Biology subjects

Winefield, C.

Publications and source records attributed to Winefield, C..

4 recordsLinked to original sources

bioRxiv2024

Dietary Bioactive Compounds Trigger Distinct Epigenetic and Metabolic Reprogramming in Lactobacillus acidophilus

Lactobacillus acidophilus ATCC 4356 (LA), a key probiotic in the human gut microbiota, offers several health benefits. While dietary bioactive compounds are known to influence gut microbiota, their specific mechanisms remain unclear. This study investigated how certain dietary bioactive compounds impact LA gene expression and metabolism. Results showed each compound produces unique transcriptional, metabolic, proteomic, and epigenetic profiles in LA. Notably, dietary compounds altered the epigenetic landscape through N4-methylcytosine (4mC) modification, a relatively underexplored form of methyl modification that may play a role in regulating gene transcription. For instance, genistein treatment up-regulated 76 genes and the down-regulated 130 genes in LA. A gene involved in mucus-binding proteins, crucial for bacterial adhesion, was up-regulated 38-fold, likely due to 4mC modifications. Additionally, the gene coding for the melibiose operon regulatory protein increased 78-fold, enhancing melibiose (a prebiotic) production with genistein, but only 1.1-fold with sodium butyrate. This study highlights the potential of dietary compounds for microbial metabolic engineering, offering a non-GMO method for modulating bacterial performance and other biotechnology applications. Graphical AbstractDietary compounds are able to modify the epigenetic landscape of Lactobacillus acidophilus ATCC 4356, resulting in significant transcriptomic, metabolic, and physiological changes. This approach differs from conventional genetic modification techniques for manipulating microbial strains. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/608491v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1d1f547org.highwire.dtl.DTLVardef@13e18a3org.highwire.dtl.DTLVardef@1c37e2dorg.highwire.dtl.DTLVardef@190be49_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Reevaluating the Concept of Aging: Long-Term Stress Adaptation as a Key Factor in Yeast Aging

It has been demonstrated that short-term stress can enhance cellular responses and promote longevity, whereas long-term stress shortens lifespan. Understanding the relationship between short-term and long-term stress could offer new insights into comprehending and modulating age-related diseases. In this study, we investigate this relationship using transcriptomic and metabolomic analyses in the yeast model system (Saccharomyces cerevisiae). We employed three metabolic treatments: firstly, treating yeast cells with threshold levels of benzoic acid for 24 hours (Short-term [ST] Stressed Cells); secondly, treating yeast cells with threshold levels of benzoic acid for 500 hours, with sub-culturing every 24 hours (Long-term [LT] Stressed Cells); and thirdly, allowing the long-term stressed cells to grow for 16 hours without any benzoic acid (Recovered Cells). Here, we propose that aging is an evolutionarily conserved cellular adaptation mechanism in response to long-term stress exposure. Under short-term stressed conditions, prominent lifespan-extending metabolites such as trehalose and metabolites linked to tumor suppression in humans, such as 5-methylthioadenosine, were overexpressed. In contrast, LT Stressed Cells activated genes such as those responsible for epigenetic regulatory enzymes that govern the aging process, and secondary stress response genes, such as heat shock proteins (HSPs) which are associated with adaptation to cell damage but also often associated with aged cells. Chronological lifespan experiments showed that LT stressed cells lived a shorter lifespan compared to ST Stressed Cells. This suggests that the markers of aging (eg. HSPs, certain epigenetic regulators) are expressed in response to long-term stress to enable cell survival but have the long-term effect of reducing lifespan. In support of this hypothesis, we also show that genes exclusively activated in ST Stressed Cells are conserved solely in eukaryotes, while those significantly expressed in LT Stressed Cells (aging related) exhibit high conservation across all domains of life, with a majority having originated from bacteria hinting at the potential evolutionary benefit of aging.

cell biology↗

bioRxiv2022

A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

Nicotiana benthamiana is an invaluable model plant and biotechnology platform. To further improve its usefulness and versatility, we have produced high quality chromosome level genome assemblies and multi-omic datasets for both the ubiquitously used LAB strain and a distantly related wild accession, QLD, as well as mapping their single nucleotide polymorphisms with two additional laboratory and four additional wild accessions. LAB and QLD have many genetic, functional, and metabolic differences. These coupled with their high inter-fertility and equally efficient transient and stable transformation and genome editing provide a powerful resource partnership. Their [~]3Gb allotetraploid genomes show advanced diploidisation with major chromosome loss and rearrangement, extensive homoeologous gene loss, and widespread segmental allopolyploidy. Recent bursts of Copia mobility, not seen in other Nicotiana genomes, have probably aided N. benthamianas adaptation to a spectrum of Australian ecologies.

plant biology↗

bioRxiv2022

Epigenetic Changes in Saccharomyces cerevisiae Alters the Aromatic Profile in Alcoholic Fermentation

Epigenetic changes in genomics provide phenotypic modification without DNA sequence alteration. This study shows that benzoic acid, a common food additive and known histone deacetylase inhibitor (HDACi), has an epigenetic effect on Saccharomyces cerevisiae. Benzoic acid stimulated formation of epigenetic histone marks H3K4Me2, H3K27Me2, H3K18ac and H3Ser10p in S. cerevisiae and altered their phenotypic behavior, resulting in increased production of phenylethyl alcohol and ester compounds during alcoholic fermentation. Our study demonstrates the HDACi activity of certain dietary compounds such as sodium butyrate, curcumin and anacardic acid, suggests the potential use of these dietary compounds in altering S. cerevisiae phenotypes without altering host-cell DNA. This study highlights the potential to use common dietary compounds to exploit epigenetic modifications for various fermentation and biotechnology applications as an alternative to genetic modification. These findings indicate that benzoic acid and other food additives may have potential epigenetic effects on human gut microbiota, in which several yeast species are involved. ImportanceThis manuscript investigates and reports for the first time utilizing microbial epigentics to alter the fermentation process of Pinot noir wines. We have experimentally demonstrated that certain dietary epigenetic compounds possess histone deacetylase (HDAC) inhibiting activity and can alter the wine characteristics by altering yeast gene expression. We have coined the term nutrifermentics to represent this newly proposed field of research, which provides insights on the effect of certain dietary compounds on microbial strains and their potential application in fermentation process. This technological approach is a novel way to manipulate microorganisms for innovative food and beverage production with quality attributes.

microbiology↗