1
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Culley S, Caballero AC, Burden JJ, Uhlmann V. Made to measure: An introduction to quantifying microscopy data in the life sciences. J Microsc 2024; 295:61-82. [PMID: 37269048 DOI: 10.1111/jmi.13208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/04/2023]
Abstract
Images are at the core of most modern biological experiments and are used as a major source of quantitative information. Numerous algorithms are available to process images and make them more amenable to be measured. Yet the nature of the quantitative output that is useful for a given biological experiment is uniquely dependent upon the question being investigated. Here, we discuss the 3 main types of information that can be extracted from microscopy data: intensity, morphology, and object counts or categorical labels. For each, we describe where they come from, how they can be measured, and what may affect the relevance of these measurements in downstream data analysis. Acknowledging that what makes a measurement 'good' is ultimately down to the biological question being investigated, this review aims at providing readers with a toolkit to challenge how they quantify their own data and be critical of conclusions drawn from quantitative bioimage analysis experiments.
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Affiliation(s)
- Siân Culley
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | | | | | - Virginie Uhlmann
- European Bioinformatics Institute (EMBL-EBI), EMBL, Cambridge, UK
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2
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Hebra T, Smrčková H, Elkatmis B, Převorovský M, Pluskal T. POMBOX: A Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology. ACS Synth Biol 2024; 13:558-567. [PMID: 37991801 PMCID: PMC10877588 DOI: 10.1021/acssynbio.3c00529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
The fission yeast Schizosaccharomyces pombe is a popular model organism in molecular biology and cell physiology. With its ease of genetic manipulation and growth, supported by in-depth functional annotations in the PomBase database and genome-wide metabolic models,S. pombe is an attractive option for synthetic biology applications. However,S. pombe currently lacks modular tools for generating genetic circuits with more than 1 transcriptional unit. We developed a toolkit to address this gap. Adapted from the MoClo-YTK plasmid kit for Saccharomyces cerevisiae and using the same modular cloning grammar, our POMBOX toolkit is designed to facilitate fast, efficient, and modular construction of genetic circuits inS. pombe. It allows for interoperability when working with DNA sequences that are functional in bothS. cerevisiae and S. pombe (e.g., protein tags, antibiotic resistance cassettes, and coding sequences). Moreover, POMBOX enables the modular assembly of multigene pathways and increases the possible pathway length from 6 to 12 transcriptional units. We also adapted the stable integration vector homology arms to Golden Gate assembly and tested the genomic integration success rates depending on different sequence sizes, from 4 to 24 kb. We included 14 S. pombe promoters that we characterized using two fluorescent proteins, in both minimally defined (EMM2─Edinburgh minimal media) and complex (YES─yeast extract with supplements) media. Then, we examined the efficacy of 6 S. cerevisiae and 6 synthetic terminators in S. pombe. Finally, we used the POMBOX kit for a synthetic biology application in metabolic engineering and expressed plant enzymes in S. pombe to produce specialized metabolite precursors, namely, methylxanthine, amorpha-4,11-diene, and cinnamic acid from the purine, mevalonate, and aromatic amino acid pathways.
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Affiliation(s)
- Téo Hebra
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Helena Smrčková
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Büsra Elkatmis
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Martin Převorovský
- Department
of Cell Biology, Faculty of Science, Charles
University, 128 00 Prague, Czech
Republic
| | - Tomáš Pluskal
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
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3
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Lera-Ramírez M, Bähler J, Mata J, Rutherford K, Hoffman CS, Lambert S, Oliferenko S, Martin SG, Gould KL, Du LL, Sabatinos SA, Forsburg SL, Nielsen O, Nurse P, Wood V. Revised fission yeast gene and allele nomenclature guidelines for machine readability. Genetics 2023; 225:iyad143. [PMID: 37758508 PMCID: PMC10627252 DOI: 10.1093/genetics/iyad143] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/24/2023] [Indexed: 09/30/2023] Open
Abstract
Standardized nomenclature for genes, gene products, and isoforms is crucial to prevent ambiguity and enable clear communication of scientific data, facilitating efficient biocuration and data sharing. Standardized genotype nomenclature, which describes alleles present in a specific strain that differ from those in the wild-type reference strain, is equally essential to maximize research impact and ensure that results linking genotypes to phenotypes are Findable, Accessible, Interoperable, and Reusable (FAIR). In this publication, we extend the fission yeast clade gene nomenclature guidelines to support the curation efforts at PomBase (www.pombase.org), the Schizosaccharomyces pombe Model Organism Database. This update introduces nomenclature guidelines for noncoding RNA genes, following those set forth by the Human Genome Organisation Gene Nomenclature Committee. Additionally, we provide a significant update to the allele and genotype nomenclature guidelines originally published in 1987, to standardize the diverse range of genetic modifications enabled by the fission yeast genetic toolbox. These updated guidelines reflect a community consensus between numerous fission yeast researchers. Adoption of these rules will improve consistency in gene and genotype nomenclature, and facilitate machine-readability and automated entity recognition of fission yeast genes and alleles in publications or datasets. In conclusion, our updated guidelines provide a valuable resource for the fission yeast research community, promoting consistency, clarity, and FAIRness in genetic data sharing and interpretation.
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Affiliation(s)
- Manuel Lera-Ramírez
- University College London, Department of Genetics Evolution and Environment, Darwin Building, 99-105 Gower Street, London WC1E 6BT, UK
| | - Jürg Bähler
- University College London, Department of Genetics Evolution and Environment, Darwin Building, 99-105 Gower Street, London WC1E 6BT, UK
| | - Juan Mata
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
| | - Kim Rutherford
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
| | | | - Sarah Lambert
- Institut Curie, Université Paris-Saclay, CNRS UMR3348, Orsay 91400, France
| | - Snezhana Oliferenko
- The Francis Crick Institute, 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
| | - Sophie G Martin
- University of Geneva, Department of Molecular and Cellular Biology, Geneva 1211, Switzerland
| | - Kathleen L Gould
- Vanderbilt University School of Medicine, Department of Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
| | - Sarah A Sabatinos
- Toronto Metropolitan University, Department of Chemistry & Biology, Toronto M5B 2K3, Canada
| | - Susan L Forsburg
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Olaf Nielsen
- Department of Biology, Cell cycle and genome stability Group, University of Copenhagen, Copenhagen N DK2100, Denmark
| | - Paul Nurse
- The Francis Crick Institute, London NW1 1AT, UK
| | - Valerie Wood
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
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4
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Malla M, Sinha D, Chowdhury P, Bisesi BT, Chen Q. The cytoplasmic tail of the mechanosensitive channel Pkd2 regulates its internalization and clustering in eisosomes. J Cell Sci 2023; 136:jcs260598. [PMID: 37259828 PMCID: PMC10323245 DOI: 10.1242/jcs.260598] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/25/2023] [Indexed: 06/02/2023] Open
Abstract
Polycystins are a family of conserved ion channels, mutations of which lead to one of the most common human genetic disorders, namely, autosomal dominant polycystic kidney disease. Schizosacchromyces pombe possesses an essential polycystin homologue, Pkd2, which directs Ca2+ influx on the cell surface in response to membrane tension, but its structure remains unsolved. Here, we analyzed the structure-function relationship of Pkd2 based on its AlphaFold-predicted structure. Pkd2 consists of three domains, the extracellular lipid-binding domain (LBD), nine-helix transmembrane domain (TMD) and C-terminal cytoplasmic domain (CCD). Our genetic and microscopy data revealed that LBD and TMD are essential for targeting Pkd2 to the plasma membrane from the endoplasmic reticulum. In comparison, CCD ensures the polarized distribution of Pkd2 by promoting its internalization and preventing its clustering in the eisosome, a caveolae-like membrane compartment. The domains of Pkd2 and their functions are conserved in other fission yeast species. We conclude that both extracellular and cytoplasmic domains of Pkd2 are crucial for its intracellular trafficking and function. We propose that mechanosensitive channels can be desensitized through either internalization or clustering in low-tension membrane compartments.
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Affiliation(s)
- Mamata Malla
- Department of Biological Sciences, The University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Debatrayee Sinha
- Department of Biological Sciences, The University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Pritha Chowdhury
- Department of Biological Sciences, The University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Benjamin Thomas Bisesi
- Department of Biological Sciences, The University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - Qian Chen
- Department of Biological Sciences, The University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
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5
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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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6
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Billault-Chaumartin I, Michon L, Anderson CA, Yde SE, Suarez C, Iwaszkiewicz J, Zoete V, Kovar DR, Martin SG. Actin assembly requirements of the formin Fus1 to build the fusion focus. J Cell Sci 2022; 135:275633. [PMID: 35673994 DOI: 10.1242/jcs.260289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 12/28/2022] Open
Abstract
In formin-family proteins, actin filament nucleation and elongation activities reside in the formin homology 1 (FH1) and FH2 domains, with reaction rates that vary by at least 20-fold between formins. Each cell expresses distinct formins that assemble one or several actin structures, raising the question of what confers each formin its specificity. Here, using the formin Fus1 in Schizosaccharomyces pombe, we systematically probed the importance of formin nucleation and elongation rates in vivo. Fus1 assembles the actin fusion focus, necessary for gamete fusion to form the zygote during sexual reproduction. By constructing chimeric formins with combinations of FH1 and FH2 domains previously characterized in vitro, we establish that changes in formin nucleation and elongation rates have direct consequences on fusion focus architecture, and that Fus1 native high nucleation and low elongation rates are optimal for fusion focus assembly. We further describe a point mutant in Fus1 FH2 that preserves native nucleation and elongation rates in vitro but alters function in vivo, indicating an additional FH2 domain property. Thus, rates of actin assembly are tailored for assembly of specific actin structures.
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Affiliation(s)
- Ingrid Billault-Chaumartin
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Laetitia Michon
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Caitlin A Anderson
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sarah E Yde
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Cristian Suarez
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Amphipôle Building, CH-1015 Lausanne, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Amphipôle Building, CH-1015 Lausanne, Switzerland.,Department of Oncology UNIL-CHUV, University of Lausanne, Ludwig Institute for Cancer Research, Route de la Corniche 9A, CH-1066 Epalinges, Switzerland
| | - David R Kovar
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Sophie G Martin
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
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7
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Varberg JM, Unruh JR, Bestul AJ, Khan AA, Jaspersen SL. Quantitative analysis of nuclear pore complex organization in Schizosaccharomyces pombe. Life Sci Alliance 2022; 5:e202201423. [PMID: 35354597 PMCID: PMC8967992 DOI: 10.26508/lsa.202201423] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 01/06/2023] Open
Abstract
The number, distribution, and composition of nuclear pore complexes (NPCs) in the nuclear envelope varies between cell types and changes during cellular differentiation and in disease. To understand how NPC density and organization are controlled, we analyzed the NPC number and distribution in the fission yeast Schizosaccharomyces pombe using structured illumination microscopy. The small size of yeast nuclei, genetic features of fungi, and our robust image analysis pipeline allowed us to study NPCs in intact nuclei under multiple conditions. Our data revealed that NPC density is maintained across a wide range of nuclear sizes. Regions of reduced NPC density are observed over the nucleolus and surrounding the spindle pole body (SPB). Lem2-mediated tethering of the centromeres to the SPB is required to maintain NPC exclusion near SPBs. These findings provide a quantitative understanding of NPC number and distribution in S. pombe and show that interactions between the centromere and the nuclear envelope influences local NPC distribution.
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Affiliation(s)
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Andrew J Bestul
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Azqa A Khan
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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8
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Larkin A, Ames A, Seman M, Ragunathan K. Investigating Mitotic Inheritance of Histone Modifications Using Tethering Strategies. Methods Mol Biol 2022; 2529:419-440. [PMID: 35733025 DOI: 10.1007/978-1-0716-2481-4_18] [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] [Indexed: 06/15/2023]
Abstract
The covalent and reversible modification of histones enables cells to establish heritable gene expression patterns without altering their genetic blueprint. Epigenetic mechanisms regulate gene expression in two separate ways: (1) establishment, which depends on sequence-specific DNA- or RNA-binding proteins that recruit histone-modifying enzymes to unique genomic loci, and (2) maintenance, which is sequence-independent and depends on the autonomous propagation of preexisting chromatin states during DNA replication. Only a subset of the vast repertoire of histone modifications in the genome is heritable. Here, we describe a synthetic biology approach to tether histone-modifying enzymes to engineer chromatin states in living cells and evaluate their potential for mitotic inheritance. In S. pombe, fusing the H3K9 methyltransferase, Clr4, to the tetracycline-inducible TetR DNA-binding domain facilitates rapid and reversible control of heterochromatin assembly. We describe a framework to successfully implement an inducible heterochromatin establishment system and evaluate its molecular properties. We anticipate that our innovative genetic strategy will be broadly applicable to the discovery of protein complexes and separation-of-function alleles of heterochromatin-associated factors with unique roles in epigenetic inheritance.
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Affiliation(s)
- Ajay Larkin
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Amanda Ames
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Melissa Seman
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Kaushik Ragunathan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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9
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Sakai K, Kondo Y, Fujioka H, Kamiya M, Aoki K, Goto Y. Near-infrared imaging in fission yeast using a genetically encoded phycocyanobilin biosynthesis system. J Cell Sci 2021; 134:273759. [PMID: 34806750 DOI: 10.1242/jcs.259315] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Near-infrared fluorescent protein (iRFP) is a bright and stable fluorescent protein with near-infrared excitation and emission maxima. Unlike the other conventional fluorescent proteins, iRFP requires biliverdin (BV) as a chromophore. Here, we report that phycocyanobilin (PCB) functions as a brighter chromophore for iRFP than BV, and that biosynthesis of PCB allows live-cell imaging with iRFP in the fission yeast Schizosaccharomyces pombe. We initially found that fission yeast cells did not produce BV and therefore did not show any iRFP fluorescence. The brightness of iRFP-PCB was higher than that of iRFP-BV both in vitro and in fission yeast. We introduced SynPCB2.1, a PCB biosynthesis system, into fission yeast, resulting in the brightest iRFP fluorescence. To make iRFP readily available in fission yeast, we developed an endogenous gene tagging system with iRFP and all-in-one integration plasmids carrying the iRFP-fused marker proteins together with SynPCB2.1. These tools not only enable the easy use of multiplexed live-cell imaging in fission yeast with a broader color palette, but also open the door to new opportunities for near-infrared fluorescence imaging in a wider range of living organisms. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Keiichiro Sakai
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Hiroyoshi Fujioka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
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10
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Zimmerli CE, Allegretti M, Rantos V, Goetz SK, Obarska-Kosinska A, Zagoriy I, Halavatyi A, Hummer G, Mahamid J, Kosinski J, Beck M. Nuclear pores dilate and constrict in cellulo. Science 2021; 374:eabd9776. [PMID: 34762489 DOI: 10.1126/science.abd9776] [Citation(s) in RCA: 151] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Christian E Zimmerli
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Matteo Allegretti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vasileios Rantos
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Sara K Goetz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Agnieszka Obarska-Kosinska
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | | | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany.,EMBL Hamburg, 22607 Hamburg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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11
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Gerganova V, Lamas I, Rutkowski DM, Vještica A, Castro DG, Vincenzetti V, Vavylonis D, Martin SG. Cell patterning by secretion-induced plasma membrane flows. SCIENCE ADVANCES 2021; 7:eabg6718. [PMID: 34533984 PMCID: PMC8448446 DOI: 10.1126/sciadv.abg6718] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/26/2021] [Indexed: 05/20/2023]
Abstract
Cells self-organize using reaction-diffusion and fluid-flow principles. Whether bulk membrane flows contribute to cell patterning has not been established. Here, using mathematical modeling, optogenetics, and synthetic probes, we show that polarized exocytosis causes lateral membrane flows away from regions of membrane insertion. Plasma membrane–associated proteins with sufficiently low diffusion and/or detachment rates couple to the flows and deplete from areas of exocytosis. In rod-shaped fission yeast cells, zones of Cdc42 GTPase activity driving polarized exocytosis are limited by GTPase activating proteins (GAPs). We show that membrane flows pattern the GAP Rga4 distribution and that coupling of a synthetic GAP to membrane flows is sufficient to establish the rod shape. Thus, membrane flows induced by Cdc42-dependent exocytosis form a negative feedback restricting the zone of Cdc42 activity.
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Affiliation(s)
- Veneta Gerganova
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
| | - Iker Lamas
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
| | | | - Aleksandar Vještica
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
| | - Daniela Gallo Castro
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
| | - Vincent Vincenzetti
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
| | - Dimitrios Vavylonis
- Department of Physics, Lehigh University, Bethlehem, PA 18015, USA
- Corresponding author. (S.G.M.); (D.V.)
| | - Sophie G. Martin
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Switzerland
- Corresponding author. (S.G.M.); (D.V.)
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Vyas A, Freitas AV, Ralston ZA, Tang Z. Fission Yeast Schizosaccharomyces pombe: A Unicellular "Micromammal" Model Organism. Curr Protoc 2021; 1:e151. [PMID: 34101381 PMCID: PMC8193909 DOI: 10.1002/cpz1.151] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The fission yeast Schizosaccharomyces pombe is a rod-shaped unicellular eukaryote, well known for its contributions as a model organism for our understanding of regulation and conservation of the eukaryotic cell cycle. As a yeast divergent from the budding yeast Saccharomyces cerevisiae, S. pombe shares more common features with humans including gene structures, chromatin dynamics, and the prevalence of introns, as well as the control of gene expression through pre-mRNA splicing, epigenetic gene silencing, and RNAi pathways. With the advent of new methodologies for research, S. pombe has become an increasingly used model to investigate various molecular and cellular processes over the last 50 years. Also, S. pombe serves as an excellent system for undergraduate students to obtain hands-on research experience. Versatile experimental approaches are amenable using the fission yeast system due to its relative ease of maintenance, its inherent cellular properties, its power in classic and molecular genetics, and its feasibility in genomics and proteomics analyses. This article provides an overview of S. pombe's rise as a valuable model organism and presents examples to highlight the significance of S. pombe as a unicellular "micromammal" in investigating biological questions. We especially focus on the advantages of and the advancements in using fission yeast for studying biological processes that are characteristic of metazoans to decipher the underlining molecular mechanisms fundamental to all eukaryotes. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- Aditi Vyas
- W.M. Keck Science Department, The Claremont Colleges, Claremont, CA 91711, USA
| | - Anna V. Freitas
- W.M. Keck Science Department, The Claremont Colleges, Claremont, CA 91711, USA
| | - Zachary A. Ralston
- W.M. Keck Science Department, The Claremont Colleges, Claremont, CA 91711, USA
| | - Zhaohua Tang
- W.M. Keck Science Department, The Claremont Colleges, Claremont, CA 91711, USA
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Vještica A, Bérard M, Liu G, Merlini L, Nkosi PJ, Martin SG. Cell cycle-dependent and independent mating blocks ensure fungal zygote survival and ploidy maintenance. PLoS Biol 2021; 19:e3001067. [PMID: 33406066 PMCID: PMC7815208 DOI: 10.1371/journal.pbio.3001067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 01/19/2021] [Accepted: 12/22/2020] [Indexed: 12/22/2022] Open
Abstract
To ensure genome stability, sexually reproducing organisms require that mating brings together exactly 2 haploid gametes and that meiosis occurs only in diploid zygotes. In the fission yeast Schizosaccharomyces pombe, fertilization triggers the Mei3-Pat1-Mei2 signaling cascade, which represses subsequent mating and initiates meiosis. Here, we establish a degron system to specifically degrade proteins postfusion and demonstrate that mating blocks not only safeguard zygote ploidy but also prevent lysis caused by aberrant fusion attempts. Using long-term imaging and flow-cytometry approaches, we identify previously unrecognized and independent roles for Mei3 and Mei2 in zygotes. We show that Mei3 promotes premeiotic S-phase independently of Mei2 and that cell cycle progression is both necessary and sufficient to reduce zygotic mating behaviors. Mei2 not only imposes the meiotic program and promotes the meiotic cycle, but also blocks mating behaviors independently of Mei3 and cell cycle progression. Thus, we find that fungi preserve zygote ploidy and survival by at least 2 mechanisms where the zygotic fate imposed by Mei2 and the cell cycle reentry triggered by Mei3 synergize to prevent zygotic mating. During sexual reproduction, fertilization must happen between exactly two gametes to ensure genome stability. This study shows that two mechanisms – establishment of zygotic fate and re-entry to the cell cycle – combine to prevent fission yeast zygotes fusing with further gametes.
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Affiliation(s)
- Aleksandar Vještica
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail: (AV); (SGM)
| | - Melvin Bérard
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gaowen Liu
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Laura Merlini
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Pedro Junior Nkosi
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sophie G. Martin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail: (AV); (SGM)
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Lamas I, Weber N, Martin SG. Activation of Cdc42 GTPase upon CRY2-Induced Cortical Recruitment Is Antagonized by GAPs in Fission Yeast. Cells 2020; 9:E2089. [PMID: 32932721 PMCID: PMC7565336 DOI: 10.3390/cells9092089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
The small GTPase Cdc42 is critical for cell polarization in eukaryotic cells. In rod-shaped fission yeast Schizosaccharomyces pombe cells, active GTP-bound Cdc42 promotes polarized growth at cell poles, while inactive Cdc42-GDP localizes ubiquitously also along cell sides. Zones of Cdc42 activity are maintained by positive feedback amplification involving the formation of a complex between Cdc42-GTP, the scaffold Scd2, and the guanine nucleotide exchange factor (GEF) Scd1, which promotes the activation of more Cdc42. Here, we use the CRY2-CIB1 optogenetic system to recruit and cluster a cytosolic Cdc42 variant at the plasma membrane and show that this leads to its moderate activation also on cell sides. Surprisingly, Scd2, which binds Cdc42-GTP, is still recruited to CRY2-Cdc42 clusters at cell sides in individual deletion of the GEFs Scd1 or Gef1. We show that activated Cdc42 clusters at cell sides are able to recruit Scd1, dependent on the scaffold Scd2. However, Cdc42 activity is not amplified by positive feedback and does not lead to morphogenetic changes, due to antagonistic activity of the GTPase activating protein Rga4. Thus, the cell architecture is robust to moderate activation of Cdc42 at cell sides.
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Affiliation(s)
| | | | - Sophie G. Martin
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore building, 1015 Lausanne, Switzerland; (I.L.); (N.W.)
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First person – Aleksandar Vještica. J Cell Sci 2020. [DOI: 10.1242/jcs.242750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Aleksandar Vještica is first author on ‘A toolbox of stable integration vectors in the fission yeast Schizosaccharomyces pombe’, published in JCS. Aleksandar is a post-doctoral fellow in the lab of Sophie G Martin at the University of Lausanne, Switzerland, where he discovered and continues to investigate fungal re-fertilization blocks.
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