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1.
PLoS Biol ; 15(8): e2002527, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28800596

RESUMO

Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing approximately 1 million annual infections globally. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large mating type (MAT) locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with 2 MAT loci (P/R and HD) located on different chromosomes. Thus, studying C. amylolentus will shed light on the transition from tetrapolar to bipolar mating systems in the pathogenic Cryptococcus species, as well as its possible link with the origin and evolution of pathogenesis. In this study, we sequenced, assembled, and annotated the genomes of 2 C. amylolentus isolates, CBS6039 and CBS6273, which are sexual and interfertile. Genome comparison between the 2 C. amylolentus isolates identified the boundaries and the complete gene contents of the P/R and HD MAT loci. Bioinformatic and chromatin immunoprecipitation sequencing (ChIP-seq) analyses revealed that, similar to those of the pathogenic Cryptococcus species, C. amylolentus has regional centromeres (CENs) that are enriched with species-specific transposable and repetitive DNA elements. Additionally, we found that while neither the P/R nor the HD locus is physically closely linked to its centromere in C. amylolentus, and the regions between the MAT loci and their respective centromeres show overall synteny between the 2 genomes, both MAT loci exhibit genetic linkage to their respective centromere during meiosis, suggesting the presence of recombinational suppressors and/or epistatic gene interactions in the MAT-CEN intervening regions. Furthermore, genomic comparisons between C. amylolentus and related pathogenic Cryptococcus species provide evidence that multiple chromosomal rearrangements mediated by intercentromeric recombination have occurred during descent of the 2 lineages from their common ancestor. Taken together, our findings support a model in which the evolution of the bipolar mating system was initiated by an ectopic recombination event mediated by similar repetitive centromeric DNA elements shared between chromosomes. This translocation brought the P/R and HD loci onto the same chromosome, and further chromosomal rearrangements then resulted in the 2 MAT loci becoming physically linked and eventually fusing to form the single contiguous MAT locus that is now extant in the pathogenic Cryptococcus species.


Assuntos
Cryptococcus/citologia , Cryptococcus/genética , Genes Fúngicos Tipo Acasalamento , Genoma Fúngico , Meiose , Translocação Genética , Imunoprecipitação da Cromatina , Biologia Computacional , Troca Genética , Cryptococcus/crescimento & desenvolvimento , Cryptococcus/fisiologia , Cryptococcus neoformans/citologia , Cryptococcus neoformans/genética , Cryptococcus neoformans/fisiologia , Epistasia Genética , Evolução Molecular , Ligação Genética , Loci Gênicos , Estruturas Genéticas , Desequilíbrio de Ligação , Anotação de Sequência Molecular , Recombinação Genética , Análise de Sequência de RNA , Especificidade da Espécie , Sintenia
2.
Genome Res ; 19(10): 1696-709, 2009 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-19525356

RESUMO

Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.


Assuntos
Genoma Fúngico , Genômica/métodos , Saccharomycetales/genética , Elementos de DNA Transponíveis/genética , Elementos de DNA Transponíveis/fisiologia , Eremothecium/genética , Duplicação Gênica , Genes Fúngicos/genética , Inteínas/genética , Kluyveromyces/genética , Dados de Sequência Molecular , Fases de Leitura Aberta/genética , Filogenia , RNA não Traduzido/genética , Saccharomyces/genética , Spliceossomos/metabolismo , Zygosaccharomyces/genética
3.
BMC Genomics ; 12: 331, 2011 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-21711526

RESUMO

BACKGROUND: Gross chromosomal rearrangements (GCRs) such as aneuploidy are key factors in genome evolution as well as being common features of human cancer. Their role in tumour initiation and progression has not yet been completely elucidated and the effects of additional chromosomes in cancer cells are still unknown. Most previous studies in which Saccharomyces cerevisiae has been used as a model for cancer cells have been carried out in the haploid context. To obtain new insights on the role of ploidy, the cellular effects of GCRs were compared between the haploid and diploid contexts. RESULTS: A total number of 21 haploid and diploid S. cerevisiae strains carrying various types of GCRs (aneuploidies, nonreciprocal translocations, segmental duplications and deletions) were studied with a view to determining the effects of ploidy on the cellular responses. Differences in colony and cell morphology as well as in the growth rates were observed between mutant and parental strains. These results suggest that cells are impaired physiologically in both contexts. We also investigated the variation in genomic expression in all the mutants. We observed that gene expression was significantly altered. The data obtained here clearly show that genes involved in energy metabolism, especially in the tricarboxylic acid cycle, are up-regulated in all these mutants. However, the genes involved in the composition of the ribosome or in RNA processing are down-regulated in diploids but up-regulated in haploids. Over-expression of genes involved in the regulation of the proteasome was found to occur only in haploid mutants. CONCLUSION: The present comparisons between the cellular responses of strains carrying GCRs in different ploidy contexts bring to light two main findings. First, GCRs induce a general stress response in all studied mutants, regardless of their ploidy. Secondly, the ploidy context plays a crucial role in maintaining the stoichiometric balance of the proteins: the translation rates decrease in diploid strains, whereas the excess protein synthesized is degraded in haploids by proteasome activity.


Assuntos
Aberrações Cromossômicas , Cromossomos Fúngicos/genética , Ploidias , Saccharomyces cerevisiae/citologia , Saccharomyces cerevisiae/genética , Trifosfato de Adenosina/biossíntese , Diploide , Proteínas Fúngicas/biossíntese , Proteínas Fúngicas/genética , Saccharomyces cerevisiae/metabolismo , Transcriptoma , Regulação para Cima
4.
FEMS Yeast Res ; 11(4): 334-44, 2011 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-21272231

RESUMO

Transposable element (TE) evolution in genomes has mostly been deduced from comparative genome analyses. TEs often account for a large proportion of the eukaryotic nuclear genome (up to 50%, depending on the species). Among the many existing genomic copies, only a small fraction may contribute to the mobility of a TE family. We have identified here, using a genetic screening procedure to trap Ty1 long terminal repeat-retrotransposon insertions in Saccharomyces cerevisiae, which among the populations of resident Ty1 copies are responsible for Ty1 mobility. Although the newly inserted Ty1 copies resulting from a single round of transposition were found to originate from a limited subset of Ty1 resident copies, they showed a high degree of diversity at the nucleotide level, mainly due to the reverse transcription-mediated recombination. In this process, highly expressed and strikingly nonautonomous mutant Ty1 were found to be the most frequently used resident copies, which suggests that nonautonomous elements play a key role in the dynamics of the Ty1 family.


Assuntos
Genoma Fúngico , Retroelementos/genética , Saccharomyces cerevisiae/genética , DNA Fúngico/genética , Variação Genética , Recombinação Genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/citologia , Alinhamento de Sequência , Sequências Repetidas Terminais/genética
5.
Nucleic Acids Res ; 37(Database issue): D550-4, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-19015150

RESUMO

The Génolevures online database (http://cbi.labri.fr/Genolevures/ and http://genolevures.org/) provides exploratory tools and curated data sets relative to nine complete and seven partial genome sequences determined and manually annotated by the Génolevures Consortium, to facilitate comparative genomic studies of Hemiascomycete yeasts. The 2008 update to the Génolevures database provides four new genomes in complete (subtelomere to subtelomere) chromosome sequences, 50,000 protein-coding and tRNA genes, and in silico analyses for each gene element. A key element is a novel classification of conserved multi-species protein families and their use in detecting synteny, gene fusions and other aspects of genome remodeling in evolution. Our purpose is to release high-quality curated data from complete genomes, with a focus on the relations between genes, genomes and proteins.


Assuntos
Ascomicetos/genética , Bases de Dados Genéticas , Proteínas Fúngicas/classificação , Proteínas Fúngicas/genética , Genoma Fúngico , Leveduras/genética , Fusão Gênica , Genômica , Proteoma/genética , Sintenia
6.
BMC Genomics ; 11: 56, 2010 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-20092627

RESUMO

BACKGROUND: This paper describes an efficient in silico method for detecting tandem gene arrays (TGAs) in fully sequenced and compact genomes such as those of prokaryotes or unicellular eukaryotes. The originality of this method lies in the search of protein sequence similarities in the vicinity of each coding sequence, which allows the prediction of tandem duplicated gene copies independently of their functionality. RESULTS: Applied to nine hemiascomycete yeast genomes, this method predicts that 2% of the genes are involved in TGAs and gene relics are present in 11% of TGAs. The frequency of TGAs with degenerated gene copies means that a significant fraction of tandem duplicated genes follows the birth-and-death model of evolution. A comparison of sequence identity distributions between sets of homologous gene pairs shows that the different copies of tandem arrayed paralogs are less divergent than copies of dispersed paralogs in yeast genomes. It suggests that paralogs included in tandem structures are more recent or more subject to the gene conversion mechanism than other paralogs. CONCLUSION: The method reported here is a useful computational tool to provide a database of TGAs composed of functional or nonfunctional gene copies. Such a database has obvious applications in the fields of structural and comparative genomics. Notably, a detailed study of the TGA catalog will make it possible to tackle the fundamental questions of the origin and evolution of tandem gene clusters.


Assuntos
Biologia Computacional/métodos , Genômica/métodos , Leveduras/genética , Algoritmos , Bases de Dados Genéticas , Evolução Molecular , Genoma Fúngico , Repetições Minissatélites , Análise de Sequência com Séries de Oligonucleotídeos , Filogenia , Análise de Sequência de DNA
7.
Curr Genet ; 56(6): 507-15, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-20830585

RESUMO

Yeasts of the Pichia genus have been isolated from different natural environments. Phylogenies based on multigene sequence analysis have shown that the genus is polyphyletic. Some species of this genus are member of the CTG group. In order to have a better insight into the relationship among species assigned to the yeast genera Pichia into the CTG group, we first sequenced the mitochondrial genome of the osmotolerant yeast Pichia farinosa. We then compared this genome with mitochondrial genomes of yeasts of the CTG group. The P. farinosa mitochondrial DNA is a circular-mapping genome of 32,065 bp, which contains 43 genes transcribed from both strands. It contains a complete set of tRNAs, the small and the large rRNAs, as well as 14 protein-coding genes. Yeasts of the CTG group contain the same core of mitochondrial genes. Phylogenetic analysis based on mitochondrial sequences clearly shows that the CTG group is divided into two distinct clades: the first one contains diploid Candida species, whereas the second mainly contains haploid Pichia species. Moreover, this analysis provides clear evidence that Pichia farinosa and Pichia sorbitophila, which were known to be unique species, are two distinct species.


Assuntos
DNA Mitocondrial/análise , Genoma Mitocondrial/genética , Pichia/genética , Sequência de Aminoácidos , Ordem dos Genes , Código Genético , Especiação Genética , Genoma Fúngico , Inteínas/genética , Modelos Biológicos , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Especificidade da Espécie , Transcrição Gênica/fisiologia
8.
BMC Genomics ; 10: 99, 2009 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-19267901

RESUMO

BACKGROUND: Chromosomal rearrangements such as duplications and deletions are key factors in evolutionary processes because they promote genomic plasticity. Although the genetic variations in the Saccharomyces cerevisiae species have been well documented, there is little known to date about the impact of the genetic background on the appearance of rearrangements. RESULTS: Using the same genetic screening, the type of rearrangements and the mutation rates observed in the S288c S. cerevisiae strain were compared to previous findings obtained in the FL100 background. Transposon-associated rearrangements, a major chromosomal rearrangement event selected in FL100, were not detected in S288c. The mechanisms involved in the occurrence of deletions and duplications in the S288c strain were also tackled, using strains deleted for genes implicated in homologous recombination (HR) or non-homologous end joining (NHEJ). Our results indicate that an Yku80p-independent NHEJ pathway is involved in the occurrence of these rearrangements in the S288c background. CONCLUSION: The comparison of two different S. cerevisiae strains, FL100 and S288c, allowed us to conclude that intra-species genomic variations have an important impact on the occurrence of chromosomal rearrangement and that this variability can partly be explained by differences in Ty1 retrotransposon activity.


Assuntos
Rearranjo Gênico , Genoma Fúngico , Saccharomyces cerevisiae/genética , Deleção Cromossômica , Cromossomos Fúngicos/genética , DNA Fúngico/genética , Duplicação Gênica , Mutação , Recombinação Genética , Retroelementos , Análise de Sequência de DNA , Especificidade da Espécie
9.
Trends Genet ; 22(1): 10-5, 2006 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-16269202

RESUMO

The DUP gene family of Saccharomyces cerevisiae comprises 23 members that can be divided into two subfamilies--DUP240 and DUP380. The location of the DUP loci suggests that at least three mechanisms were responsible for their genomic dispersion: nonreciprocal translocation at chromosomal ends, tandem duplication and Ty-associated duplication. The data we present here suggest that these nonessential genes encode proteins that facilitate membrane trafficking processes. Dup240 proteins have three conserved domains (C1, C2 and C3) and two predicted transmembrane segments (H1 and H2). A direct repetition of the C1-H1-H2-C2 module is observed in Dup380p sequences. In this article, we propose an evolutionary model to account for the emergence of the two gene subfamilies.


Assuntos
Genes Fúngicos , Saccharomyces cerevisiae/genética , Sequência de Aminoácidos , Evolução Molecular , Duplicação Gênica , Dados de Sequência Molecular , Família Multigênica , Filogenia , Proteínas de Saccharomyces cerevisiae/genética , Homologia de Sequência de Aminoácidos , Translocação Genética
10.
FEMS Yeast Res ; 9(6): 903-10, 2009 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-19594828

RESUMO

Here, we report the complete nucleotide sequence of the 39 107-bp mitochondrial genome of the yeast Pichia sorbitophila. This genome is closely related to those of Candida parapsilosis and Debaryomyces hansenii, as judged from sequence similarities and synteny conservation. It encodes three subunits of cytochrome oxidase (COX1, COX2 and COX3), three subunits of ATP synthase (ATP6, ATP8 and ATP9), the seven subunits of NADH dehydrogenase (NAD1-6 and NAD4L), the apocytochrome b (COB), the large and small rRNAs and a complete set of tRNAs. Although the mitochondrial genome of P. sorbitophila contains the same core of mitochondrial genes observed in the ascomycetous yeasts, those coding for the RNAse P and the ribosomal protein VAR1p are missing. Moreover, the mtDNA of P. sorbitophila contains several introns in its genes and has the particularity of possessing an intron, which is not linked to any upstream exon.


Assuntos
Genes Fúngicos , Genes Mitocondriais , Genoma Mitocondrial , Mitocôndrias/genética , Pichia/genética , Sequência de Aminoácidos , Candida/genética , DNA Fúngico/química , DNA Fúngico/genética , DNA Mitocondrial/química , DNA Mitocondrial/genética , Debaryomyces/genética , Dados de Sequência Molecular , Alinhamento de Sequência , Análise de Sequência de DNA , Homologia de Sequência
11.
Biochem Mol Biol Educ ; 47(5): 599-606, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31141270

RESUMO

In order to help promote instructional change at French-speaking universities in Europe, we initiated a series of 1-day events centered on learning innovations. Since 2015, these events have been taking place every 6 months at the Université Paris Descartes, with the moral support of three learned scientific societies, the French Academy of Sciences, and sponsoring by leaders in textbook editing and classroom technologies. Each event gathers ~ 40 participants (faculty members, postdocs, and educational specialists) from four countries (Belgium, France, Luxemburg, Switzerland) and invitees, who share their active learning practices, flipped classroom variations representing the most popular strategy. Their experience revealed that faculty who invest themselves in revamping teaching are still isolated at their institutions, although institutional and national support have now been gaining momentum. In particular, the role of educational specialists (known as ingénieurs pédagogiques in France) is key to help faculty move away from lecturing. Overall, our event series illustrates that a hands-off approach is effective to foster a cross-border community of committed academics in a context where the process of changing the way we teach at universities is still in its infancy. © 2019 International Union of Biochemistry and Molecular Biology, 47(5):599-606, 2019.


Assuntos
Docentes/educação , Idioma , Pesquisa/educação , Ensino/educação , França , Humanos , Aprendizagem Baseada em Problemas , Universidades
12.
DNA Repair (Amst) ; 6(10): 1441-52, 2007 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-17544927

RESUMO

The duplication of DNA sequences is a powerful determinant of genomic plasticity and is known to be one of the key factors responsible for evolution. Recent genomic sequence data demonstrate the abundance of duplicated genes in all surveyed organisms. Over the past years, experimental systems were adequately designed to explore the molecular mechanisms involved in their formation in haploid Saccharomyces cerevisiae strains. To obtain a more global and accurate view of the events leading to DNA sequence duplications, we have selected and characterized duplication occurrences in diploid S. cerevisiae cells. The molecular analysis showed that two other predominant ways lead to duplication in this context: formation of extra chimeric chromosomes and non-reciprocal translocation events. Moreover, we demonstrated that these two types of rearrangements are RAD52 independent and therefore that homologous recombination plays no part in their formation. Finally, our results show the multiplicity of mechanisms involved in duplication events and provide the first experimental evidence that these mechanisms might be ploidy dependent.


Assuntos
Diploide , Duplicação Gênica , Saccharomyces cerevisiae/genética , Southern Blotting , Cromossomos Fúngicos , DNA Fúngico/genética , Eletroforese em Gel de Campo Pulsado , Hibridização de Ácido Nucleico , Plasmídeos , Proteína Rad52 de Recombinação e Reparo de DNA/genética , Saccharomyces cerevisiae/citologia , Proteínas de Saccharomyces cerevisiae/genética
13.
Nucleic Acids Res ; 34(Database issue): D432-5, 2006 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-16381905

RESUMO

The Génolevures online database (http://cbi.labri.fr/Genolevures/) provides tools and data relative to 4 complete and 10 partial genome sequences determined and manually annotated by the Génolevures Consortium, to facilitate comparative genomic studies of hemiascomycetous yeasts. With their relatively small and compact genomes, yeasts offer a unique opportunity for exploring eukaryotic genome evolution. The new version of the Génolevures database provides truly complete (subtelomere to subtelomere) chromosome sequences, 25 000 protein-coding and tRNA genes, and in silico analyses for each gene element. A new feature of the database is a novel collection of conserved multi-species protein families and their mapping to metabolic pathways, coupled with an advanced search feature. Data are presented with a focus on relations between genes and genomes: conservation of genes and gene families, speciation, chromosomal reorganization and synteny. The Génolevures site includes an area for specific studies by members of its international community.


Assuntos
Bases de Dados Genéticas , Genoma Fúngico , Leveduras/genética , Evolução Molecular , Proteínas Fúngicas/química , Proteínas Fúngicas/classificação , Proteínas Fúngicas/genética , Genômica , Internet , Software , Integração de Sistemas , Interface Usuário-Computador
14.
Nucleic Acids Res ; 33(19): 6319-26, 2005.
Artigo em Inglês | MEDLINE | ID: mdl-16269823

RESUMO

Duplication is thought to be one of the main processes providing a substrate on which the effects of evolution are visible. The mechanisms underlying this chromosomal rearrangement were investigated here in the yeast Saccharomyces cerevisiae. Spontaneous revertants containing a duplication event were selected and analyzed. In addition to the single gene duplication described in a previous study, we demonstrated here that direct tandem duplicated regions ranging from 5 to 90 kb in size can also occur spontaneously. To further investigate the mechanisms in the duplication events, we examined whether homologous recombination contributes to these processes. The results obtained show that the mechanisms involved in segmental duplication are RAD52-independent, contrary to those involved in single gene duplication. Moreover, this study shows that the duplication of a given gene can occur in S.cerevisiae haploid strains via at least two ways: single gene or segmental duplication.


Assuntos
Duplicação Gênica , Saccharomyces cerevisiae/genética , Aspartato Carbamoiltransferase/genética , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/genética , Cromossomos Fúngicos , Deleção de Genes , Genes Fúngicos , Haploidia , Complexos Multienzimáticos/genética , Proteínas de Saccharomyces cerevisiae/genética , Análise de Sequência de DNA
15.
Nucleic Acids Res ; 32(Database issue): D315-8, 2004 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-14681422

RESUMO

The Génolevures online database (http://cbi.labri.fr/Genolevures/) provides data and tools to facilitate comparative genomic studies on hemiascomycetous yeasts. Now, four complete genome sequences recently determined (Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, Yarrowia lipolytica) have been added to the partial sequences of 13 species previously analysed by a random approach. The database also includes the reference genome Saccharomyces cerevisiae. Data are presented with a focus on relations between genes and genomes: conservation of genes and gene families, speciation, chromosomal reorganization and synteny. The Génolevures site includes a community area for specific studies by members of the international community.


Assuntos
Bases de Dados Genéticas , Evolução Molecular , Genoma Fúngico , Genômica , Leveduras/genética , Biologia Computacional , Armazenamento e Recuperação da Informação , Internet , Software
16.
Genetics ; 167(4): 1611-9, 2004 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-15342502

RESUMO

The influence of duplicated sequences on chromosomal stability is poorly understood. To characterize chromosomal rearrangements involving duplicated sequences, we compared the organization of tandem repeats of the DUP240 gene family in 15 Saccharomyces cerevisiae strains of various origins. The DUP240 gene family consists of 10 members of unknown function in the reference strain S288C. Five DUP240 paralogs on chromosome I and two on chromosome VII are arranged as tandem repeats that are highly polymorphic in copy number and sequence. We characterized DNA sequences that are likely involved in homologous or nonhomologous recombination events and are responsible for intra- and interchromosomal rearrangements that cause the creation and disappearance of DUP240 paralogs. The tandemly repeated DUP240 genes seem to be privileged sites of gene birth and death.


Assuntos
Família Multigênica , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Sequência de Bases , Cromossomos Fúngicos/genética , Primers do DNA , DNA Fúngico , Duplicação Gênica , Genes Fúngicos , Dados de Sequência Molecular , Filogenia , Reação em Cadeia da Polimerase , Saccharomyces cerevisiae/classificação
17.
Sci Rep ; 5: 11571, 2015 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-26108467

RESUMO

The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi-yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.


Assuntos
Adaptação Fisiológica/genética , Evolução Molecular , Genes Fúngicos/genética , Variação Genética , Geotrichum/genética , Leveduras/genética , Biodiversidade , DNA Fúngico/química , DNA Fúngico/genética , Proteínas Fúngicas/genética , Transferência Genética Horizontal , Genoma Fúngico/genética , Genoma Mitocondrial/genética , Geotrichum/crescimento & desenvolvimento , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA , Especificidade da Espécie , Leveduras/classificação , Leveduras/crescimento & desenvolvimento
18.
BMC Biochem ; 5: 6, 2004 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-15128434

RESUMO

BACKGROUND: The S. cerevisiae carbamylphosphate synthetase - aspartate transcarbamylase multifunctional protein catalyses the first two reactions of the pyrimidine pathway. In this organism, these two reactions are feedback inhibited by the end product UTP. In the present work, the mechanisms of these integrated inhibitions were studied. RESULTS: The results obtained show that the inhibition is competitive in the case of carbamylphosphate synthetase and non-competitive in the case of aspartate transcarbamylase. They also identify the substrate whose binding is altered by this nucleotide and the step of the carbamylphosphate synthetase reaction which is inhibited. Furthermore, the structure of the domains catalyzing these two reactions were modelled in order to localize the mutations which, specifically, alter the aspartate transcarbamylase sensitivity to the feedback inhibitor UTP. Taken together, the results make it possible to propose a model for the integrated regulation of the two activities of the complex. UTP binds to a regulatory site located in the vicinity of the carbamylphosphate synthetase catalytic subsite which catalyzes the third step of this enzyme reaction. Through a local conformational change, this binding decreases, competitively, the affinity of this site for the substrate ATP. At the same time, through a long distance signal transmission process it allosterically decreases the affinity of the aspartate transcarbamylase catalytic site for the substrate aspartate. CONCLUSION: This investigation provides informations about the mechanisms of allosteric inhibition of the two activities of the CPSase-ATCase complex. Although many allosteric monofunctional enzymes were studied, this is the first report on integrated allosteric regulation in a multifunctional protein. The positions of the point mutations which specifically abolish the sensitivity of aspartate transcarbamylase to UTP define an interface between the carbamylphosphate synthetase and aspartate transcarbamylase domains, through which the allosteric signal for the regulation of aspartate transcarbamylase must be propagated.


Assuntos
Aspartato Carbamoiltransferase/fisiologia , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/fisiologia , Complexos Multienzimáticos/fisiologia , Saccharomyces cerevisiae/enzimologia , Regulação Alostérica/fisiologia , Sequência de Aminoácidos/fisiologia , Aspartato Carbamoiltransferase/antagonistas & inibidores , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/antagonistas & inibidores , Carbamoil Fosfato Sintase (Glutamina-Hidrolizante)/química , Domínio Catalítico/fisiologia , Inibidores Enzimáticos/farmacologia , Escherichia coli/enzimologia , Proteínas de Escherichia coli/química , Modelos Moleculares , Dados de Sequência Molecular , Complexos Multienzimáticos/antagonistas & inibidores , Mutação/fisiologia , Peptídeos/química , Peptídeos/fisiologia , Mapeamento de Interação de Proteínas/métodos , Estrutura Terciária de Proteína/fisiologia , Proteínas de Saccharomyces cerevisiae/fisiologia , Alinhamento de Sequência/métodos , Homologia de Sequência de Aminoácidos , Uridina Trifosfato/farmacologia
19.
Biotechnol Biofuels ; 7: 66, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24834124

RESUMO

BACKGROUND: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant. RESULTS: The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. CONCLUSIONS: The high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications.

20.
Genome Biol Evol ; 5(12): 2524-39, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24317973

RESUMO

The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993(T)), a nitrate-assimilating Saccharomycetales of uncertain taxonomy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides. The sequence is composed of seven scaffolds, one per chromosome, totaling 11.4 Mb and containing 6,029 protein-coding genes, ~13.5% of which being interrupted by introns. This GC-rich yeast genome (45.7%) appears phylogenetically related with the few other nitrate-assimilating yeasts sequenced so far, Ogataea polymorpha, O. parapolymorpha, and Dekkera bruxellensis, with which it shares a very reduced number of tRNA genes, a novel tRNA sparing strategy, and a common nitrate assimilation cluster, three specific features to this group of yeasts. Centromeres were recognized in GC-poor troughs of each scaffold. The strain bears MAT alpha genes at a single MAT locus and presents a significant degree of conservation with Saccharomyces cerevisiae genes, suggesting that it can perform sexual cycles in nature, although genes involved in meiosis were not all recognized. The complete absence of conservation of synteny between K. capsulata and any other yeast genome described so far, including the three other nitrate-assimilating species, validates the interest of this species for long-range evolutionary genomic studies among Saccharomycotina yeasts.


Assuntos
DNA Fúngico/análise , Genoma Fúngico/genética , Saccharomycetales/genética , Animais , Composição de Bases/genética , Sequência de Bases , Centrômero/genética , Transferência Genética Horizontal , Insetos/microbiologia , Larva/microbiologia , Meiose/genética , Nitratos/metabolismo , Filogenia , RNA de Transferência , RNA não Traduzido/genética , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA
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