1
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Ishikawa K, Soejima S, Nishimura T, Saitoh S. Arrayed CRISPRi library to suppress genes required for Schizosaccharomyces pombe viability. J Cell Biol 2025; 224:e202404085. [PMID: 39378339 PMCID: PMC11465072 DOI: 10.1083/jcb.202404085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 09/06/2024] [Accepted: 09/22/2024] [Indexed: 10/10/2024] Open
Abstract
The fission yeast, Schizosaccharomyces pombe, is an excellent eukaryote model organism for studying essential biological processes. Its genome contains ∼1,200 genes essential for cell viability, most of which are evolutionarily conserved. To study these essential genes, resources enabling conditional perturbation of target genes are required. Here, we constructed comprehensive arrayed libraries of plasmids and strains to knock down essential genes in S. pombe using dCas9-mediated CRISPRi. These libraries cover ∼98% of all essential genes in fission yeast. We estimate that in ∼60% of these strains, transcription of a target gene was repressed so efficiently that cell proliferation was significantly inhibited. To demonstrate the usefulness of these libraries, we performed metabolic analyses with knockdown strains and revealed flexible interaction among metabolic pathways. Libraries established in this study enable comprehensive functional analyses of essential genes in S. pombe and will facilitate the understanding of essential biological processes in eukaryotes.
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Affiliation(s)
- Ken Ishikawa
- Department of Cell Biology, Institute of Life Science, Kurume University, Kurume, Japan
| | - Saeko Soejima
- Department of Cell Biology, Institute of Life Science, Kurume University, Kurume, Japan
| | - Takashi Nishimura
- Laboratory of Metabolic Regulation and Genetics, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Shigeaki Saitoh
- Department of Cell Biology, Institute of Life Science, Kurume University, Kurume, Japan
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2
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Cullati SN, Akizuki K, Shan Y, Zhang E, Ren L, Guillen RX, Turner LA, Chen JS, Navarrete-Perea J, Elmore ZC, Gygi SP, Gould KL. The DNA Damage Repair Function of Fission Yeast CK1 Involves Targeting Arp8, a Subunit of the INO80 Chromatin Remodeling Complex. Mol Cell Biol 2024:1-15. [PMID: 39387272 DOI: 10.1080/10985549.2024.2408016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 09/10/2024] [Accepted: 09/18/2024] [Indexed: 10/15/2024] Open
Abstract
The CK1 family are conserved serine/threonine kinases with numerous substrates and cellular functions. The fission yeast CK1 orthologues Hhp1 and Hhp2 were first characterized as regulators of DNA repair, but the mechanism(s) by which CK1 activity promotes DNA repair had not been investigated. Here, we found that deleting Hhp1 and Hhp2 or inhibiting CK1 catalytic activities in yeast or in human cells increased double-strand breaks (DSBs). The primary pathways to repair DSBs, homologous recombination and nonhomologous end joining, were both less efficient in cells lacking Hhp1 and Hhp2 activity. To understand how Hhp1 and Hhp2 promote DNA damage repair, we identified new substrates of these enzymes using quantitative phosphoproteomics. We confirmed that Arp8, a component of the INO80 chromatin remodeling complex, is a bona fide substrate of Hhp1 and Hhp2 important for DNA repair. Our data suggest that Hhp1 and Hhp2 facilitate DNA repair by phosphorylating multiple substrates, including Arp8.
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Affiliation(s)
- Sierra N Cullati
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kazutoshi Akizuki
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yufan Shan
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Eric Zhang
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Rodrigo X Guillen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lesley A Turner
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Zachary C Elmore
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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3
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Anver S, Sumit AF, Sun XM, Hatimy A, Thalassinos K, Marguerat S, Alic N, Bähler J. Ageing-associated long non-coding RNA extends lifespan and reduces translation in non-dividing cells. EMBO Rep 2024:10.1038/s44319-024-00265-9. [PMID: 39358553 DOI: 10.1038/s44319-024-00265-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 09/07/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024] Open
Abstract
Genomes produce widespread long non-coding RNAs (lncRNAs) of largely unknown functions. We characterize aal1 (ageing-associated lncRNA), which is induced in quiescent fission yeast cells. Deletion of aal1 shortens the chronological lifespan of non-dividing cells, while ectopic overexpression prolongs their lifespan, indicating that aal1 acts in trans. Overexpression of aal1 represses ribosomal-protein gene expression and inhibits cell growth, and aal1 genetically interacts with coding genes functioning in protein translation. The aal1 lncRNA localizes to the cytoplasm and associates with ribosomes. Notably, aal1 overexpression decreases the cellular ribosome content and inhibits protein translation. The aal1 lncRNA binds to the rpl1901 mRNA, encoding a ribosomal protein. The rpl1901 levels are reduced ~2-fold by aal1, which is sufficient to extend lifespan. Remarkably, the expression of the aal1 lncRNA in Drosophila boosts fly lifespan. We propose that aal1 reduces the ribosome content by decreasing Rpl1901 levels, thus attenuating the translational capacity and promoting longevity. Although aal1 is not conserved, its effect in flies suggests that animals feature related mechanisms that modulate ageing, based on the conserved translational machinery.
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Affiliation(s)
- Shajahan Anver
- Institute of Healthy Ageing, Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Ahmed Faisal Sumit
- Institute of Healthy Ageing, Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Xi-Ming Sun
- Institute of Clinical Sciences, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences (LMS), London, W12 0NN, UK
| | - Abubakar Hatimy
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Samuel Marguerat
- Institute of Clinical Sciences, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences (LMS), London, W12 0NN, UK
- UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Nazif Alic
- Institute of Healthy Ageing, Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Jürg Bähler
- Institute of Healthy Ageing, Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
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4
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Willet AH, Park JS, Snider CE, Huang JJ, Chen JS, Gould KL. Fission yeast Duc1 links to ER-PM contact sites and influences PM lipid composition and cytokinetic ring anchoring. J Cell Sci 2024; 137:jcs262347. [PMID: 39239853 PMCID: PMC11449445 DOI: 10.1242/jcs.262347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/27/2024] [Indexed: 09/07/2024] Open
Abstract
Cytokinesis is the final stage of the cell cycle that results in the physical separation of daughter cells. To accomplish cytokinesis, many organisms build an actin- and myosin-based cytokinetic ring (CR) that is anchored to the plasma membrane (PM). Defects in CR-PM anchoring can arise when the PM lipid phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] is depleted. In Schizosaccharomyces pombe, reduced PM PI(4,5)P2 results in a CR that cannot maintain a medial position and slides toward one cell end, resulting in two differently sized daughter cells. S. pombe PM PI(4,5)P2 is synthesized by the phosphatidylinositol 4-phosphate 5-kinase (PI5-kinase) Its3, but what regulates this enzyme to maintain appropriate PM PI(4,5)P2 levels in S. pombe is not known. To identify Its3 regulators, we used proximity-based biotinylation, and the uncharacterized protein Duc1 was specifically detected. We discovered that Duc1 decorates the PM except at the cell division site and that its unique localization pattern is dictated by binding to the endoplasmic reticulum (ER)-PM contact site proteins Scs2 and Scs22. Our evidence suggests that Duc1 also binds PI(4,5)P2 and helps enrich Its3 at the lateral PM, thereby promoting PM PI(4,5)P2 synthesis and robust CR-PM anchoring.
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Affiliation(s)
- Alaina H. Willet
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Joshua S. Park
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Chloe E. Snider
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Jingdian Jamie Huang
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37240, USA
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5
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Pollet L, Xia Y. Structure-guided Evolutionary Analysis of Interactome Network Rewiring at Single Residue Resolution in Yeasts. J Mol Biol 2024; 436:168641. [PMID: 38844045 DOI: 10.1016/j.jmb.2024.168641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/30/2024] [Accepted: 06/01/2024] [Indexed: 06/16/2024]
Abstract
Protein-protein interactions (PPIs) are known to rewire extensively during evolution leading to lineage-specific and species-specific changes in molecular processes. However, the detailed molecular evolutionary mechanisms underlying interactome network rewiring are not well-understood. Here, we combine high-confidence PPI data, high-resolution three-dimensional structures of protein complexes, and homology-based structural annotation transfer to construct structurally-resolved interactome networks for the two yeasts S. cerevisiae and S. pombe. We then classify PPIs according to whether they are preserved or different between the two yeast species and compare site-specific evolutionary rates of interfacial versus non-interfacial residues for these different categories of PPIs. We find that residues in PPI interfaces evolve significantly more slowly than non-interfacial residues when using lineage-specific measures of evolutionary rate, but not when using non-lineage-specific measures. Furthermore, both lineage-specific and non-lineage-specific evolutionary rate measures can distinguish interfacial residues from non-interfacial residues for preserved PPIs between the two yeasts, but only the lineage-specific measure is appropriate for rewired PPIs. Finally, both lineage-specific and non-lineage-specific evolutionary rate measures are appropriate for elucidating structural determinants of protein evolution for residues outside of PPI interfaces. Overall, our results demonstrate that unlike tertiary structures of single proteins, PPIs and PPI interfaces can be highly volatile in their evolution, thus requiring the use of lineage-specific measures when studying their evolution. These results yield insight into the evolutionary design principles of PPIs and the mechanisms by which interactions are preserved or rewired between species, improving our understanding of the molecular evolution of PPIs and PPI interfaces at the residue level.
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Affiliation(s)
- Léah Pollet
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC, Canada
| | - Yu Xia
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC, Canada.
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6
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Aydin E, Schreiner S, Böhme J, Keil B, Weber J, Žunar B, Glatter T, Kilchert C. DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3'-end of genes and involved in the recycling of cleavage factors. Nat Commun 2024; 15:6829. [PMID: 39122693 PMCID: PMC11315920 DOI: 10.1038/s41467-024-51035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
mRNA biogenesis in the eukaryotic nucleus is a highly complex process. The numerous RNA processing steps are tightly coordinated to ensure that only fully processed transcripts are released from chromatin for export from the nucleus. Here, we present the hypothesis that fission yeast Dbp2, a ribonucleoprotein complex (RNP) remodelling ATPase of the DEAD-box family, is the key enzyme in an RNP assembly checkpoint at the 3'-end of genes. We show that Dbp2 interacts with the cleavage and polyadenylation complex (CPAC) and localises to cleavage bodies, which are enriched for 3'-end processing factors and proteins involved in nuclear RNA surveillance. Upon loss of Dbp2, 3'-processed, polyadenylated RNAs accumulate on chromatin and in cleavage bodies, and CPAC components are depleted from the soluble pool. Under these conditions, cells display an increased likelihood to skip polyadenylation sites and a delayed transcription termination, suggesting that levels of free CPAC components are insufficient to maintain normal levels of 3'-end processing. Our data support a model in which Dbp2 is the active component of an mRNP remodelling checkpoint that licenses RNA export and is coupled to CPAC release.
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Affiliation(s)
- Ebru Aydin
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Silke Schreiner
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Jacqueline Böhme
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Birte Keil
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Jan Weber
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Bojan Žunar
- Department of Chemistry and Biochemistry, University of Zagreb Faculty of Food Technology and Biotechnology, Zagreb, Croatia
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Cornelia Kilchert
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany.
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7
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Acs-Szabo L, Papp LA, Miklos I. Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:288-311. [PMID: 39104724 PMCID: PMC11299203 DOI: 10.15698/mic2024.08.833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024]
Abstract
The role of model organisms such as yeasts in life science research is crucial. Although the baker's yeast (Saccharomyces cerevisiae) is the most popular model among yeasts, the contribution of the fission yeasts (Schizosaccharomyces) to life science is also indisputable. Since both types of yeasts share several thousands of common orthologous genes with humans, they provide a simple research platform to investigate many fundamental molecular mechanisms and functions, thereby contributing to the understanding of the background of human diseases. In this review, we would like to highlight the many advantages of fission yeasts over budding yeasts. The usefulness of fission yeasts in virus research is shown as an example, presenting the most important research results related to the Human Immunodeficiency Virus Type 1 (HIV-1) Vpr protein. Besides, the potential role of fission yeasts in the study of prion biology is also discussed. Furthermore, we are keen to promote the uprising model yeast Schizosaccharomyces japonicus, which is a dimorphic species in the fission yeast genus. We propose the hyphal growth of S. japonicus as an unusual opportunity as a model to study the invadopodia of human cancer cells since the two seemingly different cell types can be compared along fundamental features. Here we also collect the latest laboratory protocols and bioinformatics tools for the fission yeasts to highlight the many possibilities available to the research community. In addition, we present several limiting factors that everyone should be aware of when working with yeast models.
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Affiliation(s)
- Lajos Acs-Szabo
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
| | - Laszlo Attila Papp
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
| | - Ida Miklos
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of DebrecenDebrecen, 4032Hungary
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8
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Dinh N, Bonnefoy N. Schizosaccharomyces pombe as a fundamental model for research on mitochondrial gene expression: Progress, achievements and outlooks. IUBMB Life 2024; 76:397-419. [PMID: 38117001 DOI: 10.1002/iub.2801] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
Schizosaccharomyces pombe (fission yeast) is an attractive model for mitochondrial research. The organism resembles human cells in terms of mitochondrial inheritance, mitochondrial transport, sugar metabolism, mitogenome structure and dependence of viability on the mitogenome (the petite-negative phenotype). Transcriptions of these genomes produce only a few polycistronic transcripts, which then undergo processing as per the tRNA punctuation model. In general, the machinery for mitochondrial gene expression is structurally and functionally conserved between fission yeast and humans. Furthermore, molecular research on S. pombe is supported by a considerable number of experimental techniques and database resources. Owing to these advantages, fission yeast has significantly contributed to biomedical and fundamental research. Here, we review the current state of knowledge regarding S. pombe mitochondrial gene expression, and emphasise the pertinence of fission yeast as both a model and tool, especially for studies on mitochondrial translation.
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Affiliation(s)
- Nhu Dinh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
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9
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Mansouri-Noori F, Bayfield MA. Electrophoretic mobility shift assays (EMSAs) for in vitro detection of protein-nucleic acid interactions. STAR Protoc 2024; 5:103128. [PMID: 38875114 PMCID: PMC11227006 DOI: 10.1016/j.xpro.2024.103128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/11/2024] [Accepted: 05/23/2024] [Indexed: 06/16/2024] Open
Abstract
Protein-nucleic acid interactions drive some of the most important physiological events in cells. Here, we present a protocol for detecting protein-DNA or protein-RNA interactions in vitro. We describe steps for labeling nucleic acid species and electrophoretic mobility shift assays (EMSAs). This protocol can be used to confirm suspected in vivo interactions using recombinantly expressed/purified proteins of interest and a nucleic acid substrate. It can further be used to investigate mutations that can disrupt interaction or compensatory mutations that restore it. For complete details on the use and execution of this protocol, please refer to Mansouri-Noori et al.1.
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Affiliation(s)
| | - Mark A Bayfield
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
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10
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Zhang H, Zhang D, Li L, Willard B, Runge KW. In Vivo Proximity Labeling Identifies a New Function for the Lifespan and Autophagy-regulating Kinase Pef1, an Ortholog of Human Cdk5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598664. [PMID: 38915521 PMCID: PMC11195251 DOI: 10.1101/2024.06.12.598664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cdk5 is a highly-conserved, noncanonical cell division kinase important to the terminal differentiation of mammalian cells in multiple organ systems. We previously identified Pef1, the Schizosaccharomyces pombe ortholog of cdk5, as regulator of chronological lifespan. To reveal the processes impacted by Pef1, we developed APEX2-biotin phenol-mediated proximity labeling in S. pombe. Efficient labeling required a short period of cell wall digestion and eliminating glucose and nitrogen sources from the medium. We identified 255 high-confidence Pef1 neighbors in growing cells and a novel Pef1-interacting partner, the DNA damage response protein Rad24. The Pef1-Rad24 interaction was validated by reciprocal proximity labeling and co-immunoprecipitation. Eliminating Pef1 partially rescued the DNA damage sensitivity of cells lacking Rad24. To monitor how Pef1 neighbors change under different conditions, cells induced for autophagy were labeled and 177 high-confidence Pef1 neighbors were identified. Gene ontology (GO) analysis of the Pef1 neighbors identified proteins participating in processes required for autophagosome expansion including regulation of actin dynamics and vesicle-mediated transport. Some of these proteins were identified in both exponentially growing and autophagic cells. Pef1-APEX2 proximity labeling therefore identified a new Pef1 function in modulating the DNA damage response and candidate processes that Pef1 and other cdk5 orthologs may regulate.
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Affiliation(s)
- Haitao Zhang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at CWRU
| | - Dongmei Zhang
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Ling Li
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Belinda Willard
- Lerner Research Institute Proteomics Core and Case Comprehensive Cancer Center Cleveland Clinic Lerner College of Medicine at CWRU
| | - Kurt W. Runge
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Lerner College of Medicine at CWRU
- Department of Genomics and Genome Sciences, Case Western Reserve University School of Medicine
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11
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Davidson MK, Protacio RU, Helmlinger D, Wahls WP. Laboratory horror stories: Poison in the agars. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597796. [PMID: 38895319 PMCID: PMC11185651 DOI: 10.1101/2024.06.06.597796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The fission yeast Schizosaccharomyces pombe is a single-celled eukaryote that can be cultured as a haploid or as a diploid. Scientists employ mating, meiosis, and the plating of ascospores and cells to generate strains with novel genotypes and to discover biological processes. Our two laboratories encountered independently sudden-onset, major impediments to such research. Spore suspensions and vegetative cells no longer plated effectively on minimal media. By systematically analyzing multiple different media components from multiple different suppliers, we identified the source of the problem. Specific lots of agar, from different suppliers, were toxic. Interestingly, the inhibitory effect was attenuated on rich media. Consequently, quality control checks that use only rich media can provide false assurances on the quality of the agar. Lastly, we describe likely sources of the toxicity and we provide specific guidance for quality control measures that should be applied by all vendors as preconditions for their sale of agar.
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Affiliation(s)
- Mari K. Davidson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
| | - Reine U. Protacio
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
| | - Dominique Helmlinger
- Centre de Recherche en Biologie Cellulaire de Montpellier, University of Montpellier, CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 05, France
| | - Wayne P. Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
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12
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Grazzini A, Cavanaugh AM. Fungal microtubule organizing centers are evolutionarily unstable structures. Fungal Genet Biol 2024; 172:103885. [PMID: 38485050 DOI: 10.1016/j.fgb.2024.103885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/24/2024]
Abstract
For most Eukaryotic species the requirements of cilia formation dictate the structure of microtubule organizing centers (MTOCs). In this study we find that loss of cilia corresponds to loss of evolutionary stability for fungal MTOCs. We used iterative search algorithms to identify proteins homologous to those found in Saccharomyces cerevisiae, and Schizosaccharomyces pombe MTOCs, and calculated site-specific rates of change for those proteins that were broadly phylogenetically distributed. Our results indicate that both the protein composition of MTOCs as well as the sequence of MTOC proteins are poorly conserved throughout the fungal kingdom. To begin to reconcile this rapid evolutionary change with the rigid structure and essential function of the S. cerevisiae MTOC we further analyzed how structural interfaces among proteins influence the rates of change for specific residues within a protein. We find that a more stable protein may stabilize portions of an interacting partner where the two proteins are in contact. In summary, while the protein composition and sequences of the MTOC may be rapidly changing the proteins within the structure have a stabilizing effect on one another. Further exploration of fungal MTOCs will expand our understanding of how changes in the functional needs of a cell have affected physical structures, proteomes, and protein sequences throughout fungal evolution.
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Affiliation(s)
- Adam Grazzini
- Department of Biology, Creighton University, Omaha, Nebraska, USA
| | - Ann M Cavanaugh
- Department of Biology, Creighton University, Omaha, Nebraska, USA.
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13
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González-Esparragoza D, Carrasco-Carballo A, Rosas-Murrieta NH, Millán-Pérez Peña L, Luna F, Herrera-Camacho I. In Silico Analysis of Protein-Protein Interactions of Putative Endoplasmic Reticulum Metallopeptidase 1 in Schizosaccharomyces pombe. Curr Issues Mol Biol 2024; 46:4609-4629. [PMID: 38785548 PMCID: PMC11120530 DOI: 10.3390/cimb46050280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
Ermp1 is a putative metalloprotease from Schizosaccharomyces pombe and a member of the Fxna peptidases. Although their function is unknown, orthologous proteins from rats and humans have been associated with the maturation of ovarian follicles and increased ER stress. This study focuses on proposing the first prediction of PPI by comparison of the interologues between humans and yeasts, as well as the molecular docking and dynamics of the M28 domain of Ermp1 with possible target proteins. As results, 45 proteins are proposed that could interact with the metalloprotease. Most of these proteins are related to the transport of Ca2+ and the metabolism of amino acids and proteins. Docking and molecular dynamics suggest that the M28 domain of Ermp1 could hydrolyze leucine and methionine residues of Amk2, Ypt5 and Pex12. These results could support future experimental investigations of other Fxna peptidases, such as human ERMP1.
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Affiliation(s)
- Dalia González-Esparragoza
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química del Instituto de Ciencias (ICUAP), Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (D.G.-E.); (N.H.R.-M.); (L.M.-P.P.)
- Laboratorio de Elucidación y Síntesis en Química Orgánica, Instituto de Ciencias de la Universidad Autónoma de Puebla (ICUAP), Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Alan Carrasco-Carballo
- Laboratorio de Elucidación y Síntesis en Química Orgánica, Instituto de Ciencias de la Universidad Autónoma de Puebla (ICUAP), Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
- Consejo Nacional de Humanidades Ciencia y Tecnología, Instituto de Ciencias de la Universidad Autónoma de Puebla (ICUAP), Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Nora H. Rosas-Murrieta
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química del Instituto de Ciencias (ICUAP), Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (D.G.-E.); (N.H.R.-M.); (L.M.-P.P.)
| | - Lourdes Millán-Pérez Peña
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química del Instituto de Ciencias (ICUAP), Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (D.G.-E.); (N.H.R.-M.); (L.M.-P.P.)
| | - Felix Luna
- Laboratorio de Neuroendocrinología, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico;
| | - Irma Herrera-Camacho
- Laboratorio de Bioquímica y Biología Molecular, Centro de Química del Instituto de Ciencias (ICUAP), Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico; (D.G.-E.); (N.H.R.-M.); (L.M.-P.P.)
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14
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Cullati SN, Akizuki K, Chen JS, Johnson JL, Yaron-Barir TM, Cantley LC, Gould KL. Substrate displacement of CK1 C-termini regulates kinase specificity. SCIENCE ADVANCES 2024; 10:eadj5185. [PMID: 38728403 PMCID: PMC11086627 DOI: 10.1126/sciadv.adj5185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/05/2024] [Indexed: 05/12/2024]
Abstract
CK1 kinases participate in many signaling pathways, and their regulation is of meaningful biological consequence. CK1s autophosphorylate their C-terminal noncatalytic tails, and eliminating these tails increases substrate phosphorylation in vitro, suggesting that the autophosphorylated C-termini act as inhibitory pseudosubstrates. To test this prediction, we comprehensively identified the autophosphorylation sites on Schizosaccharomyces pombe Hhp1 and human CK1ε. Phosphoablating mutations increased Hhp1 and CK1ε activity toward substrates. Peptides corresponding to the C-termini interacted with the kinase domains only when phosphorylated, and substrates competitively inhibited binding of the autophosphorylated tails to the substrate binding grooves. Tail autophosphorylation influenced the catalytic efficiency with which CK1s targeted different substrates, and truncating the tail of CK1δ broadened its linear peptide substrate motif, indicating that tails contribute to substrate specificity as well. Considering autophosphorylation of both T220 in the catalytic domain and C-terminal sites, we propose a displacement specificity model to describe how autophosphorylation modulates substrate specificity for the CK1 family.
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Affiliation(s)
- Sierra N. Cullati
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kazutoshi Akizuki
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jared L. Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tomer M. Yaron-Barir
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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15
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Rutherford KM, Lera-Ramírez M, Wood V. PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability. Genetics 2024; 227:iyae007. [PMID: 38376816 PMCID: PMC11075564 DOI: 10.1093/genetics/iyae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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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
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16
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Kawamukai M. Regulation of sexual differentiation initiation in Schizosaccharomyces pombe. Biosci Biotechnol Biochem 2024; 88:475-492. [PMID: 38449372 DOI: 10.1093/bbb/zbae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
The fission yeast Schizosaccharomyces pombe is an excellent model organism to explore cellular events owing to rich tools in genetics, molecular biology, cellular biology, and biochemistry. Schizosaccharomyces pombe proliferates continuously when nutrients are abundant but arrests in G1 phase upon depletion of nutrients such as nitrogen and glucose. When cells of opposite mating types are present, cells conjugate, fuse, undergo meiosis, and finally form 4 spores. This sexual differentiation process in S. pombe has been studied extensively. To execute sexual differentiation, the glucose-sensing cAMP-PKA (cyclic adenosine monophosphate-protein kinase A) pathway, nitrogen-sensing TOR (target of rapamycin) pathway, and SAPK (stress-activating protein kinase) pathway are crucial, and the MAPK (mitogen-activating protein kinase) cascade is essential for pheromone sensing. These signals regulate ste11 at the transcriptional and translational levels, and Ste11 is modified in multiple ways. This review summarizes the initiation of sexual differentiation in S. pombe based on results I have helped to obtain, including the work of many excellent researchers.
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Affiliation(s)
- Makoto Kawamukai
- D epartment of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, Nishikawatsu, Matsue, Japan
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17
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Parker MD, Brunk ES, Getzler AJ, Karbstein K. The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage. PLoS Biol 2024; 22:e3001767. [PMID: 39038273 PMCID: PMC11045238 DOI: 10.1371/journal.pbio.3001767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/05/2024] [Indexed: 07/24/2024] Open
Abstract
The 18S rRNA sequence is highly conserved, particularly at its 3'-end, which is formed by the endonuclease Nob1. How Nob1 identifies its target sequence is not known, and in vitro experiments have shown Nob1 to be error-prone. Moreover, the sequence around the 3'-end is degenerate with similar sites nearby. Here, we used yeast genetics, biochemistry, and next-generation sequencing to investigate a role for the ATPase Rio1 in monitoring the accuracy of the 18S rRNA 3'-end. We demonstrate that Nob1 can miscleave its rRNA substrate and that miscleaved rRNA accumulates upon bypassing the Rio1-mediated quality control (QC) step, but not in healthy cells with intact QC mechanisms. Mechanistically, we show that Rio1 binding to miscleaved rRNA is weaker than its binding to accurately processed 18S rRNA. Accordingly, excess Rio1 results in accumulation of miscleaved rRNA. Ribosomes containing miscleaved rRNA can translate, albeit more slowly, thereby inviting collisions with trailing ribosomes. These collisions result in degradation of the defective ribosomes utilizing parts of the machinery for mRNA QC. Altogether, the data support a model in which Rio1 inspects the 3'-end of the nascent 18S rRNA to prevent miscleaved 18S rRNA-containing ribosomes from erroneously engaging in translation, where they induce ribosome collisions. The data also demonstrate how ribosome collisions purify cells of altered ribosomes with different functionalities, with important implications for the concept of ribosome heterogeneity.
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
| | - Elise S. Brunk
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
| | - Adam J. Getzler
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
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18
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Howard IV, Tavafoghi B, Igarashi MG, Ren L, Willet AH, Gould KL. Generation and characterization of temperature-sensitive alleles of the glucanosyltransferase Gas1 in Schizosaccharomyces pombe. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001144. [PMID: 38511077 PMCID: PMC10951720 DOI: 10.17912/micropub.biology.001144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
The Schizosaccharomyces pombe Gas family of β-1,3-glucanosyltransferases modify the cell wall by elongating β-1,3-glucan chains. While gas1Δ cells are inviable under standard laboratory growth conditions, they are viable in the presence of an osmotic stabilizer. Even under these conditions however, gas1Δ cells are slow-growing and display cell separation and morphology defects. Here, we isolated and characterized two gas1 temperature-sensitive alleles. Our data support that Gas1 is the primary S. pombe β-1,3-glucanosyltransferase important for cell separation and cell viability and provide useful tools for further analysis of S. pombe cell wall formation.
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Affiliation(s)
- Isaac V. Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, US
| | - Bita Tavafoghi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, US
| | - Maya G. Igarashi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, US
- Biophysical Sciences, Current address: University of Chicago, Chicago, IL, US
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, US
| | - Alaina H. Willet
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, US
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, US
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19
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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] [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.
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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
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20
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Scharl T, Grün B. A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models. BMC Bioinformatics 2024; 25:90. [PMID: 38429687 PMCID: PMC10905927 DOI: 10.1186/s12859-024-05717-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/21/2024] [Indexed: 03/03/2024] Open
Abstract
RNA sequencing of time-course experiments results in three-way count data where the dimensions are the genes, the time points and the biological units. Clustering RNA-seq data allows to extract groups of co-expressed genes over time. After standardisation, the normalised counts of individual genes across time points and biological units have similar properties as compositional data. We propose the following procedure to suitably cluster three-way RNA-seq data: (1) pre-process the RNA-seq data by calculating the normalised expression profiles, (2) transform the data using the additive log ratio transform to map the composition in the D-part Aitchison simplex to a D - 1 -dimensional Euclidean vector, (3) cluster the transformed RNA-seq data using matrix-variate Gaussian mixture models and (4) assess the quality of the overall cluster solution and of individual clusters based on cluster separation in the transformed space using density-based silhouette information and on compactness of the cluster in the original space using cluster maps as a suitable visualisation. The proposed procedure is illustrated on RNA-seq data from fission yeast and results are also compared to an analogous two-way approach after flattening out the biological units.
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Affiliation(s)
- Theresa Scharl
- Institute of Statistics, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Bettina Grün
- Institute for Statistics and Mathematics, Vienna University of Economics and Business, Vienna, Austria
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21
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Hebra T, Smrčková H, Elkatmis B, Převorovský M, Pluskal T. POMBOX: A Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology. ACS Synth Biol 2024; 13:558-567. [PMID: 37991801 PMCID: PMC10877588 DOI: 10.1021/acssynbio.3c00529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
The fission yeast Schizosaccharomyces pombe is a popular model organism in molecular biology and cell physiology. With its ease of genetic manipulation and growth, supported by in-depth functional annotations in the PomBase database and genome-wide metabolic models,S. pombe is an attractive option for synthetic biology applications. However,S. pombe currently lacks modular tools for generating genetic circuits with more than 1 transcriptional unit. We developed a toolkit to address this gap. Adapted from the MoClo-YTK plasmid kit for Saccharomyces cerevisiae and using the same modular cloning grammar, our POMBOX toolkit is designed to facilitate fast, efficient, and modular construction of genetic circuits inS. pombe. It allows for interoperability when working with DNA sequences that are functional in bothS. cerevisiae and S. pombe (e.g., protein tags, antibiotic resistance cassettes, and coding sequences). Moreover, POMBOX enables the modular assembly of multigene pathways and increases the possible pathway length from 6 to 12 transcriptional units. We also adapted the stable integration vector homology arms to Golden Gate assembly and tested the genomic integration success rates depending on different sequence sizes, from 4 to 24 kb. We included 14 S. pombe promoters that we characterized using two fluorescent proteins, in both minimally defined (EMM2─Edinburgh minimal media) and complex (YES─yeast extract with supplements) media. Then, we examined the efficacy of 6 S. cerevisiae and 6 synthetic terminators in S. pombe. Finally, we used the POMBOX kit for a synthetic biology application in metabolic engineering and expressed plant enzymes in S. pombe to produce specialized metabolite precursors, namely, methylxanthine, amorpha-4,11-diene, and cinnamic acid from the purine, mevalonate, and aromatic amino acid pathways.
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Affiliation(s)
- Téo Hebra
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Helena Smrčková
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Büsra Elkatmis
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Martin Převorovský
- Department
of Cell Biology, Faculty of Science, Charles
University, 128 00 Prague, Czech
Republic
| | - Tomáš Pluskal
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
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22
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Lopez Maury L, Ren L, Hassan S, Bähler J, Gould KL. The Cdc14 phosphatase, Clp1, does not affect genome expression. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001089. [PMID: 38415071 PMCID: PMC10897734 DOI: 10.17912/micropub.biology.001089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/29/2024]
Abstract
Schizosaccharomyces pombe Clp1 is a Cdc14-family phosphatase that reverses mitotic Cdk1 phosphorylation. Despite evolutionary conservation, Clp1 's mammalian orthologs do not share this function. Rather, higher eukaryotic Cdc14 enzymes act in DNA repair, ciliogenesis, and gene regulation. To examine if Clp1 regulates gene expression, we compared the transcriptional profiles of cells lacking Clp1 function to that of wildtype. Because clp1∆ cells are sensitive to the actin depolymerizing drug, LatrunculinA, we also investigated whether a transcriptional response was involved. Our results indicate that Clp1 does not detectably affect gene expression and highlight the organism-specific functions of this conserved phosphatase family.
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Affiliation(s)
- Luis Lopez Maury
- Department of Genetics, Evolution, and Environment, Institute of Healthy Ageing, University College London, London, UK
- Current: Instituto de Bioquimica Vegetal y Fotosintesis, Universidad de Sevilla, Sevilla, Spain
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shaimaa Hassan
- Department of Genetics, Evolution, and Environment, Institute of Healthy Ageing, University College London, London, UK
| | - Jürg Bähler
- Department of Genetics, Evolution, and Environment, Institute of Healthy Ageing, University College London, London, UK
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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23
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Putman TE, Schaper K, Matentzoglu N, Rubinetti V, Alquaddoomi F, Cox C, Caufield JH, Elsarboukh G, Gehrke S, Hegde H, Reese J, Braun I, Bruskiewich R, Cappelletti L, Carbon S, Caron A, Chan L, Chute C, Cortes K, De Souza V, Fontana T, Harris N, Hartley E, Hurwitz E, Jacobsen JB, Krishnamurthy M, Laraway B, McLaughlin J, McMurry J, Moxon ST, Mullen K, O’Neil S, Shefchek K, Stefancsik R, Toro S, Vasilevsky N, Walls R, Whetzel P, Osumi-Sutherland D, Smedley D, Robinson P, Mungall C, Haendel M, Munoz-Torres M. The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Nucleic Acids Res 2024; 52:D938-D949. [PMID: 38000386 PMCID: PMC10767791 DOI: 10.1093/nar/gkad1082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/21/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI's ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.
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Affiliation(s)
- Tim E Putman
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kevin Schaper
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Vincent P Rubinetti
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Faisal S Alquaddoomi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Corey Cox
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - J Harry Caufield
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Glass Elsarboukh
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sarah Gehrke
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Harshad Hegde
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Justin T Reese
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ian Braun
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | | | | | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anita R Caron
- European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katherina G Cortes
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Tommaso Fontana
- Dipartimento di Informatica, Università degli Studi di Milano Statale, Milano, Italy
| | - Nomi L Harris
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily L Hartley
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | - Eric Hurwitz
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Madan Krishnamurthy
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bryan J Laraway
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Julie A McMurry
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sierra A T Moxon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathleen R Mullen
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Shawn T O’Neil
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kent A Shefchek
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ray Stefancsik
- European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Sabrina Toro
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Ramona L Walls
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | - Patricia L Whetzel
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 6032, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Melissa A Haendel
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Monica C Munoz-Torres
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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24
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Badaczewska-Dawid AE, Kuriata A, Pintado-Grima C, Garcia-Pardo J, Burdukiewicz M, Iglesias V, Kmiecik S, Ventura S. A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms. Nucleic Acids Res 2024; 52:D360-D367. [PMID: 37897355 PMCID: PMC10767922 DOI: 10.1093/nar/gkad942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
Protein aggregation has been associated with aging and different pathologies and represents a bottleneck in the industrial production of biotherapeutics. Numerous past studies performed in Escherichia coli and other model organisms have allowed to dissect the biophysical principles underlying this process. This knowledge fuelled the development of computational tools, such as Aggrescan 3D (A3D) to forecast and re-design protein aggregation. Here, we present the A3D Model Organism Database (A3D-MODB) http://biocomp.chem.uw.edu.pl/A3D2/MODB, a comprehensive resource for the study of structural protein aggregation in the proteomes of 12 key model species spanning distant biological clades. In addition to A3D predictions, this resource incorporates information useful for contextualizing protein aggregation, including membrane protein topology and structural model confidence, as an indirect reporter of protein disorder. The database is openly accessible without any need for registration. We foresee A3D-MOBD evolving into a central hub for conducting comprehensive, multi-species analyses of protein aggregation, fostering the development of protein-based solutions for medical, biotechnological, agricultural and industrial applications.
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Affiliation(s)
| | - Aleksander Kuriata
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Michał Burdukiewicz
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Kilińskiego 1, 15-369, Białystok, Poland
| | - Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Sebastian Kmiecik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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25
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Pons C, van Leeuwen J. Meta-analysis of dispensable essential genes and their interactions with bypass suppressors. Life Sci Alliance 2024; 7:e202302192. [PMID: 37918966 PMCID: PMC10622647 DOI: 10.26508/lsa.202302192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023] Open
Abstract
Genes have been historically classified as essential or non-essential based on their requirement for viability. However, genomic mutations can sometimes bypass the requirement for an essential gene, challenging the binary classification of gene essentiality. Such dispensable essential genes represent a valuable model for understanding the incomplete penetrance of loss-of-function mutations often observed in natural populations. Here, we compiled data from multiple studies on essential gene dispensability in Saccharomyces cerevisiae to comprehensively characterize these genes. In analyses spanning different evolutionary timescales, dispensable essential genes exhibited distinct phylogenetic properties compared with other essential and non-essential genes. Integration of interactions with suppressor genes that can bypass the gene essentiality revealed the high functional modularity of the bypass suppression network. Furthermore, dispensable essential and bypass suppressor gene pairs reflected simultaneous changes in the mutational landscape of S. cerevisiae strains. Importantly, species in which dispensable essential genes were non-essential tended to carry bypass suppressor mutations in their genomes. Overall, our study offers a comprehensive view of dispensable essential genes and illustrates how their interactions with bypass suppressors reflect evolutionary outcomes.
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Affiliation(s)
- Carles Pons
- https://ror.org/01z1gye03 Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Jolanda van Leeuwen
- Center for Integrative Genomics, Bâtiment Génopode, University of Lausanne, Lausanne, Switzerland
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26
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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] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 10/29/2023] [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.
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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
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27
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Liang H, Mower JP, Chia CP. Functional Prokaryotic-Like Deoxycytidine Triphosphate Deaminases and Thymidylate Synthase in Eukaryotic Social Amoebae: Vertical, Endosymbiotic, or Horizontal Gene Transfer? Mol Biol Evol 2023; 40:msad268. [PMID: 38064674 PMCID: PMC10733785 DOI: 10.1093/molbev/msad268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 10/22/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023] Open
Abstract
The de novo synthesis of deoxythymidine triphosphate uses several pathways: gram-negative bacteria use deoxycytidine triphosphate deaminase to convert deoxycytidine triphosphate into deoxyuridine triphosphate, whereas eukaryotes and gram-positive bacteria instead use deoxycytidine monophosphate deaminase to transform deoxycytidine monophosphate to deoxyuridine monophosphate. It is then unusual that in addition to deoxycytidine monophosphate deaminases, the eukaryote Dictyostelium discoideum has 2 deoxycytidine triphosphate deaminases (Dcd1Dicty and Dcd2Dicty). Expression of either DcdDicty can fully rescue the slow growth of an Escherichia coli dcd knockout. Both DcdDicty mitigate the hydroxyurea sensitivity of a Schizosaccharomyces pombe deoxycytidine monophosphate deaminase knockout. Phylogenies show that Dcd1Dicty homologs may have entered the common ancestor of the eukaryotic groups of Amoebozoa, Obazoa, Metamonada, and Discoba through an ancient horizontal gene transfer from a prokaryote or an ancient endosymbiotic gene transfer from a mitochondrion, followed by horizontal gene transfer from Amoebozoa to several other unrelated groups of eukaryotes. In contrast, the Dcd2Dicty homologs were a separate horizontal gene transfer from a prokaryote or a virus into either Amoebozoa or Rhizaria, followed by a horizontal gene transfer between them. ThyXDicty, the D. discoideum thymidylate synthase, another enzyme of the deoxythymidine triphosphate biosynthesis pathway, was suggested previously to be acquired from the ancestral mitochondria or by horizontal gene transfer from alpha-proteobacteria. ThyXDicty can fully rescue the E. coli thymidylate synthase knockout, and we establish that it was obtained by the common ancestor of social amoebae not from mitochondria but from a bacterium. We propose horizontal gene transfer and endosymbiotic gene transfer contributed to the enzyme diversity of the deoxythymidine triphosphate synthesis pathway in most social amoebae, many Amoebozoa, and other eukaryotes.
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Affiliation(s)
- Heng Liang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Catherine P Chia
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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28
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Lera-Ramírez M, Bähler J, Mata J, Rutherford K, Hoffman CS, Lambert S, Oliferenko S, Martin SG, Gould KL, Du LL, Sabatinos SA, Forsburg SL, Nielsen O, Nurse P, Wood V. Revised fission yeast gene and allele nomenclature guidelines for machine readability. Genetics 2023; 225:iyad143. [PMID: 37758508 PMCID: PMC10627252 DOI: 10.1093/genetics/iyad143] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/24/2023] [Indexed: 09/30/2023] Open
Abstract
Standardized nomenclature for genes, gene products, and isoforms is crucial to prevent ambiguity and enable clear communication of scientific data, facilitating efficient biocuration and data sharing. Standardized genotype nomenclature, which describes alleles present in a specific strain that differ from those in the wild-type reference strain, is equally essential to maximize research impact and ensure that results linking genotypes to phenotypes are Findable, Accessible, Interoperable, and Reusable (FAIR). In this publication, we extend the fission yeast clade gene nomenclature guidelines to support the curation efforts at PomBase (www.pombase.org), the Schizosaccharomyces pombe Model Organism Database. This update introduces nomenclature guidelines for noncoding RNA genes, following those set forth by the Human Genome Organisation Gene Nomenclature Committee. Additionally, we provide a significant update to the allele and genotype nomenclature guidelines originally published in 1987, to standardize the diverse range of genetic modifications enabled by the fission yeast genetic toolbox. These updated guidelines reflect a community consensus between numerous fission yeast researchers. Adoption of these rules will improve consistency in gene and genotype nomenclature, and facilitate machine-readability and automated entity recognition of fission yeast genes and alleles in publications or datasets. In conclusion, our updated guidelines provide a valuable resource for the fission yeast research community, promoting consistency, clarity, and FAIRness in genetic data sharing and interpretation.
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Affiliation(s)
- Manuel Lera-Ramírez
- University College London, Department of Genetics Evolution and Environment, Darwin Building, 99-105 Gower Street, London WC1E 6BT, UK
| | - Jürg Bähler
- University College London, Department of Genetics Evolution and Environment, Darwin Building, 99-105 Gower Street, London WC1E 6BT, UK
| | - Juan Mata
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
| | - Kim Rutherford
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
| | | | - Sarah Lambert
- Institut Curie, Université Paris-Saclay, CNRS UMR3348, Orsay 91400, France
| | - Snezhana Oliferenko
- The Francis Crick Institute, London NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London SE1 1UL, UK
| | - Sophie G Martin
- University of Geneva, Department of Molecular and Cellular Biology, Geneva 1211, Switzerland
| | - Kathleen L Gould
- Vanderbilt University School of Medicine, Department of Cell and Developmental Biology, Nashville, TN 37232, USA
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
| | - Sarah A Sabatinos
- Toronto Metropolitan University, Department of Chemistry & Biology, Toronto M5B 2K3, Canada
| | - Susan L Forsburg
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Olaf Nielsen
- Department of Biology, Cell cycle and genome stability Group, University of Copenhagen, Copenhagen N DK2100, Denmark
| | - Paul Nurse
- The Francis Crick Institute, London NW1 1AT, UK
| | - Valerie Wood
- University of Cambridge, Department of Biochemistry, Cambridge CB2 1GA, UK
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29
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Willet AH, Turner LA, Park JS, Ren L, Snider CE, Gould KL. Characterization of Pik1 function in fission yeast reveals its conserved role in lipid synthesis and not cytokinesis. J Cell Sci 2023; 136:jcs261415. [PMID: 37815455 PMCID: PMC10629694 DOI: 10.1242/jcs.261415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
Phosphatidylinositol (PI)-4-phosphate (PI4P) is a lipid found at the plasma membrane (PM) and Golgi in cells from yeast to humans. PI4P is generated from PI by PI4-kinases and can be converted into PI-4,5-bisphosphate [PI(4,5)P2]. Schizosaccharomyces pombe have two essential PI4-kinases - Stt4 and Pik1. Stt4 localizes to the PM, and its loss from the PM results in a decrease of PM PI4P and PI(4,5)P2. As a result, cells divide non-medially due to disrupted cytokinetic ring-PM anchoring. However, the localization and function of S. pombe Pik1 has not been thoroughly examined. Here, we found that Pik1 localizes exclusively to the trans-Golgi and is required for Golgi PI4P production. We determined that Ncs1 regulates Pik1, but unlike in other organisms, it is not required for Pik1 Golgi localization. When Pik1 function was disrupted, PM PI4P but not PI(4,5)P2 levels were reduced, a major difference compared with Stt4. We conclude that Stt4 is the chief enzyme responsible for producing the PI4P that generates PI(4,5)P2. Also, that cells with disrupted Pik1 do not divide asymmetrically highlights the specific importance of PM PI(4,5)P2 for cytokinetic ring-PM anchoring.
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Affiliation(s)
- Alaina H. Willet
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lesley A. Turner
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Joshua S. Park
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Chloe E. Snider
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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30
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Mansouri-Noori F, Pircher A, Bilodeau D, Siniavskaia L, Grigull J, Rissland OS, Bayfield MA. The LARP1 homolog Slr1p controls the stability and expression of proto-5'TOP mRNAs in fission yeast. Cell Rep 2023; 42:113226. [PMID: 37851576 DOI: 10.1016/j.celrep.2023.113226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
Messenger RNAs (mRNAs) in higher eukaryotes that encode proteins important for the assembly of the translational apparatus (e.g., ribosomal proteins) often harbor a pyrimidine-rich motif at the extreme 5' end known as a 5' terminal oligopyrimidine (5'TOP) sequence. Members of the La-related protein 1 (LARP1) family control 5'TOP expression through a conserved DM15 motif, but the mechanism is not well understood. 5'TOP motifs have not been described in many lower organisms, and fission yeast harbors a LARP1 homolog that also lacks a DM15 motif. In this work, we show that the fission yeast LARP1 homolog, Slr1p, controls the translation and stability of mRNAs encoding proteins analogous to 5'TOP mRNAs in higher eukaryotes, which we thus refer to as proto-5'TOPs. Our data suggest that the LARP1 DM15 motif and the mRNA 5'TOP motif may be features that were scaffolded over a more fundamental mechanism of LARP1-associated control of gene expression.
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Affiliation(s)
| | | | - Danielle Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Jörg Grigull
- Department of Mathematics and Statistics, York University, Toronto, Canada
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
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31
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Stroup EK, Ji Z. Delineating yeast cleavage and polyadenylation signals using deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561764. [PMID: 37873420 PMCID: PMC10592759 DOI: 10.1101/2023.10.10.561764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
3'-end cleavage and polyadenylation is an essential process for eukaryotic mRNA maturation. In yeast species, the polyadenylation signals that recruit the processing machinery are degenerate and remain poorly characterized compared to well-defined regulatory elements in mammals. Especially, recent deep sequencing experiments showed extensive cleavage heterogeneity for some mRNAs in Saccharomyces cerevisiae and uncovered the polyA motif differences between S. cerevisiae vs. Schizosaccharomyces pombe . The findings raised the fundamental question of how polyadenylation signals are formed in yeast. Here we addressed this question by developing deep learning models to deconvolute degenerate cis -regulatory elements and quantify their positional importance in mediating yeast polyA site formation, cleavage heterogeneity, and strength. In S. cerevisiae , cleavage heterogeneity is promoted by the depletion of U-rich elements around polyA sites as well as multiple occurrences of upstream UA-rich elements. Sites with high cleavage heterogeneity show overall lower strength. The site strength and tandem site distances modulate alternative polyadenylation (APA) under the diauxic stress. Finally, we developed a deep learning model to reveal the distinct motif configuration of S. pombe polyA sites which show more precise cleavage than S. cerevisiae . Altogether, our deep learning models provide unprecedented insights into polyA site formation across yeast species.
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32
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Ader NR, Chen L, Surovtsev IV, Chadwick WL, Rodriguez EC, King MC, Lusk CP. An ESCRT grommet cooperates with a diffusion barrier to maintain nuclear integrity. Nat Cell Biol 2023; 25:1465-1477. [PMID: 37783794 PMCID: PMC11365527 DOI: 10.1038/s41556-023-01235-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
The molecular mechanisms by which the endosomal sorting complexes required for transport (ESCRT) proteins contribute to the integrity of the nuclear envelope (NE) barrier are not fully defined. We leveraged the single NE hole generated by mitotic extrusion of the Schizosaccharomyces pombe spindle pole body to reveal two modes of ESCRT function executed by distinct complements of ESCRT-III proteins, both dependent on CHMP7/Cmp7. A grommet-like function is required to restrict the NE hole in anaphase B, whereas replacement of Cmp7 by a sealing module ultimately closes the NE in interphase. Without Cmp7, nucleocytoplasmic compartmentalization remains intact despite NE discontinuities of up to 540 nm, suggesting mechanisms to limit diffusion through these holes. We implicate spindle pole body proteins as key components of a diffusion barrier acting with Cmp7 in anaphase B. Thus, NE remodelling mechanisms cooperate with proteinaceous diffusion barriers beyond nuclear pore complexes to maintain the nuclear compartment.
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Affiliation(s)
- Nicholas R Ader
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Linda Chen
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Ivan V Surovtsev
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | | | - Elisa C Rodriguez
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, CT, USA.
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
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33
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Willet AH, Wos M, Igarashi MG, Ren L, Turner LA, Gould KL. Elevated levels of sphingolipid MIPC in the plasma membrane disrupt the coordination of cell growth with cell wall formation in fission yeast. PLoS Genet 2023; 19:e1010987. [PMID: 37792890 PMCID: PMC10578601 DOI: 10.1371/journal.pgen.1010987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/16/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
Coupling cell wall expansion with cell growth is a universal challenge faced by walled organisms. Mutations in Schizosaccharomyces pombe css1, which encodes a PM inositol phosphosphingolipid phospholipase C, prevent cell wall expansion but not synthesis of cell wall material. To probe how Css1 modulates cell wall formation we used classical and chemical genetics coupled with quantitative mass spectrometry. We found that elevated levels of the sphingolipid biosynthetic pathway's final product, mannosylinositol phosphorylceramide (MIPC), specifically correlated with the css1-3 phenotype. We also found that an apparent indicator of sphingolipids and a sterol biosensor accumulated at the cytosolic face of the PM at cell tips and the division site of css1-3 cells and, in accord, the PM in css1-3 was less dynamic than in wildtype cells. Interestingly, disrupting the protein glycosylation machinery recapitulated the css1-3 phenotype and led us to investigate Ghs2, a glycosylated PM protein predicted to modify cell wall material. Disrupting Ghs2 function led to aberrant cell wall material accumulation suggesting Ghs2 is dysfunctional in css1-3. We conclude that preventing an excess of MIPC in the S. pombe PM is critical to the function of key PM-localized proteins necessary for coupling growth with cell wall formation.
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Affiliation(s)
- Alaina H. Willet
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Marcin Wos
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Maya G. Igarashi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Lesley A. Turner
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States of America
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34
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Lian Q, Maestroni L, Gaudin M, Llorente B, Mercier R. Meiotic recombination is confirmed to be unusually high in the fission yeast Schizosaccharomyces pombe. iScience 2023; 26:107614. [PMID: 37664590 PMCID: PMC10474467 DOI: 10.1016/j.isci.2023.107614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/20/2023] [Accepted: 08/09/2023] [Indexed: 09/05/2023] Open
Abstract
In most eukaryotes, meiotic crossovers (COs) are limited to 1-3 per chromosome, and are prevented from occurring close to one another by CO interference. The fission yeast Schizosaccharomyces pombe, an exception to these general rules, was reported to have the highest CO number per chromosome and no or weak interference. However, global CO frequency was indirectly estimated, calling for confirmation. Here, we used an innovative strategy to determine COs genome-wide in S. pombe. We confirmed weak CO interference, acting at physical distances compatible with the patterning of recombination precursors. We revealed a slight co-variation in CO number between chromosomes, suggesting that a limiting pro-CO factor varies between meiocytes. CO number per chromosome varies proportionally with chromosome size, with the three chromosomes having, on average, 15.9, 12.5, and 7.0 COs, respectively. This reinforces S. pombe's status as the eukaryote with the highest CO number per chromosome described to date.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Laetitia Maestroni
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Maxime Gaudin
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
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35
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Weidemann DE, Holehouse J, Singh A, Grima R, Hauf S. The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian. SCIENCE ADVANCES 2023; 9:eadh5138. [PMID: 37556551 PMCID: PMC10411910 DOI: 10.1126/sciadv.adh5138] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
Abstract
Gene expression inherently gives rise to stochastic variation ("noise") in the production of gene products. Minimizing noise is crucial for ensuring reliable cellular functions. However, noise cannot be suppressed below a certain intrinsic limit. For constitutively expressed genes, this limit is typically assumed to be Poissonian noise, wherein the variance in mRNA numbers is equal to their mean. Here, we demonstrate that several cell division genes in fission yeast exhibit mRNA variances significantly below this limit. The reduced variance can be explained by a gene expression model incorporating multiple transcription and mRNA degradation steps. Notably, in this sub-Poissonian regime, distinct from Poissonian or super-Poissonian regimes, cytoplasmic noise is effectively suppressed through a higher mRNA export rate. Our findings redefine the lower limit of eukaryotic gene expression noise and uncover molecular requirements for achieving ultralow noise, which is expected to be important for vital cellular functions.
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Affiliation(s)
- Douglas E. Weidemann
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - James Holehouse
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87510, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Silke Hauf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
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Willet AH, Turner LA, Park JS, Ren L, Snider CE, Gould KL. Characterization of Pik1 function in fission yeast reveals its conserved role in lipid synthesis and not cytokinesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550375. [PMID: 37546978 PMCID: PMC10402101 DOI: 10.1101/2023.07.24.550375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Phosphatidylinositol (PI)-4-phosphate (PI4P) is a lipid found at the plasma membrane (PM) and Golgi in cells from yeast to humans. PI4P is generated from PI by PI4-kinases and can be converted to PI-4,5-bisphosphate [PI(4,5)P 2 ]. Schizosaccharomyces pombe have 2 essential PI4-kinases: Stt4 and Pik1. Stt4 localizes to the PM and its loss from the PM results in a decrease of PM PI4P and PI(4,5)P 2 . As a result, cells divide non-medially due to disrupted cytokinetic ring-PM anchoring. However, the localization and function of S. pombe Pik1 has not been thoroughly examined. Here, we found that Pik1 localizes exclusively to the trans-Golgi and is required for Golgi PI4P production. We determined that Ncs1 regulates Pik1, but unlike in other organisms, it is not required for Pik1 Golgi localization. When Pik1 function was disrupted, PM PI4P but not PI(4,5)P 2 levels were reduced, a major difference with Stt4. We conclude that Stt4 is the chief enzyme responsible for producing the PI4P that generates PI(4,5)P 2 . Also, that cells with disrupted Pik1 do not divide asymmetrically highlights the specific importance of PM PI(4,5)P 2 for cytokinetic ring-PM anchoring. Summary statement Fission yeast Pik1 localizes exclusively to the trans-Golgi independently of Ncs1, where it contributes to PI4P but not PI(4,5)P 2 synthesis. Pik1 does not affect cytokinesis.
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Xue B, Rhee SY. Status of genome function annotation in model organisms and crops. PLANT DIRECT 2023; 7:e499. [PMID: 37426891 PMCID: PMC10326244 DOI: 10.1002/pld3.499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/21/2023] [Accepted: 05/08/2023] [Indexed: 07/11/2023]
Abstract
Since the entry into genome-enabled biology several decades ago, much progress has been made in determining, describing, and disseminating the functions of genes and their products. Yet, this information is still difficult to access for many scientists and for most genomes. To provide easy access and a graphical summary of the status of genome function annotation for model organisms and bioenergy and food crop species, we created a web application (https://genomeannotation.rheelab.org) to visualize, search, and download genome annotation data for 28 species. The summary graphics and data tables will be updated semi-annually, and snapshots will be archived to provide a historical record of the progress of genome function annotation efforts. Clear and simple visualization of up-to-date genome function annotation status, including the extent of what is unknown, will help address the grand challenge of elucidating the functions of all genes in organisms.
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Affiliation(s)
- Bo Xue
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCaliforniaUSA
- Present address:
Plant Resilience InstituteMichigan State UniversityEast LansingMI 4882
| | - Seung Y. Rhee
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCaliforniaUSA
- Present address:
Plant Resilience InstituteMichigan State UniversityEast LansingMI 4882
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38
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Cullati SN, Akizuki K, Chen JS, Gould KL. Substrate displacement of CK1 C-termini regulates kinase specificity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547285. [PMID: 37425826 PMCID: PMC10327203 DOI: 10.1101/2023.06.30.547285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
CK1 kinases participate in many signaling pathways; how these enzymes are regulated is therefore of significant biological consequence. CK1s autophosphorylate their C-terminal non-catalytic tails, and eliminating these modifications increases substrate phosphorylation in vitro, suggesting that the autophosphorylated C-termini act as inhibitory pseudosubstrates. To test this prediction, we comprehensively identified the autophosphorylation sites on Schizosaccharomyces pombe Hhp1 and human CK1ε. Peptides corresponding to the C-termini interacted with the kinase domains only when phosphorylated, and phosphoablating mutations increased Hhp1 and CK1ε activity towards substrates. Interestingly, substrates competitively inhibited binding of the autophosphorylated tails to the substrate binding grooves. The presence or absence of tail autophosphorylation influenced the catalytic efficiency with which CK1s targeted different substrates, indicating that tails contribute to substrate specificity. Combining this mechanism with autophosphorylation of the T220 site in the catalytic domain, we propose a displacement specificity model to describe how autophosphorylation regulates substrate specificity for the CK1 family.
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Affiliation(s)
- Sierra N. Cullati
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kazutoshi Akizuki
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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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] [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.
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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.
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40
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Alam S, Gu Y, Reichert P, Bähler J, Oliferenko S. Optimization of energy production and central carbon metabolism in a non-respiring eukaryote. Curr Biol 2023; 33:2175-2186.e5. [PMID: 37164017 PMCID: PMC7615655 DOI: 10.1016/j.cub.2023.04.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
Most eukaryotes respire oxygen, using it to generate biomass and energy. However, a few organisms have lost the capacity to respire. Understanding how they manage biomass and energy production may illuminate the critical points at which respiration feeds into central carbon metabolism and explain possible routes to its optimization. Here, we use two related fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, as a comparative model system. We show that although S. japonicus does not respire oxygen, unlike S. pombe, it is capable of efficient NADH oxidation, amino acid synthesis, and ATP generation. We probe possible optimization strategies through the use of stable isotope tracing metabolomics, mass isotopologue distribution analysis, genetics, and physiological experiments. S. japonicus appears to have optimized cytosolic NADH oxidation via glycerol-3-phosphate synthesis. It runs a fully bifurcated TCA pathway, sustaining amino acid production. Finally, we propose that it has optimized glycolysis to maintain high ATP/ADP ratio, in part by using the pentose phosphate pathway as a glycolytic shunt, reducing allosteric inhibition of glycolysis and supporting biomass generation. By comparing two related organisms with vastly different metabolic strategies, our work highlights the versatility and plasticity of central carbon metabolism in eukaryotes, illuminating critical adaptations supporting the preferential use of glycolysis over oxidative phosphorylation.
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Affiliation(s)
- Sara Alam
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Ying Gu
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Polina Reichert
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK; School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Jürg Bähler
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK.
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41
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Xu YJ, Bhadra S, Mahdi ATA, Dev K, Yurtsever I, Nakamura TM. Comprehensive mutational analysis of the checkpoint signaling function of Rpa1/Ssb1 in fission yeast. PLoS Genet 2023; 19:e1010691. [PMID: 37200372 DOI: 10.1371/journal.pgen.1010691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/31/2023] [Accepted: 04/24/2023] [Indexed: 05/20/2023] Open
Abstract
Replication protein A (RPA) is a heterotrimeric complex and the major single-strand DNA (ssDNA) binding protein in eukaryotes. It plays important roles in DNA replication, repair, recombination, telomere maintenance, and checkpoint signaling. Because RPA is essential for cell survival, understanding its checkpoint signaling function in cells has been challenging. Several RPA mutants have been reported previously in fission yeast. None of them, however, has a defined checkpoint defect. A separation-of-function mutant of RPA, if identified, would provide significant insights into the checkpoint initiation mechanisms. We have explored this possibility and carried out an extensive genetic screen for Rpa1/Ssb1, the large subunit of RPA in fission yeast, looking for mutants with defects in checkpoint signaling. This screen has identified twenty-five primary mutants that are sensitive to genotoxins. Among these mutants, two have been confirmed partially defective in checkpoint signaling primarily at the replication fork, not the DNA damage site. The remaining mutants are likely defective in other functions such as DNA repair or telomere maintenance. Our screened mutants, therefore, provide a valuable tool for future dissection of the multiple functions of RPA in fission yeast.
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Affiliation(s)
- Yong-Jie Xu
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, United States of America
| | - Sankhadip Bhadra
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, United States of America
| | - Alaa Taha A Mahdi
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, United States of America
| | - Kamal Dev
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, United States of America
| | - Ilknur Yurtsever
- Department of Pharmacology and Toxicology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, United States of America
| | - Toru M Nakamura
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
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42
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Mascarenhas Dos Santos AC, Julian AT, Liang P, Juárez O, Pombert JF. Telomere-to-Telomere genome assemblies of human-infecting Encephalitozoon species. BMC Genomics 2023; 24:237. [PMID: 37142951 PMCID: PMC10158259 DOI: 10.1186/s12864-023-09331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Microsporidia are diverse spore forming, fungal-related obligate intracellular pathogens infecting a wide range of hosts. This diversity is reflected at the genome level with sizes varying by an order of magnitude, ranging from less than 3 Mb in Encephalitozoon species (the smallest known in eukaryotes) to more than 50 Mb in Edhazardia spp. As a paradigm of genome reduction in eukaryotes, the small Encephalitozoon genomes have attracted much attention with investigations revealing gene dense, repeat- and intron-poor genomes characterized by a thorough pruning of molecular functions no longer relevant to their obligate intracellular lifestyle. However, because no Encephalitozoon genome has been sequenced from telomere-to-telomere and since no methylation data is available for these species, our understanding of their overall genetic and epigenetic architectures is incomplete. METHODS In this study, we sequenced the complete genomes from telomere-to-telomere of three human-infecting Encephalitozoon spp. -E. intestinalis ATCC 50506, E. hellem ATCC 50604 and E. cuniculi ATCC 50602- using short and long read platforms and leveraged the data generated as part of the sequencing process to investigate the presence of epigenetic markers in these genomes. We also used a mixture of sequence- and structure-based computational approaches, including protein structure prediction, to help identify which Encephalitozoon proteins are involved in telomere maintenance, epigenetic regulation, and heterochromatin formation. RESULTS The Encephalitozoon chromosomes were found capped by TTAGG 5-mer telomeric repeats followed by telomere associated repeat elements (TAREs) flanking hypermethylated ribosomal RNA (rRNA) gene loci featuring 5-methylcytosines (5mC) and 5-hemimethylcytosines (5hmC), themselves followed by lesser methylated subtelomeres and hypomethylated chromosome cores. Strong nucleotide biases were identified between the telomeres/subtelomeres and chromosome cores with significant changes in GC/AT, GT/AC and GA/CT contents. The presence of several genes coding for proteins essential to telomere maintenance, epigenetic regulation, and heterochromatin formation was further confirmed in the Encephalitozoon genomes. CONCLUSION Altogether, our results strongly support the subtelomeres as sites of heterochromatin formation in Encephalitozoon genomes and further suggest that these species might shutdown their energy-consuming ribosomal machinery while dormant as spores by silencing of the rRNA genes using both 5mC/5hmC methylation and facultative heterochromatin formation at these loci.
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Affiliation(s)
| | | | - Pingdong Liang
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
| | - Oscar Juárez
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
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Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, Mushayahama T, Sternberg PW, Thomas PD, Van Auken K, Ramsey J, Siegele DA, Chisholm RL, Fey P, Aspromonte MC, Nugnes MV, Quaglia F, Tosatto S, Giglio M, Nadendla S, Antonazzo G, Attrill H, Dos Santos G, Marygold S, Strelets V, Tabone CJ, Thurmond J, Zhou P, Ahmed SH, Asanitthong P, Luna Buitrago D, Erdol MN, Gage MC, Ali Kadhum M, Li KYC, Long M, Michalak A, Pesala A, Pritazahra A, Saverimuttu SCC, Su R, Thurlow KE, Lovering RC, Logie C, Oliferenko S, Blake J, Christie K, Corbani L, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Smith C, Cuzick A, Seager J, Cooper L, Elser J, Jaiswal P, Gupta P, Jaiswal P, Naithani S, Lera-Ramirez M, Rutherford K, Wood V, De Pons JL, Dwinell MR, Hayman GT, Kaldunski ML, Kwitek AE, Laulederkind SJF, Tutaj MA, Vedi M, Wang SJ, D'Eustachio P, Aimo L, Axelsen K, Bridge A, Hyka-Nouspikel N, Morgat A, Aleksander SA, Cherry JM, Engel SR, Karra K, Miyasato SR, Nash RS, Skrzypek MS, Weng S, Wong ED, Bakker E, Berardini TZ, Reiser L, Auchincloss A, Axelsen K, Argoud-Puy G, Blatter MC, Boutet E, Breuza L, Bridge A, Casals-Casas C, Coudert E, Estreicher A, Livia Famiglietti M, Feuermann M, Gos A, Gruaz-Gumowski N, Hulo C, Hyka-Nouspikel N, Jungo F, Le Mercier P, Lieberherr D, Masson P, Morgat A, Pedruzzi I, Pourcel L, Poux S, Rivoire C, Sundaram S, Bateman A, Bowler-Barnett E, Bye-A-Jee H, Denny P, Ignatchenko A, Ishtiaq R, Lock A, Lussi Y, Magrane M, Martin MJ, Orchard S, Raposo P, Speretta E, Tyagi N, Warner K, Zaru R, Diehl AD, Lee R, Chan J, Diamantakis S, Raciti D, Zarowiecki M, Fisher M, James-Zorn C, Ponferrada V, Zorn A, Ramachandran S, Ruzicka L, Westerfield M. The Gene Ontology knowledgebase in 2023. Genetics 2023; 224:iyad031. [PMID: 36866529 PMCID: PMC10158837 DOI: 10.1093/genetics/iyad031] [Citation(s) in RCA: 420] [Impact Index Per Article: 420.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 03/04/2023] Open
Abstract
The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.
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44
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Cullati SN, Zhang E, Shan Y, Guillen RX, Chen JS, Navarrete-Perea J, Elmore ZC, Ren L, Gygi SP, Gould KL. Fission yeast CK1 promotes DNA double-strand break repair through both homologous recombination and non-homologous end joining. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538600. [PMID: 37162912 PMCID: PMC10168346 DOI: 10.1101/2023.04.27.538600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The CK1 family are conserved serine/threonine kinases with numerous substrates and cellular functions. The fission yeast CK1 orthologues Hhp1 and Hhp2 were first characterized as regulators of DNA repair, but the mechanism(s) by which CK1 activity promotes DNA repair had not been investigated. Here, we found that deleting Hhp1 and Hhp2 or inhibiting CK1 catalytic activities in yeast or in human cells activated the DNA damage checkpoint due to persistent double-strand breaks (DSBs). The primary pathways to repair DSBs, homologous recombination and non-homologous end joining, were both less efficient in cells lacking Hhp1 and Hhp2 activity. In order to understand how Hhp1 and Hhp2 promote DSB repair, we identified new substrates using quantitative phosphoproteomics. We confirmed that Arp8, a component of the INO80 chromatin remodeling complex, is a bona fide substrate of Hhp1 and Hhp2 that is important for DSB repair. Our data suggest that Hhp1 and Hhp2 facilitate DSB repair by phosphorylating multiple substrates, including Arp8.
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Affiliation(s)
- Sierra N. Cullati
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Eric Zhang
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Current address: Columbia University Medical Center, New York, NY, USA
| | - Yufan Shan
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Rodrigo X. Guillen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Zachary C. Elmore
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Current address: Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Liping Ren
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Kathleen L. Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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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, MD.) 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] [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.
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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
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46
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Pham TV, Hsiao WY, Wang YT, Yeh SD, Wang SW. Protein S-palmitoylation regulates different stages of meiosis in Schizosaccharomyces pombe. Life Sci Alliance 2023; 6:e202201755. [PMID: 36650056 PMCID: PMC9845910 DOI: 10.26508/lsa.202201755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Posttranslational protein S-palmitoylation regulates the localization and function of its target proteins involved in diverse cellular processes including meiosis. In this study, we demonstrate that S-palmitoylation mediated by Erf2-Erf4 and Akr1 palmitoylacyltransferases is required at multiple meiotic stages in the fission yeast Schizosaccharomyces pombe We find that S-palmitoylation by Erf2-Erf4 is required for Ras1 localization at the cell periphery to enrich at the cell conjugation site for mating pheromone response. In the absence of Erf2 or Erf4, mutant cells are sterile. A role of Akr1 S-palmitoylating the nuclear fusion protein Tht1 to function in karyogamy is identified. We demonstrate that S-palmitoylation stabilizes and localizes Tht1 to ER, interacting with Sey1 ER fusion GTPase for proper meiotic nuclear fusion. In akr1, tht1, or sey1 mutant, meiotic cells, haploid nuclei are unfused with subsequent chromosome segregation defects. Erf2-Erf4 has an additional substrate of the spore coat protein Isp3. In the absence of Erf2, Isp3 is mislocalized from the spore coat. Together, these results highlight the versatility of the cellular processes in which protein S-palmitoylation participates.
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Affiliation(s)
- Thanh-Vy Pham
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Taiwan
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | - Wan-Yi Hsiao
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Taiwan
| | - Yi-Ting Wang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Taiwan
| | - Shu-Dan Yeh
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | - Shao-Win Wang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Taiwan
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47
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Bhattacharjee R, Hall AR, Mangione MC, Igarashi MG, Roberts-Galbraith RH, Chen JS, Vavylonis D, Gould KL. Multiple polarity kinases inhibit phase separation of F-BAR protein Cdc15 and antagonize cytokinetic ring assembly in fission yeast. eLife 2023; 12:83062. [PMID: 36749320 PMCID: PMC9904764 DOI: 10.7554/elife.83062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2023] Open
Abstract
The F-BAR protein Cdc15 is essential for cytokinesis in Schizosaccharomyces pombe and plays a key role in attaching the cytokinetic ring (CR) to the plasma membrane (PM). Cdc15's abilities to bind to the membrane and oligomerize via its F-BAR domain are inhibited by phosphorylation of its intrinsically disordered region (IDR). Multiple cell polarity kinases regulate Cdc15 IDR phosphostate, and of these the DYRK kinase Pom1 phosphorylation sites on Cdc15 have been shown in vivo to prevent CR formation at cell tips. Here, we compared the ability of Pom1 to control Cdc15 phosphostate and cortical localization to that of other Cdc15 kinases: Kin1, Pck1, and Shk1. We identified distinct but overlapping cohorts of Cdc15 phosphorylation sites targeted by each kinase, and the number of sites correlated with each kinases' abilities to influence Cdc15 PM localization. Coarse-grained simulations predicted that cumulative IDR phosphorylation moves the IDRs of a dimer apart and toward the F-BAR tips. Further, simulations indicated that the overall negative charge of phosphorylation masks positively charged amino acids necessary for F-BAR oligomerization and membrane interaction. Finally, simulations suggested that dephosphorylated Cdc15 undergoes phase separation driven by IDR interactions. Indeed, dephosphorylated but not phosphorylated Cdc15 undergoes liquid-liquid phase separation to form droplets in vitro that recruit Cdc15 binding partners. In cells, Cdc15 phosphomutants also formed PM-bound condensates that recruit other CR components. Together, we propose that a threshold of Cdc15 phosphorylation by assorted kinases prevents Cdc15 condensation on the PM and antagonizes CR assembly.
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Affiliation(s)
- Rahul Bhattacharjee
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Aaron R Hall
- Department of Physics, Lehigh UniversityBethlehemUnited States
| | - MariaSanta C Mangione
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Maya G Igarashi
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Rachel H Roberts-Galbraith
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Jun-Song Chen
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Dimitrios Vavylonis
- Department of Physics, Lehigh UniversityBethlehemUnited States,Center for Computational Biology, Flatiron InstituteNew YorkUnited States
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
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48
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Duncan C, Mata J. Translation-complex profiling of fission yeast cells reveals dynamic rearrangements of scanning ribosomal subunits upon nutritional stress. Nucleic Acids Res 2022; 50:13011-13025. [PMID: 36478272 PMCID: PMC9825154 DOI: 10.1093/nar/gkac1140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Control of mRNA translation is key for stress responses. Translation initiation is usually rate-limiting and, in eukaryotes, involves mRNA scanning by the small ribosomal subunit. Despite its importance, many aspects of translation in vivo have not been explored fully, especially at the transcriptome-wide level. A recent method termed translation-complex profiling (TCP-seq) allows transcriptome-wide views of scanning ribosomal subunits. We applied TCP-seq to nutritional stress in the fission yeast Schizosaccharomyces pombe. At initiation sites, we observed multiple complexes resembling those of mammals, and consistent with queuing of scanning subunits. In 5' UTRs, small subunit accumulations were common and may reflect impediments to scanning. A key mediator of stress responses in S. pombe is the Fil1 transcription factor, which is regulated translationally by a poorly-understood mechanism involving upstream Open Reading Frames (uORFs). TCP-seq data of fil1 shows that stress allows scanning subunits to by-pass specific uORFs and reach the fil1 coding sequence. The integration of these observations with reporter assays revealed that fil1 translational control is mediated by a combination of scanning reinitiation-repressive and permissive uORFs, and establishes fil1 as a model for uORF-mediated translational control. Altogether, our transcriptome-wide study reveals general and gene-specific features of translation in a model eukaryote.
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Affiliation(s)
| | - Juan Mata
- To whom correspondence should be addressed. Tel: +44 01223360467;
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49
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Fission Yeast Rho1p-GEFs: From Polarity and Cell Wall Synthesis to Genome Stability. Int J Mol Sci 2022; 23:ijms232213888. [PMID: 36430366 PMCID: PMC9697909 DOI: 10.3390/ijms232213888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Rho1p is a membrane-associated protein that belongs to the Rho family of small GTPases. These proteins coordinate processes such as actin remodelling and polarised secretion to maintain the shape and homeostasis of yeast cells. In response to extracellular stimuli, Rho1p undergoes conformational switching between a guanosine triphosphate (GTP)-bound active state and a guanosine diphosphate (GDP)-bound inactive state. Cycling is improved with guanine nucleotide exchange factor (GEF) activity necessary to activate signalling and GTPase activating protein (GAP) activity required for subsequent signal depletion. This review focuses on fission yeast Rho1p GEFs, Rgf1p, Rgf2p, and Rgf3p that belong to the family of DH-PH domain-containing Dbl-related GEFs. They are multi-domain proteins that detect biological signals that induce or inhibit their catalytic activity over Rho1p. Each of them activates Rho1p in different places and times. Rgf1p acts preferentially during polarised growth. Rgf2p is required for sporulation, and Rgf3p plays an essential function in septum synthesis. In addition, we outline the noncanonical roles of Rho1p-GEFs in genomic instability.
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50
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Teixeira MC, Viana R, Palma M, Oliveira J, Galocha M, Mota MN, Couceiro D, Pereira MG, Antunes M, Costa IV, Pais P, Parada C, Chaouiya C, Sá-Correia I, Monteiro PT. YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis. Nucleic Acids Res 2022; 51:D785-D791. [PMID: 36350610 PMCID: PMC9825512 DOI: 10.1093/nar/gkac1041] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
YEASTRACT+ (http://yeastract-plus.org/) is a tool for the analysis, prediction and modelling of transcription regulatory data at the gene and genomic levels in yeasts. It incorporates three integrated databases: YEASTRACT (http://yeastract-plus.org/yeastract/), PathoYeastract (http://yeastract-plus.org/pathoyeastract/) and NCYeastract (http://yeastract-plus.org/ncyeastract/), focused on Saccharomyces cerevisiae, pathogenic yeasts of the Candida genus, and non-conventional yeasts of biotechnological relevance. In this release, YEASTRACT+ offers upgraded information on transcription regulation for the ten previously incorporated yeast species, while extending the database to another pathogenic yeast, Candida auris. Since the last release of YEASTRACT+ (January 2020), a fourth database has been integrated. CommunityYeastract (http://yeastract-plus.org/community/) offers a platform for the creation, use, and future update of YEASTRACT-like databases for any yeast of the users' choice. CommunityYeastract currently provides information for two Saccharomyces boulardii strains, Rhodotorula toruloides NP11 oleaginous yeast, and Schizosaccharomyces pombe 972h-. In addition, YEASTRACT+ portal currently gathers 304 547 documented regulatory associations between transcription factors (TF) and target genes and 480 DNA binding sites, considering 2771 TFs from 11 yeast species. A new set of tools, currently implemented for S. cerevisiae and C. albicans, is further offered, combining regulatory information with genome-scale metabolic models to provide predictions on the most promising transcription factors to be exploited in cell factory optimisation or to be used as novel drug targets. The expansion of these new tools to the remaining YEASTRACT+ species is ongoing.
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Affiliation(s)
| | - Romeu Viana
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Margarida Palma
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | | | - Mónica Galocha
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Marta Neves Mota
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Diogo Couceiro
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Maria Galhardas Pereira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Miguel Antunes
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Inês V Costa
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Pedro Pais
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,iBB-Institute for BioEngineering and Biosciences, Biological Sciences Research Group, Av. Rovisco Pais, 1049-001 Lisbon, Portugal,Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Carolina Parada
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | | | - Isabel Sá-Correia
- Correspondence may also be addressed to Isabel Sá-Correia. Tel: +351 218417682;
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