Biology subjects

Nodari, R.

Publications and source records attributed to Nodari, R..

5 recordsLinked to original sources

bioRxiv2024

Does the host drive Wolbachia gene expression?

Wolbachia pipientis is an obligate intracellular bacterium, associated with several arthropods and filarial nematodes. Wolbachia establishes strict symbiotic relationships with its hosts, with the consequent loss of many genes and regulatory regions. Despite this, experimental studies show that Wolbachia gene expression is coordinated to host needs, but the mechanism is still unknown. The first published RNA-Seq study on Wolbachia evidenced a strong differential expression of a DNA methyltransferase (MTase). In bacteria, this enzyme methylates either adenines or cytosines on specific motifs, contributing to the regulation of gene expression. In this work, we tested the hypothesis that the activity of MTase modulates the expression of Wolbachia genes. We first determined the methylation motif of the Wolbachia MTase by expressing it in Escherichia coli. Surprisingly, the experiment revealed that the Wolbachia MTase methylates both adenine and cytosine, without recognising highly specific motifs. Then, re-analysing data from six RNA-Seq studies, we found that the nucleotide content of Wolbachia genes correlates with their expressions, with a pattern compatible to be a consequence of the DNA methylation. Lastly, we identified MTase as the Wolbachia gene with the most conserved binding site for the Ccka/CtrA signalling transduction system, a mechanism likely involved the host-bacterium communication. Overall, these findings suggest a cascade mechanism in which the host activates the Wolbachia Ccka/CtrA signalling system, thus inducing the expression of the MTase gene. Then, the subsequent DNA methylation will affect the expression of several Wolbachia genes on the basis of their cytosine and adenine content.

microbiology↗

bioRxiv2024

Unraveling and quantifying "Candidatus Saccharibacteria": in silico and experimental evaluation of V3-V4 16S rRNA metagenomics and qPCR protocols

BackgroundCandidate Phyla Radiation (CPR) is a large monophyletic group thought to cover about 25% of bacterial diversity. Due to peculiar characteristics and unusual 16S rRNA gene structure, they are often under-represented or lost in 16S rRNA-based microbiota surveys. Among CPR, "Candidatus Saccharibacteria" is a phylum experimentally found to modulate the immune response and enriched in the oral microbiota of subjects suffering from several immune-mediated disorders, e.g. food allergies, as reported by us in a previous work. Due to the growing evidence of "Ca. Saccharibacteria"s role in clinical settings and in order to unravel its role in host physiology and pathology, it is crucial to have a reliable method to detect and quantify this lineage. Methods and ResultsFour qPCR protocols for quantifying "Ca. Saccharibacteria" (one targeting the 23S rRNA gene and three the 16S) were selected from the literature among the few available. Efficiency and coverage of primer pairs used in these protocols were preliminary evaluated via in silico analyses on the "Ca. Saccharibacteria" known taxonomic variability, and then tested in vitro on the salivary DNA previously investigated by 16S metagenomics in the food allergy study. In silico analyses evidenced that the 23S qPCR protocol covered more "Ca. Saccharibacteria" variability compared to the 16S-based ones, and that the 16S metagenomics primers were the most comprehensive. qPCR experiments confirmed that 16S-based protocols strongly underestimated "Ca. Saccharibacteria" while the 23S protocol was the only one to yield results comparable to 16S metagenomics both in terms of correlation and absolute quantification. However, only 16S metagenomics evidenced an expansion of "Ca. Saccharibacteria" in allergic subjects compared to controls, while none of the four qPCR protocols detected it. ConclusionThese results underline the current limits in experimentally approaching "Ca. Saccharibacteria". To obtain a more realistic picture of their abundance within bacterial communities, and to enable more efficient taxonomic resolution, it is essential to find novel experimental strategies. This is a necessary premise for more targeted and systematic functional studies to clarify the role of "Ca. Saccharibacteria" and, generally, CPR bacteria, in maintaining the health of the host.

microbiology↗

bioRxiv2023

On the forces shaping diversity and adaptation in the opportunistic pathogen Serratia marcescens

Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigated the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses revealed a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets revealed only a partial ecological separation of the clusters. Globally, two clusters only showed a peculiar gene composition and evident ecological adaptations. These results suggest that genetic isolation preceded ecological adaptations in the shaping of the species diversity, suggesting an evolutionary scenario for several bacterial species.

evolutionary biology↗

bioRxiv2022

Biosynthesis and apoplast accumulation of the apocarotenoid pigment azafrin in parasitizing roots of Escobedia grandiflora

O_LIThe herbaceous hemiparasite Escobedia grandiflora (Orobanchaceae) is used in traditional medicine in the Andean region. Their roots accumulate an orange pigment with a significant relevance as a cooking dye that exhibits antioxidant and cardioprotective properties. C_LIO_LIThe present work combined metabolic and cytological analyses with de novo transcriptome assembly, gene expression studies, and phylogenetic analyses to confirm the chemical identity of the pigment and investigate its biosynthesis and function in Escobedia roots. C_LIO_LIThe pigment was conclusively shown to be azafrin, an apocarotenoid likely derived from the cleavage of {beta}-carotene. Candidate genes for the production of azafrin in Escobedia roots are proposed based on RNA-seq supported by RT-qPCR and phylogeny reconstruction analyses. In particular, our data suggest that azafrin production relies a carotenoid cleavage dioxygenase (CCD) different from CCD7 and similar to CCD4 enzymes. We also show that azafrin is delivered to the root apoplast and that it accumulates in the area where the Escobedia haustorium contacts the hosts root, suggesting a role of azafrin in the parasitization process. C_LIO_LIAltogether, our work represents an unprecedented step forward in our understanding of the Escobedia parasitization system, but it also provides vital information towards the eventual domestication of this valuable medicinal plant. C_LI

plant biology↗

bioRxiv2021

Unbiased lexicometry analyses illuminate plague dynamics during the second pandemic

Knowledge of the second plague pandemic that swept over Europe during the 14th-19th centuries, mainly relies on the exegesis of contemporary texts, prone to interpretive bias. Leveraging bioinformatic tools routinely used in biology, we here developed a quantitative lexicography of 32 texts describing two major plague outbreaks using contemporary plague-unrelated texts as negative controls. Nested, network and category analyses of a 207-word pan-lexicome over-represented in plague-related texts, indicated that "buboes" and "carbuncles" words were significantly associated with plague, signaling ectoparasite- borne plague. Moreover, plague-related words were associated with the words "merchandise", "movable", "tatters", "bed" and "clothes", while no association was found with rats and fleas. These results support the hypothesis that during the second plague pandemic, human ectoparasites were the major drivers of plague. Analyzing ancient texts using here reported method would certify plague-related historical records and indicate particularities of each plague outbreak, including sources of the causative Yersinia pestis.

bioinformatics↗