scholarly journals mRNA Transcript Analysis of Hypothesis-driven Pathways as Known Responders to Organophosphate Exposure: Rhinella Arenarum Larvae Transcriptome Study

2022 ◽  
Author(s):  
Natalia Pires ◽  
Cecilia Lascano ◽  
Danilo Ceschin ◽  
Andrés Venturino
Keyword(s):  
Organophosphorus Pesticides ◽  
A Priori ◽  
Housekeeping Genes ◽  
Antioxidant Response ◽  
Transcriptional Analysis ◽  
Polyamine Metabolism ◽  
Transcriptional Level ◽  
Regulatory Pathways ◽  
Azinphos Methyl ◽  
Rhinella Arenarum

Abstract Transcriptional analysis of the network of transcription regulators and target pathways in exposed organisms may be a hard task when their genome remains unknown. We used a whole transcriptome study on Rhinella arenarum larvae exposed to the organophosphorus pesticides azinphos-methyl and chlorpyrifos to evaluate transcriptional effects on a priori selected groups of genes. This approach allowed us to evaluate the effects on hypothesis-selected pathways such as target esterases, detoxifying enzymes, polyamine metabolism and signaling and regulatory pathways modulating them. We could then compare the responses at the transcriptional level with previously described effects at the enzymatic or metabolic levels to obtain global insight into toxicity-response mechanisms. The effects of both pesticides on the transcript levels of these pathways could be considered moderate, while the responses elicited by chlorpyrifos were more potent and earlier than those elicited by azinphos-methyl. Finally, we infer a prevailing downregulation effect of pesticides on signaling pathways and transcription factor transcripts encoding products that modulate/control the polyamine and antioxidant response pathways. We additionally tested and selected potential housekeeping genes based on those reported for other species. These results allow us to go through future confirmatory studies on pesticide gene expression modulation in toad larvae.

scholarly journals Eugenol Reduces the Expression of Virulence-Related Exoproteins in Staphylococcus aureus

2010 ◽  
Vol 76 (17) ◽  
pp. 5846-5851 ◽  
Author(s):  
Jiazhang Qiu ◽  
Haihua Feng ◽  
Jing Lu ◽  
Hua Xiang ◽  
Dacheng Wang ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Transcriptional Analysis ◽  
Pcr Analysis ◽  
Transcriptional Level ◽  
Toxic Shock ◽  
Release Assay ◽  
Subinhibitory Concentrations ◽  
Toxic Shock Syndrome Toxin ◽  
Culture Supernatants ◽  
Necrosis Factor

ABSTRACT Eugenol, an essential oil component in plants, has been demonstrated to possess activity against both Gram-positive and Gram-negative bacteria. This study examined the influence that subinhibitory concentrations of eugenol may have on the expression of the major exotoxins produced by Staphylococcus aureus. The results from a tumor necrosis factor (TNF) release assay and a hemolysin assay indicated that S. aureus cultured with graded subinhibitory concentrations of eugenol (16 to 128 μg/ml) dose dependently decreased the TNF-inducing and hemolytic activities of culture supernatants. Western blot analysis showed that eugenol significantly reduced the production of staphylococcal enterotoxin A (SEA), SEB, and toxic shock syndrome toxin 1 (the key exotoxins to induce TNF release), as well as the expression of α-hemolysin (the major hemolysin to cause hemolysis). In addition, this suppression was also evaluated at the transcriptional level via real-time reverse transcription (RT)-PCR analysis. The transcriptional analysis indicated that 128 μg/ml of eugenol remarkably repressed the transcription of the S. aureus sea, seb, tst, and hla genes. According to these results, eugenol has the potential to be rationally applied on food products as a novel food antimicrobial agent both to inhibit the growth of bacteria and to suppress the production of exotoxins by S. aureus.

DEP-induced fra-1 expression correlates with a distinct activation of AP-1-dependent gene transcription in the lung

2004 ◽  
Vol 286 (2) ◽  
pp. L427-L436 ◽  
Author(s):  
Qin Zhang ◽  
Steven R. Kleeberger ◽  
Sekhar P. Reddy
Keyword(s):  
Gene Expression ◽  
Epithelial Cell ◽  
Dna Binding ◽  
Promoter Activity ◽  
Cellular Transformation ◽  
Diesel Exhaust Particles ◽  
Transcriptional Analysis ◽  
Epithelial Cell Line ◽  
Transcriptional Level ◽  
Jun B

Recent studies indicate a potential role for Fra-1, a heterodimeric partner of activator protein (AP)-1, in toxicant-induced epithelial injury, repair, and cellular transformation. Here we have investigated the effects of diesel exhaust particles (DEP) on fra-1 expression in C10 cells, a murine lung epithelial cell line. DEP markedly upregulated fra-1, but not fra-2, expression. The increase in fra-1 mRNA expression correlated well with its protein- and DNA-binding activity. DNA-binding assays also revealed a predominant presence of Jun-B and Jun-D in the AP-1 complex. Interestingly, DEP did not alter Jun-B and Jun-D protein levels. Transcriptional analysis revealed that fra-1 induction is regulated in part at the transcriptional level. The -379 to +32 bp 5′-flanking region mediated this induction. Furthermore, inhibitors of ERK1/2, JNK1, and p38 mitogen-activated protein kinases (MAPKs) significantly suppressed DEP-stimulated fra-1 transcription, suggesting their involvement in the induction process. Consistent with this finding, DEP stimulated phosphorylation of ERK1/2, JNK1, and p38 MAPKs with a distinct activation pattern. Overexpression of Fra-1 downregulated c-Jun and Nrf2 enhanced AP-1- and ARE-mediated reporter gene expression, respectively. In contrast, Fra-1 had the opposite effect on matrix metalloproteinase (MMP)-9 promoter activity. In particular, it bound to the functional AP-1 site of the MMP-9 promoter after DEP stimulation. Consistent with this result, DEP also markedly upregulated MMP-9 promoter activity. Collectively, these findings suggest that fra-1 induction by DEP may play a role in selectively regulating gene expression involved in alveolar epithelial cell injury and repair.

scholarly journals Genome-Wide Gene Expression Analysis of Pseudomonas syringae pv. tomato DC3000 Reveals Overlapping and Distinct Pathways Regulated by hrpL and hrpRS

2006 ◽  
Vol 19 (9) ◽  
pp. 976-987 ◽  
Author(s):  
Lefu Lan ◽  
Xin Deng ◽  
Jianmin Zhou ◽  
Xiaoyan Tang
Keyword(s):  
Pseudomonas Syringae ◽  
Housekeeping Genes ◽  
The Novel ◽  
Tomato Dc3000 ◽  
Regulatory Pathways ◽  
Genome Wide ◽  
Genes Encoding ◽  
Substrate Proteins ◽  
Genome Wide Gene Expression ◽  
Insight Into

Pseudomonas syringae pv. tomato DC3000 is a model pathogen infecting tomato and Arabidopsis plants. Genes encoding the type III secretion system and substrate proteins (collectively called TTSS genes) of this bacterium are induced in plants and in minimal medium (MM). The induction of TTSS genes is mediated by HrpL, an alternative sigma factor recognizing the hrp box in the promoter of TTSS genes. The transcription of hrpL is activated by HrpR and HrpS, two homologous DNA-binding proteins encoded by the hrpRS operon. Microarray analysis was conducted to evaluate the DC3000 genes regulated by hrpL and hrpRS in MM. The analysis identified a number of novel hrpL-activated genes with a putative TTSS-independent function. Genes regulated by hrpL were mostly regulated by hrpRS in the same manner, but a large number of genes regulated by hrpRS were hrpL-independent, indicating that hrpL represents one branch of the regulatory pathways downstream of hrpRS. The induction of the TTSS genes was associated with downregulation of the housekeeping genes, indicating that the activation of the TTSS has a cost on the basic cellular activities. The novel genes and pathways identified by the microarray provide new insight into the bacterial functions coordinating with the TTSS.

scholarly journals Genome-wide transcriptomic analysis of n-caproic acid production in Ruminococcaceae bacterium CPB6 with lactate supplementation

2020 ◽  
Author(s):  
Yong Tao ◽  
Shaowen Lu ◽  
Yi Wang ◽  
Cuicui Wei ◽  
Hong Jin ◽  
...  
Keyword(s):  
Stationary Phases ◽  
Expression Patterns ◽  
Caproic Acid ◽  
Transcriptional Analysis ◽  
Chain Elongation ◽  
Transcriptional Level ◽  
Phosphotransferase System ◽  
Oxidation Pathway ◽  
Genome Wide ◽  
Genes Encoding

Abstract Background n-Caproic acid (CA) is gaining increased attention due to its high value as a chemical feedstock. Ruminococcaceae bacterium strain CPB6 is an anaerobic mesophilic bacterium that is highly prolific in its ability to perform chain elongation of lactate to CA. However, little is known about the genome-wide transcriptional analysis of strain CPB6 for CA production triggered by the supplementation of exogenous lactate. Results In this study, 0.5% lactate was supplemented into the fermentation with Ruminococcaceae bacterium CPB6 for CA production. Compared to the control (without lactate supplementation), lactate supplementation led to earlier CA production and higher final CA titer and productivity. Transcriptional analysis was carried out using RNA-Seq for the culture with and without lactate supplementation (two groups) at growth and stationary phases, respectively. It has been indicated that 295 genes whose changes in expression patterns were substrate and/or growth dependent. These genes cover crucial functional categories. Specifically, 5 genes responsible for the reverse β-oxidation pathway, 11 genes encoding ATP-binding cassette (ABC) transporters, 6 genes encoding substrate-binding protein (SBP) and 4 genes encoding phosphotransferase system (PTS) transporters were strikingly upregulated in response to the addition of lactate. These genes would be candidates for future studies aiming at understanding the regulatory mechanism of lactate conversion into CA, as well as for the improvement of CA production in strain CPB6. Conclusions This study suggested that lactate supplementation can promote CA production by altering the expression patterns of genes involved in the essential metabolic pathways, such as central pyruvate metabolism, the reverse β-oxidation pathway, ABC and PTS transports. The findings presented herein reveal unique insights into the biomolecular effects of lactate on CA production at the gene transcriptional level.

scholarly journals Molecular Genetic Basis of Ribotyping

2008 ◽  
Vol 21 (2) ◽  
pp. 262-273 ◽  
Author(s):  
Valérie Bouchet ◽  
Heather Huot ◽  
Richard Goldstein
Keyword(s):  
Genetic Basis ◽  
Fragment Length Polymorphism ◽  
A Priori ◽  
Molecular Genetic ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Sequence Variability ◽  
Gene Sequences ◽  
Molecular Genetic Basis ◽  
Pcr Ribotyping

SUMMARY Nearly 2,000 ribotyping-based studies exist, ranging from epidemiology to phylogeny and taxonomy. None precisely reveals the molecular genetic basis, with many incorrectly attributing detected polymorphisms to rRNA gene sequences. Based on in silico genomics, we demonstrate that ribotype polymorphisms result from sequence variability in neutral housekeeping genes flanking rRNA operons, with rRNA gene sequences serving solely as conserved, flank-linked tags. We also reveal that from such an informatics perspective, it is readily feasible a priori to design an interpretable ribotyping scheme for a genomically sequenced microbial species, and we discuss limitations to the basic restriction fragment length polymorphism-based method as well as alternate PCR ribotyping-based schemes.

scholarly journals Transcriptional Analysis of Major Heat Shock Genes of Helicobacter pylori

2000 ◽  
Vol 182 (15) ◽  
pp. 4257-4263 ◽  
Author(s):  
Georg Homuth ◽  
Stephanie Domm ◽  
Diethelm Kleiner ◽  
Wolfgang Schumann
Keyword(s):  
Helicobacter Pylori ◽  
Heat Shock ◽  
Transcriptional Analysis ◽  
Transcriptional Level ◽  
Heat Shock Genes ◽  
Induction Kinetic ◽  
H Pylori ◽  
Bicistronic Mrna

ABSTRACT The transcriptional organization and heat inducibility of the major heat shock genes hrcA, dnaK, dnaJ,groEL, and htpG were analyzed on the transcriptional level in Helicobacter pylori strain 69A. The strongly heat-induced dnaK operon was found to be tricistronic, consisting of the genes hrcA,grpE, and dnaK. The dnaJ gene specified one monocistronic mRNA which was also heat inducible. The genes groES and groEL were transcribed as one strongly heat-inducible bicistronic mRNA which exhibited exactly the same induction kinetic as the dnaK operon. Surprisingly, transcription of the monocistronic htpG gene was switched off after heat shock. The data presented are discussed with regard to the different mechanisms regulating expression of heat shock genes inH. pylori

scholarly journals Proteomic and Transcriptomic Analysis of Extracellular Proteins and mRNA Levels in Thermobifida fusca Grown on Cellobiose and Glucose

2007 ◽  
Vol 189 (17) ◽  
pp. 6260-6265 ◽  
Author(s):  
Shaolin Chen ◽  
David B. Wilson
Keyword(s):  
Cell Wall ◽  
Plant Cell Wall ◽  
Extracellular Proteins ◽  
Transcriptional Analysis ◽  
Thermobifida Fusca ◽  
Transcriptional Level ◽  
Mrna Levels ◽  
Egg White Lysozyme ◽  
Extracellular Proteome ◽  
Genes Encoding

ABSTRACT Thermobifida fusca secretes proteins that carry out plant cell wall degradation. Using two-dimensional electrophoresis, the extracellular proteome of T. fusca grown on cellobiose was compared to that of cells grown on glucose. Extracellular proteins, the expression of which is induced by cellobiose, mainly are cellulases and cellulose-binding proteins. Other major extracellular proteins induced by cellobiose include a xylanase (Xyl10A) and two unknown proteins, the C-terminal regions of which are homologous to a lytic transglycosylase goose egg white lysozyme domain and an NLPC_P60 domain (which defines a family of cell wall peptidases), respectively. Transcriptional analysis of genes encoding cellobiose-induced proteins suggests that their expression is controlled at the transcriptional level and that their expression also is induced by cellulose. Some other major extracellular proteins produced by T. fusca grown on both cellobiose and glucose include Lam81A and three unknown proteins that are homologous to aminopeptidases and xylanases or that contain a putative NLPC_P60 domain.

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