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Folco H, Xiao H, Wheeler D, Feng H, Bai Y, Grewal SS. The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity. Nucleic Acids Res 2024; 52:1688-1701. [PMID: 38084929 PMCID: PMC10899784 DOI: 10.1093/nar/gkad1182] [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: 05/11/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 02/29/2024] Open
Abstract
Centromeric chromatin plays a crucial role in kinetochore assembly and chromosome segregation. Centromeres are specified through the loading of the histone H3 variant CENP-A by the conserved chaperone Scm3/HJURP. The N-terminus of Scm3/HJURP interacts with CENP-A, while the C-terminus facilitates centromere localization by interacting with the Mis18 holocomplex via a small domain, called the Mis16-binding domain (Mis16-BD) in fission yeast. Fungal Scm3 proteins contain an additional conserved cysteine-rich domain (CYS) of unknown function. Here, we find that CYS binds zinc in vitro and is essential for the localization and function of fission yeast Scm3. Disrupting CYS by deletion or introduction of point mutations within its zinc-binding motif prevents Scm3 centromere localization and compromises kinetochore integrity. Interestingly, CYS alone can localize to the centromere, albeit weakly, but its targeting is greatly enhanced when combined with Mis16-BD. Expressing a truncated protein containing both Mis16-BD and CYS, but lacking the CENP-A binding domain, causes toxicity and is accompanied by considerable chromosome missegregation and kinetochore loss. These effects can be mitigated by mutating the CYS zinc-binding motif. Collectively, our findings establish the essential role of the cysteine-rich domain in fungal Scm3 proteins and provide valuable insights into the mechanism of Scm3 centromere targeting.
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Affiliation(s)
- H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Rajak N, Dey T, Sharma Y, Bellad V, Rangarajan PN. Unlocking Nature's Toolbox: glutamate-inducible recombinant protein production from the Komagatella phaffii PEPCK promoter. Microb Cell Fact 2024; 23:66. [PMID: 38402195 PMCID: PMC10893637 DOI: 10.1186/s12934-024-02340-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/17/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND Komagataella phaffii (a.k.a. Pichia pastoris) harbors a glutamate utilization pathway in which synthesis of glutamate dehydrogenase 2 and phosphoenolpyruvate carboxykinase (PEPCK) is induced by glutamate. Glutamate-inducible synthesis of these enzymes is regulated by Rtg1p, a cytosolic, basic helix-loop-helix protein. Here, we report food-grade monosodium glutamate (MSG)-inducible recombinant protein production from K. phaffii PEPCK promoter (PPEPCK) using green fluorescent protein (GFP) and receptor binding domain of SARS-CoV-2 virus (RBD) as model proteins. RESULTS PPEPCK-RBD/GFP expression cassette was integrated at two different sites in the genome to improve recombinant protein yield from PPEPCK. The traditional, methanol-inducible alcohol oxidase 1 promoter (PAOX1) was used as the benchmark. Initial studies carried out with MSG as the inducer resulted in low recombinant protein yield. A new strategy employing MSG/ethanol mixed feeding improved biomass generation as well as recombinant protein yield. Cell density of 100-120 A600 units/ml was achieved after 72 h of induction in shake flask cultivations, resulting in recombinant protein yield from PPEPCK that is comparable or even higher than that from PAOX1. CONCLUSIONS We have designed an induction medium for recombinant protein production from K. phaffii PPEPCK in shake flask cultivations. It consists of 1.0% yeast extract, 2.0% peptone, 0.17% yeast nitrogen base with ammonium sulfate, 100 mM potassium phosphate (pH 6.0), 0.4 mg/L biotin, 2.0% MSG, and 2% ethanol. Substitution of ammonium sulphate with 0.5% urea is optional. Carbon source was replenished every 24 h during 72 h induction period. Under these conditions, GFP and RBD yields from PPEPCK equaled and even surpassed those from PAOX1. Compared to the traditional methanol-inducible expression system, the inducers of glutamate-inducible expression system are non-toxic and their metabolism does not generate toxic metabolites such as formaldehyde and hydrogen peroxide. This study sets the stage for MSG-inducible, industrial scale recombinant protein production from K. phaffii PPEPCK in bioreactors.
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Affiliation(s)
- Neetu Rajak
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Trishna Dey
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Yash Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Vedanth Bellad
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Pundi N Rangarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
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3
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Sajeevan A, Pandian R, Mishra SK. Vectors with a flexible multiple cloning site and modular epitope tags for gene expression studies in Schizosaccharomyces pombe. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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4
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Dey T, Rangarajan PN. Posttranscriptional regulation of glutamate dehydrogenase 2 and phosphoenolpyruvate carboxykinase in Komagataella phaffii. Yeast 2022; 39:337-347. [PMID: 35384037 DOI: 10.1002/yea.3704] [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: 12/08/2021] [Revised: 02/25/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
The yeast Komagataella phaffii (a.k.a. Pichia pastoris) harbours a unique glutamate utilization pathway in which the cytosolic enzymes glutamate dehydrogenase 2 (GDH2), aspartate aminotransferase 2 (AAT2) and phosphoenolpyruvate carboxykinase (PEPCK) catalyze the sequential conversion of glutamate to α-ketoglutarate, oxaloacetate and phosphoenolpyruvate respectively. GDH2 and PEPCK are essential for glutamate catabolism. Their synthesis is induced by autophagy during carbon starvation and are essential for cell survival. Here, we demonstrate that GDH2 and PEPCK reciprocally regulate each other's protein levels during glutamate catabolism such that GDH2 is downregulated in Δpepck and PEPCK is downregulated in Δgdh2. We further demonstrate that sequential conversion of glutamate to α-ketoglutarate and oxaloacetate by GDH2 and AAT2, respectively, is essential for PEPCK synthesis in cells metabolizing glutamate. Our studies indicate that translation of GDH2 mRNA is induced by glutamate while oxaloacetate derived from glutamate is likely to be the inducer of PEPCK mRNA translation during glutamate catabolism. Thus, GDH2- and PEPCK-catalyzed reactions are essential for ATP generation and gluconeogenesis respectively during carbon starvation and glutamate catabolism in K. phaffii. We conclude that K. phaffii harbours a unique translational regulatory circuit in which substrates of GDH2 and PEPCK act as inducers of their synthesis, a phenomenon not reported in any yeast species.
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Affiliation(s)
- Trishna Dey
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Pundi N Rangarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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5
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Tocchini-Valentini GD, Tocchini-Valentini GP. Archaeal tRNA-Splicing Endonuclease as an Effector for RNA Recombination and Novel Trans-Splicing Pathways in Eukaryotes. J Fungi (Basel) 2021; 7:jof7121069. [PMID: 34947051 PMCID: PMC8707768 DOI: 10.3390/jof7121069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Abstract
We have characterized a homodimeric tRNA endonuclease from the euryarchaeota Ferroplasma acidarmanus (FERAC), a facultative anaerobe which can grow at temperatures ranging from 35 to 42 °C. This enzyme, contrary to the eukaryal tRNA endonucleases and the homotetrameric Methanocaldococcus jannaschii (METJA) homologs, is able to cleave minimal BHB (bulge–helix–bulge) substrates at 30 °C. The expression of this enzyme in Schizosaccharomyces pombe (SCHPO) enables the use of its properties as effectors by inserting BHB motif introns into hairpin loops normally seen in mRNA transcripts. In addition, the FERAC endonuclease can create proteins with new functionalities through the recombination of protein domains.
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Affiliation(s)
- Giuseppe D. Tocchini-Valentini
- Istituto di Biochimica e Biologia Cellulare, Campus Internazionale “A. Buzzati-Traverso”, Dipartimento Scienze Biomediche, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy;
- Dipartimento Scienze Biomediche, European Mouse Mutant Archive (EMMA), INFRAFRONTIER-IMPC, Monterotondo Mouse Clinic, Campus Internazionale “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy
- Correspondence:
| | - Glauco P. Tocchini-Valentini
- Istituto di Biochimica e Biologia Cellulare, Campus Internazionale “A. Buzzati-Traverso”, Dipartimento Scienze Biomediche, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy;
- Dipartimento Scienze Biomediche, European Mouse Mutant Archive (EMMA), INFRAFRONTIER-IMPC, Monterotondo Mouse Clinic, Campus Internazionale “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy
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6
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Veepaschit J, Viswanathan A, Bordonné R, Grimm C, Fischer U. Identification and structural analysis of the Schizosaccharomyces pombe SMN complex. Nucleic Acids Res 2021; 49:7207-7223. [PMID: 33754639 PMCID: PMC8287938 DOI: 10.1093/nar/gkab158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/11/2021] [Accepted: 02/26/2021] [Indexed: 01/20/2023] Open
Abstract
The macromolecular SMN complex facilitates the formation of Sm-class ribonucleoproteins involved in mRNA processing (UsnRNPs). While biochemical studies have revealed key activities of the SMN complex, its structural investigation is lagging behind. Here we report on the identification and structural determination of the SMN complex from the lower eukaryote Schizosaccharomyces pombe, consisting of SMN, Gemin2, 6, 7, 8 and Sm proteins. The core of the SMN complex is formed by several copies of SMN tethered through its C-terminal alpha-helices arranged with alternating polarity. This creates a central platform onto which Gemin8 binds and recruits Gemins 6 and 7. The N-terminal parts of the SMN molecules extrude via flexible linkers from the core and enable binding of Gemin2 and Sm proteins. Our data identify the SMN complex as a multivalent hub where Sm proteins are collected in its periphery to allow their joining with UsnRNA.
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Affiliation(s)
- Jyotishman Veepaschit
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Aravindan Viswanathan
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Rémy Bordonné
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier 34293, France
| | - Clemens Grimm
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Utz Fischer
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg 97074, Germany
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Masuda K, Renard-Guillet C, Shirahige K, Sutani T. Bioinformatical dissection of fission yeast DNA replication origins. Open Biol 2020; 10:200052. [PMID: 32692956 PMCID: PMC7574548 DOI: 10.1098/rsob.200052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Replication origins in eukaryotes form a base for assembly of the pre-replication complex (pre-RC), thereby serving as an initiation site of DNA replication. Characteristics of replication origin vary among species. In fission yeast Schizosaccharomyces pombe, DNA of high AT content is a distinct feature of replication origins; however, it remains to be understood what the general molecular architecture of fission yeast origin is. Here, we performed ChIP-seq mapping of Orc4 and Mcm2, two representative components of the pre-RC, and described the characteristics of their binding sites. The analysis revealed that fission yeast efficient origins are associated with two similar but independent features: a ≥15 bp-long motif with stretches of As and an AT-rich region of a few hundred bp. The A-rich motif was correlated with chromosomal binding of Orc, a DNA-binding component in the pre-RC, whereas the AT-rich region was associated with efficient binding of the DNA replicative helicase Mcm. These two features, in combination with the third feature, a transcription-poor region of approximately 1 kb, enabled to distinguish efficient replication origins from the rest of chromosome arms with high accuracy. This study, hence, provides a model that describes how multiple functional elements specify DNA replication origins in fission yeast genome.
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Affiliation(s)
- Koji Masuda
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Claire Renard-Guillet
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takashi Sutani
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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8
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Byrne DP, Shrestha S, Galler M, Cao M, Daly LA, Campbell AE, Eyers CE, Veal EA, Kannan N, Eyers PA. Aurora A regulation by reversible cysteine oxidation reveals evolutionarily conserved redox control of Ser/Thr protein kinase activity. Sci Signal 2020; 13:eaax2713. [PMID: 32636306 DOI: 10.1126/scisignal.aax2713] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Reactive oxygen species (ROS) are physiological mediators of cellular signaling and play potentially damaging roles in human diseases. In this study, we found that the catalytic activity of the Ser/Thr kinase Aurora A was inhibited by the oxidation of a conserved cysteine residue (Cys290) that lies adjacent to Thr288, a critical phosphorylation site in the activation segment. Cys is present at the equivalent position in ~100 human Ser/Thr kinases, a residue that we found was important not only for the activity of human Aurora A but also for that of fission yeast MAPK-activated kinase (Srk1) and PKA (Pka1). Moreover, the presence of this conserved Cys predicted biochemical redox sensitivity among a cohort of human CAMK, AGC, and AGC-like kinases. Thus, we predict that redox modulation of the conserved Cys290 of Aurora A may be an underappreciated regulatory mechanism that is widespread in eukaryotic Ser/Thr kinases. Given the key biological roles of these enzymes, these findings have implications for understanding physiological and pathological responses to ROS and highlight the importance of protein kinase regulation through multivalent modification of the activation segment.
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Affiliation(s)
- Dominic P Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Martin Galler
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Min Cao
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Leonard A Daly
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Amy E Campbell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Elizabeth A Veal
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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9
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Optogenetics reveals Cdc42 local activation by scaffold-mediated positive feedback and Ras GTPase. PLoS Biol 2020; 18:e3000600. [PMID: 31978045 PMCID: PMC7002011 DOI: 10.1371/journal.pbio.3000600] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 02/05/2020] [Accepted: 01/02/2020] [Indexed: 12/31/2022] Open
Abstract
Local activity of the small GTPase Cdc42 is critical for cell polarization. Whereas scaffold-mediated positive feedback was proposed to break symmetry of budding yeast cells and produce a single zone of Cdc42 activity, the existence of similar regulation has not been probed in other organisms. Here, we address this problem using rod-shaped cells of fission yeast Schizosaccharomyces pombe, which exhibit zones of active Cdc42-GTP at both cell poles. We implemented the CRY2-CIB1 optogenetic system for acute light-dependent protein recruitment to the plasma membrane, which allowed to directly demonstrate positive feedback. Indeed, optogenetic recruitment of constitutively active Cdc42 leads to co-recruitment of the guanine nucleotide exchange factor (GEF) Scd1 and endogenous Cdc42, in a manner dependent on the scaffold protein Scd2. We show that Scd2 function is dispensable when the positive feedback operates through an engineered interaction between the GEF and a Cdc42 effector, the p21-activated kinase 1 (Pak1). Remarkably, this rewired positive feedback confers viability and allows cells to form 2 zones of active Cdc42 even when otherwise essential Cdc42 activators are lacking. These cells further revealed that the small GTPase Ras1 plays a role in both localizing the GEF Scd1 and promoting its activity, which potentiates the positive feedback. We conclude that scaffold-mediated positive feedback, gated by Ras activity, confers robust polarization for rod-shape formation. The small GTPase Cdc42 is a key regulator of cell polarization. This study uses optogenetic and genetic strategies to show that Cdc42 is under positive feedback regulation potentiated by Ras GTPase activity.
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10
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Vještica A, Marek M, Nkosi PJ, Merlini L, Liu G, Bérard M, Billault-Chaumartin I, Martin SG. A toolbox of stable integration vectors in the fission yeast Schizosaccharomyces pombe. J Cell Sci 2020; 133:jcs.240754. [PMID: 31801797 DOI: 10.1242/jcs.240754] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 11/24/2019] [Indexed: 12/14/2022] Open
Abstract
Schizosaccharomyces pombe is a widely used model organism to study many aspects of eukaryotic cell physiology. Its popularity as an experimental system partially stems from the ease of genetic manipulations, where the innate homology-targeted repair is exploited to precisely edit the genome. While vectors to incorporate exogenous sequences into the chromosomes are available, most are poorly characterized. Here, we show that commonly used fission yeast vectors, which upon integration produce repetitive genomic regions, give rise to unstable genomic loci. We overcome this problem by designing a new series of stable integration vectors (SIVs) that target four different prototrophy genes. SIVs produce non-repetitive, stable genomic loci and integrate predominantly as single copy. Additionally, we develop a set of complementary auxotrophic alleles that preclude false-positive integration events. We expand the vector series to include antibiotic resistance markers, promoters, fluorescent tags and terminators, and build a highly modular toolbox to introduce heterologous sequences. Finally, as proof of concept, we generate a large set of ready-to-use, fluorescent probes to mark organelles and cellular processes with a wide range of applications in fission yeast research.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Aleksandar Vještica
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Magdalena Marek
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Pedro Junior Nkosi
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Laura Merlini
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Gaowen Liu
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Melvin Bérard
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Ingrid Billault-Chaumartin
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Sophie G Martin
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
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11
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Tong P, Pidoux AL, Toda NRT, Ard R, Berger H, Shukla M, Torres-Garcia J, Müller CA, Nieduszynski CA, Allshire RC. Interspecies conservation of organisation and function between nonhomologous regional centromeres. Nat Commun 2019; 10:2343. [PMID: 31138803 PMCID: PMC6538654 DOI: 10.1038/s41467-019-09824-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 03/27/2019] [Indexed: 01/31/2023] Open
Abstract
Despite the conserved essential function of centromeres, centromeric DNA itself is not conserved. The histone-H3 variant, CENP-A, is the epigenetic mark that specifies centromere identity. Paradoxically, CENP-A normally assembles on particular sequences at specific genomic locations. To gain insight into the specification of complex centromeres, here we take an evolutionary approach, fully assembling genomes and centromeres of related fission yeasts. Centromere domain organization, but not sequence, is conserved between Schizosaccharomyces pombe, S. octosporus and S. cryophilus with a central CENP-ACnp1 domain flanked by heterochromatic outer-repeat regions. Conserved syntenic clusters of tRNA genes and 5S rRNA genes occur across the centromeres of S. octosporus and S. cryophilus, suggesting conserved function. Interestingly, nonhomologous centromere central-core sequences from S. octosporus and S. cryophilus are recognized in S. pombe, resulting in cross-species establishment of CENP-ACnp1 chromatin and functional kinetochores. Therefore, despite the lack of sequence conservation, Schizosaccharomyces centromere DNA possesses intrinsic conserved properties that promote assembly of CENP-A chromatin.
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Affiliation(s)
- Pin Tong
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK
| | - Alison L. Pidoux
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK
| | - Nicholas R. T. Toda
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK ,0000 0001 2203 0006grid.464101.6Present Address: UPMC CNRS, Roscoff Marine Station, Place Georges Teissier, 29680 Roscoff, France
| | - Ryan Ard
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK ,0000 0001 0674 042Xgrid.5254.6Present Address: Copenhagen Plant Science Centre, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Harald Berger
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK ,0000 0001 2298 5320grid.5173.0Present Address: Symbiocyte, Universität für Bodenkultur Wien, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
| | - Manu Shukla
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK
| | - Jesus Torres-Garcia
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK
| | - Carolin A. Müller
- 0000 0004 1936 8948grid.4991.5Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE UK
| | - Conrad A. Nieduszynski
- 0000 0004 1936 8948grid.4991.5Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE UK
| | - Robin C. Allshire
- 0000 0004 1936 7988grid.4305.2Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3BF UK
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12
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Dey T, Krishna Rao K, Khatun J, Rangarajan PN. The nuclear transcription factor Rtg1p functions as a cytosolic, post-transcriptional regulator in the methylotrophic yeast Pichia pastoris. J Biol Chem 2018; 293:16647-16660. [PMID: 30185617 DOI: 10.1074/jbc.ra118.004486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 08/28/2018] [Indexed: 01/26/2023] Open
Abstract
Rtg1p and Rtg3p are two basic helix-loop-helix, retrograde transcription factors in the budding yeast Saccharomyces cerevisiae Both factors heterodimerize to activate the transcription of nuclear genes in response to mitochondrial dysfunction and glutamate auxotrophy, but are not well characterized in other yeasts. Here, we demonstrate that the Rtg1p/Rtg3p-mediated retrograde signaling pathway is absent in the methylotrophic yeast Pichia pastoris We observed that P. pastoris Rtg1p (PpRtg1p) heterodimerizes with S. cerevisiae Rtg3p and functions as a nuclear, retrograde transcription factor in S. cerevisiae, but not in P. pastoris. We noted that P. pastoris Rtg3p lacks a functional leucine zipper and interacts with neither S. cerevisiae Rtg1p (ScRtg1p) nor PpRtg1p. In the absence of an interaction with Rtg3p, PpRtg1p has apparently acquired a novel function as a cytosolic regulator of multiple P. pastoris metabolic pathways, including biosynthesis of glutamate dehydrogenase 2 and phosphoenolpyruvate carboxykinase required for the utilization of glutamate as the sole carbon source. PpRtg1p also had an essential role in methanol metabolism and regulated alcohol oxidase synthesis and was required for the metabolism of ethanol, acetate, and oleic acid, but not of glucose and glycerol. Although PpRtg1p could functionally complement ScRtg1p, ScRtg1p could not complement PpRtg1p, indicating that ScRtg1p is not a functional PpRtg1p homolog. Thus, PpRtg1p functions as a nuclear, retrograde transcription factor in S. cerevisiae and as a cytosolic, post-transcriptional regulator in P. pastoris We conclude that PpRtg1p is a key component of a signaling pathway that regulates multiple metabolic processes in P. pastoris.
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Affiliation(s)
- Trishna Dey
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 60012, India
| | - Kamisetty Krishna Rao
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 60012, India
| | - Jesminara Khatun
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 60012, India
| | - Pundi N Rangarajan
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 60012, India
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13
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Genetic interactions between the chromosome axis-associated protein Hop1 and homologous recombination determinants in Schizosaccharomyces pombe. Curr Genet 2018; 64:1089-1104. [PMID: 29550859 PMCID: PMC6153652 DOI: 10.1007/s00294-018-0827-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 11/28/2022]
Abstract
Hop1 is a component of the meiosis-specific chromosome axis and belongs to the evolutionarily conserved family of HORMA domain proteins. Hop1 and its orthologs in higher eukaryotes are a major factor in promoting double-strand DNA break formation and inter-homolog recombination. In budding yeast and mammals, they are also involved in a meiotic checkpoint kinase cascade monitoring the completion of double-strand DNA break repair. We used the fission yeast, Schizosaccharomyces pombe, which lacks a canonical synaptonemal complex to test whether Hop1 has a role beyond supporting the generation of double-strand DNA breaks and facilitating inter-homolog recombination events. We determined how mutants of homologous recombination factors genetically interact with hop1, studied the role(s) of the HORMA domain of Hop1, and characterized a bio-informatically predicted interactor of Hop1, Aho1 (SPAC688.03c). Our observations indicate that in fission yeast, Hop1 does require its HORMA domain to support wild-type levels of meiotic recombination and localization to meiotic chromatin. Furthermore, we show that hop1∆ only weakly interacts genetically with mutants of homologous recombination factors, and in fission yeast likely has no major role beyond break formation and promoting inter-homolog events. We speculate that after the evolutionary loss of the synaptonemal complex, Hop1 likely has become less important for modulating recombination outcome during meiosis in fission yeast, and that this led to a concurrent rewiring of genetic pathways controlling meiotic recombination.
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14
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Kiriya K, Tsuyuzaki H, Sato M. Module-based systematic construction of plasmids for episomal gene expression in fission yeast. Gene 2017; 637:14-24. [PMID: 28935259 DOI: 10.1016/j.gene.2017.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 12/20/2022]
Abstract
The fission yeast Schizosaccharomyces pombe is a powerful model organism for cell biology and molecular biology, as genetic manipulation is easily achieved. Introduction of exogenous genes cloned in episomal plasmids into yeast cells can be done through well-established transformation methods. For expression of genes in S. pombe cells, the multi-copy plasmid pREP1 and its derivatives, including pREP41 and pREP81, have been widely used as vectors. Although recent advancement of technology brought a number of useful genetic elements such as new promoters, selection marker genes and fluorescent protein tags, introduction of those elements into conventional pREP1 requires a large commitment of both time and effort because cloning procedures need to be repeated until the final products are constructed. Here, we introduce materials and methods to construct many pREP1-type plasmids easily and systematically using the Golden Gate shuffling method, which enables one-step ligation of many DNA fragments into a plasmid. These materials and methods support creation of expression plasmids employing a variety of novel genetic elements, which will further facilitate genetic studies using S. pombe.
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Affiliation(s)
- Keita Kiriya
- Laboratory for Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Japan
| | - Hayato Tsuyuzaki
- Laboratory for Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Japan; Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), AIST Tokyo Waterfront Main Building, 2-3-26 Aomi, Tokyo 135-0064, Japan
| | - Masamitsu Sato
- Laboratory for Cytoskeletal Logistics, Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Japan; Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan.
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15
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Ptushkina M, Poolman T, Iqbal M, Ashe M, Petersen J, Woodburn J, Rattray M, Whetton A, Ray D. A non-transcriptional role for the glucocorticoid receptor in mediating the cell stress response. Sci Rep 2017; 7:12101. [PMID: 28935859 PMCID: PMC5608759 DOI: 10.1038/s41598-017-09722-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/17/2017] [Indexed: 11/25/2022] Open
Abstract
The glucocorticoid receptor (GR) is essential for the stress response in mammals. We investigated potential non-transcriptional roles of GR in cellular stress response using fission yeast as a model.We surprisingly discovered marked heat stress resistance in yeast ectopically expressing human GR, which required expression of both the N-terminal transactivation domain, and the C-terminal ligand binding domain, but not the DNA-binding domain of the GR. This effect was not affected by GR ligand exposure, and occurred without significant GR nuclear accumulation. Mechanistically, the GR survival effect required Hsp104, and, indeed, GR expression increased Hsp104 expression. Proteomic analysis revealed GR binding to translasome components, including eIF3, a known partner for Sty1, a pattern of protein interaction which we confirmed using yeast two-hybrid studies.Taken together, we find evidence for a novel pathway conferring stress resistance in yeast that can be activated by the human GR, acting by protein-protein mechanisms in the cytoplasm. This suggests that in organisms where GR is natively expressed, GR likely contributes to stress responses through non-transcriptional mechanisms in addition to its well-established transcriptional responses.
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Affiliation(s)
- Marina Ptushkina
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK.
- Manchester Academic Health Sciences Centre, Manchester, M13 9PT, UK.
| | - Toryn Poolman
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
- Manchester Academic Health Sciences Centre, Manchester, M13 9PT, UK
| | - Mudassar Iqbal
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
- Manchester Academic Health Sciences Centre, Manchester, M13 9PT, UK
| | - Mark Ashe
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
- Manchester Academic Health Sciences Centre, Manchester, M13 9PT, UK
| | - Janni Petersen
- School of Health Science, Flinders University, South Australia Sturt Road 5042, GPO Box 2100, Adelaide, Australia
| | - Joanna Woodburn
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
- Manchester Academic Health Sciences Centre, Manchester, M13 9PT, UK
| | - Magnus Rattray
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK
- Manchester Academic Health Sciences Centre, Manchester, M13 9PT, UK
| | - Anthony Whetton
- Division of Cancer, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
- Manchester Academic Health Sciences Centre, Manchester, M13 9PT, UK
| | - David Ray
- School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, M13 9PT, UK.
- Manchester Academic Health Sciences Centre, Manchester, M13 9PT, UK.
- Department of Endocrinology, Manchester Royal Infirmary, Manchester, M13 9WL, UK.
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16
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Sahu U, Rajendra VKH, Kapnoor SS, Bhagavat R, Chandra N, Rangarajan PN. Methionine synthase is localized to the nucleus in Pichia pastoris and Candida albicans and to the cytoplasm in Saccharomyces cerevisiae. J Biol Chem 2017; 292:14730-14746. [PMID: 28701466 DOI: 10.1074/jbc.m117.783019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/10/2017] [Indexed: 11/06/2022] Open
Abstract
Methionine synthase (MS) catalyzes methylation of homocysteine, the last step in the biosynthesis of methionine, which is essential for the regeneration of tetrahydrofolate and biosynthesis of S-adenosylmethionine. Here, we report that MS is localized to the nucleus of Pichia pastoris and Candida albicans but is cytoplasmic in Saccharomyces cerevisiae The P. pastoris strain carrying a deletion of the MET6 gene encoding MS (Ppmet6) exhibits methionine as well as adenine auxotrophy indicating that MS is required for methionine as well as adenine biosynthesis. Nuclear localization of P. pastoris MS (PpMS) was abrogated by the deletion of 107 C-terminal amino acids or the R742A mutation. In silico analysis of the PpMS structure indicated that PpMS may exist in a dimer-like configuration in which Arg-742 of a monomer forms a salt bridge with Asp-113 of another monomer. Biochemical studies indicate that R742A as well as D113R mutations abrogate nuclear localization of PpMS and its ability to reverse methionine auxotrophy of Ppmet6 Thus, association of two PpMS monomers through the interaction of Arg-742 and Asp-113 is essential for catalytic activity and nuclear localization. When PpMS is targeted to the cytoplasm employing a heterologous nuclear export signal, it is expressed at very low levels and is unable to reverse methionine and adenine auxotrophy of Ppmet6 Thus, nuclear localization is essential for the stability and function of MS in P. pastoris. We conclude that nuclear localization of MS is a unique feature of respiratory yeasts such as P. pastoris and C. albicans, and it may have novel moonlighting functions in the nucleus.
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Affiliation(s)
- Umakant Sahu
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Vinod K H Rajendra
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Shankar S Kapnoor
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Raghu Bhagavat
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Pundi N Rangarajan
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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17
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Matsuo Y, Kawamukai M. cAMP-dependent protein kinase involves calcium tolerance through the regulation of Prz1 in Schizosaccharomyces pombe. Biosci Biotechnol Biochem 2017; 81:231-241. [DOI: 10.1080/09168451.2016.1246171] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
The cAMP-dependent protein kinase Pka1 is known as a regulator of glycogenesis, meiosis, and stress responses in Schizosaccharomyces pombe. We demonstrated that Pka1 is responsible for calcium tolerance. Loss of functional components of the PKA pathway such as Git3, Gpa2, Cyr1, and Pka1 yields a CaCl2-sensitive phenotype, while loss of Cgs1, a regulatory subunit of PKA, results in CaCl2 tolerance. Cytoplasmic distribution of Cgs1 and Pka1 is increased by the addition of CaCl2, suggesting that CaCl2 induces dissociation of Cgs1 and Pka1. The expression of Prz1, a transcriptional regulator in calcium homeostasis, is elevated in a pka1∆ strain and in a wild type strain under glucose-limited conditions. Accordingly, higher expression of Prz1 in the wild type strain results in a CaCl2-sensitive phenotype. These findings suggest that Pka1 is essential for tolerance to exogenous CaCl2, probably because the expression level of Prz1 needs to be properly regulated by Pka1.
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Affiliation(s)
- Yasuhiro Matsuo
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Makoto Kawamukai
- Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
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18
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Chen YH, Wang GY, Hao HC, Chao CJ, Wang Y, Jin QW. Facile manipulation of protein localization in fission yeast through binding of GFP-binding protein to GFP. J Cell Sci 2017; 130:1003-1015. [PMID: 28082423 DOI: 10.1242/jcs.198457] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/05/2017] [Indexed: 12/20/2022] Open
Abstract
GFP-binding protein (or GBP) has been recently developed in various systems and organisms as an efficient tool to purify GFP-fusion proteins. Due to the high affinity between GBP and GFP or GFP variants, this GBP-based approach is also ideally suited to alter the localization of functional proteins in live cells. In order to facilitate the wide use of the GBP-targeting approach in the fission yeast Schizosaccharomyces pombe, we developed a set of pFA6a-, pJK148- and pUC119-based vectors containing GBP- or GBP-mCherry-coding sequences and variants of inducible nmt1 or constitutive adh1 promoters that result in different levels of expression. The GBP or GBP-mCherry fragments can serve as cassettes for N- or C-terminal genomic tagging of genes of interest. We illustrated the application of these vectors in the construction of yeast strains with Dma1 or Cdc7 tagged with GBP-mCherry and efficient targeting of Dma1- or Cdc7-GBP-mCherry to the spindle pole body by Sid4-GFP. This series of vectors should help to facilitate the application of the GBP-targeting approach in manipulating protein localization and the analysis of gene function in fission yeast, at the level of single genes, as well as at a systematic scale.
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Affiliation(s)
- Ying-Hui Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Gao-Yuan Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Hao-Chao Hao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Chun-Jiang Chao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yamei Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Quan-Wen Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
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19
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Liu J, Guan T, Zheng P, Chen L, Yang Y, Huai B, Li D, Chang Q, Huang L, Kang Z. An extracellular Zn-only superoxide dismutase from Puccinia striiformis confers enhanced resistance to host-derived oxidative stress. Environ Microbiol 2016; 18:4118-4135. [PMID: 27399209 DOI: 10.1111/1462-2920.13451] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/05/2016] [Indexed: 11/30/2022]
Abstract
Accumulation of reactive oxygen species (ROS) following plant-pathogen interactions can trigger plant defence responses and directly damage pathogens. Thus, it is essential for pathogens to scavenge host-derived ROS to establish a parasitic relationship. However, the mechanisms protecting pathogens from host-derived oxidative stress remain unclear. In this study, a superoxide dismutase (SOD) gene, PsSOD1, was cloned from a wheat-Puccinia striiformis f. sp. tritici (Pst) interaction cDNA library. Transcripts of PsSOD1 were up-regulated in the early infection stage. Heterologous mutant complementation and biochemical characterization revealed that PsSOD1 encoded a Zn-only SOD. The predicted signal peptide was functional in an invertase-mutated yeast strain. Furthermore, immunoblot analysis of apoplastic proteins in Pst-infected wheat leaves and bimolecular fluorescence complementation suggested that PsSOD1 is a secreted protein that potentially forms a dimer during Pst infection. Overexpression of PsSOD1 enhanced Schizosaccharomyces pombe resistance to exogenous superoxide. Transient expression of PsSOD1 in Nicotiana benthamiana suppressed Bax-induced cell death. Knockdown of PsSOD1 using a host-induced gene silencing (HIGS) system reduced the virulence of Pst, which was associated with ROS accumulation in HIGS plants. These results suggest that PsSOD1 is an important pathogenicity factor that is secreted into the host-pathogen interface to contribute to Pst infection by scavenging host-derived ROS.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People's Republic of China
| | - Tao Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People's Republic of China
| | - Peijing Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People's Republic of China
| | - Liyang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People's Republic of China
| | - Yang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People's Republic of China
| | - Baoyu Huai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People's Republic of China
| | - Dan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People's Republic of China
| | - Qing Chang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, People's Republic of China
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20
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Landes N, Gasser B, Vorauer-Uhl K, Lhota G, Mattanovich D, Maurer M. The vitamin-sensitive promoter PTHI11enables pre-defined autonomous induction of recombinant protein production inPichia pastoris. Biotechnol Bioeng 2016; 113:2633-2643. [DOI: 10.1002/bit.26041] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Nils Landes
- Department of Biotechnology; BOKU-University of Natural Resources and Life Sciences Vienna; Muthgasse 18 Vienna 1190 Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Vienna Austria
| | - Brigitte Gasser
- Department of Biotechnology; BOKU-University of Natural Resources and Life Sciences Vienna; Muthgasse 18 Vienna 1190 Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Vienna Austria
| | - Karola Vorauer-Uhl
- Department of Biotechnology; BOKU-University of Natural Resources and Life Sciences Vienna; Muthgasse 18 Vienna 1190 Austria
| | - Gabriele Lhota
- Department of Biotechnology; BOKU-University of Natural Resources and Life Sciences Vienna; Muthgasse 18 Vienna 1190 Austria
| | - Diethard Mattanovich
- Department of Biotechnology; BOKU-University of Natural Resources and Life Sciences Vienna; Muthgasse 18 Vienna 1190 Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Vienna Austria
| | - Michael Maurer
- Austrian Centre of Industrial Biotechnology (ACIB GmbH); Vienna Austria
- School of Bioengineering; University of Applied Sciences; FH Campus Vienna Austria
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21
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Borg RM, Fenech Salerno B, Vassallo N, Bordonne R, Cauchi RJ. Disruption of snRNP biogenesis factors Tgs1 and pICln induces phenotypes that mirror aspects of SMN-Gemins complex perturbation in Drosophila, providing new insights into spinal muscular atrophy. Neurobiol Dis 2016; 94:245-58. [PMID: 27388936 DOI: 10.1016/j.nbd.2016.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 06/20/2016] [Accepted: 06/27/2016] [Indexed: 01/27/2023] Open
Abstract
The neuromuscular disorder, spinal muscular atrophy (SMA), results from insufficient levels of the survival motor neuron (SMN) protein. Together with Gemins 2-8 and Unrip, SMN forms the large macromolecular SMN-Gemins complex, which is known to be indispensable for chaperoning the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). It remains unclear whether disruption of this function is responsible for the selective neuromuscular degeneration in SMA. In the present study, we first show that loss of wmd, the Drosophila Unrip orthologue, has a negative impact on the motor system. However, due to lack of a functional relationship between wmd/Unrip and Gemin3, it is likely that Unrip joined the SMN-Gemins complex only recently in evolution. Second, we uncover that disruption of either Tgs1 or pICln, two cardinal players in snRNP biogenesis, results in viability and motor phenotypes that closely resemble those previously uncovered on loss of the constituent members of the SMN-Gemins complex. Interestingly, overexpression of both factors leads to motor dysfunction in Drosophila, a situation analogous to that of Gemin2. Toxicity is conserved in the yeast S. pombe where pICln overexpression induces a surplus of Sm proteins in the cytoplasm, indicating that a block in snRNP biogenesis is partly responsible for this phenotype. Importantly, we show a strong functional relationship and a physical interaction between Gemin3 and either Tgs1 or pICln. We propose that snRNP biogenesis is the pathway connecting the SMN-Gemins complex to a functional neuromuscular system, and its disturbance most likely leads to the motor dysfunction that is typical in SMA.
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Affiliation(s)
- Rebecca M Borg
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta; Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Université Montpellier 1 and 2, Montpellier, France
| | - Benji Fenech Salerno
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Neville Vassallo
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
| | - Rémy Bordonne
- Institut de Génétique Moléculaire de Montpellier, CNRS-UMR5535, Université Montpellier 1 and 2, Montpellier, France
| | - Ruben J Cauchi
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta.
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22
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Abstract
The field of fluorescent proteins (FPs) is constantly developing. The use of FPs changed the field of life sciences completely, starting a new era of direct observation and quantification of cellular processes. The broad spectrum of FPs (see Fig. 1) with a wide range of characteristics allows their use in many different experiments. This review discusses the use of FPs for imaging in budding yeast (Saccharomyces cerevisiae) and fission yeast Schizosaccharomyces pombe). The information included in this review is relevant for both species unless stated otherwise.
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Affiliation(s)
- Maja Bialecka-Fornal
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94158, USA
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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23
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Ivan B, Lajdova D, Abelovska L, Balazova M, Nosek J, Tomaska L. Mdm31 protein mediates sensitivity to potassium ionophores but does not regulate mitochondrial morphology or phospholipid trafficking inSchizosaccharomyces pombe. Yeast 2015; 32:345-54. [DOI: 10.1002/yea.3062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 11/20/2014] [Accepted: 11/28/2014] [Indexed: 01/31/2023] Open
Affiliation(s)
- Branislav Ivan
- Departments of Biochemistry and Genetics; Comenius University, Faculty of Natural Sciences; Bratislava Slovakia
| | - Dana Lajdova
- Departments of Biochemistry and Genetics; Comenius University, Faculty of Natural Sciences; Bratislava Slovakia
| | - Lenka Abelovska
- Departments of Biochemistry and Genetics; Comenius University, Faculty of Natural Sciences; Bratislava Slovakia
| | - Maria Balazova
- Institute of Animal Biochemistry and Genetics; Slovak Academy of Sciences; Ivanka pri Dunaji Slovakia
| | - Jozef Nosek
- Departments of Biochemistry and Genetics; Comenius University, Faculty of Natural Sciences; Bratislava Slovakia
| | - Lubomir Tomaska
- Departments of Biochemistry and Genetics; Comenius University, Faculty of Natural Sciences; Bratislava Slovakia
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24
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Převorovský M. pREPORT: a multi-readout transcription reporter vector for fission yeast. Yeast 2014; 32:327-34. [PMID: 25395321 DOI: 10.1002/yea.3055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/08/2014] [Accepted: 11/10/2014] [Indexed: 11/08/2022] Open
Abstract
Transcription factors are prominent regulators of gene expression that execute responses to various intracellular and extracellular stimuli. Recombinant transcription reporter systems can be conveniently used to study the DNA binding preferences and regulatory activity of a transcription factor under a range of conditions. Several reporter genes have been used to study transcription regulation in the fission yeast Schizosaccharomyces pombe. Each of these reporters has distinct advantages, such as high sensitivity or ease of use, and limitations, such as prohibitive costs or use of hazardous substances. To combine the strengths and mitigate the weaknesses of individual reporter genes, we have created pREPORT, a flexible multi-readout transcription reporter vector for fission yeast that employs an enhanced GFP-lacZ fusion and a customizable minimal promoter. With pREPORT, gene expression driven by the transcription factor of interest can be quantified in a number of ways, both in live cells and in vitro, using a single reporter construct.
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Affiliation(s)
- Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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Gadaleta MC, Iwasaki O, Noguchi C, Noma KI, Noguchi E. New vectors for epitope tagging and gene disruption in Schizosaccharomyces pombe. Biotechniques 2014; 55:257-63. [PMID: 24215641 DOI: 10.2144/000114100] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 10/16/2013] [Indexed: 12/31/2022] Open
Abstract
We describe a series of new vectors for PCR-based epitope tagging and gene disruption in the fission yeast Schizosaccharomyces pombe, an exceptional model organism for the study of cellular processes. The vectors are designed for amplification of gene-targeting DNA cassettes and integration into specific genetic loci, allowing expression of proteins fused to 12 tandem copies of the Pk (V5) epitope or 5 tandem copies of the FLAG epitope with a glycine linker. These vectors are available with various antibiotic or nutritional markers and are useful for protein studies using biochemical and cell biological methods. We also describe new vectors for fluorescent protein-tagging and gene disruption using ura4MX6, LEU2MX6, and his3MX6 selection markers, allowing researchers in the S. pombe community to disrupt genes and manipulate genomic loci using primer sets already available for the widely used pFA6a-MX6 system. Our new vectors may also be useful for gene manipulation in Saccharomyces cerevisiae.
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Affiliation(s)
- Mariana C Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA
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Fennessy D, Grallert A, Krapp A, Cokoja A, Bridge AJ, Petersen J, Patel A, Tallada VA, Boke E, Hodgson B, Simanis V, Hagan IM. Extending the Schizosaccharomyces pombe molecular genetic toolbox. PLoS One 2014; 9:e97683. [PMID: 24848109 PMCID: PMC4029729 DOI: 10.1371/journal.pone.0097683] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 04/09/2014] [Indexed: 12/13/2022] Open
Abstract
Targeted alteration of the genome lies at the heart of the exploitation of S. pombe as a model system. The rate of analysis is often determined by the efficiency with which a target locus can be manipulated. For most loci this is not a problem, however for some loci, such as fin1+, rates of gene targeting below 5% can limit the scope and scale of manipulations that are feasible within a reasonable time frame. We now describe a simple modification of transformation procedure for directing integration of genomic sequences that leads to a 5-fold increase in the transformation efficiency when antibiotic based dominant selection markers are used. We also show that removal of the pku70+ and pku80+ genes, which encode DNA end binding proteins required for the non-homologous end joining DNA repair pathway, increases the efficiency of gene targeting at fin1+ to around 75-80% (a 16-fold increase). We describe how a natMX6/rpl42+ cassette can be used for positive and negative selection for integration at a targeted locus. To facilitate the evaluation of the impact of a series of mutations on the function of a gene of interest we have generated three vector series that rely upon different selectable markers to direct the expression of tagged/untagged molecules from distinct genomic integration sites. pINTL and pINTK vectors use ura4+ selection to direct disruptive integration of leu1+ and lys1+ respectively, while pINTH vectors exploit nourseothricin resistance to detect the targeted disruption of a hygromycin B resistance conferring hphMX6 cassette that has been integrated on chromosome III. Finally, we have generated a series of multi-copy expression vectors that use resistance to nourseothricin or kanamycin/G418 to select for propagation in prototrophic hosts. Collectively these protocol modifications and vectors extend the versatility of this key model system.
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Affiliation(s)
- Dorota Fennessy
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Agnes Grallert
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Andrea Krapp
- Swiss Institute for Experimental Cancer Research, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Adisa Cokoja
- Swiss Institute for Experimental Cancer Research, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Alan J. Bridge
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Janni Petersen
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Avinash Patel
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Victor A. Tallada
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Elvan Boke
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Ben Hodgson
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Viesturs Simanis
- Swiss Institute for Experimental Cancer Research, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Iain M. Hagan
- Cell Division Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
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Steinhauf D, Rodriguez A, Vlachakis D, Virgo G, Maksimov V, Kristell C, Olsson I, Linder T, Kossida S, Bongcam-Rudloff E, Bjerling P. Silencing motifs in the Clr2 protein from fission yeast, Schizosaccharomyces pombe. PLoS One 2014; 9:e86948. [PMID: 24475199 PMCID: PMC3903592 DOI: 10.1371/journal.pone.0086948] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 12/16/2013] [Indexed: 01/01/2023] Open
Abstract
The fission yeast, Schizosaccharomyces pombe, is a well-established model for heterochromatin formation, but the exact sequence of events for initiation remains to be elucidated. The essential factors involved include RNA transcribed from repeated sequences together with the methyltransferase Clr4. In addition, histone deacetylases, like Clr3, found in the SHREC complex are also necessary for transcriptional silencing. Clr2 is another crucial factor required for heterochromatin formation found in the SHREC complex. The function of Clr2 has been difficult to establish due to the lack of conserved domains or homology to proteins of known molecular function. Using a bioinformatics approach, three conserved motifs in Clr2 were identified, which contained amino acids important for transcriptional repression. Analysis of clr2 mutant strains revealed a major role for Clr2 in mating-type and rDNA silencing, and weaker effects on centromeric silencing. The effect on mating-type silencing showed variegation in several of the strains with mutated versions of Clr2 indicating an establishment or maintenance defect. Moreover, the critical amino acids in Clr2 were also necessary for transcriptional repression in a minimal system, by the tethering of Clr4 upstream of a reporter gene, inserted into the euchromatic part of the genome. Finally, in silico modeling suggested that the mutations in Clr2 cause disruption of secondary structures in the Clr2 protein. Identification of these critical amino acids in the protein provides a useful tool to explore the molecular mechanism behind the role of Clr2 in heterochromatin formation.
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Affiliation(s)
- Daniel Steinhauf
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, University of Uppsala, Uppsala, Sweden
| | - Alejandro Rodriguez
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, University of Uppsala, Uppsala, Sweden
| | - Dimitrios Vlachakis
- Bioinformatics and Medical Informatics Laboratory, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Gordon Virgo
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, University of Uppsala, Uppsala, Sweden
| | - Vladimir Maksimov
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, University of Uppsala, Uppsala, Sweden
| | - Carolina Kristell
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, University of Uppsala, Uppsala, Sweden
| | - Ida Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, University of Uppsala, Uppsala, Sweden
| | - Tomas Linder
- Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sophia Kossida
- Bioinformatics and Medical Informatics Laboratory, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, SLU Global Bioinformatics Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pernilla Bjerling
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, University of Uppsala, Uppsala, Sweden
- * E-mail:
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Overcoming the metabolic burden of protein secretion in Schizosaccharomyces pombe – A quantitative approach using 13C-based metabolic flux analysis. Metab Eng 2014; 21:34-45. [DOI: 10.1016/j.ymben.2013.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/27/2013] [Accepted: 11/11/2013] [Indexed: 01/20/2023]
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Characterization and in vivo functional analysis of the Schizosaccharomyces pombe ICLN gene. Mol Cell Biol 2013; 34:595-605. [PMID: 24298023 DOI: 10.1128/mcb.01407-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the early steps of snRNP biogenesis, the survival motor neuron (SMN) complex acts together with the methylosome, an entity formed by the pICln protein, WD45, and the PRMT5 methyltransferase. To expand our understanding of the functional relationship between pICln and SMN in vivo, we performed a genetic analysis of an uncharacterized Schizosaccharomyces pombe pICln homolog. Although not essential, the S. pombe ICln (SpICln) protein is important for optimal yeast cell growth. The human ICLN gene complements the Δicln slow-growth phenotype, demonstrating that the identified SpICln sequence is the bona fide human homolog. Consistent with the role of human pICln inferred from in vitro experiments, we found that the SpICln protein is required for optimal production of the spliceosomal snRNPs and for efficient splicing in vivo. Genetic interaction approaches further demonstrate that modulation of ICln activity is unable to compensate for growth defects of SMN-deficient cells. Using a genome-wide approach and reverse transcription (RT)-PCR validation tests, we also show that splicing is differentially altered in Δicln cells. Our data are consistent with the notion that splice site selection and spliceosome kinetics are highly dependent on the concentration of core spliceosomal components.
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Poly(A) tail-mediated gene regulation by opposing roles of Nab2 and Pab2 nuclear poly(A)-binding proteins in pre-mRNA decay. Mol Cell Biol 2013; 33:4718-31. [PMID: 24081329 DOI: 10.1128/mcb.00887-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The 3' end of most eukaryotic transcripts is decorated by poly(A)-binding proteins (PABPs), which influence the fate of mRNAs throughout gene expression. However, despite the fact that multiple PABPs coexist in the nuclei of most eukaryotes, how functional interplay between these nuclear PABPs controls gene expression remains unclear. By characterizing the ortholog of the Nab2/ZC3H14 zinc finger PABP in Schizosaccharomyces pombe, we show here that the two major fission yeast nuclear PABPs, Pab2 and Nab2, have opposing roles in posttranscriptional gene regulation. Notably, we find that Nab2 functions in gene-specific regulation in a manner opposite to that of Pab2. By studying the ribosomal-protein-coding gene rpl30-2, which is negatively regulated by Pab2 via a nuclear pre-mRNA decay pathway that depends on the nuclear exosome subunit Rrp6, we show that Nab2 promotes rpl30-2 expression by acting at the level of the unspliced pre-mRNA. Our data support a model in which Nab2 impedes Pab2/Rrp6-mediated decay by competing with Pab2 for polyadenylated transcripts in the nucleus. The opposing roles of Pab2 and Nab2 reveal that interplay between nuclear PABPs can influence gene regulation.
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Yu ZY, Zhang MT, Wang GY, Xu D, Keifenheim D, Franco A, Cansado J, Masuda H, Rhind N, Wang Y, Jin QW. Fission yeast nucleolar protein Dnt1 regulates G2/M transition and cytokinesis by downregulating Wee1 kinase. J Cell Sci 2013; 126:4995-5004. [PMID: 24006256 DOI: 10.1242/jcs.132845] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cytokinesis involves temporally and spatially coordinated action of the cell cycle, cytoskeletal and membrane systems to achieve separation of daughter cells. The septation initiation network (SIN) and mitotic exit network (MEN) signaling pathways regulate cytokinesis and mitotic exit in the yeasts Schizosaccharomyces pombe and Saccharomyces cerevisiae, respectively. Previously, we have shown that in fission yeast, the nucleolar protein Dnt1 negatively regulates the SIN pathway in a manner that is independent of the Cdc14-family phosphatase Clp1/Flp1, but how Dnt1 modulates this pathway has remained elusive. By contrast, it is clear that its budding yeast relative, Net1/Cfi1, regulates the homologous MEN signaling pathway by sequestering Cdc14 phosphatase in the nucleolus before mitotic exit. In this study, we show that dnt1(+) positively regulates G2/M transition during the cell cycle. By conducting epistasis analyses to measure cell length at septation in double mutant (for dnt1 and genes involved in G2/M control) cells, we found a link between dnt1(+) and wee1(+). Furthermore, we showed that elevated protein levels of the mitotic inhibitor Wee1 kinase and the corresponding attenuation in Cdk1 activity is responsible for the rescuing effect of dnt1Δ on SIN mutants. Finally, our data also suggest that Dnt1 modulates Wee1 activity in parallel with SCF-mediated Wee1 degradation. Therefore, this study reveals an unexpected missing link between the nucleolar protein Dnt1 and the SIN signaling pathway, which is mediated by the Cdk1 regulator Wee1 kinase. Our findings also define a novel mode of regulation of Wee1 and Cdk1, which is important for integration of the signals controlling the SIN pathway in fission yeast.
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Affiliation(s)
- Zhi-Yong Yu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
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Cruz S, Muñoz S, Manjón E, García P, Sanchez Y. The fission yeast cell wall stress sensor-like proteins Mtl2 and Wsc1 act by turning on the GTPase Rho1p but act independently of the cell wall integrity pathway. Microbiologyopen 2013; 2:778-94. [PMID: 23907979 PMCID: PMC3831639 DOI: 10.1002/mbo3.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 12/27/2022] Open
Abstract
Sensing stressful conditions that affect the cell wall reorganization is important for yeast survival. Here, we studied two proteins SpWsc1p and SpMtl2p with structural features indicative of plasma membrane-associated cell wall sensors. We found that Mtl2p and Wsc1p act by turning on the Rho1p GTPase. Each gene could be deleted individually without affecting viability, but the deletion of both was lethal and this phenotype was rescued by overexpression of the genes encoding either Rho1p or its GDP/GTP exchange factors (GEFs). In addition, wsc1Δ and mtl2Δ cells showed a low level of Rho1p-GTP under cell wall stress. Mtl2p-GFP (green fluorescent protein) localized to the cell periphery and was necessary for survival under different types of cell wall stress. Wsc1p-GFP was concentrated in patches at the cell tips, it interacted with the Rho-GEF Rgf2p, and its overexpression activated cell wall biosynthesis. Our results are consistent with the notion that cell wall assembly is regulated by two different networks involving Rho1p. One includes signaling from Mtl2p through Rho1p to Pck1p, while the second one implicates signaling from Wsc1p and Rgf2p through Rho1p to activate glucan synthase (GS). Finally, signaling through the mitogen-activated protein kinase (MAPK) Pmk1p remained active in mtl2Δ and wsc1Δ disruptants exposed to cell wall stress, suggesting that the cell wall stress-sensing spectrum of Schizosaccharomyces pombe sensor-like proteins differs from that of Saccharomyces cerevisiae.
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Affiliation(s)
- Sandra Cruz
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca, C/Zacarías González s/n., Salamanca, Spain
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Dziadkowiec D, Kramarz K, Kanik K, Wisniewski P, Carr AM. Involvement of Schizosaccharomyces pombe rrp1+ and rrp2+ in the Srs2- and Swi5/Sfr1-dependent pathway in response to DNA damage and replication inhibition. Nucleic Acids Res 2013; 41:8196-209. [PMID: 23828040 PMCID: PMC3783160 DOI: 10.1093/nar/gkt564] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Previously we identified Rrp1 and Rrp2 as two proteins required for the Sfr1/Swi5-dependent branch of homologous recombination (HR) in Schizosaccharomyces pombe. Here we use a yeast two-hybrid approach to demonstrate that Rrp1 and Rrp2 can interact with each other and with Swi5, an HR mediator protein. Rrp1 and Rrp2 form co-localizing methyl methanesulphonate-induced foci in nuclei, further suggesting they function as a complex. To place the Rrp1/2 proteins more accurately within HR sub-pathways, we carried out extensive epistasis analysis between mutants defining Rrp1/2, Rad51 (recombinase), Swi5 and Rad57 (HR-mediators) plus the anti-recombinogenic helicases Srs2 and Rqh1. We confirm that Rrp1 and Rrp2 act together with Srs2 and Swi5 and independently of Rad57 and show that Rqh1 also acts independently of Rrp1/2. Mutants devoid of Srs2 are characterized by elevated recombination frequency with a concomitant increase in the percentage of conversion-type recombinants. Strains devoid of Rrp1 or Rrp2 did not show a change in HR frequency, but the number of conversion-type recombinants was increased, suggesting a possible function for Rrp1/2 with Srs2 in counteracting Rad51 activity. Our data allow us to propose a model placing Rrp1 and Rrp2 functioning together with Swi5 and Srs2 in a synthesis-dependent strand annealing HR repair pathway.
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Affiliation(s)
- Dorota Dziadkowiec
- Faculty of Biotechnology, Wrocław University, Przybyszewskiego 63-77, 51-148 Wrocław, Poland, Institute of Low Temperature and Structure Research, Polish Academy of Sciences, PO Box 1410, 50-950 Wrocław, Poland and Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
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Oravcová M, Teska M, Půta F, Folk P, Převorovský M. Fission yeast CSL proteins function as transcription factors. PLoS One 2013; 8:e59435. [PMID: 23555033 PMCID: PMC3598750 DOI: 10.1371/journal.pone.0059435] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/14/2013] [Indexed: 12/29/2022] Open
Abstract
Background Transcription factors of the CSL (CBF1/RBP-Jk/Suppressor of Hairless/LAG-1) family are key regulators of metazoan development and function as the effector components of the Notch receptor signalling pathway implicated in various cell fate decisions. CSL proteins recognize specifically the GTG[G/A]AA sequence motif and several mutants compromised in their ability to bind DNA have been reported. In our previous studies we have identified a number of novel putative CSL family members in fungi, organisms lacking the Notch pathway. It is not clear whether these represent genuine CSL family members. Methodology/Principal Findings Using a combination of in vitro and in vivo approaches we characterized the DNA binding properties of Cbf11 and Cbf12, the antagonistic CSL paralogs from the fission yeast, important for the proper coordination of cell cycle events and the regulation of cell adhesion. We have shown that a mutation of a conserved arginine residue abolishes DNA binding in both CSL paralogs, similar to the situation in mouse. We have also demonstrated the ability of Cbf11 and Cbf12 to activate gene expression in an autologous fission yeast reporter system. Conclusions/Significance Our results indicate that the fission yeast CSL proteins are indeed genuine family members capable of functioning as transcription factors, and provide support for the ancient evolutionary origin of this important protein family.
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Affiliation(s)
- Martina Oravcová
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Mikoláš Teska
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- * E-mail:
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Minde DP, Halff EF, Tans S. Designing disorder: Tales of the unexpected tails. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e26790. [PMID: 28516025 PMCID: PMC5424805 DOI: 10.4161/idp.26790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 10/11/2013] [Accepted: 10/11/2013] [Indexed: 12/24/2022]
Abstract
Protein tags of various sizes and shapes catalyze progress in biosciences. Well-folded tags can serve to solubilize proteins. Small, unfolded, peptide-like tags have become invaluable tools for protein purification as well as protein-protein interaction studies. Intrinsically Disordered Proteins (IDPs), which lack unique 3D structures, received exponentially increasing attention during the last decade. Recently, large ID tags have been developed to solubilize proteins and to engineer the pharmacological properties of protein and peptide pharmaceuticals. Here, we contrast the complementary benefits and applications of both folded and ID tags based on predictions of ID. Less structure often means more function in a shorter tag.
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Affiliation(s)
| | - Els F Halff
- Crystal and Structural Chemistry; Bijvoet Center for Biomolecular Research; Utrecht University; Utrecht, The Netherlands
| | - Sander Tans
- FOM Institute AMOLF; Amsterdam, The Netherlands
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Blt1 and Mid1 provide overlapping membrane anchors to position the division plane in fission yeast. Mol Cell Biol 2012; 33:418-28. [PMID: 23149940 DOI: 10.1128/mcb.01286-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Spatial control of cytokinesis is essential for proper cell division. The molecular mechanisms that anchor the dynamic assembly and constriction of the cytokinetic ring at the plasma membrane remain unclear. In the fission yeast Schizosaccharomyces pombe, the cytokinetic ring is assembled in the cell middle from cortical node precursors that are positioned by the anillin-like protein Mid1. During mitotic entry, cortical nodes mature and then compact into a contractile ring positioned in the cell middle. The molecular link between Mid1 and medial cortical nodes remains poorly defined. Here we show that Blt1, a previously enigmatic cortical node protein, promotes the robust association of Mid1 with cortical nodes. Blt1 interacts with Mid1 through the RhoGEF Gef2 to stabilize nodes at the cell cortex during the early stages of contractile ring assembly. The Blt1 N terminus is required for localization and function, while the Blt1 C terminus promotes cortical localization by interacting with phospholipids. In cells lacking membrane binding by both Mid1 and Blt1, nodes detach from the cell cortex and generate aberrant cytokinetic rings. We conclude that Blt1 acts as a scaffolding protein for precursors of the cytokinetic ring and that Blt1 and Mid1 provide overlapping membrane anchors for proper division plane positioning.
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Kim JY, Kwon ES, Roe JH. A homeobox protein Phx1 regulates long-term survival and meiotic sporulation in Schizosaccharomyces pombe. BMC Microbiol 2012; 12:86. [PMID: 22646093 PMCID: PMC3438059 DOI: 10.1186/1471-2180-12-86] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 04/09/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the fission yeast Schizosaccharomyces pombe, the phx1+ (pombe homeobox) gene was initially isolated as a multi-copy suppressor of lysine auxotrophy caused by depletion of copper/zinc-containing superoxide dismutase (CuZn-SOD). Overproduction of Phx1 increased the synthesis of homocitrate synthase, the first enzyme in lysine biosynthetic pathway, which is labile to oxidative stress. Phx1 has a well conserved DNA-binding domain called homeodomain at the N-terminal region and is predicted to be a transcription factor in S. pombe. However, its role has not been revealed in further detail. Here we examined its expression pattern and the phenotype of its null mutant to get clues on its function. RESULTS Fluorescence from the Phx1-GFP expressed from a chromosomal fusion gene demonstrated that it is localized primarily in the nucleus, and is distinctly visible during the stationary phase. When we replaced the N-terminal homeobox domain of Phx1 with the DNA binding domain of Pap1, a well-characterized transcription factor, the chimeric protein caused the elevation of transcripts from Pap1-dependent genes such as ctt1+ and trr1+, suggesting that Phx1 possesses transcriptional activating activity when bound to DNA. The amount of phx1+ transcripts sharply increased as cells entered the stationary phase and was maintained at high level throughout the stationary phase. Nutrient shift down to low nitrogen or carbon sources caused phx1+ induction during the exponential phase, suggesting that cells need Phx1 for maintenance function during nutrient starvation. The Δphx1 null mutant showed decreased viability in long-term culture, whereas overproduction of Phx1 increased viability. Decrease in long-term survival was also observed for Δphx1 under N- or C-starved conditions. In addition, Δphx1 mutant was more sensitive to various oxidants and heat shock. When we examined sporulation of the Δphx1/Δphx1 diploid strain, significant decrease in the formation of meiotic spores was observed. CONCLUSIONS Phx1 is a transcriptional regulator whose synthesis is elevated during stationary phase and by nutrient starvation in S. pombe. It supports long-term survival and stress tolerance against oxidation and heat, and plays a key role in the formation of meiotic spores.
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Affiliation(s)
- Ji-Yoon Kim
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, South Korea
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Korvald H, Falnes PØ, Laerdahl JK, Bjørås M, Alseth I. The Schizosaccharomyces pombe AlkB homolog Abh1 exhibits AP lyase activity but no demethylase activity. DNA Repair (Amst) 2012; 11:453-62. [PMID: 22365419 DOI: 10.1016/j.dnarep.2012.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/26/2012] [Accepted: 01/26/2012] [Indexed: 11/24/2022]
Abstract
2-Oxoglutarate (2OG) and iron (Fe(II)) dependent dioxygenases catalyze a wide range of biological oxidations, including hydroxylation and demethylation of proteins and nucleic acids. AlkB from Escherichia coli directly reverses certain methyl lesions in DNA, and defines a subfamily of 2OG/Fe(II) dioxygenases that has so far been shown to be involved in both nucleic acid repair and modification. The human genome encodes nine AlkB homologs and the function of most of these is still unknown. The fission yeast Schizosaccharomyces pombe has two AlkB homologs and here we have addressed the function of one of these, Abh1, which appears not to possess a classical AlkB-like repair activity. No enzymatic activity was found toward methylated DNA or etheno adducts, nor was the yeast abh1- mutant sensitive toward alkylating agents. Interestingly, heterologous expression of E. coli AlkB protected the fission yeast cells from alkylation induced cytotoxicity, suggesting that S. pombe lacks systems for efficient repair of lesions that are AlkB substrates. Further, we show that Abh1 possesses an unexpected DNA incision activity at apurinic/apyrimidinic (AP) sites. This AP lyase activity did not depend on 2OG and Fe(II) and was not repressed by dioxygenase inhibitors. Survival and complementation analyses failed to reveal any biological role for AP lyase cleavage by Abh1. It appears that in vitro AP lyase activity can be detected for a number of enzymes belonging to structurally and functionally unrelated families, but the in vivo significance of such activities may be questionable.
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Affiliation(s)
- Hanne Korvald
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, and Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
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Tamm T, Grallert A, Grossman EPS, Alvarez-Tabares I, Stevens FE, Hagan IM. Brr6 drives the Schizosaccharomyces pombe spindle pole body nuclear envelope insertion/extrusion cycle. ACTA ACUST UNITED AC 2012; 195:467-84. [PMID: 22042620 PMCID: PMC3206342 DOI: 10.1083/jcb.201106076] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Insertion into and release of the cytoplasmic domain of the Schizosaccharomyces pombe spindle pole body from a nuclear envelope fenestra during mitosis requires Brr6. The fission yeast interphase spindle pole body (SPB) is a bipartite structure in which a bulky cytoplasmic domain is separated from a nuclear component by the nuclear envelope. During mitosis, the SPB is incorporated into a fenestra that forms within the envelope during mitotic commitment. Closure of this fenestra during anaphase B/mitotic exit returns the cytoplasmic component to the cytoplasmic face of an intact interphase nuclear envelope. Here we show that Brr6 is transiently recruited to SPBs at both SPB insertion and extrusion. Brr6 is required for both SPB insertion and nuclear envelope integrity during anaphase B/mitotic exit. Genetic interactions with apq12 and defective sterol assimilation suggest that Brr6 may alter envelope composition at SPBs to promote SPB insertion and extrusion. The restriction of the Brr6 domain to eukaryotes that use a polar fenestra in an otherwise closed mitosis suggests a conserved role in fenestration to enable a single microtubule organizing center to nucleate both cytoplasmic and nuclear microtubules on opposing sides of the nuclear envelope.
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Affiliation(s)
- Tiina Tamm
- Cancer Research UK Cell Division Group, Paterson Institute for Cancer Research, Manchester M20 4BX, England, UK
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Abstract
Schizosaccharomyces pombe, the fission yeast, has been a popular and useful model system for investigating the mechanisms of biological processes for a long time. To facilitate purification, localization, and functional analysis of gene products, a wide range of expression vectors have been developed. Several of these vectors utilize the inducible/repressible promoter systems and enable the episomal expression of proteins as fusion proteins with epitope tags attached to their N terminus or C terminus.This chapter provides a detailed protocol for expression of the epitope-tagged proteins from thiamine-regulatable nmt promoter in fission yeast. The yeast culture conditions and procedures for yeast transformation, expression induction, preparation of whole-cell extracts, and analysis of epitope-tagged protein expression by Western blotting are described.
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Affiliation(s)
- Tiina Tamm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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Cheetham J, MacCallum DM, Doris KS, da Silva Dantas A, Scorfield S, Odds F, Smith DA, Quinn J. MAPKKK-independent regulation of the Hog1 stress-activated protein kinase in Candida albicans. J Biol Chem 2011; 286:42002-42016. [PMID: 21994942 PMCID: PMC3234903 DOI: 10.1074/jbc.m111.265231] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Hog1 stress-activated protein kinase regulates both stress responses and morphogenesis in Candida albicans and is essential for the virulence of this major human pathogen. Stress-induced Hog1 phosphorylation is regulated by the upstream MAPKK, Pbs2, which in turn is regulated by the MAPKKK, Ssk2. Here, we have investigated the role of phosphorylation of Hog1 and Pbs2 in Hog1-mediated processes in C. albicans. Mutation of the consensus regulatory phosphorylation sites of Hog1 (Thr-174/Tyr-176) and Pbs2 (Ser-355/Thr-359), to nonphosphorylatable residues, resulted in strains that phenocopied hog1Δ and pbs2Δ cells. Consistent with this, stress-induced phosphorylation of Hog1 was abolished in cells expressing nonphosphorylatable Pbs2 (Pbs2AA). However, mutation of the consensus sites of Pbs2 to phosphomimetic residues (Pbs2DD) failed to constitutively activate Hog1. Furthermore, Ssk2-independent stress-induced Hog1 activation was observed in Pbs2DD cells. Collectively, these data reveal a previously uncharacterized MAPKKK-independent mechanism of Hog1 activation in response to stress. Although Pbs2DD cells did not exhibit high basal levels of Hog1 phosphorylation, overexpression of an N-terminal truncated form of Ssk2 did result in constitutive Hog1 activation, which was further increased upon stress. Significantly, both Pbs2AA and Pbs2DD cells displayed impaired stress resistance and attenuated virulence in a mouse model of disease, whereas only Pbs2AA cells exhibited the morphological defects associated with loss of Hog1 function. This indicates that Hog1 mediates C. albicans virulence by conferring stress resistance rather than regulating morphogenesis.
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Affiliation(s)
- Jill Cheetham
- Institute for Cell and Molecular Biosciences, Faculty of Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Donna M MacCallum
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
| | - Kathryn S Doris
- Institute for Cell and Molecular Biosciences, Faculty of Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Alessandra da Silva Dantas
- Institute for Cell and Molecular Biosciences, Faculty of Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Susan Scorfield
- Institute for Cell and Molecular Biosciences, Faculty of Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Frank Odds
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
| | - Deborah A Smith
- Institute for Cell and Molecular Biosciences, Faculty of Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Janet Quinn
- Institute for Cell and Molecular Biosciences, Faculty of Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom.
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Korvald H, Mølstad Moe AM, Cederkvist FH, Thiede B, Laerdahl JK, Bjørås M, Alseth I. Schizosaccharomyces pombe Ofd2 is a nuclear 2-oxoglutarate and iron dependent dioxygenase interacting with histones. PLoS One 2011; 6:e25188. [PMID: 21949882 PMCID: PMC3175000 DOI: 10.1371/journal.pone.0025188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 08/29/2011] [Indexed: 11/18/2022] Open
Abstract
2-oxoglutarate (2OG) dependent dioxygenases are ubiquitous iron containing enzymes that couple substrate oxidation to the conversion of 2OG to succinate and carbon dioxide. They participate in a wide range of biological processes including collagen biosynthesis, fatty acid metabolism, hypoxic sensing and demethylation of nucleic acids and histones. Although substantial progress has been made in elucidating their function, the role of many 2OG dioxygenases remains enigmatic. Here we have studied the 2OG and iron (Fe(II)) dependent dioxygenase Ofd2 in Schizosaccharomyces pombe, a member of the AlkB subfamily of dioxygenases. We show that decarboxylation of 2OG by recombinant Ofd2 is dependent on Fe(II) and a histidine residue predicted to be involved in Fe(II) coordination. The decarboxylase activity of Ofd2 is stimulated by histones, and H2A has the strongest effect. Ofd2 interacts with all four core histones, however, only very weakly with H4. Our results define a new subclass of AlkB proteins interacting with histones, which also might comprise some of the human AlkB homologs with unknown function.
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Affiliation(s)
- Hanne Korvald
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
| | - Anne Margrethe Mølstad Moe
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
| | - F. Henning Cederkvist
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
- Department of Medical Biochemistry, University of Oslo, Oslo, Norway
| | - Bernd Thiede
- The Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway
| | - Jon K. Laerdahl
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
- Department of Medical Biochemistry, University of Oslo, Oslo, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
- * E-mail:
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Kelly FD, Nurse P. Spatial control of Cdc42 activation determines cell width in fission yeast. Mol Biol Cell 2011; 22:3801-11. [PMID: 21849474 PMCID: PMC3192860 DOI: 10.1091/mbc.e11-01-0057] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe is a rod-shaped cell that grows by linear extension at the cell tips, with a nearly constant width throughout the cell cycle. This simple geometry makes it an ideal system for studying the control of cellular dimensions. In this study, we carried out a near-genome-wide screen for mutants wider than wild-type cells. We found 11 deletion mutants that were wider; seven of the deleted genes are implicated in the control of the small GTPase Cdc42, including the Cdc42 guanine nucleotide exchange factor (GEF) Scd1 and the Cdc42 GTPase-activating protein (GAP) Rga4. Deletions of rga4 and scd1 had additive effects on cell width, and the proteins localized independently of one another, with Rga4 located at the cell sides and Scd1 at the cell tips. Activated Cdc42 localization is altered in rga4Δ, scd1Δ, and scd2Δ mutants. Delocalization and ectopic retargeting experiments showed that the localizations of Rga4 and Scd1 are crucial for their roles in determining cell width. We propose that the GAP Rga4 and the GEF Scd1 establish a gradient of activated Cdc42 within the cellular tip plasma membrane, and it is this gradient that determines cell growth-zone size and normal cell width.
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Quinn J, Malakasi P, Smith DA, Cheetham J, Buck V, Millar JBA, Morgan BA. Two-component mediated peroxide sensing and signal transduction in fission yeast. Antioxid Redox Signal 2011; 15:153-65. [PMID: 20919928 DOI: 10.1089/ars.2010.3345] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Two-component related proteins play a major role in regulating the oxidative stress response in the fission yeast, Schizosaccharomyces pombe. For example, the peroxide-sensing Mak2 and Mak3 histidine kinases regulate H(2)O(2)-induced activation of the Sty1 stress-activated protein kinase pathway, and the Skn7-related response regulator transcription factor, Prr1, is essential for activation of the core oxidative stress response genes. Here, we investigate the mechanism by which the S. pombe two-component system senses H(2)O(2), and the potential role of two-component signaling in the regulation of Prr1. Significantly, we demonstrate that PAS and GAF domains present in the Mak2 histidine kinase are essential for redox-sensing and activation of Sty1. In addition, we find that Prr1 is required for the transcriptional response to a wide range of H(2)O(2) concentrations and, furthermore, that two-component regulation of Prr1 is specifically required for the response of cells to high levels of H(2)O(2). Significantly, this provides the first demonstration that the conserved two-component phosphorylation site on Skn7-related proteins influences resistance to oxidative stress and oxidative stress-induced gene expression. Collectively, these data provide new insights into the two-component mediated sensing and signaling mechanisms underlying the response of S. pombe to oxidative stress.
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Affiliation(s)
- Janet Quinn
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
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Meyer CL, Peisker D, Courbot M, Craciun AR, Cazalé AC, Desgain D, Schat H, Clemens S, Verbruggen N. Isolation and characterization of Arabidopsis halleri and Thlaspi caerulescens phytochelatin synthases. PLANTA 2011; 234:83-95. [PMID: 21369921 DOI: 10.1007/s00425-011-1378-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 02/07/2011] [Indexed: 05/13/2023]
Abstract
The synthesis of phytochelatins (PC) represents a major metal and metalloid detoxification mechanism in various species. PC most likely play a role in the distribution and accumulation of Cd and possibly other metals. However, to date, no studies have investigated the phytochelatin synthase (PCS) genes and their expression in the Cd-hyperaccumulating species. We used functional screens in two yeast species to identify genes expressed by two Cd hyperaccumulators (Arabidopsis halleri and Thlaspi caerulescens) and involved in cellular Cd tolerance. As a result of these screens, PCS genes were identified for both species. PCS1 was in each case the dominating cDNA isolated. The deduced sequences of AhPCS1 and TcPCS1 are very similar to AtPCS1 and their identity is particularly high in the proposed catalytic N-terminal domain. We also identified in A. halleri and T. caerulescens orthologues of AtPCS2 that encode functional PCS. As compared to A. halleri and A. thaliana, T. caerulescens showed the lowest PCS expression. Furthermore, concentrations of PC in Cd-treated roots were the highest in A. thaliana, intermediate in A. halleri and the lowest in T. caerulescens. This mirrors the known capacity of these species to translocate Cd to the shoot, with T. caerulescens being the best translocator. Very low or undetectable concentrations of PC were measured in A. halleri and T. caerulescens shoots, contrary to A. thaliana. These results suggest that extremely efficient alternative Cd sequestration pathways in leaves of Cd hyperaccumulators prevent activation of PC synthase by Cd²⁺ ions.
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Affiliation(s)
- Claire-Lise Meyer
- Faculté des Sciences, Laboratoire de Physiologie & de Génétique moléculaire des Plantes, Université Libre de Bruxelles, Campus Plaine CP242, 1050 Brussels, Belgium
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A Phosphorylation Cycle Shapes Gradients of the DYRK Family Kinase Pom1 at the Plasma Membrane. Cell 2011; 145:1116-28. [DOI: 10.1016/j.cell.2011.05.014] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/23/2011] [Accepted: 05/04/2011] [Indexed: 12/25/2022]
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Biotechnological Production of 20-alpha-Dihydrodydrogesterone at Pilot Scale. Appl Biochem Biotechnol 2011; 165:190-203. [DOI: 10.1007/s12010-011-9243-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 04/04/2011] [Indexed: 01/20/2023]
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48
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Garlapati S, Saraiya AA, Wang CC. A La autoantigen homologue is required for the internal ribosome entry site mediated translation of giardiavirus. PLoS One 2011; 6:e18263. [PMID: 21479239 PMCID: PMC3066225 DOI: 10.1371/journal.pone.0018263] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 02/28/2011] [Indexed: 12/11/2022] Open
Abstract
Translation of Giardiavirus (GLV) mRNA is initiated at an internal ribosome entry site (IRES) in the viral transcript. The IRES localizes to a downstream portion of 5′ untranslated region (UTR) and a part of the early downstream coding region of the transcript. Recent studies indicated that the IRES does not require a pre-initiation complex to initiate translation but may directly recruit the small ribosome subunit with the help of a number of trans-activating protein factors. A La autoantigen homologue in the viral host Giardia lamblia, GlLa, was proposed as one of the potential trans-activating factors based on its specific binding to GLV-IRES in vitro. In this study, we further elucidated the functional role of GlLa in GLV-IRES mediated translation in Giardia by knocking down GlLa with antisense morpholino oligo, which resulted in a reduction of GLV-IRES activity by 40%. An over-expression of GlLa in Giardia moderately stimulated GLV-IRES activity by 20%. A yeast inhibitory RNA (IRNA), known to bind mammalian and yeast La autoantigen and inhibit Poliovirus and Hepatitis C virus IRES activities in vitro and in vivo, was also found to bind to GlLa protein in vitro and inhibited GLV-IRES function in vivo. The C-terminal domain of La autoantigen interferes with the dimerization of La and inhibits its function. An over-expression of the C-terminal domain (200–348aa) of GlLa in Giardia showed a dominant-negative effect on GLV-IRES activity, suggesting a potential inhibition of GlLa dimerization. HA tagged GlLa protein was detected mainly in the cytoplasm of Giardia, thus supporting a primary role of GlLa in translation initiation in Giardiavirus.
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Affiliation(s)
- Srinivas Garlapati
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Ashesh A. Saraiya
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Ching C. Wang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Sayrac S, Vengrova S, Godfrey EL, Dalgaard JZ. Identification of a novel type of spacer element required for imprinting in fission yeast. PLoS Genet 2011; 7:e1001328. [PMID: 21423720 PMCID: PMC3053322 DOI: 10.1371/journal.pgen.1001328] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 02/07/2011] [Indexed: 11/18/2022] Open
Abstract
Asymmetrical segregation of differentiated sister chromatids is thought to be important for cellular differentiation in higher eukaryotes. Similarly, in fission yeast, cellular differentiation involves the asymmetrical segregation of a chromosomal imprint. This imprint has been shown to consist of two ribonucleotides that are incorporated into the DNA during lagging-strand synthesis in response to a replication pause, but the underlying mechanism remains unknown. Here we present key novel discoveries important for unravelling this process. Our data show that cis-acting sequences within the mat1 cassette mediate pausing of replication forks at the proximity of the imprinting site, and the results suggest that this pause dictates specific priming at the position of imprinting in a sequence-independent manner. Also, we identify a novel type of cis-acting spacer region important for the imprinting process that affects where subsequent primers are put down after the replication fork is released from the pause. Thus, our data suggest that the imprint is formed by ligation of a not-fully-processed Okazaki fragment to the subsequent fragment. The presented work addresses how differentiated sister chromatids are established during DNA replication through the involvement of replication barriers.
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Affiliation(s)
- Suha Sayrac
- Clinical Sciences Research Institute, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Sonya Vengrova
- Clinical Sciences Research Institute, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Emma L. Godfrey
- Clinical Sciences Research Institute, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Jacob Z. Dalgaard
- Clinical Sciences Research Institute, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
- * E-mail:
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Abstract
We developed a series of plasmids that allow C-terminal tagging of any gene in its endogenous locus in Giardia intestinalis, with different epitope tags (triple hemagglutinin [3HA] and triple Myc [3Myc]) and selection markers (puromycin, neomycin, and a newly developed marker, blasticidin). Using these vectors, cyclin B and aurora kinase were tagged, expressed, and localized.
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