RESUMEN
This study employs simple approaches involving melt blending and Fused Deposition Modeling (FDM) 3D printing to fabricate a light-responsive shape memory composite. And, this composite material is used for the design of optically controlled devices that mimics the blooming of flowers in the natural environment. The composite material utilizes poly(ε-caprolactone) (PCL) and thermoplastic polyurethane (TPU) as the matrix, with lignin (L) serving as a functional filler. The analysis indicates that, due to the excellent photothermal conversion efficiency of lignin, under constant illumination the shape memory materials heat up to 50⯰C within 40â¯s, the shape recovery rate exceeds 95.06â¯%. Lignin ameliorated the rheological deficiencies of TPU, with the composite material viscosity decreasing from 103 to 101 at an angular frequency of 100â¯rad/s, enhancing its compatibility with FDM processes. This research offers greater economic efficiency compared to conventional light-responsive materials and a simpler production method.
Asunto(s)
Luz , Lignina , Poliésteres , Impresión Tridimensional , Lignina/química , Poliésteres/química , Poliuretanos/química , Materiales Inteligentes/química , Viscosidad , ReologíaRESUMEN
Canavanine resistance has been used to analyze mutation rates in the fission yeast Schizosaccharomyces pombe . However, the genetic basis of canavanine resistance in this organism remains incompletely understood. Here, we performed whole genome sequencing on five spontaneously arising canavanine-resistant S. pombe mutants, including the can2-1 mutant isolated in the 1970s. This analysis revealed that three mutants, including can2-1 , experienced terminal deletions of the left arm of chromosome II, leading to the loss of multiple amino acid transporter genes. Interestingly, these three mutants underwent chromosome terminal deletion through distinct mechanisms, including homology-driven translocation, homology-independent chromosome fusion, and de novo telomere addition. Our findings shed new light on the genetic basis of canavanine resistance and mechanisms underlying chromosome terminal deletions in fission yeast.
RESUMEN
Killer meiotic drivers (KMDs) skew allele transmission in their favor by killing meiotic progeny not inheriting the driver allele. Despite their widespread presence in eukaryotes, the molecular mechanisms behind their selfish behavior are poorly understood. In several fission yeast species, single-gene KMDs belonging to the wtf gene family exert selfish killing by expressing a toxin and an antidote through alternative transcription initiation. Here we investigate how the toxin and antidote products of a wtf-family KMD gene can act antagonistically. Both the toxin and the antidote are multi-transmembrane proteins, differing only in their N-terminal cytosolic tails. We find that the antidote employs PY motifs (Leu/Pro-Pro-X-Tyr) in its N-terminal cytosolic tail to bind Rsp5/NEDD4 family ubiquitin ligases, which ubiquitinate the antidote. Mutating PY motifs or attaching a deubiquitinating enzyme transforms the antidote into a toxic protein. Ubiquitination promotes the transport of the antidote from the trans-Golgi network to the endosome, thereby preventing it from causing toxicity. A physical interaction between the antidote and the toxin enables the ubiquitinated antidote to translocate the toxin to the endosome and neutralize its toxicity. We propose that post-translational modification-mediated protein localization and/or activity changes may be a common mechanism governing the antagonistic duality of single-gene KMDs.
Asunto(s)
Schizosaccharomyces , Schizosaccharomyces/genética , Schizosaccharomyces/metabolismo , Antídotos , Ubiquitinación , Aparato de Golgi/metabolismo , Ubiquitina/metabolismo , Complejos de Clasificación Endosomal Requeridos para el Transporte/metabolismo , Ubiquitina-Proteína Ligasas/metabolismoRESUMEN
Selective macroautophagy of the endoplasmic reticulum (ER) and the nucleus, known as ER-phagy and nucleophagy, respectively, are processes whose mechanisms remain inadequately understood. Through an imaging-based screen, we find that in the fission yeast Schizosaccharomyces pombe, Yep1 (also known as Hva22 or Rop1), the ortholog of human REEP1-4, is essential for ER-phagy and nucleophagy but not for bulk autophagy. In the absence of Yep1, the initial phase of ER-phagy and nucleophagy proceeds normally, with the ER-phagy/nucleophagy receptor Epr1 coassembling with Atg8. However, ER-phagy/nucleophagy cargos fail to reach the vacuole. Instead, nucleus- and cortical-ER-derived membrane structures not enclosed within autophagosomes accumulate in the cytoplasm. Intriguingly, the outer membranes of nucleus-derived structures remain continuous with the nuclear envelope-ER network, suggesting a possible outer membrane fission defect during cargo separation from source compartments. We find that the ER-phagy role of Yep1 relies on its abilities to self-interact and shape membranes and requires its C-terminal amphipathic helices. Moreover, we show that human REEP1-4 and budding yeast Atg40 can functionally substitute for Yep1 in ER-phagy, and Atg40 is a divergent ortholog of Yep1 and REEP1-4. Our findings uncover an unexpected mechanism governing the autophagosomal enclosure of ER-phagy/nucleophagy cargos and shed new light on the functions and evolution of REEP family proteins.
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Schizosaccharomyces , Humanos , Schizosaccharomyces/genética , Schizosaccharomyces/metabolismo , Autofagia/genética , Retículo Endoplásmico/metabolismo , Autofagosomas/metabolismo , Familia de las Proteínas 8 Relacionadas con la Autofagia/genética , Familia de las Proteínas 8 Relacionadas con la Autofagia/metabolismo , Estrés del Retículo Endoplásmico , Proteínas de Transporte de Membrana/metabolismoRESUMEN
In Schizosaccharomyces pombe, the can1-1 mutation confers resistance to the toxic arginine analog canavanine. This mutation has been assumed to disrupt a gene encoding an arginine transporter. In PomBase, the gene SPBC18H10.16 is currently designated can1. Here, we sequenced the genomes of three can1-1 strains. No mutations were found in SPBC18H10.16. Instead, these strains harbor an R175C mutation in the gene any1 (SPBC18H10.20c). any1 encodes an α-arrestin that acts as a ubiquitin ligase adaptor to downregulate plasma membrane amino acid transporters. Our findings indicate that can1-1 is not a loss-of-function mutation in an amino acid transporter gene, but a possible gain-of-function mutation in a gene encoding a negative regulator of amino acid transporters.
RESUMEN
Hybridization is thought to reactivate transposable elements (TEs) that were efficiently suppressed in the genomes of the parental hosts. Here, we provide evidence for this "genomic shock hypothesis" in the fission yeast Schizosaccharomyces pombe In this species, two divergent lineages (Sp and Sk) have experienced recent, likely human-induced, hybridization. We used long-read sequencing data to assemble genomes of 37 samples derived from 31 S. pombe strains spanning a wide range of ancestral admixture proportions. A comprehensive TE inventory revealed exclusive presence of long terminal repeat (LTR) retrotransposons. Sequence analysis of active full-length elements, as well as solo LTRs, revealed a complex history of homologous recombination. Population genetic analyses of syntenic sequences placed insertion of many solo LTRs before the split of the Sp and Sk lineages. Most full-length elements were inserted more recently, after hybridization. With the exception of a single full-length element with signs of positive selection, both solo LTRs and, in particular, full-length elements carry signatures of purifying selection indicating effective removal by the host. Consistent with reactivation upon hybridization, the number of full-length LTR retrotransposons, varying extensively from zero to 87 among strains, significantly increases with the degree of genomic admixture. This study gives a detailed account of global TE diversity in S. pombe, documents complex recombination histories within TE elements, and provides evidence for the "genomic shock hypothesis."
Asunto(s)
Schizosaccharomyces , Elementos Transponibles de ADN/genética , Evolución Molecular , Genoma Fúngico , Humanos , Retroelementos/genética , Schizosaccharomyces/genética , Secuencias Repetidas Terminales/genéticaRESUMEN
Conditional degron technologies, which allow a protein of interest to be degraded in an inducible manner, are important tools for biological research, and are especially useful for creating conditional loss-of-function mutants of essential genes. The auxin-inducible degron (AID) technology, which utilizes plant auxin signaling components to control protein degradation in nonplant species, is a widely used small-molecular-controlled degradation method in yeasts and animals. However, the currently available AID systems still have room for further optimization. Here, we have improved the AID system for the fission yeast Schizosaccharomyces pombe by optimizing all three components: the AID degron, the small-molecule inducer, and the inducer-responsive F-box protein. We chose a 36-amino-acid sequence of the Arabidopsis IAA17 protein as the degron and employed three tandem copies of it to enhance efficiency. To minimize undesirable side effects of the inducer, we adopted a bulky analog of auxin, 5-adamantyl-IAA, and paired it with the F-box protein OsTIR1 that harbors a mutation (F74A) at the auxin-binding pocket. 5-adamantyl-IAA, when utilized with OsTIR1-F74A, is effective at concentrations thousands of times lower than auxin used in combination with wild-type OsTIR1. We tested our improved AID system on 10 essential genes and achieved inducible lethality for all of them, including ones that could not be effectively inactivated using a previously published AID system. Our improved AID system should facilitate the construction of conditional loss-of-function mutants in fission yeast.
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Proteínas F-Box , Schizosaccharomyces , Animales , Proteínas F-Box/genética , Ácidos Indolacéticos/metabolismo , Ácidos Indolacéticos/farmacología , Mutación , Proteolisis , Schizosaccharomyces/genética , Schizosaccharomyces/metabolismoRESUMEN
Using genetic mutations to study protein functions in vivo is a central paradigm of modern biology. Single-domain camelid antibodies generated against GFP have been engineered as nanobodies or GFP-binding proteins (GBPs) that can bind GFP as well as some GFP variants with high affinity and selectivity. In this study, we have used GBP-mCherry fusion protein as a tool to perturb the natural functions of a few kinetochore proteins in the fission yeast Schizosaccharomyces pombe. We found that cells simultaneously expressing GBP-mCherry and the GFP-tagged inner kinetochore protein Cnp1 are sensitive to high temperature and microtubule drug thiabendazole (TBZ). In addition, kinetochore-targeted GBP-mCherry by a few major kinetochore proteins with GFP tags causes defects in faithful chromosome segregation. Thus, this setting compromises the functions of kinetochores and renders cells to behave like conditional mutants. Our study highlights the potential of using GBP as a general tool to perturb the function of some GFP-tagged proteins in vivo with the objective of understanding their functional relevance to certain physiological processes, not only in yeasts, but also potentially in other model systems.
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Proteínas de Schizosaccharomyces pombe , Schizosaccharomyces , Proteínas Portadoras , Proteínas Cromosómicas no Histona/metabolismo , Segregación Cromosómica , Cinetocoros/metabolismo , Schizosaccharomyces/genética , Schizosaccharomyces/metabolismo , Proteínas de Schizosaccharomyces pombe/genética , Proteínas de Schizosaccharomyces pombe/metabolismoRESUMEN
Objective: Several studies have suggested an involvement of the immune system in the occurrence and development of chronic obstructive pulmonary disease (COPD), but the mechanism is still unclear. The aim of this study was to explore the mechanism of ginsenoside in inhibiting inflammation by regulating FOXP3 in COPD. Methods: Eighty COPD patients were selected and 35 healthy people were enrolled in the study to determine clinical efficacy, observation index, and SGRQ scores. Percentage of Treg and Th17 cells were detected by flow cytometry; HE staining was used to detect the effect of ginsenoside therapy on pathological changes of COPD in mice. Additionally, we transfected FOXP3 inhibitor; RT-PCR and western blot were used to detect the inflammation related genes and proteins. Results: The basic information of the patients were comparable. The clinical outcome in the treatment group was better than that in the control group, which indicated that ginsenoside has a certain therapeutic effect on COPD patients. The lung function and 6MWT distance results indicated that ginsenoside could stabilize the clinical symptoms of COPD patients and improve their quality of life. Flow cytometry results showed that ginsenoside can increase Treg expression while reducing Th17 cell expression. RT-PCR and western blot results showed that the expression of TNF-α and IL-17 in the model group was significantly increased after treatment, obviously caused by an increased expression of FOXP3. Conclusion: Ginsenoside can inhibit inflammation in COPD by up-regulating FOXP3.
Asunto(s)
Antiinflamatorios/farmacología , Ginsenósidos/farmacología , Inflamación/tratamiento farmacológico , Enfermedad Pulmonar Obstructiva Crónica/tratamiento farmacológico , Animales , Antiinflamatorios/administración & dosificación , Estudios de Casos y Controles , Femenino , Factores de Transcripción Forkhead/genética , Ginsenósidos/administración & dosificación , Humanos , Inflamación/fisiopatología , Masculino , Ratones , Ratones Endogámicos C57BL , Enfermedad Pulmonar Obstructiva Crónica/fisiopatología , Calidad de Vida , Linfocitos T Reguladores/inmunología , Células Th17/inmunologíaRESUMEN
Autophagic degradation of the endoplasmic reticulum (ER-phagy) is triggered by ER stress in diverse organisms. However, molecular mechanisms governing ER stress-induced ER-phagy remain insufficiently understood. Here we report that ER stress-induced ER-phagy in the fission yeast Schizosaccharomyces pombe requires Epr1, a soluble Atg8-interacting ER-phagy receptor. Epr1 localizes to the ER through interacting with integral ER membrane proteins VAPs. Bridging an Atg8-VAP association is the main ER-phagy role of Epr1, as it can be bypassed by an artificial Atg8-VAP tether. VAPs contribute to ER-phagy not only by tethering Atg8 to the ER membrane, but also by maintaining the ER-plasma membrane contact. Epr1 is upregulated during ER stress by the unfolded protein response (UPR) regulator Ire1. Loss of Epr1 reduces survival against ER stress. Conversely, increasing Epr1 expression suppresses the ER-phagy defect and ER stress sensitivity of cells lacking Ire1. Our findings expand and deepen the molecular understanding of ER-phagy.
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Estrés del Retículo Endoplásmico/genética , Endorribonucleasas/genética , Proteínas R-SNARE/genética , Autofagosomas/metabolismo , Autofagia/genética , Familia de las Proteínas 8 Relacionadas con la Autofagia/genética , Retículo Endoplásmico/genética , Regulación Fúngica de la Expresión Génica/genética , Proteolisis , Schizosaccharomyces/genética , Proteínas de Schizosaccharomyces pombe/genética , Respuesta de Proteína Desplegada/genéticaRESUMEN
Structure-specific endonucleases (SSEs) play key roles in DNA replication, recombination, and repair. SSEs must be tightly regulated to ensure genome stability but their regulatory mechanisms remain incompletely understood. Here, we show that in the fission yeast Schizosaccharomyces pombe, the activities of two SSEs, Dna2 and Rad16 (ortholog of human XPF), are temporally controlled during the cell cycle by the CRL4Cdt2 ubiquitin ligase. CRL4Cdt2 targets Pxd1, an inhibitor of Dna2 and an activator of Rad16, for degradation in S phase. The ubiquitination and degradation of Pxd1 is dependent on CRL4Cdt2, PCNA, and a PCNA-binding degron motif on Pxd1. CRL4Cdt2-mediated Pxd1 degradation prevents Pxd1 from interfering with the normal S-phase functions of Dna2. Moreover, Pxd1 degradation leads to a reduction of Rad16 nuclease activity in S phase, and restrains Rad16-mediated single-strand annealing, a hazardous pathway of repairing double-strand breaks. These results demonstrate a new role of the CRL4Cdt2 ubiquitin ligase in genome stability maintenance and shed new light on how SSE activities are regulated during the cell cycle.
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Proteínas de Unión al ADN/genética , Endonucleasas de ADN Solapado/genética , Proteínas Nucleares/genética , Proteínas de Schizosaccharomyces pombe/genética , Reparación del ADN/genética , Replicación del ADN/genética , Inestabilidad Genómica/genética , Humanos , Fase S/genética , Schizosaccharomyces/genética , Ubiquitina/genética , Ubiquitina-Proteína Ligasas/genética , Ubiquitinación/genéticaRESUMEN
The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analyzing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the data sets generated in this study will facilitate future research on genome evolution.
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Evolución Molecular , Variación Genética , Genoma Mitocondrial , Metagenómica , Recombinación Genética , Schizosaccharomyces/clasificación , Schizosaccharomyces/genética , FilogeniaRESUMEN
Gene essentiality is a variable phenotypic trait, but to what extent and how essential genes can become dispensable for viability remain unclear. Here, we investigate 'bypass of essentiality (BOE)' - an underexplored type of digenic genetic interaction that renders essential genes dispensable. Through analyzing essential genes on one of the six chromosome arms of the fission yeast Schizosaccharomyces pombe, we find that, remarkably, as many as 27% of them can be converted to non-essential genes by BOE interactions. Using this dataset we identify three principles of essentiality bypass: bypassable essential genes tend to have lower importance, tend to exhibit differential essentiality between species, and tend to act with other bypassable genes. In addition, we delineate mechanisms underlying bypassable essentiality, including the previously unappreciated mechanism of dormant redundancy between paralogs. The new insights gained on bypassable essentiality deepen our understanding of genotype-phenotype relationships and will facilitate drug development related to essential genes.
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Epistasis Genética , Genes Esenciales , Genes Fúngicos/genética , Schizosaccharomyces/genética , Mapeo Cromosómico , Cromosomas , Bases de Datos Genéticas , Evolución Molecular , Redes Reguladoras de Genes , Genotipo , Modelos Genéticos , Fenotipo , Plásmidos/genética , Especificidad de la EspecieRESUMEN
Hexavalent chromium [Cr(VI)] damages DNA and causes cancer, but it is unclear which DNA damage responses (DDRs) most critically protect cells from chromate toxicity. Here, genome-wide quantitative functional profiling, DDR measurements and genetic interaction assays in Schizosaccharomyces pombe reveal a chromate toxicogenomic profile that closely resembles the cancer chemotherapeutic drug camptothecin (CPT), which traps Topoisomerase 1 (Top1)-DNA covalent complex (Top1cc) at the 3' end of single-stand breaks (SSBs), resulting in replication fork collapse. ATR/Rad3-dependent checkpoints that detect stalled and collapsed replication forks are crucial in Cr(VI)-treated cells, as is Mus81-dependent sister chromatid recombination (SCR) that repairs single-ended double-strand breaks (seDSBs) at broken replication forks. Surprisingly, chromate resistance does not require base excision repair (BER) or interstrand crosslink (ICL) repair, nor does co-elimination of XPA-dependent nucleotide excision repair (NER) and Rad18-mediated post-replication repair (PRR) confer chromate sensitivity in fission yeast. However, co-elimination of Tdp1 tyrosyl-DNA phosphodiesterase and Rad16-Swi10 (XPF-ERCC1) NER endonuclease synergistically enhances chromate toxicity in top1Δ cells. Pnk1 polynucleotide kinase phosphatase (PNKP), which restores 3'-hydroxyl ends to SSBs processed by Tdp1, is also critical for chromate resistance. Loss of Tdp1 ameliorates pnk1Δ chromate sensitivity while enhancing the requirement for Mus81. Thus, Tdp1 and PNKP, which prevent neurodegeneration in humans, repair an important class of Cr-induced SSBs that collapse replication forks.
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Roturas del ADN de Cadena Simple , Replicación del ADN , Hidrolasas Diéster Fosfóricas/metabolismo , Proteínas de Schizosaccharomyces pombe/metabolismo , Schizosaccharomyces/genética , Camptotecina/farmacología , Ciclo Celular/efectos de los fármacos , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Quinasa 1 Reguladora del Ciclo Celular (Checkpoint 1)/genética , Quinasa de Punto de Control 2/efectos de los fármacos , Cromatos/toxicidad , Cromátides/metabolismo , Reparación del ADN/efectos de los fármacos , ADN-Topoisomerasas de Tipo I/genética , ADN-Topoisomerasas de Tipo I/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Farmacorresistencia Fúngica , Endonucleasas/genética , Endonucleasas/metabolismo , Humanos , Hidrolasas Diéster Fosfóricas/genética , Polinucleótido 5'-Hidroxil-Quinasa/genética , Polinucleótido 5'-Hidroxil-Quinasa/metabolismo , Schizosaccharomyces/metabolismo , Proteínas de Schizosaccharomyces pombe/efectos de los fármacos , Proteínas de Schizosaccharomyces pombe/genéticaRESUMEN
Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast Schizosaccharomyces pombe. Both killers belong to the previously uncharacterized wtf gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them. Spores carrying one killer are protected from its killing effect but not that of the other killer. The killing and protecting activities can be uncoupled by mutation. The numbers and sequences of wtf genes vary considerably between S. pombe isolates, indicating rapid divergence. We propose that wtf genes contribute to the extensive intraspecific reproductive isolation in S. pombe, and represent ideal models for understanding how segregation-distorting elements act and evolve.
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Genes Fúngicos , Venenos/metabolismo , Schizosaccharomyces/efectos de los fármacos , Schizosaccharomyces/genética , Selección Genética , Esporas Fúngicas/efectos de los fármacos , Viabilidad Microbiana/efectos de los fármacos , Schizosaccharomyces/metabolismoRESUMEN
The action of DNA topoisomerase II (Top2) creates transient DNA breaks that are normally concealed inside Top2-DNA covalent complexes. Top2 poisons, including ubiquitously present natural compounds and clinically used anti-cancer drugs, trap Top2-DNA complexes. Here, we show that cells actively prevent Top2 degradation to avoid the exposure of concealed DNA breaks. A genome-wide screen revealed that fission yeast cells lacking Rrp2, an Snf2-family DNA translocase, are strongly sensitive to Top2 poisons. Loss of Rrp2 enhances SUMOylation-dependent ubiquitination and degradation of Top2, which in turn increases DNA damage at sites where Top2-DNA complexes are trapped. Rrp2 possesses SUMO-binding ability and prevents excessive Top2 degradation by competing against the SUMO-targeted ubiquitin ligase (STUbL) for SUMO chain binding and by displacing SUMOylated Top2 from DNA. The budding yeast homolog of Rrp2, Uls1, plays a similar role, indicating that this genome protection mechanism is widely employed, a finding with implications for cancer treatment.
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Daño del ADN , ADN-Topoisomerasas de Tipo II/metabolismo , ADN de Hongos/metabolismo , Proteínas de Unión al ADN/metabolismo , Genoma Fúngico , Inestabilidad Genómica , Proteínas de Schizosaccharomyces pombe/metabolismo , Schizosaccharomyces/enzimología , Sumoilación , Daño del ADN/efectos de los fármacos , ADN Helicasas/genética , ADN Helicasas/metabolismo , ADN-Topoisomerasas de Tipo II/genética , ADN de Hongos/efectos de los fármacos , ADN de Hongos/genética , Proteínas de Unión al ADN/genética , Resistencia a Medicamentos , Etopósido/farmacología , Genoma Fúngico/efectos de los fármacos , Inestabilidad Genómica/efectos de los fármacos , Mutación , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Proteolisis , Saccharomyces cerevisiae/enzimología , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Schizosaccharomyces/efectos de los fármacos , Schizosaccharomyces/genética , Proteínas de Schizosaccharomyces pombe/genética , Inhibidores de Topoisomerasa II/farmacología , Ubiquitina-Proteína Ligasas/genética , Ubiquitina-Proteína Ligasas/metabolismo , UbiquitinaciónRESUMEN
Heavy metals and metalloids such as cadmium [Cd(II)] and arsenic [As(III)] are widespread environmental toxicants responsible for multiple adverse health effects in humans. However, the molecular mechanisms underlying metal-induced cytotoxicity and carcinogenesis, as well as the detoxification and tolerance pathways, are incompletely understood. Here, we use global fitness profiling by barcode sequencing to quantitatively survey the Schizosaccharomyces pombe haploid deletome for genes that confer tolerance of cadmium or arsenic. We identified 106 genes required for cadmium resistance and 110 genes required for arsenic resistance, with a highly significant overlap of 36 genes. A subset of these 36 genes account for almost all proteins required for incorporating sulfur into the cysteine-rich glutathione and phytochelatin peptides that chelate cadmium and arsenic. A requirement for Mms19 is explained by its role in directing iron-sulfur cluster assembly into sulfite reductase as opposed to promoting DNA repair, as DNA damage response genes were not enriched among those required for cadmium or arsenic tolerance. Ubiquinone, siroheme, and pyridoxal 5'-phosphate biosynthesis were also identified as critical for Cd/As tolerance. Arsenic-specific pathways included prefoldin-mediated assembly of unfolded proteins and protein targeting to the peroxisome, whereas cadmium-specific pathways included plasma membrane and vacuolar transporters, as well as Spt-Ada-Gcn5-acetyltransferase (SAGA) transcriptional coactivator that controls expression of key genes required for cadmium tolerance. Notable differences are apparent with corresponding screens in the budding yeast Saccharomyces cerevisiae, underscoring the utility of analyzing toxic metal defense mechanisms in both organisms.
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Adaptación Biológica , Arsénico/farmacología , Cadmio/farmacología , Aptitud Genética , Schizosaccharomyces/efectos de los fármacos , Schizosaccharomyces/genética , Arsénico/metabolismo , Transporte Biológico , Cadmio/metabolismo , Análisis por Conglomerados , Biología Computacional/métodos , Cisteína/biosíntesis , Daño del ADN , Perfilación de la Expresión Génica , Regulación Fúngica de la Expresión Génica , Ontología de Genes , Intoxicación por Metales Pesados , Proteínas de Transporte de Membrana/metabolismo , Redes y Vías Metabólicas , Pruebas de Sensibilidad Microbiana , Mitocondrias/metabolismo , Mutación , Oxidación-Reducción , Estrés Oxidativo , Peroxisomas/metabolismo , Fenotipo , Fitoquelatinas/biosíntesis , Intoxicación , Schizosaccharomyces/metabolismo , Proteínas de Schizosaccharomyces pombe/metabolismo , Factores de Transcripción/metabolismo , Vitamina B 6/metabolismoRESUMEN
Although the fission yeast Schizosaccharomyces pombe is a well-established model organism, studies of natural trait variations in this species remain limited. To assess the feasibility of segregant-pool-based mapping of phenotype-causing genes in natural strains of fission yeast, we investigated the cause of a maltose utilization defect (Mal(-)) of the S. pombe strain CBS5557 (originally known as Schizosaccharomyces malidevorans). Analyzing the genome sequence of CBS5557 revealed 955 nonconservative missense substitutions, and 61 potential loss-of-function variants including 47 frameshift indels, 13 early stop codons, and 1 splice site mutation. As a side benefit, our analysis confirmed 146 sequence errors in the reference genome and improved annotations of 27 genes. We applied bulk segregant analysis to map the causal locus of the Mal(-) phenotype. Through sequencing the segregant pools derived from a cross between CBS5557 and the laboratory strain, we located the locus to within a 2.23-Mb chromosome I inversion found in most S. pombe isolates including CBS5557. To map genes within the inversion region that occupies 18% of the genome, we created a laboratory strain containing the same inversion. Analyzing segregants from a cross between CBS5557 and the inversion-containing laboratory strain narrowed down the locus to a 200-kb interval and led us to identify agl1, which suffers a 5-bp deletion in CBS5557, as the causal gene. Interestingly, loss of agl1 through a 34-kb deletion underlies the Mal(-) phenotype of another S. pombe strain CGMCC2.1628. This work adapts and validates the bulk segregant analysis method for uncovering trait-gene relationship in natural fission yeast strains.
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Ligamiento Genético , Variación Genética , Genoma Fúngico , Carácter Cuantitativo Heredable , Schizosaccharomyces/genética , Maltosa/genética , Maltosa/metabolismo , Mutación , Fenotipo , Schizosaccharomyces/metabolismoRESUMEN
Genetic factors underlying aging are remarkably conserved from yeast to human. The fission yeast Schizosaccharomyces pombe is an emerging genetic model to analyze cellular aging. Chronological lifespan (CLS) has been studied in stationary-phase yeast cells depleted for glucose, which only survive for a few days. Here, we analyzed CLS in quiescent S. pombe cells deprived of nitrogen, which arrest in a differentiated, G0-like state and survive for more than 2 months. We applied parallel mutant phenotyping by barcode sequencing (Bar-seq) to assay pooled haploid deletion mutants as they aged together during long-term quiescence. As expected, mutants with defects in autophagy or quiescence were under-represented or not detected. Lifespan scores could be calculated for 1199 mutants. We focus the discussion on the 48 most long-lived mutants, including both known aging genes in other model systems and genes not previously implicated in aging. Genes encoding membrane proteins were particularly prominent as pro-aging factors. We independently verified the extended CLS in individual assays for 30 selected mutants, showing the efficacy of the screen. We also applied Bar-seq to profile all pooled deletion mutants for proliferation under a standard growth condition. Unlike for stationary-phase cells, no inverse correlation between growth and CLS of quiescent cells was evident. These screens provide a rich resource for further studies, and they suggest that the quiescence model can provide unique, complementary insights into cellular aging.
Asunto(s)
Mutación , Schizosaccharomyces/genética , Código de Barras del ADN Taxonómico , ADN de Hongos/genética , Schizosaccharomyces/crecimiento & desarrolloRESUMEN
Nonhomologous end joining (NHEJ) is the main means for repairing DNA double-strand breaks (DSBs) in human cells. Molecular understanding of NHEJ has benefited from analyses in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In human cells, the DNA ligation reaction of the classical NHEJ pathway is carried out by a protein complex composed of DNA ligase IV (LigIV) and XRCC4. In S. cerevisiae, this reaction is catalyzed by a homologous complex composed of Dnl4 and Lif1. Intriguingly, no homolog of XRCC4 has been found in S. pombe, raising the possibility that such a factor may not always be required for classical NHEJ. Here, through screening the ionizing radiation (IR) sensitivity phenotype of a genome-wide fission yeast deletion collection in both the vegetative growth state and the spore state, we identify Xrc4, a highly divergent homolog of human XRCC4. Like other fission yeast NHEJ factors, Xrc4 is critically important for IR resistance of spores, in which no homologous recombination templates are available. Using both extrachromosomal and chromosomal DSB repair assays, we show that Xrc4 is essential for classical NHEJ. Exogenously expressed Xrc4 colocalizes with the LigIV homolog Lig4 at the chromatin region of the nucleus in a mutually dependent manner. Furthermore, like their human counterparts, Xrc4 and Lig4 interact with each other and this interaction requires the inter-BRCT linker and the second BRCT domain of Lig4. Our discovery of Xrc4 suggests that an XRCC4 family protein is universally required for classical NHEJ in eukaryotes.