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Xiong Y, Zhang H, Zhou S, Ma L, Xiao W, Wu Y, Yuan YJ. Structural Variations and Adaptations of Synthetic Chromosome Ends Driven by SCRaMbLE in Haploid and Diploid Yeasts. ACS Synth Biol 2023; 12:689-699. [PMID: 36821394 DOI: 10.1021/acssynbio.2c00424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Variations and adaptations of chromosome ends play an important role in eukaryotic karyotype evolution. Traditional experimental studies of the adaptations of chromosome ends mainly rely on the strategy of introducing defects; thus, the adaptation methods of survivors may vary depending on the initial defects. Here, using the SCRaMbLE strategy, we obtained a library of haploid and diploid synthetic strains with variations in chromosome ends. Analysis of the SCRaMbLEd survivors revealed four routes of adaptation: homologous recombination between nonhomologous chromosome arms (haploids) or homologous chromosome arms (diploids), site-specific recombination between intra- or interchromosomal ends, circularization of chromosomes, and loss of whole chromosomes (diploids). We also found that circularization of synthetic chromosomes can be generated by SCRaMbLE. Our study of various adaptation routes of chromosome ends provides insight into eukaryotic karyotype evolution from the viewpoint of synthetic genomics.
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Affiliation(s)
- Yao Xiong
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hui Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Sijie Zhou
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Lu Ma
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wenhai Xiao
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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2
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Kolářová K, Nešpor Dadejová M, Loja T, Lochmanová G, Sýkorová E, Dvořáčková M. Disruption of NAP1 genes in Arabidopsis thaliana suppresses the fas1 mutant phenotype, enhances genome stability and changes chromatin compaction. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:56-73. [PMID: 33368779 DOI: 10.1111/tpj.15145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/21/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Histone chaperones mediate the assembly and disassembly of nucleosomes and participate in essentially all DNA-dependent cellular processes. In Arabidopsis thaliana, loss-of-function of FAS1 or FAS2 subunits of the H3-H4 histone chaperone complex CHROMATIN ASSEMBLY FACTOR 1 (CAF-1) has a dramatic effect on plant morphology, growth and overall fitness. CAF-1 dysfunction can lead to altered chromatin compaction, systematic loss of repetitive elements or increased DNA damage, clearly demonstrating its severity. How chromatin composition is maintained without functional CAF-1 remains elusive. Here we show that disruption of the H2A-H2B histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 (NAP1) suppresses the FAS1 loss-of-function phenotype. The quadruple mutant fas1 nap1;1 nap1;2 nap1;3 shows wild-type growth, decreased sensitivity to genotoxic stress and suppression of telomere and 45S rDNA loss. Chromatin of fas1 nap1;1 nap1;2 nap1;3 plants is less accessible to micrococcal nuclease and the nuclear H3.1 and H3.3 histone pools change compared to fas1. Consistently, association between NAP1 and H3 occurs in the cytoplasm and nucleus in vivo in protoplasts. Altogether we show that NAP1 proteins play an essential role in DNA repair in fas1, which is coupled to nucleosome assembly through modulation of H3 levels in the nucleus.
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Affiliation(s)
- Karolína Kolářová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
- Molecular Cytology and Cytometry, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, Brno, CZ-61265, Czech Republic
| | - Martina Nešpor Dadejová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
| | - Tomáš Loja
- Centre for Molecular Medicine, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
| | - Eva Sýkorová
- Molecular Cytology and Cytometry, Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, Brno, CZ-61265, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology/Masaryk University, Kamenice 5, Brno, CZ-62500, Czech Republic
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3
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Baek S, Utomo JC, Lee JY, Dalal K, Yoon YJ, Ro DK. The yeast platform engineered for synthetic gRNA-landing pads enables multiple gene integrations by a single gRNA/Cas9 system. Metab Eng 2021; 64:111-121. [PMID: 33549837 DOI: 10.1016/j.ymben.2021.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 12/28/2020] [Accepted: 01/30/2021] [Indexed: 12/25/2022]
Abstract
Saccharomyces cerevisiae is a versatile microbial platform to build synthetic metabolic pathways for production of diverse chemicals. To expedite the construction of complex metabolic pathways by multiplex CRISPR-Cas9 genome-edit, eight desirable intergenic loci, located adjacent to highly expressed genes selected from top 100 expressers, were identified and fully characterized for three criteria after integrating green fluorescent protein (GFP) gene - CRISPR-mediated GFP integration efficiency, expression competency assessed by levels of GFP fluorescence, and assessing growth rates of GFP integrated strains. Five best performing intergenic loci were selected to build a multiplex CRISPR platform, and a synthetic 23-bp DNA comprised of 20-bp synthetic DNA with a protospacer adjacent motif (PAM) was integrated into the five loci using CRISPR-Cas9 in a sequential manner. This process resulted in five different yeast strains harbouring 1-5 synthetic gRNA-binding sites in their genomes. Using these pre-engineered yeast strains, simultaneous integrations of 2-, 3-, 4-, or 5-genes to the targeted loci were demonstrated with efficiencies from 85% to 98% using beet pigment betalain (3-gene pathway), hygromycin and geneticin resistance markers. Integrations of the multiple, foreign genes in the targeted loci with 100% precision were validated by genotyping. Finally, we further developed the strain to have 6th synthetic gRNA-binding site, and the resulting yeast strain was used to generate a yeast strain producing a sesquiterpene lactone, kauniolide by simultaneous 6-gene integrations. This study demonstrates the effectiveness of a single gRNA-mediated CRISPR platform to build complex metabolic pathways in yeast.
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Affiliation(s)
- Sihyun Baek
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | | | - Ji Young Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Kunal Dalal
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada.
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4
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Yu EY, Hsu M, Holloman WK, Lue NF. Contributions of recombination and repair proteins to telomere maintenance in telomerase-positive and negative Ustilago maydis. Mol Microbiol 2017; 107:81-93. [PMID: 29052918 DOI: 10.1111/mmi.13866] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/13/2017] [Accepted: 10/14/2017] [Indexed: 11/26/2022]
Abstract
Homologous recombination and repair factors are known to promote both telomere replication and recombination-based telomere extension. Herein, we address the diverse contributions of several recombination/repair proteins to telomere maintenance in Ustilago maydis, a fungus that bears strong resemblance to mammals with respect to telomere regulation and recombination mechanisms. In telomerase-positive U. maydis, deletion of rad51 and blm separately caused shortened but stably maintained telomeres, whereas deletion of both engendered similar telomere loss, suggesting that the repair proteins help to resolve similar problems in telomere replication. In telomerase-negative cells, the loss of Rad51 or Brh2 caused accelerated senescence and failure to generate survivors on semi-solid medium. However, slow growing survivors can be isolated through continuous liquid culturing, and these survivors exhibit type II-like as well as ALT-like telomere features. In contrast, the trt1Δ blmΔ double mutant gives rise to survivors as readily as the trt1Δ single mutant, and like the single mutant survivors, exhibit almost exclusively type I-like telomere features. In addition, we observed direct physical interactions between Blm and two telomere-binding proteins, which may thus recruit or regulate Blm at telomeres. Our findings provide the basis for further analyzing the interplays between telomerase, telomere replication, and telomere recombination.
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Affiliation(s)
- Eun Young Yu
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center Weill Medical College of Cornell University, New York, NY, USA
| | - Min Hsu
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center Weill Medical College of Cornell University, New York, NY, USA
| | - William K Holloman
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center Weill Medical College of Cornell University, New York, NY, USA
| | - Neal F Lue
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center Weill Medical College of Cornell University, New York, NY, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
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5
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Pathways and Mechanisms that Prevent Genome Instability in Saccharomyces cerevisiae. Genetics 2017; 206:1187-1225. [PMID: 28684602 PMCID: PMC5500125 DOI: 10.1534/genetics.112.145805] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 04/26/2017] [Indexed: 12/13/2022] Open
Abstract
Genome rearrangements result in mutations that underlie many human diseases, and ongoing genome instability likely contributes to the development of many cancers. The tools for studying genome instability in mammalian cells are limited, whereas model organisms such as Saccharomyces cerevisiae are more amenable to these studies. Here, we discuss the many genetic assays developed to measure the rate of occurrence of Gross Chromosomal Rearrangements (called GCRs) in S. cerevisiae. These genetic assays have been used to identify many types of GCRs, including translocations, interstitial deletions, and broken chromosomes healed by de novo telomere addition, and have identified genes that act in the suppression and formation of GCRs. Insights from these studies have contributed to the understanding of pathways and mechanisms that suppress genome instability and how these pathways cooperate with each other. Integrated models for the formation and suppression of GCRs are discussed.
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6
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Jalal D, Chalissery J, Hassan AH. Genome maintenance in Saccharomyces cerevisiae: the role of SUMO and SUMO-targeted ubiquitin ligases. Nucleic Acids Res 2017; 45:2242-2261. [PMID: 28115630 PMCID: PMC5389695 DOI: 10.1093/nar/gkw1369] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/02/2017] [Indexed: 01/08/2023] Open
Abstract
The genome of the cell is often exposed to DNA damaging agents and therefore requires an intricate well-regulated DNA damage response (DDR) to overcome its deleterious effects. The DDR needs proper regulation for its timely activation, repression, as well as appropriate choice of repair pathway. Studies in Saccharomyces cerevisiae have advanced our understanding of the DNA damage response, as well as the mechanisms the cell employs to maintain genome stability and how these mechanisms are regulated. Eukaryotic cells utilize post-translational modifications as a means for fine-tuning protein functions. Ubiquitylation and SUMOylation involve the attachment of small protein molecules onto proteins to modulate function or protein–protein interactions. SUMO in particular, was shown to act as a molecular glue when DNA damage occurs, facilitating the assembly of large protein complexes in repair foci. In other instances, SUMOylation alters a protein's biochemical activities, and interactions. SUMO-targeted ubiquitin ligases (STUbLs) are enzymes that target SUMOylated proteins for ubiquitylation and subsequent degradation, providing a function for the SUMO modification in the regulation and disassembly of repair complexes. Here, we discuss the major contributions of SUMO and STUbLs in the regulation of DNA damage repair pathways as well as in the maintenance of critical regions of the genome, namely rDNA regions, telomeres and the 2 μm circle in budding yeast.
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Affiliation(s)
- Deena Jalal
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE
| | - Jisha Chalissery
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE
| | - Ahmed H Hassan
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE
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Beletsky AV, Malyavko AN, Sukhanova MV, Mardanova ES, Zvereva MI, Petrova OA, Parfenova YY, Rubtsova MP, Mardanov AV, Lavrik OI, Dontsova OA, Ravin NV. The genome-wide transcription response to telomerase deficiency in the thermotolerant yeast Hansenula polymorpha DL-1. BMC Genomics 2017; 18:492. [PMID: 28659185 PMCID: PMC5490237 DOI: 10.1186/s12864-017-3889-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 06/21/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND In the course of replication of eukaryotic chromosomes, the telomere length is maintained due to activity of telomerase, the ribonucleoprotein reverse transcriptase. Abolishing telomerase function causes progressive shortening of telomeres and, ultimately, cell cycle arrest and replicative senescence. To better understand the cellular response to telomerase deficiency, we performed a transcriptomic study for the thermotolerant methylotrophic yeast Hansenula polymorpha DL-1 lacking telomerase activity. RESULTS Mutant strain of H. polymorpha carrying a disrupted telomerase RNA gene was produced, grown to senescence and analyzed by RNA-seq along with wild type strain. Telomere shortening induced a transcriptional response involving genes relevant to telomere structure and maintenance, DNA damage response, information processing, and some metabolic pathways. Genes involved in DNA replication and repair, response to environmental stresses and intracellular traffic were up-regulated in senescent H. polymorpha cells, while strong down-regulation was observed for genes involved in transcription and translation, as well as core histones. CONCLUSIONS Comparison of the telomerase deletion transcription responses by Saccharomyces cerevisiae and H. polymorpha demonstrates that senescence makes different impact on the main metabolic pathways of these yeast species but induces similar changes in processes related to nucleic acids metabolism and protein synthesis. Up-regulation of a subunit of the TORC1 complex is clearly relevant for both types of yeast.
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Affiliation(s)
- Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia
| | - Alexander N Malyavko
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia.,Center of Functional Genomics, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
| | - Eugenia S Mardanova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia
| | - Maria I Zvereva
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia
| | - Olga A Petrova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1, bld. 40, Moscow, 119992, Russia
| | - Yulia Yu Parfenova
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia
| | - Maria P Rubtsova
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Olga A Dontsova
- Faculty of Chemistry, Moscow State University, Leninskie Gory 1, bld. 3, Moscow, 119991, Russia.,Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1, bld. 40, Moscow, 119992, Russia.,Center of Functional Genomics, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld 2, Moscow, 119071, Russia.
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8
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Reider Apel A, d'Espaux L, Wehrs M, Sachs D, Li RA, Tong GJ, Garber M, Nnadi O, Zhuang W, Hillson NJ, Keasling JD, Mukhopadhyay A. A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae. Nucleic Acids Res 2017; 45:496-508. [PMID: 27899650 PMCID: PMC5224472 DOI: 10.1093/nar/gkw1023] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/12/2016] [Accepted: 10/18/2016] [Indexed: 01/08/2023] Open
Abstract
Despite the extensive use of Saccharomyces cerevisiae as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locus and promoter selection, as well as protein localization and solubility. The toolkit includes 23 Cas9-sgRNA plasmids, 37 promoters of various strengths and temporal expression profiles, and 10 protein-localization, degradation and solubility tags. We facilitated the use of these parts via a web-based tool, that automates the generation of DNA fragments for integration. Our system builds upon existing gene editing methods in the thoroughness with which the parts are standardized and characterized, the types and number of parts available and the ease with which our methodology can be used to perform genetic edits in yeast. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important enzyme, taxadiene synthase (TXS). This approach enabled us to diagnose an issue with TXS solubility, the resolution of which yielded a 25-fold improvement in taxadiene production.
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Affiliation(s)
- Amanda Reider Apel
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Leo d'Espaux
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Maren Wehrs
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Daniel Sachs
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Rachel A Li
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, CA 94720, USA
| | - Gary J Tong
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Megan Garber
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - Oge Nnadi
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
| | - William Zhuang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, CA 94720, USA
| | - Nathan J Hillson
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
- DOE Joint Genome Institute, Walnut Creek, California, CA 94598, USA
| | - Jay D Keasling
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, CA 94720, USA
- DOE Joint Genome Institute, Walnut Creek, California, CA 94598, USA
- The Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Aindrila Mukhopadhyay
- DOE Joint BioEnergy Institute, Emeryville, California, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, CA 94720, USA
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9
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Lue NF, Yu EY. Telomere recombination pathways: tales of several unhappy marriages. Curr Genet 2016; 63:401-409. [PMID: 27666406 DOI: 10.1007/s00294-016-0653-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 01/29/2023]
Abstract
All happy families are alike; each unhappy family is unhappy in its own way.-Leo Tolstoy, Anna Karenina.
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Affiliation(s)
- Neal F Lue
- Department of Microbiology and Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, NY, USA. .,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Eun Young Yu
- Department of Microbiology and Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, New York, NY, USA
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10
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Qi Z, Redding S, Lee JY, Gibb B, Kwon Y, Niu H, Gaines WA, Sung P, Greene EC. DNA sequence alignment by microhomology sampling during homologous recombination. Cell 2015; 160:856-869. [PMID: 25684365 DOI: 10.1016/j.cell.2015.01.029] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/18/2014] [Accepted: 01/09/2015] [Indexed: 11/19/2022]
Abstract
Homologous recombination (HR) mediates the exchange of genetic information between sister or homologous chromatids. During HR, members of the RecA/Rad51 family of recombinases must somehow search through vast quantities of DNA sequence to align and pair single-strand DNA (ssDNA) with a homologous double-strand DNA (dsDNA) template. Here, we use single-molecule imaging to visualize Rad51 as it aligns and pairs homologous DNA sequences in real time. We show that Rad51 uses a length-based recognition mechanism while interrogating dsDNA, enabling robust kinetic selection of 8-nucleotide (nt) tracts of microhomology, which kinetically confines the search to sites with a high probability of being a homologous target. Successful pairing with a ninth nucleotide coincides with an additional reduction in binding free energy, and subsequent strand exchange occurs in precise 3-nt steps, reflecting the base triplet organization of the presynaptic complex. These findings provide crucial new insights into the physical and evolutionary underpinnings of DNA recombination.
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Affiliation(s)
- Zhi Qi
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Sy Redding
- Department of Chemistry, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Ja Yil Lee
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - Bryan Gibb
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Hengyao Niu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - William A Gaines
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA.
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11
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Fallet E, Jolivet P, Soudet J, Lisby M, Gilson E, Teixeira MT. Length-dependent processing of telomeres in the absence of telomerase. Nucleic Acids Res 2014; 42:3648-65. [PMID: 24393774 PMCID: PMC3973311 DOI: 10.1093/nar/gkt1328] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In the absence of telomerase, telomeres progressively shorten with every round of DNA replication, leading to replicative senescence. In telomerase-deficient Saccharomyces cerevisiae, the shortest telomere triggers the onset of senescence by activating the DNA damage checkpoint and recruiting homologous recombination (HR) factors. Yet, the molecular structures that trigger this checkpoint and the mechanisms of repair have remained elusive. By tracking individual telomeres, we show that telomeres are subjected to different pathways depending on their length. We first demonstrate a progressive accumulation of subtelomeric single-stranded DNA (ssDNA) through 5'-3' resection as telomeres shorten. Thus, exposure of subtelomeric ssDNA could be the signal for cell cycle arrest in senescence. Strikingly, early after loss of telomerase, HR counteracts subtelomeric ssDNA accumulation rather than elongates telomeres. We then asked whether replication repair pathways contribute to this mechanism. We uncovered that Rad5, a DNA helicase/Ubiquitin ligase of the error-free branch of the DNA damage tolerance (DDT) pathway, associates with native telomeres and cooperates with HR in senescent cells. We propose that DDT acts in a length-independent manner, whereas an HR-based repair using the sister chromatid as a template buffers precocious 5'-3' resection at the shortest telomeres.
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Affiliation(s)
- Emilie Fallet
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, FRE3354, 75005 Paris, France, Laboratoire de Biologie Moléculaire de la Cellule, Centre National de la Recherche Scientifique, Ecole Normale Supérieure de Lyon, Université de Lyon 1, UMR5239, 69364 Lyon Cedex 07, France, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark, Institute for Research on Cancer and Aging, Nice (IRCAN), University of Nice Sophia-Antipolis, CNRS UMR7284/INSERM U1081, Faculty of Medicine, Nice F-06107, France and Department of Medical Genetics, CHU Nice, 06202 Nice cedex 3, France
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Reactivation of chromosomally integrated human herpesvirus-6 by telomeric circle formation. PLoS Genet 2013; 9:e1004033. [PMID: 24367281 PMCID: PMC3868596 DOI: 10.1371/journal.pgen.1004033] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/01/2013] [Indexed: 11/23/2022] Open
Abstract
More than 95% of the human population is infected with human herpesvirus-6 (HHV-6) during early childhood and maintains latent HHV-6 genomes either in an extra-chromosomal form or as a chromosomally integrated HHV-6 (ciHHV-6). In addition, approximately 1% of humans are born with an inheritable form of ciHHV-6 integrated into the telomeres of chromosomes. Immunosuppression and stress conditions can reactivate latent HHV-6 replication, which is associated with clinical complications and even death. We have previously shown that Chlamydia trachomatis infection reactivates ciHHV-6 and induces the formation of extra-chromosomal viral DNA in ciHHV-6 cells. Here, we propose a model and provide experimental evidence for the mechanism of ciHHV-6 reactivation. Infection with Chlamydia induced a transient shortening of telomeric ends, which subsequently led to increased telomeric circle (t-circle) formation and incomplete reconstitution of circular viral genomes containing single viral direct repeat (DR). Correspondingly, short t-circles containing parts of the HHV-6 DR were detected in cells from individuals with genetically inherited ciHHV-6. Furthermore, telomere shortening induced in the absence of Chlamydia infection also caused circularization of ciHHV-6, supporting a t-circle based mechanism for ciHHV-6 reactivation. Human herpesviruses (HHVs) can reside in a lifelong non-infectious state displaying limited activity in their host and protected from immune responses. One possible way by which HHV-6 achieves this state is by integrating into the telomeric ends of human chromosomes, which are highly repetitive sequences that protect the ends of chromosomes from damage. Various stress conditions can reactivate latent HHV-6 thus increasing the severity of multiple human disorders. Recently, we have identified Chlamydia infection as a natural cause of latent HHV-6 reactivation. Here, we have sought to elucidate the molecular mechanism of HHV-6 reactivation. HHV-6 efficiently utilizes the well-organized telomere maintenance machinery of the host cell to exit from its inactive state and initiate replication to form new viral DNA. We provide experimental evidence that the shortening of telomeres, as a consequence of interference with telomere maintenance, triggers the release of the integrated virus from the chromosome. Our data provide a mechanistic basis to understand HHV-6 reactivation scenarios, which in light of the high prevalence of HHV-6 infection and the possibility of chromosomal integration of other common viruses like HHV-7 have important medical consequences for several million people worldwide.
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