Biology subjects

Bähler, J.

Publications and source records attributed to Bähler, J..

9 recordsLinked to original sources

bioRxiv2023

Genetic and environmental determinants of multicellular-like phenotypes in fission yeast

Multicellular fungi have repeatedly given rise to primarily unicellular yeast species. Some of these, including Schizosaccharomyces pombe, are able to revert to multicellular-like phenotypes (MLP). Our bioinformatic analysis of existing data suggested that, besides some regulatory proteins, most proteins involved in MLP formation are not functionally conserved between S. pombe and budding yeast. We developed high-throughput assays for two types of MLP in S. pombe: flocculation and surface adhesion, which correlated in minimal medium, suggesting a common mechanism. Using a library of 57 natural S. pombe isolates, we found MLP formation to widely vary across different nutrient and drug conditions. Next, in a segregant S. pombe library generated from an adhesive natural isolate and the standard laboratory strain, MLP formation correlated with expression levels of the transcription-factor gene mbx2 and several flocculins. Quantitative trait locus mapping of MLP formation located a causal frameshift mutation in the srb11 gene encoding cyclin C, a part of the Cdk8 kinase module (CKM) of the Mediator complex. Other CKM deletions also resulted in MLP formation, consistently through upregulation of mbx2, and only in minimal media. We screened a library of 3721 gene-deletion strains, uncovering additional genes involved in surface adhesion on minimal media. We identified 31 high-confidence hits, including 19 genes that have not been associated with MLPs in fission or budding yeast. Notably, deletion of srb11, unlike deletions of the 31 hits, did not compromise cell growth, which might explain its natural occurrence as a QTL for MLP formation.

genetics↗

bioRxiv2023

Broad functional profiling of fission yeast proteins using phenomics and machine learning

Many proteins remain poorly characterized even in well-studied organisms, presenting a bottleneck for research. We applied phenomics and machine-learning approaches with Schizosaccharomyces pombe for broad cues on protein functions. We assayed colony-growth phenotypes to measure the fitness of deletion mutants for 3509 non-essential genes in 131 conditions with different nutrients, drugs, and stresses. These analyses exposed phenotypes for 3492 mutants, including 124 mutants of priority unstudied proteins conserved in humans, providing varied functional clues. For example, over 900 proteins were newly implicated in the resistance to oxidative stress. Phenotype-correlation networks suggested roles for poorly characterized proteins through guilt by association with known proteins. For complementary functional insights, we predicted Gene Ontology (GO) terms using machine learning methods exploiting protein-network and protein-homology data (NET-FF). We obtained 56,594 high-scoring GO predictions, of which 22,060 also featured high information content. Our phenotype-correlation data and NET-FF predictions showed a strong concordance with existing PomBase GO annotations and protein networks, with integrated analyses revealing 1,675 novel GO predictions for 783 genes, including 47 predictions for 23 priority unstudied proteins. Experimental validation identified new proteins involved in cellular ageing, showing that these predictions and phenomics data provide a rich resource to uncover new protein functions.

genetics↗

bioRxiv2022

Large-scale changes of molecular network states explain complex traits

The complexity of many cellular and organismal traits results from poorly understood mechanisms integrating genetic and environmental factors via molecular networks. Here, we show when and how genetic perturbations lead to molecular changes that are confined to small parts of a network versus when they lead to large-scale adaptations of global network states. Integrating multi-omics profiling of genetically heterogeneous budding and fission yeast strains with an array of cellular traits identified a central state transition of the yeast molecular network that is related to PKA and TOR (PT) signaling. Genetic variants affecting this PT state globally shifted the molecular network along a single-dimensional axis, thereby modulating processes including energy- and amino acid metabolism, transcription, translation, cell cycle control and cellular stress response. We propose that genetic effects can propagate through large parts of molecular networks because of the functional requirement to centrally coordinate the activity of fundamental cellular processes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/519111v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@18d3323org.highwire.dtl.DTLVardef@1185111org.highwire.dtl.DTLVardef@17238c7org.highwire.dtl.DTLVardef@1edc6e6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Genetic variants directly or indirectly affecting the activity of PKA and/or TOR signaling cause global changes of transcriptomic and proteomic network states by modulating the activity of diverse cellular functions and network modules. Using marker genes acting downstream of PKA and TOR signaling we are able to quantify the activity status of combined PKA and TOR signaling (PT Score). This PT Score correlates with major transcriptomic and proteomic changes in response to genetic variability. Those large-scale molecular adaptations correlate with and explain phenotypic consequences for multiple cellular traits. Variants affecting the stoichiometry of proteins within a specific module have regional effects that remain confined to smaller parts of the molecular network. Variants affecting only one or very few proteins change molecular networks only locally. The global reorganization of network states caused by variants of the first type result in consequences for many cellular traits (i.e. pleiotropic effects), such as growth on different carbon sources, stress response, energy metabolism and replicative lifespan. (Created with BioRender.com) C_FIG

systems biology↗

bioRxiv2022

Perturbed fatty-acid metabolism is linked to localized chromatin hyperacetylation, increased stress-response gene expression and resistance to oxidative stress

Oxidative stress is associated with cardiovascular and neurodegenerative diseases, diabetes, cancer, psychiatric disorders and aging. In order to counteract, eliminate and/or adapt to the sources of stress, cells possess elaborate stress-response mechanisms, which also operate at the level of regulating transcription. Interestingly, it is becoming apparent that the metabolic state of the cell and certain metabolites can directly control the epigenetic information and gene expression. In the fission yeast Schizosaccharomyces pombe, the conserved Sty1 stress-activated protein kinase cascade is the main pathway responding to most types of stresses, and regulates the transcription of hundreds of genes via the Atf1 transcription factor. Here we report that fission yeast cells defective in fatty acid synthesis (cbf11, mga2 and ACC/cut6 mutants) show increased expression of a subset of stress-response genes. This altered gene expression depends on Sty1, and the Gcn5 and Mst1 histone acetyltransferases, is associated with increased acetylation of histone H3 at lysine 9 in the corresponding gene promoters, and results in increased cellular resistance to oxidative stress. Since both fatty-acid synthesis and histone acetylation compete for the same substrate, acetyl-CoA, we propose that changes in lipid metabolism can regulate the chromatin and transcription of specific stress-response genes, which in turn might help cells to maintain redox homeostasis.

molecular biology↗

bioRxiv2021

Fission stories: Using PomBase to understand Schizosaccharomyces pombe biology

PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualisation, PomBase also drives innovation in the MOD community.

bioinformatics↗

bioRxiv2020

C. elegans hermaphrodites undergo semelparous reproductive death

Ageing in the nematode Caenorhabditis elegans is unusual in terms of the severity and early onset of senescent pathology, particularly affecting organs involved in reproduction (Ezcurra et al., 2018; Garigan et al., 2002; Herndon et al., 2002). In post-reproductive C. elegans hermaphrodites, intestinal biomass is converted into yolk leading to intestinal atrophy and yolk steatosis (Ezcurra et al., 2018; Sornda et al., 2019). We recently showed that post-reproductive mothers vent yolk which functions as a milk (yolk milk), supporting larval growth that is consumed by larvae (Kern et al., 2020). This form of massive reproductive effort involving biomass repurposing leading to organ degeneration is characteristic of semelparous organisms (i.e. that exhibit only a single reproductive episode) ranging from monocarpic plants to Pacific salmon where it leads to rapid death (reproductive death) (Finch, 1990; Gems et al., 2020). Removal of the germline greatly increases lifespan in both C. elegans and Pacific salmon, in the latter case by suppressing semelparous reproductive death (Hsin and Kenyon, 1999; Robertson, 1961). Here we present evidence that reproductive death occurs in C. elegans, and that it is suppressed by germline removal, leading to extension of lifespan. Comparing three Caenorhabditis sibling species pairs with hermaphrodites and females, we show that lactation and massive early pathology only occurs in the former. In each case, hermaphrodites are shorter lived and only in hermaphrodites does germline removal markedly increase lifespan. Semelparous reproductive death has previously been viewed as distinct from ageing; however, drawing on recent theories of ageing (Blagosklonny, 2006; de Magalhaes and Church, 2005; Maklakov and Chapman, 2019), we argue that it involves exaggerated versions of programmatic mechanisms that to a smaller extent contribute to ageing in non-semelparous species. Thus, despite the presence of reproductive death, mechanisms of ageing in C. elegans are informative about ageing in general.

genetics↗

bioRxiv2020

C. elegans provide milk for their young

Adult C. elegans hermaphrodites exhibit severe senescent pathology that begins to develop within days of reaching sexual maturity (Ezcurra et al., 2018; Garigan et al., 2002; Herndon et al., 2002; Wang et al., 2018). For example, after depletion of self-sperm, intestinal biomass is converted into yolk leading to intestinal atrophy and yolk steatosis (pseudocoelomic lipoprotein pools, PLPs) (Ezcurra et al., 2018; Garigan et al., 2002; Herndon et al., 2002; Sornda et al., 2019). These senescent pathologies are promoted by insulin/IGF-1 signalling (IIS), which also shortens lifespan (Ezcurra et al., 2018; Kenyon, 2010). This pattern of rapid and severe pathology in organs linked to reproduction is reminiscent of semelparous organisms where massive reproductive effort leads to rapid death (reproductive death) as in Pacific salmon (Finch, 1990; Gems et al., 2020). Moreover, destructive conversion of somatic biomass to support reproduction is a hallmark of reproductive death (Gems et al., 2020). Yet arguing against the occurrence of reproductive death in C. elegans is the apparent futility of post-reproductive yolk production. Here we show that this effort is not futile, since post-reproductive mothers vent yolk through their vulva, which is consumed by progeny and supports their growth; thus vented yolk functions as a milk, and C. elegans mothers exhibit a form of lactation. Moreover, IIS promotes lactation, thereby effecting a costly process of resource transfer from postreproductive mothers to offspring. These results support the view that C. elegans hermaphrodites exhibit reproductive death involving a self-destructive process of lactation that is promoted by IIS. They also provide new insight into how the strongly life-shortening effects of IIS in C. elegans evolved.

genetics↗

bioRxiv2019

Temporal Transcriptome and Promoter Architecture ofthe African Swine Fever Virus

The African Swine Fever Virus causes haemorrhagic fever in domestic pigs and presents the biggest global threat to animal farming in recorded history. Despite its importance, very little is known the mechanisms and temporal regulation of transcription in ASFV. Here we report the first detailed viral transcriptome analysis of ASFV during early and late infection of Vero cells. In addition to total RNA sequencing, we have characterised the transcription start sites and transcription termination sites at nucleotide-resolution, revealing the distinct DNA consensus motifs of early and late promoters, as well as the sequence determinants for transcription termination. ASFV can utilise alternative promoters to generate distinct proteins from the same transcription unit that differ with respect to the polypeptide N-terminus. Finally, our results reveal that the ASFV-RNAP undergoes transcript slippage at the 5 end of transcription units that in a promoter sequence-specific manner results in the addition of 5-AT and 5-ATAT tails to mRNAs.

genomics↗

bioRxiv2018

Single-cell phenotyping and RNA sequencing reveal novel patterns of gene expression heterogeneity and regulation during growth and stress adaptation in a unicellular eukaryote

Cell-to-cell variability is central for microbial populations and contributes to cell function, stress adaptation and drug resistance. Gene-expression heterogeneity underpins this variability, but has been challenging to study genome-wide. Here, we report an integrated approach for imaging of individual fission yeast cells followed by single-cell RNA sequencing (scRNA-seq) and novel Bayesian normalisation. We analyse >2000 single cells and >700 matching RNA controls in various environmental conditions and identify sets of highly variable genes. Combining scRNA-seq with cell-size measurements provides unique insights into genes regulated during cell growth and division in single cells, including genes whose expression does not scale with cell size. We further analyse the heterogeneity and dynamics of gene expression during adaptive and acute responses to changing environments. Entry into stationary phase is preceded by a gradual, synchronised adaptation in gene regulation, followed by highly variable gene expression when growth decreases. Conversely, a sudden and acute heat-shock leads to a stronger and coordinated response and adaptation across cells. This analysis reveals that the extent and dynamics of global gene-expression heterogeneity is regulated in response to different physiological conditions within populations of a unicellular eukaryote. In summary, this works illustrates the potential of combined transcriptomics and imaging analysis in single cells to provide comprehensive and unbiased mechanistic understanding of cell-to-cell variability in microbial communities.

genomics↗