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2.
Int J Syst Evol Microbiol ; 70(5): 3379-3390, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32375944

RESUMO

During a survey of fungi in native forests in Chile, several unidentified isolates of Diaporthe were collected from different hosts. The isolates were characterized based on DNA comparisons, morphology, culture characteristics and host affiliation, in accordance with previous descriptions. Phylogenetic analysis of the ITS region, combined with partial tub2 and tef1 genes, showed that the isolates formed three distinct groups representing three new taxa. The three new species of Diaporthe, Diaporthe araucanorum on Araucaria araucana, Diaporthe foikelawen on Drimys winteri and Diaporthe patagonica on Aristotelia chilensis are described and illustrated in the present study.


Assuntos
Florestas , Filogenia , Saccharomycetales/classificação , Chile , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Genes Fúngicos , RNA Ribossômico 16S/genética , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA
3.
Int J Syst Evol Microbiol ; 70(5): 3491-3496, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32374249

RESUMO

During studies on the endophytic yeast communities associated with fruits from Vietnam, three fermenting yeast strains were isolated from fruits of the coconut palm (Cocos nucifera). Phylogenetic analysis based on the sequences of the ITS regions and D1/D2 domains of the large subunit rRNA gene showed that these strains represented a single species of the Yamadazyma clade that was distinct from the other related species. The new species represented a basal branch of the clade formed by the Yamadazyma species i.e. Y. insecticola and Y. takamatsuzukensis. Based on the phylogenetic analysis and phenotypic characteristics, the studied strains were assigned to a novel species of the genus Yamadazyma, for which the name Yamadazyma cocois f.a., sp. nov. is proposed. The holotype is VCIM 4241, with the ex-type cultures VTCC 920004=VKM Y-3049=KBP Y-6091 code 17-68. The MycoBank number is MB 834435.


Assuntos
Cocos/microbiologia , Filogenia , Saccharomycetales/classificação , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Fermentação , Técnicas de Tipagem Micológica , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA , Vietnã
4.
PLoS Biol ; 18(5): e3000627, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32421706

RESUMO

Despite over a billion years of evolutionary divergence, several thousand human genes possess clearly identifiable orthologs in yeast, and many have undergone lineage-specific duplications in one or both lineages. These duplicated genes may have been free to diverge in function since their expansion, and it is unclear how or at what rate ancestral functions are retained or partitioned among co-orthologs between species and within gene families. Thus, in order to investigate how ancestral functions are retained or lost post-duplication, we systematically replaced hundreds of essential yeast genes with their human orthologs from gene families that have undergone lineage-specific duplications, including those with single duplications (1 yeast gene to 2 human genes, 1:2) or higher-order expansions (1:>2) in the human lineage. We observe a variable pattern of replaceability across different ortholog classes, with an obvious trend toward differential replaceability inside gene families, and rarely observe replaceability by all members of a family. We quantify the ability of various properties of the orthologs to predict replaceability, showing that in the case of 1:2 orthologs, replaceability is predicted largely by the divergence and tissue-specific expression of the human co-orthologs, i.e., the human proteins that are less diverged from their yeast counterpart and more ubiquitously expressed across human tissues more often replace their single yeast ortholog. These trends were consistent with in silico simulations demonstrating that when only one ortholog can replace its corresponding yeast equivalent, it tends to be the least diverged of the pair. Replaceability of yeast genes having more than 2 human co-orthologs was marked by retention of orthologous interactions in functional or protein networks as well as by more ancestral subcellular localization. Overall, we performed >400 human gene replaceability assays, revealing 50 new human-yeast complementation pairs, thus opening up avenues to further functionally characterize these human genes in a simplified organismal context.


Assuntos
Evolução Molecular , Genes Duplicados , Genes Fúngicos , Família Multigênica , Saccharomycetales/genética , Expressão Gênica , Teste de Complementação Genética , Humanos , Homologia de Sequência do Ácido Nucleico
5.
Int J Food Microbiol ; 325: 108647, 2020 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-32361480

RESUMO

Yeasts are one of the main organisms in the food industry and effective components of many ecosystems. The method for identifying and detecting certain yeast species or strains is a crucial step for the food industry and should be simple, reliable, fast, and inexpensive. In our study, inter-priming binding sites (iPBS) retrotransposon marker system was employed to elucidate the genetic variability at intraspecies and interspecies levels among 112 yeast strains belonging to eight species previously obtained from fermented foods. The molecular identification of yeast strains was firstly confirmed by sequencing the D1/D2 domain of the 26S rRNA. The eight selected retrotransposon-based primers produced 278 bands, all of which were polymorphic with an average of 34.75 polymorphic fragments per primer. The averages of polymorphism information contents and the resolving power values for the iPBS marker system were 0.23 and 10.11, respectively. The genetic parameters within each yeast species obtained from iPBS markers were observed as; the percentage of polymorphic loci for each species ranging from 19.23% to 71.21%, Nei's gene diversity from 0.085 to 0.228, while Shannon's information index values ranging from 0.125 to 0.349. The value of gene flow (0.09) and genetic variation among the populations (0.85) showed higher genetic variation among the species. UPGMA analyses demonstrated considerable genetic variability in the yeast strains, clustered them according to their species, and revealed the intraspecific variation. Each of the selected iPBS primer provided enough species-discrimination. Present evaluations suggest the utility of iPBS marker system to estimate the genetic variation of yeast strains. This study is a preliminary point for further studies on the identification methodology, and population genetics of yeast species having importance in the food industry with iPBS markers.


Assuntos
Retroelementos/genética , Saccharomycetales/genética , Fermento Seco/genética , Sítios de Ligação , Primers do DNA/genética , Ecossistema , Variação Genética/genética , Filogenia , Polimorfismo Genético/genética , Saccharomycetales/classificação
6.
J Nat Med ; 74(3): 545-549, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32236853

RESUMO

Fungal co-culture is a strategy to induce the production of secondary metabolites by activating cryptic genes. We discovered the production of a new compound, talarodone A (1), along with five known compounds 2-6 in co-culture of Talaromyces pinophilus and Paraphaeosphaeria sp. isolated from soil collected in Miyazaki Prefecture, Japan. Among them, the productions of penicidones C (2) and D (3) were enhanced 27- and sixfold, respectively, by the co-culture. The structure of 3 should be represented as a γ-pyridol form with the reported chemical shifts, but not as a γ-pyridone form, based on DFT calculation.


Assuntos
Piridonas/metabolismo , Saccharomycetales/metabolismo , Talaromyces/metabolismo , Técnicas de Cocultura , Japão , Piridonas/química , Saccharomycetales/crescimento & desenvolvimento , Saccharomycetales/isolamento & purificação , Microbiologia do Solo , Talaromyces/crescimento & desenvolvimento , Talaromyces/isolamento & purificação
7.
Int J Syst Evol Microbiol ; 70(2): 1372-1397, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32122458

RESUMO

Fourteen novel lipomycetaceous yeasts species were isolated from soil samples collected from the Hokkaido, Chiba and Okinawa prefectures of Japan. Phylogenetic analyses of the D1/D2 domains of the large subunit rRNAs and translation elongation factor 1 alpha genes (TEF1-α) revealed that five strains of two species from the soil in Furano-shi, Hokkaido were related to Dipodascopsis anomala and 29 strains representing 12 species from soils in Kamogawa-shi, Chiba and Iriomote Island, Okinawa were in the Myxozyma clade. The two species of Dipodascopsis form globose or ellipsoid ascospores in their sac-like ascus and pseudohyphae. Furthermore, these species produce ascospores in their pseudohyphae and do not produce an acicular ascus, which is common among the three species including D. anomala. Therefore, we propose transferring D. anomala to the genus Babjevia and amending Babjevia. Two novel species were described and included in the genus Babjevia: Babjevia hyphoforaminiformans sp. nov. (holotype NBRC 111233; MycoBank no. MB 829051) and Babjevia hyphasca sp. nov. (holotype NBRC 112965; MycoBank no. MB 829053). The 12 species in the Myxozyma clade produce neither ascospores nor pseudohyphae and have different characteristics in assimilating several carbon sources from each other. Thus, we propose that the novel species of Lipomyces be classified as forma asexualis (f.a.). From Kamogawa-shi, Chiba (19 strains representing five species): Lipomyces melibiosiraffinosiphilus f.a., sp. nov. (holotype NBRC 111411; MycoBank no. MB 829034), Lipomyces kiyosumicus f.a., sp. nov. (holotype NBRC 111424; MycoBank no. MB 829035), Lipomyces chibensis f.a., sp. nov. (holotype NBRC 111413; MycoBank no. MB 829036), Lipomyces kamogawensis f.a., sp. nov. (holotype NBRC 112967; MycoBank no. MB 829037), Lipomyces amatsuensis f.a., sp. nov. (holotype NBRC 111420; MycoBank no. MB 829041). From Iriomote island, Okinawa (10 strains representing seven species): Lipomyces taketomicus f.a., sp. nov. (holotype NBRC 112966; MycoBank no. MB 829042), Lipomyces yaeyamensis f.a., sp. nov. (holotype NBRC 110433; MycoBank no. MB 829050), Lipomyces iriomotensis f.a., sp. nov. (holotype NBRC 110436; MycoBank no. MB 829045), Lipomyces haiminakanus f.a., sp. nov. (holotype NBRC 110435; MycoBank no. MB 829046), Lipomyces komiensis f.a., sp. nov. (holotype NBRC 110440; MycoBank no. MB 829047), Lipomyces nakamensis f.a., sp. nov. (holotype NBRC 110434; MycoBank no. MB 829048), Lipomyces sakishimensis f.a., sp. nov. (holotype NBRC 110439; MycoBank no. MB 829049).


Assuntos
Lipomyces/classificação , Filogenia , Microbiologia do Solo , DNA Fúngico/genética , Genes Fúngicos , Japão , Lipomyces/isolamento & purificação , Técnicas de Tipagem Micológica , Fator 1 de Elongação de Peptídeos/genética , Fenótipo , Saccharomycetales/classificação , Análise de Sequência de DNA , Esporos Fúngicos
8.
Nucleic Acids Res ; 48(8): 4081-4099, 2020 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-32187373

RESUMO

Cytosine methylation is a ubiquitous modification in mammalian DNA generated and maintained by several DNA methyltransferases (DNMTs) with partially overlapping functions and genomic targets. To systematically dissect the factors specifying each DNMT's activity, we engineered combinatorial knock-in of human DNMT genes in Komagataella phaffii, a yeast species lacking endogenous DNA methylation. Time-course expression measurements captured dynamic network-level adaptation of cells to DNMT3B1-induced DNA methylation stress and showed that coordinately modulating the availability of S-adenosyl methionine (SAM), the essential metabolite for DNMT-catalyzed methylation, is an evolutionarily conserved epigenetic stress response, also implicated in several human diseases. Convolutional neural networks trained on genome-wide CpG-methylation data learned distinct sequence preferences of DNMT3 family members. A simulated annealing interpretation method resolved these preferences into individual flanking nucleotides and periodic poly(A) tracts that rotationally position highly methylated cytosines relative to phased nucleosomes. Furthermore, the nucleosome repeat length defined the spatial unit of methylation spreading. Gene methylation patterns were similar to those in mammals, and hypo- and hypermethylation were predictive of increased and decreased transcription relative to control, respectively, in the absence of mammalian readers of DNA methylation. Introducing controlled epigenetic perturbations in yeast thus enabled characterization of fundamental genomic features directing specific DNMT3 proteins.


Assuntos
DNA (Citosina-5-)-Metiltransferases/metabolismo , Metilação de DNA , Epigênese Genética , Saccharomycetales/genética , Engenharia Celular , Centrômero , Cromatina/química , DNA (Citosina-5-)-Metiltransferases/genética , Técnicas de Introdução de Genes , Genoma Fúngico , Humanos , Redes Neurais de Computação , S-Adenosilmetionina/metabolismo , Saccharomycetales/metabolismo , Estresse Fisiológico/genética , Telômero , Transcrição Genética
9.
Nat Ecol Evol ; 4(4): 601-611, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32152531

RESUMO

Mutations that a population accumulates during evolution in one 'home' environment may cause fitness gains or losses in other environments. Such pleiotropic fitness effects determine the evolutionary fate of the population in variable environments and can lead to ecological specialization. It is unclear how the pleiotropic outcomes of evolution are shaped by the intrinsic randomness of the evolutionary process and by the deterministic variation in selection pressures across environments. Here, to address this question, we evolved 20 replicate populations of the yeast Saccharomyces cerevisiae in 11 laboratory environments and measured their fitness across multiple conditions. We found that evolution led to diverse pleiotropic fitness gains and losses, driven by multiple types of mutations. Approximately 60% of this variation is explained by the home environment of a clone and the most common parallel genetic changes, whereas about 40% is attributed to the stochastic accumulation of mutations whose pleiotropic effects are unpredictable. Although populations are typically specialized to their home environment, generalists also evolved in almost all of the conditions. Our results suggest that the mutations that accumulate during evolution incur a variety of pleiotropic costs and benefits with different probabilities. Thus, whether a population evolves towards a specialist or a generalist phenotype is heavily influenced by chance.


Assuntos
Saccharomycetales , Aclimatação , Adaptação Fisiológica , Fenótipo , Probabilidade
10.
Int J Syst Evol Microbiol ; 70(4): 2589-2594, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32134373

RESUMO

Seven yeast strains, DMKU VGT1-14T, DMKU VGT1-19T, DMKU-JMGT1-28, DMKU-JMGT1-32, DMKU VGT2-06, DMKU VGT2-19 and DMKU VGT6-14, were isolated from a grease trap in Thailand and two strains, SJ-1 and SN-102 were isolated from the sea surface microlayer in Taiwan. On the basis of phenotypic characteristics and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, these strains represented two novel yeast species of the genus Wickerhamiella. In terms of pairwise sequence similarity, four strains, DMKU VGT1-14, DMKU-JMGT1-32, DMKU VGT6-14 and SN-102, were closely related to Wickerhamiella infanticola NRRL Y-17858T but differed by 13 nucleotide substitutions with one gap (2.46 %) in the D1/D2 domain of the LSU rRNA gene and 15 nucleotide substitutions with 23 gaps (4.2 %) in the ITS region. The strains DMKU VGT1-19T, DMKU-JMGT1-28, DMKU VGT2-06, DMKU VGT2-19 and SJ-1, differed from the type strain of the most closely related species, Wickerhamiella sorbophila NRRL Y-7921T, by nine nucleotide substitutions with one gap (1.66 %) in the D1/D2 domain of the LSU rRNA gene and nine nucleotide substitutions with 17 gaps (2.52%) in the ITS region. Hence, the names Wickerhamiella osmotolerans sp. nov. and Wickerhamiella tropicalis sp. nov. are proposed to accommodate these species in the genus Wickerhamiella. The holotypes are W. osmotolerans DMKU VGT1-14T (ex-type strain TBRC 11425=PYCC 8359=CGMCC 2.6179; Mycobank number 833394) and W. tropicalis DMKU VGT1-19T (ex-type strain TBRC 11426=PYCC 8360=CGMCC 2.6180; Mycobank number 833393).


Assuntos
Filogenia , Saccharomycetales/classificação , Água do Mar/microbiologia , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Técnicas de Tipagem Micológica , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA , Taiwan , Tailândia
11.
Int J Syst Evol Microbiol ; 70(4): 2677-2681, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32207678

RESUMO

Six strains of a novel yeast species were isolated from tree bark collected in the Atlantic Forest and the Amazon Rainforest in Brazil. Analyses of the sequences of D1/D2 domains of the large subunit rRNA gene showed that the strains belong to a species in the genus Zygotorulaspora. The species differed by 5.54 % sequence divergence (25 substitutions and five indels out of 542 bp) in the D1/D2 sequences from Zygotorulaspora mrakii, its closest relative. The ITS sequence of the type strain of the novel species differs by 27-69 nucleotide substitutions/indels from the other Zygotorulaspora species. The novel species is able to grow on trehalose, maltose, l-sorbose, inulin and at 37 °C, which are negative in Z. mrakii. The name Zygotorulaspora cariocana sp. nov. is proposed. The holotype of Z. cariocana sp. nov. is CBS 16118T. The MycoBank number is MB 833702.


Assuntos
Filogenia , Casca de Planta/microbiologia , Saccharomycetales/classificação , Brasil , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Técnicas de Tipagem Micológica , Floresta Úmida , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA , Árvores/microbiologia
12.
J Agric Food Chem ; 68(8): 2418-2425, 2020 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-32011876

RESUMO

Two biosynthetically related new metabolites, eucalyptacid A (1) and eucalactam B (2), along with six known compounds (3-8), eugenitol (3), cytosporone C (4), 4-hydroxyphenethyl alcohol (5), 1-(4-hydroxyphenyl)ethane-1,2-diol (6), N-(2-hydroxy-2-phenylethyl)acetamide (7), and phomopene (8), were isolated from the solid rice cultures of the endophytic fungus Diaporthe eucalyptorum KY-9 that had been isolated from Melia azedarach. Also, two further new derivatives (2a, 2b) were prepared from 2. The structures were elucidated by exhaustive analysis of NMR and ESIMS data and chemical methods such as Marfey's protocol. Compound 1 was identified as a rare polyketide fatty acid, (8E)-3,5,11-trihydroxy-2,10,12-trimethyltetradecenoic acid, and 2 was determined to be the first cyclic depsipeptide containing the same fatty acid unit as 1 and a Gly-Gly-Thr tripeptide chain. Its N-terminal end is N-acylated by an 11-hydroxy fatty acid with a branch alkyl chain of 14:1. The 11-hydroxyl group connects to the carboxylic group of the C-terminal amino acid to form a 22-membered lactone ring. A hypothetical biosynthetic pathway for the new polyketides is proposed. The isolated compounds were assayed for their inhibition against four plant pathogenic fungi, Alternaria solani, Botrytis cinerea, Fusarium solani, and Gibberella saubinettii. Compounds 1, 4, 6, and 7 exhibited antifungal activities against Alternaria solani, with minimal inhibitory concentration (MIC) values from 6.25 to 50 µM. Thus, strain KY-9 represents an untapped source for the development of biological control agents to prevent the infection of pathogenic fungus A. solani.


Assuntos
Fungicidas Industriais/metabolismo , Fungicidas Industriais/farmacologia , Melia azedarach/microbiologia , Saccharomycetales/química , Alternaria/efeitos dos fármacos , Alternaria/crescimento & desenvolvimento , Botrytis/efeitos dos fármacos , Botrytis/crescimento & desenvolvimento , Fungicidas Industriais/química , Fungicidas Industriais/isolamento & purificação , Fusarium/efeitos dos fármacos , Fusarium/crescimento & desenvolvimento , Testes de Sensibilidade Microbiana , Saccharomycetales/isolamento & purificação , Saccharomycetales/metabolismo
13.
Lett Appl Microbiol ; 70(6): 431-439, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32031273

RESUMO

This study was performed to evaluate the effects of dietary probiotics on growth, non-specific immune responses and disease resistance in olive flounder, Paralichthys olivaceus. During 8 weeks, the fish were fed the five experimental diets such as a basal commercial diet (CON), oxytetracycline (OTC) and three basal diets containing Bacillus subtilis (BS), a commercial microbial product (CES) and a mixture of yeast and bacterium (PI), respectively. Fish fed all the probiotics diets and OTC showed a significantly higher growth than fish-fed CON (P < 0·05). Fish-fed PI had a significantly higher nitroblue tetrazolium activity, whereas fish-fed CES showed a higher lysozyme level (P < 0·05). A 7-day challenge test also showed that fish-fed PI had a cumulative survival rate equivalent to that of fish-fed OTC (P < 0·05). Moreover, the diet (PI) appeared to increase the diversity of microbial community in the fish. All these results suggest that the probiotics diet could function as a potential antibiotic replacer in the olive flounder. SIGNIFICANCE AND IMPACT OF THE STUDY: This study is unique in revealing that a diet mixture of yeast, Groenewaldozyma salmanticensis and bacterium Gluconacetobacter liquefaciens can enhance growth, innate immunity and diversity of microbial community including dominant species in the olive flounder. All these indicate that the diet mixture could function as a potential antibiotic replacer in one of the most commercially important fisheries in South Korea.


Assuntos
Ração Animal/microbiologia , Linguado/crescimento & desenvolvimento , Linguado/imunologia , Gluconacetobacter/fisiologia , Probióticos/farmacologia , Saccharomycetales/fisiologia , Ração Animal/análise , Animais , Bacillus subtilis/fisiologia , Dieta , Resistência à Doença/fisiologia , Doenças dos Peixes/microbiologia , Linguado/microbiologia , República da Coreia
14.
Int J Syst Evol Microbiol ; 70(4): 2420-2425, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32100691

RESUMO

Yeast strains belonging to a novel anamorphic yeast species were isolated from subsoil groundwater contaminated with hydrocarbons in a metal working factory located in northern Spain, and from a human infection in the USA. Comparison of ITS sequences between the isolates revealed 0.2 % divergence between the Spanish isolates and 0.46 % divergence between those and the USA isolate. Phylogenetic analysis based on the D1/D2 domains of the LSU rRNA gene showed that these isolates belong to the Wickerhamiella clade with W. sorbophila and W. infanticola as their closest relatives. Sequence divergence between the new isolates and W. sorbophila and W. infanticola was 1.97 and 1.79 %, respectively. The isolates in the novel species are not fermentative and pseudohyphae were not produced. Sexual reproduction was not observed for individual isolates or in mixtures of isolates. Conjugation between the isolates in the novel species and close relatives W. sorbophila and W. infanticola was not observed. These data support the proposal of Wickerhamiella verensis as a novel species, with CECT 12028T as the holotype.


Assuntos
Água Subterrânea/microbiologia , Micoses/microbiologia , Filogenia , Saccharomycetales/classificação , DNA Fúngico/genética , Fermentação , Georgia , Humanos , Hidrocarbonetos , Lactente , Técnicas de Tipagem Micológica , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA , Espanha , Poluentes Químicos da Água
15.
Int J Syst Evol Microbiol ; 70(3): 2103-2107, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31995468

RESUMO

Four strains of anamorphic yeasts isolated from the fruiting bodies of mushrooms collected in Taiwan were found to represent two novel yeast species belonging to the genus Teunomyces, which was formally known as the Candida kruisii clade. Strains NY13M09T and NY14M14 were related to the type strains of Teunomyces panamensis, T. pallodes, T. tritomae and T. lycoperdinae, and strains GG4M07T and GG6M14 were related to T. kruisii NRRL Y-17087T and T. cretensis NRRL Y-27777T. However, strains NY13M09T and NY14M14 differed from their closest phylogenetic neighbours by 2.9-3.7 % in the D1/D2 domain sequence of the LSU rRNA gene and by 6.6-13.7 % in the internal transcribed spacer (ITS); GG4M07T and GG6M14 differed from their closest known species by 2.4 % in the D1/D2 domain sequence of the LSU rRNA gene and by 8.7-10.0 % in the ITS. Meanwhile, these strains were also clearly distinguished from their closest relatives based on the results of physiological tests. Based on the characteristics described above, the strains could be regarded as representing two novel species of the genus Teunomyces, for which the names Teunomyces basidiocarpi sp. nov. and Teunomyces luguensis sp. nov. are proposed. The holotypes are Teunomyces basidiocarpi BCRC 23475T and Teunomyces luguensis BCRC 23476T.


Assuntos
Agaricales , Filogenia , Saccharomycetales/classificação , Composição de Bases , DNA Fúngico/genética , Técnicas de Tipagem Micológica , RNA Ribossômico/genética , RNA Ribossômico 16S/genética , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA , Taiwan
16.
BMC Bioinformatics ; 21(1): 34, 2020 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-31996136

RESUMO

BACKGROUND: To develop mechanistic dynamic models in systems biology, one often needs to identify all (or minimal) representations of the biological processes that are consistent with experimental data, out of a potentially large set of hypothetical mechanisms. However, a simple enumeration of all alternatives becomes quickly intractable when the number of model parameters grows. Selecting appropriate dynamic models out of a large ensemble of models, taking the uncertainty in our biological knowledge and in the experimental data into account, is therefore a key current problem in systems biology. RESULTS: The TopoFilter package addresses this problem in a heuristic and automated fashion by implementing the previously described topological filtering method for Bayesian model selection. It includes a core heuristic for searching the space of submodels of a parametrized model, coupled with a sampling-based exploration of the parameter space. Recent developments of the method allow to balance exhaustiveness and speed of the model space search, to efficiently re-sample parameters, to parallelize the search, and to use custom scoring functions. We use a theoretical example to motivate these features and then demonstrate TopoFilter's applicability for a yeast signaling network with more than 250'000 possible model structures. CONCLUSIONS: TopoFilter is a flexible software framework that makes Bayesian model selection and reduction efficient and scalable to network models of a complexity that represents contemporary problems in, for example, cell signaling. TopoFilter is open-source, available under the GPL-3.0 license at https://gitlab.com/csb.ethz/TopoFilter. It includes installation instructions, a quickstart guide, a description of all package options, and multiple examples.


Assuntos
Modelos Biológicos , Transdução de Sinais , Software , Biologia de Sistemas/métodos , Algoritmos , Teorema de Bayes , Saccharomycetales/metabolismo
17.
Nat Commun ; 11(1): 316, 2020 01 16.
Artigo em Inglês | MEDLINE | ID: mdl-31949281

RESUMO

Here we propose an experimental setup based on operando X-ray absorption spectroscopy (XAS) to understand why copper-containing oxidoreductase enzymes show exceptional performance as catalysts for the oxygen reduction reaction (ORR). An electrode based on carbon nanoparticles organized in mesoporous structures with bilirubin oxidase (BOD) was developed to be used in a home-made operando XAS electrochemical cell, and we probed the electron transfer under ORR regime. In the presence of molecular oxygen, the BOD cofactor containing 4 copper ions require an overpotential about 150 mV to be reduced as compared to that in the absence of oxygen. A second electron transfer step, which occurs faster than the cofactor reduction, suggests that the cooper ions act as a tridimensional redox active electronic bridges for the electron transfer reaction.


Assuntos
Cobre/química , Transporte de Elétrons , Elétrons , Metaloproteínas/química , Oxirredutases/química , Espectroscopia por Absorção de Raios X/métodos , Catálise , Eletrodos , Modelos Químicos , Oxirredução , Oxirredutases atuantes sobre Doadores de Grupo CH-CH/química , Oxigênio/química , Saccharomycetales
18.
Nucleic Acids Res ; 48(1): 421-431, 2020 01 10.
Artigo em Inglês | MEDLINE | ID: mdl-31724694

RESUMO

COMPlex ASsociating with SET1 (COMPASS) is a histone H3 Lys-4 methyltransferase that typically marks the promoter region of actively transcribed genes. COMPASS is a multi-subunit complex in which the catalytic unit, SET1, is required for H3K4 methylation. An important subunit known to regulate SET1 methyltransferase activity is the CxxC zinc finger protein 1 (Cfp1). Cfp1 binds to COMPASS and is critical to maintain high level of H3K4me3 in cells but the mechanisms underlying its stimulatory activity is poorly understood. In this study, we show that Cfp1 only modestly activates COMPASS methyltransferase activity in vitro. Binding of Cfp1 to COMPASS is in part mediated by a new type of monovalent zinc finger (ZnF). This ZnF interacts with the COMPASS's subunits RbBP5 and disruption of this interaction blunts its methyltransferase activity in cells and in vivo. Collectively, our studies reveal that a novel form of ZnF on Cfp1 enables its integration into COMPASS and contributes to epigenetic signaling.


Assuntos
Proteínas Fúngicas/química , Histona-Lisina N-Metiltransferase/química , Histonas/química , Fatores de Transcrição/química , Dedos de Zinco , Sequência de Aminoácidos , Sítios de Ligação , Chaetomium/genética , Chaetomium/metabolismo , Clonagem Molecular , Cristalografia por Raios X , Epigênese Genética , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Histona-Lisina N-Metiltransferase/genética , Histona-Lisina N-Metiltransferase/metabolismo , Histonas/genética , Histonas/metabolismo , Cinética , Metilação , Modelos Moleculares , Regiões Promotoras Genéticas , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Saccharomycetales/genética , Saccharomycetales/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Zinco/metabolismo
19.
Int J Syst Evol Microbiol ; 70(2): 977-981, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31724935

RESUMO

Strain SY-07 was isolated from decaying leaves of Avicennia marina collected from Syhat mangroves, Dammam city, Arabian Gulf, Saudi Arabia. Phylogenetic analyses of three genes [D1/D2 region of the LSU and SSU rRNA genes and internal transcribed spacer (ITS) region] showed that strain SY-07 represents a novel species of the genus Saturnispora distinct from closely related species. Saturnispora mendoncae was the most closely related species with an LSU gene sequence similarity of 89.3 % (58 nucleotide substitutions and four indels out of 578 nt), 97 % similarity for the SSU gene (42 nucleotide substitutions and 10 indels out of 1614 nt) and 88 % similarity for the ITS region (15 nucleotide substitutions and eight indels out of 430 nt). In addition, strain SY-07 differed from S. mendoncae by its ability to assimilate d-galactose (weak), d-xylose (weak), meso-erythritol (delayed), glucono-δ-lactone, citrate (delayed) and ethylamine. S. mendoncae produced persistent asci that contain two to four spherical ascospores and lacked pseudohyphae, while sexual reproduction was not observed in strain SY-07 and extensive and pseudohyphae were present. Strain SY-07 was able to grow at between 25 and 40 °C, while S. mendoncae did not grow at 37 °C. The name Saturnispora mangrovi f.a., sp. nov. is proposed for strain SY-07. The holotype is CBS 15874, with the ex-type culture AUMC 12005. The MycoBank number for Saturnispora mangrovi f.a., sp. nov. is MB 827036.


Assuntos
Avicennia/microbiologia , Filogenia , Folhas de Planta/microbiologia , Saccharomycetales/classificação , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Técnicas de Tipagem Micológica , Saccharomycetales/isolamento & purificação , Arábia Saudita , Análise de Sequência de DNA , Esporos Fúngicos
20.
J Appl Microbiol ; 128(3): 853-861, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31733170

RESUMO

AIM: The aim of the present study was to investigate the in vitro antioxidant activity of yeast strains isolated from virgin olive oil. METHODS AND RESULTS: The 2,2-diphenyl-1-picryl-hydrazyl (DPPH) free-radical scavenging activity of single cultures of 24 yeast strains belonging to eight species isolated from virgin olive oil was evaluated and compared with that of the reference yeast Saccharomyces boulardii. All the yeasts studied in vitro showed antioxidant activity similar to or superior to that of the reference yeast. The highest antioxidant activity was observed in Nakazawaea wickerhamii, which exceeded the value reached by the reference strain S. boulardii, while the significantly lowest values were observed in the Candida adriatica, Candida diddensiae and Barnettozyma californica strains. Tests performed with virgin olive oil enriched with Wickerhamomyces anomalus and S. boulardii yeast biomasses showed a positive correlation between the microbial biomass used and the percentage of antioxidant activity observed during 60 days of storage. Survival in virgin olive oil was also significantly higher for W. anomalus compared to S. boulardii. CONCLUSIONS: All the oil-borne yeasts studied showed DPPH free-radical scavenging activity in both aqueous and oily media. SIGNIFICANCE AND IMPACT OF THE STUDY: For the first time, the antioxidant activity of the microbiota of virgin olive oil is reported. This activity may indicate the probiotic characteristics of the microbiota.


Assuntos
Antioxidantes/metabolismo , Azeite de Oliva , Saccharomycetales/isolamento & purificação , Saccharomycetales/metabolismo , Biomassa , Compostos de Bifenilo/metabolismo , Microbiologia de Alimentos , Microbiota , Picratos/metabolismo , Probióticos , Saccharomycetales/classificação , Saccharomycetales/crescimento & desenvolvimento
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