scholarly journals Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes

mSystems ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Taylor Reiter ◽  
Rachel Montpetit ◽  
Shelby Byer ◽  
Isadora Frias ◽  
Esmeralda Leon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Environmental Factors ◽  
Ribosomal Dna ◽  
Amplicon Sequencing ◽  
Content Type ◽  
Genetic Signatures ◽  
Insight Into ◽  
Regional Wine ◽  
Grape Musts

ABSTRACT Ribosomal DNA amplicon sequencing of grape musts has demonstrated that microorganisms occur nonrandomly and are associated with the vineyard of origin, suggesting a role for the vineyard, grape, and wine microbiome in shaping wine fermentation outcomes. Here, ribosomal DNA amplicon sequencing from grape musts and RNA sequencing of eukaryotic transcripts from primary fermentations inoculated with the wine yeast Saccharomyces cerevisiae RC212 were used to profile fermentations from 15 vineyards in California and Oregon across two vintages. These data demonstrate that the relative abundance of fungal organisms detected by ribosomal DNA amplicon sequencing correlated with neither transcript abundance from those same organisms within the RNA sequencing data nor gene expression of the inoculated RC212 yeast strain. These data suggest that the majority of the fungi detected in must by ribosomal DNA amplicon sequencing were not active during the primary stage of these inoculated fermentations and were not a major factor in determining RC212 gene expression. However, unique genetic signatures were detected within the ribosomal DNA amplicon and eukaryotic transcriptomic sequencing that were predictive of vineyard site and region. These signatures included S. cerevisiae gene expression patterns linked to nitrogen, sulfur, and thiamine metabolism. These genetic signatures of site offer insight into specific environmental factors to consider with respect to fermentation outcomes and vineyard site and regional wine characteristics. IMPORTANCE The wine industry generates billions of dollars of revenue annually, and economic productivity is in part associated with regional distinctiveness of wine sensory attributes. Microorganisms associated with grapes and wineries are influenced by region of origin, and given that some microorganisms play a role in fermentation, it is thought that microbes may contribute to the regional distinctiveness of wine. In this work, as in previous studies, it is demonstrated that specific bacteria and fungi are associated with individual wine regions and vineyard sites. However, this work further shows that their presence is not associated with detectable fungal gene expression during the primary fermentation or the expression of specific genes by the inoculate Saccharomyces cerevisiae strain RC212. The detected RC212 gene expression signatures associated with region and vineyard site also allowed the identification of flavor-associated metabolic processes and environmental factors that could impact primary fermentation outcomes. These data offer novel insights into the complexities and subtleties of vineyard-specific inoculated wine fermentation and starting points for future investigations into factors that contribute to regional wine distinctiveness.

scholarly journals Transcriptomics provides a genetic signature of vineyard site with insight into vintage-independent regional wine characteristics

2021 ◽  
Author(s):  
Taylor Reiter ◽  
Rachel Montpetit ◽  
Shelby Byer ◽  
Isadora Frias ◽  
Esmeralda Leon ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Ribosomal Dna ◽  
Transcript Abundance ◽  
Amplicon Sequencing ◽  
Sequencing Data ◽  
Fungal Organisms ◽  
Genetic Signatures ◽  
Insight Into ◽  
Regional Wine ◽  
Grape Musts

In wine fermentations, the metabolic activity of both Saccharomyces cerevisiae and non-Saccharomyces organisms impact wine chemistry. Ribosomal DNA amplicon sequencing of grape musts has demonstrated that microorganisms occur non-randomly and are associated with the vineyard of origin, suggesting a role for the vineyard, grape, and wine microbiome in shaping wine fermentation outcomes. We used ribosomal DNA amplicon sequencing of grape must and RNA sequencing of primary fermentations to profile fermentations from 15 vineyards in California and Oregon across two vintages. We find that the relative abundance of fungal organisms detected by ribosomal DNA amplicon sequencing did not correlate with transcript abundance from those organisms within the RNA sequencing data, suggesting that the majority of the fungi detected in must by ribosomal DNA amplicon sequencing are not active during these inoculated fermentations. Additionally, we detect genetic signatures of vineyard site and region during fermentation that are predictive for each vineyard site, identifying nitrogen, sulfur, and thiamine metabolism as important factors for distinguishing vineyard site and region.

scholarly journals Determination of the Global Pattern of Gene Expression in Yeast Cells by Intracellular Levels of Guanine Nucleotides

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Andy Hesketh ◽  
Marta Vergnano ◽  
Stephen G. Oliver
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Carbon Source ◽  
Gene Transcription ◽  
Adenine Nucleotide ◽  
High Energy ◽  
Yeast Cells ◽  
Purine Nucleotides ◽  
Global Pattern ◽  
Content Type

ABSTRACT Correlations between gene transcription and the abundance of high-energy purine nucleotides in Saccharomyces cerevisiae have often been noted. However, there has been no systematic investigation of this phenomenon in the absence of confounding factors such as nutrient status and growth rate, and there is little hard evidence for a causal relationship. Whether transcription is fundamentally responsive to prevailing cellular energetic conditions via sensing of intracellular purine nucleotides, independently of specific nutrition, remains an important question. The controlled nutritional environment of chemostat culture revealed a strong correlation between ATP and GTP abundance and the transcription of genes required for growth. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into S. cerevisiae, permitting analysis of the transcriptional effect of an increased demand for these nucleotides. During steady-state growth using the fermentable carbon source glucose, the futile consumption of ATP led to a decrease in intracellular ATP concentration but an increase in GTP and the guanylate energy charge (GEC). Expression of transcripts encoding proteins involved in ribosome biogenesis, and those controlled by promoters subject to SWI/SNF-dependent chromatin remodelling, was correlated with these nucleotide pool changes. Similar nucleotide abundance changes were observed using a nonfermentable carbon source, but an effect on the growth-associated transcriptional programme was absent. Induction of the GTP-cycling pathway had only marginal effects on nucleotide abundance and gene transcription. The transcriptional response of respiring cells to glucose was dampened in chemostats induced for ATP cycling, but not GTP cycling, and this was primarily associated with altered adenine nucleotide levels. IMPORTANCE This paper investigates whether, independently of the supply of any specific nutrient, gene transcription responds to the energy status of the cell by monitoring ATP and GTP levels. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into the yeast Saccharomyces cerevisiae, and the effect of an increased demand for these purine nucleotides on gene transcription was analyzed. The resulting changes in transcription were most consistently associated with changes in GTP and GEC levels, although the reprogramming in gene expression during glucose repression is sensitive to adenine nucleotide levels. The results show that GTP levels play a central role in determining how genes act to respond to changes in energy supply and that any comprehensive understanding of the control of eukaryotic gene expression requires the elucidation of how changes in guanine nucleotide abundance are sensed and transduced to alter the global pattern of transcription.

scholarly journals Interplay of a Ligand Sensor and an Enzyme in Controlling Expression of the Saccharomyces cerevisiae GAL Genes

2011 ◽  
Vol 11 (3) ◽  
pp. 334-342 ◽  
Author(s):  
Dariusz Abramczyk ◽  
Stacey Holden ◽  
Christopher J. Page ◽  
Richard J. Reece
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Transcriptional Control ◽  
Transcriptional Response ◽  
Content Type ◽  
Considerable Debate ◽  
Active Transcription ◽  
Gal Genes ◽  
The Subject

ABSTRACT The regulation of the Saccharomyces cerevisiae GAL genes in response to galactose as a source of carbon has served as a paradigm for eukaryotic transcriptional control over the last 50 years. Three proteins—a transcriptional activator (Gal4p), an inhibitor (Gal80p), and a ligand sensor (Gal3p)—control the switch between inert and active gene expression. The molecular mechanism by which the recognition of galactose within the cell is converted into a transcriptional response has been the subject of considerable debate. In this study, using a novel and powerful method of localizing active transcription factors within the nuclei of cells, we show that a short-lived complex between Gal4p, Gal80p, and Gal3p occurs soon after the addition of galactose to cells to activate GAL gene expression. Gal3p is subsequently replaced in this complex by Gal1p, and a Gal4p-Gal80p-Gal1p complex is responsible for the continued expression of the GAL genes. The transient role of the ligand sensor indicates that current models for the induction and continued expression of the yeast GAL genes need to be reevaluated.

scholarly journals High-Resolution Genome-Wide Occupancy in Candida spp. Using ChEC-seq

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Faiza Tebbji ◽  
Inès Khemiri ◽  
Adnane Sellam
Keyword(s):  
Public Health ◽  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Candida Albicans ◽  
High Resolution ◽  
Transcriptional Regulator ◽  
Candida Auris ◽  
Content Type ◽  
Genome Wide ◽  
Public Health Threat

ABSTRACT To persist in their dynamic human host environments, fungal pathogens must sense and adapt by modulating their gene expression to fulfill their cellular needs. Understanding transcriptional regulation on a global scale would uncover cellular processes linked to persistence and virulence mechanisms that could be targeted for antifungal therapeutics. Infections associated with the yeast Candida albicans, a highly prevalent fungal pathogen, and the multiresistant related species Candida auris are becoming a serious public health threat. To define the set of a gene regulated by a transcriptional regulator in C. albicans, chromatin immunoprecipitation (ChIP)-based techniques, including ChIP with microarray technology (ChIP-chip) or ChIP-DNA sequencing (ChIP-seq), have been widely used. Here, we describe a new set of PCR-based micrococcal nuclease (MNase)-tagging plasmids for C. albicans and other Candida spp. to determine the genome-wide location of any transcriptional regulator of interest using chromatin endogenous cleavage (ChEC) coupled to high-throughput sequencing (ChEC-seq). The ChEC procedure does not require protein-DNA cross-linking or sonication, thus avoiding artifacts related to epitope masking or the hyper-ChIPable euchromatic phenomenon. In a proof-of-concept application of ChEC-seq, we provided a high-resolution binding map of the SWI/SNF chromatin remodeling complex, a master regulator of fungal fitness in C. albicans, in addition to the transcription factor Nsi1 that is an ortholog of the DNA-binding protein Reb1 for which genome-wide occupancy was previously established in Saccharomyces cerevisiae. The ChEC-seq procedure described here will allow a high-resolution genomic location definition which will enable a better understanding of transcriptional regulatory circuits that govern fungal fitness and drug resistance in these medically important fungi. IMPORTANCE Systemic fungal infections caused by Candida albicans and the “superbug” Candida auris are becoming a serious public health threat. The ability of these yeasts to cause disease is linked to their faculty to modulate the expression of genes that mediate their escape from the immune surveillance and their persistence in the different unfavorable niches within the host. Comprehensive knowledge on gene expression control of fungal fitness is consequently an interesting framework for the identification of essential infection processes that could be hindered by chemicals as potential therapeutics. Here, we expanded the use of ChEC-seq, a technique that was initially developed in the yeast model Saccharomyces cerevisiae to identify genes that are modulated by a transcriptional regulator, in pathogenic yeasts from the genus Candida. This robust technique will allow a better characterization of key gene expression regulators and their contribution to virulence and antifungal resistance in these pathogenic yeasts.

scholarly journals The Epigenetic Pathways to Ribosomal DNA Silencing

2016 ◽  
Vol 80 (3) ◽  
pp. 545-563 ◽  
Author(s):  
Rakesh Srivastava ◽  
Rashmi Srivastava ◽  
Seong Hoon Ahn
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromosome Segregation ◽  
Ribosomal Dna ◽  
Genome Stability ◽  
Cellular Aging ◽  
Content Type ◽  
Eukaryotic Chromatin ◽  
Normal Life Span ◽  
Protein Components ◽  
Dna Silencing

SUMMARYHeterochromatin is the transcriptionally repressed portion of eukaryotic chromatin that maintains a condensed appearance throughout the cell cycle. At sites of ribosomal DNA (rDNA) heterochromatin, epigenetic states contribute to gene silencing and genome stability, which are required for proper chromosome segregation and a normal life span. Here, we focus on recent advances in the epigenetic regulation of rDNA silencing inSaccharomyces cerevisiaeand in mammals, including regulation by several histone modifications and several protein components associated with the inner nuclear membrane within the nucleolus. Finally, we discuss the perturbations of rDNA epigenetic pathways in regulating cellular aging and in causing various types of diseases.

scholarly journals Mitochondrial Genomic Dysfunction Causes Dephosphorylation of Sch9 in the Yeast Saccharomyces cerevisiae

2011 ◽  
Vol 10 (10) ◽  
pp. 1367-1369 ◽  
Author(s):  
Shigeyuki Kawai ◽  
Jörg Urban ◽  
Manuele Piccolis ◽  
Nicolas Panchaud ◽  
Claudio De Virgilio ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Molecular Mechanisms ◽  
Retrograde Signaling ◽  
Yeast Saccharomyces Cerevisiae ◽  
Content Type ◽  
Insight Into

ABSTRACTTORC1-dependent phosphorylation ofSaccharomyces cerevisiaeSch9 was dramatically reduced upon exposure to a protonophore or in respiration-incompetent ρ0cells but not in respiration-incompetentpetmutants, providing important insight into the molecular mechanisms governing interorganellar signaling in general and retrograde signaling in particular.

scholarly journals RNA Sequencing Data Sets Identifying Differentially Expressed Transcripts during Campylobacter jejuni Biofilm Formation

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Greg Tram ◽  
William P. Klare ◽  
Joel A. Cain ◽  
Basem Mourad ◽  
Stuart J. Cordwell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Campylobacter Jejuni ◽  
Biofilm Formation ◽  
Foodborne Pathogen ◽  
Data Sets ◽  
Sequencing Data ◽  
Content Type ◽  
Differential Gene ◽  
Insight Into

Campylobacter jejuni is a foodborne pathogen and an important contributor to gastroenteritis in humans. C. jejuni readily forms biofilms which may play a role in the transmission of the pathogen from animals to humans. Herein, we present RNA sequencing data investigating differential gene expression in biofilm and planktonic C. jejuni. These data provide insight into pathways which may be important to biofilm formation in this organism.

scholarly journals Stenotrophomonas maltophiliaDifferential Gene Expression in Synthetic Cystic Fibrosis Sputum Reveals Shared and Cystic Fibrosis Strain-Specific Responses to the Sputum Environment

2019 ◽  
Vol 201 (15) ◽  
Author(s):  
Graham G. Willsey ◽  
Korin Eckstrom ◽  
Annette E. LaBauve ◽  
Lauren A. Hinkel ◽  
Kristin Schutz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cystic Fibrosis ◽  
Stress Responses ◽  
Metabolic Pathways ◽  
Stenotrophomonas Maltophilia ◽  
Acute Infection ◽  
Survival Strategies ◽  
Transcriptional Responses ◽  
Content Type ◽  
Insight Into

ABSTRACTStenotrophomonas maltophiliais a Gram-negative opportunistic pathogen that can infect the lungs of people with cystic fibrosis (CF). The highly viscous mucus in the CF lung, expectorated as sputum, serves as the primary nutrient source for microbes colonizing this site and induces virulence-associated phenotypes and gene expression in several CF pathogens. Here, we characterized the transcriptional responses of threeS. maltophiliastrains during exposure to synthetic CF sputum medium (SCFM2) to gain insight into how this organism interacts with the host in the CF lung. These efforts led to the identification of 881 transcripts differentially expressed by all three strains, many of which reflect the metabolic pathways used byS. maltophiliain sputum, as well as altered stress responses. The latter correlated with increased resistance to peroxide exposure after pregrowth in SCFM2 for two of the strains. We also compared the SCFM2 transcriptomes of twoS. maltophiliaCF isolates to that of the acute infection strain,S. maltophiliaK279a, allowing us to identify CF isolate-specific signatures in differential gene expression. The expression of genes from the accessory genomes was also differentially altered in response to SCFM2. Finally, a number of biofilm-associated genes were differentially induced in SCFM2, particularly in K279a, which corresponded to increased aggregation and biofilm formation in this strain relative to both CF strains. Collectively, this work details the response ofS. maltophiliato an environment that mimics important aspects of the CF lung, identifying potential survival strategies and metabolic pathways used byS. maltophiliaduring infections.IMPORTANCEStenotrophomonas maltophiliais an important infecting bacterium in the airways of people with cystic fibrosis (CF). However, compared to the other CF pathogens,S. maltophiliahas been relatively understudied. The significance of our research is to provide insight into the global transcriptomic changes ofS. maltophiliain response to a medium that was designed to mimic important aspects of the CF lung. This study elucidates the overall metabolic changes that occur whenS. maltophiliaencounters the CF lung and generates a road map of candidate genes to test usingin vitroandin vivomodels of CF.

Applying the demand-control-support model on burnout in managers and non-managers

2016 ◽  
Vol 9 (1) ◽  
pp. 110-122 ◽  
Author(s):  
Victoria Blom ◽  
Lennart Bodin ◽  
Gunnar Bergström ◽  
Pia Svedberg
Keyword(s):  
Environmental Factors ◽  
Family Environment ◽  
Shared Environment ◽  
Content Type ◽  
Female Managers ◽  
Managerial Status ◽  
And Control ◽  
Demand Control ◽  
Insight Into ◽  
Swedish Twin Registry

Purpose – The purpose of this paper is to study the demand-control-support (DCS) model on burnout in male and female managers and non-managers, taking into account genetic and shared family environmental factors, contributing to the understanding of mechanisms of how and when work stress is related to burnout. Design/methodology/approach – A total of 5,510 individuals in complete same-sex twin pairs from the Swedish Twin Registry were included in the analyses. Co-twin control analyses were performed using linear mixed modeling, comparing between-pairs and within-pair effects, stratified by zygosity and sex. Findings – Managers scored higher on demands and control in their work than non-managers, and female managers seem to be particularly at risk for burnout facing more demands which are not reduced by a higher control as in their male counterparts. Co-twin analyses showed that associations between control and burnout as well as between demands and burnout seem to be affected by shared family environmental factors in male non-managers but not in male managers in which instead the associations between social support and burnout seem to be influenced by shared family environment. Practical implications – Taken together, the study offers knowledge that shared environment as well as sex and managerial status are important factors to consider in how DCS is associated to exhaustion. Originality/value – Using twin data with possibilities to control for genetics, shared environment, sex and age, this study offers unique insight into the DCS research, which focusses primarily on the workplace environment rather than individual factors.

scholarly journals The CCR4 and CAF1 Proteins of the CCR4-NOT Complex Are Physically and Functionally Separated from NOT2, NOT4, and NOT5

1999 ◽  
Vol 19 (10) ◽  
pp. 6642-6651 ◽  
Author(s):  
Yongli Bai ◽  
Christopher Salvadore ◽  
Yueh-Chin Chiang ◽  
Martine A. Collart ◽  
Hai-Yan Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Rna Polymerase Ii ◽  
Genetic Interactions ◽  
Physical Separation ◽  
Amino Acid Region ◽  
Rna Polymerase Ii Holoenzyme ◽  
Insight Into ◽  
Acid Region

ABSTRACT The CCR4-NOT complex (1 mDa in size), consisting of the proteins CCR4, CAF1, and NOT1 to NOT5, regulates gene expression both positively and negatively and is distinct from other large transcriptional complexes in Saccharomyces cerevisiae such as SNF/SWI, TFIID, SAGA, and RNA polymerase II holoenzyme. The physical and genetic interactions between the components of the CCR4-NOT complex were investigated in order to gain insight into how this complex affects the expression of diverse genes and processes. The CAF1 protein was found to be absolutely required for CCR4 association with the NOT proteins, and CCR4 and CAF1, in turn, physically interacted with NOT1 through its central amino acid region from positions 667 to 1152. The NOT3, NOT4, and NOT5 proteins had no significant effect on the association of CCR4, CAF1, and NOT1 with each other. In contrast, the NOT2, NOT4, and NOT5 interacted with the C-terminal region (residues 1490 to 2108) of NOT1 in which NOT2 and NOT5 physically associated in the absence of CAF1, NOT3, and NOT4. These and other data indicate that the physical ordering of these proteins in the complex is CCR4-CAF1-NOT1-(NOT2, NOT5), with NOT4 and NOT3 more peripheral to NOT2 and NOT5. The physical separation of CCR4 and CAF1 from other components of the CCR4-NOT complex correlated with genetic analysis indicating partially separate functions for these two groups of proteins. ccr4or caf1 deletion suppressed the increased 3-aminotriazole resistance phenotype conferred by not mutations, resulted in opposite effects on gene expression as compared to severalnot mutations, and resulted in a number of synthetic phenotypes in combination with not mutations. These results define the CCR4-NOT complex as consisting of at least two physically and functionally separated groups of proteins.

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