Overexpression of Genes of the Cell Wall Stimulon in Clinical Isolates of Staphylococcus aureus Exhibiting Vancomycin-Intermediate- S. aureus-Type Resistance to Vancomycin

ABSTRACT Custom-designed gene chips (Affymetrix) were used to determine genetic relatedness and gene expression profiles in Staphylococcus aureus isolates with increasing MICs of vancomycin that were recovered over a period of several weeks from the blood and heart valve of a patient undergoing extensive vancomycin therapy. The isolates were found to be isogenic as determined by the GeneChip based genotyping approach and thus represented a unique opportunity to study changes in gene expression that may contribute to the vancomycin resistance phenotype. No differences in gene expression were detected between the parent strain, JH1, and JH15, isolated from the nares of a patient contact. Few expression changes were observed between blood and heart valve isolates with identical vancomycin MICs. A large number of genes had altered expression in the late stage JH9 isolate (MIC = 8 μg/ml) compared to JH1 (MIC = 1 μg/ml). Most genes with altered expression were involved in housekeeping functions or cell wall biosynthesis and regulation. The sortase-encoding genes, srtA and srtB, as well as several surface protein-encoding genes were downregulated in JH9. Two hypothetical protein-encoding genes, SAS016 and SA2343, were dramatically overexpressed in JH9. Interestingly, 27 of the genes with altered expression in JH9 grown in drug-free medium were found to be also overexpressed when the parental strain JH1 was briefly exposed to inhibitory concentrations of vancomycin, and more than half (17 of 27) of the genes with altered expression belonged to determinants that were proposed to form part of a general cell wall stress stimulon (S. Utaida et al., Microbiology 149:2719-2732, 2003).

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Formation of Staphylococcus aureus Biofilm in the Presence of Sublethal Concentrations of Disinfectants Studied via a Transcriptomic Analysis Using Transcriptome Sequencing (RNA-seq)

Applied and Environmental Microbiology ◽

10.1128/aem.01643-17 ◽

2017 ◽

Vol 83 (24) ◽

Cited By ~ 12

Author(s):

M. Slany ◽

J. Oppelt ◽

L. Cincarova

Keyword(s):

Gene Expression ◽

Staphylococcus Aureus ◽

Biofilm Formation ◽

Transcriptome Sequencing ◽

Expression Profiles ◽

Bacterial Species ◽

Rna Seq ◽

Altered Expression ◽

Content Type ◽

Sublethal Concentrations

ABSTRACT Staphylococcus aureus is a common biofilm-forming pathogen. Low doses of disinfectants have previously been reported to promote biofilm formation and to increase virulence. The aim of this study was to use transcriptome sequencing (RNA-seq) analysis to investigate global transcriptional changes in S. aureus in response to sublethal concentrations of the commonly used food industry disinfectants ethanol (EtOH) and chloramine T (ChT) and their combination (EtOH_ChT) in order to better understand the effects of these agents on biofilm formation. Treatment with EtOH and EtOH_ChT resulted in more significantly altered expression profiles than treatment with ChT. Our results revealed that EtOH and EtOH_ChT treatments enhanced the expression of genes responsible for regulation of gene expression (sigB), cell surface factors (clfAB), adhesins (sdrDE), and capsular polysaccharides (cap8EFGL), resulting in more intact biofilm. In addition, in this study we were able to identify the pathways involved in the adaptation of S. aureus to the stress of ChT treatment. Further, EtOH suppressed the effect of ChT on gene expression when these agents were used together at sublethal concentrations. These data show that in the presence of sublethal concentrations of tested disinfectants, S. aureus cells trigger protective mechanisms and try to cope with them. IMPORTANCE So far, the effect of disinfectants is not satisfactorily explained. The presented data will allow a better understanding of the mode of disinfectant action with regard to biofilm formation and the ability of bacteria to survive the treatment. Such an understanding could contribute to the effort to eliminate possible sources of bacteria, making disinfectant application as efficient as possible. Biofilm formation plays significant role in the spread and pathogenesis of bacterial species.

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Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase

Microbial Genomics ◽

10.1099/mgen.0.000445 ◽

2020 ◽

Vol 6 (10) ◽

Cited By ~ 1

Author(s):

Domenico Giosa ◽

Maria Rosa Felice ◽

Letterio Giuffrè ◽

Riccardo Aiese Cigliano ◽

Andreu Paytuví-Gallart ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Sporothrix Schenckii ◽

Gene Expression Profiles ◽

Transcriptional Networks ◽

Dimorphic Fungus ◽

Genome Database ◽

Strong Basis ◽

Protein Encoding ◽

Encoding Genes

Sporothrix schenckii is a dimorphic fungus existing as mould in the environment and as yeast in the host. The morphological shift between mycelial/yeast phases is crucial for its virulence, but the transcriptional networks implicated in dimorphic transition are still not fully understood. Here, we report the global transcriptomic differences occurring between mould and yeast phases of S. schenckii, including changes in gene expression profiles associated with these distinct cellular phenotypes. Moreover, we also propose a new genome annotation, which reveals a more complex transcriptional architecture than previously assumed. Using RNA-seq, we identified a total of 17 307 genes, of which 11 217 were classified as protein-encoding genes, whereas 6090 were designated as non-coding RNAs (ncRNAs). Approximately ~71 % of all annotated genes were found to overlap and the different-strand overlapping type was the most common. Gene expression analysis revealed that 8795 genes were differentially regulated among yeast and mould forms. Differential gene expression was also observed for antisense ncRNAs overlapping neighbouring protein-encoding genes. The release of transcriptome-wide data and the establishment of the Sporothrix Genome DataBase (http://sporothrixgenomedatabase.unime.it) represent an important milestone for Sporothrix research, because they provide a strong basis for future studies on the molecular pathways involved in numerous biological processes.

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The Oral Intake of Organic Germanium, Ge-132, Elevates α-Tocopherol Levels in the Plas-ma and Modulates Hepatic Gene Expression Profiles to Promote Immune Activation in Mice

International Journal for Vitamin and Nutrition Research ◽

10.1024/0300-9831/a000205 ◽

2014 ◽

Vol 84 (3-4) ◽

pp. 0183-0195 ◽

Cited By ~ 12

Author(s):

Takashi Nakamura ◽

Tomoya Takeda ◽

Yoshihiko Tokuji

Keyword(s):

Gene Expression ◽

Immune Activation ◽

Expression Profiles ◽

Water Soluble ◽

Alpha Tocopherol ◽

Hepatic Gene Expression ◽

Tocopherol Concentration ◽

Altered Expression ◽

Atp Production ◽

Transfer Protein

The common water-soluble organic germanium compound poly-trans-[(2-carboxyethyl) germasesquioxane] (Ge-132) exhibits activities related to immune responses and antioxidant induction. In this study, we evaluated the antioxidative effect of dietary Ge-132 in the plasma of mice. Male ICR mice (seven mice per group) received an AIN-76 diet with 0.05 % Ge-132; three groups received the Ge-132-containing diet for 0, 1 or 4 days. The plasma alpha-tocopherol (α-tocopherol) concentration increased from 6.85 to 9.60 μg/ml after 4 days of Ge-132 intake (p < 0.05). We evaluated the changes in hepatic gene expression related to antioxidative activity as well as in the entire expression profile after one day of Ge-132 intake, using DNA microarray technology. We identified 1,220 genes with altered expression levels greater than 1.5-fold (increased or decreased) as a result of Ge-132 intake, and α-tocopherol transfer protein (Ttpa) gene expression was increased 1.62-fold. Immune activation was identified as the category with the most changes (containing 60 Gene Ontology (GO) term biological processes (BPs), 41 genes) via functional clustering analysis of altered gene expression. Ge-132 affected genes in clusters related to ATP production (22 GO term BPs, 21 genes), lipid metabolism (4 GO term BPs, 38 genes) and apoptosis (5 GO term BPs). Many GO term BPs containing these categories were significantly affected by the Ge-132 intake. Oral Ge-132 intake may therefore have increased plasma α-tocopherol levels by up-regulating α-tocopherol transfer protein (Ttpa) gene expression.

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Enhanced surface display efficiency of β-glucosidase in Saccharomyces cerevisiae by disruption of cell wall protein-encoding genes YGP1 and CWP2

Biochemical Engineering Journal ◽

10.1016/j.bej.2021.108305 ◽

2021 ◽

pp. 108305

Author(s):

Jantima Arnthong ◽

Jatupong Ponjarat ◽

Piyada Bussadee ◽

Pacharawan Deenarn ◽

Parichat Prommana ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Wall ◽

Surface Display ◽

Cell Wall Protein ◽

Protein Encoding ◽

Encoding Genes ◽

Enhanced Surface

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Dose-response relationships in gene expression profiles in a harbor seal B lymphoma cell line exposed to 17α-ethinyl estradiol

Journal of Xenobiotics ◽

10.4081/xeno.2017.6702 ◽

2017 ◽

Vol 7 (1) ◽

Author(s):

Christine Kleinert ◽

Matthieu Blanchet ◽

François Gagné ◽

Michel Fournier

Keyword(s):

Gene Expression ◽

Cell Line ◽

Ethinyl Estradiol ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Harbor Seal ◽

Lymphoma Cell ◽

Lymphoma Cell Line ◽

Altered Expression ◽

B Lymphoma

The determination of changes in gene expression profiles with xenobiotic dose will allow identifying biomarkers and modes of toxicant action. The harbor seal (Phoca vitulina) 11B7501 B lymphoma cell line was exposed to 1, 10, 100, 1000, 10,000, or 25,000 μg/L 17α-ethinyl estradiol (EE2, the active compound of the contraceptive pill) for 24 h. Following exposure, RNA was extracted and transformed into cDNA. Transcript expression in exposed vs. control lymphocytes was analyzed via RT-qPCR to identify genes with altered expression. Our analysis indicates that gene expression for all but the reference gene varied with dose, suggesting that different doses induce distinct physiological responses. These findings demonstrate that RT-qPCR could be used to identify immunotoxicity and relative dose in harbor seal leukocytes.

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Transcriptome Analysis Unveils the Effects of Proline on Gene Expression in the Yeast Komagataella phaffii

Microorganisms ◽

10.3390/microorganisms10010067 ◽

2021 ◽

Vol 10 (1) ◽

pp. 67

Author(s):

Andrey Rumyantsev ◽

Anton Sidorin ◽

Artemii Volkov ◽

Ousama Al Shanaa ◽

Elena Sambuk ◽

...

Keyword(s):

Gene Expression ◽

Recombinant Proteins ◽

Gene Promoter ◽

Energy Sources ◽

Experimental Conditions ◽

Komagataella Phaffii ◽

Protein Encoding ◽

Modern Biotechnology ◽

Encoding Genes ◽

Transcriptome Level

Komagataella phaffii yeast is one of the most important biocompounds producing microorganisms in modern biotechnology. Optimization of media recipes and cultivation strategies is key to successful synthesis of recombinant proteins. The complex effects of proline on gene expression in the yeast K. phaffii was analyzed on the transcriptome level in this work. Our analysis revealed drastic changes in gene expression when K. phaffii was grown in proline-containing media in comparison to ammonium sulphate-containing media. Around 18.9% of all protein-encoding genes were differentially expressed in the experimental conditions. Proline is catabolized by K. phaffii even in the presence of other nitrogen, carbon and energy sources. This results in the repression of genes involved in the utilization of other element sources, namely methanol. We also found that the repression of AOX1 gene promoter with proline can be partially reversed by the deletion of the KpPUT4.2 gene.

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Effects of Collagen–Glycosaminoglycan Mesh on Gene Expression as Determined by Using Principal Component Analysis-Based Unsupervised Feature Extraction

Polymers ◽

10.3390/polym13234117 ◽

2021 ◽

Vol 13 (23) ◽

pp. 4117

Author(s):

Y-h. Taguchi ◽

Turki Turki

Keyword(s):

Gene Expression ◽

Principal Component Analysis ◽

Feature Extraction ◽

Cell Lines ◽

Time Course ◽

Expression Profiles ◽

Principal Component ◽

Component Analysis ◽

Altered Expression ◽

Unsupervised Feature Extraction

The development of the medical applications for substances or materials that contact cells is important. Hence, it is necessary to elucidate how substances that surround cells affect gene expression during incubation. In the current study, we compared the gene expression profiles of cell lines that were in contact with collagen–glycosaminoglycan mesh and control cells. Principal component analysis-based unsupervised feature extraction was applied to identify genes with altered expression during incubation in the treated cell lines but not in the controls. The identified genes were enriched in various biological terms. Our method also outperformed a conventional methodology, namely, gene selection based on linear regression with time course.

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Transcriptome profiling of aSaccharomyces cerevisiaemutant with a constitutively activated Ras/cAMP pathway

Physiological Genomics ◽

10.1152/physiolgenomics.00139.2003 ◽

2003 ◽

Vol 16 (1) ◽

pp. 107-118 ◽

Cited By ~ 37

Author(s):

D. L. Jones ◽

J. Petty ◽

D. C. Hoyle ◽

A. Hayes ◽

E. Ragni ◽

...

Keyword(s):

Gene Expression ◽

Cell Wall ◽

Microarray Analysis ◽

Cellular Response ◽

Ribosome Biogenesis ◽

Biological Significance ◽

Altered Expression ◽

Wall Functions ◽

Constitutive Activation ◽

Camp Pathway

Often changes in gene expression levels have been considered significant only when above/below some arbitrarily chosen threshold. We investigated the effect of applying a purely statistical approach to microarray analysis and demonstrated that small changes in gene expression have biological significance. Whole genome microarray analysis of a pde2Δ mutant, constructed in the Saccharomyces cerevisiae reference strain FY23, revealed altered expression of ∼11% of protein encoding genes. The mutant, characterized by constitutive activation of the Ras/cAMP pathway, has increased sensitivity to stress, reduced ability to assimilate nonfermentable carbon sources, and some cell wall integrity defects. Applying the Munich Information Centre for Protein Sequences (MIPS) functional categories revealed increased expression of genes related to ribosome biogenesis and downregulation of genes in the cell rescue, defense, cell death and aging category, suggesting a decreased response to stress conditions. A reduced level of gene expression in the unfolded protein response pathway (UPR) was observed. Cell wall genes whose expression was affected by this mutation were also identified. Several of the cAMP-responsive orphan genes, upon further investigation, revealed cell wall functions; others had previously unidentified phenotypes assigned to them. This investigation provides a statistical global transcriptome analysis of the cellular response to constitutive activation of the Ras/cAMP pathway.

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ABA accelerates blackberry (Rubus spp.) fruit ripening by positively affecting ripening-related gene expression and metabolite profiles

Journal of Berry Research ◽

10.3233/jbr-210725 ◽

2021 ◽

pp. 1-16

Author(s):

Chunhong Zhang ◽

Yaqiong Wu ◽

Zhenghao Xiong ◽

Weilin Li ◽

Wenlong Wu ◽

...

Keyword(s):

Gene Expression ◽

Cell Wall ◽

Fruit Ripening ◽

Plant Hormone ◽

Expression Profiles ◽

Related Gene ◽

Commercial Use ◽

Metabolite Profiles ◽

Metabolite Accumulation ◽

Aba Synthesis

BACKGROUND: The softness of blackberry fruits limits their postharvest shelf-life and commercial use, and abscisic acid (ABA) is considered one of the key hormones involved in fruit ripening. OBJECTIVE: This study aimed to explore the underlying physiological and molecular actions of ABA on blackberry fruit ripening and softening. METHODS: Various physiological indices of and plant hormone levels in treated and untreated blackberry fruits were determined simultaneously. The differentially expressed genes (DEGs) were analyzed by RNA-sequencing, and their expression profiles were detected. The ripening mechanism was elucidated by UHPLC-MS using two groups of fruits at 28 d. RESULTS: After 25 d, the ABA concentration and polygalacturonase (PG) and beta-1,4-endoglucanase (EG) activities in ABA-treated fruits were significantly higher than those in untreated fruits. Large differences in the expression profiles were detected at 28 d. The expression of DEGs related to cell wall softening and ABA synthesis was largely triggered after 25 or 28 d. Sixty-nine differentially accumulated metabolites were ultimately annotated as related to fruit ripening. CONCLUSIONS: ABA stimulates blackberry fruit ripening by promoting cell wall enzyme activities, the expression of various ripening-related genes and metabolite accumulation.

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