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Brysch-Herzberg M, Jia GS, Sipiczki M, Seidel M, Zhang WC, Du LL. Reinstatement of the fission yeast species Schizosaccharomyces versatilis Wickerham et Duprat, a sibling species of Schizosaccharomyces japonicus. Yeast 2024; 41:108-127. [PMID: 38450805 DOI: 10.1002/yea.3922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 03/08/2024] Open
Abstract
Schizosaccharomyces japonicus Yukawa et Maki (1931) and Schizosaccharomyces versatilis Wickerham et Duprat (1945) have been treated as varieties of S. japonicus or as conspecific, based on various approaches including mating trials and nDNA/nDNA optical reassociation studies. However, the type strains of S. japonicus and S. versatilis differ by five substitutions (99.15% identity) and one 1-bp indel in the sequences of the D1/D2 domain of the 26S rRNA gene, and 23 substitutions (96.3% identity) and 31-bp indels in the sequences of internal transcribed spacer (ITS) of rRNA, suggesting that they may not be conspecific. To reassess their taxonomic status, we conducted mating trials and whole-genome analyses. Mating trials using the type strains showed a strong but incomplete prezygotic sterility barrier, yielding interspecies mating products at two orders of magnitude lower efficiency than intraspecies matings. These mating products, which were exclusively allodiploid hybrids, were unable to undergo the haplontic life cycle of the parents. We generated chromosome-level gap-less genome assemblies for both type strains. Whole genome sequences yielded an average nucleotide identity (ANI) of 86.4%, indicating clear separation of S. japonicus and S. versatilis. Based on these findings, we propose the reinstatement of S. versatilis as a distinct species (holotype strain: CBS 103T and ex-types: NRRL Y-1026, NBRC 1607, ATCC 9987, PYCC 7100; Mycobank no.: 847838).
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Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn, Germany
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn, Germany
| | - Wen-Cai Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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D'Angiolo M, Bähler J. New species, genome assemblies, and tools shed fresh light on fission yeasts. Yeast 2024; 41:69-72. [PMID: 38466717 DOI: 10.1002/yea.3930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 03/13/2024] Open
Affiliation(s)
- Melania D'Angiolo
- Department of Genetics, Evolution & Environment, Institute of Healthy Ageing, University College London, London, UK
| | - Jürg Bähler
- Department of Genetics, Evolution & Environment, Institute of Healthy Ageing, University College London, London, UK
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Rutkowski D, Weston M, Vannette RL. Bees just wanna have fungi: a review of bee associations with nonpathogenic fungi. FEMS Microbiol Ecol 2023; 99:fiad077. [PMID: 37422442 PMCID: PMC10370288 DOI: 10.1093/femsec/fiad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/15/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023] Open
Abstract
Bee-fungus associations are common, and while most studies focus on entomopathogens, emerging evidence suggests that bees associate with a variety of symbiotic fungi that can influence bee behavior and health. Here, we review nonpathogenic fungal taxa associated with different bee species and bee-related habitats. We synthesize results of studies examining fungal effects on bee behavior, development, survival, and fitness. We find that fungal communities differ across habitats, with some groups restricted mostly to flowers (Metschnikowia), while others are present almost exclusively in stored provisions (Zygosaccharomyces). Starmerella yeasts are found in multiple habitats in association with many bee species. Bee species differ widely in the abundance and identity of fungi hosted. Functional studies suggest that yeasts affect bee foraging, development, and pathogen interactions, though few bee and fungal taxa have been examined in this context. Rarely, fungi are obligately beneficial symbionts of bees, whereas most are facultative bee associates with unknown or ecologically contextual effects. Fungicides can reduce fungal abundance and alter fungal communities associated with bees, potentially disrupting bee-fungi associations. We recommend that future study focus on fungi associated with non-honeybee species and examine multiple bee life stages to document fungal composition, abundance, and mechanistic effects on bees.
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Affiliation(s)
- Danielle Rutkowski
- 367 Briggs Hall, Department of Entomology and Nematology, University of California Davis, Davis, CA 95616, United States
| | - Makena Weston
- 367 Briggs Hall, Department of Entomology and Nematology, University of California Davis, Davis, CA 95616, United States
| | - Rachel L Vannette
- 367 Briggs Hall, Department of Entomology and Nematology, University of California Davis, Davis, CA 95616, United States
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Brysch-Herzberg M, Jia GS, Sipiczki M, Seidel M, Li W, Assali I, Du LL. Schizosaccharomyces lindneri sp. nov., a fission yeast occurring in honey. Yeast 2023. [PMID: 37243506 DOI: 10.1002/yea.3857] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/29/2023] Open
Abstract
Two strains of fission yeast were isolated from honey. They differ from the type strain of Schizosaccharomyces octosporus by three substitutions in the D1/D2 domain of the nuclear 26S large subunit ribosomal RNA (rRNA) gene sequence, resulting in a 99.5% identity. In the internal transcribed spacer (ITS) region (consisting of ITS1, 5.8S rDNA, and ITS2), the strains differ from S. octosporus by 16 gaps and 91 substitutions, which is equivalent to an identity of 88.1%. Genome sequencing on one of the new strains revealed that the average nucleotide identity (ANI) between its genome and the reference genome of S. octosporus is 90.43% and there exist major genome rearrangements between the two genomes. Mating analysis revealed that S. octosporus and one of the new strains are completely reproductively separated. A strong prezygotic barrier exists and the few mating products consist of diploid hybrids that do not form recombinant ascospores. In the new strains, asci are either zygotic, arising from conjugation, or they develop without conjugation from asexual cells (azygotic). Compared to the currently recognized Schizosaccharomyces species, the spectrum of nutrients that are assimilated by the new strains is restricted. Of the 43 carbohydrates that were included in the physiological standard tests, only 7 were assimilated. According to the results of the genome sequence analysis, the mating trials, and the phenotypic characterization, the new species Schizosaccharomyces lindneri is described to accommodate the two strains (holotype: CBS 18203T and ex-type: MUCL 58363; MycoBank no.: MB 847838).
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Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, Debrecen, Hungary
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Wen Li
- National Institute of Biological Sciences, Beijing, China
| | - Imen Assali
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University of Applied Sciences, Heilbronn, Germany
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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Jia GS, Zhang WC, Liang Y, Liu XH, Rhind N, Pidoux A, Brysch-Herzberg M, Du LL. A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus. G3 (BETHESDA, MD.) 2023; 13:jkad028. [PMID: 36748990 PMCID: PMC10085805 DOI: 10.1093/g3journal/jkad028] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/08/2023]
Abstract
Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes of S. pombe and 3 other fission yeast species S. japonicus, S. octosporus, and S. cryophilus has enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast species S. osmophilus and obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5,098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed that S. osmophilus is most closely related to S. octosporus and these 2 species diverged around 16 million years ago. To demonstrate the utility of this S. osmophilus reference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of 2 types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of 2 types of mitochondrial selfish elements.
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Affiliation(s)
- Guo-Song Jia
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wen-Cai Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yue Liang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xi-Han Liu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Nicholas Rhind
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alison Pidoux
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Heilbronn 74081, Germany
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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Seike T, Niki H. Pheromone Response and Mating Behavior in Fission Yeast. Microbiol Mol Biol Rev 2022; 86:e0013022. [PMID: 36468849 PMCID: PMC9769774 DOI: 10.1128/mmbr.00130-22] [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] [Indexed: 12/12/2022] Open
Abstract
Most ascomycete fungi, including the fission yeast Schizosaccharomyces pombe, secrete two peptidyl mating pheromones: C-terminally modified and unmodified peptides. S. pombe has two mating types, plus and minus, which secrete two different pheromones, P-factor (unmodified) and M-factor (modified), respectively. These pheromones are specifically recognized by receptors on the cell surface of cells of opposite mating types, which trigger a pheromone response. Recognition between pheromones and their corresponding receptors is important for mate discrimination; therefore, genetic changes in pheromone or receptor genes affect mate recognition and cause reproductive isolation that limits gene flow between populations. Such genetic variation in recognition via the pheromone/receptor system may drive speciation. Our recent studies reported that two pheromone receptors in S. pombe might have different stringencies in pheromone recognition. In this review, we focus on the molecular mechanism of pheromone response and mating behavior, emphasizing pheromone diversification and its impact on reproductive isolation in S. pombe and closely related fission yeast species. We speculate that the "asymmetric" system might allow flexible adaptation to pheromone mutational changes while maintaining stringent recognition of mating partners. The loss of pheromone activity results in the extinction of an organism's lineage. Therefore, genetic changes in pheromones and their receptors may occur gradually and/or coincidently before speciation. Our findings suggest that the M-factor plays an important role in partner discrimination, whereas P-factor communication allows flexible adaptation to create variations in S. pombe. Our inferences provide new insights into the evolutionary mechanisms underlying pheromone diversification.
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Affiliation(s)
- Taisuke Seike
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka, Japan
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De Carvalho M, Jia GS, Nidamangala Srinivasa A, Billmyre RB, Xu YH, Lange JJ, Sabbarini IM, Du LL, Zanders SE. The wtf meiotic driver gene family has unexpectedly persisted for over 100 million years. eLife 2022; 11:e81149. [PMID: 36227631 PMCID: PMC9562144 DOI: 10.7554/elife.81149] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Meiotic drivers are selfish elements that bias their own transmission into more than half of the viable progeny produced by a driver+/driver- heterozygote. Meiotic drivers are thought to exist for relatively short evolutionary timespans because a driver gene or gene family is often found in a single species or in a group of very closely related species. Additionally, drivers are generally considered doomed to extinction when they spread to fixation or when suppressors arise. In this study, we examine the evolutionary history of the wtf meiotic drivers first discovered in the fission yeast Schizosaccharomyces pombe. We identify homologous genes in three other fission yeast species, S. octosporus, S. osmophilus, and S. cryophilus, which are estimated to have diverged over 100 million years ago from the S. pombe lineage. Synteny evidence supports that wtf genes were present in the common ancestor of these four species. Moreover, the ancestral genes were likely drivers as wtf genes in S. octosporus cause meiotic drive. Our findings indicate that meiotic drive systems can be maintained for long evolutionary timespans.
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Affiliation(s)
- Mickaël De Carvalho
- Stowers Institute for Medical ResearchKansas CityUnited States
- Open UniversityMilton KeynesUnited Kingdom
| | - Guo-Song Jia
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua UniversityBeijingChina
- National Institute of Biological Sciences, BeijingBeijingChina
| | - Ananya Nidamangala Srinivasa
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular and Integrative Physiology, University of Kansas Medical CenterKansas CityUnited States
| | | | - Yan-Hui Xu
- National Institute of Biological Sciences, BeijingBeijingChina
| | - Jeffrey J Lange
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | - Li-Lin Du
- National Institute of Biological Sciences, BeijingBeijingChina
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua UniversityBeijingChina
| | - Sarah E Zanders
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular and Integrative Physiology, University of Kansas Medical CenterKansas CityUnited States
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8
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Brysch-Herzberg M, Jia GS, Seidel M, Assali I, Du LL. Insights into the ecology of Schizosaccharomyces species in natural and artificial habitats. Antonie van Leeuwenhoek 2022; 115:661-695. [PMID: 35359202 PMCID: PMC9007792 DOI: 10.1007/s10482-022-01720-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
Abstract
The fission yeast genus Schizosaccharomyces contains important model organisms for biological research. In particular, S. pombe is a widely used model eukaryote. So far little is known about the natural and artificial habitats of species in this genus. Finding out where S. pombe and other fission yeast species occur and how they live in their habitats can promote better understanding of their biology. Here we investigate in which substrates S. pombe, S. octosporus, S. osmophilus and S. japonicus are present. To this end about 2100 samples consisting of soil, tree sap fluxes, fresh fruit, dried fruit, honey, cacao beans, molasses and other substrates were analyzed. Effective isolation methods that allow efficient isolation of the above mentioned species were developed. Based on the frequency of isolating different fission yeast species in various substrates and on extensive literature survey, conclusions are drawn on their ecology. The results suggest that the primary habitat of S. pombe and S. octosporus is honeybee honey. Both species were also frequently detected on certain dried fruit like raisins, mango or pineapple to which they could be brought by the honey bees during ripening or during drying. While S. pombe was regularly isolated from grape mash and from fermented raw cacao beans S. octosporus was never isolated from fresh fruit. The main habitat of S. osmophilus seems to be solitary bee beebread. It was rarely isolated from raisins. S. japonicus was mainly found in forest substrates although it occurs on fruit and in fruit fermentations, too.
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Affiliation(s)
- Michael Brysch-Herzberg
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, 102206 China
| | - Martin Seidel
- Laboratory for Wine Microbiology, Department International Business, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany
| | - Imen Assali
- Department of Bioengineering, National Engineering School of Sfax, University of Sfax, Soukra, km 4, 3038 Sfax, Tunisia
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, 102206 China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206 China
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9
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Shraim R, Nieuwenhuis BPS. The search for Schizosaccharomyces fission yeasts in environmental meta-transcriptomes. Yeast 2021; 39:83-94. [PMID: 34967063 DOI: 10.1002/yea.3689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/09/2021] [Accepted: 12/23/2021] [Indexed: 11/07/2022] Open
Abstract
Fission yeast is an important model organism in evolutionary genetics and cell biology research. Nevertheless, most research is limited to a single laboratory strain and knowledge of its natural occurrence is limited, which reduces our understanding of its life history and hinders isolation of new strains from nature. Understanding the natural diversity of fission yeast can provide insight into its genetic and phenotypic diversity and the evolutionary processes that shaped these. Here we aimed to identify candidate natural habitats of fission yeasts by searching through a large collection of publicly available environmental metatranscriptomic datasets. Using a custom pipeline, we processed over 13,000 NCBI SRA accessions, from a wide range of 34 different environmental categories. Overall, we found a very low abundance of putative yeast transcripts, with most fission yeast signatures coming from the categories of 'food' and 'terrestrial arthropods'. Additionally, a signal could be found in a variety of marine and fresh aquatic habitats. Our results do not provide a conclusive answer on the natural habitat of fission yeasts, but our analysis further narrows the range of locations where fission yeasts naturally occur.
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Affiliation(s)
- Rasha Shraim
- The SFI Centre for Research Training in Genomics Data Sciences, National University of Ireland Galway and Department of Public Health and Primary Care, School of Medicine, Trinity College Dublin, Republic of Ireland.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Germany
| | - Bart P S Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Germany
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Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection. J Fungi (Basel) 2021; 7:jof7100864. [PMID: 34682285 PMCID: PMC8537764 DOI: 10.3390/jof7100864] [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: 09/10/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
Fission yeasts have a unique life history and exhibit distinct evolutionary patterns from other yeasts. Besides, the species demonstrate stable genome structures despite the relatively fast evolution of their genomic sequences. To reveal what could be the reason for that, comparative genomic analyses were carried out. Our results provided evidence that the structural and sequence evolution of the fission yeasts were correlated. Moreover, we revealed ancestral locally collinear blocks (aLCBs), which could have been inherited from their last common ancestor. These aLCBs proved to be the most conserved regions of the genomes as the aLCBs contain almost eight genes/blocks on average in the same orientation and order across the species. Gene order of the aLCBs is mainly fission-yeast-specific but supports the idea of filamentous ancestors. Nevertheless, the sequences and gene structures within the aLCBs are as mutable as any sequences in other parts of the genomes. Although genes of certain Gene Ontology (GO) categories tend to cluster at the aLCBs, those GO enrichments are not related to biological functions or high co-expression rates, they are, rather, determined by the density of essential genes and Rec12 cleavage sites. These data and our simulations indicated that aLCBs might not only be remnants of ancestral gene order but are also maintained by natural selection.
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Wang X, Xu R, Wang Y, Liu Z, Lou R, Sugiyama T. Yesprit and Yeaseq: Applications for designing primers and browsing sequences for research using the four Schizosaccharomyces species. Yeast 2021; 38:583-591. [PMID: 34251689 DOI: 10.1002/yea.3660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/17/2021] [Accepted: 05/27/2021] [Indexed: 11/05/2022] Open
Abstract
The polymerase chain reaction (PCR)-based gene targeting method, which can delete a specific gene or introduce tags, has been widely utilized to study gene function in fission yeast. One of the critical steps in this method is to design primers for amplifying DNA fragments of deletion or tagging modules and for checking the integration of those DNA fragments at designated loci. Although the primer design tool Pombe PCR Primer Program (PPPP) is available for Schizosaccharomyces pombe, there is no such publicly available application for the other three fission yeast species, S. cryophilus, S. japonicus, and S. octosporus. Likewise, no application enabling DNA/protein sequence retrieval for these three fission yeast species is available either. Therefore, access to such functionality would substantially assist in retrieval of gene sequences of interest and primer design in these fission yeast species. In this report, we describe two applications for fission yeast study: Yesprit and Yeaseq. Yesprit is a primer design tool for strain construction using the PCR-based method, and Yeaseq is a sequence viewer that can acquire the DNA/protein sequences of specific genes. Both tools can be run on the Windows, macOS, and Linux platforms. We believe that the Yesprit and Yeaseq will facilitate research using the four fission yeast species.
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Affiliation(s)
- Xindi Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ruoming Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yichen Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ziyue Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ronghui Lou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Tomoyasu Sugiyama
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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12
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Fukunaga T, Tanaka N, Furumoto T, Nakakita S, Ohashi T, Higuchi Y, Maekawa H, Takegawa K. Substrate specificities of α1,2- and α1,3-galactosyltransferases and characterization of Gmh1p and Otg1p in Schizosaccharomyces pombe. Glycobiology 2021; 31:1037-1045. [PMID: 33909078 DOI: 10.1093/glycob/cwab028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 12/26/2022] Open
Abstract
In the fission yeast Schizosaccharomyces pombe, α1,2- and α1,3-linked D-galactose (Gal) residues are transferred to N- and O-linked oligosaccharides of glycoproteins by galactosyltransferases. Although the galactomannans are important for cell-cell communication in S. pombe (e.g., in non-sexual aggregation), the mechanisms underlying galactosylation in cells remain unclear. S. pombe has 10 galactosyltransferase-related genes: seven belonging to glycosyltransferase (GT) family 34 and three belonging GT family 8. Disruption of all 10 α-galactosyltransferases (strain Δ10GalT) has been shown to result in a complete lack of α-Gal residues. Here, we have investigated the function and substrate specificities of galactosyltransferases in S pombe by using strains expressing single α-galactosyltransferases in the Δ10GalT background. High-performance liquid chromatography (HPLC) analysis of pyridylaminated O-linked oligosaccharides showed that two GT family 34 α1,2-galactosyltransferases (Gma12p and Gmh6p) and two GT family 8 α1,3-galactosyltransferases (Otg2p and Otg3p) are involved in galactosylation of O-linked oligosaccharide. Moreover, 1H-NMR of N-glycans revealed that three GT family 34 α1,2-galactosyltransferases (Gmh1p, Gmh2p, and Gmh3p) are required for galactosylation of N-linked oligosaccharides. Furthermore, HPLC and lectin-blot analysis revealed that Otg1p showed α1,3-galactosyltransferase activity under conditions of co-expression with Gmh6p, indicating that α-1,2-linked galactose is required for the galactosylation activity of Otg1p in S. pombe. In conclusion, eight galactosyltransferases have been shown to have activity in S. pombe with different substrate specificities. These findings will be useful for genetically tailoring the galactosylation of both N- and O- glycans in fission yeast.
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Affiliation(s)
- Takamasa Fukunaga
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Naotaka Tanaka
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa, Japan
| | - Toshio Furumoto
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Kagawa, Japan
| | - Shinichi Nakakita
- Department of Endocrinology; Department of Immunology and Immunopathology, Faculty of Medicine, Kagawa University, Kagawa, Japan; and Life Science Research Center, Kagawa University, Kagawa, Japan
| | - Takao Ohashi
- Faculty of Science and Engineering Department of Life Science, Setsunan University, Osaka, Japan
| | - Yujiro Higuchi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Hiromi Maekawa
- Centre for Promotion of International Education and Research, Faculty of Agriculture, Kyushu university, Fukuoka, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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Fukunaga T, Tanaka N, Furumoto T, Nakakita S, Ohashi T, Higuchi Y, Maekawa H, Takegawa K. Characterization of N- and O-linked galactosylated oligosaccharides from fission yeast species. J Biosci Bioeng 2020; 130:128-136. [DOI: 10.1016/j.jbiosc.2020.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/04/2020] [Accepted: 03/14/2020] [Indexed: 10/24/2022]
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