P421 Whole-transcriptome analysis of Sporothrix brasiliensis grown in mold- and yeast-inducing conditions

Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM

 

Objectives

Sporothrix brasiliensis is an emerging Sporothrix species limited to Brazil capable of causing sporotrichosis in humans and animals, especially in cats. Like other pathogenic Sporothrix species, S. brasiliensis exhibits a temperature-dependent dimorphic switch and is therefore, able to undergo a reversible morphological transition (mold and yeast), in response to environmental thermal stimuli.

While dimorphism appears to be essential for virulence in Sporothrix spp, the molecular mechanisms involved in this phenomenon have not yet been fully elucidated.

In this study, we used the strand-specific RNA-Seq technique and bioinformatics analysis to investigate the transcriptomic signatures associated with mold and yeast phases of S. brasiliensis. Furthermore, we generated an accurate version of the S. brasiliensis genome annotation in order to perform high-quality gene expression analysis and other functional or structural genomic studies.

Methods

The whole transcriptome of S. brasiliensis ATCC-MYA-4823, grown in both yeast-inducing (YPD medium at 37°C) and mold-inducing (YPD medium at 25°C) conditions, was sequenced in this study. High-quality RNA was used to prepare Illumina TruSeq Stranded mRNA-paired-end sequencing libraries (2 × 150 bp) that were sequenced using the HiSeq-2500 platform. A total of three biological replicates were sequenced for each condition.

Before transcriptome assembly, adapters and low-quality reads (Phred-score <25) were removed. The StringTie software was used to assemble the transcriptomes imported into the Apollo webtool to manually curate the genome annotation. Transcripts were investigated using TransDecoder and CPC2 programs to determine whether a gene was potentially protein-coding or non-coding. Finally, differential gene expression analysis between yeast and mold forms of S. brasiliensis was conducted using the edgeR package.

Results

Illumina sequencing resulted in a total of ∼217 million raw reads. After quality filtering and trimming, ∼99.5% of reads were used for downstream bioinformatics analysis. The updated S. brasiliensis genome annotation consisted of a total of 14 664 genes of which 10 243 protein-coding genes, 4259 lncRNAs, 140 tRNAs, and 22 rRNAs.

Gene expression analysis revealed a total of 13 838 and 13 938 transcripts expressed in mold- and yeast-form, respectively. Of these, 192 and 292 were expressed exclusively in the mold and yeast-phase, respectively. Moreover, a total of 6802 genes (FDR <0.05) were differentially expressed between the two examined conditions. In particular, 3420 of these genes were up-regulated in the yeast-form (2450 coding, 970 non-coding), and 3382 genes in the filamentous form (2507 coding, 875 non-coding). The raw reads have been deposited into the SRA database and are available under BioProjectID: PRJNA646214.

Conclusions

The characterization of the whole-transcriptome of S. brasiliensis mycelial and yeast-like forms represents an essential starting point for investigating the molecular pathways and regulatory frameworks associated with these two morphological stages. Our results provide new insight into global gene expression profiles of S. brasiliensis, emphasizing the role of non-coding RNAs in its complex transcriptional network.

All transcriptomic data have also been integrated into the ‘Sporothrix Genome DataBase’ (www. sporothrixgenomedatabase.unime.it) in order to expand the current knowledge of Sporothrix genomics and to allow a more in-depth structural exploration of S. brasiliensis gene models, including gene expression patterns related to its saprophytic and pathogenic lifestyle.

The Effect of Metal Cations on the Aqueous Behavior of Dopamine. Thermodynamic Investigation of the Binary and Ternary Interactions with Cd2+, Cu2+ and UO22+ in NaCl at Different Ionic Strengths and Temperatures

The interactions of dopamine [2-(3,4-Dihydroxyphenyl)ethylamine, (Dop-)] with cadmium(II), copper(II) and uranyl(VI) were studied in NaCl(aq) at different ionic strengths (0 ≤ I/mol dm-3 ≤ 1.0) and temperatures (288.15 ≤ T/K ≤ 318.15). From the elaboration of the experimental data, it was found that the speciation models are featured by species of different stoichiometry and stability. In particular for cadmium, the formation of only MLH, ML and ML2 (M = Cd2+; L = dopamine) species was obtained. For uranyl(VI) (UO22+), the speciation scheme is influenced by the use of UO2(acetate)2 salt as a chemical; in this case, the formation of ML2, MLOH and the ternary MLAc (Ac = acetate) species in a wide pH range was observed. The most complex speciation model was obtained for the interaction of Cu2+ with dopamine; in this case we observed the formation of the following species: ML2, M2L, M2L2, M2L2(OH)2, M2LOH and ML2OH. These speciation models were determined at each ionic strength and temperature investigated. As a further contribution to this kind of investigation, the ternary interactions of dopamine with UO22+/Cd2+ and UO22+/Cu2+ were investigated at I = 0.15 mol dm-3 and T = 298.15K. These systems have different speciation models, with the MM'L and M2M'L2OH [M = UO22+; M' = Cd2+ or Cu2+, L = dopamine] common species; the species of the mixed Cd2+ containing system have a higher stability with respect the Cu2+ containing one. The dependence on the ionic strength of complex formation constants was modelled by using both an extended Debye-Hückel equation that included the Van't Hoff term for the calculation of the formation enthalpy change values and the Specific Ion Interaction Theory (SIT). The results highlighted that, in general, the entropy is the driving force of the process. The quantification of the effective sequestering ability of dopamine towards the studied cations was evaluated by using a Boltzmann-type equation and the calculation of pL0.5 parameter. The sequestering ability was quantified at different ionic strengths, temperatures and pHs, and this resulted, in general, that the pL0.5 trend was always: UO22+ > Cu2+ > Cd2+.

The Solution Behavior of Dopamine in the Presence of Mono and Divalent Cations: A Thermodynamic Investigation in Different Experimental Conditions

The interactions of dopamine [2-(3,4-Dihydroxyphenyl)ethylamine, (Dop⁻)] with methylmercury(II) (CH₃Hg⁺), magnesium(II), calcium(II), and tin(II) were studied in NaCl(aq) at different ionic strengths and temperatures. Different speciation models were obtained, mainly characterized by mononuclear species. Only for Sn²⁺ we observed the formation of binuclear complexes (M₂L₂ and M₂LOH (charge omitted for simplicity); M = Sn²⁺, L = Dop⁻). For CH₃Hg⁺, the speciation model reported the ternary MLCl (M = CH₃Hg⁺) complex. The dependence on the ionic strength of complex formation constants was modeled by using both an extended Debye–Hückel equation that included the Van’t Hoff term for the calculation of enthalpy change values of the formation and the Specific Ion Interaction Theory (SIT). The results highlighted that, in general, the entropy is the driving force of the process. The sequestering ability of dopamine towards the investigated cations was evaluated using the calculation of pL_0.5 parameter. The sequestering ability trend resulted to be: Sn²⁺ > CH₃Hg⁺ > Ca²⁺ > Mg²⁺. For example, at I = 0.15 mol dm⁻³, T = 298.15 K and pH = 7.4, pL_0.5 = 3.46, 2.63, 1.15, and 2.27 for Sn²⁺, CH₃Hg⁺, Ca²⁺ and Mg²⁺ (pH = 9.5 for Mg²⁺), respectively. For the Ca²⁺/Dop⁻ system, the precipitates collected at the end of the potentiometric titrations were analyzed by thermogravimetry (TGA). The thermogravimetric calculations highlighted the formation of solid with stoichiometry dependent on the different metal:ligand ratios and concentrations of the starting solutions.

Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase

Sporothrix schenckii is a dimorphic fungus existing as mould in the environment and as yeast in the host. The morphological shift between mycelial/yeast phases is crucial for its virulence, but the transcriptional networks implicated in dimorphic transition are still not fully understood. Here, we report the global transcriptomic differences occurring between mould and yeast phases of S. schenckii, including changes in gene expression profiles associated with these distinct cellular phenotypes. Moreover, we also propose a new genome annotation, which reveals a more complex transcriptional architecture than previously assumed. Using RNA-seq, we identified a total of 17 307 genes, of which 11 217 were classified as protein-encoding genes, whereas 6090 were designated as non-coding RNAs (ncRNAs). Approximately ~71 % of all annotated genes were found to overlap and the different-strand overlapping type was the most common. Gene expression analysis revealed that 8795 genes were differentially regulated among yeast and mould forms. Differential gene expression was also observed for antisense ncRNAs overlapping neighbouring protein-encoding genes. The release of transcriptome-wide data and the establishment of the Sporothrix Genome DataBase (http://sporothrixgenomedatabase.unime.it) represent an important milestone for Sporothrix research, because they provide a strong basis for future studies on the molecular pathways involved in numerous biological processes.

Citrus Flavones: An Update on Sources, Biological Functions, and Health Promoting Properties

Citrus spp. are among the most widespread plants cultivated worldwide and every year millions of tons of fruit, juices, or processed compounds are produced and consumed, representing one of the main sources of nutrients in human diet. Among these, the flavonoids play a key role in providing a wide range of health beneficial effects. Apigenin, diosmetin, luteolin, acacetin, chrysoeriol, and their respective glycosides, that occur in concentrations up to 60 mg/L, are the most common flavones found in Citrus fruits and juices. The unique characteristics of their basic skeleton and the nature and position of the substituents have attracted and stimulated vigorous investigations as a consequence of an enormous biological potential, that manifests itself as (among other properties) antioxidant, anti-inflammatory, antiviral, antimicrobial, and anticancer activities. This review analyzes the biochemical, pharmacological, and biological properties of Citrus flavones, emphasizing their occurrence in Citrus spp. fruits and juices, on their bioavailability, and their ability to modulate signal cascades and key metabolic enzymes both in vitro and in vivo. Electronic databases including PubMed, Scopus, Web of Science, and SciFinder were used to investigate recent published articles on Citrus spp. in terms of components and bioactivity potentials.

Looking for New Antifungal Drugs from Flavonoids: Impact of the Genetic Diversity of Candida albicans on the in-vitro Response

BACKGROUND

In an era in which antimicrobial resistance is increasing at an alarming pace, it is very important to find new antimicrobial agents effective against pathogenic microrganisms resistant to traditional treatments. Among the notable breakthroughs in the past years of research in natural-drug discovery, there is the identification and testing of flavonoids, a group of plant-derived substances capable of promoting many beneficial effects on humans. These compounds show different biological activities such as inhibition of neuroinflammation and tumor growth as well as antimicrobial activity against many microbial pathogens.

METHODS

We undertook a review of protocols and standard strains used in studies reporting the inhibitory effects of flavonoids against Candida albicans by focusing our attention on genetic characterization of the strains examined. Moreover, using the C. albicans MLST-database, we performed a phylogenetic analysis showing the genetic variation occurring in this species.

RESULTS

Today, we have enough information to estimate genetic diversity within microbial species and recent data revealed that most of fungal pathogens show complex population structures in which not a single isolate can be designated as representative of the entire taxon. This is especially true for the highly divergent fungal pathogen C. albicans, in which the assumption that one or few "standard strains" can represent the whole species is overly unrealistic and should be laid to rest.

CONCLUSION

The goal of this article is to shed light on the extent of genetic variation in C. albicans and how this phenomenon can largely influence the activity of flavonoids against this species.

Genetic diversity of Candida albicans isolates recovered from hospital environments and patients with severe acquired brain injuries

Although the epidemiology of pathogenic Candida species causing invasive human diseases is changing, Candida albicans still remains the most common cause of bloodstream infections worldwide. The propensity of this pathogen to cause infections is undoubtedly the result of its unique genetic plasticity that allow it to adapt and respond quickly to a myriad of changing conditions both in the host and in the environment. For this reason, we decided to investigate the genetic diversity of this important fungal pathogen in a particular category of patients with severe neurological deficits including the hospital environments where they are hospitalized. Genetic diversity of 21 C. albicans isolates recovered from blood, hands of healthcare workers and hospital environments was evaluated by using multilocus sequence typing (MLST) which revealed a high genetic heterogeneity with a set of 18 diploid sequence types (DSTs) recovered among 21 isolates investigated. Interestingly, 13 of these 18 MLST genotypes were completely new and added to the C. albicans MLST central database. Six eBURST clonal complexes (CC-1, CC-2, CC-6, CC-9, CC-27 and CC-42) and three singletons contained all DSTs found in this study. Among all the new DSTs identified, DST3388 was the most intriguing as this genotype was recovered from a typical C. albicans isolate clustering within the MLST-Clade 13, the most divergent evolutionary lineage within C. albicans population containing only isolates with unusual phenotypes originally known as Candida africana. In conclusion, the results of this study expand our understanding of the molecular epidemiology and global population structure of C. albicans suggesting that further studies on different categories of patients and hospital environments are needed to better understand how the population of this species adapts and evolves in heterogeneous hosts and changing environments.

Whole RNA-Sequencing and Transcriptome Assembly of Candida albicans and Candida africana under Chlamydospore-Inducing Conditions

Candida albicans is the most common cause of life-threatening fungal infections in humans, especially in immunocompromised individuals. Crucial to its success as an opportunistic pathogen is the considerable dynamism of its genome, which readily undergoes genetic changes generating new phenotypes and shaping the evolution of new strains. Candida africana is an intriguing C. albicans biovariant strain that exhibits remarkable genetic and phenotypic differences when compared with standard C. albicans isolates. Candida africana is well-known for its low degree of virulence compared with C. albicans and for its inability to produce chlamydospores that C. albicans, characteristically, produces under certain environmental conditions. Chlamydospores are large, spherical structures, whose biological function is still unknown. For this reason, we have sequenced, assembled, and annotated the whole transcriptomes obtained from an efficient C. albicans chlamydospore-producing clinical strain (GE1), compared with the natural chlamydospore-negative C. africana clinical strain (CBS 11016). The transcriptomes of both C. albicans (GE1) and C. africana (CBS 11016) clinical strains, grown under chlamydospore-inducing conditions, were sequenced and assembled into 7,442 (GE1 strain) and 8,370 (CBS 11016 strain) high quality transcripts, respectively. The release of the first assembly of the C. africana transcriptome will allow future comparative studies to better understand the biology and evolution of this important human fungal pathogen.

Whole Genome-Based Amplified Fragment Length Polymorphism Analysis Reveals Genetic Diversity in Candida africana

This study aimed at investigating the genetic diversity of a panel of Candida africana strains recovered from vaginal samples in different countries. All fungal strains were heterozygous at the mating-type-like locus and belonged to the genotype A of Candida albicans. Moreover, all examined C. africana strains lack N-acetylglucosamine assimilation and sequence analysis of the HXK1 gene showed a distinctive polymorphism that impair the utilization of this amino sugar in this yeast. Multi-locus sequencing of seven housekeeping genes revealed a substantial genetic homogeneity among the strains, except for the CaMPIb, SYA1 and VPS13 loci which contributed significantly to the classification of our set of C. africana strains into six existing diploid sequence types. Amplified fragment length polymorphism fingerprint analysis yielded greater genotypic heterogeneity among the C. africana strains. Overall the data reported here show that in C. africana genetic diversity occurs and the existence of this intriguing group of C. albicans strains with specific phenotypes associated could be useful for future comparative studies in order to better understand the genetics and evolution of this important human pathogen.

Copper chelation and interleukin-6 proinflammatory cytokine effects on expression of different proteins involved in iron metabolism in HepG2 cell line

Background

In vertebrates, there is an intimate relationship between copper and iron homeostasis. Copper deficiency, which leads to a defect in ceruloplasmin enzymatic activity, has a strong effect on iron homeostasis resulting in cellular iron retention. Much is known about the mechanisms underlying cellular iron retention under “normal” conditions, however, less is known about the effect of copper deficiency during inflammation.

Results

We show that copper deficiency and the inflammatory cytokine interleukin-6 have different effects on the expression of proteins involved in iron and copper metabolism such as the soluble and glycosylphosphtidylinositol anchored forms of ceruloplasmin, hepcidin, ferroportin1, transferrin receptor1, divalent metal transporter1 and H-ferritin subunit. We demonstrate, using the human HepG2 cell line, that in addition to ceruloplasmin isoforms, copper deficiency affects other proteins, some posttranslationally and some at the transcriptional level. The addition of interleukin-6, moreover, has different effects on expression of ferroportin1 and ceruloplasmin, in which ferroportin1 is decreased while ceruloplasmin is increased. These effects are stronger when a copper chelating agent and IL-6 are used simultaneously.

Conclusions

These results suggest that copper chelation has effects not only on ceruloplasmin but also on other proteins involved in iron metabolism, sometimes at the mRNA level and, in inflammatory conditions, the functions of ferroportin and ceruloplasmin may be independent.

Cytotoxicity, haemolymphatic parameters, and oxidative stress following exposure to sub-lethal concentrations of quaternium-15 in Mytilus galloprovincialis

The presence of a xenobiotic in the environment can often represent a risk for living organisms. Quaternium-15, a preservative, is one of the most used substances and is added to several cosmetics and other industrial products. For this reason,kwowing the bio-indicator of the marine environment, the toxicological effects potentially elicited by this preservative on the marine invertebrate Mytilus galloprovincialis were studied. The results of this work confirm that quaternium-15, used at 0.1 and 1mg/l concentrations, while metabolized in M. galloprovincialis, causes a decrease in cellular viability, and remarkable changes to the defense and antioxidant system. In fact, haemocyte viability is dramatically reduced, and haemolymphatic parameter measurements indicate a stress on the animal. Moreover, an increase in radical species production, in Thiobarbituric Acid Reactive Species (TBARS) concentration, and in the Heat Shock Protein 70 amount, were observed in hepatopancreas. These changes suggest that the antioxidant systems are activated to overwhelm the oxidative damage induced by quaternium-15. Quaternium-15 jeopardizes both the defense and antioxidant systems. These results provide essential information with the biological fate of quaternium-15 in aquatic organisms, and confirm that biomarkers represent an important tool for modern environmental assessments as they can help with the prediction of pollutants involved in the monitoring program.

Molecular Characterization of the N-Acetylglucosamine Catabolic Genes in Candida africana, a Natural N-Acetylglucosamine Kinase (HXK1) Mutant

Background

In this study we report the genetic characterization, including expression analysis, of the genes involved in the uptake (NGT1) and catabolism (HXK1/NAG5, DAC1/NAG2, NAG1) of the aminosugar N-acetylglucosamine (GlcNAc) in Candida africana, a pathogenic biovariant of Candida albicans that is naturally unable to assimilate the GlcNAc.

Results

DNA sequence analysis of these genes revealed a number of characteristic nucleotide substitutions including a unique and distinctive guanine insertion that shifts the reading frame and generates a premature stop codon (TGA) 154 bp downstream of the ATG start codon of the HXK1 gene encoding the GlcNAc-kinase, a key enzyme of the GlcNAc catabolic pathway. However, all examined genes produced transcripts even though different levels of expression were observed among the Candida isolates examined. In particular, we found an HXK1-idependent relationship of the NGT1 gene and a considerable influence of the GlcNAc-kinase functionality on the transcription of the DAC1 and NAG1 genes. Additional phenotypic analysis revealed that C. africana isolates are hyperfilamentous in the first 24-48h of growth on filament-inducing media and revert to the yeast morphological form after 72h of incubation on these media.

Conclusions

Our results show that C. africana is a natural HXK1 mutant, displaying a number of phenotypic characteristics distinct from typical C. albicans isolates.

Specific aspartate residues in FET3 control high-affinity iron transport inSaccharomyces cerevisiae

Site-directed mutagenesis was performed on a set of six aspartate residues of Fet3, the multicopper ferroxidase involved in high-affinity iron transport in Saccharomyces cerevisiae, in order to comprehend the molecular determinants of the protein function. Asp312, Asp315, Asp319 and Asp320 were predicted by homology modelling to be located in a negatively charged surface-exposed loop of the protein. Other two aspartate residues (Asp278 and Asp279) are placed close to the type 1 copper- and iron-binding sites, possibly linking these sites to the negatively charged region. In vivo results showed that mutation of Asp319 and Asp320 to yield D319N and D320N derivatives strongly impairs the ability of the yeast to grow under iron-limiting conditions. In particular, substitution of Asp320 with asparagine essentially abolished the Fet3-dependent iron transport activity. All other mutants (D278Q, D279N, D312N and D315I) behaved essentially as the wild-type protein. The electron paramagnetic resonance spectrum of the soluble forms of D319N and D320N showed significant changes of the copper sites' geometry in D319N but not in D320N. At variance with the membrane-bound forms, soluble D319N and D320N derivatives were highly susceptible to proteolytic degradation, suggesting that replacement of Asp319 or Asp320 locally modifies the structure of Fet3, making the protein sensitive to proteolysis when it is not protected by the membrane environment. In turn, this might be evidence of a shielding role of the permease Ftr1, which could interact with Fet3 at the level of the aspartate-rich negatively charged region.

Regulation of prostaglandin generation in carrageenan-induced pleurisy by inducible nitric oxide synthase in knockout mice

In the present study, by comparing the responses in wild-type mice (iNOSWT) and mice lacking (iNOSKO) the inducible (or type 2) nitric oxide synthase (iNOS), we investigated the correlation between endogenous nitric oxide (NO) and prostaglandin (PG) generation in carrageenan-induced pleurisy. The inflammatory response in iNOSKO mice was significantly reduced in respect to iNOSWT animals, as demonstrated by the exudate volume (-63%) and numbers of infiltrating cells (-62%). The levels of NOx in the pleural exudate from carrageenan-treated mice were significantly (p < 0.01) decreased in iNOSKO mice (16 +/- 7.6 nmoles/mice) compared to iNOSWT animals (133 +/- 9 nmoles/mice). Similarly, the amounts of PGE2 in the pleural exudates of carrageenan-treated animals were significantly (p < 0.01) lower in iNOSKO compared to iNOSWT mice (120 +/- 20 pg/mice vs. 308 +/- 51 pg/mice). Also the amounts of 6-keto-PGF(1 alpha) produced by lungs from carrageenan-treated iNOSKO mice (1.01 +/- 0.10 ng/tissue mg) were significantly (p < 0.01) reduced compared to iNOSWT carrageenan-treated mice (2.1 +/- 0.09 ng/tissue mg). In conclusion our results confirm, by the use of iNOSKO mice that in carrageenan-induced pleurisy NO positively modulates PG biosynthesis.

Mutational analysis of the iron binding site of Saccharomyces cerevisiae ferroxidase Fet3. An in vivo study

The role of residues predicted to be involved in the binding of iron by the yeast ferroxidase Fet3 has been studied by site-directed mutagenesis. The effect of Fet3 mutations E185A, E185Q, Y354F, D409V and H489D has been investigated in vivo by kinetic analyses of high affinity iron uptake. Our results indicate that Glu-185 is critical for the binding of iron, since substitution of this residue with Ala or Gln strongly affects both growth and the kinetic parameters of high affinity iron uptake, greatly increasing K(m). Mutations Y354F and D409V result in less severe alteration of high affinity iron uptake, while mutant H489D is unable to grow under conditions of iron limitation.

The essential role of Glu-185 and Tyr-354 residues in the ferroxidase activity of Saccharomyces cerevisiae Fet3

The structural determinants required for ferroxidase activity by the yeast multicopper oxidase Fet3 have been partially clarified by site-directed mutagenesis based on homology modeling. Glu-185 and Tyr-354 were substituted with Ala and Phe, respectively. Fet3 E185A retained ca. 5% residual ferroxidase catalytic efficiency, and almost 40% oxidase efficiency. On the other hand, Fet3 Y354F exhibited 50% residual efficiency as a ferroxidase and more than 70% as an oxidase. These results provide new insights in the mechanism of iron binding and oxidation by Fet3, establishing the essential role of Glu-185 and Tyr-354, and allowing to dissect ferroxidase from non-iron oxidase activity.