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 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.

Different roles for the stress-activated protein kinase pathway in the regulation of trehalose metabolism in Schizosaccharomyces pombe

Microbiology ◽  
2003 ◽  
Vol 149 (7) ◽  
pp. 1745-1752 ◽  
Author(s):  
V. Paredes ◽  
A. Franco ◽  
T. Soto ◽  
J. Vicente-Soler ◽  
M. Gacto ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Transcription Factors ◽  
Protein Kinase ◽  
Osmotic Stress ◽  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Stress Responses ◽  
Mitogen Activated Protein Kinase ◽  
Wide Range ◽  
Trehalose Metabolism

The Wis1p-Sty1p mitogen-activated protein kinase cascade is a major signalling system in the fission yeast Schizosaccharomyces pombe for a wide range of stress responses. It is known that trehalose functions as a protective metabolite to counteract deleterious effects of environmental stresses. Herein it is reported that the expression of genes related to trehalose metabolism in S. pombe, ntp1 + (neutral trehalase) and tps1 + [trehalose-6-phosphate (T6P) synthase], is partially regulated by the Sty1p kinase under salt-induced osmotic stress and conditions of slight oxidative stress and is fully dependent on this kinase under severe oxidative stress. This control is carried out through transcription factors Atf1p/Pcr1p during osmotic stress and through Pap1p during exposure to low levels of oxidative stress. However, all three transcription factors are needed for gene expression under conditions of extreme oxidative stress. In addition, a role for Sty1p in the modulation of post-transcriptional activation of trehalase mediated by Pka1p/Sck1p kinases, as well as in the activity of T6P synthase under such stressful conditions has been demonstrated. These results reveal a novel dual action of the Wis1p-Sty1p pathway in the regulation of trehalose metabolism in fission yeast.

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.

scholarly journals A toolbox of stable integration vectors in the fission yeast Schizosaccharomyces pombe

2019 ◽  
Vol 133 (1) ◽  
pp. jcs240754 ◽  
Author(s):  
Aleksandar Vještica ◽  
Magdalena Marek ◽  
Pedro Junior Nkosi ◽  
Laura Merlini ◽  
Gaowen Liu ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Stable Integration

scholarly journals Schizosaccharomyces pombe Hat1 (Kat1) Is Associated with Mis16 and Is Required for Telomeric Silencing

2012 ◽  
Vol 11 (9) ◽  
pp. 1095-1103 ◽  
Author(s):  
Kevin Tong ◽  
Thomas Keller ◽  
Charles S. Hoffman ◽  
Anthony T. Annunziato
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Trichostatin A ◽  
Tail Domain ◽  
Histone H4 ◽  
Type Locus ◽  
Content Type ◽  
Telomeric Silencing ◽  
Deacetylase Inhibitor ◽  
Wide Range

ABSTRACT The Hat1 histone acetyltransferase has been implicated in the acetylation of histone H4 during chromatin assembly. In this study, we have characterized the Hat1 complex from the fission yeast Schizosaccharomyces pombe and have examined its role in telomeric silencing. Hat1 is found associated with the RbAp46 homologue Mis16, an essential protein. The Hat1 complex acetylates lysines 5 and 12 of histone H4, the sites that are acetylated in newly synthesized H4 in a wide range of eukaryotes. Deletion of hat1 in S. pombe is itself sufficient to cause the loss of silencing at telomeres. This is in contrast to results obtained with an S. cerevisiae hat1Δ strain, which must also carry mutations of specific acetylatable lysines in the H3 tail domain for loss of telomeric silencing to occur. Notably, deletion of hat1 from S. pombe resulted in an increase of acetylation of histone H4 in subtelomeric chromatin, concomitant with derepression of this region. A similar loss of telomeric silencing was also observed after growing cells in the presence of the deacetylase inhibitor trichostatin A. However, deleting hat1 did not cause loss of silencing at centromeres or the silent mating type locus. These results point to a direct link between Hat1, H4 acetylation, and the establishment of repressed telomeric chromatin in fission yeast.

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
Sign in / Sign up

Export Citation Format

Share Document