccharomyces cerevisiae chromosome III. Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling. SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATα allele on synIII. The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.
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Affiliation(s)
- Narayana Annaluru
- Department of Environmental Health Sciences, Johns Hopkins University (JHU) School of Public Health, Baltimore, MD 21205, USA
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Agmon N, Liefshitz B, Zimmer C, Fabre E, Kupiec M. Effect of nuclear architecture on the efficiency of double-strand break repair. Nat Cell Biol 2013; 15:694-9. [PMID: 23644470 DOI: 10.1038/ncb2745] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/02/2013] [Indexed: 12/15/2022]
Abstract
The most dangerous insults to the genome's integrity are those that break both strands of the DNA. Double-strand breaks can be repaired by homologous recombination; in this conserved mechanism, a global genomic homology search finds sequences similar to those near the break, and uses them as a template for DNA synthesis and ligation. Chromosomes occupy restricted territories within the nucleus. We show that yeast genomic regions whose nuclear territories overlap recombine more efficiently than sequences located in spatially distant territories. Tethering of telomeres and centromeres reduces the efficiency of recombination between distant genomic loci, lowering the chances of non-allelic recombination. Our results challenge present models that posit an active scanning of the whole nuclear volume by the broken chromosomal end; they demonstrate that the search for homology is a limiting step in homologous recombination, and emphasize the importance of nuclear organization in genome maintenance.
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Affiliation(s)
- Neta Agmon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
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15
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Agmon N, Yovel M, Harari Y, Liefshitz B, Kupiec M. The role of Holliday junction resolvases in the repair of spontaneous and induced DNA damage. Nucleic Acids Res 2011; 39:7009-19. [PMID: 21609961 PMCID: PMC3167605 DOI: 10.1093/nar/gkr277] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/07/2011] [Accepted: 04/07/2011] [Indexed: 12/02/2022] Open
Abstract
DNA double-strand breaks (DSBs) and other lesions occur frequently during cell growth and in meiosis. These are often repaired by homologous recombination (HR). HR may result in the formation of DNA structures called Holliday junctions (HJs), which need to be resolved to allow chromosome segregation. Whereas HJs are present in most HR events in meiosis, it has been proposed that in vegetative cells most HR events occur through intermediates lacking HJs. A recent screen in yeast has shown HJ resolution activity for a protein called Yen1, in addition to the previously known Mus81/Mms4 complex. Yeast strains deleted for both YEN1 and MMS4 show a reduction in growth rate, and are very sensitive to DNA-damaging agents. In addition, we investigate the genetic interaction of yen1 and mms4 with mutants defective in different repair pathways. We find that in the absence of Yen1 and Mms4 deletion of RAD1 or RAD52 have no further effect, whereas additional sensitivity is seen if RAD51 is deleted. Finally, we show that yeast cells are unable to carry out meiosis in the absence of both resolvases. Our results show that both Yen1 and Mms4/Mus81 play important (although not identical) roles during vegetative growth and in meiosis.
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Affiliation(s)
| | | | | | | | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69979, Israel
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16
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Cohen S, Agmon N, Sobol O, Segal D. Extrachromosomal circles of satellite repeats and 5S ribosomal DNA in human cells. Mob DNA 2010; 1:11. [PMID: 20226008 PMCID: PMC3225859 DOI: 10.1186/1759-8753-1-11] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [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: 05/07/2009] [Accepted: 03/08/2010] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Extrachomosomal circular DNA (eccDNA) is ubiquitous in eukaryotic organisms and was detected in every organism tested, including in humans. A two-dimensional gel electrophoresis facilitates the detection of eccDNA in preparations of genomic DNA. Using this technique we have previously demonstrated that most of eccDNA consists of exact multiples of chromosomal tandemly repeated DNA, including both coding genes and satellite DNA. RESULTS Here we report the occurrence of eccDNA in every tested human cell line. It has heterogeneous mass ranging from less than 2 kb to over 20 kb. We describe eccDNA homologous to human alpha satellite and the SstI mega satellite. Moreover, we show, for the first time, circular multimers of the human 5S ribosomal DNA (rDNA), similar to previous findings in Drosophila and plants. We further demonstrate structures that correspond to intermediates of rolling circle replication, which emerge from the circular multimers of 5S rDNA and SstI satellite. CONCLUSIONS These findings, and previous reports, support the general notion that every chromosomal tandem repeat is prone to generate eccDNA in eukryoric organisms including humans. They suggest the possible involvement of eccDNA in the length variability observed in arrays of tandem repeats. The implications of eccDNA on genome biology may include mechanisms of centromere evolution, concerted evolution and homogenization of tandem repeats and genomic plasticity.
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Affiliation(s)
- Sarit Cohen
- Department of Molecular Microbiology & Biotechnology Tel-Aviv University, Tel-Aviv 69978, Israel.
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17
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Ben-Aroya S, Agmon N, Yuen K, Kwok T, McManus K, Kupiec M, Hieter P. Proteasome nuclear activity affects chromosome stability by controlling the turnover of Mms22, a protein important for DNA repair. PLoS Genet 2010; 6:e1000852. [PMID: 20174551 PMCID: PMC2824753 DOI: 10.1371/journal.pgen.1000852] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [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: 09/09/2009] [Accepted: 01/20/2010] [Indexed: 11/18/2022] Open
Abstract
To expand the known spectrum of genes that maintain genome stability, we screened a recently released collection of temperature sensitive (Ts) yeast mutants for a chromosome instability (CIN) phenotype. Proteasome subunit genes represented a major functional group, and subsequent analysis demonstrated an evolutionarily conserved role in CIN. Analysis of individual proteasome core and lid subunit mutations showed that the CIN phenotype at semi-permissive temperature is associated with failure of subunit localization to the nucleus. The resultant proteasome dysfunction affects chromosome stability by impairing the kinetics of double strand break (DSB) repair. We show that the DNA repair protein Mms22 is required for DSB repair, and recruited to chromatin in a ubiquitin-dependent manner as a result of DNA damage. Moreover, subsequent proteasome-mediated degradation of Mms22 is necessary and sufficient for cell cycle progression through the G2/M arrest induced by DNA damage. Our results demonstrate for the first time that a double strand break repair protein is a proteasome target, and thus link nuclear proteasomal activity and DSB repair. Chromosome Instability (CIN) is a genome phenotype that involves changes in chromosome number or structure, and accounts for most malignancies. In this paper, we describe a screen to identify a set of novel CIN genes and find that proteasomal subunits represent a major functional group. We show that proteasome dysfunction affects CIN by impairing DNA double strand break (DSB) repair. Previous studies speculated that the proteasome is required to degrade one or more components of the DSB repair machinery; however, until now, no such target has been identified. Here we identify the previously described CIN gene MMS22 as a proteasomal target. We found that, as a result of DNA damage, Mms22 is ubiquitinated and recruited to chromatin. Mms22 then undergoes polyubiquitination and subsequent proteasome-mediated degradation. We also provide evidence that the degradation of Mms22 is important for the normal course of DNA repair and for exit from the G2/M arrest induced by DNA damage. Our results demonstrate for the first time that a DSB repair protein is a proteasome target, linking nuclear proteasomal activity and DSB repair. The mechanism of regulation of Mms22 may serve as a paradigm to understand how these additional proteins are regulated by the proteasome.
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Affiliation(s)
- Shay Ben-Aroya
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Neta Agmon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Karen Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Teresa Kwok
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Kirk McManus
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- * E-mail:
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18
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Abstract
Double-strand breaks (DSBs) occur frequently during cell growth. Due to the presence of repeated sequences in the genome, repair of a single DSB can result in gene conversion, translocation, deletion or tandem duplication depending on the mechanism and the sequence chosen as partner for the recombinational repair. Here, we study how yeast cells repair a single, inducible DSB when there are several potential donors to choose from, in the same chromosome and elsewhere in the genome. We systematically investigate the parameters that affect the choice of mechanism, as well as its genetic regulation. Our results indicate that intrachromosomal homologous sequences are always preferred as donors for repair. We demonstrate the occurrence of a novel tri-partite repair product that combines ectopic gene conversion and deletion. In addition, we show that increasing the distance between two repeated sequences enhances the dependence on Rad51 for colony formation after DSB repair. This is due to a role of Rad51 in the recovery from the checkpoint signal induced by the DSB. We suggest a model for the competition between the different homologous recombination pathways. Our model explains how different repair mechanisms are able to compensate for each other during DSB repair.
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Affiliation(s)
- Neta Agmon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
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19
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Abstract
Extrachromosomal circular DNA (eccDNA) is one characteristic of the plasticity of the eukaryotic genome. It is found in various organisms and contains sequences derived primarily from repetitive chromosomal DNA. Using 2D gel electrophoresis, we have previously detected eccDNA composed of chromosomal tandem repeats throughout the life cycle of Drosophila. Here, we report for the first time evidence suggesting the occurrence of rolling circle replication of eccDNA in Drosophila. We show, on 2D gels, specific structures that can be enriched by benzoylated naphthoylated DEAE-cellulose chromatography and were identified in other systems as rolling circle intermediates (RCIs). These RCIs are homologous to histone genes, Stellate and Suppressor of Stellate, which are all organized in the chromosomes as tandem repeats. RCIs are detected throughout the life cycle of Drosophila and in cultured fly cells. These structures are found regardless of the expression of the replicated gene or of its chromosomal copy number.
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Affiliation(s)
- Sarit Cohen
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University Tel Aviv 69978, Israel.
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20
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Solntsev KM, Huppert D, Agmon N. Experimental evidence for a kinetic transition in reversible reactions. Phys Rev Lett 2001; 86:3427-3430. [PMID: 11327987 DOI: 10.1103/physrevlett.86.3427] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2000] [Indexed: 05/23/2023]
Abstract
We provide a first experimental verification of a theoretical prediction of a kinetic transition in a reversible binding reaction, AB right harpoon over left harpoon A+B, driven by the difference in effective lifetimes of the bound and the unbound states. We consider the kinetics of excited-state proton transfer to solvent from a photoacid whose conjugate anionic base possesses an extremely short unbound anion lifetime. Its solvent variation relative to the overall dissociation rate coefficient induces a transition in the kinetics, from power law to exponential.
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Affiliation(s)
- K M Solntsev
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
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21
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Abstract
Using an iterative solution in Laplace-Fourier space, we supply a rigorous mathematical proof for the long-time asymptotics of reversible binding in one dimension. The asymptotic power law and its concentration dependent prefactor result from diffusional and many-body effects which, unlike for the corresponding irreversible reaction and in classical chemical kinetics, play a dominant role in shaping the approach to equilibrium.
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Affiliation(s)
- IV Gopich
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel
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22
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Abstract
A quantitative model, which involves diffusion on a temperature-dependent potential, is utilized to analyze the time-dependence of geminate CO recombination to sperm whale myoglobin in a trehalose glass and the accompanying spectral shifts. Most of the recombination is inhomogeneous. This is due to higher geminate reactivity rather than slower protein relaxation. A fraction of the hemes undergoes relaxation with a concomitant increase in the barrier height for recombination. The activation energy for conformational diffusion (relaxation) is considerably lower than in glycerol/water. "Protein collapse", manifested in glycerol/water by a decrease in the equilibrium conformational separation between the bound and deoxy states, is completely prevented in trehalose. We postulate that the high internal viscosity in glycerol/water is due to dehydration of the heme pocket. Trehalose prevents the escape of the few vital internal water molecules and thus preserves the internal lability of the protein. This might be important in understanding the ability of trehalose to protect against the adverse effects of dehydration.
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Affiliation(s)
- G M Sastry
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem, Israel
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23
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Abstract
Binding kinetics of receptor arrays can differ dramatically from that of the isolated receptor. We simulate synaptic transmission using a microscopically accurate Brownian dynamics routine. We study the factors governing the rise and decay of the activation probability as a function of the number of transmitter molecules released. Using a realistic receptor array geometry, the simulation reproduces the time course of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor-mediated excitatory postsynaptic currents. A consistent interpretation of experimentally observed synaptic currents in terms of rebinding and spatial correlations is discussed.
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Affiliation(s)
- N Agmon
- Department of Physical Chemistry, Hebrew University, Jerusalem, Israel.
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24
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Abstract
We investigate the various reactivity patterns possible when several transmitter molecules, released at one side of a synaptic gap, diffuse and bind reversibly to a single receptor at the other end. In the framework of a one-dimensional approximation, the complete time, reactivity, concentration and gap-width dependence are determined, using a rigorous theoretical and computational approach to the many-body aspects of this problem. The time dependence of the survival probability is found to consist of up to four phases. These include a short delay followed by gaussian, power-law, and exponential decay phases. A rigorous expression is derived for the long-time exponent and approximate expressions are obtained for describing the short-time gaussian phase.
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Affiliation(s)
- N Agmon
- Department of Physical Chemistry, Hebrew University, Jerusalem, Israel
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25
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Abstract
Heme proteins react inhomogeneously with ligands at cryogenic temperatures and homogeneously at room temperature. We have identified and characterized a transition from inhomogeneous to homogeneous behavior at intermediate temperatures in the time dependence of CO binding to horse myoglobin. The turnover is attributed to a functionally important tertiary protein relaxation process during which the barrier increases dynamically. This is verified by a combination of theory and multipulse measurements. A likely biological significance of this effect is in the autocatalysis of the ligand release process.
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Affiliation(s)
- N Agmon
- Department of Physical Chemistry, Hebrew University, Jerusalem, Israel
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Rabinovich S, Agmon N. Scaling and critical-like behavior in multidimensional diffusive dynamics. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1993; 47:3717-3720. [PMID: 9960428 DOI: 10.1103/physreve.47.3717] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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28
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Agmon N. Competitive and noncompetitive reversible binding processes. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1993; 47:2415-2429. [PMID: 9960273 DOI: 10.1103/physreve.47.2415] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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29
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Huppert D, Goldberg SY, Masad A, Agmon N. Experimental determination of the long-time behavior in reversible binary chemical reactions. Phys Rev Lett 1992; 68:3932-3935. [PMID: 10045841 DOI: 10.1103/physrevlett.68.3932] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Abstract
The temporal shift in the near-IR absorption peak of myoglobin (Mb) following flash photolysis of MbCO at cryogenic temperatures appears to be due largely to an inhomogeneous reactive process rather than to relaxation. This conclusion, which follows from a new analysis of the experimental data, is based on the following three points: First, at very low temperatures (60 K) a transient line-narrowing effect can be detected. Second, there is a universal, temperature-independent, correlation between spectral shift and survival probability in the rebinding kinetics, and third, the same quantitative model which accounts for rebinding accounts semiquantitatively for the temporal shift in the peak. A fit to the model indicates that the inhomogeneous broadening of the near-IR peak in myoglobin is 15-20% of the total width. The same rebinding process which governs the loss of intensity of this peak is therefore most likely responsible for the shift in its center wavelength.
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Affiliation(s)
- N Agmon
- Department of Physical Chemistry, Hebrew University, Jerusalem, Israel
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Agmon N, Glasser ML. Complete asymptotic expansion for integrals arising from one-dimensional diffusion with random traps. Phys Rev A Gen Phys 1986; 34:656-658. [PMID: 9897304 DOI: 10.1103/physreva.34.656] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Abstract
We present a simple model which extends the Michaelis-Menten mechanism by incorporating a continuous protein conformational change in enzymatic catalysis. This model can represent a quantitative version for "rack" or "induced fit" mechanisms. In the steady-state it leads to an equation of the Michaelis-Menten form, but with the catalytic step at the active site showing strong dependence on solvent viscosity. We suggest that a careful examination of solvent viscosity effects on enzymatic activity may serve as a test for the conformational change hypothesis.
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Agmon N, Feinberg D. [Treatment of colostomy patients]. Acta Biochim Biophys Acad Sci Hung 1973; 21:26-34. [PMID: 4763835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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