Biology subjects

Pontes, A.

Publications and source records attributed to Pontes, A..

5 recordsLinked to original sources

bioRxiv2025

Discovery of additional ancient genome duplications in yeasts

Whole genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages1,2, preceding adaptive radiations in vertebrates3-5, teleost fish6,7, and angiosperms8,9. In contrast to the many known ancient WGDs in animals10,11 and especially plants12-14, we are aware of evidence for only four in fungi15,16. The oldest of these occurred [~]100 million years ago (mya) and is shared by [~]60 extant Saccharomycetales species17,18, including the bakers yeast Saccharomyces cerevisiae (Fig. 1). Notably, this is the only known ancient WGD in the yeast subphylum Saccharomycotina. The dearth of ancient WGD events in fungi remains a mystery15. Some studies have suggested that fungal lineages that experience chromosome19 and genome15 duplication quickly go extinct, leaving no trace in the genomic record, while others contend that the lack of known WGD is due to an absence of data15,16. Under the second hypothesis, additional sampling and deeper sequencing of fungal genomes should lead to the discovery of more WGD events. Coupling hundreds of recently published genomes from nearly every described Saccharomycotina species with three additional long-read assemblies, we discovered three novel WGD events. While the functions of retained duplicate genes originating from these events are broad, they bear many similarities to the well-known WGD that occurred in the Saccharomycetales17. Our results suggest that WGD may be a more common evolutionary force in fungi than previously believed. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/673279v1_fig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@6a8f47org.highwire.dtl.DTLVardef@1e4a790org.highwire.dtl.DTLVardef@b4e0eforg.highwire.dtl.DTLVardef@11b7795_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Three additional whole genome duplications in Saccharomycotina yeasts. Rates of gene duplication are mapped onto Saccharomycetales (left) and Dipodascales (right) phylogenies. Whole genome duplications indicated along the lineages in which they are predicted to occur. Trees have been pruned for visualization purposes. C_FIG HighlightsO_LIEvidence for three whole genome duplications (WGDs) in Dipodascales yeasts C_LIO_LIImpacts of WGD are broad but bear many similarities to the known WGD in Saccharomycetales yeasts C_LIO_LIDuplicates with many protein-protein interactions are more likely to be retained over long timescales C_LIO_LIWGD in fungi is likely underreported C_LI

evolutionary biology↗

bioRxiv2025

FrlP, an ABC type I importer component of Bacillus subtilis: regulation and impact in bacterial fitness

Bacillus subtilis is able to catabolize fructosamines, also known as Amadori rearrangement products. The frlBONMD-frlP operon mediates this process and is subjected to specific and global regulation. Although the degradation pathway favoring -glycated amino acids is known, the mechanisms of substrate uptake have remained unclear. In this study, mutagenic and functional analyses revealed that FrlONM, a type I ABC importer, along with the nucleotide-binding domain (NBD) FrlP, is required for the uptake of fructosevaline. Transcriptional and translation frlP-lacZ fusions indicated that frlP is induced by fructosevaline and negatively regulated by the FrlR repressor. Furthermore, by targeting an RNA molecule (S1254) encoded upstream from frlP and overlapping the repressor flrR gene transcribed in the opposite direction, we provide evidence for the dual regulation of frlP by this anti-sense RNA and FrlR. This result adds a posttranscriptional layer to the intricate regulation of the fructosamines operon. In addition, we show that MsmX, a multitask NBD of B. subtilis, is also able to serve as energy motor of this type I ABC importer, and that its presence alongside FrlP is vital for optimal growth on fructosevaline. To address the physiological significance of this functional redundancy we assessed the distribution of ABC type I NBDs FrlP and MsmX across the Bacillaceae family. MsmX is homogeneously distributed in Bacillaceae family tree, while FrlP is restricted to the Bacillus subtilis group, suggesting that the presence of FrlP together with other components of the fructosamines operon is important for bacteria fitness in plant-associated ecological niches. ImportanceBacillus subtilis is widely applied in the industry as a microbial cell factory, as a biofertilizer for sustainable agriculture, in the animal feed industry and as human probiotic. In its natural environment B. subtilis helps to shape the gut microbiome and the phytomicrobiome. Fructosamines, or Amadori rearrangement products, are ubiquitously found in nature and serve as precursors of toxic cell end-products implicated in the pathology of human diseases. This study provides a solid contribution to a deep knowledge of transport mechanisms, genetic regulation and physiological relevance of fructosamines utilization in B. subtilis. Moreover, it highlights an unusual strategy to adapt to alterations in nutrient availability by swapping the energy providing domain of ABC transporters.

microbiology↗

bioRxiv2024

Convergent reductive evolution in bee-associated lactic acid bacteria

AbstractDistantly related organisms may evolve similar traits when exposed to similar environments or engaging in certain lifestyles. Several members of the Lactobacillaceae (LAB) family are frequently isolated from the floral niche, mostly from bees and flowers. In some floral LAB species (henceforth referred to as bee- associated), distinctive genomic (e.g., genome reduction) and phenotypic (e.g., preference for fructose over glucose or fructophily) features were recently documented. These features are found across distantly related species, raising the hypothesis that specific genomic and phenotypic traits evolved convergently during adaptation to the floral environment. To test this hypothesis, we examined representative genomes of 369 species of bee-associated and non-bee-associated LAB. Phylogenomic analysis unveiled seven independent ecological shifts towards the floral niche in LAB. In these bee-associated LAB, we observed pervasive, significant reductions of genome size, gene repertoire, and GC content. Using machine leaning, we could distinguish bee-associated from non-bee-associated species with 94% accuracy, based on the absence of genes involved in metabolism, osmotic stress, or DNA repair. Moreover, we found that the most important genes for the machine learning classifier were seemingly lost, independently, in multiple bee-associated lineages. One of these genes, adhE, encodes a bifunctional aldehyde-alcohol dehydrogenase associated with the evolution of fructophily, a rare phenotypic trait that was recently identified in many floral LAB species. These results suggest that the independent evolution of distinctive phenotypes in bee- associated LAB has been largely driven by independent loss of the same set of genes. ImportanceSeveral lactic acid bacteria (LAB) species are intimately associated with bees and exhibit unique biochemical properties with potential for food applications and honeybee health. Using a machine-learning based approach, our study shows that adaptation of LAB to the bee environment was accompanied by a distinctive genomic trajectory deeply shaped by gene loss. Several of these gene losses occurred independently in distantly related species and are linked to some of their unique biotechnologically relevant traits, such as the preference of fructose over glucose (fructophily). This study underscores the potential of machine learning in identifying fingerprints of adaptation and detecting instances of convergent evolution. Furthermore, it sheds light onto the genomic and phenotypic particularities of bee-associated bacteria, thereby deepening the understanding of their positive impact on honeybee health.

evolutionary biology↗

bioRxiv2020

New insights into the paradoxical distribution of IRC7 in Saccharomyces cerevisiae and its associated phenotypic and genomic landscapes

Biotic and abiotic factors of wine fermentations have led to the accumulation of numerous genomic hallmarks of domestication in Saccharomyces cerevisiae wine strains. Here we have studied the paradoxical distribution of a dominant allele of IRC7 in wine yeast strains. This gene encodes a cysteine-S-{beta}-lyase and presents two alleles: a wild full-length allele (IRC7F) and a mutated one (IRC7S), harboring a 38bp-deletion. Interestingly, IRC7S-coding for a less active enzyme-appears in the great majority of wine strains. Studying its global distribution among phylogenetic clades, we observed that IRC7S allele is dominant just in wine strains, having a moderate presence in other domesticated clades (Beer, Bread and Wine-PDM), but being completely absent in wild clades, appearing as a new hallmark of domestication. To explain this paradoxical distribution, we performed an IRC7-rooted phenotypic-wide survey, demonstrating that IRC7S-homozygous (HS) wine strains have both fitness (lower lag phases and higher growth rates) and competitive (killer toxin resistance, pseudohyphal growth) advantages. Hence, we performed a genome-wide survey across domesticated clades, finding a set of mutations that are conserved among wine strains and potentially associated to IRC7S allele, which can help to explain the outstanding phenotype of HS strains and their dominant distribution in wines. Originality-Significance StatementS. cerevisiae is one of the best studied microbes due to its industrial importance and its use as a eukaryotic model organism. S. cerevisiae is also an interesting model for studying the effects of domestication in yeast genomic, phenotype and ecology. The study of how wild S. cerevisiae strains evolved into a greatly adapted domesticated strains and changed its lifestyle drastically is still of great interest. In the case of wine populations, strains have accumulated numerous hallmarks of domestication in their genome, related with their great phenotypic adaptation to this environment. Here, we report a new hallmark of domestication in wine strains; the IRC7 deleted allele (IRC7S) and present the first insights about its unexpected global distribution among phylogenetic clades, understanding the genomic context and the phenotypic implications of this allele in wine strains.

microbiology↗

bioRxiv2017

A library of structurally homogeneous human N-glycans synthesized from microbial oligosaccharide precursors

Synthesis of homogenous glycans in quantitative yields represents a major bottleneck to the production of molecular tools for glycoscience, such as glycan microarrays, affinity resins, and reference standards. Here, we describe a combined biological/enzymatic method termed bioenzymatic synthesis that is capable of efficiently converting microbially-derived precursor oligosaccharides into structurally uniform human-type N-glycans. Unlike starting material obtained by chemical synthesis or direct isolation from natural sources, which can be time consuming and costly to generate, bioenzymatic synthesis involves precursors derived from renewable sources including wild-type Saccharomyces cerevisiae glycoproteins and lipid-linked oligosaccharides from glycoengineered Escherichia coli. Following deglycosylation of these biosynthetic precursors, the resulting microbial oligosaccharides are subjected to a greatly simplified purification scheme followed by structural remodeling using commercially available and recombinantly produced glycosyltransferases including key N- acetylglucosaminyltransferases (e.g., GnTI, GnTII, and GnTIV) involved in early remodeling of glycans in the mammalian glycosylation pathway. Using this approach, preparative quantities of hybrid and complex-type N-glycans including asymmetric multi-antennary structures were generated all without the need of a specialized skillset. Collectively, our results reveal bioenzymatic synthesis to be a user-friendly methodology for rapidly supplying homogeneous oligosaccharide structures that can be used to understand the human glycome and probe the biological roles of glycans in health and disease.

biochemistry↗