scholarly journals Transcriptomic Analysis of Staphylococcus xylosus in Solid Dairy Matrix Reveals an Aerobic Lifestyle Adapted to Rind

2020 ◽  
Vol 8 (11) ◽  
pp. 1807
Author(s):  
Sabine Leroy ◽  
Sergine Even ◽  
Pierre Micheau ◽  
Anne de La Foye ◽  
Valérie Laroute ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Antioxidant Enzymes ◽  
Dairy Products ◽  
Molecular Mechanisms ◽  
Iron Acquisition ◽  
Carbon Sources ◽  
Original System ◽  
Staphylococcus Xylosus ◽  
Genes Encoding

Staphylococcus xylosus is found in the microbiota of traditional cheeses, particularly in the rind of soft smeared cheeses. Despite its frequency, the molecular mechanisms allowing the growth and adaptation of S. xylosus in dairy products are still poorly understood. A transcriptomic approach was used to determine how the gene expression profile is modified during the fermentation step in a solid dairy matrix. S. xylosus developed an aerobic metabolism perfectly suited to the cheese rind. It overexpressed genes involved in the aerobic catabolism of two carbon sources in the dairy matrix, lactose and citrate. Interestingly, S. xylosus must cope with nutritional shortage such as amino acids, peptides, and nucleotides, consequently, an extensive up-regulation of genes involved in their biosynthesis was observed. As expected, the gene sigB was overexpressed in relation with general stress and entry into the stationary phase and several genes under its regulation, such as those involved in transport of anions, cations and in pigmentation were up-regulated. Up-regulation of genes encoding antioxidant enzymes and glycine betaine transport and synthesis systems showed that S. xylosus has to cope with oxidative and osmotic stresses. S. xylosus expressed an original system potentially involved in iron acquisition from lactoferrin.

scholarly journals Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Karolina Stępniak ◽  
Magdalena A. Machnicka ◽  
Jakub Mieczkowski ◽  
Anna Macioszek ◽  
Bartosz Wojtaś ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Molecular Mechanisms ◽  
Genome Mapping ◽  
Malignant Gliomas ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Multiple Tumor ◽  
Genes Encoding ◽  
Methylation Patterns

AbstractChromatin structure and accessibility, and combinatorial binding of transcription factors to regulatory elements in genomic DNA control transcription. Genetic variations in genes encoding histones, epigenetics-related enzymes or modifiers affect chromatin structure/dynamics and result in alterations in gene expression contributing to cancer development or progression. Gliomas are brain tumors frequently associated with epigenetics-related gene deregulation. We perform whole-genome mapping of chromatin accessibility, histone modifications, DNA methylation patterns and transcriptome analysis simultaneously in multiple tumor samples to unravel epigenetic dysfunctions driving gliomagenesis. Based on the results of the integrative analysis of the acquired profiles, we create an atlas of active enhancers and promoters in benign and malignant gliomas. We explore these elements and intersect with Hi-C data to uncover molecular mechanisms instructing gene expression in gliomas.

scholarly journals Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes

Genetics ◽  
2019 ◽  
Vol 213 (4) ◽  
pp. 1545-1563 ◽  
Author(s):  
Ramona Lütkenhaus ◽  
Stefanie Traeger ◽  
Jan Breuer ◽  
Laia Carreté ◽  
Alan Kuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruiting Body ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Comparative Transcriptomics ◽  
Fruiting Bodies ◽  
Body Development ◽  
Fruiting Body Development ◽  
Genes Encoding

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora. With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.

scholarly journals Dynamics of Gene Expression Revealed by Comparison of Serial Analysis of Gene Expression Transcript Profiles from Yeast Grown on Two Different Carbon Sources

1999 ◽  
Vol 10 (6) ◽  
pp. 1859-1872 ◽  
Author(s):  
Arnoud J. Kal ◽  
Anton Jan van Zonneveld ◽  
Vladimir Benes ◽  
Marlene van den Berg ◽  
Marian Groot Koerkamp ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adaptive Response ◽  
Carbon Sources ◽  
Differentially Expressed ◽  
Mitochondrial Enzymes ◽  
A Genome ◽  
Redox Shuttles ◽  
Genes Encoding ◽  
Transcript Profiles ◽  
Yeast Genes

We describe a genome-wide characterization of mRNA transcript levels in yeast grown on the fatty acid oleate, determined using Serial Analysis of Gene Expression (SAGE). Comparison of this SAGE library with that reported for glucose grown cells revealed the dramatic adaptive response of yeast to a change in carbon source. A major fraction (>20%) of the 15,000 mRNA molecules in a yeast cell comprised differentially expressed transcripts, which were derived from only 2% of the total number of ∼6300 yeast genes. Most of the mRNAs that were differentially expressed code for enzymes or for other proteins participating in metabolism (e.g., metabolite transporters). In oleate-grown cells, this was exemplified by the huge increase of mRNAs encoding the peroxisomal β-oxidation enzymes required for degradation of fatty acids. The data provide evidence for the existence of redox shuttles across organellar membranes that involve peroxisomal, cytoplasmic, and mitochondrial enzymes. We also analyzed the mRNA profile of a mutant strain with deletions of the PIP2and OAF1 genes, encoding transcription factors required for induction of genes encoding peroxisomal proteins. Induction of genes under the immediate control of these factors was abolished; other genes were up-regulated, indicating an adaptive response to the changed metabolism imposed by the genetic impairment. We describe a statistical method for analysis of data obtained by SAGE.

scholarly journals The Activator of GntII Genes for Gluconate Metabolism, GntH, Exerts Negative Control of GntR-Regulated GntI Genes in Escherichia coli

2003 ◽  
Vol 185 (6) ◽  
pp. 1783-1795 ◽  
Author(s):  
Ryouichi Tsunedomi ◽  
Hanae Izu ◽  
Takuya Kawai ◽  
Kazunobu Matsushita ◽  
Thomas Ferenci ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Cell Growth ◽  
Mutational Analysis ◽  
Carbon Sources ◽  
Negative Control ◽  
Rna Analysis ◽  
Target Sites ◽  
Genes Encoding ◽  
Transcriptional Fusions

ABSTRACT Gluconate is one of the preferred carbon sources of Escherichia coli, and two sets of gnt genes (encoding the GntI and GntII systems) are involved in its transport and metabolism. GntR represses the GntI genes gntKU and gntT, whereas GntH was previously suggested to be an activator for the GntII genes gntV and idnDO-gntWH. The helix-turn-helix residues of the two regulators GntR and GntH exhibit extensive homologies. The similarity between the two regulators prompted analysis of the cross-regulation of the GntI genes by GntH. Repression of gntKU and gntT by GntH, as well as GntR, was indeed observed using transcriptional fusions and RNA analysis. High GntH expression, from cloned gntH or induced through 5-ketogluconate, was required to observe repression of GntI genes. Two GntR-binding elements were identified in the promoter-operator region of gntKU and were also shown to be the target sites of GntH by mutational analysis. However, the GntI genes were not induced by gluconate in the presence of enhanced amounts of GntH, whereas repression by GntR was relieved by gluconate. The repression of GntI genes by GntH is thus unusual in that it is not relieved by the availability of substrate. These results led us to propose that GntH activates GntII and represses the GntI genes in the presence of metabolites derived from gluconate, allowing the organism to switch from the GntI to the GntII system. This cross-regulation may explain the progressive changes in gnt gene expression along with phases of cell growth in the presence of gluconate.

scholarly journals Amino acid limitation regulates gene expression

1999 ◽  
Vol 58 (3) ◽  
pp. 625-632 ◽  
Author(s):  
Alain Bruhat ◽  
Céline Jousse ◽  
Pierre Fafournoux
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Amino Acid ◽  
Molecular Mechanisms ◽  
Binding Protein ◽  
Regulation Of Gene Expression ◽  
Essential Amino Acids ◽  
Mrna Levels ◽  
Dependent Manner ◽  
Control Of Gene Expression

In mammals, the plasma concentration of amino acids is affected by nutritional or pathological conditions. For example, an alteration in the amino acid profile has been reported when there is a deficiency of any one or more of the essential amino acids, a dietary imbalance of amino acids, or an insufficient intake of protein. We examined the role of amino acid limitation in regulating mammalian gene expression. Depletion of arginine, cystine and all essential amino acids leads to induction of insulin-like growth factor-binding protein-1 (IGFBP-1) mRNA and protein expression in a dose-dependent manner. Moreover, exposure of HepG2 cells to amino acids at a concentration reproducing the amino acid concentration found in portal blood of rats fed on a low-protein diet leads to a significantly higher (P < 0·0002) expression of IGFBP-1. Using CCAAT/enhancer-binding protein homologous protein (CHOP) induction by leucine deprivation as a model, we have characterized the molecular mechanisms involved in the regulation of gene expression by amino acids. We have shown that leucine limitation leads to induction of CHOP mRNA and protein. Elevated mRNA levels result from both an increase in the rate of CHOP transcription and an increase in mRNA stability. We have characterized two elements of the CHOP gene that are essential to the transcriptional activation produced by an amino acid limitation. These findings demonstrate that an amino acid limitation, as occurs during dietary protein deficiency, can induce gene expression. Thus, amino acids by themselves can play, in concert with hormones, an important role in the control of gene expression.

scholarly journals Gene Expression Response ofTrichophyton rubrumduring Coculture on Keratinocytes Exposed to Antifungal Agents

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Tatiana Takahasi Komoto ◽  
Tamires Aparecida Bitencourt ◽  
Gabriel Silva ◽  
Rene Oliveira Beleboni ◽  
Mozart Marins ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Citrate Synthase ◽  
Isocitrate Lyase ◽  
Glyoxylate Cycle ◽  
Serine Proteinase ◽  
Gene Expression Response ◽  
Fungal Host ◽  
Host Interaction ◽  
Genes Encoding

Trichophyton rubrumis the most common causative agent of dermatomycoses worldwide, causing infection in the stratum corneum, nails, and hair. Despite the high prevalence of these infections, little is known about the molecular mechanisms involved in the fungal-host interaction, particularly during antifungal treatment. The aim of this work was to evaluate the gene expression ofT. rubrumcocultured with keratinocytes and treated with the flavonoidtrans-chalcone and the glycoalkaloidα-solanine. Both substances showed a marked antifungal activity againstT. rubrumstrain CBS (MIC = 1.15 and 17.8 µg/mL, resp.). Cytotoxicity assay against HaCaT cells produced IC50values of 44.18 totrans-chalcone and 61.60 µM toα-solanine. The interaction of keratinocytes withT. rubrumconidia upregulated the expression of genes involved in the glyoxylate cycle, ergosterol synthesis, and genes encoding proteases but downregulated the ABC transporterTruMDR2 gene. However, both antifungals downregulated the ERG1 and ERG11, metalloprotease 4, serine proteinase, andTruMDR2 genes. Furthermore, thetrans-chalcone downregulated the genes involved in the glyoxylate pathway, isocitrate lyase, and citrate synthase. Considering the urgent need for more efficient and safer antifungals, these results contribute to a better understanding of fungal-host interactions and to the discovery of new antifungal targets.

scholarly journals Global Gene Expression Responses to Cadmium Toxicity in Escherichia coli

2005 ◽  
Vol 187 (9) ◽  
pp. 3259-3266 ◽  
Author(s):  
Anyou Wang ◽  
David E. Crowley
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Ribosomal Proteins ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Cadmium Toxicity ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Temporal Gene Expression ◽  
Genes Encoding

ABSTRACT Genome-wide analysis of temporal gene expression profiles in Escherichia coli following exposure to cadmium revealed a shift to anaerobic metabolism and induction of several stress response systems. Disruption in the transcription of genes encoding ribosomal proteins and zinc-binding proteins may partially explain the molecular mechanisms of cadmium toxicity.

scholarly journals Iron and Fur Regulation in Vibrio cholerae and the Role of Fur in Virulence

2005 ◽  
Vol 73 (12) ◽  
pp. 8167-8178 ◽  
Author(s):  
Alexandra R. Mey ◽  
Elizabeth E. Wyckoff ◽  
Vanamala Kanukurthy ◽  
Carolyn R. Fisher ◽  
Shelley M. Payne
Keyword(s):  
Gene Expression ◽  
Vibrio Cholerae ◽  
Iron Acquisition ◽  
Bacterial Species ◽  
Regulation Of Gene Expression ◽  
Transport Systems ◽  
Infant Mouse ◽  
Genes Encoding ◽  
Regulatory Functions

ABSTRACT Regulation of iron uptake and utilization is critical for bacterial growth and for prevention of iron toxicity. In many bacterial species, this regulation depends on the iron-responsive master regulator Fur. In this study we report the effects of iron and Fur on gene expression in Vibrio cholerae. We show that Fur has both positive and negative regulatory functions, and we demonstrate Fur-independent regulation of gene expression by iron. Nearly all of the known iron acquisition genes were repressed by Fur under iron-replete conditions. In addition, genes for two newly identified iron transport systems, Feo and Fbp, were found to be negatively regulated by iron and Fur. Other genes identified in this study as being induced in low iron and in the fur mutant include those encoding superoxide dismutase (sodA), fumarate dehydratase (fumC), bacterioferritin (bfr), bacterioferritin-associated ferredoxin (bfd), and multiple genes of unknown function. Several genes encoding iron-containing proteins were repressed in low iron and in the fur mutant, possibly reflecting the need to reserve available iron for the most critical functions. Also repressed in the fur mutant, but independently of iron, were genes located in the V. cholerae pathogenicity island, encoding the toxin-coregulated pilus (TCP), and genes within the V. cholerae mega-integron. The fur mutant exhibited very weak autoagglutination, indicating a possible defect in expression or assembly of the TCP, a major virulence factor of V. cholerae. Consistent with this observation, the fur mutant competed poorly with its wild-type parental strain for colonization of the infant mouse gut.

scholarly journals CtaM Is Required for Menaquinol Oxidaseaa3Function inStaphylococcus aureus

mBio ◽  
2016 ◽  
Vol 7 (4) ◽  
Author(s):  
Neal D. Hammer ◽  
Lici A. Schurig-Briccio ◽  
Svetlana Y. Gerdes ◽  
Robert B. Gennis ◽  
Eric P. Skaar
Keyword(s):  
Staphylococcus Aureus ◽  
Electron Transport ◽  
Electron Transport Chain ◽  
Molecular Mechanisms ◽  
Carbon Sources ◽  
Spectroscopic Studies ◽  
Uncharacterized Protein ◽  
Terminal Oxidases ◽  
Transport Chain ◽  
Genes Encoding

ABSTRACTStaphylococcus aureusis the leading cause of skin and soft tissue infections, bacteremia, osteomyelitis, and endocarditis in the developed world. The ability ofS. aureusto cause substantial disease in distinct host environments is supported by a flexible metabolism that allows this pathogen to overcome challenges unique to each host organ. One feature of staphylococcal metabolic flexibility is a branched aerobic respiratory chain composed of multiple terminal oxidases. Whereas previous biochemical and spectroscopic studies reported the presence of three different respiratory oxygen reductases (otype,bdtype, andaa3type), the genome contains genes encoding only two respiratory oxygen reductases,cydABandqoxABCD. Previous investigation showed thatcydABandqoxABCDare required to colonize specific host organs, the murine heart and liver, respectively. This work seeks to clarify the relationship between the genetic studies showing the unique roles of thecydABandqoxABCDin virulence and the respiratory reductases reported in the literature. We establish that QoxABCD is anaa3-type menaquinol oxidase but that this enzyme is promiscuous in that it can assemble as abo3-type menaquinol oxidase. However, thebo3form of QoxABCD restricts the carbon sources that can support the growth ofS. aureus. In addition, QoxABCD function is supported by a previously uncharacterized protein, which we have named CtaM, that is conserved in aerobically respiringFirmicutes. In total, these studies establish the heme A biosynthesis pathway inS. aureus, determine that QoxABCD is a typeaa3menaquinol oxidase, and reveal CtaM as a new protein required for typeaa3menaquinol oxidase function in multiple bacterial genera.IMPORTANCEStaphylococcus aureusrelies upon the function of two terminal oxidases, CydAB and QoxABCD, to aerobically respire and colonize distinct host tissues. Previous biochemical studies support the conclusion that a third terminal oxidase is also present. We establish the components of theS. aureuselectron transport chain by determining the heme cofactors that interact with QoxABCD. This insight explains previous observations by revealing that QoxABCD can utilize different heme cofactors and confirms that the electron transport chain ofS. aureusis comprised of two terminal menaquinol oxidases. In addition, a newly identified protein, CtaM, is found to be required for the function of QoxABCD. These results provide a more complete assessment of the molecular mechanisms that support staphylococcal respiration.

scholarly journals Overexpression of Barley Transcription Factor HvERF2.11 in Arabidopsis Enhances Plant Waterlogging Tolerance

2020 ◽  
Vol 21 (6) ◽  
pp. 1982
Author(s):  
Haiye Luan ◽  
Baojian Guo ◽  
Huiquan Shen ◽  
Yuhan Pan ◽  
Yi Hong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Transcription Factor ◽  
Antioxidant Enzymes ◽  
Transgenic Plants ◽  
Waterlogging Tolerance ◽  
Waterlogging Stress ◽  
Ethylene Responsive Factor ◽  
Growth Development ◽  
Do So

Waterlogging stress significantly affects the growth, development, and productivity of crop plants. However, manipulation of gene expression to enhance waterlogging tolerance is very limited. In this study, we identified an ethylene-responsive factor from barley, which was strongly induced by waterlogging stress. This transcription factor named HvERF2.11 was 1158 bp in length and encoded 385 amino acids, and mainly expressed in the adventitious root and seminal root. Overexpression of HvERF2.11 in Arabidopsis led to enhanced tolerance to waterlogging stress. Further analysis of the transgenic plants showed that the expression of AtSOD1, AtPOD1 and AtACO1 increased rapidly, while the same genes did not do so in non-transgenic plants, under waterlogging stress. Activities of antioxidant enzymes and alcohol dehydrogenase (ADH) were also significantly higher in the transgenic plants than in the non-transgenic plants under waterlogging stress. Therefore, these results indicate that HvERF2.11 plays a positive regulatory role in plant waterlogging tolerance through regulation of waterlogging-related genes, improving antioxidant and ADH enzymes activities.

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