1
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Boob AG, Zhu Z, Intasian P, Jain M, Petrov V, Lane ST, Tan SI, Xun G, Zhao H. CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration. Nucleic Acids Res 2024; 52:e30. [PMID: 38346683 PMCID: PMC11014336 DOI: 10.1093/nar/gkae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 04/14/2024] Open
Abstract
The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search, and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.
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Affiliation(s)
- Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhixin Zhu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pattarawan Intasian
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wangchan Valley, Rayong 21210, Thailand
| | - Manan Jain
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Vassily Andrew Petrov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephan Thomas Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Guanhua Xun
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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2
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Matsuyama A, Hashimoto A, Nishimura S, Yoshida M. A set of vectors and strains for chromosomal integration in fission yeast. Sci Rep 2023; 13:9295. [PMID: 37291244 PMCID: PMC10250367 DOI: 10.1038/s41598-023-36267-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023] Open
Abstract
The expression of heterologous genes is an important technique in yeast genetics. In fission yeast, the leu1 and ura4 genes have been used mainly as selectable markers for heterologous expression. To expand the repertoire of selection markers available for heterologous expression of genes, here we developed new host-vector systems employing lys1 and arg3. By employing genome editing with the CRISPR/Cas9 system, we isolated several alleles of lys1 and arg3, each having a critical mutation in the ORF region. In parallel, we developed a set of vectors that complement the amino acid auxotrophy of lys1 and arg3 mutants when integrated into each locus. Using these vectors in combination with the previously developed integration vector pDUAL, we successfully observed the localization of three proteins in a cell simultaneously by fusing them with different fluorescent proteins. Thus, these vectors enable combinatorial expression of heterologous genes, which addresses increasingly diverse experimental challenges.
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Affiliation(s)
- Akihisa Matsuyama
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan.
- Laboratory of Microbiology, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Atsushi Hashimoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinichi Nishimura
- Laboratory of Microbiology, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
- Laboratory of Microbiology, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan
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3
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Hatano T, Lim TC, Billault-Chaumartin I, Dhar A, Gu Y, Massam-Wu T, Scott W, Adishesha S, Chapa-y-Lazo B, Springall L, Sivashanmugam L, Mishima M, Martin SG, Oliferenko S, Palani S, Balasubramanian MK. mNG-tagged fusion proteins and nanobodies to visualize tropomyosins in yeast and mammalian cells. J Cell Sci 2022; 135:jcs260288. [PMID: 36148799 PMCID: PMC9592052 DOI: 10.1242/jcs.260288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Tropomyosins are structurally conserved α-helical coiled-coil proteins that bind along the length of filamentous actin (F-actin) in fungi and animals. Tropomyosins play essential roles in the stability of actin filaments and in regulating myosin II contractility. Despite the crucial role of tropomyosin in actin cytoskeletal regulation, in vivo investigations of tropomyosin are limited, mainly due to the suboptimal live-cell imaging tools currently available. Here, we report on an mNeonGreen (mNG)-tagged tropomyosin, with native promoter and linker length configuration, that clearly reports tropomyosin dynamics in Schizosaccharomyces pombe (Cdc8), Schizosaccharomyces japonicus (Cdc8) and Saccharomyces cerevisiae (Tpm1 and Tpm2). We also describe a fluorescent probe to visualize mammalian tropomyosin (TPM2 isoform). Finally, we generated a camelid nanobody against S. pombe Cdc8, which mimics the localization of mNG-Cdc8 in vivo. Using these tools, we report the presence of tropomyosin in previously unappreciated patch-like structures in fission and budding yeasts, show flow of tropomyosin (F-actin) cables to the cytokinetic actomyosin ring and identify rearrangements of the actin cytoskeleton during mating. These powerful tools and strategies will aid better analyses of tropomyosin and F-actin cables in vivo.
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Affiliation(s)
- Tomoyuki Hatano
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Tzer Chyn Lim
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Ingrid Billault-Chaumartin
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Anubhav Dhar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
| | - Teresa Massam-Wu
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - William Scott
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Sushmitha Adishesha
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Bernardo Chapa-y-Lazo
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Luke Springall
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Lavanya Sivashanmugam
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Masanori Mishima
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
| | - Sophie G. Martin
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
| | - Saravanan Palani
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Mohan K. Balasubramanian
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, Warwick CV4 7AL, UK
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4
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Yu ZQ, Liu XM, Zhao D, Xu DD, Du LL. Visual detection of binary, ternary and quaternary protein interactions in fission yeast using a Pil1 co-tethering assay. J Cell Sci 2021; 134:272452. [PMID: 34499173 DOI: 10.1242/jcs.258774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/03/2021] [Indexed: 01/28/2023] Open
Abstract
Protein-protein interactions are vital for executing nearly all cellular processes. To facilitate the detection of protein-protein interactions in living cells of the fission yeast Schizosaccharomyces pombe, here we present an efficient and convenient method termed the Pil1 co-tethering assay. In its basic form, we tether a bait protein to mCherry-tagged Pil1, which forms cortical filamentary structures, and examine whether a GFP-tagged prey protein colocalizes with the bait. We demonstrate that this assay is capable of detecting pairwise protein-protein interactions of cytosolic proteins and nuclear proteins. Furthermore, we show that this assay can be used for detecting not only binary protein-protein interactions, but also ternary and quaternary protein-protein interactions. Using this assay, we systematically characterized the protein-protein interactions in the Atg1 complex and in the phosphatidylinositol 3-kinase (PtdIns3K) complexes and found that Atg38 is incorporated into the PtdIns3K complex I via an Atg38-Vps34 interaction. Our data show that this assay is a useful and versatile tool and should be added to the routine toolbox of fission yeast researchers. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Zhong-Qiu Yu
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Dan Zhao
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Dan-Dan Xu
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, 102206 Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206 Beijing, China
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5
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Kurokawa Y, Murayama Y. DNA Binding by the Mis4 Scc2 Loader Promotes Topological DNA Entrapment by the Cohesin Ring. Cell Rep 2020; 33:108357. [PMID: 33176147 DOI: 10.1016/j.celrep.2020.108357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 12/27/2022] Open
Abstract
Cohesin, a critical mediator of genome organization including sister chromatid cohesion, is a ring-shaped multi-subunit ATPase that topologically embraces DNA. Its loading and function on chromosomes require the Scc2-Scc4 loader. Using biochemical reconstitution, we show here that the ability of the loader to bind DNA plays a critical role in promoting cohesin loading. Two distinct sites within the Mis4Scc2 subunit are found to cooperatively bind DNA. Mis4Scc2 initially forms a tertiary complex with cohesin on DNA and promotes subsequent topological DNA entrapment by cohesin through its DNA binding activity, a process that requires an additional DNA binding surface provided by Psm3Smc3, the ATPase domain of cohesin. Furthermore, we show that mutations in the two DNA binding sites of Mis4 impair the chromosomal loading of cohesin. These observations demonstrate the physiological importance of DNA binding by the loader and provide mechanistic insights into the process of topological cohesin loading.
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Affiliation(s)
- Yumiko Kurokawa
- Center for Frontier Research, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yasuto Murayama
- Center for Frontier Research, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111, Yata, Mishima, Shizuoka 411-8540, Japan.
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6
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Systematic analysis reveals the prevalence and principles of bypassable gene essentiality. Nat Commun 2019; 10:1002. [PMID: 30824696 PMCID: PMC6397241 DOI: 10.1038/s41467-019-08928-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/07/2019] [Indexed: 12/12/2022] Open
Abstract
Gene essentiality is a variable phenotypic trait, but to what extent and how essential genes can become dispensable for viability remain unclear. Here, we investigate 'bypass of essentiality (BOE)' - an underexplored type of digenic genetic interaction that renders essential genes dispensable. Through analyzing essential genes on one of the six chromosome arms of the fission yeast Schizosaccharomyces pombe, we find that, remarkably, as many as 27% of them can be converted to non-essential genes by BOE interactions. Using this dataset we identify three principles of essentiality bypass: bypassable essential genes tend to have lower importance, tend to exhibit differential essentiality between species, and tend to act with other bypassable genes. In addition, we delineate mechanisms underlying bypassable essentiality, including the previously unappreciated mechanism of dormant redundancy between paralogs. The new insights gained on bypassable essentiality deepen our understanding of genotype-phenotype relationships and will facilitate drug development related to essential genes.
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7
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Hu W, Jiang ZD, Suo F, Zheng JX, He WZ, Du LL. A large gene family in fission yeast encodes spore killers that subvert Mendel's law. eLife 2017; 6:e26057. [PMID: 28631610 PMCID: PMC5478263 DOI: 10.7554/elife.26057] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/06/2017] [Indexed: 12/12/2022] Open
Abstract
Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast Schizosaccharomyces pombe. Both killers belong to the previously uncharacterized wtf gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them. Spores carrying one killer are protected from its killing effect but not that of the other killer. The killing and protecting activities can be uncoupled by mutation. The numbers and sequences of wtf genes vary considerably between S. pombe isolates, indicating rapid divergence. We propose that wtf genes contribute to the extensive intraspecific reproductive isolation in S. pombe, and represent ideal models for understanding how segregation-distorting elements act and evolve.
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Affiliation(s)
- Wen Hu
- National Institute of Biological Sciences, Beijing, China
| | - Zhao-Di Jiang
- National Institute of Biological Sciences, Beijing, China
- PTN Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Jin-Xin Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Wan-Zhong He
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
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8
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Zhao D, Liu XM, Yu ZQ, Sun LL, Xiong X, Dong MQ, Du LL. Atg20- and Atg24-family proteins promote organelle autophagy in fission yeast. J Cell Sci 2016; 129:4289-4304. [PMID: 27737912 DOI: 10.1242/jcs.194373] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/06/2016] [Indexed: 12/17/2022] Open
Abstract
Autophagy cargos include not only soluble cytosolic materials but also bulky organelles, such as ER and mitochondria. In budding yeast, two proteins that contain the PX domain and the BAR domain, Atg20 and Atg24 (also known as Snx42 and Snx4, respectively) are required for organelle autophagy and contribute to general autophagy in a way that can be masked by compensatory mechanisms. It remains unclear why these proteins are important for organelle autophagy. Here, we show that in a distantly related fungal organism, the fission yeast Schizosaccharomyces pombe, autophagy of ER and mitochondria is induced by nitrogen starvation and is promoted by three Atg20- and Atg24-family proteins - Atg20, Atg24 and SPBC1711.11 (named here as Atg24b). These proteins localize at the pre-autophagosomal structure, or phagophore assembly site (PAS), during starvation. S. pombe Atg24 forms a homo-oligomer and acts redundantly with Atg20 and Atg24b, and the latter two proteins can form a hetero-oligomer. The organelle autophagy defect caused by the loss of these proteins is associated with a reduction of autophagosome size and a decrease in Atg8 accumulation at the PAS. These results provide new insights into the autophagic function of Atg20- and Atg24-family proteins.
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Affiliation(s)
- Dan Zhao
- PTN Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China.,National Institute of Biological Sciences, Beijing 102206, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhong-Qiu Yu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ling-Ling Sun
- National Institute of Biological Sciences, Beijing 102206, China
| | | | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
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9
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Kakui Y, Sunaga T, Arai K, Dodgson J, Ji L, Csikász-Nagy A, Carazo-Salas R, Sato M. Module-based construction of plasmids for chromosomal integration of the fission yeast Schizosaccharomyces pombe. Open Biol 2016; 5:150054. [PMID: 26108218 PMCID: PMC4632507 DOI: 10.1098/rsob.150054] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Integration of an external gene into a fission yeast chromosome is useful to investigate the effect of the gene product. An easy way to knock-in a gene construct is use of an integration plasmid, which can be targeted and inserted to a chromosome through homologous recombination. Despite the advantage of integration, construction of integration plasmids is energy- and time-consuming, because there is no systematic library of integration plasmids with various promoters, fluorescent protein tags, terminators and selection markers; therefore, researchers are often forced to make appropriate ones through multiple rounds of cloning procedures. Here, we establish materials and methods to easily construct integration plasmids. We introduce a convenient cloning system based on Golden Gate DNA shuffling, which enables the connection of multiple DNA fragments at once: any kind of promoters and terminators, the gene of interest, in combination with any fluorescent protein tag genes and any selection markers. Each of those DNA fragments, called a ‘module’, can be tandemly ligated in the order we desire in a single reaction, which yields a circular plasmid in a one-step manner. The resulting plasmids can be integrated through standard methods for transformation. Thus, these materials and methods help easy construction of knock-in strains, and this will further increase the value of fission yeast as a model organism.
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Affiliation(s)
- Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Tomonari Sunaga
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University TWIns, 2-2 Wakamatsucho, Shinjuku, Tokyo 162-0056, Japan
| | - Kunio Arai
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University TWIns, 2-2 Wakamatsucho, Shinjuku, Tokyo 162-0056, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - James Dodgson
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Liang Ji
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University TWIns, 2-2 Wakamatsucho, Shinjuku, Tokyo 162-0056, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Attila Csikász-Nagy
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige 38010, Italy Randall Division of Cell and Molecular Biophysics and Institute for Mathematical and Molecular Biomedicine, King's College London, London SE1 1UL, UK
| | - Rafael Carazo-Salas
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Masamitsu Sato
- Laboratory of Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University TWIns, 2-2 Wakamatsucho, Shinjuku, Tokyo 162-0056, Japan Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
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10
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Hu W, Suo F, Du LL. Bulk Segregant Analysis Reveals the Genetic Basis of a Natural Trait Variation in Fission Yeast. Genome Biol Evol 2015; 7:3496-510. [PMID: 26615217 PMCID: PMC4700965 DOI: 10.1093/gbe/evv238] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although the fission yeast Schizosaccharomyces pombe is a well-established model organism, studies of natural trait variations in this species remain limited. To assess the feasibility of segregant-pool-based mapping of phenotype-causing genes in natural strains of fission yeast, we investigated the cause of a maltose utilization defect (Mal(-)) of the S. pombe strain CBS5557 (originally known as Schizosaccharomyces malidevorans). Analyzing the genome sequence of CBS5557 revealed 955 nonconservative missense substitutions, and 61 potential loss-of-function variants including 47 frameshift indels, 13 early stop codons, and 1 splice site mutation. As a side benefit, our analysis confirmed 146 sequence errors in the reference genome and improved annotations of 27 genes. We applied bulk segregant analysis to map the causal locus of the Mal(-) phenotype. Through sequencing the segregant pools derived from a cross between CBS5557 and the laboratory strain, we located the locus to within a 2.23-Mb chromosome I inversion found in most S. pombe isolates including CBS5557. To map genes within the inversion region that occupies 18% of the genome, we created a laboratory strain containing the same inversion. Analyzing segregants from a cross between CBS5557 and the inversion-containing laboratory strain narrowed down the locus to a 200-kb interval and led us to identify agl1, which suffers a 5-bp deletion in CBS5557, as the causal gene. Interestingly, loss of agl1 through a 34-kb deletion underlies the Mal(-) phenotype of another S. pombe strain CGMCC2.1628. This work adapts and validates the bulk segregant analysis method for uncovering trait-gene relationship in natural fission yeast strains.
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Affiliation(s)
- Wen Hu
- PTN Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China National Institute of Biological Sciences, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
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11
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Isakova EP, Epova EY, Sekova VY, Trubnikova EV, Kudykina YK, Zylkova MV, Guseva MA, Deryabina YI. The engineering of a Yarrowia lipolytica yeast strain capable of homologous recombination of the mitochondrial genome. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815030096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Etheridge TJ, Boulineau RL, Herbert A, Watson AT, Daigaku Y, Tucker J, George S, Jönsson P, Palayret M, Lando D, Laue E, Osborne MA, Klenerman D, Lee SF, Carr AM. Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy. Nucleic Acids Res 2014; 42:e146. [PMID: 25106872 PMCID: PMC4231725 DOI: 10.1093/nar/gku726] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/09/2014] [Accepted: 07/28/2014] [Indexed: 12/25/2022] Open
Abstract
Development of single-molecule localization microscopy techniques has allowed nanometre scale localization accuracy inside cells, permitting the resolution of ultra-fine cell structure and the elucidation of crucial molecular mechanisms. Application of these methodologies to understanding processes underlying DNA replication and repair has been limited to defined in vitro biochemical analysis and prokaryotic cells. In order to expand these techniques to eukaryotic systems, we have further developed a photo-activated localization microscopy-based method to directly visualize DNA-associated proteins in unfixed eukaryotic cells. We demonstrate that motion blurring of fluorescence due to protein diffusivity can be used to selectively image the DNA-bound population of proteins. We designed and tested a simple methodology and show that it can be used to detect changes in DNA binding of a replicative helicase subunit, Mcm4, and the replication sliding clamp, PCNA, between different stages of the cell cycle and between distinct genetic backgrounds.
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Affiliation(s)
- Thomas J Etheridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Sussex, UK
| | - Rémi L Boulineau
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Sussex, UK
| | - Alex Herbert
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Sussex, UK
| | - Adam T Watson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Sussex, UK
| | - Yasukazu Daigaku
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Sussex, UK
| | - Jem Tucker
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Sussex, UK
| | - Sophie George
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Sussex, UK
| | - Peter Jönsson
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - David Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ernest Laue
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mark A Osborne
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Sussex, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Sussex, UK
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13
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Murayama Y, Uhlmann F. Biochemical reconstitution of topological DNA binding by the cohesin ring. Nature 2014; 505:367-71. [PMID: 24291789 PMCID: PMC3907785 DOI: 10.1038/nature12867] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 11/13/2013] [Indexed: 01/06/2023]
Abstract
Cohesion between sister chromatids, mediated by the chromosomal cohesin complex, is a prerequisite for faithful chromosome segregation in mitosis. Cohesin also has vital roles in DNA repair and transcriptional regulation. The ring-shaped cohesin complex is thought to encircle sister DNA strands, but its molecular mechanism of action is poorly understood and the biochemical reconstitution of cohesin activity in vitro has remained an unattained goal. Here we reconstitute cohesin loading onto DNA using purified fission yeast cohesin and its loader complex, Mis4(Scc2)-Ssl3(Scc4) (Schizosaccharomyces pombe gene names appear throughout with their more commonly known Saccharomyces cerevisiae counterparts added in superscript). Incubation of cohesin with DNA leads to spontaneous topological loading, but this remains inefficient. The loader contacts cohesin at multiple sites around the ring circumference, including the hitherto enigmatic Psc3(Scc3) subunit, and stimulates cohesin's ATPase, resulting in efficient topological loading. The in vitro reconstitution of cohesin loading onto DNA provides mechanistic insight into the initial steps of the establishment of sister chromatid cohesion and other chromosomal processes mediated by cohesin.
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Affiliation(s)
- Yasuto Murayama
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
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14
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Matsuyama A, Yoshida M. Heterologous gene expression by chromosomal integration in fission yeast. Methods Mol Biol 2012; 824:433-50. [PMID: 22160913 DOI: 10.1007/978-1-61779-433-9_23] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Thanks to the convenience and flexibility of the multicopy plasmid-based approach for heterologous gene expression, this technique has long been used for biological studies, especially in prokaryotes and lower eukaryotes. For better understanding of biological mechanisms, however, there are increasing demands on the experimental technologies enabling fine-tuned expression of introduced heterologous genes or serving conditions that are closer to the physiological conditions. For this purpose, the use of direct tagging of a chromosomal gene has been gradually increasing, although the use conditions of this approach are relatively limited compared to plasmid-based methods. Expression of a cloned gene using chromosomal integration has a property intermediate between multicopy plasmid-based method and direct tagging of an endogenous gene. Here, we describe the principle and methods of introduction of a cloned gene into the targeting loci of the chromosome in fission yeast.
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15
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Buttrick GJ, Meadows JC, Lancaster TC, Vanoosthuyse V, Shepperd LA, Hoe KL, Kim DU, Park HO, Hardwick KG, Millar JBA. Nsk1 ensures accurate chromosome segregation by promoting association of kinetochores to spindle poles during anaphase B. Mol Biol Cell 2011; 22:4486-502. [PMID: 21965289 PMCID: PMC3226469 DOI: 10.1091/mbc.e11-07-0608] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nsk1 is a novel fission yeast protein that binds the nucleolus during interphase and the nucleoplasm during early mitosis. After anaphase and following dephosphorylation by Clp1, Nsk1 binds the kinetochore–spindle pole junction and maintains accurate chromosome segregation by promoting the association of kinetochores to spindle poles during anaphase B. Type 1 phosphatase (PP1) antagonizes Aurora B kinase to stabilize kinetochore–microtubule attachments and to silence the spindle checkpoint. We screened for factors that exacerbate the growth defect of Δdis2 cells, which lack one of two catalytic subunits of PP1 in fission yeast, and identified Nsk1, a novel protein required for accurate chromosome segregation. During interphase, Nsk1 resides in the nucleolus but spreads throughout the nucleoplasm as cells enter mitosis. Following dephosphorylation by Clp1 (Cdc14-like) phosphatase and at least one other phosphatase, Nsk1 localizes to the interface between kinetochores and the inner face of the spindle pole body during anaphase. In the absence of Nsk1, some kinetochores become detached from spindle poles during anaphase B. If this occurs late in anaphase B, then the sister chromatids of unclustered kinetochores segregate to the correct daughter cell. These unclustered kinetochores are efficiently captured, retrieved, bioriented, and segregated during the following mitosis, as long as Dis2 is present. However, if kinetochores are detached from a spindle pole early in anaphase B, then these sister chromatids become missegregated. These data suggest Nsk1 ensures accurate chromosome segregation by promoting the tethering of kinetochores to spindle poles during anaphase B.
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Affiliation(s)
- Graham J Buttrick
- Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
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16
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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