Biology subjects

Staats, C. C.

Publications and source records attributed to Staats, C. C..

6 recordsLinked to original sources

bioRxiv2026

Complete genome sequence and metabolic features of Vreelandella zhaodongensis BS253: A new isolate from hypersaline lakes from Brazilian Pantanal

The urgent need for sustainable solutions to mitigate climate change has intensified research into carbon capture, utilization, and storage (CCUS) strategies. Biological approaches, particularly involving extremophilic microorganisms, offer promising alternatives to conventional methods due to their adaptability and potential for bioproduct synthesis. In this study, we report the complete genome sequencing and functional characterization of isolate BS253, derived from a hypersaline alkaline lake in Brazils Pantanal region. Using a hybrid sequencing strategy combining Oxford Nanopore long reads and Illumina short reads, we assembled a circular chromosome of 3.76 Mb and identified two plasmids. Phylogenetic and comparative genomic analyses identified the isolate as Vreelandella zhaodongensis. Digital DNA-DNA hybridization (dDDH % = 71.4%) and ANI (96,83%) values supported the designation of BS253 as a distinct subspecies of V. zhaodongensis. The genome reveals genes associated with salt and alkali tolerance, hydrocarbon and plastic degradation, and the biosynthesis of secondary metabolites. Phenotypically, BS253 is a moderately halophilic, facultatively anaerobic, Gram-negative rod exhibiting biosurfactant activity, with an emulsification index of 51.7% under defined culture conditions. These findings highlight BS253 as a metabolically versatile extremophile with potential applications in different types of industries and biotechnological CCUS systems. ImportanceMicroorganisms adapted to extreme environments represent an untapped source of biotechnologically valuable traits. Vreelandella zhaodongensis BS253, isolated from a hypersaline alkaline lake in the Brazilian Pantanal, expands the known diversity of extremophiles and offers metabolic features with relevance to sustainable bioprocesses. Its complete genome reveals genes involved in salt and alkali tolerance, plastic and hydrocarbon degradation, and the biosynthesis of biosurfactant-like compounds, positioning this strain as a promising chassis for applications in emerging carbon capture, utilization, and storage (CCUS) strategies. The ability of BS253 to produce bioemulsifying molecules under defined nutritional conditions, combined with pathways for degrading recalcitrant pollutants, reinforces its potential for environmentally friendly industrial processes. By characterizing BS253 at the genomic and physiological levels, this work provides foundational information for future exploitation of extremophiles in biotechnological innovations aimed at reducing carbon emissions and supporting circular bioeconomy initiatives.

microbiology↗

bioRxiv2022

Extracellular vesicle formation in Cryptococcus deuterogattii impacts fungal virulence and requires the NOP16 gene

Small molecules are components of fungal extracellular vesicles (EVs), but their biological roles are only superficially known. NOP16 is a eukaryotic gene that is required for the activity of benzimidazoles against Cryptococcus deuterogattii. In this study, during the phenotypic characterization of C. deuterogattii mutants lacking NOP16 expression, we observed that this gene was required for EV production. Analysis of the small molecule composition of EVs produced by wild-type cells and two independent nop16{Delta} mutants revealed that the deletion of NOP16 resulted not only in a reduced number of EVs but also an altered small molecule composition. In a Galleria mellonella model of infection, the nop16{Delta} mutants were hypovirulent. The hypovirulent phenotype was reverted when EVs produced by wild-type cells, but not mutant EVs, were co-injected with the nop16{Delta} cells in G. mellonella. These results reveal a role for NOP16 in EV biogenesis and cargo, and also indicate that the composition of EVs is determinant for cryptococcal virulence.

microbiology↗

bioRxiv2020

Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss

Evaluating the quality of a de novo annotation of a complex fungal genome based on RNA-seq data remains a challenge. In this study, we sequentially optimized a Cufflinks-CodingQuary based bioinformatics pipeline fed with RNA-seq data using the manually annotated model pathogenic yeasts Cryptococcus neoformans and Cryptococcus deneoformans as test cases. Our results demonstrate that the quality of the annotation is sensitive to the quantity of RNA-seq data used and that the best quality is obtained with 5 to 10 million reads per RNA-seq replicate. We also demonstrated that the number of introns predicted is an excellent a priori indicator of the quality of the final de novo annotation. We then used this pipeline to annotate the genome of the RNAi-deficient species Cryptococcus deuterogattii strain R265 using RNA-seq data. Dynamic transcriptome analysis revealed that intron retention is more prominent in C. deuterogattii than in the other RNAi-proficient species C. neoformans and C. deneoformans. In contrast, we observed that antisense transcription was not higher in C. deuterogattii than in the two other Cryptococcus species. Comparative gene content analysis identified 21 clusters enriched in transcription factors and transporters that have been lost. Interestingly, analysis of the subtelomeric regions in these three annotated species identified a similar gene enrichment, reminiscent of the structure of primary metabolic clusters. Our data suggest that there is active exchange between subtelomeric regions, and that other chromosomal regions might participate in adaptive diversification of Cryptococcus metabolite assimilation potential.

microbiology↗

bioRxiv2020

Calcium binding protein Ncs1 is calcineurin-regulated in Cryptococcus neoformans and essential for cell division and virulence

Intracellular calcium (Ca2+) is crucial for signal transduction in Cryptococcus neoformans, the major cause of fatal fungal meningitis. The calcineurin pathway is the only Ca2+-requiring signalling cascade implicated in cryptococcal stress adaptation and virulence, with Ca2+-binding mediated by the EF-hand domains of the Ca2+ sensor protein calmodulin. In this study, we identified the cryptococcal ortholog of neuronal calcium sensor-1 (Ncs1) as a member of the EF-hand superfamily. We demonstrated that Ncs1 has a role in Ca2+ homeostasis under stress and non-stress conditions, as the ncs1{Delta} mutant is sensitive to a high Ca2+ concentration and has an elevated basal Ca2+ level that correlates with increased expression of the Ca2+ transporter genes, CCH1 and MID1. Furthermore, NCS1 expression is induced by Ca2+, with the Ncs1 protein adopting a punctate subcellular distribution. We also demonstrate that, in contrast to Saccharomyces cerevisiae, NCS1 expression in C. neoformans is regulated by the calcineurin pathway via the transcription factor Crz1, as NCS1 expression is reduced by FK506 treatment and CRZ1 deletion. Moreover, the ncs1{Delta} mutant shares a high temperature and high Ca2+ sensitivity phenotype with the calcineurin and calmodulin mutants (cna1{Delta} and cam1{Delta}) and the NCS1 promoter contains two calcineurin/Crz1-dependent response elements (CDRE1). Ncs1-deficency coincided with reduced growth, characterized by delayed bud emergence and aberrant cell division, and hypovirulence in a mouse infection model. In summary, our data shows that Ncs1 plays distinct roles in Ca2+ sensing in C. neoformans despite widespread functional conservation of Ncs1 and other regulators of Ca2+ homeostasis. ImportanceCryptococcus neoformans is the major cause of fungal meningitis in HIV infected patients. Several studies have highlighted the important contribution of Ca2+ signalling and homeostasis to the virulence of C. neoformans. Here, we identify the cryptococcal ortholog of neuronal calcium sensor-1 (Ncs1) and demonstrate its role in Ca2+ homeostasis, bud emergence, cell cycle progression and virulence. We also show that Ncs1 function is regulated by the calcineurin/Crz1 signalling cascade. Our work provides evidence of a link between Ca2+ homeostasis and cell cycle progression in C. neoformans.

microbiology↗

bioRxiv2020

Gender, race and parenthood impact academic productivity during the COVID-19 pandemic: from survey to action.

While the Coronavirus disease 2019 (COVID-19) pandemic is altering academia dynamics, those juggling remote work and domestic demands - including childcare - have already felt the impacts on productivity. Female authors are facing a decrease in papers submission rates since the beginning of the pandemic period. The reasons for this decline in women productivity need to be further investigated. Here we show the influence of gender, parenthood and race in academics productivity during the pandemic period, based on a survey answered by 3,345 Brazilian academics from various knowledge areas and research institutions. Findings revealed that male academics - especially childless ones - were the least affected group, whereas female academics, especially Black women and mothers, were the most impacted group. This scenario will leave long-term effects on the career progression of the most affected groups. The results presented here are crucial for the development of actions and policies that aim to avoid further deepening the gender gap in science. This particular situation we are facing during the pandemic demands institutional flexibility and academia should foster the discussion about actions to benefit Black scientists and academics with families in the post-pandemic scenario.

scientific communication and education↗

bioRxiv2019

A novel protocol for the isolation of fungal extracellular vesicles reveals the participation of a putative scramblase in polysaccharide export and capsule construction in Cryptococcus gattii.

Regular protocols for the isolation of fungal extracellular vesicles (EVs) are time-consuming, hard to reproduce, and produce low yields. In an attempt to improve the protocols used for EV isolation, we explored a model of vesicle production after growth of Cryptococcus gattii and C. neoformans on solid media. Nanoparticle tracking analysis in combination with transmission electron microscopy revealed that C. gattii and C. neoformans produced EVs in solid media. These results were reproduced with an acapsular mutant of C. neoformans, as well as with isolates of Candida albicans, Histoplasma capsulatum, and Saccharomyces cerevisiae. Cryptococcal EVs produced in solid media were biologically active and contained regular vesicular components, including the major polysaccharide glucuronoxylomannan (GXM) and RNA. Since the protocol had higher yields and was much faster than the regular methods used for the isolation of fungal EVs, we asked if it would be applicable to address fundamental questions related to cryptococcal secretion. On the basis that polysaccharide export in Cryptococcus requires highly organized membrane traffic culminating with EV release, we analyzed the participation of a putative scramblase (Aim25, CNBG_3981) in EV-mediated GXM export and capsule formation in C. gattii. EVs from a C. gattii aim25{Delta} strain differed from those obtained from wild-type (WT) cells in physical-chemical properties and cargo. In a model of surface coating of an acapsular cryptococcal strain with vesicular GXM, EVs obtained from the aim25{Delta} mutant were more efficiently used as a source of capsular polysaccharides. Lack of the Aim25 scramblase resulted in disorganized membranes and increased capsular dimensions. These results associate the description of a novel protocol for the isolation of fungal EVs with the identification of a previously unknown regulator of polysaccharide release. IMPORTANCEExtracellular vesicles (EVs) are fundamental components of the physiology of cells from all kingdoms. In pathogenic fungi, they participate in important mechanisms of transfer of antifungal resistance and virulence, as well as in immune stimulation and prion transmission. However, studies on the functions of fungal EVs are still limited by the lack of efficient methods for isolation of these compartments. In this study, we developed an alternative protocol for isolation of fungal EVs and demonstrated an application of this new methodology in the study of the physiology of the fungal pathogen Cryptococcus gattii. Our results describe a fast and reliable method for the study of fungal EVs and reveal the participation of scramblase, a phospholipid translocating enzyme, in secretory processes of C. gattii.

microbiology↗