PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information

Nucleic Acids Research, Год журнала: 2018, Номер 47(D1), С. D821 - D827

Опубликована: Окт. 11, 2018

PomBase (www.pombase.org), the model organism database for fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in more fully integrated, better-performing service. The new infrastructure supports daily data updates as well fast, efficient querying and smoother navigation within between pages. New pages publications genotypes provide routes to all curated from single source phenotypes associated with specific genotype, respectively. For ontology-based annotations, improved displays balance comprehensive coverage ease of use. default view now uses ontology structure concise, non-redundant summary that can be expanded reveal underlying details metadata. phenotype annotation display also offers filtering options allow users focus on areas interest. An instance JBrowse genome browser been facilitating loading intuitive access to, genome-scale datasets. Taken together, pages, along improvements querying, probe connections among different types form biology. implementation provides rich set modular, reusable tools deployed create new, or enhance existing, organism-specific databases.

Язык: Английский

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CRISPR/Cas system for yeast genome engineering: advances and applications

FEMS Yeast Research, Год журнала: 2017, Номер 17(5)

Опубликована: Май 13, 2017

The methods based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system have quickly gained popularity for genome editing and transcriptional regulation in many organisms, including yeast. This review aims to provide a comprehensive overview of CRISPR application different yeast species: from basic principles genetic design applications.

Язык: Английский

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1,2,4-Triazole and 1,3,4-oxadiazole analogues: Synthesis, MO studies, in silico molecular docking studies, antimalarial as DHFR inhibitor and antimicrobial activities

Bioorganic & Medicinal Chemistry, Год журнала: 2017, Номер 25(15), С. 4064 - 4075

Опубликована: Май 30, 2017

Язык: Английский

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Proximity-dependent biotinylation mediated by TurboID to identify protein–protein interaction networks in yeast

Journal of Cell Science, Год журнала: 2019, Номер 132(11)

Опубликована: Май 7, 2019

ABSTRACT The use of proximity-dependent biotinylation assays coupled to mass spectrometry (PDB-MS) has changed the field protein–protein interaction studies. However, despite recurrent and successful BioID-based interactions screening in mammalian cells, implementation PDB-MS yeast not been effective. Here, we report a simple rapid approach effectively screen for proximal interacting proteins their natural cellular environment by using TurboID, recently described version BirA biotin ligase. Using protein arginine methyltransferase Rmt3 RNA exosome subunits, Rrp6 Dis3, application TurboID was able recover previously identified other biochemical approaches provided new complementary information given bait. development effective PDB assay that can systematically analyze living cells opens way large-scale proteomics studies this powerful model organism.

Язык: Английский

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Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution

New Phytologist, Год журнала: 2024, Номер 242(4), С. 1448 - 1475

Опубликована: Апрель 6, 2024

Summary Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have developing Suillus , widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into model system for studying ectomycorrhizal (ECM) associations. Over last decade, compiled extensive genomic resources, culture libraries, phenotype database, protocols manipulating fungi without their tree partners. Our efforts already resulted in large number publicly available genomes, transcriptomes, respective annotations, as well advances our understanding partner specificity host communication, nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, biological invasions. Here, highlight most significant recent findings enabled present suite working genus, discuss how is emerging an important to elucidate ecology evolution ECM interactions.

Язык: Английский

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Benzothiazole analogues: Synthesis, characterization, MO calculations with PM6 and DFT, in silico studies and in vitro antimalarial as DHFR inhibitors and antimicrobial activities

Bioorganic & Medicinal Chemistry, Год журнала: 2017, Номер 25(20), С. 5396 - 5406

Опубликована: Июль 30, 2017

Язык: Английский

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Cellular factories for coenzyme Q10 production

Microbial Cell Factories, Год журнала: 2017, Номер 16(1)

Опубликована: Март 2, 2017

Coenzyme Q10 (CoQ10), a benzoquinone present in most organisms, plays an important role the electron-transport chain, and its deficiency is associated with various neuropathies muscular disorders. CoQ10 only lipid-soluble antioxidant found humans, for this, it gaining popularity cosmetic healthcare industries. To meet growing demand CoQ10, there has been considerable interest ways to enhance production, effective of which remains microbial fermentation. Previous attempts increase production industrial scale have thus far conformed strategies used typical metabolic engineering endeavors. However, emergence new tools expanding field synthetic biology provided suite possibilities that extend beyond traditional modes engineering. In this review, we cover currently undertaken upscale discuss some potential novel areas future research.

Язык: Английский

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G-rich telomeric and ribosomal DNA sequences from the fission yeast genome form stable G-quadruplex DNA structuresin vitroand are unwound by the Pfh1 DNA helicase

Nucleic Acids Research, Год журнала: 2016, Номер 44(13), С. 6213 - 6231

Опубликована: Май 16, 2016

Certain guanine-rich sequences have an inherent propensity to form G-quadruplex (G4) structures. G4 structures are e.g. involved in telomere protection and gene regulation. However, they also constitute obstacles during replication if remain unresolved. To overcome these threats genome integrity, organisms harbor specialized unwinding helicases. In Schizosaccharomyces pombe, one such candidate helicase is Pfh1, evolutionarily conserved Pif1 homolog. Here, we addressed whether putative S. pombe can adopt and, so, Pfh1 resolve them. We tested two sequences, derived from ribosomal telomeric DNA regions, demonstrated that inter- intramolecular structures, respectively. Also, was enriched vivo at the sites. The nuclear isoform of (nPfh1) unwound both types structure, although G4-stabilizing compound Phen-DC3 significantly enhanced their stability, nPfh1 still resolved them efficiently. stable inhibited adenosine triphosphate hydrolysis by nPfh1. Because contain regions yeasts humans, our studies support important role structure formation provide further evidence for a helicases resolving

Язык: Английский

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

Journal of Cell Science, Год журнала: 2019, Номер 133(1)

Опубликована: Дек. 4, 2019

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 genetic manipulations, where innate homology-targeted repair exploited precisely edit genome. While vectors incorporate exogenous sequences into chromosomes are available, most poorly characterized. Here, we show that commonly fission yeast vectors, which upon integration produce repetitive genomic regions, give rise unstable loci. We overcome this problem by designing new series stable (SIVs) target four different prototrophy genes. SIVs non-repetitive, loci and integrate predominantly single copy. Additionally, develop set complementary auxotrophic alleles preclude false-positive events. expand vector include antibiotic resistance markers, promoters, fluorescent tags terminators, build highly modular toolbox introduce heterologous sequences. Finally, proof concept, generate large ready-to-use, probes mark organelles cellular processes with wide range applications in research. This article has associated First Person interview first author paper.

Язык: Английский

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Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast

Molecular Biology and Evolution, Год журнала: 2019, Номер 36(9), С. 1975 - 1989

Опубликована: Май 10, 2019

Mutation and recombination are key evolutionary processes governing phenotypic variation reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20-60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset intensified transcontinental trade. Species-wide heritable explained near-exclusively by strain-specific arrangements alternating ancestry components evidence for transgressive segregation. Reproductive compatibility likewise predicted degree shared ancestry. To assess genetic determinants block distribution across genome, we characterized type, frequency, position structural genomic using nanopore single-molecule real-time sequencing. Despite being associated double-strand break initiation points, over 800 segregating variants exerted overall little influence on introgression landscape or strains. In contrast, found strong disequilibrium negative epistatic selection shaping combinations during course hybridization. This study provides a detailed, experimentally tractable example genomes natural populations mosaics reflecting different histories. Exploiting genome-wide heterogeneity in history lineage-specific mutations sheds new light population S. highlights importance as creative force generating biodiversity.

Язык: Английский

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