Pitarch, A. | bioRxiv Science

bioRxiv2023

Plasticity of the MFS1 promotor is not the only driver of Multidrug resistance in Zymoseptoria tritici

Multidrug resistance (MDR) in fungal pathogens poses a growing threat to fungicide efficacy and sustainable agriculture. In the wheat pathogen Zymoseptoria tritici, MDR is primarily linked to overexpression of the MFS1 transporter gene, driven by transposable element (TE) insertions in its promoter or their remnants. Here, we provide a comprehensive analysis of MFS1 promoter polymorphism and its phenotypic impact on MDR across 374 field isolates collected in Europe between 2020 and 2021. We identify six novel structural variants derived from diverse TE types, confirming that the MFS1 promoter undergoes recurrent and independent insertion events. While previously characterized inserts consistently confer resistance, other variants show limited or variable phenotypic effects. Genetic crosses and quantitative phenotyping further reveal that MDR behaves as a quantitative trait and genome-wide association study confirmed MFS1 as the major resistance locus but also identified additional candidate genes involved in xenobiotic detoxification and membrane transport, supporting a polygenic basis for MDR. Our findings highlight the interplay between TE-driven structural variation and background polygenic architecture in shaping resistance phenotypes. In parallel, this study highlights the need to improve MDR monitoring beyond single-locus genotyping and re-evaluate current resistance management strategies that may inadvertently select for broad-spectrum resistance.

molecular biology↗

bioRxiv2020

Distinct human gut microbial taxonomic signatures uncovered with different sample processing and microbial cell disruption methods for metaproteomic analysis

Metaproteomics is as a promising technique for studying the human gut microbiota, because it can reveal the taxonomic profile and also shed light on the functional role of the microbial community. Nevertheless, methods for extracting proteins from stool samples continue to evolve, in the pursuit of optimal protocols for moistening and dispersing the stool sample and for disrupting microbial cells which are two critical steps for ensuring good protein recovery. Here, we evaluated different stool sample processing and microbial cell disruption methods for metaproteomic analyses of human gut microbiota. An unsupervised principal component analysis showed that different methods produced similar human gut microbial taxonomic profiles. An unsupervised two-way hierarchical clustering analysis identified the microbial taxonomic signatures associated with each method. Proteobacteria and Bacteroidetes identification was favored by moistening the stool samples during processing and by disrupting cells with medium-sized glass beads. Ascomycota identification was enhanced by using large-sized glass beads during sample processing for stool dispersion. Euryarchaeota identification was improved with a combination of small and medium-sized glass beads for cell disruption. Assessments of the relative abundance of Firmicutes, Actinobacteria and Spirochaetes improved when ultrasonication was performed before cell disruption with glass beads. The latter method also increased the overall number of identified proteins. Taxonomic and protein functional analyses of metaproteomic data derived from stool samples from six healthy individuals showed common taxonomic profiles. We also detected certain proteins involved in microbial functions relevant to the host and related mostly to particular taxa, such as B12 biosynthesis and short chain fatty acid production carried out mainly by members in the Prevotella genus and the Firmicutes phylum, respectively. Finally, in this metaproteomic study we identified several human proteins, mostly related to the anti-microbial response, which could contribute to determining the beneficial and detrimental relationships between gut microbiota and human cells in particular human diseases.

microbiology↗