Ana C. Gomes

Comparative genomics of wild type yeast strains unveils important genome diversity

BackgroundGenome variability generates phenotypic heterogeneity and is of relevance for adaptation to environmental change, but the extent of such variability in natural populations is still poorly understood. For example, selected Saccharomyces cerevisiae strains are variable at the ploidy level, have gene amplifications, changes in chromosome copy number, and gross chromosomal rearrangements. This suggests that genome plasticity provides important genetic diversity upon which natural selection mechanisms can operate.ResultsIn this study, we have used wild-type S. cerevisiae (yeast) strains to investigate genome variation in natural and artificial environments. We have used comparative genome hybridization on array (aCGH) to characterize the genome variability of 16 yeast strains, of laboratory and commercial origin, isolated from vineyards and wine cellars, and from opportunistic human infections. Interestingly, sub-telomeric instability was associated with the clinical phenotype, while Ty element insertion regions determined genomic differences of natural wine fermentation strains. Copy number depletion of ASP3 and YRF1 genes was found in all wild-type strains. Other gene families involved in transmembrane transport, sugar and alcohol metabolism or drug resistance had copy number changes, which also distinguished wine from clinical isolates.ConclusionWe have isolated and genotyped more than 1000 yeast strains from natural environments and carried out an aCGH analysis of 16 strains representative of distinct genotype clusters. Important genomic variability was identified between these strains, in particular in sub-telomeric regions and in Ty-element insertion sites, suggesting that this type of genome variability is the main source of genetic diversity in natural populations of yeast. The data highlights the usefulness of yeast as a model system to unravel intraspecific natural genome diversity and to elucidate how natural selection shapes the yeast genome.

Unravelling the diversity of grapevine microbiome.

Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines.

Large Scale Comparative Codon-Pair Context Analysis Unveils General Rules that Fine-Tune Evolution of mRNA Primary Structure

Background Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. Methodologies/Principal Findings We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. Conclusions The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.

A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans

BackgroundGenetic code alterations have been reported in mitochondrial, prokaryotic, and eukaryotic cytoplasmic translation systems, but their evolution and how organisms cope and survive such dramatic genetic events are not understood.ResultsHere we used an unusual decoding of leucine CUG codons as serine in the main human fungal pathogen Candida albicans to elucidate the global impact of genetic code alterations on the proteome. We show that C. albicans decodes CUG codons ambiguously and tolerates partial reversion of their identity from serine back to leucine on a genome-wide scale.ConclusionSuch codon ambiguity expands the proteome of this human pathogen exponentially and is used to generate important phenotypic diversity. This study highlights novel features of C. albicans biology and unanticipated roles for codon ambiguity in the evolution of the genetic code.

Parallel DNA pyrosequencing unveils new zebrafish microRNAs

BackgroundMicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. Their small size, low abundance and high instability complicated early identification, however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes.ResultsWe have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish (Danio rerio). For this, a series of cDNA libraries were prepared from miRNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics. Twenty five novel miRNAs were predicted, 107 miRNA star sequences and also 41 candidate miRNA targets were identified. A miRNA expression profile built on the basis of pyrosequencing read numbers showed high expression of most miRNAs throughout zebrafish development and identified tissue specific miRNAs.ConclusionThis study increases the number of zebrafish miRNAs from 192 to 217 and demonstrates that a single DNA mini-chip pyrosequencing run is effective in miRNA identification in zebrafish. This methodology also produced sufficient information to elucidate miRNA expression patterns during development and in differentiated organs. Moreover, some zebrafish miRNA star sequences were more abundant than their corresponding miRNAs, suggesting a functional role for the former in gene expression control in this vertebrate model organism.

Thermal Transformation of a Layered Multifunctional Network into a Metal–Organic Framework Based on a Polymeric Organic Linker

The preparation of layered [La(H(3)nmp)] as microcrystalline powders from optimized microwave-assisted synthesis or dynamic hydrothermal synthesis (i.e., with constant rotation of the autoclaves) from the reaction of nitrilotris(methylenephosphonic acid) (H(6)nmp) with LaCl(3)·7H(2)O is reported. Thermogravimetry in conjunction with thermodiffractometry showed that the material undergoes a microcrystal-to-microcrystal phase transformation above 300 °C, being transformed into either a three-dimensional or a two-dimensional network (two models are proposed based on dislocation of molecular units) formulated as [La(L)] (where L(3-) = [-(PO(3)CH(2))(2)(NH)(CH(2)PO(2))O(1/2)-](n)(3n-)). The two crystal structures were solved from ab initio methods based on powder X-ray diffraction data in conjunction with structural information derived from (13)C and (31)P solid-state NMR, electron microscopy (SEM and EDS mapping), FT-IR spectroscopy, thermodiffractometry, and photoluminescence studies. It is shown that upon heating the coordinated H(3)nmp(3-) anionic organic ligand undergoes a polymerization (condensation) reaction to form in situ a novel and unprecedented one-dimensional polymeric organic ligand. The lanthanum oxide layers act, thus, simultaneously as insulating and templating two-dimensional scaffolds. A rationalization of the various steps involved in these transformations is provided for the two models. Photoluminescent materials, isotypical with both the as-prepared ([(La(0.95)Eu(0.05))(H(3)nmp)] and [(La(0.95)Tb(0.05))(H(3)nmp)]) and the calcined ([(La(0.95)Eu(0.05))(L)]) compounds and containing stoichiometric amounts of optically active lanthanide centers, have been prepared and their photoluminescent properties studied in detail. The lifetimes of Eu(3+) vary between 2.04 ± 0.01 and 2.31 ± 0.01 ms (considering both ambient and low-temperature studies). [La(H(3)nmp)] is shown to be an effective heterogeneous catalyst in the ring opening of styrene oxide with methanol or ethanol, producing 2-methoxy-2-phenylethanol or 2-ethoxy-2-phenylethanol, respectively, in quantitative yields in the temperature range 40-70 °C. The material exhibits excellent regioselectivity to the β-alkoxy alcohol products even in the presence of water. Catalyst recycling and leaching tests performed for [La(H(3)nmp)] confirm the heterogeneous nature of the catalytic reaction. Catalytic activity may be attributed to structural defect sites. This assumption is somewhat supported by the much higher catalytic activity of [La(L)] in comparison to [La(H(3)nmp)].

Wine fermentation microbiome: a landscape from different Portuguese wine appellations

Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation – Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of regional wines.

Critical roles for a genetic code alteration in the evolution of the genus Candida

During the last 30 years, several alterations to the standard genetic code have been discovered in various bacterial and eukaryotic species. Sense and nonsense codons have been reassigned or reprogrammed to expand the genetic code to selenocysteine and pyrrolysine. These discoveries highlight unexpected flexibility in the genetic code, but do not elucidate how the organisms survived the proteome chaos generated by codon identity redefinition. In order to shed new light on this question, we have reconstructed a Candida genetic code alteration in Saccharomyces cerevisiae and used a combination of DNA microarrays, proteomics and genetics approaches to evaluate its impact on gene expression, adaptation and sexual reproduction. This genetic manipulation blocked mating, locked yeast in a diploid state, remodelled gene expression and created stress cross‐protection that generated adaptive advantages under environmental challenging conditions. This study highlights unanticipated roles for codon identity redefinition during the evolution of the genus Candida, and strongly suggests that genetic code alterations create genetic barriers that speed up speciation.

Multi-functional metal–organic frameworks assembled from a tripodal organic linker

The reaction between (benzene-1,3,5-triyltris(methylene))triphosphonic acid (H6bmt) and lanthanide chlorides, under typical hydrothermal conditions (180 °C for 3 days) or using microwave heating (5 minutes above 150 °C), led to the isolation of an isotypical series of compounds formulated as [Ln2(H3bmt)2(H2O)2]·H2O [where Ln3+ = La3+ (1), Ce3+ (2), Pr3+ (3), Nd3+ (4), (La0.95Eu0.05)3+ (5) and (La0.95Tb0.05)3+ (6)]. Compounds 1 to 4 have been readily isolated as large single-crystals and their structures determined in the monoclinic C2/c space group using single-crystal X-ray diffraction. All compounds were thoroughly characterized in the solid-state using powder X-ray diffraction, FT-IR spectroscopy, thermogravimetry, scanning electron microscopy (SEM and EDS) and elemental analysis. Solid-state NMR (31P MAS and 13C{1H} CP MAS) and thermodiffractometry studies have been performed on the La3+-based material. [Ln2(H3bmt)2(H2O)2]·H2O were found to be three-dimensional frameworks with water molecules (both of crystallization and coordinated to the lanthanide center), which could be reversibly removed by either heating the materials or by applying high vacuum. This typical zeolitic behaviour was confirmed experimentally by determining the crystal structure of the evacuated La3+-based material (1-dehyd) using single-crystal X-ray diffraction. This series of materials was found to exhibit dual functionality: photoluminescence and catalytic activity. Small amounts (5%) of Eu3+ and Tb3+ cations were engineered into the La3+-based matrices, promoting the isolation of optically active materials. The H6−xbmtx− residues were found to be good sensitizers of Tb3+, with 6 having the remarkable absolute emission quantum yield of ca. 46% (at 280 nm excitation). The zeolitic properties of the Eu3+-based material allowed an increase of the quantum efficiency from ca. 15% to 54% by removing under vacuum all water molecules in the material. Based on studies of the La3+-based material, these compounds can be employed as effective heterogeneous catalysts in the ring-opening reaction of styrene oxide with methanol, showing excellent regioselectivity, recyclability and structural stability in consecutive catalytic runs.

Multifunctional micro- and nanosized metal–organic frameworks assembled from bisphosphonates and lanthanides

Phase-pure and highly crystalline [Ln(Hpmd)(H2O)] materials [where Ln3+ = Eu3+ (1), Gd3+ (2) and Tb3+ (3); H4pmd = 1,4-phenylenebis(methylene)diphosphonic acid] were prepared by using three distinct approaches: (i) conventional hydrothermal synthesis (180 °C, 3 days); (ii) microwave-assisted heating (50 W irradiation power, 40 °C, 5 seconds; nano-sized aggregates with sizes ranging between 100 and 150 nm); and (iii) ultrasound-assisted synthesis which, for highly diluted reactive mixtures (Ln3+ : H4pmd : H2O of 1 : 1 : 7200), permitted the preparation of isolated nano-crystals at ambient temperature with 5 minutes of ultrasonic irradiation. Compounds were structurally characterized by powder X-ray diffraction (Rietveld refinement and variable-temperature studies), thermogravimetry, vibrational spectroscopy, elemental analysis and electron microscopy (SEM and EDS). The magnetic behavior of 1 and 2 was investigated between ambient temperature and ca. 2 K revealing that the Ln3+ cations act as isolated centers. A strategy to calculate the vibrational spectra of MOF structures and based on the known embedded-clusters approach is proposed and applied to [Ln(Hpmd)(H2O)]. This allowed the identification, along with deuteration of the materials, of the vibrational modes of the confined water molecule in the structure. Compound 1 was tested in the methanolysis of styrene oxide at 55 °C: it is shown that microcrystalline 1 (1-m) does not possess significant catalytic activity; on the other hand, the nano-sized counterpart (1-n) exhibits relatively high catalytic activity and excellent selectivity to 2-methoxy-2-phenylethanol (100% yield within 48 h of reaction time). Photoluminescence studies both at ambient and low temperatures showed, on the one hand, that bulk materials are composed of a single lanthanide site and, on the other hand, that the organic linker is a suitable sensitizer of Tb3+ (absolute quantum yield of ca. 14% for 3). It is further demonstrated that the coordinated water molecule has a pivotal role in the quenching of the photoluminescence of Eu3+ in 1: deuteration of the material results in a ca. 3.4 times improvement of the decay time (e.g., at 300 K the lifetime improves from 0.58 ± 0.01 ms to 1.98 ± 0.01 ms).