Paula Gonçalves - Academia.edu (original) (raw)

Papers by Paula Gonçalves

Fructophily is a rare trait that consists in the preference for fructose over other carbon source... more Fructophily is a rare trait that consists in the preference for fructose over other carbon sources. Here we show that in a yeast lineage (theWickerhamiella/Starmerella, W/S clade) formed by fructophilic species thriving in the floral niche, the acquisition of fructophily is part of a wider process of adaptation of central carbon metabolism to the high sugar environment. Coupling comparative genomics with biochemical and genetic approaches, we show that the alcoholic fermentation pathway was profoundly remodeled in the W/S clade, as genes required for alcoholic fermentation were lost and subsequently re-acquired from bacteria through horizontal gene transfer. We further show that the reinstated fermentative pathway is functional and that an enzyme required for sucrose assimilation is also of bacterial origin, reinforcing the adaptive nature of the genetic novelties identified in the W/S clade. This work shows how even central carbon metabolism can be remodeled by a surge of HGT events.

Genome biology and evolution, Jan 18, 2016

The natural biology of Saccharomyces cerevisiae, the best known unicellular model eukaryote, rema... more The natural biology of Saccharomyces cerevisiae, the best known unicellular model eukaryote, remains poorly documented and understood although recent progress has started to change this situation. Studies carried out recently in the Northern Hemisphere revealed the existence of wild populations associated with oak trees in North America, Asia and in the Mediterranean region. However, in spite of these advances, the global distribution of natural populations of S. cerevisiae, especially in regions were oaks and other members of the Fagaceae are absent, is not well understood. Here we investigate the occurrence of S. cerevisiae in Brazil, a tropical region where oaks and other Fagaceae are absent. We report a candidate natural habitat of S. cerevisiae in South America and, using whole genome data, we uncover new lineages that appear to have as closest relatives the wild populations found in North America and Japan. A population structure analysis revealed the penetration of the wine g...

Genetics, Jan 14, 2015

In most fungi, sexual reproduction is bipolar, that is, two alternate sets of genes at a single m... more In most fungi, sexual reproduction is bipolar, that is, two alternate sets of genes at a single mating-type (MAT) locus determine two mating types. However, in the Basidiomycota, a unique (tetrapolar) reproductive system emerged in which sexual identity is governed by two unlinked MAT loci, each of which controls independent mechanisms of self/nonself recognition. Tetrapolar to bipolar transitions have occurred on multiple occasions in the Basidiomycota, resulting for instance, from linkage of the two MAT loci into a single inheritable unit. Nevertheless, owing to the scarcity of molecular data regarding tetrapolar systems in the earliest-branching lineage of the Basidiomycota (subphylum Pucciniomycotina), it is presently unclear if the last common ancestor was tetrapolar or bipolar. Here, we address this question, by investigating the mating system of the Pucciniomycotina yeast Leucosporidium scottii. Using whole-genome sequencing and chromoblot analysis, we discovered that sexual ...

FEMS yeast research, 2015

Species of Leucosporidiales are a group of psychrotolerant yeasts with biotechnological potential... more Species of Leucosporidiales are a group of psychrotolerant yeasts with biotechnological potential. In the present work, we studied the phenotypic, genetic and sexual characteristics of three species of this genus (Leucosporidium scottii, Leucosporidiella creatinivora and Le. yakutica) to clarify the evolutionary relationship among these closely related taxa. From the results obtained, it becomes clear that these yeasts can interbreed. Although genetic delimitation is possible for the three species, the extent of nucleotide substitutions and phenotypic differences observed between them are lower than that expected for species that have ended the speciation process. Our taxonomic conclusion is to maintain the three taxa until further genomic data are gathered. However, the concept of L. scottii species complex is proposed for this group of species. Finally, we transfer all Leucosporidiella and Mastigobasidium species to Leucosporidium (Leucosporidiales), and, in order to end the polyp...

mBio, 2013

Our understanding of the interactions between normal skin microbiota and the human host has been ... more Our understanding of the interactions between normal skin microbiota and the human host has been greatly extended by recent investigations. In their recent study in mBio , A. Gioti et al. (mBio 4[1]:e00572-12, 2013) sequenced the genome of the atopic eczema-associated yeast, Malassezia sympodialis , and compared its gene content and organization with that of Malassezia globosa , a species implicated in dandruff. Their findings were also contrasted with those previously obtained for Ustilago maydis , which is a close relative but ecologically distinct plant parasite. Besides gaining additional insight into key host-specific adaptations and the particular function and molecular evolution of allergens related to atopic eczema, Gioti et al. also uncovered several lines of evidence that elegantly suggest the presence of an extant sexual cycle, with important implications in disease.

BMC genomics, Nov 9, 2016

The class Tremellomycete (Agaricomycotina) encompasses more than 380 fungi. Although there are a ... more The class Tremellomycete (Agaricomycotina) encompasses more than 380 fungi. Although there are a few edible Tremella spp., the only species with current biotechnological use is the astaxanthin-producing yeast Phaffia rhodozyma (Cystofilobasidiales). Besides astaxanthin, a carotenoid pigment with potent antioxidant activity and great value for aquaculture and pharmaceutical industries, P. rhodozyma possesses multiple exceptional traits of fundamental and applied interest. The aim of this study was to obtain, and analyze two new genome sequences of representative strains from the northern (CBS 7918(T), the type strain) and southern hemispheres (CRUB 1149) and compre them to a previously published genome sequence (strain CBS 6938). Photoprotection and antioxidant related genes, as well as genes involved in sexual reproduction were analyzed. Both genomes had ca. 19 Mb and 6000 protein coding genes, similar to CBS 6938. Compared to other fungal genomes P. rhodozyma strains and other Cyst...

Proceedings of the National Academy of Sciences, 1991

Using the "tagged" rRNA gene system, which allows in vivo mutational analysis of Saccha... more Using the "tagged" rRNA gene system, which allows in vivo mutational analysis of Saccharomyces cerevisiae rRNA, we studied the role of two distinct structural elements of 26S rRNA in ribosome biogenesis and function--namely, the evolutionarily highly conserved "GTPase center" located in domain II and the eukaroyote-specific variable region V9 in domain III. Replacement of the S. cerevisiae GTPase center with its counterpart from Escherichia coli did not affect the assembly of the mutant 26S rRNA into functional (as judged by their polysomal distribution) 60S subunits, indicating that the E. coli GTPase center functions efficiently in the context of the heterologous rRNA. Removal of most of the S. cerevisiae V9 region or replacement of this segment by the equivalent segment from mouse 28S rRNA also did not affect the formation of functional 60S subunits carrying the mutant 26S rRNA. Therefore, the V9 region does not seem to play a role in the biological functionin...

Nucleic Acids Research, 1992

ABF1 is a multifunctional protein present in Saccharomyces cerevisiae, involved in transcriptiona... more ABF1 is a multifunctional protein present in Saccharomyces cerevisiae, involved in transcriptionactivation and-repression as well as in DNA-replication. Several lines of evidence indicate the occurrence in the related species Kluyveromyces lactis of a protein having similar properties to those of ABF1 in S.cerevisiae. In order to identify conserved functional domains in ABF1, we have cloned and sequenced the gene encoding the ABFI-homologue from K. lactis. KIABF1 is much smaller than ScABF1 (54.6 vs. 81.7 kD). It exhibits extensive homology with its S. cerevisiae counterpart in the N-terminal region. The Cterminal domain however, is divergent, with the striking exception of a stretch of 20 amino acids, which is virtually identical in the two proteins. KIABF1 can substitute ABF1 in S. cerevisiae, emphasizing the conservation of the multiple functions of this protein.

Nature, 2010

Local adaptations within species are often governed by several interacting genes scattered throug... more Local adaptations within species are often governed by several interacting genes scattered throughout the genome. Single-locus models of selection cannot explain the maintenance of such complex variation because recombination separates co-adapted alleles. Here we report a novel type of intraspecific multi-locus genetic variation that has been maintained over a vast period of time. The galactose (GAL) utilization gene network of the brewer's yeast relative Saccharomyces kudriavzevii exists in two distinct states: a functional gene network in Portuguese strains and, in Japanese strains, a non-functional gene network of allelic pseudogenes. Genome sequencing of all available S. kudriavzevii strains revealed that none of the functional GAL genes were acquired from other species. Rather, these polymorphisms have been maintained for nearly the entire history of the species, despite more recent gene flow genome-wide. Experimental evidence suggests that inactivation of the GAL3 and GAL80 regulatory genes facilitated the origin and longterm maintenance of the two gene network states. This striking example of a balanced unlinked gene network polymorphism introduces a remarkable type of intraspecific variation that may be widespread. Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

Microbiology, 2008

Two glucose/xylose transporter genes from Candida intermedia were recently cloned and characteriz... more Two glucose/xylose transporter genes from Candida intermedia were recently cloned and characterized: GXF1, which encodes a glucose/xylose facilitator; and GXS1, which encodes a glucose/xylose proton symporter. Here we report the functional expression of these transporters in Saccharomyces cerevisiae. While Gxf1p seems to be fully functional in S. cerevisiae, the symporter Gxs1p exhibits very low glucose/xylose transport activity, which could not be ascribed to insufficient production of the protein or incorrect subcellular localization. In addition, coexpression of glucose/xylose facilitators with Gxs1p strongly reduced GXS1 mRNA levels, and consequently symport activity, in glucose-grown, but not in ethanol-grown, cells. The observed decrease in GXS1 transcript levels seems to be related to an enhanced glucose influx mediated by glucose facilitator protein(s), and not to a specific interaction between Gxs1p and other transporters. We found GXS1 mRNA levels to be severely reduced as a result of glucose addition, and we show that this effect takes place at the level of GXS1 mRNA stability. Our results suggest that a decrease in mRNAs encoding high-affinity/active sugar transport systems may be a widespread and conserved mechanism in yeasts, limiting expression of these proteins whenever their activity is dispensable.

Applied and Environmental Microbiology, 2008

Here we report the isolation of four Saccharomyces species (former Saccharomyces sensu stricto gr... more Here we report the isolation of four Saccharomyces species (former Saccharomyces sensu stricto group) from tree bark. The employment of two temperatures (10°C in addition to the more commonly used 30°C) resulted in the isolation of S. kudriavzevii and S. uvarum , two species that grow at low temperatures, in addition to S. cerevisiae and S. paradoxus . A clear bias was found toward the bark of certain trees, particularly certain oak species. Very often, more than one Saccharomyces species was found in one locality and occasionally even in the same bark sample. Our evidence strongly suggests that (markedly) different growth temperature preferences play a fundamental role in the sympatric associations of Saccharomyces species uncovered in this survey. S. kudriavzevii was isolated at most of the sites sampled in Portugal, indicating that the geographic distribution of this species is wider than the distribution assumed thus far. However, the Portuguese S. kudriavzevii population exhibi...

mSphere

Microbes usually have flexible metabolic capabilities and are able to use different compounds to ... more Microbes usually have flexible metabolic capabilities and are able to use different compounds to meet their needs. The yeasts belonging to the Wickerhamiella and Starmerella genera (forming the so-called W/S clade) are usually found in flowers or insects that visit flowers and are known for having acquired many genes from bacteria by a process called horizontal gene transfer.

This is a gzip/tar compressed data archive containing the concatenated SNP alignment of the restr... more This is a gzip/tar compressed data archive containing the concatenated SNP alignment of the restricted dataset with S. paradoxus as outgroup, related to Figure 3. SNP alignments for each chromosome are also provided, together with the corresponding list of SNP positions

Trends in Microbiology, 1998

Molecular Microbiology, 1996

Abf1p and Rap1p are global regulatory factors which play an essential role in the transcription a... more Abf1p and Rap1p are global regulatory factors which play an essential role in the transcription activation of yeast ribosomal protein genes. This functional link prompted us to investigate whether these factors may be functionally interchangeable. We focused on the indispensable C-terminal portions of both factors and performed mutual domain swaps. The functional capacity of the resulting hybrid proteins was subsequently examined using yeast strains conditionally expressing either the ABF1 or the RAP1 gene. Both the Abf1p-Rap1p and the Rap1p-Abf1p fusion proteins were found to be able to complement the growth defect of the respective strains. Furthermore, Abf1p and Rap1p are both able to promote transcription of a reporter gene through a combination of the respective binding site and a T-rich promoter element. These data strongly suggest that the C-terminal domains of Abf1p and Rap1p have, at least partially, identical functions. Finally, a deletion analysis of the so far largely uncharacterized C-terminal domain of Abf1p was performed, which revealed that two regions of 50 amino acids can perform all essential Abf1p functions.

Journal of Bacteriology, 2000

A novel gene, FSY1 , encoding a permease involved in active fructose uptake by a proton symport m... more A novel gene, FSY1 , encoding a permease involved in active fructose uptake by a proton symport mechanism in the type strain of Saccharomyces carlsbergensis has been isolated. Fsy1p is only distantly related to the Hxt proteins that mediate facilitated diffusion of glucose and fructose in Saccharomyces cerevisiae and related species.

Biochemistry and Cell Biology, 1995

Three abundant ubiquitous DNA-binding protein factors appear to play a major role in the control ... more Three abundant ubiquitous DNA-binding protein factors appear to play a major role in the control of ribosome biosynthesis in yeast. Two of these factors mediate the regulation of transcription of ribosomal protein genes (rp-genes) in yeasts. Most yeast rp-genes are under transcriptional control of Rap1p (repressor–activator protein), while a small subset of rp-genes is activated through Abf1p (ARS binding factor). The third protein, designated Reb1p (rRNA enhancer binding protein), which binds strongly to two sites located upstream of the enhancer and the promoter of the rRNA operon, respectively, appears to play a crucial role in the efficient transcription of the chromosomal rDNA. All three proteins, however, have many target sites on the yeast genome, in particular, in the upstream regions of several Pol II transcribed genes, suggesting that they play a much more general role than solely in the regulation of ribosome biosynthesis. Furthermore, some evidence has been obtained sugg...

Sexual reproduction in fungi relies on proteins with well-known functions encoded by the mating-t... more Sexual reproduction in fungi relies on proteins with well-known functions encoded by the mating-type (MAT) loci. In the Basidiomycota,MATloci are often bipartite, with theP/Rlocus encoding pheromone precursors and pheromone receptors and theHDlocus encoding heterodimerizing homeodomain transcription factors (Hd1/Hd2). The interplay between different alleles of these genes within a single species usually generates at least two compatible mating types. However, a minority of species are homothallic, reproducing sexually without an obligate need for a compatible partner. Here we examine the organization and function of theMATloci ofCystofilobasidium capitatum, a species in the order Cystofilobasidiales, which is unusually rich in homothallic species. We determinedMATgene content and organization inC. capitatumand found that it resembles a mating type of the closely related heterothallic speciesCystofilobasidium ferigula. To explain the homothallic sexual reproduction observed inC. capi...

This is a gzip/tar compressed data archive containing the results of polydNdS from the libsequenc... more This is a gzip/tar compressed data archive containing the results of polydNdS from the libsequence analysis package (http://molpopgen.org/) (Thornton 2003), related to Table S2. The archive contains results for coding sequences (CDS) in the Mediterranean oak population (MO) and the wine population (wine), with one file per locus. The SGD systematic name is used to identify CDS