Biology subjects

Louis, E. J.

Publications and source records attributed to Louis, E. J..

4 recordsLinked to original sources

bioRxiv2024

Impact of inter-species hybridisation on antifungal drug response in the Saccharomyces genus.

Antifungal drug resistance across fungal and yeast pathogens presents one of the major concerns for global public health. Understanding the interactions between genetic background and environment is important for the development of new, effective treatments of infections. Allelic variation within populations of Ascomycota as well as hybridisation impacts the phenotype in response to stressful conditions, including to antifungal drugs. We exploited recent advances in multigenerational breeding of Saccharomyces interspecies hybrids to study the impact of hybridisation on antifungal resistance and identify quantitative trait loci (QTL) responsible for the phenotypes observed. A library of Saccharomyces cerevisiae x S. kudriavzevii hybrid offspring was screened in the presence of sub-lethal concentrations of six antifungal drugs and revealed a broad phenotypic diversity across the progeny. QTL analysis was carried out comparing alleles between the pools of high and low fitness offspring, identifying hybrid-specific genetic regions involved in resistance to fluconazole, micafungin and flucytosine. We found both drug specific and pleiotropic regions, and through gene ontology and SIFT analysis we identify potential causal genes, such as BCK2 and DNF1 that were validated via reciprocal hemizygosity analysis. We highlight 41 regions that contain genes not previously associated with resistance phenotypes in the literature. The results of this screening will help identify new pathways contributing to drug resistance, and lead to greater understanding of how allelic variation, hybridisation and evolution affect antifungal drug resistance in yeast and fungi.

genetics↗

bioRxiv2023

Humanized yeast to study the role of human ECE-1 isoforms in apoptosis in congenital heart diseases

Endothelin convert enzyme-1(ECE-1) plays a significant role in cardiovascular development including four isoforms with unclear function. Therefore, we are interested in studying the function of ECE-1 isoforms through mitochondria due to the high correlation between congenital heart disease (CHD) and apoptosis. Since the expression of human Bax and Bcl-xL in budding yeast (Saccharomyces cerevisiae) results in similar effects in mammalian cells, a yeast system was generated for mimicking human Bax-induced apoptosis and the expression of human ECE-1 isoforms was involved. The correlation between Bax-induced growth defect and the candidates of apoptosis via mitochondrial pathway was preliminarily investigated in this system. Furthermore, the phenotypes of ECE-1 isoforms have been identified through yeast growth defect. Individual ECE-1 isoform does not affect yeast growth but act as enhancers for the Bax-induced growth defect. ECE-1c is the strongest enhancer that affect the expression of candidates of outer membrane translocases. This study indicates that ECE-1 might play an important role in inducing apoptosis and we speculate these findings are possible to provide new perspectives with clarifying the mechanism of CHD.

molecular biology↗

bioRxiv2021

Restoring fertility in yeast hybrids: breeding and quantitative genetics of beneficial traits

Hybrids species can harbour a combination of beneficial traits from each parent and may exhibit hybrid vigour, more readily adapting to new harsher environments. Inter-species hybrids are also sterile and therefore an evolutionary dead-end unless fertility is restored, usually via auto-polyploidisation events. In the Saccharomyces genus, hybrids are readily found in nature and in industrial settings, where they have adapted to severe fermentative conditions. Due to their hybrid sterility, the development of new commercial yeast strains has so far been primarily conducted via selection methods rather than breeding. In this study, we overcame infertility by creating tetraploid intermediates of Saccharomyces inter-species hybrids, to allow continuous multigenerational breeding. We incorporated nuclear and mitochondrial genetic diversity within each parental species, allowing for quantitative genetic analysis of traits exhibited by the hybrids, and for nuclear-mitochondrial interactions to be assessed. Using pooled F12 generation segregants of different hybrids with extreme phenotype distributions, we identified QTLs for tolerance to high and low temperatures, high sugar concentration, high ethanol concentration, and acetic acid levels. We identified QTLs that are species specific, that are shared between species, as well as hybrid specific, where the variants do not exhibit phenotypic differences in the original parental species. Moreover, we could distinguish between mitochondria-type dependent and independent traits. This study tackles the complexity of the genetic interactions and traits in hybrid species, bringing hybrids into the realm of full genetic analysis of diploid species, and paves the road for the biotechnological exploitation of yeast biodiversity.

genetics↗

bioRxiv2017

PHENOS: a high-throughput and flexible tool for microorganism growth phenotyping on solid media

BACKGROUNDMicrobial arrays, with a large number of different strains on a single plate printed with robotic precision, underpin an increasing number of genetic and genomic approaches. These include Synthetic Genetic Array analysis, high-throughput Quantitative Trait Loci (QTL) analysis and 2-hybrid techniques. Measuring the growth of individual colonies within these arrays is an essential part of many of these techniques but is useful for any work with arrays. Measurement is typically done using intermittent imagery fed into complex image analysis software, which is not especially accurate and is challenging to use effectively. We have developed a simple and fast alternative technique that uses a pinning robot and a commonplace microplate reader to continuously measure the thickness of colonies growing on solid agar, complemented by a technique for normalizing the amount of cells initially printed to each spot of the array in the first place. We have developed software to automate the process of combining multiple sets of readings, subtracting agar absorbance, and visualizing colony thickness changes in a number of informative ways.\n\nRESULTSThe \"PHENOS\" pipeline (PHENotyping On Solid media), optimized for Saccharomyces yeasts, produces highly reproducible growth curves and is particularly sensitive to low-level growth. We have empirically determined a formula to estimate colony cell count from an absorbance measurement, and shown this to be comparable with estimates from measurements in liquid. We have also validated the technique by reproducing the results of an earlier QTL study done with conventional liquid phenotyping, and found PHENOS to be considerably more sensitive.\n\nCONCLUSIONS\"PHENOS\" is a cost effective and reliable high-throughput technique for quantifying growth of yeast arrays, and is likely to be equally very useful for a range of other types of microbial arrays. A detailed guide to the pipeline and software is provided with the installation files at https://github.com/gact/phenos.

microbiology↗