scholarly journals Fission stories: Using PomBase to understand Schizosaccharomyces pombe biology

Genetics ◽  
2021 ◽  
Author(s):  
Midori A Harris ◽  
Kim M Rutherford ◽  
Jacqueline Hayles ◽  
Antonia Lock ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism ◽  
Biological Knowledge ◽  
Model Organism Database ◽  
Comprehensive Data ◽  
Data Collections ◽  
Data Summaries

Abstract PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualisation, PomBase also drives innovation in the MOD community.

scholarly journals Fission stories: Using PomBase to understand Schizosaccharomyces pombe biology

2021 ◽  
Author(s):  
Midori A. Harris ◽  
Kim M. Rutherford ◽  
Jacqueline Hayles ◽  
Antonia Lock ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism ◽  
Biological Knowledge ◽  
Model Organism Database ◽  
Link Type ◽  
Comprehensive Data ◽  
Data Collections ◽  
Data Summaries

AbstractPomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualisation, PomBase also drives innovation in the MOD community.

scholarly journals A toolbox of Stable Integration Vectors (SIV) in the fission yeast Schizosaccharomyces pombe

2019 ◽  
Author(s):  
Aleksandar Vještica ◽  
Magdalena Marek ◽  
Pedro N’kosi ◽  
Laura Merlini ◽  
Gaowen Liu ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism ◽  
Experimental System ◽  
Single Copy ◽  
Cell Physiology ◽  
Large Set ◽  
Stable Integration ◽  
Wide Range ◽  
Fluorescent Tags

AbstractSchizosaccharomyces pombe is a widely used model organism that resembles higher eukaryotes in many aspects of 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, yield unstable genomic loci. We overcome this problem by designing a new series of Stable Integration Vectors (SIV) that target four different prototrophy genes. SIV 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.

scholarly journals Website Review: How to Get the Best From Fission Yeast Genome Data

2002 ◽  
Vol 3 (3) ◽  
pp. 282-288 ◽  
Author(s):  
Valerie Wood ◽  
Jürg Bähler
Keyword(s):  
Functional Genomics ◽  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism ◽  
Research Community ◽  
Yeast Genome ◽  
Biological Databases ◽  
Genome Data ◽  
Internet Resources ◽  
Continuous Feedback

Researchers are increasingly depending on various centralized resources to access the vast amount of information reported in the literature and generated by systematic sequencing and functional genomics projects. Biological databases have become everyday working tools for many researchers. This dependency goes both ways in that the databases require continuous feedback from the research community to maintain accurate, reliable, and upto- date information. The fission yeastSchizosaccharomyces pombehas recently been sequenced, setting the stage for the post-genome era of this popular model organism. Here, we provide an overview of relevant databases available, or being developed, together with a compilation of Internet resources containing useful information and tools for fission yeast.

scholarly journals Variables Influencing Differences in Sequence Conservation in the Fission Yeast Schizosaccharomyces pombe

2021 ◽  
Author(s):  
Simon Emanuel Harnqvist ◽  
Cooper Alastair Grace ◽  
Daniel Charlton Jeffares
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Protein Interactions ◽  
Model Organism ◽  
Sequence Conservation ◽  
Rate Variation ◽  
Sequence Evolution ◽  
Least Squares Regression ◽  
Protein Protein Interactions ◽  
Partial Correlations

AbstractWhich variables determine the constraints on gene sequence evolution is one of the most central questions in molecular evolution. In the fission yeast Schizosaccharomyces pombe, an important model organism, the variables influencing the rate of sequence evolution have yet to be determined. Previous studies in other single celled organisms have generally found gene expression levels to be most significant, with numerous other variables such as gene length and functional importance identified as having a smaller impact. Using publicly available data, we used partial least squares regression, principal components regression, and partial correlations to determine the variables most strongly associated with sequence evolution constraints. We identify centrality in the protein–protein interactions network, amino acid composition, and cellular location as the most important determinants of sequence conservation. However, each factor only explains a small amount of variance, and there are numerous variables having a significant or heterogeneous influence. Our models explain more than half of the variance in dN, raising the possibility that future refined models could quantify the role of stochastics in evolutionary rate variation.

scholarly journals JaponicusDB: Rapid deployment of a model organism database for an emerging model species

Genetics ◽  
2021 ◽  
Author(s):  
Kim M Rutherford ◽  
Midori A Harris ◽  
Snezhana Oliferenko ◽  
Valerie Wood
Keyword(s):  
Fission Yeast ◽  
Model Organism ◽  
Full Potential ◽  
Model Species ◽  
Model Organism Database ◽  
Cellular Processes ◽  
Growing Body ◽  
Central Resource ◽  
Ready Access ◽  
Rapid Deployment

Abstract The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realise the full potential of studying a newly emerging model species, and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.

scholarly journals imp2, a New Component of the Actin Ring in the Fission Yeast Schizosaccharomyces pombe

1998 ◽  
Vol 143 (2) ◽  
pp. 415-427 ◽  
Author(s):  
Janos Demeter ◽  
Shelley Sazer
Keyword(s):  
Cell Division ◽  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism ◽  
Eukaryotic Cell ◽  
Actin Ring ◽  
Daughter Cells ◽  
Isolation And Characterization ◽  
Ring Structures

Cytokinesis is the part of the cell cycle in which the cell is cleaved to form two daughter cells. The unicellular yeast, Schizosaccharomyces pombe is an excellent model organism in which to study cell division, since it shows the general features of eukaryotic cell division and is amenable to genetic analysis. In this manuscript we describe the isolation and characterization of a new protein, imp2, which is required for normal septation in fission yeast. imp2, which colocalizes with the medial ring during septation, is structurally similar to a group of proteins including the S. pombe cdc15 and the mouse PSTPIP that are localized to, and thought to be involved in actin ring organization. Cells in which the imp2 gene is deleted or overexpressed have septation and cell separation defects. An analysis of the actin cytoskeleton shows the lack of a medial ring in septating cells that overexpress imp2, and the appearance of abnormal medial ring structures in septated cells that lack imp2. These observations suggest that imp2 destabilizes the medial ring during septation. imp2 also shows genetic interactions with several, previously characterized septation genes, strengthening the conclusion that it plays a role in normal fission yeast septation.

Fission Yeast Schizosaccharomyces pombe : A Unicellular “Micromammal” Model Organism

2021 ◽  
Vol 1 (6) ◽  
Author(s):  
Aditi Vyas ◽  
Anna V. Freitas ◽  
Zachary A. Ralston ◽  
Zhaohua Tang
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism

scholarly journals Mutational Analysis of N-Ethyl-N-Nitrosourea (ENU) in the Fission Yeast Schizosaccharomyces pombe

2020 ◽  
Vol 10 (3) ◽  
pp. 917-923
Author(s):  
Rafael Hoyos-Manchado ◽  
Sergio Villa-Consuegra ◽  
Modesto Berraquero ◽  
Juan Jiménez ◽  
Víctor A. Tallada
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Mutational Analysis ◽  
Alkylating Agents ◽  
Model Organism ◽  
Forward Genetics ◽  
Model Organisms ◽  
Temperature Sensitive ◽  
Aminoglycoside Resistance ◽  
Research Fields

Forward genetics in model organisms has boosted our knowledge of the genetic bases of development, aging, and human diseases. In this experimental pipeline, it is crucial to start by inducing a large number of random mutations in the genome of the model organism to search for phenotypes of interest. Many chemical mutagens are used to this end because most of them display particular reactivity properties and act differently over DNA. Here we report the use of N-ethyl-N-nitrosourea (ENU) as a mutagen in the fission yeast Schizosaccharomyces pombe. As opposed to many other alkylating agents, ENU only induces an SN1-type reaction with a low s constant (s = 0.26), attacking preferentially O2 and O4 in thymine and O6 deoxyguanosine, leading to base substitutions rather than indels, which are extremely rare in its resulting mutagenic repertoire. Using ENU, we gathered a collection of 13 temperature-sensitive mutants and 80 auxotrophic mutants including two deleterious alleles of the human ortholog ATIC. Defective alleles of this gene cause AICA-ribosiduria, a severe genetic disease. In this screen, we also identified 13 aminoglycoside-resistance inactivating mutations in APH genes. Mutations reported here may be of interest for metabolism related diseases and antibiotic resistance research fields.

Hydrogen peroxide-induced oxidative damages in Schizosaccharomyces pombe

Biologia ◽  
2008 ◽  
Vol 63 (2) ◽  
Author(s):  
Murat Pekmez ◽  
Nazlı Arda ◽  
İsmail Hamad ◽  
Cenk Kiğ ◽  
Güler Temizkan
Keyword(s):  
Oxidative Stress ◽  
Hydrogen Peroxide ◽  
Lipid Peroxidation ◽  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Mammalian Cells ◽  
Model Organism ◽  
Cell Number ◽  
Protein Carbonyl ◽  
Protein Carbonyls

AbstractOxidative stress causes damage to proteins, lipids and nucleic acids, and thereby compromises cell viability. Some of the oxidative stress markers in an eukaryotic model organism, fission yeast Schizosaccharomyces pombe, were evaluated in this study. Intracellular oxidation, protein carbonyls, lipid peroxidation and reduced glutathione (GSH) levels were investigated in H2O2-treated and non-treated control cells. It was observed that increased H2O2 concentration proportionally lowered the cell number and increased the intracellular oxidation, lipid peroxidation and protein carbonyl levels in S. pombe. A dose-dependent decrease in GSH level was also detected. The fission yeast S. pombe is best known for its contribution to understanding of eukaryotic cell cycle control. S. pombe displays a different physiology from Saccharomyces cerevisiae in several ways and is thus probably more closely related to higher eukaryotes. The purpose of this study was to provide some data about the effects of hydrogen peroxide on the proteins and lipids in the fission yeast. The data obtained here is expected to constitute a basis for the further studies on redox balance and related processes in yeast and mammalian cells.

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