Academic literature on the topic 'Saccharomycetales'

Lignin, which is a component of wood, is difficult to degrade in nature. However, serious decay caused by microbial consortia can happen to wooden antiques during the preservation process. This study successfully screened four microbial consortia with lignin degradation capabilities (J-1, J-6, J-8 and J-15) from decayed wooden antiques. Their compositions were identified by genomic sequencing, while the degradation products were analyzed by GC-MS. The lignin degradation efficiency of J-6 reached 54% after 48 h with an initial lignin concentration of 0.5 g/L at pH 4 and rotation speed of 200 rpm. The fungal consortium of J-6 contained Saccharomycetales (98.92%) and Ascomycota (0.56%), which accounted for 31% of the total biomass. The main bacteria in J-6 were Shinella sp. (47.38%), Cupriavidus sp. (29.84%), and Bosea sp. (7.96%). The strongest degradation performance of J-6 corresponded to its composition, where Saccharomycetales likely adapted to the system and improved lignin degradation enzymes activities, and the abundant bacterial consortium accelerated lignin decomposition. Our work demonstrated the potential utilization of microbial consortia via the synergy of microbial consortia, which may overcome the shortcomings of traditional lignin biodegradation when using a single strain, and the potential use of J-6 for lignin degradation/removal applications.

Spathaspora is an important genus of d-xylose-fermenting yeasts that are poorly studied in China. During recent yeast collections in Yunnan Province in China, 13 isolates of Spathaspora were obtained from rotting wood and all represent undescribed taxa. Based on morphological and phylogenetic analyses (ITS and nuc 28S), five new species are proposed: Spathaspora elongata, Sp. mengyangensis, Sp. jiuxiensis, Sp. parajiuxiensis and Sp. rosae. Our results indicate a high species diversity of Spathaspora waiting to be discovered in rotting wood from tropical and subtropical southwest China. In addition, the two Candida species, C. jeffriesii and C. materiae, which are members of the Spathaspora clade based on phylogeny, are transferred to Spathaspora as new combinations.

A total of 175 yeast isolates were obtained from grease samples. Based on the D1/D2 region of the large subunit (LSU) ribosomal RNA (rRNA) gene analysis, 150 yeast isolates were identified as belonging to 36 described yeast species, whereas 25 isolates required more analysis. Among the described species, Rhodotorula mucilaginosa was the only Basidiomycetous yeast, whereas 149 isolates were identified as belonging to 35 described species of 15 genera in the phylum Ascomycota, and Candida tropicalis was the most abundant species. A study of lipase production indicated that strain DMKU-JMGT1-45 showed volumetric activity of 38.89 ± 9.62 and 155.56 ± 14.70 U/mL when grown in yeast extract malt extract (YM) and YM supplemented with 1% olive oil, respectively. In addition, this strain intracellularly accumulated lipid, of which the fatty acid profile revealed the major fatty acids to be 39.9% oleic acid (C18:1), 27.61% palmitoleic acid (C16:1) and 14.97% palmitic acid (C16:0). A phylogenetic analysis of the combined multi-locus gene sequences showed that the strains DMKU-JMGT1-45T and DMKU-JMGT4-14 formed a well-separated lineage and could not be assigned to any of the currently recognized genera of the Saccharomycetales. Limtongella siamensis gen. nov., sp. nov. is therefore proposed to accommodate these two strains as members of the order Saccharomycetales.

Eight strains of a novel yeast species were isolated from tree saps of ‘Coihue’ (Nothofagus dombeyi, Nothofagaceae) and glacial meltwater (Castaño Overo River) in the Nahuel Huapi National Park, Patagonia, Argentina. The sequences of the D1/D2 domains of the large subunit of the rRNA gene showed that this novel yeast species belongs to the Wickerhamomyces genus (Order Saccharomycetales, Family Wickerhamomycetaceae). The closest related species were Candida ponderosae and Wickerhamomyces chambardii. Wickerhamomyces patagonicus sp. nov. is proposed to accommodate these novel strains, with the type strain CRUB 1724T (=CBS 11398T =JCM 16381T).

Three species of yeasts are taxonomically described for strains isolated from marine environments. Candida spencermartinsiae sp. nov. (type strain CBS 10894T =NRRL Y-48663T) and Candida taylorii sp. nov. (type strain CBS 8508T =NRRL Y-27213T) are anamorphic ascomycetous yeasts in a phylogenetic cluster of marine yeasts in the Debaryomyces/Lodderomyces clade of the Saccharomycetales. The two species were isolated from multiple locations among coral reefs and mangrove habitats. Pseudozyma abaconensis sp. nov. (type strain CBS 8380T =NRRL Y-17380T) is an anamorphic basidiomycete that is related to the smut fungi of the genus Ustilago in the Ustilaginales. P. abaconensis was collected from waters adjacent to a coral reef.

Species of the genus Sugiyamaella (Trichomonascaceae, Saccharomycetales), found in rotting wood in China, were investigated using morphology and the molecular phylogeny of a combined ITS and nrLSU dataset. Nine taxa were collected in China: two were new species (viz. Sugiyamaella chuxiongsp. nov. and S. yunanensissp. nov.) and seven were known species, S. americana, S. ayubii, S. novakii, S. paludigena, S. valenteae, S. valdiviana and S. xiaguanensis. The two new species are illustrated and their morphology and phylogenetic relationships with other Sugiyamaella species are discussed. Our results indicate a potentially great diversity of Sugiyamaella spp. inhabiting rotting wood in China just waiting to be discovered.

A hierarchy of different chromosome conformations plays a role in many biological systems. These conformations contribute to the regulation of gene expression, cellular development, chromosome transmission, and defects can lead to human disease. The highest functional level of this hierarchy is the partitioning of the genome into compartments of active and inactive chromatin domains (1’s -10’s Mb). These compartments are further partitioned into Topologically Associating Domains (TADs) that spatially cluster co-regulated genes (100’s kb – 1’s Mb). The final level that has been observed is long range loops formed between regulatory elements and promoters (10’s kb – 100’s Mb). At all of these levels, mechanisms that establish these conformations remain poorly understood. To gain new insights into processes that determine chromosome folding I used the mating type switching system in budding yeast to study the chromosome conformation at length scales analogous to looping interaction. I specifically examined the role in chromosome conformation in the mating type switching system. Budding yeast cells can have two sexes: MATa and MATα. The mating types are determined by allele-specific expression of the MAT locus on chromosome III. The MATa allele encodes for transcription factors responsible for the MATa mating type and the MATα allele encodes transcription factors responsible for the MATα mating type. Yeast cells can switch their mating type by a process that repairs a break at MAT using one of two silent loci, HML or HMR, as a donor to convert the allele at the MAT locus. When MATa cells switch they prefer to use HML, which contains the MATα allele, located at the end of the left arm. MATα cells prefer to use HMR, which contains the MATa allele, located on the end of the right arm of chromosome III. The sequences of the HM loci are not important for donor preference. Instead the cell chooses the donor on the left arm in MATa cells and chooses the donor on the right arm in MATα cells. This lack of sequence specificity has led to the hypothesis that the conformation of the chromosome may play a role in donor preference. I found that the conformation of chromosome III is, indeed, different between the two mating types. In MATa cells the chromosomes displays a more crumpled conformation in which the left arm of the chromosome interacts with a large region of the right arm which includes the centromere and the MAT locus. In MATα cells, on the other hand, the left arm of the chromosomes displays a more extend conformation. I found that the Recombination Enhancer (RE), which enhances recombination along the left arm of the chromosome in MATa cells, is responsible for these mating type-specific conformations. Deleting the RE affects the conformation of the chromosomes in both MATa and MATα cells. The left portion of the RE, which is essential for donor preference during the switching reaction in MATa cells, does not contribute to the conformation in MATa. This region does have a minor effect on the conformation in MATα cells. However, I found that the right portion of the RE is responsible for the conformation of chromosome III in both mating types prior to initiation of switching. This work demonstrates that chromosome conformation is determined by specific cis regulatory elements that drive cell-type specific chromosome conformation.

La dérégulation du cycle cellulaire peut entraîner d'importants dommages pour la cellule elle-même, ainsi que pour tout l'organisme : il s'agit en effet d'un des signes avant-coureurs du cancer. Par ailleurs, la souplesse des mécanismes de contrôle permet à la cellule de s'adapter à des signaux internes et externes variés. La réponse à ces signaux peut aller de l'arrêt du cycle à la possibilité de "sauter" une phase du cycle canonique, comme dans le cas des endocycles, des cycles syncytiaux ou de la méiose. Les données qualitatives étant les plus nombreuses, nous avons choisi le formalisme logique pour étudier le cycle cellulaire d'un point de vue théorique. La relative simplicité de ce formalisme nous permet de construire rapidement des modèles impliquant des dizaines de composants. De plus, des outils analytiques spécifiques permettent d'identifier les états stables ou d'analyser le rôle dynamique des circuits de régulation. Après une introduction au cycle cellulaire et au formalisme logique, je présente les résultats obtenus au cours de mon doctorat, articulés autour des articles auxquels j'ai collaboré. La première partie traite d'un modèle schématique du cycle cellulaire chez les mammifères et du système de priorités développé à cette occasion. La seconde partie traite de la levure bourgeonnante, et de l'approche modulaire utilisée pour étendre le modèle avec des modules de régulation supplémentaires. Pour finir, la troisième partie présente ma contribution à la dernière version publique du logiciel de modélisation logique GINsim. Au cours de la discussion, j'analyse la conservation de la fonctionnalité des circuits de régulation dans des modèles du cycle cellulaire de différents organismes. Ensuite, je discute les perspectives de développement des modèles levure et mammifères ouvertes par l'approche modulaire. Enfin, j'aborde les questions de modularité, de fonctionnalité des circuits et de robustesse
Deregulation of the cell cycle can lead to important damage to the cell itself, or to the whole organism. Indeed, unrestricted proliferation is one of the hallmarks of cancer. Moreover, cell cycle control is very flexible, allowing the cell to adapt to many different external and internal signals. Response to these signals may involve profound modifications, including cell cycle arrest, or yet the possibility to “skip” one phase of the canonical cycle, as in endocycles, syncytial cycles or meiosis. In regard to the scarcity of quantitative data, we chose the logical formalism to study the cell cycle from a theoretical point of view. Moreover, the relative simplicity of this formalism allows us to rapidly build large models involving tens of components. Last but not least, this formalism comes with specific analytical tools, including the possibility to identify stable states and analyse the dynamical role of specific regulatory circuits. After an introduction to both the cell cycle and the logical formalism, I present the results obtained during my Ph. D, articulated around the articles I co-authored. The first part of my work deals with a schematic logical model of the mammalian cell cycle and the prioritisation system developed in this context. The second part deals with budding yeast and a modular approach used to extend and update a model of the core cell cycle engine with regulatory modules developed separately. Finally, the third part presents my contribution to the latest public version of the logical modelling software GINsim. In the discussion, I analyse the conservation of functional regulatory circuits in various logical models of the cell cycle in different organisms. Next I discuss perspectives of extension of the budding yeast and mammalian models open by the modular approach. Finally I consider the questions raised by my work in terms of modularity, circuit functionality and robustness