The past determines the future: sugar source history and transcriptional memory

Bheda, Poonam; Kirmizis, Antonis; Schneider, Robert

doi:10.1007/s00294-020-01094-8

Cited by 10 publications

(5 citation statements)

References 18 publications

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“…Another important feature of the S. cerevisiae GAL response, which accounts for its environmental adaptability, is its enhanced activation after previous galactose encounter or transcriptional memory (25, 26). In naïve yeast cells, GAL gene induction is slow and inefficient especially at low galactose concentrations.…”

Section: Introductionmentioning

confidence: 99%

Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast

Fita-Torró

Swamy

Pascual-Ahuir

et al. 2023

Preprint

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Optimized nutrient utilization is crucial for the progression of microorganisms in competing communities. Here we investigate how different budding yeast species and ecological isolates have established divergent preferences for two alternative sugar substrates: Glucose, which is fermented preferentially by yeast, and galactose, which is alternatively used upon induction of the relevantGALmetabolic genes. We quantified the dose-dependent induction of theGAL1gene encoding the central galactokinase enzyme, and found that a very large diversification exists between different yeast ecotypes and species. The sensitivity ofGAL1induction correlates with the growth performance of the respective yeasts with the alternative sugar. We further define some of the mechanisms, which have established different glucose/galactose consumption strategies in representative yeast strains by modulating the activity of the Gal3 inducer. (1) Optimal galactose consumers, such asSaccharomyces bayanus, contain a hyperactiveGAL3promoter, sustaining highly sensitiveGAL1expression, which is not further improved upon repetitive galactose encounters. (2) Desensitized galactose consumers, such asS. cerevisiaeY12, contain a less sensitive Gal3 sensor, causing a shift of the galactose response towards higher sugar concentrations even in galactose experienced cells. (3) Galactose insensitive sugar consumers, such asS. cerevisiaeDBVPG6044, contain an interruptedGAL3gene, causing extremely reluctant galactose consumption, which however still is improved upon repeated galactose availability. In summary, different yeast strains and natural isolates have evolved galactose utilization strategies, which cover the whole range of possible sensitivities by modulating the expression and/or activity of the inducible galactose sensor Gal3.

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Section: Introductionmentioning

confidence: 99%

Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast

Fita-Torró

Swamy

Pascual-Ahuir

et al. 2023

Preprint

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“…The critical features of INO1 memory, including interaction with the nuclear pore protein Nup100, histone mark H3K4me2, and binding of poised Pol II at the promoter, are evolutionarily conserved and widespread ( D'Urso and Brickner, 2017 ; Sood et al, 2017 ; Sump et al, 2022 ). Evidence indicates that in yeast GAL memory (galactose-induced transcriptional memory in GAL genes: GAL1 , GAL2 , GAL7 , and GAL10 ), along with other mechanisms, epigenetically inheritable changes such as the incorporation of H2A.Z, H3K4me2, and poised Pol II at the promoter contribute to primed reactivation ( Sood et al, 2017 ; Cerulus et al, 2018 ; Bheda et al, 2020 ). Further, the primed reactivation of oxidative stress-induced genes in yeast previously exposed to high salt concentration requires interaction with nuclear pore protein (Nup42 instead of Nup100) ( Guan et al, 2012 ; D'Urso et al, 2016 ).…”

Section: Transcriptional Memory: Possible Contributor To Late-onset D...mentioning

confidence: 99%

Epigenetic memory contributing to the pathogenesis of AKI-to-CKD transition

Tanemoto

Nangaku

Mimura

2022

Front. Mol. Biosci.

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Epigenetic memory, which refers to the ability of cells to retain and transmit epigenetic marks to their daughter cells, maintains unique gene expression patterns. Establishing programmed epigenetic memory at each stage of development is required for cell differentiation. Moreover, accumulating evidence shows that epigenetic memory acquired in response to environmental stimuli may be associated with diverse diseases. In the field of kidney diseases, the “memory” of acute kidney injury (AKI) leads to progression to chronic kidney disease (CKD); epidemiological studies show that patients who recover from AKI are at high risk of developing CKD. The underlying pathological processes include nephron loss, maladaptive epithelial repair, inflammation, and endothelial injury with vascular rarefaction. Further, epigenetic alterations may contribute as well to the pathophysiology of this AKI-to-CKD transition. Epigenetic changes induced by AKI, which can be recorded in cells, exert long-term effects as epigenetic memory. Considering the latest findings on the molecular basis of epigenetic memory and the pathophysiology of AKI-to-CKD transition, we propose here that epigenetic memory contributing to AKI-to-CKD transition can be classified according to the presence or absence of persistent changes in the associated regulation of gene expression, which we designate “driving” memory and “priming” memory, respectively. “Driving” memory, which persistently alters the regulation of gene expression, may contribute to disease progression by activating fibrogenic genes or inhibiting renoprotective genes. This process may be involved in generating the proinflammatory and profibrotic phenotypes of maladaptively repaired tubular cells after kidney injury. “Priming” memory is stored in seemingly successfully repaired tubular cells in the absence of detectable persistent phenotypic changes, which may enhance a subsequent transcriptional response to the second stimulus. This type of memory may contribute to AKI-to-CKD transition through the cumulative effects of enhanced expression of profibrotic genes required for wound repair after recurrent AKI. Further understanding of epigenetic memory will identify therapeutic targets of future epigenetic intervention to prevent AKI-to-CKD transition.

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“…Eukaryotes, however, exhibit more sophisticated epigenetic regulation of gene expression than prokaryotes (Willbanks et al, 2016). This regulation likely preceded the evolution of multicellularity as single-celled eukaryotic species change their epigenetic states in fluctuating environments without altering genome sequences (Kundu et al, 2007;Payne et al, 2019;Bheda et al, 2020).…”

Section: Epigeneticsmentioning

confidence: 99%

Major Evolutionary Transitions and the Roles of Facilitation and Information in Ecosystem Transformations

et al. 2021

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A small number of extraordinary “Major Evolutionary Transitions” (METs) have attracted attention among biologists. They comprise novel forms of individuality and information, and are defined in relation to organismal complexity, irrespective of broader ecosystem-level effects. This divorce between evolutionary and ecological consequences qualifies unicellular eukaryotes, for example, as a MET although they alone failed to significantly alter ecosystems. Additionally, this definition excludes revolutionary innovations not fitting into either MET type (e.g., photosynthesis). We recombine evolution with ecology to explore how and why entire ecosystems were newly created or radically altered – as Major System Transitions (MSTs). In doing so, we highlight important morphological adaptations that spread through populations because of their immediate, direct-fitness advantages for individuals. These are Major Competitive Transitions, or MCTs. We argue that often multiple METs and MCTs must be present to produce MSTs. For example, sexually-reproducing, multicellular eukaryotes (METs) with anisogamy and exoskeletons (MCTs) significantly altered ecosystems during the Cambrian. Therefore, we introduce the concepts of Facilitating Evolutionary Transitions (FETs) and Catalysts as key events or agents that are insufficient themselves to set a MST into motion, but are essential parts of synergies that do. We further elucidate the role of information in MSTs as transitions across five levels: (I) Encoded; (II) Epigenomic; (III) Learned; (IV) Inscribed; and (V) Dark Information. The latter is ‘authored’ by abiotic entities rather than biological organisms. Level IV has arguably allowed humans to produce a MST, and V perhaps makes us a FET for a future transition that melds biotic and abiotic life into one entity. Understanding the interactive processes involved in past major transitions will illuminate both current events and the surprising possibilities that abiotically-created information may produce.

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The past determines the future: sugar source history and transcriptional memory

Cited by 10 publications

References 18 publications

Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast

Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast

Epigenetic memory contributing to the pathogenesis of AKI-to-CKD transition

Major Evolutionary Transitions and the Roles of Facilitation and Information in Ecosystem Transformations

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