1
|
Ohtsuka H, Kawai S, Otsubo Y, Shimasaki T, Yamashita A, Aiba H. Metarhizium robertsii COH1 functionally complements Schizosaccharomyces pombe Ecl family proteins. J GEN APPL MICROBIOL 2024; 69:335-338. [PMID: 37813640 DOI: 10.2323/jgam.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The fission yeast Schizosaccharomyces pombe ecl family genes respond to various starvation signals and induce appropriate intracellular responses, including the extension of chronological lifespan and induction of sexual differentiation. Herein, we propose that the colonization of hemocoel 1 (COH1) protein of Metarhizium robertsii, an insect-pathogenic fungus, is a functional homolog of S. pombe Ecl1 family proteins.
Collapse
Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Sawa Kawai
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Yoko Otsubo
- Interdisciplinary Research Unit, National Institute for Basic Biology
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Akira Yamashita
- Interdisciplinary Research Unit, National Institute for Basic Biology
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
| |
Collapse
|
2
|
Nageshan RK, Krogan N, Cooper JP. Parallel genetic screens identify nuclear envelope homeostasis as a key determinant of telomere entanglement resolution in fission yeast. G3 (Bethesda) 2024:jkae078. [PMID: 38657142 DOI: 10.1093/g3journal/jkae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
In fission yeast lacking the telomere binding protein, Taz1, replication forks stall at telomeres, triggering deleterious downstream events. Strand invasion from one taz1Δ telomeric stalled fork to another on a separate (non-sister) chromosome leads to telomere entanglements, which are resolved in mitosis at 32°C; however, entanglement resolution fails at ≤20°C, leading to cold-specific lethality. Previously, we found that loss of the mitotic function of Rif1, a conserved DNA replication and repair factor, suppresses cold sensitivity by promoting resolution of entanglements without affecting entanglement formation. To understand the underlying pathways of mitotic entanglement resolution, we performed a series of genomewide synthetic genetic array screens to generate a comprehensive list of genetic interactors of taz1Δ and rif1Δ. We modified a previously described screening method to ensure that the queried cells were kept in log phase growth. In addition to recapitulating previously identified genetic interactions, we find that loss of genes encoding components of the nuclear pore complex (NPC) promotes telomere disentanglement and suppresses taz1Δ cold sensitivity. We attribute this to more rapid anaphase midregion nuclear envelope (NE) breakdown in the absence of these NPC components. Loss of genes involved in lipid metabolism reverses the ability of rif1+ deletion to suppress taz1Δ cold sensitivity, again pinpointing NE modulation. A rif1+ separation-of-function mutant that specifically loses Rif1's mitotic functions yields similar genetic interactions. Genes promoting membrane fluidity were enriched in a parallel taz1+ synthetic lethal screen at permissive temperature, cementing the idea that the cold specificity of taz1Δ lethality stems from altered NE homeostasis.
Collapse
Affiliation(s)
- Rishi Kumar Nageshan
- Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, NCI, NIH, Bethesda, MD 20892, USA
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, 308D, San Francisco, CA 94158, USA
| | - Julia Promisel Cooper
- Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, NCI, NIH, Bethesda, MD 20892, USA
| |
Collapse
|
3
|
Kumar A, Gok MO, Nguyen KN, Connor OM, Reese ML, Wideman JG, Muñoz-Gómez SA, Friedman JR. A dynamin superfamily-like pseudoenzyme coordinates with MICOS to promote cristae architecture. Curr Biol 2024:S0960-9822(24)00468-8. [PMID: 38692277 DOI: 10.1016/j.cub.2024.04.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/19/2024] [Accepted: 04/10/2024] [Indexed: 05/03/2024]
Abstract
Mitochondrial cristae architecture is crucial for optimal respiratory function of the organelle. Cristae shape is maintained in part by the mitochondrial contact site and cristae organizing system (MICOS) complex. While MICOS is required for normal cristae morphology, the precise mechanistic role of each of the seven human MICOS subunits, and how the complex coordinates with other cristae-shaping factors, has not been fully determined. Here, we examine the MICOS complex in Schizosaccharomyces pombe, a minimal model whose genome only encodes for four core subunits. Using an unbiased proteomics approach, we identify a poorly characterized inner mitochondrial membrane protein that interacts with MICOS and is required to maintain cristae morphology, which we name Mmc1. We demonstrate that Mmc1 works in concert with MICOS to promote normal mitochondrial morphology and respiratory function. Mmc1 is a distant relative of the dynamin superfamily of proteins (DSPs), GTPases, which are well established to shape and remodel membranes. Similar to DSPs, Mmc1 self-associates and forms high-molecular-weight assemblies. Interestingly, however, Mmc1 is a pseudoenzyme that lacks key residues required for GTP binding and hydrolysis, suggesting that it does not dynamically remodel membranes. These data are consistent with the model that Mmc1 stabilizes cristae architecture by acting as a scaffold to support cristae ultrastructure on the matrix side of the inner membrane. Our study reveals a new class of proteins that evolved early in fungal phylogeny and is required for the maintenance of cristae architecture. This highlights the possibility that functionally analogous proteins work with MICOS to establish cristae morphology in metazoans.
Collapse
Affiliation(s)
- Abhishek Kumar
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mehmet Oguz Gok
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kailey N Nguyen
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Olivia M Connor
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael L Reese
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jeremy G Wideman
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Sergio A Muñoz-Gómez
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jonathan R Friedman
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
4
|
Ushiyama Y, Nishida I, Tomiyama S, Tanaka H, Kume K, Hirata D. Search for protein kinase(s) related to cell growth or viability maintenance in the presence of ethanol in budding and fission yeasts. Biosci Biotechnol Biochem 2024:zbae044. [PMID: 38592956 DOI: 10.1093/bbb/zbae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Alcohol fermentation comprises two phases: phase 1, alcohol fermentation occurs while yeast cells proliferate; phase 2, growth stops and alcohol fermentation continues. We categorized genes related to proliferation in low ethanol (phase 1) and viability in high ethanol (phase 2) as Alcohol Growth Ability (AGA) and Alcohol Viability (ALV), respectively. Although genes required for phase 1 are examined in budding yeast, those for phase 2 are unknown. We set conditions for ALV screening, searched for protein kinases (PKs) related to ALV in budding yeast, and expanded two screenings to fission yeast. Bub1 kinase was important for proliferation in low ethanol but not for viability in high ethanol, suggesting that the important PKs differ between the two phases. It was indeed the case. Further, three common PKs were identified as AGA in both yeasts, suggesting that the important cellular mechanism in phase 1 is conserved in both yeasts, at least partially.
Collapse
Affiliation(s)
- Yuto Ushiyama
- Sakeology Course, Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Niigata, 950-2181, Japan
| | - Ikuhisa Nishida
- Sakeology Center, Niigata University, 2-8050, Ikarashi, Niigata, 950-2181, Japan
| | - Saki Tomiyama
- Sakeology Course, Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Niigata, 950-2181, Japan
| | - Hitomi Tanaka
- Sakeology Course, Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Niigata, 950-2181, Japan
| | - Kazunori Kume
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Dai Hirata
- Sakeology Course, Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Niigata, 950-2181, Japan
- Sakeology Center, Niigata University, 2-8050, Ikarashi, Niigata, 950-2181, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| |
Collapse
|
5
|
Sakai K, Aoki K, Goto Y. Live-cell fluorescence imaging and optogenetic control of PKA kinase activity in fission yeast Schizosaccharomyces pombe. Yeast 2024. [PMID: 38583078 DOI: 10.1002/yea.3937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/21/2024] [Accepted: 03/20/2024] [Indexed: 04/08/2024] Open
Abstract
The cAMP-PKA signaling pathway plays a crucial role in sensing and responding to nutrient availability in the fission yeast Schizosaccharomyces pombe. This pathway monitors external glucose levels to control cell growth and sexual differentiation. However, the temporal dynamics of the cAMP-PKA pathway in response to external stimuli remains unclear mainly due to the lack of tools to quantitatively visualize the activity of the pathway. Here, we report the development of the kinase translocation reporter (KTR)-based biosensor spPKA-KTR1.0, which allows us to measure the dynamics of PKA activity in fission yeast cells. The spPKA-KTR1.0 is derived from the transcription factor Rst2, which translocates from the nucleus to the cytoplasm upon PKA activation. We found that spPKA-KTR1.0 translocates between the nucleus and cytoplasm in a cAMP-PKA pathway-dependent manner, indicating that the spPKA-KTR1.0 is a reliable indicator of the PKA activity in fission yeast cells. In addition, we implemented a system that simultaneously visualizes and manipulates the cAMP-PKA signaling dynamics by introducing bPAC, a photoactivatable adenylate cyclase, in combination with spPKA-KTR1.0. This system offers an opportunity for investigating the role of the signaling dynamics of the cAMP-PKA pathway in fission yeast cells with higher temporal resolution.
Collapse
Affiliation(s)
- Keiichiro Sakai
- Quantitative Biology Research Group, Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| |
Collapse
|
6
|
Rasheed MA, Mohy-Ud-Din R, Anwar T, Faiz M. A novel cell biological tool to explain mechanics and dynamics in fission yeast. J Basic Microbiol 2024; 64:e2300605. [PMID: 38168868 DOI: 10.1002/jobm.202300605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/24/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]
Abstract
The Rho guanosine triphosphatase hydrolase enzyme (GTPase) is required for the control of the actin cytoskeleton, but its activation in vivo condition is unknown. The study's goal was to find a new synthetic nanobody VHH (P-36 tagged with mNeonGreen) that interacts strongly with the Rho GTPase. We present the first novel synthetic nanobody, VHH (P-36 tagged with mNeonGreen), tested in fission yeast cells and found to have a particular interaction with Rho1GTPase. Plasmids were constructed by using of certain enzymes to digest the pDUAL-pef1a vector plasmid to produce a protein that was encoded by cloned genes. A varied VHH library was created synthetically, then transformed into yeast cells, and positive clones were chosen using chemical agents. To investigate protein interactions and cellular reactions, several studies were carried out, such as live cell imaging, growth curve analysis, coimmunoprecipitation, structural analysis, and cell therapies. Prism and RStudio were used for the statistical analysis. The presence of VHH (P-36) has no effect on the growth pattern making it an appropriate model for studying cytokinesis in vivo. According to a computational biological study, its affinity to interact with Rho1GTPase with all the complementarity-determining region (CDR) regions found on VHH (P-36) is extremely strong. We were able to track its subcellular target by localization using a fluorescent confocal microscope, ensuring the maintenance of cell polarity and morphology. Spheroplast analysis revealed a circular-shaped cell with an even distribution of Rho1 tagged VHH (P-36), indicating that the interaction occurs near the plasma membrane. The introduction of latrunculin-A (Lat-A) disrupted Rho GTPase localization, demonstrating the control over actin production, and the cell did not show evidence of mitotic phase commencement while Lat-A was present. Finally, this important biological tool can aid in our understanding of the mechanics and dynamics of cytokinesis in relation to Rho1GTPase.
Collapse
Affiliation(s)
| | - Raza Mohy-Ud-Din
- Institute of Biochemistry and Biotechnology, Faculty of Bio-Sciences, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | - Tehreem Anwar
- Lahore Medical Research Center LLP, Lahore, Punjab, Pakistan
| | - Muhammad Faiz
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences BUITEMS, Quetta, Balochistan, Pakistan
| |
Collapse
|
7
|
Fang Y, Hua X, Shan CM, Toda T, Qiao F, Zhang Z, Jia S. Coordination of histone chaperones for parental histone segregation and epigenetic inheritance. Genes Dev 2024; 38:189-204. [PMID: 38479839 PMCID: PMC10982699 DOI: 10.1101/gad.351278.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/20/2024] [Indexed: 04/02/2024]
Abstract
Chromatin-based epigenetic memory relies on the accurate distribution of parental histone H3-H4 tetramers to newly replicated DNA strands. Mcm2, a subunit of the replicative helicase, and Dpb3/4, subunits of DNA polymerase ε, govern parental histone H3-H4 deposition to the lagging and leading strands, respectively. However, their contribution to epigenetic inheritance remains controversial. Here, using fission yeast heterochromatin inheritance systems that eliminate interference from initiation pathways, we show that a Mcm2 histone binding mutation severely disrupts heterochromatin inheritance, while mutations in Dpb3/4 cause only moderate defects. Surprisingly, simultaneous mutations of Mcm2 and Dpb3/4 stabilize heterochromatin inheritance. eSPAN (enrichment and sequencing of protein-associated nascent DNA) analyses confirmed the conservation of Mcm2 and Dpb3/4 functions in parental histone H3-H4 segregation, with their combined absence showing a more symmetric distribution of parental histone H3-H4 than either single mutation alone. Furthermore, the FACT histone chaperone regulates parental histone transfer to both strands and collaborates with Mcm2 and Dpb3/4 to maintain parental histone H3-H4 density and faithful heterochromatin inheritance. These results underscore the importance of both symmetric distribution of parental histones and their density at daughter strands for epigenetic inheritance and unveil distinctive properties of parental histone chaperones during DNA replication.
Collapse
Affiliation(s)
- Yimeng Fang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University, New York, New York 10027, USA
- Department of Pediatrics, Columbia University, New York, New York 10027, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Chun-Min Shan
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Takenori Toda
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Feng Qiao
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University, New York, New York 10027, USA;
- Department of Pediatrics, Columbia University, New York, New York 10027, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA;
| |
Collapse
|
8
|
Etherington GJ, Wu PS, Oliferenko S, Uhlmann F, Nieduszynski CA. Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features. Yeast 2024; 41:73-86. [PMID: 38451028 DOI: 10.1002/yea.3912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 03/08/2024] Open
Abstract
Schizosaccharomyces japonicus belongs to the single-genus class Schizosaccharomycetes, otherwise known as "fission yeasts." As part of a composite model system with its widely studied S. pombe sister species, S. japonicus has provided critical insights into the workings and the evolution of cell biological mechanisms. Furthermore, its divergent biology makes S. japonicus a valuable model organism in its own right. However, the currently available genome assembly contains gaps and has been unable to resolve centromeres and other repeat-rich chromosomal regions. Here we present a telomere-to-telomere long-read genome assembly of the S. japonicus genome. This includes the three megabase-length chromosomes, with centromeres hundreds of kilobases long, rich in 5S ribosomal RNA genes, transfer RNA genes, long terminal repeats, and short repeats. We identify a gene-sparse region on chromosome 2 that resembles a 331 kb centromeric duplication. We revise the genome size of S. japonicus to at least 16.6 Mb and possibly up to 18.12 Mb, at least 30% larger than previous estimates. Our whole genome assembly will support the growing S. japonicus research community and facilitate research in new directions, including centromere and DNA repeat evolution, and yeast comparative genomics.
Collapse
Affiliation(s)
| | | | - Snezhana Oliferenko
- The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Frank Uhlmann
- The Francis Crick Institute, London, UK
- Cell Biology Centre, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, Japan
| | - Conrad A Nieduszynski
- The Earlham Institute, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| |
Collapse
|
9
|
Kume K, Nishikawa K, Furuyama R, Fujimoto T, Koyano T, Matsuyama M, Mizunuma M, Hirata D. The fission yeast NDR kinase Orb6 and its signalling pathway MOR regulate cytoplasmic microtubule organization during the cell cycle. Open Biol 2024; 14:230440. [PMID: 38442865 PMCID: PMC10914512 DOI: 10.1098/rsob.230440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/04/2024] [Indexed: 03/07/2024] Open
Abstract
Microtubule organization and reorganization during the cell cycle are achieved by regulation of the number, distribution and activity of microtubule-organizing centres (MTOCs). In fission yeast, the Mto1/2 complex determines the activity and distribution of cytoplasmic MTOCs. Upon mitosis, cytoplasmic microtubule nucleation ceases; inactivation of the Mto1/2 complex is triggered by Mto2 hyperphosphorylation. However, the protein kinase(s) that phosphorylates Mto2 remains elusive. Here we show that a conserved signalling network, called MOR (morphogenesis Orb6 network) in fission yeast, negatively regulates cytoplasmic MTOCs through Mto2 phosphorylation to ensure proper microtubule organization. Inactivation of Orb6 kinase, the most downstream MOR component, by attenuation of MOR signalling leads to reduced Mto2 phosphorylation, coincident with increased number of both Mto2 puncta and cytoplasmic microtubules. These defects cause the emergence of uncoordinated mitotic cells with cytoplasmic microtubules, resulting in reduced spindle assembly. Thus, the regulation of Mto2 by the MOR is crucial for cytoplasmic microtubule organization and contributes to reorganization of the microtubule cytoskeletons during the cell cycle.
Collapse
Affiliation(s)
- Kazunori Kume
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Kenji Nishikawa
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Rikuto Furuyama
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takahiro Fujimoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takayuki Koyano
- Division of Cell Biology, Shigei Medical Research Institute, 2117 Yamada, Minami-ku, Okayama 701-0202, Japan
| | - Makoto Matsuyama
- Division of Molecular Genetics, Shigei Medical Research Institute, 2117 Yamada, Minami-ku, Okayama 701-0202, Japan
| | - Masaki Mizunuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Dai Hirata
- Faculty of Agriculture, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan
- Sakeology Center, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan
| |
Collapse
|
10
|
Etherington GJ, Gil EG, Haerty W, Oliferenko S, Nieduszynski CA. Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast. Yeast 2024; 41:95-107. [PMID: 38146786 DOI: 10.1002/yea.3919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023] Open
Abstract
The fission yeast species Schizosaccharomyces japonicus is currently divided into two varieties-S. japonicus var. japonicus and S. japonicus var. versatilis. Here we examine the var. versatilis isolate CBS5679. The CBS5679 genome shows 88% identity to the reference genome of S. japonicus var. japonicus at the coding sequence level, with phylogenetic analyses suggesting that it has split from the S. japonicus lineage 25 million years ago. The CBS5679 genome contains a reciprocal translocation between chromosomes 1 and 2, together with several large inversions. The products of genes linked to the major translocation are associated with 'metabolism' and 'cellular assembly' ontology terms. We further show that CBS5679 does not generate viable progeny with the reference strain of S. japonicus. Although CBS5679 shares closer similarity to the 'type' strain of var. versatilis as compared to S. japonicus, it is not identical to the type strain, suggesting population structure within var. versatilis. We recommend that the taxonomic status of S. japonicus var. versatilis is raised, with it being treated as a separate species, Schizosaccharomyces versatilis.
Collapse
Affiliation(s)
| | - Elisa Gomez Gil
- Oliferenko Lab, The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Wilfried Haerty
- Research Faculty, The Earlham Institute, Norwich Research Park, Norwich, UK
| | - Snezhana Oliferenko
- Oliferenko Lab, The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Conrad A Nieduszynski
- Research Faculty, The Earlham Institute, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| |
Collapse
|
11
|
García-Ruano D, Hsu I, Leray B, Billard B, Liti G, Coudreuse D. Engineering heterothallic strains in fission yeast. Yeast 2024; 41:87-94. [PMID: 38099423 DOI: 10.1002/yea.3914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/18/2023] [Accepted: 11/15/2023] [Indexed: 02/24/2024] Open
Abstract
In poor nitrogen conditions, fission yeast cells mate, undergo meiosis and form spores that are resistant to deleterious environments. Natural isolates of Schizosaccharomyces pombe are homothallic. This allows them to naturally switch between the two h- and h+ mating types with a high frequency, thereby ensuring the presence of both mating partners in a population of cells. However, alteration of the mating type locus can abolish mating type switching or reduce it to a very low frequency. Such heterothallic strains have been isolated and are common in research laboratories due to the simplicity of their use for Mendelian genetics. In addition to the standard laboratory strains, a large collection of natural S. pombe isolates is now available, representing a powerful resource for investigating the genetic diversity and biology of fission yeast. However, most of these strains are homothallic, and only tedious or mutagenic strategies have been described to obtain heterothallic cells from a homothallic parent. Here, we describe a simple approach to generate heterothallic strains. It takes advantage of an alteration of the mating type locus that was previously identified in a mating type switching-deficient strain and the CRISPR-Cas9 editing tool, allowing for a one-step engineering of heterothallic cells with high efficiency.
Collapse
Affiliation(s)
- Daniel García-Ruano
- Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, University of Bordeaux, Bordeaux, France
| | - Ian Hsu
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Baptiste Leray
- Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, University of Bordeaux, Bordeaux, France
| | | | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
| | - Damien Coudreuse
- Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, University of Bordeaux, Bordeaux, France
| |
Collapse
|
12
|
Sugiyama H, Goto Y, Kondo Y, Coudreuse D, Aoki K. Live-cell imaging defines a threshold in CDK activity at the G2/M transition. Dev Cell 2024; 59:545-557.e4. [PMID: 38228139 DOI: 10.1016/j.devcel.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 10/05/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024]
Abstract
Cyclin-dependent kinase (CDK) determines the temporal ordering of the cell cycle phases. However, despite significant progress in studying regulators of CDK and phosphorylation patterns of CDK substrates at the population level, it remains elusive how CDK regulators coordinately affect CDK activity at the single-cell level and how CDK controls the temporal order of cell cycle events. Here, we elucidate the dynamics of CDK activity in fission yeast and mammalian cells by developing a CDK activity biosensor, Eevee-spCDK. We find that although CDK activity does not necessarily correlate with cyclin levels, it converges to the same level around mitotic onset in several mutant backgrounds, including pom1Δ cells and wee1 or cdc25 overexpressing cells. These data provide direct evidence that cells enter the M phase when CDK activity reaches a high threshold, consistent with the quantitative model of cell cycle progression in fission yeast.
Collapse
Affiliation(s)
- Hironori Sugiyama
- 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
| | - 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; Basic Biology Program, Graduate Institute for Advanced Studies, SOKENDAI, 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; Basic Biology Program, Graduate Institute for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Damien Coudreuse
- Institute of Biochemistry and Cellular Genetics, UMR 5095, CNRS, Bordeaux University, 33077 Bordeaux, France
| | - 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; Basic Biology Program, Graduate Institute for Advanced Studies, SOKENDAI, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan.
| |
Collapse
|
13
|
Rutherford KM, Lera-Ramírez M, Wood V. PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability. Genetics 2024:iyae007. [PMID: 38376816 DOI: 10.1093/genetics/iyae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/13/2024] [Indexed: 02/21/2024] Open
Abstract
PomBase (https://www.pombase.org), the model organism database (MOD) for fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition (GBC; https://globalbiodata.org/) after a rigorous selection process. In this MOD review, we present PomBase's continuing growth and improvement over the last 2 years. We describe these improvements in the context of the qualitative GCBR indicators related to scientific quality, comprehensivity, accelerating science, user stories, and collaborations with other biodata resources. This review also showcases the depth of existing connections both within the biocuration ecosystem and between PomBase and its user community.
Collapse
Affiliation(s)
- Kim M Rutherford
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Manuel Lera-Ramírez
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Valerie Wood
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| |
Collapse
|
14
|
Rezig IM, Yaduma WG, McInerny CJ. Processes Controlling the Contractile Ring during Cytokinesis in Fission Yeast, Including the Role of ESCRT Proteins. J Fungi (Basel) 2024; 10:154. [PMID: 38392827 PMCID: PMC10890238 DOI: 10.3390/jof10020154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Cytokinesis, as the last stage of the cell division cycle, is a tightly controlled process amongst all eukaryotes, with defective division leading to severe cellular consequences and implicated in serious human diseases and conditions such as cancer. Both mammalian cells and the fission yeast Schizosaccharomyces pombe use binary fission to divide into two equally sized daughter cells. Similar to mammalian cells, in S. pombe, cytokinetic division is driven by the assembly of an actomyosin contractile ring (ACR) at the cell equator between the two cell tips. The ACR is composed of a complex network of membrane scaffold proteins, actin filaments, myosin motors and other cytokinesis regulators. The contraction of the ACR leads to the formation of a cleavage furrow which is severed by the endosomal sorting complex required for transport (ESCRT) proteins, leading to the final cell separation during the last stage of cytokinesis, the abscission. This review describes recent findings defining the two phases of cytokinesis in S. pombe: ACR assembly and constriction, and their coordination with septation. In summary, we provide an overview of the current understanding of the mechanisms regulating ACR-mediated cytokinesis in S. pombe and emphasize a potential role of ESCRT proteins in this process.
Collapse
Affiliation(s)
- Imane M Rezig
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Davidson Building, Glasgow G12 8QQ, UK
| | - Wandiahyel G Yaduma
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Davidson Building, Glasgow G12 8QQ, UK
- Department of Chemistry, School of Sciences, Adamawa State College of Education, Hong 640001, Adamawa State, Nigeria
| | - Christopher J McInerny
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Davidson Building, Glasgow G12 8QQ, UK
| |
Collapse
|
15
|
Bednor L, Sanchez AM, Garg A, Shuman S, Schwer B. Genetic suppressor screen identifies Tgp1 (glycerophosphocholine transporter), Kcs1 (IP 6 kinase), and Plc1 (phospholipase C) as determinants of inositol pyrophosphate toxicosis in fission yeast. mBio 2024; 15:e0306223. [PMID: 38133430 PMCID: PMC10865970 DOI: 10.1128/mbio.03062-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
The inositol pyrophosphate signaling molecule 1,5-IP8 is an agonist of RNA 3'-processing and transcription termination in fission yeast that regulates the expression of phosphate acquisition genes pho1, pho84, and tgp1. IP8 is synthesized from 5-IP7 by the Asp1 N-terminal kinase domain and catabolized by the Asp1 C-terminal pyrophosphatase domain. asp1-STF mutations that delete or inactivate the Asp1 pyrophosphatase domain elicit growth defects in yeast extract with supplements (YES) medium ranging from severe sickness to lethality. We now find that the toxicity of asp1-STF mutants is caused by a titratable constituent of yeast extract. Via a genetic screen for spontaneous suppressors, we identified a null mutation of glycerophosphodiester transporter tgp1 that abolishes asp1-STF toxicity in YES medium. This result, and the fact that tgp1 mRNA expression is increased by >40-fold in asp1-STF cells, prompted discovery that: (i) glycerophosphocholine (GPC) recapitulates the toxicity of yeast extract to asp1-STF cells in a Tgp1-dependent manner, and (ii) induced overexpression of tgp1 in asp1+ cells also elicits toxicity dependent on GPC. asp1-STF suppressor screens yielded a suite of single missense mutations in the essential IP6 kinase Kcs1 that generates 5-IP7, the immediate precursor to IP8. Transcription profiling of the kcs1 mutants in an asp1+ background revealed the downregulation of the same phosphate acquisition genes that were upregulated in asp1-STF cells. The suppressor screen also returned single missense mutations in Plc1, the fission yeast phospholipase C enzyme that generates IP3, an upstream precursor for the synthesis of inositol pyrophosphates.IMPORTANCEThe inositol pyrophosphate metabolite 1,5-IP8 governs repression of fission yeast phosphate homeostasis genes pho1, pho84, and tgp1 by lncRNA-mediated transcriptional interference. Asp1 pyrophosphatase mutations that increase IP8 levels elicit precocious lncRNA termination, leading to derepression of the PHO genes. Deletions of the Asp1 pyrophosphatase domain result in growth impairment or lethality via IP8 agonism of transcription termination. It was assumed that IP8 toxicity ensues from dysregulation of essential genes. In this study, a suppressor screen revealed that IP8 toxicosis of Asp1 pyrophosphatase mutants is caused by: (i) a >40-fold increase in the expression of the inessential tgp1 gene encoding a glycerophosphodiester transporter and (ii) the presence of glycerophosphocholine in the growth medium. The suppressor screen yielded missense mutations in two upstream enzymes of inositol polyphosphate metabolism: the phospholipase C enzyme Plc1 that generates IP3 and the essential Kcs1 kinase that converts IP6 to 5-IP7, the immediate precursor of IP8.
Collapse
Affiliation(s)
- Lauren Bednor
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, USA
- Molecular Biology Program, Sloan-Kettering Institute, New York, USA
- Weill Cornell Graduate School of Medical Sciences, New York, USA
| | - Ana M. Sanchez
- Molecular Biology Program, Sloan-Kettering Institute, New York, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, USA
| | - Angad Garg
- Molecular Biology Program, Sloan-Kettering Institute, New York, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, USA
| |
Collapse
|
16
|
Hall AR, Choi YK, Im W, Vavylonis D. Anillin-related Mid1 as an adaptive and multimodal contractile ring anchoring protein: A simulation study. Structure 2024; 32:242-252.e2. [PMID: 38103546 PMCID: PMC10872332 DOI: 10.1016/j.str.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 10/13/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
Abstract
Cytokinesis of animal and fungi cells depends crucially on the anillin scaffold proteins. Fission yeast anillin-related Mid1 anchors cytokinetic ring precursor nodes to the membrane. However, it is unclear if both of its Pleckstrin Homology (PH) and C2 C-terminal domains bind to the membrane as monomers or dimers, and if one domain plays a dominant role. We studied Mid1 membrane binding with all-atom molecular dynamics near a membrane with yeast-like lipid composition. In simulations with the full C terminal region started away from the membrane, Mid1 binds through the disordered L3 loop of C2 in a vertical orientation, with the PH away from the membrane. However, a configuration with both C2 and PH initially bound to the membrane remains associated with the membrane. Simulations of C2-PH dimers show extensive asymmetric membrane contacts. These multiple modes of binding may reflect Mid1's multiple interactions with membranes, node proteins, and ability to sustain mechanical forces.
Collapse
Affiliation(s)
- Aaron R Hall
- Department of Physics, Lehigh University, Bethlehem, PA 18017, USA
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18017, USA
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18017, USA
| | - Dimitrios Vavylonis
- Department of Physics, Lehigh University, Bethlehem, PA 18017, USA; Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA.
| |
Collapse
|
17
|
Sun L, Liu L, Song C, Wang Y, Jin QW. Heat stress-induced activation of MAPK pathway attenuates Atf1-dependent epigenetic inheritance of heterochromatin in fission yeast. eLife 2024; 13:e90525. [PMID: 38289024 PMCID: PMC10863984 DOI: 10.7554/elife.90525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/29/2024] [Indexed: 02/15/2024] Open
Abstract
Eukaryotic cells are constantly exposed to various environmental stimuli. It remains largely unexplored how environmental cues bring about epigenetic fluctuations and affect heterochromatin stability. In the fission yeast Schizosaccharomyces pombe, heterochromatic silencing is quite stable at pericentromeres but unstable at the mating-type (mat) locus under chronic heat stress, although both loci are within the major constitutive heterochromatin regions. Here, we found that the compromised gene silencing at the mat locus at elevated temperature is linked to the phosphorylation status of Atf1, a member of the ATF/CREB superfamily. Constitutive activation of mitogen-activated protein kinase (MAPK) signaling disrupts epigenetic maintenance of heterochromatin at the mat locus even under normal temperature. Mechanistically, phosphorylation of Atf1 impairs its interaction with heterochromatin protein Swi6HP1, resulting in lower site-specific Swi6HP1 enrichment. Expression of non-phosphorylatable Atf1, tethering Swi6HP1 to the mat3M-flanking site or absence of the anti-silencing factor Epe1 can largely or partially rescue heat stress-induced defective heterochromatic maintenance at the mat locus.
Collapse
Affiliation(s)
- Li Sun
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Libo Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Chunlin Song
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Yamei Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Quan-wen Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| |
Collapse
|
18
|
Takado M, Yamamoto TG, Chikashige Y, Matsumoto T. Fission yeast Wee1 is required for stable kinetochore-microtubule attachment. Open Biol 2024; 14:230379. [PMID: 38166399 PMCID: PMC10762435 DOI: 10.1098/rsob.230379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/21/2023] [Indexed: 01/04/2024] Open
Abstract
Wee1 is a cell cycle regulator that phosphorylates Cdk1/Cdc2 and inhibits G2/M transition. Loss of Wee1 in fission yeast results in an early onset of mitosis. Interestingly, we found that cells lacking Wee1 require the functional spindle checkpoint for their viability. Genetic analysis indicated that the requirement is not attributable to the early onset of mitosis. Live-cell imaging revealed that some kinetochores are not attached or bioriented in the wee1 mutant. Furthermore, Mad2, a component of the spindle checkpoint known to recognize unattached kinetochores, accumulates in the vicinity of the spindle, representing activation of the spindle checkpoint in the mutant. It appears that the wee1 mutant cannot maintain stable kinetochore-microtubule attachment, and relies on the delay imposed by the spindle checkpoint for establishing biorientation of kinetochores. This study revealed a role of Wee1 in ensuring accurate segregation of chromosomes during mitosis, and thus provided a basis for a new principle of cancer treatment with Wee1 inhibitors.
Collapse
Affiliation(s)
- Masahiro Takado
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Takaharu G. Yamamoto
- Kobe Frontier Research Center, Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Yuji Chikashige
- Kobe Frontier Research Center, Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Tomohiro Matsumoto
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| |
Collapse
|
19
|
Wang K, Okada H, Wloka C, Bi E. Unraveling the mechanisms and evolution of a two-domain module in IQGAP proteins for controlling eukaryotic cytokinesis. Cell Rep 2023; 42:113510. [PMID: 38041816 PMCID: PMC10809011 DOI: 10.1016/j.celrep.2023.113510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/17/2023] [Accepted: 11/13/2023] [Indexed: 12/04/2023] Open
Abstract
The IQGAP family of proteins plays a crucial role in cytokinesis across diverse organisms, but the underlying mechanisms are not fully understood. In this study, we demonstrate that IQGAPs in budding yeast, fission yeast, and human cells use a two-domain module to regulate their localization as well as the assembly and disassembly of the actomyosin ring during cytokinesis. Strikingly, the calponin homology domains (CHDs) in these IQGAPs bind to distinct cellular F-actin structures with varying specificity, whereas the non-conserved domains immediately downstream of the CHDs in these IQGAPs all target the division site, but differ in timing, localization strength, and binding partners. We also demonstrate that human IQGAP3 acts in parallel to septins and myosin-IIs to mediate the role of anillin in cytokinesis. Collectively, our findings highlight the two-domain mechanism by which IQGAPs regulate cytokinesis in distantly related organisms as well as their evolutionary conservation and divergence.
Collapse
Affiliation(s)
- Kangji Wang
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Hiroki Okada
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Carsten Wloka
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA; Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin, Germany
| | - Erfei Bi
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA.
| |
Collapse
|
20
|
Xu R, Pan Z, Nakagawa T. Gross Chromosomal Rearrangement at Centromeres. Biomolecules 2023; 14:28. [PMID: 38254628 PMCID: PMC10813616 DOI: 10.3390/biom14010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Centromeres play essential roles in the faithful segregation of chromosomes. CENP-A, the centromere-specific histone H3 variant, and heterochromatin characterized by di- or tri-methylation of histone H3 9th lysine (H3K9) are the hallmarks of centromere chromatin. Contrary to the epigenetic marks, DNA sequences underlying the centromere region of chromosomes are not well conserved through evolution. However, centromeres consist of repetitive sequences in many eukaryotes, including animals, plants, and a subset of fungi, including fission yeast. Advances in long-read sequencing techniques have uncovered the complete sequence of human centromeres containing more than thousands of alpha satellite repeats and other types of repetitive sequences. Not only tandem but also inverted repeats are present at a centromere. DNA recombination between centromere repeats can result in gross chromosomal rearrangement (GCR), such as translocation and isochromosome formation. CENP-A chromatin and heterochromatin suppress the centromeric GCR. The key player of homologous recombination, Rad51, safeguards centromere integrity through conservative noncrossover recombination between centromere repeats. In contrast to Rad51-dependent recombination, Rad52-mediated single-strand annealing (SSA) and microhomology-mediated end-joining (MMEJ) lead to centromeric GCR. This review summarizes recent findings on the role of centromere and recombination proteins in maintaining centromere integrity and discusses how GCR occurs at centromeres.
Collapse
Affiliation(s)
- Ran Xu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Ziyi Pan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| |
Collapse
|
21
|
Tai YT, Fukuda T, Morozumi Y, Hirai H, Oda AH, Kamada Y, Akikusa Y, Kanki T, Ohta K, Shiozaki K. Fission Yeast TORC1 Promotes Cell Proliferation through Sfp1, a Transcription Factor Involved in Ribosome Biogenesis. Mol Cell Biol 2023; 43:675-692. [PMID: 38051102 PMCID: PMC10761059 DOI: 10.1080/10985549.2023.2282349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
Target of rapamycin complex 1 (TORC1) is activated in response to nutrient availability and growth factors, promoting cellular anabolism and proliferation. To explore the mechanism of TORC1-mediated proliferation control, we performed a genetic screen in fission yeast and identified Sfp1, a zinc-finger transcription factor, as a multicopy suppressor of temperature-sensitive TORC1 mutants. Our observations suggest that TORC1 phosphorylates Sfp1 and protects Sfp1 from proteasomal degradation. Transcription analysis revealed that Sfp1 positively regulates genes involved in ribosome production together with two additional transcription factors, Ifh1/Crf1 and Fhl1. Ifh1 physically interacts with Fhl1, and the nuclear localization of Ifh1 is regulated in response to nutrient levels in a manner dependent on TORC1 and Sfp1. Taken together, our data suggest that the transcriptional regulation of the genes involved in ribosome biosynthesis by Sfp1, Ifh1, and Fhl1 is one of the key pathways through which nutrient-activated TORC1 promotes cell proliferation.
Collapse
Affiliation(s)
- Yen Teng Tai
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Tomoyuki Fukuda
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yuichi Morozumi
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hayato Hirai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Arisa H. Oda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshiaki Kamada
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa, Japan
| | - Yutaka Akikusa
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Tomotake Kanki
- Department of Cellular Physiology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Shiozaki
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA
| |
Collapse
|
22
|
Zhang X, Fawwal DV, Spangle JM, Corbett AH, Jones CY. Exploring the Molecular Underpinnings of Cancer-Causing Oncohistone Mutants Using Yeast as a Model. J Fungi (Basel) 2023; 9:1187. [PMID: 38132788 PMCID: PMC10744705 DOI: 10.3390/jof9121187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Understanding the molecular basis of cancer initiation and progression is critical in developing effective treatment strategies. Recently, mutations in genes encoding histone proteins that drive oncogenesis have been identified, converting these essential proteins into "oncohistones". Understanding how oncohistone mutants, which are commonly single missense mutations, subvert the normal function of histones to drive oncogenesis requires defining the functional consequences of such changes. Histones genes are present in multiple copies in the human genome with 15 genes encoding histone H3 isoforms, the histone for which the majority of oncohistone variants have been analyzed thus far. With so many wildtype histone proteins being expressed simultaneously within the oncohistone, it can be difficult to decipher the precise mechanistic consequences of the mutant protein. In contrast to humans, budding and fission yeast contain only two or three histone H3 genes, respectively. Furthermore, yeast histones share ~90% sequence identity with human H3 protein. Its genetic simplicity and evolutionary conservation make yeast an excellent model for characterizing oncohistones. The power of genetic approaches can also be exploited in yeast models to define cellular signaling pathways that could serve as actionable therapeutic targets. In this review, we focus on the value of yeast models to serve as a discovery tool that can provide mechanistic insights and inform subsequent translational studies in humans.
Collapse
Affiliation(s)
- Xinran Zhang
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
| | - Dorelle V. Fawwal
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Jennifer M. Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Anita H. Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Celina Y. Jones
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
23
|
Hati D, Brault A, Gupta M, Fletcher K, Jacques JF, Labbé S, Outten CE. Iron homeostasis proteins Grx4 and Fra2 control activity of the Schizosaccharomyces pombe iron repressor Fep1 by facilitating [2Fe-2S] cluster removal. J Biol Chem 2023; 299:105419. [PMID: 37923140 PMCID: PMC10704371 DOI: 10.1016/j.jbc.2023.105419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/12/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023] Open
Abstract
The Bol2 homolog Fra2 and monothiol glutaredoxin Grx4 together play essential roles in regulating iron homeostasis in Schizosaccharomyces pombe. In vivo studies indicate that Grx4 and Fra2 act as coinhibitory partners that inactivate the transcriptional repressor Fep1 in response to iron deficiency. In Saccharomyces cerevisiae, Bol2 is known to form a [2Fe-2S]-bridged heterodimer with the monothiol Grxs Grx3 and Grx4, with the cluster ligands provided by conserved residues in Grx3/4 and Bol2 as well as GSH. In this study, we characterized this analogous [2Fe-2S]-bridged Grx4-Fra2 complex in S. pombe by identifying the specific residues in Fra2 that act as ligands for the Fe-S cluster and are required to regulate Fep1 activity. We present spectroscopic and biochemical evidence confirming the formation of a [2Fe-2S]-bridged Grx4-Fra2 heterodimer with His66 and Cys29 from Fra2 serving as Fe-S cluster ligands in S. pombe. In vivo transcription and growth assays confirm that both His66 and Cys29 are required to fully mediate the response of Fep1 to low iron conditions. Furthermore, we analyzed the interaction between Fep1 and Grx4-Fra2 using CD spectroscopy to monitor changes in Fe-S cluster coordination chemistry. These experiments demonstrate unidirectional [2Fe-2S] cluster transfer from Fep1 to Grx4-Fra2 in the presence of GSH, revealing the Fe-S cluster dependent mechanism of Fep1 inactivation mediated by Grx4 and Fra2 in response to iron deficiency.
Collapse
Affiliation(s)
- Debolina Hati
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Ariane Brault
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Malini Gupta
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Kylie Fletcher
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA
| | - Jean-François Jacques
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Simon Labbé
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Caryn E Outten
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, USA.
| |
Collapse
|
24
|
Hirai H, Sen Y, Tamura M, Ohta K. TOR inactivation triggers heterochromatin formation in rDNA during glucose starvation. Cell Rep 2023; 42:113320. [PMID: 37913773 DOI: 10.1016/j.celrep.2023.113320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/29/2023] [Accepted: 10/05/2023] [Indexed: 11/03/2023] Open
Abstract
In response to environmental cues, such as nutrient starvation, living organisms modulate gene expression through mechanisms involving histone modifications. Specifically, nutrient depletion inactivates the TOR (target of rapamycin) pathway, leading to reduced expression of ribosomal genes. While these regulatory mechanisms are well elucidated in budding yeast Saccharomyces cerevisiae, their conservation across diverse organisms remains unclear. In this study, we demonstrate that fission yeast Schizosaccharomyces pombe cells repress ribosomal gene transcription through a different mechanism. TORC1, which accumulates in the rDNA region, dissociates upon starvation, resulting in enhanced methylation of H3K9 and heterochromatin formation, facilitated by dissociation of the stress-responsive transcription factor Atf1 and accumulation of the histone chaperone FACT. We propose that this mechanism might be adapted in mammals that possess Suv39H1 and HP1, which are absent in budding yeast.
Collapse
Affiliation(s)
- Hayato Hirai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan.
| | - Yuki Sen
- Department of Integrated Sciences, College of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan
| | - Miki Tamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan; Universal Biology Institute, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.
| |
Collapse
|
25
|
Nguyen LAC, Mori M, Yasuda Y, Galipon J. Functional Consequences of Shifting Transcript Boundaries in Glucose Starvation. Mol Cell Biol 2023; 43:611-628. [PMID: 37937348 PMCID: PMC10761120 DOI: 10.1080/10985549.2023.2270406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Glucose is a major source of carbon and essential for the survival of many organisms, ranging from yeast to human. A sudden 60-fold reduction of glucose in exponentially growing fission yeast induces transcriptome-wide changes in gene expression. This regulation is multilayered, and the boundaries of transcripts are known to vary, with functional consequences at the protein level. By combining direct RNA sequencing with 5'-CAGE and short-read sequencing, we accurately defined the 5'- and 3'-ends of transcripts that are both poly(A) tailed and 5'-capped in glucose starvation, followed by proteome analysis. Our results confirm previous experimentally validated loci with alternative isoforms and reveal several transcriptome-wide patterns. First, we show that sense-antisense gene pairs are more strongly anticorrelated when a time lag is taken into account. Second, we show that the glucose starvation response initially elicits a shortening of 3'-UTRs and poly(A) tails, followed by a shortening of the 5'-UTRs at later time points. These result in domain gains and losses in proteins involved in the stress response. Finally, the relatively poor overlap both between differentially expressed genes (DEGs), differential transcript usage events (DTUs), and differentially detected proteins (DDPs) highlight the need for further study on post-transcriptional regulation mechanisms in glucose starvation.
Collapse
Affiliation(s)
- Lan Anh Catherine Nguyen
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
- Institute of Innovation for Future Society, Nagoya University, Aichi, Nagoya, Japan
| | - Yuji Yasuda
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Faculty of Environment and Information Studies, Keio University, Kanagawa, Fujisawa, Japan
| | - Josephine Galipon
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
- Graduate School of Science and Engineering, Yamagata University, Yamagata, Yonezawa, Japan
| |
Collapse
|
26
|
Koyano T, Fujimoto T, Onishi K, Matsuyama M, Fukushima M, Kume K. Pkd2, mutations linking to autosomal dominant polycystic kidney disease, localizes to the endoplasmic reticulum and regulates calcium signaling in fission yeast. Genes Cells 2023; 28:811-820. [PMID: 37723847 DOI: 10.1111/gtc.13069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a renal disorder caused by mutations in the PKD2 gene, which encodes polycystin-2/Pkd2, a transient receptor potential channel. The precise role of Pkd2 in cyst formation remains unclear. The fission yeast Schizosaccharomyces pombe has a putative transient receptor potential channel, Pkd2, which shares similarities with human Pkd2. In this study, truncation analyses of fission yeast Pkd2 were conducted to investigate its localization and function. The results revealed that Pkd2 localizes not only to the plasma membrane but also to the endoplasmic reticulum (ER) in fission yeast. Furthermore, Pkd2 regulates calcium signaling in fission yeast, with the transmembrane domains of Pkd2 being sufficient for these processes. Specifically, the C-terminal region of Pkd2 plays a crucial role in the regulation of calcium signaling. Interestingly, human Pkd2 also localized to the ER and had some impact on calcium signaling in fission yeast. However, human Pkd2 failed to suppress the loss of fission yeast Pkd2. These findings indicate that hPkd2 may not completely substitute for cellular physiology of fission yeast Pkd2. This study provides insights into the localization and functional characteristics of Pkd2 in fission yeast, contributing to our understanding of the pathogenesis of ADPKD.
Collapse
Affiliation(s)
- Takayuki Koyano
- Division of Cell Biology, Shigei Medical Research Institute, Minami-ku, Okayama, Japan
| | - Takahiro Fujimoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Kaori Onishi
- Division of Cell Biology, Shigei Medical Research Institute, Minami-ku, Okayama, Japan
| | - Makoto Matsuyama
- Division of Molecular Genetics, Shigei Medical Research Institute, Minami-ku, Okayama, Japan
| | - Masaki Fukushima
- Division of Molecular Genetics, Shigei Medical Research Institute, Minami-ku, Okayama, Japan
- Shigei Medical Research Hospital, Minami-ku, Okayama, Japan
| | - Kazunori Kume
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Hiroshima Research Center for Healthy Aging (HiHA), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| |
Collapse
|
27
|
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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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.
Collapse
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
| |
Collapse
|
28
|
Ohtsuka H, Otsubo Y, Shimasaki T, Yamashita A, Aiba H. ecl family genes: Factors linking starvation and lifespan extension in Schizosaccharomyces pombe. Mol Microbiol 2023; 120:645-657. [PMID: 37525511 DOI: 10.1111/mmi.15134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/02/2023]
Abstract
In the fission yeast Schizosaccharomyces pombe, the duration of survival in the stationary phase, termed the chronological lifespan (CLS), is affected by various environmental factors and the corresponding gene activities. The ecl family genes were identified in the genomic region encoding non-coding RNA as positive regulators of CLS in S. pombe, and subsequently shown to encode relatively short proteins. Several studies revealed that ecl family genes respond to various nutritional starvation conditions via different mechanisms, and they are additionally involved in stress resistance, autophagy, sexual differentiation, and cell cycle control. Recent studies reported that Ecl family proteins strongly suppress target of rapamycin complex 1, which is a conserved eukaryotic nutrient-sensing kinase complex that also regulates longevity in a variety of organisms. In this review, we introduce the regulatory mechanisms of Ecl family proteins and discuss their emerging findings.
Collapse
Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Yoko Otsubo
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Akira Yamashita
- Interdisciplinary Research Unit, National Institute for Basic Biology, Okazaki, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| |
Collapse
|
29
|
Lam UTF, Nguyen TTT, Raechell R, Yang J, Singer H, Chen ES. A Normalization Protocol Reduces Edge Effect in High-Throughput Analyses of Hydroxyurea Hypersensitivity in Fission Yeast. Biomedicines 2023; 11:2829. [PMID: 37893202 PMCID: PMC10604075 DOI: 10.3390/biomedicines11102829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Edge effect denotes better growth of microbial organisms situated at the edge of the solid agar media. Although the precise reason underlying edge effect is unresolved, it is generally attributed to greater nutrient availability with less competing neighbors at the edge. Nonetheless, edge effect constitutes an unavoidable confounding factor that results in misinterpretation of cell fitness, especially in high-throughput screening experiments widely employed for genome-wide investigation using microbial gene knockout or mutant libraries. Here, we visualize edge effect in high-throughput high-density pinning arrays and report a normalization approach based on colony growth rate to quantify drug (hydroxyurea)-hypersensitivity in fission yeast strains. This normalization procedure improved the accuracy of fitness measurement by compensating cell growth rate discrepancy at different locations on the plate and reducing false-positive and -negative frequencies. Our work thus provides a simple and coding-free solution for a struggling problem in robotics-based high-throughput screening experiments.
Collapse
Affiliation(s)
- Ulysses Tsz-Fung Lam
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Thi Thuy Trang Nguyen
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Raechell Raechell
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Jay Yang
- Singer Instruments, Roadwater, Watchet TA23 0RE, UK; (J.Y.); (H.S.)
| | - Harry Singer
- Singer Instruments, Roadwater, Watchet TA23 0RE, UK; (J.Y.); (H.S.)
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
- NUS Center for Cancer Research, National University of Singapore, Singapore 117599, Singapore
- NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI), Life Science Institute, National University of Singapore, Singapore 117456, Singapore
- National University Health System (NUHS), Singapore 119228, Singapore
| |
Collapse
|
30
|
Vahsen T, Brault A, Mourer T, Labbé S. A novel role of the fission yeast sulfiredoxin Srx1 in heme acquisition. Mol Microbiol 2023; 120:608-628. [PMID: 37644673 DOI: 10.1111/mmi.15146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
The transporter Str3 promotes heme import in Schizosaccharomyces pombe cells that lack the heme receptor Shu1 and are deficient in heme biosynthesis. Under microaerobic conditions, the peroxiredoxin Tpx1 acts as a heme scavenger within the Str3-dependent pathway. Here, we show that Srx1, a sulfiredoxin known to interact with Tpx1, is essential for optimal growth in the presence of hemin. The expression of Srx1 is induced in response to low iron and repressed under iron repletion. Coimmunoprecipitation and bimolecular fluorescence complementation experiments show that Srx1 interacts with Str3. Although the interaction between Srx1 and Str3 is weakened, it is still observed in tpx1Δ mutant cells or when Str3 is coexpressed with a mutant form of Srx1 (mutD) that cannot bind Tpx1. Further analysis by absorbance spectroscopy and hemin-agarose pull-down assays confirms the binding of Srx1 to hemin, with an equilibrium constant value of 2.56 μM. To validate the Srx1-hemin association, we utilize a Srx1 mutant (mutH) that fails to interact with hemin. Notably, when Srx1 binds to hemin, it partially shields hemin from degradation caused by hydrogen peroxide. Collectively, these findings elucidate an additional function of the sulfiredoxin Srx1, beyond its conventional role in oxidative stress defense.
Collapse
Affiliation(s)
- Tobias Vahsen
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Ariane Brault
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Thierry Mourer
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Simon Labbé
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| |
Collapse
|
31
|
Rahayu AF, Hayashi A, Yoshimura Y, Nakagawa R, Arita K, Nakayama JI. Cooperative DNA-binding activities of Chp2 are critical for its function in heterochromatin assembly. J Biochem 2023; 174:371-382. [PMID: 37400983 DOI: 10.1093/jb/mvad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Heterochromatin protein 1 (HP1) is an evolutionarily conserved protein that plays a critical role in heterochromatin assembly. HP1 proteins share a basic structure consisting of an N-terminal chromodomain (CD) and a C-terminal chromoshadow domain (CSD) linked by a disordered hinge region. The CD recognizes histone H3 lysine 9 methylation, a hallmark of heterochromatin, while the CSD forms a dimer to recruit other chromosomal proteins. HP1 proteins have been shown to bind DNA or RNA primarily through the hinge region. However, how DNA or RNA binding contributes to their function remains elusive. Here, we focus on Chp2, one of the two HP1 proteins in fission yeast, and investigate how Chp2's DNA-binding ability contributes to its function. Similar to other HP1 proteins, the Chp2 hinge exhibits clear DNA-binding activity. Interestingly, the Chp2 CSD also shows robust DNA-binding activity. Mutational analysis revealed that basic residues in the Chp2 hinge and at the N-terminus of the CSD are essential for DNA binding, and the combined amino acid substitutions of these residues alter Chp2 stability, impair Chp2 heterochromatin localization and lead to a silencing defect. These results demonstrate that the cooperative DNA-binding activities of Chp2 play an important role in heterochromatin assembly in fission yeast.
Collapse
Affiliation(s)
- Anisa Fitri Rahayu
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - Aki Hayashi
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - Yuriko Yoshimura
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| | - Reiko Nakagawa
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Kyohei Arita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Kanagawa 230-0045, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
| |
Collapse
|
32
|
Gergely ZR, Jones MH, Zhou B, Cash C, McIntosh JR, Betterton MD. Distinct regions of the kinesin-5 C-terminal tail are essential for mitotic spindle midzone localization and sliding force. Proc Natl Acad Sci U S A 2023; 120:e2306480120. [PMID: 37725645 PMCID: PMC10523502 DOI: 10.1073/pnas.2306480120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/05/2023] [Indexed: 09/21/2023] Open
Abstract
Kinesin-5 motor proteins play essential roles during mitosis in most organisms. Their tetrameric structure and plus-end-directed motility allow them to bind to and move along antiparallel microtubules, thereby pushing spindle poles apart to assemble a bipolar spindle. Recent work has shown that the C-terminal tail is particularly important to kinesin-5 function: The tail affects motor domain structure, ATP hydrolysis, motility, clustering, and sliding force measured for purified motors, as well as motility, clustering, and spindle assembly in cells. Because previous work has focused on presence or absence of the entire tail, the functionally important regions of the tail remain to be identified. We have therefore characterized a series of kinesin-5/Cut7 tail truncation alleles in fission yeast. Partial truncation causes mitotic defects and temperature-sensitive growth, while further truncation that removes the conserved BimC motif is lethal. We compared the sliding force generated by cut7 mutants using a kinesin-14 mutant background in which some microtubules detach from the spindle poles and are pushed into the nuclear envelope. These Cut7-driven protrusions decreased as more of the tail was truncated, and the most severe truncations produced no observable protrusions. Our observations suggest that the C-terminal tail of Cut7p contributes to both sliding force and midzone localization. In the context of sequential tail truncation, the BimC motif and adjacent C-terminal amino acids are particularly important for sliding force. In addition, moderate tail truncation increases midzone localization, but further truncation of residues N-terminal to the BimC motif decreases midzone localization.
Collapse
Affiliation(s)
- Zachary R Gergely
- Department of Physics, University of Colorado, Boulder, CO 80309
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Michele H Jones
- Department of Physics, University of Colorado, Boulder, CO 80309
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Bojun Zhou
- Department of Physics, University of Colorado, Boulder, CO 80309
| | - Cai Cash
- Department of Physics, University of Colorado, Boulder, CO 80309
| | - J Richard McIntosh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Meredith D Betterton
- Department of Physics, University of Colorado, Boulder, CO 80309
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309
| |
Collapse
|
33
|
Cao M, Day AM, Galler M, Latimer HR, Byrne DP, Foy TW, Dwyer E, Bennett E, Palmer J, Morgan BA, Eyers PA, Veal EA. A peroxiredoxin-P38 MAPK scaffold increases MAPK activity by MAP3K-independent mechanisms. Mol Cell 2023; 83:3140-3154.e7. [PMID: 37572670 DOI: 10.1016/j.molcel.2023.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 05/19/2023] [Accepted: 07/14/2023] [Indexed: 08/14/2023]
Abstract
Peroxiredoxins (Prdxs) utilize reversibly oxidized cysteine residues to reduce peroxides and promote H2O2 signal transduction, including H2O2-induced activation of P38 MAPK. Prdxs form H2O2-induced disulfide complexes with many proteins, including multiple kinases involved in P38 MAPK signaling. Here, we show that a genetically encoded fusion between a Prdx and P38 MAPK is sufficient to hyperactivate the kinase in yeast and human cells by a mechanism that does not require the H2O2-sensing cysteine of the Prdx. We demonstrate that a P38-Prdx fusion protein compensates for loss of the yeast scaffold protein Mcs4 and MAP3K activity, driving yeast into mitosis. Based on our findings, we propose that the H2O2-induced formation of Prdx-MAPK disulfide complexes provides an alternative scaffold and signaling platform for MAPKK-MAPK signaling. The demonstration that formation of a complex with a Prdx is sufficient to modify the activity of a kinase has broad implications for peroxide-based signal transduction in eukaryotes.
Collapse
Affiliation(s)
- Min Cao
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Alison M Day
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Martin Galler
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Heather R Latimer
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Dominic P Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Thomas W Foy
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Emilia Dwyer
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Elise Bennett
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jeremy Palmer
- Newcastle University Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Brian A Morgan
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Patrick A Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Elizabeth A Veal
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| |
Collapse
|
34
|
Boronat S, Cabrera M, Vega M, Alcalá J, Salas-Pino S, Daga RR, Ayté J, Hidalgo E. Formation of Transient Protein Aggregate-like Centers Is a General Strategy Postponing Degradation of Misfolded Intermediates. Int J Mol Sci 2023; 24:11202. [PMID: 37446379 DOI: 10.3390/ijms241311202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
When misfolded intermediates accumulate during heat shock, the protein quality control system promotes cellular adaptation strategies. In Schizosaccharomyces pombe, thermo-sensitive proteins assemble upon stress into protein aggregate-like centers, PACs, to escape from degradation. The role of this protein deposition strategy has been elusive due to the use of different model systems and reporters, and to the addition of artificial inhibitors, which made interpretation of the results difficult. Here, we compare fission and budding yeast model systems, expressing the same misfolding reporters in experiments lacking proteasome or translation inhibitors. We demonstrate that mild heat shock triggers reversible PAC formation, with the collapse of both reporters and chaperones in a process largely mediated by chaperones. This assembly postpones proteasomal degradation of the misfolding reporters, and their Hsp104-dependent disassembly occurs during stress recovery. Severe heat shock induces formation of cytosolic PACs, but also of nuclear structures resembling nucleolar rings, NuRs, presumably to halt nuclear functions. Our study demonstrates that these distantly related yeasts use very similar strategies to adapt and survive to mild and severe heat shock and that aggregate-like formation is a general cellular scheme to postpone protein degradation and facilitate exit from stress.
Collapse
Affiliation(s)
- Susanna Boronat
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Margarita Cabrera
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
- Centro de Biología Molecular Severo Ochoa and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
| | - Montserrat Vega
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Jorge Alcalá
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Silvia Salas-Pino
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Carretera de Utrera, km1, 41013 Seville, Spain
| | - Rafael R Daga
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Carretera de Utrera, km1, 41013 Seville, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Elena Hidalgo
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 08003 Barcelona, Spain
| |
Collapse
|
35
|
Vaurs M, Naiman K, Bouabboune C, Rai S, Ptasińska K, Rives M, Matmati S, Carr AM, Géli V, Coulon S. Stn1-Ten1 and Taz1 independently promote replication of subtelomeric fragile sequences in fission yeast. Cell Rep 2023; 42:112537. [PMID: 37243596 DOI: 10.1016/j.celrep.2023.112537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/01/2023] [Accepted: 05/03/2023] [Indexed: 05/29/2023] Open
Abstract
Efficient replication of terminal DNA is crucial to maintain telomere stability. In fission yeast, Taz1 and the Stn1-Ten1 (ST) complex play prominent roles in DNA-ends replication. However, their function remains elusive. Here, we have analyzed genome-wide replication and show that ST does not affect genome-wide replication but is crucial for the efficient replication of a subtelomeric region called STE3-2. We further show that, when ST function is compromised, a homologous recombination (HR)-based fork restart mechanism becomes necessary for STE3-2 stability. While both Taz1 and Stn1 bind to STE3-2, we find that the STE3-2 replication function of ST is independent of Taz1 but relies on its association with the shelterin proteins Pot1-Tpz1-Poz1. Finally, we demonstrate that the firing of an origin normally inhibited by Rif1 can circumvent the replication defect of subtelomeres when ST function is compromised. Our results help illuminate why fission yeast telomeres are terminal fragile sites.
Collapse
Affiliation(s)
- Mélina Vaurs
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France
| | - Karel Naiman
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France; Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, UK
| | - Chaïnez Bouabboune
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France
| | - Sudhir Rai
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France
| | - Katarzyna Ptasińska
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, UK
| | - Marion Rives
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France
| | - Samah Matmati
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France
| | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, UK
| | - Vincent Géli
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France.
| | - Stéphane Coulon
- CNRS, INSERM, Aix Marseille Univ, Institut Paoli-Calmettes, CRCM, Ligue Nationale Contre le Cancer (équipe labellisée), Marseille, France.
| |
Collapse
|
36
|
Lim KK, Koh NZH, Zeng YB, Chuan JK, Raechell R, Chen ES. Resistance to Chemotherapeutic 5-Fluorouracil Conferred by Modulation of Heterochromatic Integrity through Ino80 Function in Fission Yeast. Int J Mol Sci 2023; 24:10687. [PMID: 37445861 DOI: 10.3390/ijms241310687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
5-Fluorouracil (5-FU) is a conventional chemotherapeutic drug widely used in clinics worldwide, but development of resistance that compromises responsiveness remains a major hurdle to its efficacy. The mechanism underlying 5-FU resistance is conventionally attributed to the disruption of nucleotide synthesis, even though research has implicated other pathways such as RNA processing and chromatin dysregulation. Aiming to clarify resistance mechanisms of 5-FU, we tested the response of a collection of fission yeast (Schizosaccharomyces pombe) null mutants, which confer multiple environmental factor responsiveness (MER). Our screen identified disruption of membrane transport, chromosome segregation and mitochondrial oxidative phosphorylation to increase cellular susceptibility towards 5-FU. Conversely, we revealed several null mutants of Ino80 complex factors exhibited resistance to 5-FU. Furthermore, attenuation of Ino80 function via deleting several subunit genes reversed loss of chromosome-segregation fidelity in 5-FU in the loss-of-function mutant of the Argonaute protein, which regulates RNA interference (RNAi)-dependent maintenance of pericentromeric heterochromatin. Our study thus uncovered a critical role played by chromatin remodeling Ino80 complex factors in 5-FU resistance, which may constitute a possible target to modulate in reversing 5-FU resistance.
Collapse
Affiliation(s)
- Kim Kiat Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Nathaniel Zhi Hao Koh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Yi Bing Zeng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Jun Kai Chuan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Raechell Raechell
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- National University Health System (NUHS), Singapore 119228, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- NUS Graduate School-Integrative Sciences & Engineering Programme, National University of Singapore, Singapore 119077, Singapore
| |
Collapse
|
37
|
Kanoh J. Roles of Specialized Chromatin and DNA Structures at Subtelomeres in Schizosaccharomyces pombe. Biomolecules 2023; 13:biom13050810. [PMID: 37238680 DOI: 10.3390/biom13050810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Eukaryotes have linear chromosomes with domains called telomeres at both ends. The telomere DNA consists of a simple tandem repeat sequence, and multiple telomere-binding proteins including the shelterin complex maintain chromosome-end structures and regulate various biological reactions, such as protection of chromosome ends and control of telomere DNA length. On the other hand, subtelomeres, which are located adjacent to telomeres, contain a complex mosaic of multiple common segmental sequences and a variety of gene sequences. This review focused on roles of the subtelomeric chromatin and DNA structures in the fission yeast Schizosaccharomyces pombe. The fission yeast subtelomeres form three distinct chromatin structures; one is the shelterin complex, which is localized not only at the telomeres but also at the telomere-proximal regions of subtelomeres to form transcriptionally repressive chromatin structures. The others are heterochromatin and knob, which have repressive effects in gene expression, but the subtelomeres are equipped with a mechanism that prevents these condensed chromatin structures from invading adjacent euchromatin regions. On the other hand, recombination reactions within or near subtelomeric sequences allow chromosomes to be circularized, enabling cells to survive in telomere shortening. Furthermore, DNA structures of the subtelomeres are more variable than other chromosomal regions, which may have contributed to biological diversity and evolution while changing gene expression and chromatin structures.
Collapse
Affiliation(s)
- Junko Kanoh
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| |
Collapse
|
38
|
Willet AH, Chen JS, Ren L, Gould KL. Membrane binding of endocytic myosin-1s is inhibited by a class of ankyrin repeat proteins. bioRxiv 2023:2023.04.26.538419. [PMID: 37163016 PMCID: PMC10168314 DOI: 10.1101/2023.04.26.538419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Myosin-1s are monomeric actin-based motors that function at membranes. Myo1 is the single myosin-1 isoform in Schizosaccharomyces pombe that works redundantly with Wsp1-Vrp1 to activate the Arp2/3 complex for endocytosis. Here, we identified Ank1 as an uncharacterized cytoplasmic Myo1 binding partner. We found that in ank1Δ cells, Myo1 dramatically redistributed from endocytic patches to decorate the entire plasma membrane and endocytosis was defective. Biochemical analysis and structural predictions suggested that the Ank1 ankyrin repeats bind the Myo1 lever arm and the Ank1 acidic tail binds the Myo1 TH1 domain to prevent TH1-dependent Myo1 membrane binding. Indeed, Ank1 over-expression precluded Myo1 membrane localization and recombinant Ank1 blocked purified Myo1 liposome binding in vitro. Based on biochemical and cell biology analyses, we propose budding yeast Ank1 and human OSTF1 are functional Ank1 orthologs and that cytoplasmic sequestration by small ankyrin repeat proteins is a conserved mechanism regulating myosin-1s in endocytosis. Summary Fission yeast long-tailed myosin-1 binds Ank1. Ank1 ankyrin repeats associate with the Myo1 lever arm and Ank1 acidic tail binds the Myo1 TH1 domain to inhibit Myo1 membrane binding. Ank1 orthologs exists in budding yeast (Ank1) and humans (OSTF1).
Collapse
Affiliation(s)
- Alaina H Willet
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| |
Collapse
|
39
|
Ishikawa K, Saitoh S. Transcriptional Regulation Technology for Gene Perturbation in Fission Yeast. Biomolecules 2023; 13:biom13040716. [PMID: 37189462 DOI: 10.3390/biom13040716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023] Open
Abstract
Isolation and introduction of genetic mutations is the primary approach to characterize gene functions in model yeasts. Although this approach has proven very powerful, it is not applicable to all genes in these organisms. For example, introducing defective mutations into essential genes causes lethality upon loss of function. To circumvent this difficulty, conditional and partial repression of target transcription is possible. While transcriptional regulation techniques, such as promoter replacement and 3' untranslated region (3'UTR) disruption, are available for yeast systems, CRISPR-Cas-based technologies have provided additional options. This review summarizes these gene perturbation technologies, including recent advances in methods based on CRISPR-Cas systems for Schizosaccharomyces pombe. We discuss how biological resources afforded by CRISPRi can promote fission yeast genetics.
Collapse
Affiliation(s)
- Ken Ishikawa
- Department of Cell Biology, Institute of Life Science, Kurume University, Asahi-machi 67, Fukuoka 830-0011, Japan
| | - Shigeaki Saitoh
- Department of Cell Biology, Institute of Life Science, Kurume University, Asahi-machi 67, Fukuoka 830-0011, Japan
| |
Collapse
|
40
|
Zahedi Y, Zeng S, Ekwall K. An essential role for the Ino80 chromatin remodeling complex in regulation of gene expression during cellular quiescence. Chromosome Res 2023; 31:14. [PMID: 37043046 PMCID: PMC10097750 DOI: 10.1007/s10577-023-09723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 03/15/2023] [Accepted: 03/31/2023] [Indexed: 04/13/2023]
Abstract
Cellular quiescence is an important physiological state both in unicellular and multicellular eukaryotes. Quiescent cells are halted for proliferation and stop the cell cycle at the G0 stage. Using fission yeast as a model organism, we have previously found that several subunits of a conserved chromatin remodeling complex, Ino80C (INOsitol requiring nucleosome remodeling factor), are required for survival in quiescence. Here, we demonstrate that Ino80C has a key function in the regulation of gene expression in G0 cells. We show that null mutants for two Ino80C subunits, Iec1 and Ies2, a putative subunit Arp42, a null mutant for the histone variant H2A.Z, and a null mutant for the Inositol kinase Asp1 have very similar phenotypes in quiescence. These mutants show reduced transcription genome-wide and specifically fail to activate 149 quiescence genes, of which many are localized to the subtelomeric regions. Using spike in normalized ChIP-seq experiments, we show that there is a global reduction of H2A.Z levels in quiescent wild-type cells but not in iec1∆ cells and that a subtelomeric chromosome boundary element is strongly affected by Ino80C. Based on these observations, we propose a model in which Ino80C is evicting H2A.Z from chromatin in quiescent cells, thereby inactivating the subtelomeric boundary element, leading to a reorganization of the chromosome structure and activation of genes required to survive in quiescence.
Collapse
Affiliation(s)
- Yasaman Zahedi
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo Building, 141 83, Huddinge, Sweden
| | - Shengyuan Zeng
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo Building, 141 83, Huddinge, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo Building, 141 83, Huddinge, Sweden.
| |
Collapse
|
41
|
Jia GS, Zhang WC, Liang Y, Liu XH, Rhind N, Pidoux A, Brysch-Herzberg M, Du LL. A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus. G3 (Bethesda) 2023; 13:jkad028. [PMID: 36748990 PMCID: PMC10085805 DOI: 10.1093/g3journal/jkad028] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/08/2023]
Abstract
Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes of S. pombe and 3 other fission yeast species S. japonicus, S. octosporus, and S. cryophilus has enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast species S. osmophilus and obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5,098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed that S. osmophilus is most closely related to S. octosporus and these 2 species diverged around 16 million years ago. To demonstrate the utility of this S. osmophilus reference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of 2 types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of 2 types of mitochondrial selfish elements.
Collapse
Affiliation(s)
- Guo-Song Jia
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wen-Cai Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yue Liang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xi-Han Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alison Pidoux
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn 74081, Germany
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| |
Collapse
|
42
|
Arcangioli B, Gangloff S. The Fission Yeast Mating-Type Switching Motto: "One-for-Two" and "Two-for-One". Microbiol Mol Biol Rev 2023; 87:e0000821. [PMID: 36629411 PMCID: PMC10029342 DOI: 10.1128/mmbr.00008-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Schizosaccharomyces pombe is an ascomycete fungus that divides by medial fission; it is thus commonly referred to as fission yeast, as opposed to the distantly related budding yeast Saccharomyces cerevisiae. The reproductive lifestyle of S. pombe relies on an efficient genetic sex determination system generating a 1:1 sex ratio and using alternating haploid/diploid phases in response to environmental conditions. In this review, we address how one haploid cell manages to generate two sister cells with opposite mating types, a prerequisite to conjugation and meiosis. This mating-type switching process depends on two highly efficient consecutive asymmetric cell divisions that rely on DNA replication, repair, and recombination as well as the structure and components of heterochromatin. We pay special attention to the intimate interplay between the genetic and epigenetic partners involved in this process to underscore the importance of basic research and its profound implication for a better understanding of chromatin biology.
Collapse
Affiliation(s)
- Benoît Arcangioli
- Genome Dynamics Unit, Genomes and Genetics Department, Pasteur Institute, Paris, France
| | - Serge Gangloff
- Genome Dynamics Unit, Genomes and Genetics Department, Pasteur Institute, Paris, France
- UMR3525, Genetics of Genomes, CNRS-Pasteur Institute, Paris, France
| |
Collapse
|
43
|
Şeylan C, Tarhan Ç. Metformin extends the chronological lifespan of fission yeast by altering energy metabolism and stress resistance capacity. FEMS Yeast Res 2023; 23:7081309. [PMID: 36941121 PMCID: PMC10103822 DOI: 10.1093/femsyr/foad018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/23/2023] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
The anti-aging properties of metformin used for the treatment of type 2 diabetes mellitus have been studied extensively but there is more to discover regarding underlying mechanisms. Here we show that metformin significantly prolongs the chronological lifespan (CLS) of Schizosaccharomyces pombe through mechanisms similar to those observed in mammalian cells and other model organisms. While the presence of metformin in the medium caused an increase in carbohydrate consumption and ATP production, it reduced reactive oxygen species production and alleviate oxidative damage parameters such as lipid peroxidation and carbonylated proteins. We also tested whether the effect of metformin changed with the time it was added to the medium and observed that the lifespan-prolonging effect of metformin was related to the glucose concentration in the medium and did not prolong lifespan when added after glucose was completely depleted in the medium. On the other hand, cells inoculated in glucose-free medium containing metformin also showed extended lifespan suggesting that mechanisms other than that solely depend on glucose availability may be involved in extending the lifespan. These results suggest that metformin prolongs lifespan especially affecting energy metabolism and stress resistance capacity and that fission yeast can be effectively used when investigating the anti-aging mechanisms of metformin.
Collapse
Affiliation(s)
- Ceren Şeylan
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, 34134 Vezneciler, Istanbul, Turkey
| | - Çağatay Tarhan
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, 34134 Vezneciler, Istanbul, Turkey
| |
Collapse
|
44
|
Wu K, Li H, Wang Y, Liu D, Li H, Zhang Y, Lynch M, Long H. Silver nanoparticles elevate mutagenesis of eukaryotic genomes. G3 (Bethesda) 2023; 13:6986423. [PMID: 36635051 PMCID: PMC9997555 DOI: 10.1093/g3journal/jkad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 11/28/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023]
Abstract
Metal nanoparticles, especially silver, have been used in various medical scenarios, due to their excellent antimicrobial effects. Recent studies have shown that AgNPs do not exert mutagenic effects on target bacteria, but the degree to which they compromise eukaryotic genomes remains unclear. To study this, we evaluated the mutagenic effects of AgNPs on the fission yeast Schizosaccharomyces pombe ATCC-16979, of which ∼23% genes are homologous to human ones, at single-nucleotide resolution, and whole-genome scale by running 283 mutation accumulation lines for ∼260,000 cell divisions in total. We also explored the action and mutagenesis mechanisms using differential gene-expression analysis based on RNAseq. Upon AgNPs treatment, the genomic base-substitution mutation rate of S. pombe at four-fold degenerate sites increased by 3.46×, and small indels were prone to occur in genomic regions that are not simple sequence repeats. The G:C → T:A transversion rate was also significantly increased, likely mostly from oxidative damage. Thus, in addition to their antimicrobial potency, AgNPs might pose slight genotoxicity threats to eukaryotic and possibly human genomes, though at a low magnitude.
Collapse
Affiliation(s)
- Kun Wu
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China.,Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province 266237, China
| | - Haichao Li
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Yaohai Wang
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Dan Liu
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Hui Li
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Yu Zhang
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China.,School of Mathematics Science, Ocean University of China, Qingdao, Shandong Province 266000, China
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Hongan Long
- KLMME, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong Province 266003, China.,Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province 266237, China
| |
Collapse
|
45
|
Maruyama T, Hayashi K, Matsui K, Maekawa Y, Shimasaki T, Ohtsuka H, Shigeaki S, Aiba H. Characterization of hexose transporter genes in the views of the chronological life span and glucose uptake in fission yeast. J GEN APPL MICROBIOL 2023; 68:270-277. [PMID: 35781263 DOI: 10.2323/jgam.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fission yeast, Schizosaccharomyces pombe, possesses eight hexose transporters, Ght1~8. In order to clarify the role of each hexose transporter on glucose uptake, a glucose uptake assay system was established and the actual glucose uptake activity of each hexose transporter-deletion mutant was measured. Under normal growth condition containing 2% glucose, ∆ght5 and ∆ght2 mutants showed large and small decrease in glucose uptake activity, respectively. On the other hand, the other deletion mutants did not show any decrease in glucose uptake activity indicating that, in the presence of Ght5 and Ght2, the other hexose transporters do not play a significant role in glucose uptake. To understand the relevance between glucose uptake and lifespan regulation, we measured the chronological lifespan of each hexose transporter deletion mutant, and found that only ∆ght5 mutant showed a significant lifespan extension. Based on these results we showed that Ght5 is mainly involved in the glucose uptake in Schizosaccharomyces pombe, and suggested that the ∆ght5 mutant has prolonged lifespan due to physiological changes similar to calorie restriction.
Collapse
Affiliation(s)
- Teppei Maruyama
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Kanako Hayashi
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Kotaro Matsui
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Yasukichi Maekawa
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| | | | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University
| |
Collapse
|
46
|
Fujita I, Kimura A, Yamashita A. A force balance model for a cell size-dependent meiotic nuclear oscillation in fission yeast. EMBO Rep 2023; 24:e55770. [PMID: 36622644 PMCID: PMC9986818 DOI: 10.15252/embr.202255770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 01/10/2023] Open
Abstract
Fission yeast undergoes premeiotic nuclear oscillation, which is dependent on microtubules and is driven by cytoplasmic dynein. Although the molecular mechanisms have been analyzed, how a robust oscillation is generated despite the dynamic behaviors of microtubules has yet to be elucidated. Here, we show that the oscillation exhibits cell length-dependent frequency and requires a balance between microtubule and viscous drag forces, as well as proper microtubule dynamics. Comparison of the oscillations observed in living cells with a simulation model based on microtubule dynamic instability reveals that the period of oscillation correlates with cell length. Genetic alterations that reduce cargo size suggest that the nuclear movement depends on viscous drag forces. Deletion of a gene encoding Kinesin-8 inhibits microtubule catastrophe at the cell cortex and results in perturbation of oscillation, indicating that nuclear movement also depends on microtubule dynamic instability. Our findings link numerical parameters from the simulation model with cellular functions required for generating the oscillation and provide a basis for understanding the physical properties of microtubule-dependent nuclear movements.
Collapse
Affiliation(s)
- Ikumi Fujita
- Laboratory for Cell Asymmetry, Center for Biosystems Dynamics ResearchRIKENKobeJapan
| | - Akatsuki Kimura
- Cell Architecture LaboratoryNational Institute of GeneticsMishimaJapan
- Department of Genetics, School of Life ScienceSOKENDAI (The Graduate University for Advanced Studies)MishimaJapan
| | - Akira Yamashita
- Interdisciplinary Research UnitNational Institute for Basic BiologyOkazakiJapan
- Center for Low‐temperature Plasma SciencesNagoya UniversityNagoyaJapan
| |
Collapse
|
47
|
Morishita J, Nurse P. Identification of a small RhoA GTPase inhibitor effective in fission yeast and human cells. Open Biol 2023; 13:220185. [PMID: 36854376 PMCID: PMC9974304 DOI: 10.1098/rsob.220185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The Rho GTPase family proteins are key regulators of cytoskeletal dynamics. Deregulated activity of Rho GTPases is associated with cancers and neurodegenerative diseases, and their potential as drug targets has long been recognized. Using an economically effective drug screening workflow in fission yeast and human cells, we have identified a Rho GTPase inhibitor, O1. By a suppressor mutant screen in fission yeast, we find a point mutation in the rho1 gene that confers resistance to O1. Consistent with the idea that O1 is the direct inhibitor of Rho1, O1 reduced the cellular amount of activated, GTP-bound Rho1 in wild-type cells, but not in the O1-resistant mutant cells, in which the evolutionarily conserved Ala62 residue is mutated to Thr. Similarly, O1 inhibits activity of the human orthologue RhoA GTPase in tissue culture cells. Our studies illustrate the power of yeast phenotypic screens in the identification and characterization of drugs relevant to human cells and have identified a novel GTPase inhibitor for fission yeast and human cells.
Collapse
Affiliation(s)
- Jun Morishita
- Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, New York, NY 10065, USA
| | - Paul Nurse
- Laboratory of Yeast Genetics and Cell Biology, Rockefeller University, New York, NY 10065, USA
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| |
Collapse
|
48
|
Abstract
Cytokinesis is the final stage of cell division cycle when cellular constituents are separated to produce two daughter cells. This process is driven by the formation and constriction of a contractile ring. Progression of these events is controlled by mechanisms and proteins that are evolutionary conserved in eukaryotes from fungi to humans. Genetic and molecular studies in different model organisms identified essential cytokinesis genes, with several conserved proteins, including the anillin/Mid1p proteins, constituting the core cytokinetic machinery. The fission yeast Schizosaccharomyces pombe represents a well-established model organism to study eukaryotic cell cycle regulation. Cytokinesis in fission yeast and mammalian cells depends on the placement, assembly, maturation, and constriction of a medially located actin-myosin contractile ring (ACR). Here, we review aspects of the ACR assembly and cytokinesis process in fission yeast and consider the regulation of such events in mammalian cells. First, we briefly describe the role of anillin during mammalian ACR assembly and cytokinesis. Second, we describe different aspects of the anillin-like protein Mid1p regulation during the S. pombe cell cycle, including its structure, function, and phospho-regulation. Third, we briefly discuss Mid1pindependent ACR assembly in S. pombe. Fourth, we highlight emerging studies demonstrating the roles of anillin in human tumourigenesis introducing anillin as a potential drug target for cancer treatment. Collectively, we provide an overview of the current understanding of medial division and cytokinesis in S. pombe and suggest the implications of these observations in other eukaryotic organisms, including humans.
Collapse
Affiliation(s)
- Imane M. Rezig
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, UK
| | - Wandiahyel G. Yaduma
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, UK,Department of Chemistry, School of Sciences, Adamawa State College of Education Hong, Nigeria
| | - Gwyn W. Gould
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Christopher J. McInerny
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Davidson Building, University of Glasgow, Glasgow, UK,CONTACT Christopher J. McInerny School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Davidson Building, University of Glasgow, GlasgowG12 8QQ, UK
| |
Collapse
|
49
|
Prieto-Ruiz F, Gómez-Gil E, Martín-García R, Pérez-Díaz AJ, Vicente-Soler J, Franco A, Soto T, Pérez P, Madrid M, Cansado J. Myosin II regulatory light chain phosphorylation and formin availability modulate cytokinesis upon changes in carbohydrate metabolism. eLife 2023; 12:83285. [PMID: 36825780 PMCID: PMC10005788 DOI: 10.7554/elife.83285] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/23/2023] [Indexed: 02/25/2023] Open
Abstract
Cytokinesis, the separation of daughter cells at the end of mitosis, relies in animal cells on a contractile actomyosin ring (CAR) composed of actin and class II myosins, whose activity is strongly influenced by regulatory light chain (RLC) phosphorylation. However, in simple eukaryotes such as the fission yeast Schizosaccharomyces pombe, RLC phosphorylation appears dispensable for regulating CAR dynamics. We found that redundant phosphorylation at Ser35 of the S. pombe RLC homolog Rlc1 by the p21-activated kinases Pak1 and Pak2, modulates myosin II Myo2 activity and becomes essential for cytokinesis and cell growth during respiration. Previously, we showed that the stress-activated protein kinase pathway (SAPK) MAPK Sty1 controls fission yeast CAR integrity by downregulating formin For3 levels (Gómez-Gil et al., 2020). Here, we report that the reduced availability of formin For3-nucleated actin filaments for the CAR is the main reason for the required control of myosin II contractile activity by RLC phosphorylation during respiration-induced oxidative stress. Thus, the restoration of For3 levels by antioxidants overrides the control of myosin II function regulated by RLC phosphorylation, allowing cytokinesis and cell proliferation during respiration. Therefore, fine-tuned interplay between myosin II function through Rlc1 phosphorylation and environmentally controlled actin filament availability is critical for a successful cytokinesis in response to a switch to a respiratory carbohydrate metabolism.
Collapse
Affiliation(s)
- Francisco Prieto-Ruiz
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de MurciaMurciaSpain
| | - Elisa Gómez-Gil
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de MurciaMurciaSpain
- The Francis Crick InstituteLondonUnited Kingdom
| | - Rebeca Martín-García
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas, Universidad de SalamancaSalamancaSpain
| | - Armando Jesús Pérez-Díaz
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de MurciaMurciaSpain
| | - Jero Vicente-Soler
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de MurciaMurciaSpain
| | - Alejandro Franco
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de MurciaMurciaSpain
| | - Teresa Soto
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de MurciaMurciaSpain
| | - Pilar Pérez
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas, Universidad de SalamancaSalamancaSpain
| | - Marisa Madrid
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de MurciaMurciaSpain
| | - José Cansado
- Yeast Physiology Group. Department of Genetics and Microbiology. Campus de Excelencia Internacional de Ámbito Regional (CEIR) Campus Mare Nostrum, Universidad de MurciaMurciaSpain
| |
Collapse
|
50
|
San-Quirico E, Curto MÁ, Gómez-Delgado L, Moreno MB, Pérez P, Ribas JC, Cortés JCG. Analysis of the Localization of Schizosaccharomyces pombe Glucan Synthases in the Presence of the Antifungal Agent Caspofungin. Int J Mol Sci 2023; 24:ijms24054299. [PMID: 36901728 PMCID: PMC10002279 DOI: 10.3390/ijms24054299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
In recent years, invasive fungal infections have emerged as a common source of infections in immunosuppressed patients. All fungal cells are surrounded by a cell wall that is essential for cell integrity and survival. It prevents cell death and lysis resulting from high internal turgor pressure. Since the cell wall is not present in animal cells, it is an ideal target for selective invasive fungal infection treatments. The antifungal family known as echinocandins, which specifically inhibit the synthesis of the cell wall β(13)glucan, has been established as an alternative treatment for mycoses. To explore the mechanism of action of these antifungals, we analyzed the cell morphology and glucan synthases localization in Schizosaccharomyces pombe cells during the initial times of growth in the presence of the echinocandin drug caspofungin. S. pombe are rod-shaped cells that grow at the poles and divide by a central division septum. The cell wall and septum are formed by different glucans, which are synthesized by four essential glucan synthases: Bgs1, Bgs3, Bgs4, and Ags1. Thus, S. pombe is not only a perfect model for studying the synthesis of the fungal β(1-3)glucan, but also it is ideal for examining the mechanisms of action and resistance of cell wall antifungals. Herein, we examined the cells in a drug susceptibility test in the presence of either lethal or sublethal concentrations of caspofungin, finding that exposure to the drug for long periods at high concentrations (>10 µg/mL) induced cell growth arrest and the formation of rounded, swollen, and dead cells, whereas low concentrations (<10 µg/mL) permitted cell growth with a mild effect on cell morphology. Interestingly, short-term treatments with either high or low concentrations of the drug induced effects contrary to those observed in the susceptibility tests. Thus, low drug concentrations induced a cell death phenotype that was not observed at high drug concentrations, which caused transient fungistatic cell growth arrest. After 3 h, high concentrations of the drug caused the following: (i) a decrease in the GFP-Bgs1 fluorescence level; (ii) altered locations of Bgs3, Bgs4, and Ags1; and (iii) a simultaneous accumulation of cells with calcofluor-stained incomplete septa, which at longer times resulted in septation uncoupling from plasma membrane ingression. The incomplete septa revealed with calcofluor were found to be complete when observed via the membrane-associated GFP-Bgs or Ags1-GFP. Finally, we found that the accumulation of incomplete septa depended on Pmk1, the last kinase of the cell wall integrity pathway.
Collapse
|