Convergent adaptation of Saccharomyces uvarum to sulfite, an antimicrobial preservative widely used in human-driven fermentations.

Different species can find convergent solutions to adapt their genome to the same evolutionary constraints, although functional convergence promoted by chromosomal rearrangements in different species has not previously been found. In this work, we discovered that two domesticated yeast species, Saccharomyces cerevisiae, and Saccharomyces uvarum, acquired chromosomal rearrangements to convergently adapt to the presence of sulfite in fermentation environments. We found two new heterologous chromosomal translocations in fermentative strains of S. uvarum at the SSU1 locus, involved in sulfite resistance, an antimicrobial additive widely used in food production. These are convergent events that share similarities with other SSU1 locus chromosomal translocations previously described in domesticated S. cerevisiae strains. In S. uvarum, the newly described VIIXVI and XIXVI chromosomal translocations generate an overexpression of the SSU1 gene and confer increased sulfite resistance. This study highlights the relevance of chromosomal rearrangements to promote the adaptation of yeast to anthropic environments.

A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event.

BACKGROUND: Horizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes. RESULTS: Through a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces. CONCLUSIONS: The presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.

Phenotypic and genomic differences among S. cerevisiae strains in nitrogen requirements during wine fermentations.

Nitrogen requirements by S. cerevisiae during wine fermentation are highly strain-dependent. Different approaches were applied to explore the nitrogen requirements of 28 wine yeast strains. Based on the growth and fermentation behaviour displayed at different nitrogen concentrations, high and low nitrogen-demanding strains were selected and further verified by competition fermentation. Biomass production with increasing nitrogen concentrations in the exponential fermentation phase was analysed by chemostat cultures. Low nitrogen-demanding (LND) strains produced a larger amount of biomass in nitrogen-limited synthetic grape musts, whereas high nitrogen-demanding (HND) strains achieved a bigger biomass yield when the YAN concentration was above 100 mg/L. Constant rate fermentation was carried out with both strains to determine the amount of nitrogen required to maintain the highest fermentation rate. Large differences appeared in the analysis of the genomes of low and high-nitrogen demanding strains showed for heterozygosity and the amino acid substitutions between orthologous proteins, with nitrogen recycling system genes showing the widest amino acid divergences. The CRISPR/Cas9-mediated genome modification method was used to validate the involvement of GCN1 in the yeast strain nitrogen needs. However, the allele swapping of gene GCN1 from low nitrogen-demanding strains to high nitrogen-demanding strains did not significantly influence the fermentation rate.

Kluyveromyces osmophilus is not a synonym of Zygosaccharomyces mellis; reinstatement as Zygosaccharomyces osmophilus comb. nov.

Kluyveromyces osmophilus, a single-strain species isolated from Mozambique sugar, has been treated a synonym of Zygosaccharomyces mellis. Analyses of D1/D2 LSU rRNA gene sequences confirmed that the species belongs to the genus Zygosaccharomyces but showed it to be distinct from strains of Z. mellis. During studies of yeasts associated with stingless bees in Brazil, nine additional isolates of the species were obtained from unripe and ripe honey and pollen of Scaptotrigona cfr. bipunctata, as well as ripe honey of Tetragonisca angustula. The D1/D2 sequences of the Brazilian isolates were identical to those of the type strain of K. osmophilus CBS 5499 (=ATCC 22027), indicating that they represent the same species. Phylogenomic analyses using 4038 orthologous genes support the reinstatement of K. osmophilus as a member of the genus Zygosaccharomyces. We, therefore, propose the name Zygosaccharomyces osmophilus comb. nov. (lectotype ATCC 22027; MycoBank no. MB 833739).

Functional divergence in the proteins encoded by ARO80 from S. uvarum, S. kudriavzevii and S. cerevisiae explain differences in the aroma production during wine fermentation.

Phenylethanol (PE) and phenylethyl acetate (PEA) are commonly desired compounds in wine because of their rose-like aroma. The yeast S. cerevisiae produces the PE either through de novo biosynthesis by shikimate pathway followed by the Ehrlich pathway or the direct phenylalanine catabolism via Ehrlich pathway, and then converted into PEA. Previous work demonstrated that, compared to S. cerevisiae, other Saccharomyces species, such as S. kudriavzevii and S. uvarum, produce higher concentrations of PE and PEA from the precursor phenylalanine, which indicates differential activities of the biosynthetic-involved enzymes. A previous in-silico analysis suggested that the transcriptional activator Aro80p is one of the best candidates to explain these differences. An improved functional analysis identified significant radical amino acid changes in the S. uvarum and S. kudriavzevii Aro80p that could impact the expression of the catabolic genes ARO9 and ARO10, and hence, the production of PE from phenylalanine. Indeed, wine S. cerevisiae strains carrying the S. uvarum and S. kudriavzevii ARO80 alleles increased the production of both compounds in the presence of phenylalanine by increasing the expression of ARO9 and ARO10. This study provides novel insights of the unidentified Aro80p regulatory region and the potential usage of alternatives ARO80 alleles to enhance the PE and PEA concentration in wine.

Adaptive evolution in the Saccharomyces kudriavzevii Aro4p promoted a reduced production of higher alcohols.

The use of unconventional yeast species in human-driven fermentations has attracted a lot of attention in the last few years. This tool allows the alcoholic beverage industries to solve problems related to climate change or the consumer demand for newer high-quality products. In this sense, one of the most attractive species is Saccharomyces kudriavzevii, which shows interesting fermentative traits such as the increased and diverse aroma compound production in wines. Specifically, it has been observed that different isolates of this species can produce higher amounts of higher alcohols such as phenylethanol compared with Saccharomyces cerevisiae. In this work, we have shed light on this feature relating it to the S. kudriavzevii aromatic amino acid anabolic pathway in which the enzyme Aro4p plays an essential role. Unexpectedly, we observed that the presence of the S. kudriavzevii ARO4 variant reduces phenylethanol production compared with the S. cerevisiae ARO4 allele. Our experiments suggest that this can be explained by increased feedback inhibition, which might be a consequence of the changes detected in the Aro4p amino end such as L26 Q24 that have been under positive selection in the S. kudriavzevii specie.

A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different Redox Balancing among Yeast Species of the Saccharomyces Genus in Fermentation.

Yeasts constitute over 1,500 species with great potential for biotechnology. Still, the yeast Saccharomyces cerevisiae dominates industrial applications, and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts' metabolic specificity in batch cultures. Here, we propose a multiphase multiobjective dynamic genome-scale model of yeast batch cultures that describes the uptake of carbon and nitrogen sources and the production of primary and secondary metabolites. The model integrates a specific metabolic reconstruction, based on the consensus Yeast8, and a kinetic model describing the time-varying culture environment. In addition, we proposed a multiphase multiobjective flux balance analysis to compute the dynamics of intracellular fluxes. We then compared the metabolism of S. cerevisiae and Saccharomyces uvarum strains in a rich medium fermentation. The model successfully explained the experimental data and brought novel insights into how cryotolerant strains achieve redox balance. The proposed model (along with the corresponding code) provides a comprehensive picture of the main steps occurring inside the cell during batch cultures and offers a systematic approach to prospect or metabolically engineering novel yeast cell factories. IMPORTANCE Nonconventional yeast species hold the promise to provide novel metabolic routes to produce industrially relevant compounds and tolerate specific stressors, such as cold temperatures. This work validated the first multiphase multiobjective genome-scale dynamic model to describe carbon and nitrogen metabolism throughout batch fermentation. To test and illustrate its performance, we considered the comparative metabolism of three yeast strains of the Saccharomyces genus in rich medium fermentation. The study revealed that cryotolerant Saccharomyces species might use the γ-aminobutyric acid (GABA) shunt and the production of reducing equivalents as alternative routes to achieve redox balance, a novel biological insight worth being explored further. The proposed model (along with the provided code) can be applied to a wide range of batch processes started with different yeast species and media, offering a systematic and rational approach to prospect nonconventional yeast species metabolism and engineering novel cell factories.

GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level.

One of the most widely used programs for detecting positive selection, at the molecular level, is the program codeml, which is implemented in the Phylogenetic Analysis by Maximum Likelihood (PAML) package. However, it has a limitation when it comes to genome-wide studies, as it runs on a gene-by-gene basis. Furthermore, the size of such studies will depend on the number of orthologous genes the genomes have income and these are often restricted to only account for instances where a one-to-one relationship is observed between the genomes. In this work, we present GWideCodeML, a Python package, which runs a genome-wide codeml with the option of parallelization. To maximize the number of analyzed genes, the package allows for a variable number of taxa in the alignments and will automatically prune the topology to fit each of them, before running codeml.

Comparative Genomics Between Saccharomyces kudriavzevii and S. cerevisiae Applied to Identify Mechanisms Involved in Adaptation.

Yeasts belonging to the Saccharomyces genus play an important role in human-driven fermentations. The species S. cerevisiae has been widely studied because it is the dominant yeast in most fermentations and it has been widely used as a model eukaryotic organism. Recently, other species of the Saccharomyces genus are gaining interest to solve the new challenges that the fermentation industry are facing. One of these species is S. kudriavzevii, which exhibits interesting physiological properties compared to S. cerevisiae, such as a better adaptation to grow at low temperatures, a higher glycerol synthesis and lower ethanol production. The aim of this study is to understand the molecular basis behind these phenotypic differences of biotechnological interest by using a species-based comparative genomics approach. In this work, we sequenced, assembled and annotated two new genomes of S. kudriavzevii. We used a combination of different statistical methods to identify functional divergence, signatures of positive selection and acceleration of substitution rates at specific amino acid sites of proteins in S. kudriavzevii when compared to S. cerevisiae, and vice versa. We provide a list of candidate genes in which positive selection could be acting during the evolution of both S. cerevisiae and S. kudriavzevii clades. Some of them could be related to certain important differences in metabolism previously reported by other authors such us DAL3 and ARO4, involved in nitrogen assimilation and amino acid biosynthesis. In addition, three of those genes (FBA1, ZIP1, and RQC2) showed accelerated evolutionary rates in Sk branch. Finally, genes of the riboflavin biosynthesis were also among those genes with a significant higher rate of nucleotide substitution and those proteins have amino acid positions contributing to functional divergence.

Aneuploidy and Ethanol Tolerance in Saccharomyces cerevisiae.

Response to environmental stresses is a key factor for microbial organism growth. One of the major stresses for yeasts in fermentative environments is ethanol. Saccharomyces cerevisiae is the most tolerant species in its genus, but intraspecific ethanol-tolerance variation exists. Although, much effort has been done in the last years to discover evolutionary paths to improve ethanol tolerance, this phenotype is still hardly understood. Here, we selected five strains with different ethanol tolerances, and used comparative genomics to determine the main factors that can explain these phenotypic differences. Surprisingly, the main genomic feature, shared only by the highest ethanol-tolerant strains, was a polysomic chromosome III. Transcriptomic data point out that chromosome III is important for the ethanol stress response, and this aneuploidy can be an advantage to respond rapidly to ethanol stress. We found that chromosome III copy numbers also explain differences in other strains. We show that removing the extra chromosome III copy in an ethanol-tolerant strain, returning to euploidy, strongly compromises its tolerance. Chromosome III aneuploidy appears frequently in ethanol-tolerance evolution experiments, and here, we show that aneuploidy is also used by natural strains to enhance their ethanol tolerance.

Short-Spindled Cell Haemangioblastoma with CD34 Expression: New Histopathological Variant or Just a Stochastic Cytological Singularity?

Haemangioblastomas are neoplasms of uncertain histogenesis with cellular and reticular variants advocated in current lore. Herein we describe an intriguing cerebellar specimen with unusual traits including spindle cell morphology and CD34 positivity. A thirty-nine-year old man had an infratentorial tumour discovered incidentally and resected three times. In all the instances, histopathological diagnosis was haemangioblastoma; nonetheless, he had neither physical stigmata nor family history of von Hippel-Lindau disease. By histology, the lesion was composed of areas of conventional stromal cells admixed with territories populated by short-spindled cells packed in lobules, sometimes giving the appearance of gomitoli. Immunoperoxidase-coupled reactions confirmed the expression of inhibin A, neuron-specific enolase (NSE), PS100, and CD57 but also revealed focal immunolabeling for CD34, CD99, and FXIIIa. This case highlights the potential phenotypical diversity that can be found within these neoplasms. Rather than uncertain histogenesis, it may in fact reflect multiple lines of differentiation-histomimesis-prone to adopt unusual morpho- and immunophenotypes in a subset of haemangioblastomas.

Paediatric Primary Pachymeningeal Xanthogranuloma with Scattered Foci Displaying Reticulohistiocytoma-like Features.

We report a unique case of a 4-year-old girl with an intriguing fibrohistiocytic tumour. Magnetic resonance imaging scans showed a dural mass of variegated intensity compressing the left occipital pole and apparently extending toward the superior sagittal sinus. Grossly, the cut surface of the surgical specimen was yellow, pale, and soft with reddish kernel-like crusts. Histologically, the yellow areas resembled cholesterol granulomas with widespread coagulative necrosis, cholesterol clefts, powdery calcification, foreign body-type giant cells, and foamy macrophages, while the scattered red spots contained numerous multinucleated giant cells of foreign-body and Touton types, the former with amphophilic to slightly eosinophilic cytoplasm. Immunoperoxidase reactions confirmed the expression of histiocytic markers and vimentin. As far as we know, no tumour displaying these peculiar morphological features has yet been described.

Erratum: WHO Grade IV Gliofibroma: A Grading Label Denoting Malignancy for an Otherwise Commonly Misinterpreted Neoplasm.

[This corrects the article on p. 325 in vol. 49, PMID: 26081826.].

WHO Grade IV Gliofibroma: A Grading Label Denoting Malignancy for an Otherwise Commonly Misinterpreted Neoplasm.

We report a 50-year-old woman with no relevant clinical history who presented with headache and loss of memory. Magnetic resonance imaging showed a left parieto-temporal mass with annular enhancement after contrast media administration, rendering a radiological diagnosis of high-grade astrocytic neoplasm. Tumour sampling was performed but the patient ultimately died as a result of disease. Microscopically, the lesion had areas of glioblastoma mixed with a benign mesenchymal constituent; the former showed hypercellularity, endothelial proliferation, high mitotic activity and necrosis, while the latter showed fascicles of long spindle cells surrounded by collagen and reticulin fibers. With approximately 40 previously reported cases, gliofibroma is a rare neoplasm defined as either glio-desmoplastic or glial/benign mesenchymal. As shown in our case, its prognosis is apparently determined by the degree of anaplasia of the glial component.

El espectro morfológico del complejo esclerosis tuberosa: análisis de cuatro casos de autopsia / The morphological spectrum of the tuberous sclerosis complex: analysis of four necropsy cases

Se informan cuatro casos de esclerosis tuberosa. Los hallazgos post mortem más frecuentes fueron hamartomas subependimarios y angiofibromas faciales. También se encontraron astrocitomas subependimarios de células gigantes, rabdomiomas cardiacos múltiples, riñones poliquísticos, fibromas subungueales, manchas hipopigmentadas y angiomiolipomas renales. La presentación clínica y morfológica de la esclerosis tuberosa es variada y heterogénea y en esta breve serie se revisan los aspectos patológicos más importantes para su diagnóstico.

Enfermedad de Devic (Neuromielitis óptica) Hallazgos clínico-patológicos de diez casos de autopsia / (Devic disease (optic neuromyelitis). Clinical and pathologic features in 10 autopsy cases)

Se presentan los hallazgos clínico-pathológicos de diez casos de enfermedad de Devic. La enfermedad fue más frecuente en mujeres adultas y el tiempo de evolución promedio en esta serie fue de diez meses. Las manifestaciones por lesión de la médula espinal fueron las más sobresalientes y casi todos los enfermos murieron por complicaciones pulmonares. Los hallazgos neuropatológicos más importantes fueron desmielinización, infiltrado linfocitario perivascular y cavitación del quiasma óptico y de la médula espinal. Algunos autores consideran la enfermedad de Devic como una forma de esclerosis múltiple y otros como entidad aparte, pero se sabe que es una enfermedad desmielinizante primaria confinada a nervios, quiasma y bandeletas ópticos y a la médula espina, en que el grado de destrucción es mayor aún que en las placas más antiguas de la esclerosis múltiple

Corea de Huntington. Rasgos sobresalientes de dos casos de autopsia / Huntington chorea. Prominent features in two autopsy cases

Se presentan dos casos de Corea de Huntington con autopsia completa, en dos hombres de 70 y 43 años en quienes no se hizo el diagnóstico en vida. Los hallazgos macroscópicos son muy característicos en los dos encéfalos, con atrofia principalmente del caudado y en menor grado del putamen y el globus pallidus, que microscópicamente se corrobora por la presencia de pérdida neuronal, rarefacción y gliosis poco acentuada. Se comenta acerca del diagnóstico premortem y la hipótesis actual sobre el mecanismo de la enfermedad

Tuberculomas biliares de la tienda del cerebelo asociados a neuralgia del trigémino: informe de un caso / Bilateral tuberculomas of the tentorium associated with trigeminal neuralgia: a case report

La neuralgia del trigénio (NT) se asocia con múltiples lesiones intra y extracraneanas como son la compresión vascular arterial o venosa, ateroesclerosis, esclerosis múltiple, malformaciones arteriovenosas, etc. Se piensa que algunas de estas lesiones intervienen en la patogenia de la NT. Se presenta el caso de una mujer de 72 años con NT unilateral secundaria a la presencia de tuberculomas bilaterales de la tienda del cerebelo, y del surco olfatorio. Murió como consecuencia de leptomeningitis tuberculosa. Se revisan los conceptos actuales de la patogenia de la NT

Malformaciones arteriovenosas cerebrales: datos sobresalientes de 113 casos de autopsia / Arteriovenous in the brain: salient features in 113 autopsy cases

Se informa una serie grande de malformaciones arteriovenosas cerebrales estudiadas en un periodo de 20 años. En un total de 15,026 autopsias se diagnostiocaron 113 casos, lo que indica una frecuencia más alta de la que ha sido informada en otras series. Se señalan los resultados del análisis de manifestaciones clínicas, estudios de gabinete y tratamiento. Del estudio anatomopatológico se indican su localización, tamaño, presencia o ausencia de hemorragia, cambios en el parénquima vecino y enfermedades asociadas. No se hizo la distinción en los cuatro tipos clásicos de malgormación arteriovenosa, ya que se ha demostrado que la presentación clínica, los datos obtenidos por imagen y el pronóstico son similares en todos ellos.

Arteritis segmentaria y focal de arterias intracraneanas: Informe de cuatro casos de autopsia / Segmental and focal arteritis of intracranial arteries: A report of four autopsy cases

El sistema nervioso central puede ser afectado por diversos tipos de vasculitis, ya sea como parte de una afección sistémica o de manera aislada. Se informan cuatro casos de arteritis segmentarias y focales de arterias intracraneanas, todos los pacientes fueron jóvenes y no presentaron datos clínicos de afección, ni lesiones en arterias extracraneanas. La afección de las arterias cerebrales fue focal y segmentaria y produjo trombosis con el consiguiente infarto isquémico en el territorio irrigado por el vaso afectado. Se revisan los conceptos sobre patogenía y clasificación de las vasculitis que afectan al sistema nervioso central, con especial atención de aquellas producidas por complejos inmunes circulantes