Biology subjects

Gabaldon, T.

Publications and source records attributed to Gabaldon, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Genome-wide RNA structural determination in Candida yeast pathogens

Understanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions in diverse species, more is needed to know about the structure of pathogen RNAs. This is particularly true for fungal pathogens, including pathogenic yeasts of the Candida genus, which are the leading cause of hospital-acquired fungal infections. Deciphering the relation between RNA structure and their biology remains a significant gap. Despite advancements in transcriptional regulation studies, especially for fungal pathogens like Candida, the structural aspects of pathogenic RNAs remain understudied. Our work addresses this gap by employing genome-wide structure probing to comprehensively explore the structural landscape of mRNAs and long non-coding RNAs (lncRNAs) in the four major Candida pathogens. Specifically focusing on mRNA, we observe a robust correlation between sequence conservation and structural characteristics in orthologous transcripts, significantly when sequence identity exceeds 50%, highlighting structural feature conservation among closely related species. We investigate the impact of single nucleotide polymorphisms (SNPs) on mRNA secondary structure. SNPs within 5 untranslated regions (UTRs) tend to occur in less structured positions, suggesting structural constraints influencing transcript regulation. Furthermore, we compare the structural properties of coding regions and UTRs, noting that coding regions are generally more structured than UTRs, consistent with similar trends in other species. Additionally, we provide the first experimental characterization of lncRNA structures in Candida species. Most lncRNAs form independent subdomains, similar to human lncRNAs. Notably, we identify hairpin-like structures in lncRNAs, a feature known to be functionally significant. Comparing hairpin prevalence between lncRNAs and protein-coding genes, we find enrichment in lncRNAs across Candida species, humans, and Arabidopsis thaliana, suggesting a conserved role for these structures. In summary, our study offers valuable insights into the interplay between RNA sequence, structure, and function in Candida pathogens, with implications for gene expression regulation and potential therapeutic strategies against Candida infections.

microbiology↗

bioRxiv2023

A yeast love triangle: multiple hybridizations shape genome evolution in the Pichia cactophila species complex.

Hybrids are chimeric organisms carrying genetic material from at least two divergent parental lineages. Hybridization can contribute to the emergence of novel lineages with unique phenotypic traits that may facilitate their adaptation to new environments. In recent years, genomic analyses have revealed the hybrid nature of several opportunistic human pathogenic yeasts. One of them is Candida inconspicua, a member of the Pichia cactophila species complex, for which all sequenced strains are hybrids isolated from Europe with so far unknown parentals. It has been recently proposed that C. inconspicua and P. cactophila s.s. should be ranked as the same species due to their genetic similarity. To obtain a better understanding of the evolution of this clade, we sequenced the genomes of the P. cactophila type strain, of its close-relative Pichia pseudocactophila, and of a putative C. inconspicua clinical isolate from Alaska and compared them with the previously sequenced genomes of Pichia norvegensis, C. inconspicua and the recently described Pichia galeolata. Our results show evidence for the existence of distinct hybrid lineages within this clade and suggest an intricate scenario of recurrent hybridizations in this species complex, some of them giving rise to lineages with the ability to infect humans. Given their different hybridization histories, we propose that C. inconspicua, P. cactophila, and the new clinical isolate from Alaska should represent three distinct species and suggest the name Pichia alaskaensis for the new taxon. Moreover, the name C. inconspicua is recombined in the genus Pichia as P. inconspicua. Our results clarify the evolutionary relationships within the P. cactophila species complex and underscore the importance of non-vertical evolution.

microbiology↗

bioRxiv2023

Stability of Oral and Fecal Microbiome at Room Temperature: Impact on Diversity

When collecting oral and fecal samples for large epidemiological microbiome studies, optimal storage conditions such as immediate freezing, are not always feasible. It is fundamental to study the impact of temporary room temperature (RT) storage and shipping on the microbiome diversity obtained in different types of samples. We performed a pilot study aimed at validating the sampling protocol based on the viability of the 16S rRNA gene sequencing in microbiome samples. Fecal and oral samples from five participants were collected and preserved in different conditions: a) 70% ethanol; b) in a FIT tube for stool samples; and c) in a chlorhexidine solution for oral wash samples. Four aliquots were prepared per sample, which were stored at RT, and frozen at days 0, 5, 10 and 15, respectively. In terms of alpha diversity, the maximum average decrease in 5 days was 0.3%, 1.6% and 1.7% for oral, stool in ethanol and stool in FIT, respectively. Furthermore, the relative abundances of the most important phyla and orders remained stable over the two weeks. The stability of fecal and oral samples for microbiome studies preserved at RT with 70% ethanol, chlorhexidine and in FIT tubes was verified for a 15-day window, with no substantial changes in terms of alpha diversity and relative abundances.

microbiology↗

bioRxiv2023

A multidimensional assessment of in-host fitness costs of drug resistance in the opportunistic fungal pathogen Candida glabrata

The global rise of antimicrobial resistance poses a serious threat to public health. Because drug-resistant (DR) pathogens typically carry mutations in genes involved in critical cellular functions, they may be less fit under drug-free conditions than their susceptible counterparts. As such, the limited use of antimicrobial drugs has been proposed as a practical strategy to diminish the prevalence of DR strains. However, in many cases the fitness of DR pathogens under host conditions is unknown. Candida (Nakaseomyces) glabrata is a prevalent opportunistic fungal pathogen notable for its high rate of fluconazole resistance (FLZR), echinocandin resistance (ECR), and multidrug resistance (MDR) relative to other Candida pathogens. Nonetheless, the fitness of C. glabrata MDR isolates is poorly characterized, and studies of FLZR isolate fitness have produced contradictory findings. Two important host niches for C. glabrata are macrophages, in which it can survive and proliferate, and the gut. Herein, by employing a comprehensive collection of clinical and isogenic C. glabrata isolates, we show that FLZR C. glabrata isolates are less fit inside macrophages than susceptible isolates and that this fitness cost is reversed by acquiring ECR mutations in FKS1/2 genes. Interestingly, dual-RNAseq revealed that macrophages infected with DR isolates mount an inflammatory response whereas the intracellular DR cells downregulate processes required for in-host adaptation. Consistently, DR isolates were outcompeted by their susceptible counterparts in the context of gut colonization and in the kidneys of systemically infected mice, whereas they showed comparable fitness in the spleen. Collectively, our study shows that macrophage-rich organs, such as the spleen, favor the retention of DR isolates, potentially reducing the utility of limited antifungal use to decrease the burden of DR C. glabrata in the context of candidemia. Author summaryThe rise of multidrug resistant (MDR) strains of fungal pathogens, notably Candida glabrata, poses a significant clinical challenge because of the limited number of antifungal drugs available for use. Thus, it is vital to minimize the prevalence of drug resistance in the clinic. Because in some bacterial and fungal species drug resistance is accompanied by a fitness cost, implementation of limited antibiotic or antifungal drug use in the clinic has been suggested as a practical way to favor the spread of susceptible isolates. However, it is not clear whether this strategy can work for MDR C. glabrata, as its fitness costs have not been systematically examined, particularly in the context of the host. Herein, we show that MDR C. glabrata isolates can replicate within macrophages as well as susceptible isolates, and this result was consistent with gene expression changes in the infected macrophages. In animal models, MDR strains were unfit in the context of the gastrointestinal tract and kidney, but their fitness in the spleen was comparable to that of susceptible strains. Accordingly, the potential of limited antifungal use to reduce the prevalence of MDR strains of C. glabrata strongly depends on the host reservoir of infection.

microbiology↗

bioRxiv2023

Overlooked Candida glabrata petites are echinocandin tolerant, induce host inflammatory responses, and display poor in vivo fitness

Small colony variants (SCVs) are relatively common among some bacterial species and are associated with poor prognosis and recalcitrant infections. Similarly, Candida glabrata - a major intracellular fungal pathogen - produces small and slow-growing respiratory-deficient colonies, termed "petite." Despite reports of clinical petite C. glabrata strains, our understanding of petite behavior in the host remains obscure. Moreover, controversies exist regarding in-host petite fitness and its clinical relevance. Herein, we employed whole-genome sequencing (WGS), dual-RNAseq, and extensive ex vivo and in vivo studies to fill this knowledge gap. WGS identified multiple petite-specific mutations in nuclear and mitochondrially-encoded genes. Consistent with dual-RNAseq data, petite C. glabrata cells did not replicate inside host macrophages and were outcompeted by their non-petite parents in macrophages and in gut colonization and systemic infection mouse models. The intracellular petites showed hallmarks of drug tolerance and were relatively insensitive to the fungicidal activity of echinocandin drugs. Petite-infected macrophages exhibited a pro-inflammatory and type I IFN-skewed transcriptional program. Interrogation of international C. glabrata blood isolates (n=1000) showed that petite prevalence varies by country, albeit at an overall low prevalence (0-3.5%). Collectively, our study sheds new light on the genetic basis, drug susceptibility, clinical prevalence, and host-pathogen responses of a clinically overlooked phenotype in a major fungal pathogen. ImportanceCandida glabrata is a major fungal pathogen, which is able to lose mitochondria and form small and slow-growing colonies, called "petite". This attenuated growth rate has created controversies and questioned the clinical importance of petiteness. Herein, we have employed multiple omicstechnologies and in vivo mouse models to critically assess the clinical importance of petite phenotype. Our WGS identifies multiple genes potentially underpinning petite phenotype. Interestingly, petite C. glabrata cells engulfed by macrophages are dormant and therefore are not killed by the frontline antifungal drugs. Interestingly, macrophages infected with petite cells mount distinct transcriptomic responses. Consistent with our ex-vivo observations, mitochondrial-proficient parental strains outcompete petites during systemic and gut colonization. Retrospective examination of C. glabrata isolates identified petite prevalence a rare entity, can significantly vary from country to country. Collectively, our study overcomes the existing controversies and provides novel insights regarding the clinical relevance of petite C. glabrata isolates.

microbiology↗

bioRxiv2023

JLOH: Inferring Loss of Heterozygosity Blocks from Sequencing Data

Heterozygosity is a genetic condition in which two or more alleles are found at a genomic locus. Among the organisms that are more prone to heterozygosity are hybrids, i.e. organisms that are the offspring of genetically divergent yet still interfertile individuals. One of the most studied aspects is the loss of heterozygosity (LOH) within genomes, where multi-allelic sites lose one of their two alleles by converting it to the other, or by remaining hemizygous at that site. LOH is deeply interconnected with adaptation, especially in hybrids, but the in silico techniques to infer LOH blocks are hardly standardized, and a general tool to infer and analyse them in most genomic contexts and species is missing. Here, we present JLOH, a computational toolkit for the inference and exploration of LOH blocks which only requires commonly available genomic data as input. Starting from mapped reads, called variants and a reference genome sequence, JLOH infers candidate LOH blocks based on single-nucleotide polymorphism density (SNPs/kbp) and read coverage per position. If working with a hybrid organism of known parentals, JLOH is also able to assign each LOH block to its subgenome of origin.

bioinformatics↗

bioRxiv2022

Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus

Aspergillus fumigatus is both an environmental saprobe and an opportunistic human fungal pathogen. Knowledge of genomic variation across A. fumigatus isolates is essential for understanding the evolution of pathogenicity, virulence, and resistance to antifungal drugs. Here, we investigated 206 A. fumigatus isolates (133 clinical and 73 environmental isolates) aiming to identify genes with variable presence across isolates and test whether this variation was related to the clinical or environmental origin of isolates. The PanCore genome of A. fumigatus constitutes 13,085 ortholog groups, of which 7,773 (59.4%) are shared by all isolates (CORE) and 5,312 (40.6%) vary in their gene presence across isolates (ACCESSORY). Despite differences in the distribution of orthologs across all isolates, no significant differences were observed among clinical vs. environmental isolates when accounting for phylogeny. Orthologs that differ in their distribution across isolates tend to occur in low frequency and/or be restricted to specific isolates; thus, the degree of genomic conservation between orthologs of A. fumigatus is high. These results suggest that differences in the distribution of orthologs within A. fumigatus cannot be associated with the clinical or environmental origin of isolates. ImportanceAspergillus fumigatus is a cosmopolitan species of fungi responsible for thousands of cases of invasive disease. Clinical and environmental isolates of A. fumigatus exhibit extensive phenotypic differences, including differences related to virulence and antifungal drug resistance. A comprehensive survey of the genomic diversity present in A. fumigatus and its relationship to the clinical or environmental origin of isolates can contribute to the prediction of the mechanisms of evolution and infection of the species. Our results suggest that there is no significant variation in ortholog distribution between clinical and environmental isolates when accounting for evolutionary history. The work supports the hypothesis that environmental and clinical isolates of A. fumigatus do not differ in their gene contents.

bioinformatics↗

bioRxiv2022

Gamete interaction protein evolution evinces Pantherines hybridizing history

The absence of robust interspecific isolation barriers among pantherines, including the iconic South American jaguar (Panthera onca), led us to study molecular evolution of typically rapidly evolving reproductive proteins within this subfamily and related groups. In this study, we delved into the evolutionary forces acting on the Zona Pellucida (ZP) gamete interaction protein family and the sperm-oocyte fusion protein pair IZUMO1-JUNO across the Carnivora order, distinguishing between Caniformia and Feliformia suborders and anticipating few significant diversifying changes in the Pantherinae subfamily. A chromosome-resolved jaguar genome assembly facilitated coding sequences, enabling the reconstruction of protein evolutionary histories. Examining sequence variability across more than 30 Carnivora species revealed that Feliformia exhibited significantly lower diversity compared to its sister taxa, Caniformia. Molecular evolution analyses of ZP2 and ZP3, subunits directly involved in sperm-recognition, unveiled diversifying positive selection in Feliformia, Caniformia, and Pantherinae, although no significant changes were linked to sperm binding. Structural cross-linking ZP subunits, ZP4, and ZP1 exhibited lower levels or complete absence of positive selection. Notably, the fusion protein IZUMO1 displayed prominent positive selection signatures and sites in basal lineages of both Caniformia and Feliformia, extending along the Caniformia subtree but absent in Pantherinae. Conversely, JUNO did not exhibit any positive selection signatures across tested lineages and clades. Eight Caniformia-specific positive selected sites in IZUMO1 were detected within two JUNO-interaction clusters. Our findings provide for the first time insights into the evolutionary trajectories of ZP proteins and the IZUMO1-JUNO gamete interaction pair within the Carnivora order.

evolutionary biology↗

bioRxiv2022

The little skate genome and the evolutionary emergence of wing-like fin appendages

Skates are cartilaginous fish whose novel body plan features remarkably enlarged wing-like pectoral fins that allow them to thrive in benthic environments. The molecular underpinnings of this unique trait, however, remain elusive. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins - gene expression, chromatin occupancy and three-dimensional (3D) conformation - we find skate-specific genomic rearrangements that alter the 3D regulatory landscape of genes involved in the planar cell polarity (PCP) pathway. Functional inhibition of PCP signaling resulted in marked reduction of anterior fin size, confirming this pathway as a major contributor of batoid fin morphology. We also identified a fin-specific enhancer that interacts with 3 HOX genes, consistent with the redeployment of Hox gene expression in anterior pectoral fins, and confirmed the potential of this element to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganizations and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

evolutionary biology↗

bioRxiv2021

PerSVade: Personalized Structural Variation detection in your species of interest

Structural variants (SVs) like translocations, deletions, and other rearrangements underlie genetic and phenotypic variation. SVs are often overlooked due to difficult detection from short-read sequencing. Most algorithms yield low recall on humans, but the performance in other organisms is unclear. Similarly, despite remarkable differences across species genomes, most approaches use parameters optimized for humans. To overcome this and enable species-tailored approaches, we developed perSVade (personalized Structural Variation Detection), a pipeline that identifies SVs in a way that is optimized for any input sample. Starting from short reads, perSVade uses simulations on the reference genome to choose the best SV calling parameters. The output includes the optimally-called SVs and the accuracy, useful to assess the confidence in the results. In addition, perSVade can call small variants and copy-number variations. In summary, perSVade automatically identifies several types of genomic variation from short reads using sample-optimized parameters. We validated that perSVade increases the SV calling accuracy on simulated variants for six diverse eukaryotes, and on datasets of validated human variants. Importantly, we found no universal set of "optimal" parameters, which underscores the need for species-specific parameter optimization. PerSVade will improve our understanding about the role of SVs in non-human organisms.

bioinformatics↗

bioRxiv2021

Multiple hybridization events punctuate the evolutionary trajectory of Malassezia furfur

Malassezia species are important fungal skin commensals and are part of the normal microbiota of humans and other animals. However, under certain circumstances these fungi can also display a pathogenic behaviour. For example, Malassezia furfur is a common commensal of human skin, and yet is often responsible for skin disorders but also systemic infections. Comparative genomics analysis of M. furfur revealed that some isolates have a hybrid origin, similar to several other recently described hybrid fungal pathogens. Because hybrid species exhibit genomic plasticity that can impact phenotypes, we sought to elucidate the genomic evolution and phenotypic characteristics of M. furfur hybrids in comparison to their parental lineages. To this end, we performed a comparative genomics analysis between hybrid strains and their presumptive parental lineages, and assessed phenotypic characteristics. Our results provide evidence that at least two distinct hybridization events occurred between the same parental lineages, and that the parental strains may have originally been hybrids themselves. Analysis of the mating-type locus reveals that M. furfur has a pseudobipolar mating system, and provides evidence that after sexual liaisons of mating compatible cells, hybridization involved cell-cell fusion leading to a diploid/aneuploid state. This study provides new insights into the evolutionary trajectory of M. furfur and contributes with valuable genomic resources for future pathogenicity studies. ImportanceMalassezia furfur is a common commensal member of human/animal microbiota that is also associated with several pathogenic states. Recent studies report involvement of Malassezia species in Crohns disease, a type of inflammatory bowel disease, pancreatic cancer progression, and exacerbation of Cystic fibrosis. A recent genomics analysis of M. furfur revealed the existence of hybrid isolates and identified their putative parental lineages. In this study, we explored the genomic and phenotypic features of these hybrids in comparison to their putative parental lineages. Our results revealed the existence of a pseudobipolar mating system in this species and showed evidence for the occurrence of multiple hybridization events in the evolutionary trajectory of M. furfur. These findings significantly advance our understanding of the evolution of this commensal microbe and are relevant for future studies exploring the role of hybridization in the adaptation to new niches or environments, including the emergence of pathogenicity.

evolutionary biology↗

bioRxiv2021

Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources

Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. The yeast Candida parapsilosis metabolizes these compounds via the 3-oxoadipate and gentisate pathways, whose components are encoded by two metabolic gene clusters. In this study, we determine the chromosome level assembly of the C. parapsilosis strain CLIB214 and use it for transcriptomic and proteomic investigation of cells cultivated on hydroxyaromatic substrates. We demonstrate that the genes coding for enzymes and plasma membrane transporters involved in the 3-oxoadipate and gentisate pathways are highly upregulated and their expression is controlled in a substrate-specific manner. However, regulatory proteins involved in this process are not known. Using the knockout mutants, we show that putative transcriptional factors encoded by the genes OTF1 and GTF1 located within these gene clusters function as transcriptional activators of the 3-oxoadipate and gentisate pathway, respectively. We also show that the activation of both pathways is accompanied by upregulation of genes for the enzymes involved in {beta}-oxidation of fatty acids, glyoxylate cycle, amino acid metabolism, and peroxisome biogenesis. Transcriptome and proteome profiles of the cells grown on 4-hydroxybenzoate and 3-hydroxybenzoate, which are metabolized via the 3-oxoadipate and gentisate pathway, respectively, reflect their different connection to central metabolism. Yet we find that the expression profiles differ also in the cells assimilating 4-hydroxybenzoate and hydroquinone, which are both metabolized in the same pathway. This finding is consistent with the phenotype of the Otf1p-lacking mutant, which exhibits impaired growth on hydroxybenzoates, but still utilizes hydroxybenzenes, thus indicating that additional, yet unidentified transcription factor could be involved in the 3-oxoadipate pathway regulation. Moreover, we propose that bicarbonate ions resulting from decarboxylation of hydroxybenzoates also contribute to differences in the cell responses to hydroxybenzoates and hydroxybenzenes. Finally, our phylogenetic analysis highlights evolutionary paths leading to metabolic adaptations of yeast cells assimilating hydroxyaromatic substrates. Author summaryBenzene and its derivatives are simple aromatic compounds representing key substances for the chemical industry. While benzene itself is toxic and carcinogenic, benzoic acid is commonly used in the food industry and some of its derivatives are used in pharmacology (aspirin) or cosmetics (parabens). The benzene ring of aromatic molecules is relatively stable, but many microorganisms including yeasts break it enzymatically and, in a series of biochemical reactions, utilize resulting metabolites as carbon sources. Understanding the genetic basis of corresponding metabolic pathways and their regulation opens a venue for applications in biotechnology and bioremediation of polluted environments. Here we investigate the yeast Candida parapsilosis which assimilates various hydroxybenzenes and hydroxybenzoates via the 3-oxoadipate and gentisate pathways. We show that the genes coding for the substrate transporters and enzymes involved in both pathways are co-expressed and regulated by the transcriptional activators Otf1p and Gtf1p, respectively. Our results also reveal the connections of both pathways to central metabolism and organelle biogenesis and provide an insight into evolution of metabolism of hydroxyaromatic compounds.

genomics↗

bioRxiv2021

Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other non-standard architectures in genome assemblies.

Recent technological developments have made genome sequencing and assembly accessible to many groups. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, polyploidy, aneuploidy, or heterokaryosis can challenge current standard assembly procedures and result in highly fragmented assemblies. Hence, we hypothesized that genome databases must contain a non-negligible fraction of low-quality assemblies that result from such type of intrinsic genomic factors. Here we present Karyon, a Python-based toolkit that uses raw sequencing data and de novo genome assembly to assess several parameters and generate informative plots to assist in the identification of non-chanonical genomic traits. Karyon includes automated de novo genome assembly and variant calling pipelines. We tested Karyon by diagnosing 35 highly fragmented publicly available assemblies from 19 different Mucorales (Fungi) species. Our results show that 6 (17%) of the assemblies presented signs of unusual genomic configurations, suggesting that these are common, at least within the Fungi.

genomics↗

bioRxiv2021

Chromatin profiling reveals genome stability heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus

Invasive Pulmonary aspergillosis is a life-threatening infection in immunosuppressed patients caused by the filamentous fungus Aspergillus fumigatus. Chromatin structure regulation is important for genome stability maintenance and has the potential to lead to genome rearrangements driving differences in virulence and pathogenesis of different A. fumigatus isolates. Here, we compared the chromatin activities of the most investigated clinical isolates Af293 and CEA17 and uncovered striking differences in the number, locations and expression of transposable elements. We found evidence for higher genome instability in Af293 as compared to CEA17 and identified a spontaneous Af293 variant that exhibits gross chromosomal alterations including the loss of a 320 kb long segment in chromosome VIII and the amplification of a biosynthetic gene cluster. As a consequence of these re-arrangements, the variant shows increased secondary metabolites production, growth and virulence. Our work emphasizes genome stability heterogeneity as an evolutionary driver of A. fumigatus fitness and virulence.

molecular biology↗

bioRxiv2021

Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units.

Long non-coding RNAs (IncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the function of IncRNAS are largely mediated by their structures. However, our structural knowledge for most IncRNAS is limited to sequence-based computational predictions. Non-coding RNA activated by DNA damage (NORAD) is an atypical IncRNA due to its abundant expression and high sequence conservation. NORAD regulates genomic stability by interacting with proteins and microRNAs. Previous sequence-based characterization has identified a modular organization of NORAD composed of several NORAD repeat units (NRUs). These units comprise the protein-binding elements and are separated by regular spacers of unknown function. Here, we experimentally determine for the first time the secondary structure of NORAD using the nextPARS approach. Our results suggest that the spacer regions provide structural stability to NRUs. Furthermore, we uncover two previously-unreported NRUs, and determine the core structural motifs conserved across NRUs. Overall, these findings will help to elucidate the function and evolution of NORAD.

genomics↗

bioRxiv2021

The genome sequence of the cereal pest Sitophilus oryzae: an unprecedented transposable element content

BackgroundThe rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. ResultsWe sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis. ConclusionsHere we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

genomics↗

bioRxiv2021

Transient mitochondria dysfunction confers fungal cross-resistance between macrophages and fluconazole

Loss or inactivation of antivirulence genes is an adaptive strategy in pathogen evolution. Candida glabrata is an important opportunistic pathogen related to bakers yeast, with the ability to both, quickly increase its intrinsic high level of azole resistance and persist within phagocytes. During C. glabratas evolution as a pathogen, the mitochondrial DNA polymerase, CgMip1, has been under positive selection. We show that CgMIP1 deletion not only triggers loss of mitochondrial function and a petite phenotype, but increases C. glabratas azole and ER stress resistance, and importantly, its survival in phagocytes. The same phenotype is induced by fluconazole and by exposure to macrophages, conferring a cross-resistance between antifungals and immune cells, and can be found in clinical isolates despite its slow growth. This suggests that petite constitutes a bet-hedging strategy of C. glabrata, and potentially a relevant cause of azole resistance. Mitochondrial function may therefore be considered a potential antivirulence factor.

evolutionary biology↗

bioRxiv2020

Impact of sleep fragmentation, heart failure, and their combination, on the gut microbiome

Heart failure (HF) is a common condition associated with a high rate of hospitalizations and adverse outcomes. HF is characterized by impairments of the cardiac ventricular filling and/or ejection of blood capacity. Sleep fragmentation (SF) involves a series of short sleep interruptions that lead to fatigue and contribute to cognitive impairments and dementia. Both conditions are known to be associated with increased inflammation and dysbiosis of the gut microbiota. In the present study, male mice were distributed into four groups, and subjected for four weeks to either HF, SF, both HF and SF, or left unperturbed as controls. We used 16S metabarcoding to assess fecal microbiome composition before and after the experiments. Evidence for distinct alterations in several bacterial groups and an overall decrease in alpha diversity emerged in HF and SF treatment groups. Combined HF and SF conditions, however, showed no synergism, and observed changes were not always additive, suggesting that some of the individual effects of either HF or SF cancel each other out when applied concomitantly. IMPORTANCEThe study demonstrates the potential of the gut microbiome as a source of molecular markers for the diagnosis, prevention, and treatment of both heart failure and sleep fragmentation conditions in isolation. Our results provide the first evidence of an antagonistic effect of the presence of both conditions in the gut microbiome dysbiosis, showing an attenuation of the alterations that are observed when considering them separately.

microbiology↗