Biology subjects

Balarezo-Cisneros, L. N.

Publications and source records attributed to Balarezo-Cisneros, L. N..

9 recordsLinked to original sources

bioRxiv2025

SWR1C loss promotes longevity through tRNA-mediated proteostasis

The conserved SWR1C chromatin remodeling complex promotes cellular aging, yet the mechanisms linking its activity to lifespan control remain poorly defined. Although SWR1C shapes chromatin architecture and regulates non-coding RNA expression, how these activities relate to its role in aging remains unclear. Here, we combine genetic and lifespan-epistasis analyses to identify the cellular processes that underlie SWR1C-dependent chronological longevity in Saccharomyces cerevisiae. Loss of subunits specifically required for H2A.Z deposition robustly extends longevity, and this effect is functionally linked to cytosolic translation and proteostasis pathways. Lifespan profiling of ncRNA deletions reveals a substantial fraction of aging phenotypes and prevalent genetic interactions with SWR1, with tRNAs emerging as key determinants of its long-lived phenotype. The expression of specific tRNA genes is dysregulated in swr1{Delta} cells, and interactions with tyrosine-decoding tRNA genes are linked to ER proteotoxic stress, suggesting that altered tRNA pools affect proteostasis during aging. These findings establish tRNAs as central mediators of SWR1C-associated longevity, revealing a fundamental connection between chromatin remodeling, RNA biology, and proteostasis stress responses in lifespan regulation.

cell biology↗

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↗

bioRxiv2025

Unveiling the genetic basis of the low pH response in the acidophilic yeast Maudiozyma bulderi as a potential host for biorefinery

Non-conventional yeasts represent a great genetic and phenotypic diversity with potential for industrial strain development in the bio-production of green chemicals. In recent years, mass genome sequencing of non-conventional yeasts has opened avenues to improved understanding of transcriptional networks and phenotypic plasticity and gene function, including the discovery of novel genes. Here, we investigated the expressional and morphological changes at low-pH in three strains of the acidophilic yeast Maudiozyma bulderi (previously Kazachstania bulderi and Saccharomyces bulderi): CBS 8638, CBS 8639 and NRRL Y-27205. The comparison of the transcriptome of cells growing in a bioreactor at pH=5.5 vs pH= 2.5, primarily showed dysregulation of genes involved in cell wall integrity, with NRRL Y-27205 the least acidophilic strain, showing the largest transcriptional response when compared to the other two strains. We identified four uncharacterised genes, unique to M. bulderi, and predicted function as transporters, upregulated at low pH. Microscopy studies showed that M. bulderi cell wall is not damaged in acidic environment, and the membrane lipid composition remains stable at low pH, unlike S. cerevisiae. Overall, our data on transcriptional variability in M. bulderi highlights genes and cellular pathways involved in the acidophilic adaptation of this species and can aid further strain development.

genomics↗

bioRxiv2024

Exploring adaptation routes to low temperatures in the Saccharomyces genus

The identification of traits that affect adaptation of microbial species to external abiotic factors, such as temperature, is key for our understanding of how biodiversity originates and can be maintained in a constantly changing environment. The Saccharomyces genus, which includes eight species with different thermotolerant profiles, represent an ideal experimental platform to study the impact of adaptive alleles in different genetic backgrounds. Previous studies identified a group of genes important for maintenance of growth at lower temperatures. Here, we carried out a genus-wide functional analysis in all eight Saccharomyces species for six candidate genes. We showed that the cold tolerance trait of S. kudriavzevii and S. eubayanus is likely to be evolved from different routes, involving genes important for the conservation of redox-balance, and for the long-chain fatty acid metabolism, respectively. For several loci, temperature- and species-dependent epistasis was detected, underlying the plasticity and complexity of the genetic interactions. The natural isolates of S. kudriavzevii, S. jurei and S. mikatae had a significantly higher expression of the genes involved in the redox balance compared to S. cerevisiae, raising the question of what proportion of the trait is accounted for solely due to transcriptional strength. To tease apart the role of gene expression from that of allelic variation, for two genes we independently replaced in four yeast species either the promoters or the alleles with those derived from S. kudriavzevii. Our data consistently showed a significant fitness improvement at cold temperatures in the strains carrying the S. kudriavzevii promoter, while growth was lower upon allele swapping. These results suggest that transcriptional strength plays a bigger role in growth maintenance at cold over the allele type and supports a model of adaptation centred on stochastic tuning of the expression network. Author summaryThe decline in biodiversity due to environmental changes influences the stability of ecosystems by altering the geographic distribution of several microbial and fungal species. Temperature is one of the leading factors that drive adaptation and different organisms share the same habitat because of their different thermal profiles. It is therefore important to study the genes that affect the fitness of microorganisms at different temperatures in order to understand both how biodiversity originated and how can be maintained. The Saccharomyces genus, which includes species with different thermotolerant profiles, represent an ideal experimental platform to investigate the impact of adaptive alleles in response to temperature changes. Here, we carried out a functional analysis for putative cold-tolerant genes and showed that this trait is likely to be evolved from different routes in different species, involving the conservation of redox-balance and alteration of membrane fluidity. Furthermore, for several species, genetic interactions display fitness tradeoffs in different environments. Finally, by unravelling the interplay between gene expression, allele variation, genetic background and environment, this study shed light on the intricate nature of transcriptional regulation and its pivotal role in facilitating cold adaptation in Saccharomyces species.

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

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

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↗