Biology subjects

Timouma, S.

Publications and source records attributed to Timouma, S..

9 recordsLinked to original sources

bioRxiv2025

Construction of a reference genome for Starmerella batistae and annotation of Starmerella species reveal a close evolutionary relationship with Schizosaccharomyces pombe and suggest an alternative pathway for sophorolipid production.

The Starmerella clade is known for displaying osmotolerant and acidophilic traits from their association with bees. Several species in this genus can produce sophorolipids, which are commercially produced as biosurfactants. Here, we isolated a yeast contaminant from the laboratory environment, identified as Starmerella batistae, able to thrive under low pH, including high concentrations of lactic acid, and relative high temperatures. We have sequenced and conducted a de novo genome assembly in three chromosomes and a mitochondrial genome for S. batistae (ca 9.3 Mb). Based on this reference genome we functionally annotated 29 different Starmerella species, using the publicly available sequences. Phylogenetic analysis across different yeast clades revealed a close relationship of Starmerella species with Schizosaccharomyces yeasts. Fifteen genes were uniquely shared between Sz. pombe and S. batistae, of which twelve were involved in cell morphology. Interestingly, the shape of S. batistae cells is elongated rather than round, similar to the Sz. pombe. Additionally, we found that all the Starmerella strains capable of producing sophorolipids shared a last common ancestor. Such clustering can help identify other sophorolipid-producing Starmerella yeasts that have not yet been characterised. We did not find the one-to-one orthologs of S. bombicola sophorolipid pathway in any of the Starmerella sp. with the exception of S. kuoi, S. powellii and S. floricola. In S. etchelsii, the antisense and telomeric pair UGTA1/CYP52M1 was found to be structurally conserved although not functionally. These findings support the notion that alternative pathways for the production of sophorolipids have evolved in different Starmerella lineages.

genomics↗

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

Development of a genome scale metabolic model for the lager hybrid yeast S. pastorianus to understand evolution of metabolic pathways in industrial settings.

In silico tools such as genome-scale metabolic models (GSMM) have shown to be powerful for metabolic engineering of microorganisms. Here, we created the iSP_1513 GSMM for the aneuploid hybrid S. pastorianus CBS1513 to allow top-down computational approaches to predict the evolution of metabolic pathways and to aid strain optimisation and media engineering in production processes. The iSP_1513 comprises 4062 reactions, 1808 alleles and 2747 metabolites, and takes into account the functional redundancy in the gene-protein-reaction rule caused by the presence of orthologous genes. Moreover, a universal algorithm to constrain GSMM reactions using transcriptome data was developed as a python library and enabled the integration of temperature as parameter. Essentiality datasets, growth data on various carbohydrates and volatile metabolites secretion were used to validate the model. Overall, the iSP_1513 GSMM represent an important step towards understanding the metabolic capabilities, evolutionary trajectories and adaptation potential of S. pastorianus in different industrial settings.

systems biology↗

bioRxiv2023

High quality de novo genome assembly of non-conventional yeast Kazachstania bulderi a new potential low pH production host for biorefineries.

Kazachstania bulderi is a yeast species belonging to a ubiquitous group of non-conventional yeasts which has the ability to grow efficiently on glucose and {delta}-gluconolactone at low pH. This unique trait makes K. bulderi an ideal candidate as a new host for low pH fermentation processes for sustainable production of green chemicals such as organic acids. To accelerate strain development with this species, detailed information of its genetics is needed. Here, by employing high accuracy long read sequencing we report a high-quality phased genome assembly for three strains belonging to K. bulderi species, including the type strain. The sequences were assembled into 12 chromosomes with a total length of 14Mb, and the genome was fully annotated at structural and functional levels, including allelic and structural variants, ribosomal array, centromeres and mating type locus. This high-quality reference genome provides an essential resource to advance our fundamental knowledge of biotechno-logically relevant non-conventional yeasts and to support the development of genetic tools for manipulating such strains towards their use as production hosts biotechnological processes.

genomics↗

bioRxiv2022

Analysis of synthetic genetic interactions of non-coding RNAs in Saccharomyces cerevisiae

Non-coding RNAs (ncRNAs) with unknown function have been found to be responsible for fitness changes in yeast. With the help of synthetic genetic array (SGA) methodology, genetic interaction screenings between protein-coding genes have contributed to the understanding of complex genetic pathways in eukaryotes. By extending this approach to the ncRNAs, we created more than 15,000 ncRNA double mutants and scored their epistasis in different environments. More than 90% of ncRNA interactions did not correlate with the epistasis of their neighbouring protein-coding genes, showing that the ncRNA and protein interaction networks are largely independent. In the presence of different stressors, epistatic changes were observed with an overall increase in negative interactions. Such network plasticity supports the notion that these ncRNAs may have environmentally dependent functions and can contribute to phenotypic adaptation. The U3 paralogs, SNR17A and SNR17B, share most interactions in rich media, as expected, however, in stressful conditions, there was an increase of paralog-unique interactions, suggesting that SNR17A and SNR17B may have diverged cellular roles under different environmental pressures and may have neo-functionalised after genome duplication. Further investigation of the interaction networks between SNR17 and protein-coding genes revealed the emergence of paralog-specific interactions under stress conditions. Gene Ontology enrichment analysis suggested a novel potential role of SNR17B in chromatin structural remodelling and DNA topology under osmotic and oxidative stress. Overall, this genome-wide study uncovers the level of epistasis involving ncRNA mutants aiding functional assignment and expanding our fundamental knowledge of these genetic elements.

genetics↗

bioRxiv2021

Aneuploidy influences the gene expression profiles in Saccharomyces pastorianus group I and II strains during fermentation.

The lager yeasts, Saccharomyces pastorianus, are hybrids of Saccharomyces cerevisiae and Saccharomyces eubayanus and are divided into two broad groups, Group I and II. The two groups evolved from at least one common hybridisation event but have subsequently diverged with Group I strains losing many S. cerevisiae chromosomes while the Group II strains retain both sub-genomes. The complex genomes, containing orthologous alleles from the parental chromosomes, pose interesting questions regarding gene regulation and its impact on the fermentation properties of the strains. Superimposed on the presence of orthologous alleles are complexities of gene dosage due to the aneuploid nature of the genomes. We examined the contribution of the S. cerevisiae and S. eubayanus alleles to the gene expression patterns of Group I and II strains during fermentation. We show that the relative expression of S. cerevisiae and S. eubayanus orthologues is positively correlated with gene copy number. Despite the reduced S. cerevisiae content in the Group I strain, S. cerevisiae orthologues contribute to biochemical pathways upregulated during fermentation which may explain the retention of specific chromosomes in the strain. Conversely, S. eubayanus genes are significantly overrepresented in the upregulated gene pool in the Group II strain. Comparison of the transcription profiles of Group I and II strains during fermentation identified both common and unique gene expression patterns, with gene copy number being a dominant contributory factor. Thus, the aneuploid genomes create complex patterns of gene expression during fermentation with gene dosage playing a crucial role both within and between strains.

genetics↗

bioRxiv2021

Transcriptional network of the industrial hybrid Saccharomyces pastorianus reveals temperature-dependent allele expression bias and preferential orthologous protein assemblies

Saccharomyces pastorianus is an industrial natural yeast evolved from different hybridisation events between the mesophilic S. cerevisiae and the cold-tolerant S. eubayanus. This complex aneuploid hybrid carries multiple copies of the parental alleles alongside specific hybrid genes and encodes for multiple protein isoforms which impart novel phenotypes, such as the strong ability to ferment at low temperature. These characteristics lead to agonistic or antagonistic competition for substrates and a plethora of biochemical activities, resulting in a unique cellular metabolism. Here, we investigated the transcriptional signature of the different orthologous alleles in S. pastorianus during temperature shifts. We identified temperature-dependent media-independent genes and showed that 35% have their regulation dependent on extracellular leucine uptake, suggesting an interplay between leucine metabolism and temperature response. The analysis of the expression of ortholog parental alleles unveiled that the majority of the genes express preferentially one parental allele over the other, and that S. eubayanus-like alleles are significantly over-represented among the genes involved in cold acclimatisation. The presence of functionally redundant parental alleles may impact on the nature of protein complexes established in the hybrid, where both parental alleles are competing. Our expression data indicate that the majority of the protein complexes in the hybrid are likely to be either exclusively chimeric or uni-specific, and that the redundancy is discouraged, a scenario which fits well with the stoichiometric balance-hypothesis. This study offers the first overview of the transcriptional pattern of S. pastorianus and provide a rationalisation for its unique industrial traits at expression level.

genomics↗

bioRxiv2020

HybridMine: pipeline for allele inheritance and gene copy number prediction in industrial yeast hybrids

Saccharomyces pastorianus is an allopolyploid sterile yeast hybrid used in brewing to produce lager-style beers. The development of new yeast strains with valuable industrial traits such as improved maltose utilization or balanced flavour profiles are now a major ambition and challenge in craft brewing and distilling industries. Genome-scale computational approaches are opening opportunities to model and predict favourable combination of traits for strain development. However, mining the genome of these complex hybrids is not currently an easy task, due to the high level of redundancy and presence of homologous. Moreover, no genome annotation for these industrial strains have been published. Here, we developed HybridMine, a new user-friendly, open-source tool for functional annotation of hybrid aneuploid genomes of any species by predicting parental alleles including paralogs. As proof of principle, we carried out a comprehensive structural and functional annotation of complex yeast hybrids to enable system biology prediction studies. HybridMine is developed in Python, Perl and Bash programming languages and is available at https://github.com/Sookie-S/HybridMine.

genomics↗

bioRxiv2020

Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and widespread in trans effects on the protein regulatory network

Non-coding RNAs (ncRNAs), including the more recently identified Stable Unannotated Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs), are increasingly being shown to play pivotal roles in the transcriptional and post-transcriptional regulation of genes in eukaryotes. Here, we carried out a large-scale screening of ncRNAs in Saccharomyces cerevisiae, and provide evidence for SUT and CUT function. Phenotypic data on 372 ncRNA deletion strains in 23 different growth conditions were collected, identifying ncRNAs responsible for significant cellular fitness changes. Transcriptome profiles were assembled for 18 haploid ncRNA deletion mutants and 2 essential ncRNA heterozygous deletants. Guided by the resulting RNA-seq data we analysed the genome-wide dysregulation of protein coding genes and non-coding transcripts. Novel functional ncRNAs, SUT125, SUT126, SUT035 and SUT532 that act in trans by modulating transcription factors were identified. Furthermore, we described the impact of SUTs and CUTs in modulating coding gene expression in response of different environmental conditions, regulating important biological process such as respiration (SUT125, SUT126, SUT035, SUT432), steroid biosynthesis (CUT494, SUT530, SUT468) or rRNA processing (SUT075 and snR30). Overall, this data captures and integrates the regulatory and phenotypic network of ncRNAs and protein coding genes, providing genome-wide evidence of the impact of ncRNAs on cellular homeostasis. Author SummaryThe yeast genome contains 25% of non-coding RNA molecules (ncRNAs), which do not translate into proteins but are involved in regulation of gene expression. ncRNAs can affect nearby genes by physically interfering with their transcription (cis mode of action), or they interact with DNA, proteins or others RNAs to regulate the expression of distant genes (trans mode of action). Examples of cis-acting ncRNAs have been broadly described, however genome-wide studies to identify functional trans-acting ncRNAs involved in global gene regulation are still lacking. Here, we used the ncRNA yeast deletion collection to score their impact on cellular function in different environmental conditions. A group of 20 ncRNAs mutants with broad fitness diversity were selected to investigate their effect on the protein and ncRNA expression network. We showed a high correlation between altered phenotypes and global transcriptional changes, in an environmental dependent manner. We confirmed the widespread trans acting expressional regulation of ncRNAs in the genome and their role in affecting transcription factors. These findings support the notion of the involvement on ncRNAs in fine tuning the cellular expression via regulations of TFs, as an advantageous RNA-mediated mechanism that can be fast and cost-effective for the cells.

genomics↗