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Kaberdin, V. R.

Publications and source records attributed to Kaberdin, V. R..

4 recordsLinked to original sources

Effect of pH on the secretome profile of the human pathogen

Secreted virulence factors (e.g., hydrolytic enzymes, toxins, agglutinins) play an important role in human diseases. Nevertheless, their secretion by some pathogenic fungi, especially some virulent Candida-related species such as Candidozyma auris, is still only partly characterized. Here we used high-throughput mass-spectroscopy analysis to identify polypeptides secreted by C. auris into growth medium under two physiologically relevant pH conditions: pH 5.5 and pH 7.5. This analysis revealed that many secreted polypeptides belong to putative virulence factors and enzymes involved in cell wall biogenesis. Moreover, we found that 13 and 27 polypeptides were detected only at pH 5.5 or pH 7.5, respectively. Furthermore, our findings indicate that lower pH (pH 5.5) favours secretion of several putative virulence factors including aspartic proteases and polypeptides potentially facilitating host-pathogen interactions. In contrast, the majority of polypeptides detected only at pH 7.5 are involved in N-glycosylation and protein folding. Thus, this secretome analysis reveals numerous C. auris polypeptides with putative roles in infection and host-pathogen interactions. Moreover, their differential secretion at pH 5.5 and pH 7.5 may reflect different strategies used by C. auris to elicit infections in different anatomical sites.

microbiology↗

Universal single-copy genes and 16S rDNA present incongruent evolutionary histories in Vibrio

A common technique for the study of the diversity and evolution of microbial communities is 16S rDNA sequencing. However, high sequence identity and variable copy number constrain the application of 16S rDNA in differentiation of closely related taxa and estimation of species relative abundance in environmental samples. A promising alternative is the use of universal single-copy genes (USCGs) as phylogenetic markers. We develop this by analyzing a set of USCG loci from the genus Vibrio, which holds over 100 species of substantial ecological and epidemiological relevance. The phylogenetic histories of these loci, of representative copies of 16S and 23S rDNA genes, and of a collection of 16S rDNA partial sequences were reconstructed using Bayesian inference. Taxon resolution was assessed according to consensus tree topology and clade credibility values. In addition, the congruence among posterior distributions of phylogenetic estimates of the different loci was calculated using Robinson-Foulds distances and visualized with non-metric multidimensional scaling (NMDS). Phylogenetic analyses reveal that USCG loci produce highly resolved trees in comparison to those of 16S and 23S rDNA sequences. We also observe relatively high congruence among phylogenies of USCG loci while rDNA phylogenies diverge from these. The loci mfd and uvrC are highlighted for further research on Vibrio evolution and analysis of environmental samples. Moreover, possible sources of phylogenetic incongruence between USCG and rDNA loci include differential susceptibility to horizontal gene transfer, as potentially explained by the complexity hypothesis, or lack of phylogenetic information due to limited sequence variability in rDNA sequences.

microbiology↗

Independent colonisations of serpentine habitats highlight species-specific evolutionary histories of lineage diversification

Serpentine soils are characterized by high levels of heavy metals, low nutrient availability, and water scarcity, presenting significant ecological challenges for plant species. Nonetheless, some species have adapted successfully to these conditions. We investigate the population genomic structure, evolutionary history and phenotypic differentiation of three diploid generalist plant species, Lavandula stoechas L., Halimium atriplicifolium (Lam) Spach. subsp. atriplicifolium, and Phlomis purpurea L., all of which inhabit adjacent serpentine and non-serpentine soils in the Malaga region in the southern Iberian Peninsula (Spain). We explore whether populations from serpentine and non-serpentine soils represent distinct evolutionary lineages and whether there is genomic and phenotypic differentiation associated with serpentine conditions. We measured plant height and specific leaf area (SLA) to detect potential ecotypic variation associated with soil type. A ddRADseq SNP dataset was generated for each species, representing 10 populations from serpentine and 10 from non-serpentine soils. We ordinated genotype data to assess genomic variation, conducted an ADMIXTURE analysis to infer ancestral groups, and used Treemix analyses to investigate phylogenetic relationships and gene flow events between populations. Isolation by distance (IBD) analyses evaluated the role of geographic separation in observed genomic differentiation. Our results reveal species-specific patterns of genomic, and to some extent phenotypic, differentiation between serpentine and non-serpentine populations, with evidence of multiple colonisations of serpentine sites in all three species. The study highlights the role of historical differentiation and subsequent gene flow in shaping the genomic structure of plant populations, alongside observed variation in phenotypic traits across environments.

evolutionary biology↗

NAD+ capping of RNA in Archaea and Mycobacteria

Chemical modifications of RNA affect essential properties of transcripts, such as their translation, localization and stability. 5-end RNA capping with the ubiquitous redox cofactor nicotinamide adenine dinucleotide (NAD+) has been discovered in organisms ranging from bacteria to mammals. However, the hypothesis that NAD+ capping might be universal in all domains of life has not been proven yet, as information on this RNA modification is missing for Archaea. Likewise, this RNA modification has not been studied in the clinically important Mycobacterium genus. Here, we demonstrate that NAD+ capping occurs in the archaeal and mycobacterial model organisms Methanosarcina barkeri and Mycobacterium smegmatis. Moreover, we identify the NAD+-capped transcripts in M. smegmatis, showing that this modification is more prevalent in stationary phase, and revealing that mycobacterial NAD+-capped transcripts include non-coding small RNAs, such as Ms1. Furthermore, we show that mycobacterial RNA polymerase incorporates NAD+ into RNA, and that the genes of NAD+-capped transcripts are preceded by promoter elements compatible with {sigma}A/{sigma}F dependent expression. Taken together, our findings demonstrate that NAD+ capping exists in the archaeal domain of life, suggesting that it is universal to all living organisms, and define the NAD+-capped RNA landscape in mycobacteria, providing a basis for its future exploration.

molecular biology↗