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1.
Food Chem ; 292: 81-89, 2019 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-31054696

RESUMO

How to effectively increase or decrease the ability of A. oryzae to produce enzymes was the key to improve the quality of soy sauce. However, multi-core property of A. oryzae resulted in genetic instability of the new strain. Here, A. oryzae 3.042-3 which can stably produce mononuclear spores was constructed based on A. oryzae 3.042. A. oryzae 3.042-3-c obtained by transformation of the fragment of cis-CreA into A. oryzae 3.042-3 exhibited genetic stability. The fragment containing the cis-acting and the promoter CreA from A. oryzae was connected to chromosome VII in A. oryzae 3.042-3-c. Compared with A. oryzae 3.042-3, the cellulase activity of A. oryzae 3.042-3-c was reduced by 50.5% and the pectinase activity was decreased by 10.0%. At the end of the soy sauce fermentation, the salt-free solid content of A. oryzae 3.042-3-c was higher 58.9% than that of A. oryzae 3.042-3. The kinds and contents of the flavor components of the soy sauce from the fermentation by A. oryzae 3.042-3-c were higher than those of the A. oryzae 3.042 and A. oryzae 3.042-3, especially in alcohols and esters. HEMF was only found in the soy sauce from A. oryzae 3.042-3-c. The results indicated that the new strain A. oryzae 3.042-3-c could improve the quality of soy sauce from the low-salt solid fermentation by decreasing enzyme activity of cellulase and pectinase.


Assuntos
Aspergillus oryzae/enzimologia , Proteínas Fúngicas/metabolismo , Alimentos de Soja/análise , Aspergillus oryzae/genética , Celulase/genética , Celulase/metabolismo , Cromossomos Fúngicos , Qualidade dos Alimentos , Proteínas Fúngicas/genética , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Alimentos de Soja/microbiologia
2.
Appl Microbiol Biotechnol ; 103(12): 4869-4880, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31053912

RESUMO

The yeast Saccharomyces cerevisiae has been widely used as a model system for studying the physiological and pharmacological action of small-molecular drugs. Here, a heterozygous diploid S. cerevisiae strain QSS4 was generated to determine whether drugs could induce chromosomal instability by determining the frequency of mitotic recombination. Using the combination of a custom SNP microarray and yeast screening system, the patterns of chromosomal instability induced by drugs were explored at the whole genome level in QSS4. We found that Zeocin (a member of the bleomycin family) treatment increased the rate of genomic alterations, including aneuploidy, loss of heterozygosity (LOH), and chromosomal rearrangement over a hundred-fold. Most recombination events are likely to be initiated by DNA double-stand breaks directly generated by Zeocin. Another remarkable finding is that G4-motifs and low GC regions were significantly underrepresented within the gene conversion tracts of Zeocin-induced LOH events, indicating that certain DNA regions are less preferred Zeocin-binding sites in vivo. This study provides a novel paradigm for evaluating genetic toxicity of small-molecular drugs using yeast models.


Assuntos
Instabilidade Cromossômica/efeitos dos fármacos , Cromossomos Fúngicos , Saccharomyces cerevisiae/efeitos dos fármacos , Saccharomyces cerevisiae/genética , Bibliotecas de Moléculas Pequenas/farmacologia , Aneuploidia , Bleomicina/farmacologia , Divisão Celular , Rearranjo Gênico , Instabilidade Genômica , Perda de Heterozigosidade , Recombinação Genética
3.
Mol Plant Microbe Interact ; 32(10): 1273-1276, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31125281

RESUMO

Alternaria alternata is a generally saprophytic fungus. Its genome consists of 10 autosomes, while some strains have one or two additional chromosomes, called a conditionally dispensable chromosome (CDC). A CDC is not required for reproduction but confers host-specific pathogenicity. We sequenced the genome of the peach pathotype of A. alternata using Nanopore and assembled it into 20 sequences. The 10 largest sequences corresponded to 10 gapless sequences of A. solani autosomes, and 1 sequence was a mitochondrial genome. Nine other sequences may be derived from CDCs because of lack of similarity with autosomes of other Alternaria spp. The sequence information could provide novel insights into genomes of Alternaria spp. and on the biosynthesis of a novel host-specific toxin in the peach pathotype of A. alternata.


Assuntos
Alternaria , Cromossomos Fúngicos , Prunus persica , Alternaria/genética , Cromossomos Fúngicos/genética , Prunus persica/microbiologia
4.
PLoS Genet ; 15(4): e1008093, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-31009462

RESUMO

Chromosome and genome stability are important for normal cell function as instability often correlates with disease and dysfunction of DNA repair mechanisms. Many organisms maintain supernumerary or accessory chromosomes that deviate from standard chromosomes. The pathogenic fungus Zymoseptoria tritici has as many as eight accessory chromosomes, which are highly unstable during meiosis and mitosis, transcriptionally repressed, show enrichment of repetitive elements, and enrichment with heterochromatic histone methylation marks, e.g., trimethylation of H3 lysine 9 or lysine 27 (H3K9me3, H3K27me3). To elucidate the role of heterochromatin on genome stability in Z. tritici, we deleted the genes encoding the methyltransferases responsible for H3K9me3 and H3K27me3, kmt1 and kmt6, respectively, and generated a double mutant. We combined experimental evolution and genomic analyses to determine the impact of these deletions on chromosome and genome stability, both in vitro and in planta. We used whole genome sequencing, ChIP-seq, and RNA-seq to compare changes in genome and chromatin structure, and differences in gene expression between mutant and wildtype strains. Analyses of genome and ChIP-seq data in H3K9me3-deficient strains revealed dramatic chromatin reorganization, where H3K27me3 is mostly relocalized into regions that are enriched with H3K9me3 in wild type. Many genome rearrangements and formation of new chromosomes were found in the absence of H3K9me3, accompanied by activation of transposable elements. In stark contrast, loss of H3K27me3 actually increased the stability of accessory chromosomes under normal growth conditions in vitro, even without large scale changes in gene activity. We conclude that H3K9me3 is important for the maintenance of genome stability because it disallows H3K27me3 in regions considered constitutive heterochromatin. In this system, H3K27me3 reduces the overall stability of accessory chromosomes, generating a "metastable" state for these quasi-essential regions of the genome.


Assuntos
Instabilidade Genômica , Histonas/metabolismo , Lisina/metabolismo , Ascomicetos/genética , Ascomicetos/metabolismo , Cromossomos Fúngicos , Deleção de Genes , Heterocromatina/genética , Heterocromatina/metabolismo , Histona-Lisina N-Metiltransferase/genética , Histonas/química , Metilação , Sequências Repetitivas de Ácido Nucleico , Ativação Transcricional
5.
mSphere ; 4(2)2019 03 06.
Artigo em Inglês | MEDLINE | ID: mdl-30842269

RESUMO

The ability to generate autonomously replicating plasmids has been elusive in Candida albicans, a prevalent human fungal commensal and pathogen. Instead, plasmids generally integrate into the genome. Here, we assessed plasmid and transformant properties, including plasmid geometry, transformant colony size, four selectable markers, and potential origins of replication, for their ability to drive autonomous plasmid maintenance. Importantly, linear plasmids with terminal telomere repeats yielded many more autonomous transformants than circular plasmids with the identical sequences. Furthermore, we could distinguish (by colony size) transient, autonomously replicating, and chromosomally integrated transformants (tiny, medium, and large, respectively). Candida albicans URA3 and a heterologous marker, ARG4, yielded many transient transformants indicative of weak origin activity; the replication of the plasmid carrying the heterologous LEU2 marker was highly dependent upon the addition of a bona fide origin sequence. Several bona fide chromosomal origins, with an origin fragment of ∼100 bp as well as a heterologous origin, panARS, from Kluyveromyces lactis, drove autonomous replication, yielding moderate transformation efficiency and plasmid stability. Thus, C. albicans maintains linear plasmids that yield high transformation efficiency and are maintained autonomously in an origin-dependent manner.IMPORTANCE Circular plasmids are important tools for molecular manipulation in model fungi such as baker's yeast, yet, in Candida albicans, an important yeast pathogen of humans, prior studies were not able to generate circular plasmids that were autonomous (duplicated without inserting themselves into the chromosome). Here, we found that linearizing circular plasmids with sequences from telomeres, the chromosome ends, allows the plasmids to duplicate and segregate in C. albicans We used this system to identify chromosomal sequences that facilitate the initiation of plasmid replication (origins) and to show that an ∼100-bp fragment of a C. albicans origin and an origin sequence from a distantly related yeast can both function as origins in C. albicans Thus, the requirements for plasmid geometry, but not necessarily for origin sequences, differ between C. albicans and baker's yeast.


Assuntos
Candida albicans/genética , Cromossomos Fúngicos/genética , Replicação do DNA , Plasmídeos/genética , Origem de Replicação , Kluyveromyces/genética , Telômero/genética
6.
Proc Natl Acad Sci U S A ; 116(13): 6270-6279, 2019 03 26.
Artigo em Inglês | MEDLINE | ID: mdl-30850541

RESUMO

In budding yeast, which possesses simple point centromeres, we discovered that all of its centromeres express long noncoding RNAs (cenRNAs), especially in S phase. Induction of cenRNAs coincides with CENP-ACse4 loading time and is dependent on DNA replication. Centromeric transcription is repressed by centromere-binding factor Cbf1 and histone H2A variant H2A.ZHtz1 Deletion of CBF1 and H2A.Z HTZ1 results in an up-regulation of cenRNAs; an increased loss of a minichromosome; elevated aneuploidy; a down-regulation of the protein levels of centromeric proteins CENP-ACse4, CENP-A chaperone HJURPScm3, CENP-CMif2, SurvivinBir1, and INCENPSli15; and a reduced chromatin localization of CENP-ACse4, CENP-CMif2, and Aurora BIpl1 When the RNA interference system was introduced to knock down all cenRNAs from the endogenous chromosomes, but not the cenRNA from the circular minichromosome, an increase in minichromosome loss was still observed, suggesting that cenRNA functions in trans to regulate centromere activity. CenRNA knockdown partially alleviates minichromosome loss in cbf1Δ, htz1Δ, and cbf1Δ htz1Δ in a dose-dependent manner, demonstrating that cenRNA level is tightly regulated to epigenetically control point centromere function.


Assuntos
Centrômero/metabolismo , Segregação de Cromossomos/fisiologia , RNA não Traduzido/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Saccharomycetales/metabolismo , Aurora Quinases/metabolismo , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/genética , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/metabolismo , Proteínas de Transporte/metabolismo , Centrômero/genética , Cromatina/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Cromossomos Fúngicos , Replicação do DNA , Proteínas de Ligação a DNA/metabolismo , Deleção de Genes , Histonas/genética , Histonas/metabolismo , Proteínas Associadas aos Microtúbulos/metabolismo , Interferência de RNA/fisiologia , Fase S , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Regulação para Cima
7.
Mol Biol Evol ; 36(6): 1148-1161, 2019 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-30835262

RESUMO

Pyricularia is a fungal genus comprising several pathogenic species causing the blast disease in monocots. Pyricularia oryzae, the best-known species, infects rice, wheat, finger millet, and other crops. As past comparative and population genomics studies mainly focused on isolates of P. oryzae, the genomes of the other Pyricularia species have not been well explored. In this study, we obtained a chromosomal-level genome assembly of the finger millet isolate P. oryzae MZ5-1-6 and also highly contiguous assemblies of Pyricularia sp. LS, P. grisea, and P. pennisetigena. The differences in the genomic content of repetitive DNA sequences could largely explain the variation in genome size among these new genomes. Moreover, we found extensive gene gains and losses and structural changes among Pyricularia genomes, including a large interchromosomal translocation. We searched for homologs of known blast effectors across fungal taxa and found that most avirulence effectors are specific to Pyricularia, whereas many other effectors share homologs with distant fungal taxa. In particular, we discovered a novel effector family with metalloprotease activity, distinct from the well-known AVR-Pita family. We predicted 751 gene families containing putative effectors in 7 Pyricularia genomes and found that 60 of them showed differential expression in the P. oryzae MZ5-1-6 transcriptomes obtained under experimental conditions mimicking the pathogen infection process. In summary, this study increased our understanding of the structural, functional, and evolutionary genomics of the blast pathogen and identified new potential effector genes, providing useful data for developing crops with durable resistance.


Assuntos
Evolução Biológica , Genoma Fúngico , Família Multigênica , Pyricularia grisea/genética , Cromossomos Fúngicos , Metaloproteases/genética , Milhetes/microbiologia , Doenças das Plantas , Homologia de Sequência do Ácido Nucleico , Transcriptoma
8.
Nat Commun ; 10(1): 970, 2019 02 27.
Artigo em Inglês | MEDLINE | ID: mdl-30814509

RESUMO

Faithful meiotic chromosome inheritance and fertility rely on the stimulation of meiotic crossover recombination by potentially genotoxic DNA double-strand breaks (DSBs). To avoid excessive damage, feedback mechanisms down-regulate DSBs, likely in response to initiation of crossover repair. In Saccharomyces cerevisiae, this regulation requires the removal of the conserved DSB-promoting protein Hop1/HORMAD during chromosome synapsis. Here, we identify privileged end-adjacent regions (EARs) spanning roughly 100 kb near all telomeres that escape DSB down-regulation. These regions retain Hop1 and continue to break in pachynema despite normal synaptonemal complex deposition. Differential retention of Hop1 requires the disassemblase Pch2/TRIP13, which preferentially removes Hop1 from telomere-distant sequences, and is modulated by the histone deacetylase Sir2 and the nucleoporin Nup2. Importantly, the uniform size of EARs among chromosomes contributes to disproportionately high DSB and repair signals on short chromosomes in pachynema, suggesting that EARs partially underlie the curiously high recombination rate of short chromosomes.


Assuntos
Cromossomos Fúngicos/genética , Quebras de DNA de Cadeia Dupla , Meiose/genética , Saccharomyces cerevisiae/genética , Telômero/genética , Pareamento Cromossômico/genética , Cromossomos Fúngicos/metabolismo , Proteínas de Ligação a DNA/metabolismo , Complexo de Proteínas Formadoras de Poros Nucleares/metabolismo , Proteínas Nucleares/metabolismo , Recombinação Genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas Reguladoras de Informação Silenciosa de Saccharomyces cerevisiae/metabolismo , Sirtuína 2/metabolismo , Telômero/metabolismo
9.
mSphere ; 4(1)2019 02 13.
Artigo em Inglês | MEDLINE | ID: mdl-30760617

RESUMO

The heterozygous diploid genome of Candida albicans is highly plastic, with frequent loss of heterozygosity (LOH) events. In the SC5314 laboratory strain, while LOH events are ubiquitous, a chromosome homozygosis bias is observed for certain chromosomes, whereby only one of the two homologs can occur in the homozygous state. This suggests the occurrence of recessive lethal allele(s) (RLA) preventing large-scale LOH events on these chromosomes from being stably maintained. To verify the presence of an RLA on chromosome 7 (Chr7), we utilized a system that allows (i) DNA double-strand break (DSB) induction on Chr7 by the I-SceI endonuclease and (ii) detection of the resulting long-range homozygosis. I-SceI successfully induced a DNA DSB on both Chr7 homologs, generally repaired by gene conversion. Notably, cells homozygous for the right arm of Chr7B were not recovered, confirming the presence of RLA(s) in this region. Genome data mining for RLA candidates identified a premature nonsense-generating single nucleotide polymorphism (SNP) within the HapB allele of C7_03400c whose Saccharomyces cerevisiae ortholog encodes the essential Mtr4 RNA helicase. Complementation with a wild-type copy of MTR4 rescued cells homozygous for the right arm of Chr7B, demonstrating that the mtr4K880* RLA is responsible for the Chr7 homozygosis bias in strain SC5314. Furthermore, we observed that the major repeat sequences (MRS) on Chr7 acted as hot spots for interhomolog recombination. Such recombination events provide C. albicans with increased opportunities to survive DNA DSBs whose repair can lead to homozygosis of recessive lethal or deleterious alleles. This might explain the maintenance of MRS in this species.IMPORTANCE Candida albicans is a major fungal pathogen, whose mode of reproduction is mainly clonal. Its genome is highly tolerant to rearrangements, in particular loss of heterozygosity events, known to unmask recessive lethal and deleterious alleles in heterozygous diploid organisms such as C. albicans By combining a site-specific DSB-inducing system and mining genome sequencing data of 182 C. albicans isolates, we were able to ascribe the chromosome 7 homozygosis bias of the C. albicans laboratory strain SC5314 to an heterozygous SNP introducing a premature STOP codon in the MTR4 gene. We have also proposed genome-wide candidates for new recessive lethal alleles. We additionally observed that the major repeat sequences (MRS) on chromosome 7 acted as hot spots for interhomolog recombination. Maintaining MRS in C. albicans could favor haplotype exchange, of vital importance to LOH events, leading to homozygosis of recessive lethal or deleterious alleles that inevitably accumulate upon clonality.


Assuntos
Candida albicans/genética , Genes Letais , Genes Recessivos , Genoma Fúngico , Sequências Repetitivas de Ácido Nucleico , Alelos , Cromossomos Fúngicos , Diploide , Perda de Heterozigosidade , Polimorfismo de Nucleotídeo Único , Recombinação Genética
10.
Mol Cell ; 73(5): 900-914.e9, 2019 03 07.
Artigo em Inglês | MEDLINE | ID: mdl-30733119

RESUMO

Post-replication repair (PRR) allows tolerance of chemical- and UV-induced DNA base lesions in both an error-free and an error-prone manner. In classical PRR, PCNA monoubiquitination recruits translesion synthesis (TLS) DNA polymerases that can replicate through lesions. We find that PRR responds to DNA replication stress that does not cause base lesions. Rad5 forms nuclear foci during normal S phase and after exposure to types of replication stress where DNA base lesions are likely absent. Rad5 binds to the sites of stressed DNA replication forks, where it recruits TLS polymerases to repair single-stranded DNA (ssDNA) gaps, preventing mitotic defects and chromosome breaks. In contrast to the prevailing view of PRR, our data indicate that Rad5 promotes both mutagenic and error-free repair of undamaged ssDNA that arises during physiological and exogenous replication stress.


Assuntos
Quebras de DNA de Cadeia Simples , DNA Helicases/metabolismo , Reparo do DNA , Replicação do DNA , DNA Fúngico/metabolismo , DNA de Cadeia Simples/metabolismo , Mutação , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/enzimologia , Sítios de Ligação , Cromossomos Fúngicos , DNA Helicases/genética , DNA Fúngico/genética , DNA de Cadeia Simples/genética , DNA Polimerase Dirigida por DNA/genética , DNA Polimerase Dirigida por DNA/metabolismo , Mitose , Nucleotidiltransferases/genética , Nucleotidiltransferases/metabolismo , Antígeno Nuclear de Célula em Proliferação/genética , Antígeno Nuclear de Célula em Proliferação/metabolismo , Ligação Proteica , Reparo de DNA por Recombinação , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crescimento & desenvolvimento , Proteínas de Saccharomyces cerevisiae/genética , Ubiquitinação
11.
PLoS Genet ; 15(2): e1007959, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30763303

RESUMO

The nuclear division takes place in the daughter cell in the basidiomycetous budding yeast Cryptococcus neoformans. Unclustered kinetochores gradually cluster and the nucleus moves to the daughter bud as cells enter mitosis. Here, we show that the evolutionarily conserved Aurora B kinase Ipl1 localizes to the nucleus upon the breakdown of the nuclear envelope during mitosis in C. neoformans. Ipl1 is shown to be required for timely breakdown of the nuclear envelope as well. Ipl1 is essential for viability and regulates structural integrity of microtubules. The compromised stability of cytoplasmic microtubules upon Ipl1 depletion results in a significant delay in kinetochore clustering and nuclear migration. By generating an in silico model of mitosis, we previously proposed that cytoplasmic microtubules and cortical dyneins promote atypical nuclear division in C. neoformans. Improving the previous in silico model by introducing additional parameters, here we predict that an effective cortical bias generated by cytosolic Bim1 and dynein regulates dynamics of kinetochore clustering and nuclear migration. Indeed, in vivo alterations of Bim1 or dynein cellular levels delay nuclear migration. Results from in silico model and localization dynamics by live cell imaging suggests that Ipl1 spatio-temporally influences Bim1 or/and dynein activity along with microtubule stability to ensure timely onset of nuclear division. Together, we propose that the timely breakdown of the nuclear envelope by Ipl1 allows its own nuclear entry that helps in spatio-temporal regulation of nuclear division during semi-open mitosis in C. neoformans.


Assuntos
Aurora Quinase B/metabolismo , Divisão do Núcleo Celular/fisiologia , Cryptococcus neoformans/metabolismo , Proteínas Fúngicas/metabolismo , Transporte Ativo do Núcleo Celular , Aurora Quinase B/genética , Divisão do Núcleo Celular/genética , Segregação de Cromossomos , Cromossomos Fúngicos/genética , Simulação por Computador , Cryptococcus neoformans/citologia , Cryptococcus neoformans/genética , Dineínas/metabolismo , Proteínas Fúngicas/genética , Genes Fúngicos , Cinetocoros/metabolismo , Microtúbulos/metabolismo , Mitose , Modelos Biológicos , Mutação , Análise Espaço-Temporal
12.
BMC Genomics ; 20(1): 120, 2019 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-30732559

RESUMO

BACKGROUND: Genes involved in production of secondary metabolites (SMs) in fungi are exceptionally diverse. Even strains of the same species may exhibit differences in metabolite production, a finding that has important implications for drug discovery. Unlike in other eukaryotes, genes producing SMs are often clustered and co-expressed in fungal genomes, but the genetic mechanisms involved in the creation and maintenance of these secondary metabolite biosynthetic gene clusters (SMBGCs) remains poorly understood. RESULTS: In order to address the role of genome architecture and chromosome scale structural variation in generating diversity of SMBGCs, we generated chromosome scale assemblies of six geographically diverse isolates of the insect pathogenic fungus Tolypocladium inflatum, producer of the multi-billion dollar lifesaving immunosuppressant drug cyclosporin, and utilized a Hi-C chromosome conformation capture approach to address the role of genome architecture and structural variation in generating intraspecific diversity in SMBGCs. Our results demonstrate that the exchange of DNA between heterologous chromosomes plays an important role in generating novelty in SMBGCs in fungi. In particular, we demonstrate movement of a polyketide synthase (PKS) and several adjacent genes by translocation to a new chromosome and genomic context, potentially generating a novel PKS cluster. We also provide evidence for inter-chromosomal recombination between nonribosomal peptide synthetases located within subtelomeres and uncover a polymorphic cluster present in only two strains that is closely related to the cluster responsible for biosynthesis of the mycotoxin aflatoxin (AF), a highly carcinogenic compound that is a major public health concern worldwide. In contrast, the cyclosporin cluster, located internally on chromosomes, was conserved across strains, suggesting selective maintenance of this important virulence factor for infection of insects. CONCLUSIONS: This research places the evolution of SMBGCs within the context of whole genome evolution and suggests a role for recombination between chromosomes in generating novel SMBGCs in the medicinal fungus Tolypocladium inflatum.


Assuntos
Cromossomos Fúngicos/genética , Ciclosporina/metabolismo , Rearranjo Gênico , Variação Genética , Hypocreales/genética , Hypocreales/metabolismo , Metabolismo Secundário/genética , Duplicação Cromossômica , Evolução Molecular , Genoma Fúngico/genética , Família Multigênica/genética , Recombinação Genética , Especificidade da Espécie
13.
Proc Natl Acad Sci U S A ; 116(11): 4973-4982, 2019 03 12.
Artigo em Inglês | MEDLINE | ID: mdl-30718387

RESUMO

Each genomic locus in a eukaryotic cell has a distinct average time of replication during S phase that depends on the spatial and temporal pattern of replication initiation events. Replication timing can affect genomic integrity because late replication is associated with an increased mutation rate. For most eukaryotes, the features of the genome that specify the location and timing of initiation events are unknown. To investigate these features for the fission yeast, Schizosaccharomyces pombe, we developed an integrative model to analyze large single-molecule and global genomic datasets. The model provides an accurate description of the complex dynamics of S. pombe DNA replication at high resolution. We present evidence that there are many more potential initiation sites in the S. pombe genome than previously identified and that the distribution of these sites is primarily determined by two factors: the sequence preferences of the origin recognition complex (ORC), and the interference of transcription with the assembly or stability of prereplication complexes (pre-RCs). We suggest that in addition to directly interfering with initiation, transcription has driven the evolution of the binding properties of ORC in S. pombe and other eukaryotic species to target pre-RC assembly to regions of the genome that are less likely to be transcribed.


Assuntos
Replicação do DNA , Células Eucarióticas/metabolismo , Schizosaccharomyces/metabolismo , Sequência Rica em At , Cromossomos Fúngicos/genética , Simulação por Computador , Período de Replicação do DNA , RNA Polimerases Dirigidas por DNA/metabolismo , Células Eucarióticas/citologia , Genoma Fúngico , Modelos Biológicos , Complexo de Reconhecimento de Origem/genética , Probabilidade , Schizosaccharomyces/citologia , Proteínas de Schizosaccharomyces pombe/metabolismo , Transcrição Genética
14.
J Microbiol ; 57(4): 221-231, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30671743

RESUMO

During meiosis, crossing over allows for the exchange of genes between homologous chromosomes, enabling their segregation and leading to genetic variation in the resulting gametes. Spo11, a topoisomerase-like protein expressed in eukaryotes, and diverse accessory factors induce programmed double-strand breaks (DSBs) to initiate meiotic recombination during the early phase of meiosis after DNA replication. DSBs are further repaired via meiosis-specific homologous recombination. Studies on budding yeast have provided insights into meiosis and genetic recombination and have improved our understanding of higher eukaryotic systems. Cohesin, a chromosome-associated multiprotein complex, mediates sister chromatid cohesion (SCC), and is conserved from yeast to humans. Diverse cohesin subunits in budding yeast have been identified in DNA metabolic pathways, such as DNA replication, chromosome segregation, recombination, DNA repair, and gene regulation. During cell cycle, SCC is established by multiple cohesin subunits, which physically bind sister chromatids together and modulate proteins that involve in the capturing and separation of sister chromatids. Cohesin components include at least four core subunits that establish and maintain SCC: two structural maintenance chromosome subunits (Smc1 and Smc3), an α-kleisin subunit (Mcd1/Scc1 during mitosis and Rec8 during meiosis), and Scc3/Irr1 (SA1 and SA2). In addition, the cohesin-associated factors Pds5 and Rad61 regulate structural modifications and cell cyclespecific dynamics of chromatin to ensure accurate chromosome segregation. In this review, we discuss SCC and the recombination pathway, as well as the relationship between the two processes in budding yeast, and we suggest a possible conserved mechanism for meiotic chromosome dynamics from yeast to humans.


Assuntos
Cromossomos Fúngicos/genética , Meiose , Recombinação Genética , Saccharomycetales/citologia , Saccharomycetales/genética , Cromossomos Fúngicos/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Saccharomycetales/metabolismo
15.
Nucleic Acids Res ; 47(7): 3521-3535, 2019 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-30668788

RESUMO

Oxidative DNA damage is a threat to genome stability. Using a genetic system in yeast that allows detection of mitotic recombination, we found that the frequency of crossovers is greatly elevated when cells are treated with hydrogen peroxide (H2O2). Using a combination of microarray analysis and genomic sequencing, we mapped the breakpoints of mitotic recombination events and other chromosome rearrangements at a resolution of about 1 kb. Gene conversions and crossovers were the two most common types of events, but we also observed deletions, duplications, and chromosome aneuploidy. In addition, H2O2-treated cells had elevated rates of point mutations (particularly A to T/T to A and C to G/G to C transversions) and small insertions/deletions (in/dels). In cells that underwent multiple rounds of H2O2 treatments, we identified a genetic alteration that resulted in improved H2O2 tolerance by amplification of the CTT1 gene that encodes cytosolic catalase T. Lastly, we showed that cells grown in the absence of oxygen have reduced levels of recombination. This study provided multiple novel insights into how oxidative stress affects genomic instability and phenotypic evolution in aerobic cells.


Assuntos
Catalase/genética , Dano ao DNA/efeitos dos fármacos , Conversão Gênica/genética , Estresse Oxidativo/efeitos dos fármacos , Cromossomos Fúngicos/genética , Citosol/enzimologia , Reparo do DNA/efeitos dos fármacos , Replicação do DNA/efeitos dos fármacos , Genoma Fúngico/efeitos dos fármacos , Instabilidade Genômica/efeitos dos fármacos , Peróxido de Hidrogênio/farmacologia , Mitose/genética , Mutação Puntual/genética , Saccharomyces cerevisiae/genética
16.
Yeast ; 36(5): 275-283, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30557459

RESUMO

Point centromeres, found in some ascomycete yeasts such Saccharomyces cerevisiae, are very different in structure from the centromeres of other eukaryotes. They are tiny and nonrepetitive and contain only two short conserved sequence motifs. Until recently, point centromeres were thought to have a single evolutionary origin, in the budding yeast family Saccharomycetaceae. Most yeasts outside this family have centromeres that are many kilobases in size. Some have centromeres consisting of a large inverted repeat sequence, others have centromeric clusters of retrotransposons, and a third group including Candida albicans has centromeres with no conserved sequence features. It was recently reported that Scheffersomyces stipitis has point centromeres with a strongly conserved 125-bp core sequence, which is unexpected because S. stipitis is only distantly related to the known point-centromere species. We show here that the 125-bp core sequence is actually part of the long terminal repeat (LTR) of the Ty5-like retrotransposon Tps5, which forms a cluster in the centromeric region of each S. stipitis chromosome. Thus, the LTR of a centromere-associated retrotransposon confers centromere-like mitotic stability when cloned into a plasmid. The centromeric regions of S. stipitis contain three types of Tps5 element (Tps5a, Tps5b, and Tps5c) and a noncoding nonautonomous large retrotransposon derivative.


Assuntos
Centrômero , Cromossomos Fúngicos , Retroelementos , Sequências Repetidas Terminais , Leveduras/genética , Evolução Molecular , Saccharomycetales/genética
17.
Biol Pharm Bull ; 42(2): 289-294, 2019 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-30531092

RESUMO

In eukaryotic genomes, the nucleosome is the structural and functional unit, and its position and dynamics are important for gene expression control and epigenetic regulation. Epigenetics is an important mechanism in development and homeostasis, and aberrant epigenetics is a common feature in cancer. Although understanding the mechanistic basis that determines nucleosome positioning in vivo is important for elucidating chromatin function and epigenetic regulation, a suitable experimental system to examine such mechanisms is still being developed. Herein, we examined nucleosome organization in yeast minichromosomes, using a parallel mapping method we previously developed that involve site-directed chemical cleavage and micrococcal nuclease digestion. This parallel mapping is capable of revealing the differences in the occupancy and the stability of individual nucleosomes in the minichromosome. Based on the previously characterized minichromosome, we engineered a set of new minichromosomes, aimed at strengthening the positioning of the nucleosomes. The site-directed chemical mapping method demonstrated that the nucleosome positioning in the newly designed yeast minichromosome system was significantly more stable. This system will be useful for elucidating the determinants of nucleosome organization, such as DNA sequences and/or nucleosome binding proteins, and for determining the relationships between nucleosome dynamics and epigenetic regulation, which are targets for therapeutic agents.


Assuntos
Nucleossomos/genética , Saccharomyces cerevisiae/genética , Leveduras/genética , Cromatina/genética , Cromatina/metabolismo , Mapeamento Cromossômico/métodos , Cromossomos Fúngicos , Nuclease do Micrococo/metabolismo , Nucleossomos/metabolismo , Saccharomyces cerevisiae/metabolismo , Leveduras/metabolismo
18.
Elife ; 72018 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-30543518

RESUMO

Meiosis is a key cellular process of sexual reproduction that includes pairing of homologous sequences. In many species however, meiosis can also involve the segregation of supernumerary chromosomes, which can lack a homolog. How these unpaired chromosomes undergo meiosis is largely unknown. In this study we investigated chromosome segregation during meiosis in the haploid fungus Zymoseptoria tritici that possesses a large complement of supernumerary chromosomes. We used isogenic whole chromosome deletion strains to compare meiotic transmission of chromosomes when paired and unpaired. Unpaired chromosomes inherited from the male parent as well as paired supernumerary chromosomes in general showed Mendelian inheritance. In contrast, unpaired chromosomes inherited from the female parent showed non-Mendelian inheritance but were amplified and transmitted to all meiotic products. We concluded that the supernumerary chromosomes of Z. tritici show a meiotic drive and propose an additional feedback mechanism during meiosis, which initiates amplification of unpaired female-inherited chromosomes.


Assuntos
Ascomicetos/citologia , Ascomicetos/genética , Cromossomos Fúngicos/genética , Padrões de Herança/genética , Meiose , Segregação de Cromossomos/genética , Marcadores Genéticos , Mitocôndrias/genética , Polimorfismo de Nucleotídeo Único/genética , Sequenciamento Completo do Genoma
19.
BMC Syst Biol ; 12(Suppl 8): 140, 2018 12 21.
Artigo em Inglês | MEDLINE | ID: mdl-30577873

RESUMO

BACKGROUND: Chromatin interactions medicated by genomic elements located throughout the genome play important roles in gene regulation and can be identified with the technologies such as high-throughput chromosome conformation capture (Hi-C), followed by next-generation sequencing. These techniques were wildly used to reveal the relative spatial disposition of chromatins in human, mouse and yeast. Unlike metazoan where CTCF plays major roles in mediating chromatin interactions, in yeast, the transcription factors (TFs) involved in this biological process are poorly known. RESULTS: Here, we presented two computational approaches to estimate the TFs enriched in the chromatin physical inter-chromosomal interactions in yeast. Through the Chi-square method, we found TFs whose binding data are differentially distributed in different interaction groups, including Cin5, Stp1 and Sut1, whose binding data are negatively correlated with the chromosome spatial distance. A multivariate linear regression model was employed to estimate the potential contribution of different transcription factors against the physical distance of chromosomes. Rlr1, Set12 and Dig1 were found to be top positively participated in these chromosomal interactions. Ste12 was highlighted to be involved in gene reposition. Overall, we found 10 TFs enriched from both computational approaches, potentially to be involved in inter-chromosomal interactions. CONCLUSIONS: No transcription factor (TF) in our study was found to have a dominant impact on the inter-chromosomal interaction as CTCF did in human or other metazoan, suggesting species without CTCF might have different regulatory systems in mediating inter-chromosomal interactions. In summary, we presented a systematic examination of TFs involved in chromatin interaction in yeast and the results provide candidate TFs for future studies.


Assuntos
Cromossomos Fúngicos/genética , Biologia Computacional , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Fatores de Transcrição/metabolismo , Cromatina/metabolismo
20.
Elife ; 72018 12 17.
Artigo em Inglês | MEDLINE | ID: mdl-30556807

RESUMO

RNA polymerase (RNAPII) transcription occurs pervasively, raising the important question of its functional impact on other DNA-associated processes, including replication. In budding yeast, replication originates from Autonomously Replicating Sequences (ARSs), generally located in intergenic regions. The influence of transcription on ARSs function has been studied for decades, but these earlier studies have neglected the role of non-annotated transcription. We studied the relationships between pervasive transcription and replication origin activity using high-resolution transcription maps. We show that ARSs alter the pervasive transcription landscape by pausing and terminating neighboring RNAPII transcription, thus limiting the occurrence of pervasive transcription within origins. We propose that quasi-symmetrical binding of the ORC complex to ARS borders and/or pre-RC formation are responsible for pausing and termination. We show that low, physiological levels of pervasive transcription impact the function of replication origins. Overall, our results have important implications for understanding the impact of genomic location on origin function.


Assuntos
Replicação do DNA/genética , Complexo de Reconhecimento de Origem/genética , Origem de Replicação/genética , Saccharomyces cerevisiae/genética , Transcrição Genética , Sítios de Ligação , Mapeamento Cromossômico , Cromossomos Fúngicos/genética , DNA Fúngico/genética , DNA Fúngico/metabolismo , Modelos Genéticos , Complexo de Reconhecimento de Origem/metabolismo , RNA Polimerase II/metabolismo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo
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