scholarly journals Aspergillus nigercitrate exporter revealed by comparison of two alternative citrate producing conditions

2018 ◽  
Author(s):  
Dorett I Odoni ◽  
Thanaporn Laothanachareon ◽  
Marta Vazquez-Vilar ◽  
Merlijn P van Gaal ◽  
Tom Schonewille ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Aspergillus Niger ◽  
Expression Patterns ◽  
Cell Factory ◽  
Complex Interplay ◽  
Gene Encoding ◽  
Organic Acid Production ◽  
Combining Data ◽  
Citrate Accumulation

AbstractCurrently, there is no consensus regarding the mechanism underlyingAspergillus nigercitrate biosynthesis and secretion, although it is amongst the most studied biotechnological production processes. Carbon excess relative to various other medium constituents is key, but the complex interplay between the limiting factors required for extracellular citrate accumulation remains elusive. It is thought that one of the industrial bottlenecks for citrate production is citrate export, however, noA. nigercitrate exporter has yet been identified. Here, we show that the phenotype of increased extracellular citrate accumulation can have fundamentally different underlying mechanisms, depending on how this response is triggered, and that combining gene expression analyses of the different conditions can lead to the compilation of a shortlist of the most promising citrate exporter candidates. Specifically, we found that varying the amount and type of supplement of an arginine auxotrophicA. nigerstrain shows down-regulation of citrate metabolising enzymes in the condition in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations triggered by iron limitation, which also induces increasedA. nigercitrate production. By combining data obtained from these two manners of inducing comparatively high extracellular citrate accumulation, we were able to compile a shortlist of the most likely citrate transporter candidates. Two of the most promising candidates were tested in the yeastSaccharomyces cerevisiae, one of which showed the ability to secrete citrate. Deletion of the endogenousA. nigergene encoding the corresponding transporter abolished the ability of this fungus to secrete citrate. Instead, under conditions that usually favourA. nigercitrate production, we found increased accumulation of extracellular oxalate. Our findings provide steps in untangling the complex interplay of different mechanisms underlyingA. nigercitrate accumulation, and we identify, for the first time, a fungal citrate exporter, offering a valuable tool for improvement ofA. nigeras biotechnological cell-factory for organic acid production.Author SummaryCitrate is widely applied as acidifier, flavouring and chelating agent. Industrial citrate production currently relies on the filamentous fungusAspergillus niger. Although the industrial production process usingA. niger has vastly improved since initiated almost 100 years ago, citrate export remains a bottleneck. Here, we studied the gene expression pattern ofA. nigerunder various citrate producing conditions. Using these expression patterns and different computational approaches, we compiled a shortlist of putative citrate exporter candidates. In this way, we were able to identify a gene encoding a transporter protein capable of citrate export. We show that the yeastSaccharomyces cerevisiae, normally a citrate non-producer, secretes detectable amounts of citrate when harbouring this gene. In addition, we verify the biological function of this gene inA. nigeritself, as removing this gene resulted in a citrate non-producing phenotype, which is atypical for this fungus. This finding is particularly exciting, as it is the first identification of a eukaryotic citrate exporter. With this, we not only provide a tool for improvement of industrial citrate production, but knowledge of this gene should help develop new methods for improvement ofA. nigeras biotechnological cell-factory for the production of other organic acids.

scholarly journals Mapping global shifts in Saccharomyces cerevisiae gene expression across asynchronous time trajectories with diffusion maps

2021 ◽  
Author(s):  
Taylor Reiter ◽  
Rachel Montpetit ◽  
Ron Runnebaum ◽  
C. Titus Brown ◽  
Ben Montpetit
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Expression Patterns ◽  
Pinot Noir ◽  
Wine Fermentation ◽  
Gene Expression Patterns ◽  
Expression Data ◽  
Site Specific ◽  
Time Series Gene Expression ◽  
Specific Factors

AbstractGrapes grown in a particular geographic region often produce wines with consistent characteristics, suggesting there are site-specific factors driving recurrent fermentation outcomes. However, our understanding of the relationship between site-specific factors, microbial metabolism, and wine fermentation outcomes are not well understood. Here, we used differences in Saccharomyces cerevisiae gene expression as a biosensor for differences among Pinot noir fermentations from 15 vineyard sites. We profiled time series gene expression patterns of primary fermentations, but fermentations proceeded at different rates, making analyzes of these data with conventional differential expression tools difficult. This led us to develop a novel approach that combines diffusion mapping with continuous differential expression analysis. Using this method, we identified vineyard specific deviations in gene expression, including changes in gene expression correlated with the activity of the non-Saccharomyces yeast Hanseniaspora uvarum, as well as with initial nitrogen concentrations in grape musts. These results highlight novel relationships between site-specific variables and Saccharomyces cerevisiae gene expression that are linked to repeated wine fermentation outcomes. In addition, we demonstrate that our analysis approach can extract biologically relevant gene expression patterns in other contexts (e.g., hypoxic response of Saccharomyces cerevisiae), indicating that this approach offers a general method for investigating asynchronous time series gene expression data.ImportanceWhile it is generally accepted that foods, in particular wine, possess sensory characteristics associated with or derived from their place of origin, we lack knowledge of the biotic and abiotic factors central to this phenomenon. We have used Saccharomyces cerevisiae gene expression as a biosensor to capture differences in fermentations of Pinot noir grapes from 15 vineyards across two vintages. We find that gene expression by non-Saccharomyces yeasts and initial nitrogen content in the grape must correlates with differences in gene expression among fermentations from these vintages. These findings highlight important relationships between site-specific variables and gene expression that can be used to understand, or possibly modify, wine fermentation outcomes. Our work also provides a novel analysis method for investigating asynchronous gene expression data sets that is able to reveal both global shifts and subtle differences in gene expression due to varied cell – environment interactions.

scholarly journals Saccharomyces cerevisiae gene expression during fermentation of Pinot noir wines at industrially relevant scale

2021 ◽  
Author(s):  
Taylor Reiter ◽  
Rachel Montpetit ◽  
Shelby Byer ◽  
Isadora Frias ◽  
Esmeralda Leon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Expression Patterns ◽  
Pilot Scale ◽  
Pinot Noir ◽  
Wine Fermentation ◽  
Gene Expression Program ◽  
Gene Expression Patterns ◽  
Grape Must ◽  
Expression Program

Saccharomyces cerevisiae metabolism produces ethanol and other compounds during the fermentation of grape must into wine. Thousands of genes change expression over the course of a wine fermentation, allowing S. cerevisiae to adapt to and dominate the fermentation environment. Investigations into these gene expression patterns have previously revealed genes that underlie cellular adaptation to the grape must and wine environment involving metabolic specialization and ethanol tolerance. However, the majority of studies detailing gene expression patterns have occurred in controlled environments that may not recapitulate the biological and chemical complexity of fermentations performed at production scale. Here, an analysis of the S. cerevisiae RC212 gene expression program is presented, drawing from 40 pilot-scale fermentations (150 liters) using Pinot noir grapes from 10 California vineyards across two vintages. A core gene expression program was observed across all fermentations irrespective of vintage similar to that of laboratory fermentations, in addition to novel gene expression patterns likely related to the presence of non-Saccharomyces microorganisms and oxygen availability during fermentation. These gene expression patterns, both common and diverse, provide insight into Saccharomyces cerevisiae biology critical to fermentation outcomes under industry-relevant conditions. Importance This study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using industry-relevant conditions. The reported gene expression patterns of RC212 are generally similar to that observed in laboratory fermentation conditions, but also contain gene expression signatures related to yeast-environment interactions found in a production setting (e.g., presence of non-Saccharomyces microorganisms). Key genes and pathways highlighted by this work remain under-characterized, raising the need for further research to understand the roles of these genes and their impact on industrial wine fermentation outcomes.

scholarly journals Flavin Mononucleotide-Based Fluorescent Protein as an Oxygen-Independent Reporter in Candida albicans and Saccharomyces cerevisiae

2009 ◽  
Vol 8 (6) ◽  
pp. 913-915 ◽  
Author(s):  
D. Tielker ◽  
I. Eichhof ◽  
K.-E. Jaeger ◽  
J. F. Ernst
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Candida Albicans ◽  
Fluorescent Protein ◽  
Flavin Mononucleotide ◽  
Gene Encoding

ABSTRACT Hypoxia is encountered frequently by pathogenic and apathogenic fungi. A codon-adapted gene encoding flavin mononucleotide-based fluorescent protein (CaFbFP) was expressed in Candida albicans and Saccharomyces cerevisiae. Both species produced CaFbFP and fluoresced even during hypoxia, suggesting that oxygen-independent CaFbFP is a useful, novel tool for monitoring hypoxic gene expression in fungi.

scholarly journals Extracted Trans-Resveratrol from Arachis hypogaea Enhances Expression of Sirtuin Gene and Replicative Life Span in Saccharomyces cerevisiae

2020 ◽  
pp. 48-59
Author(s):  
Mritunjay Kumar Singh ◽  
Ravi Deval
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Aspergillus Niger ◽  
Life Span ◽  
Arachis Hypogaea ◽  
Plant Extract ◽  
Yeast Culture ◽  
Replicative Life Span ◽  
Peanut Plant ◽  
Rp Hplc

Aims: Biotic stress given by Aspergillus niger enhances trans-resveratrol production in Arachis hypogaea plant. This plant extract  increases sir2 gene expression and Replicative Life Span in  Saccharomyces cerevisiae. Design of Study: Peanut plant was grown in aseptic environment, infected by Aspergillus niger. Plant extract used for quantification of trans-resveratrol by RP-HPLC. Yeast culture was grown in Potato dextrose media along with plant extract. Sir2 gene expression fold calculated by real time pcr. Replicative Life Span of yeast was measured by spectrophotometer. Place and Duration of Study: Allele Life Sciences Pvt. Ltd., Department of Biotechnology between February 2017 to March 2020. Methodology: Biotic stress in Arachis hypogaea plant was induced by wounding the leaves and introducing Aspergillus niger to enhance trans-resveratrol production. Tran-resveratrol was quantified by Reverse Phase High Pressure Liquid Chromatography (RP-HPLC). Two methods conducted to check reverse ageing, first one epigenetic based, when extracted trans-resveratrol from infected Arachis hypogaea plant extract added to Saccharomyces cerevisiae culture, it enhanced expression of Sir2 gene in Saccharomyces cerevisiae measured by qPCR, ABI applied biosystem. Process included RNA isolation, cDNA synthesis and thereafter qPCR. Enhanced expression of sirtuin responsible for gene silencing as sirtuin (Sir2 gene product) is a class of Histone deacetylase transferase enzyme. Second method, Replicative Life Span of Saccharomyces cerevisiae culture increased when Aspergillus niger infected peanut plant extract added to yeast culture which was measured through spectrophotometer at 600nm and showed high absorbance value. Results: Tran-resveratrol was quantified by Reverse Phase High Pressure Liquid Chromatography (RP-HPLC) and yield was 2.24 mg/g. Sir2 gene expression increased by 1.56 fold in yeast grown in infected peanut plant extract. Absorbance of yeast culture grown in infected peanut plant extract was 0.522±0.008 which was higher than control. Conclusion: Sir2 gene expression enhances along with replicative life span in yeast in presence of peanut plant extract.

scholarly journals microRNA-138 modulates cardiac patterning during embryonic development

2008 ◽  
Vol 105 (46) ◽  
pp. 17830-17835 ◽  
Author(s):  
Sarah U. Morton ◽  
Paul J. Scherz ◽  
Kimberly R. Cordes ◽  
Kathryn N. Ivey ◽  
Didier Y. R. Stainier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Retinoic Acid ◽  
Embryonic Development ◽  
Expression Patterns ◽  
Acid Synthesis ◽  
Specific Gene ◽  
Protein Activity ◽  
Gene Encoding ◽  
Small Noncoding Rnas ◽  
Discrete Domains

Organ patterning during embryonic development requires precise temporal and spatial regulation of protein activity. microRNAs (miRNAs), small noncoding RNAs that typically inhibit protein expression, are broadly important for proper development, but their individual functions during organogenesis are largely unknown. We report that miR-138 is expressed in specific domains in the zebrafish heart and is required to establish appropriate chamber-specific gene expression patterns. Disruption of miR-138 function led to ventricular expansion of gene expression normally restricted to the atrio-ventricular valve region and, ultimately, to disrupted ventricular cardiomyocyte morphology and cardiac function. Temporal-specific knockdown of miR-138 by antagomiRs showed miR-138 function was required during a discrete developmental window, 24–34 h post-fertilization (hpf). miR-138 functioned partially by repressing the retinoic acid synthesis enzyme, aldehyde dehydrogenase-1a2, in the ventricle. This activity was complemented by miR-138-mediated ventricular repression of the gene encoding versican (cspg2), which was positively regulated by retinoic-acid signaling. Our findings demonstrate that miR-138 helps establish discrete domains of gene expression during cardiac morphogenesis by targeting multiple members of a common pathway, and also establish the use of antagomiRs in fish for temporal knockdown of miRNA function.

scholarly journals Differential Expression of Three α-Galactosidase Genes and a Single β-Galactosidase Gene from Aspergillus niger

1999 ◽  
Vol 65 (6) ◽  
pp. 2453-2460 ◽  
Author(s):  
Ronald P. de Vries ◽  
Hetty C. van den Broeck ◽  
Ester Dekkers ◽  
Paloma Manzanares ◽  
Leo H. de Graaff ◽  
...  
Keyword(s):  
Amino Acids ◽  
Aspergillus Niger ◽  
Signal Sequence ◽  
Expression Patterns ◽  
Carbon Sources ◽  
Gene Encoding ◽  
Calculated Molecular Mass ◽  
Reading Frame ◽  
Polymeric Compounds ◽  
Elevated Expression

ABSTRACT A gene encoding a third α-galactosidase (AglB) fromAspergillus niger has been cloned and sequenced. The gene consists of an open reading frame of 1,750 bp containing six introns. The gene encodes a protein of 443 amino acids which contains a eukaryotic signal sequence of 16 amino acids and seven putative N-glycosylation sites. The mature protein has a calculated molecular mass of 48,835 Da and a predicted pI of 4.6. An alignment of the AglB amino acid sequence with those of other α-galactosidases revealed that it belongs to a subfamily of α-galactosidases that also includesA. niger AglA. A. niger AglC belongs to a different subfamily that consists mainly of prokaryotic α-galactosidases. The expression of aglA,aglB, aglC, and lacA, the latter of which encodes an A. niger β-galactosidase, has been studied by using a number of monomeric, oligomeric, and polymeric compounds as growth substrates. Expression of aglA is only detected on galactose and galactose-containing oligomers and polymers. The aglB gene is expressed on all of the carbon sources tested, including glucose. Elevated expression was observed on xylan, which could be assigned to regulation via XlnR, the xylanolytic transcriptional activator. Expression of aglC was only observed on glucose, fructose, and combinations of glucose with xylose and galactose. High expression of lacA was detected on arabinose, xylose, xylan, and pectin. Similar to aglB, the expression on xylose and xylan can be assigned to regulation via XlnR. All four genes have distinct expression patterns which seem to mirror the natural substrates of the encoded proteins.

scholarly journals Acute Systemic Inflammatory Response Alters Transcription Profile of Genes Related to Immune Response and Ca2+ Homeostasis in Hippocampus; Relevance to Neurodegenerative Disorders

2020 ◽  
Vol 21 (21) ◽  
pp. 7838
Author(s):  
Grzegorz A. Czapski ◽  
Yuhai Zhao ◽  
Walter J. Lukiw ◽  
Joanna B. Strosznajder
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Inflammatory Response ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Systemic Inflammatory Response ◽  
Lipocalin 2 ◽  
Gene Encoding ◽  
Expression Of Genes

Acute systemic inflammatory response (SIR) triggers an alteration in the transcription of brain genes related to neuroinflammation, oxidative stress and cells death. These changes are also characteristic for Alzheimer’s disease (AD) neuropathology. Our aim was to evaluate gene expression patterns in the mouse hippocampus (MH) by using microarray technology 12 and 96 h after SIR evoked by lipopolysaccharide (LPS). The results were compared with microarray analysis of human postmortem hippocampal AD tissues. It was found that 12 h after LPS administration the expression of 231 genes in MH was significantly altered (FC > 2.0); however, after 96 h only the S100a8 gene encoding calgranulin A was activated (FC = 2.9). Gene ontology enrichment analysis demonstrated the alteration of gene expression related mostly to the immune-response including the gene Lcn2 for Lipocalin 2 (FC = 237.8), involved in glia neurotoxicity. The expression of genes coding proteins involved in epigenetic regulation, histone deacetylases (Hdac4,5,8,9,11) and bromo- and extraterminal domain protein Brd3 were downregulated; however, Brd2 was found to be upregulated. Remarkably, the significant increase in expression of Lcn2, S100a8, S100a9 and also Saa3 and Ch25h, was found in AD brains suggesting that early changes of immune-response genes evoked by mild SIR could be crucial in AD pathogenesis.

Evaluation of common gene expression patterns in the rat nervous system

2003 ◽  
Vol 16 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Sergio Kaiser ◽  
Laura K. Nisenbaum
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Transcript Profiling ◽  
Nerve Tissue ◽  
Gene Expression Patterns ◽  
Published Data ◽  
Common Gene ◽  
Neuropsychiatric Diseases ◽  
Combining Data ◽  
Microarray Studies

In the postgenomic era, integrating data obtained from array technologies (e.g., oligonucleotide microarrays) with published information on eukaryotic genomes is beginning to yield biomarkers and therapeutic targets that are key for the diagnosis and treatment of disease. Nevertheless, identifying and validating these drug targets has not been a trivial task. Although a plethora of bioinformatics tools and databases are available, major bottlenecks for this approach reside in the interpretation of vast amounts of data, its integration into biologically representative models, and ultimately the identification of pathophysiologically and therapeutically useful information. In the field of neuroscience, accomplishing these goals has been particularly challenging because of the complex nature of nerve tissue, the relatively small adaptive nature of induced-gene expression changes, as well as the polygenic etiology of most neuropsychiatric diseases. This report combines published data sets from multiple transcript profiling studies that used GeneChip microarrays to illustrate a postanalysis approach for the interpretation of data from neuroscience microarray studies. By defining common gene expression patterns triggered by diverse events (administration of psychoactive drugs and trauma) in different nerve tissues (telencephalic brain areas and spinal cord), we broaden the conclusions derived from each of the original studies. In addition, the evaluation of the identified overlapping gene lists provides a foundation for generating hypotheses relating alterations in specific sets of genes to common physiological processes. Our approach demonstrates the significance of interpreting transcript profiling data within the context of common pathways and mechanisms rather than specific to a given tissue or stimulus. We also highlight the use of gene expression patterns in predictive biology (e.g., in toxicogenomics) as well as the utility of combining data derived from multiple microarray studies that examine diverse biological events for a broader interpretation of data from a particular microarray study.

scholarly journals The Saccharomyces cerevisiae SPT13/GAL11 gene has both positive and negative regulatory roles in transcription.

1989 ◽  
Vol 9 (12) ◽  
pp. 5602-5609 ◽  
Author(s):  
J S Fassler ◽  
F Winston
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Gene Encoding

To understand the function of SPT13, a gene encoding a trans-acting factor involved in regulation of Ty-mediated gene expression, we have cloned and sequenced the gene. Our analysis revealed that SPT13 is the same gene as GAL11, a gene in which mutations cause reduced expression of some GAL4-regulated genes. Further analysis of spt13/gal11 mutants suggested that the SPT13 gene also affects transcription of genes involved in mating-type specialization. We show here that SPT13 has both positive and negative regulatory roles in transcription.

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