Biology subjects

Sterzi, L.

Publications and source records attributed to Sterzi, L..

3 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↗