scholarly journals Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23

2019 ◽  
Author(s):  
Nidhi Shah ◽  
April Gislason ◽  
Michael Becker ◽  
Mark F. Belmonte ◽  
W.G. Dilantha Fernando ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Pseudomonas Chlororaphis ◽  
Phenotypic Analysis ◽  
Promoter Regions ◽  
Altered Expression ◽  
Inhibitory Compounds ◽  
General Metabolism ◽  
Rot Disease

AbstractPseudomonas chlororaphis strain PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungal pathogen Sclerotinia sclerotiorum. PA23 produces several of inhibitory compounds that are under control of a complex regulatory network. Included in this cascade is the PhzRI quorum sensing (QS) system, which plays an essential role in PA23 biocontrol. The focus of the current study was to employ RNA sequencing to explore the spectrum of PA23 genes under QS control. Transcriptomic profiling revealed 545 differentially expressed genes (365 downregulated; 180 upregulated) in the phzR mutant and 534 genes (382 downregulated; 152 upregulated) in the AHL-deficient PA23-6863. In both strains, decreased expression of phenazine, pyrrolnitrin, and exoprotease biosynthetic genes was observed. We have previously reported that QS activates expression of these genes and their encoded products. In addition, elevated siderophore and decreased chitinase gene expression was observed in the QS-deficient stains, which was confirmed by phenotypic analysis. Inspection of the promoter regions revealed the presence of “phz-box” sequences in only 58 of the 807 differentially expressed genes, suggesting that much of the QS regulon is indirectly regulated. Consistent with this notion, 41 transcriptional regulators displayed altered expression in one or both of the QS-deficient strains. Collectively, our findings indicate that QS governs expression of approximately 13% of the PA23 genome affecting diverse functions ranging from secondary metabolite production to general metabolism. To the best of our knowledge, this represents the first global transcriptomic analysis of the QS regulon of a biocontrol pseudomonad.

scholarly journals Assessment of Embryo-Induced Transcriptomic Changes in Hamster Uterus Using RNA-Seq

2018 ◽  
Vol 46 (5) ◽  
pp. 1868-1878 ◽  
Author(s):  
Ming-Yu Huang ◽  
Wen-Qian Zhang ◽  
Miao Zhao ◽  
Can Zhu ◽  
Jia-Peng He ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Embryo Implantation ◽  
Bioinformatic Analysis ◽  
Differentially Expressed ◽  
Implantation Site ◽  
Rna Seq ◽  
Promoter Regions ◽  
Functional Clustering ◽  
Gene Network Analysis ◽  
Transcriptomic Changes

Background/Aims: The mouse is widely used as an animal model for studying human embryo implantation. However, the mouse is unique in that both ovarian progesterone and estrogen are critical to implantation, whereas in the majority of species (e.g. human and hamster) implantation can occur in the presence of progesterone alone. Methods: In this study, we analyzed embryo-induced transcriptomic changes in the hamster uterus during embryo implantation by using RNA-seq. Differentially expressed genes were characterized by bioinformatic analysis. Results: We identified a total of 781 differentially expressed genes, of which 367 genes were up-regulated and 414 genes were down-regulated at the implantation site compared to the inter-implantation site. Functional clustering and gene network analysis highlighted the cell cycle process in uterus upon embryo implantation. By examining of the promoter regions of differentially expressed genes, we identified 7 causal transcription factors. Additionally, through connectivity map (CMap) analysis, multiple compounds were identified to have potential anti-implantation effects due to their ability to reverse embryo-induced transcriptomic changes. Conclusion: Our study provides a valuable resource for in-depth understanding of the mechanism underlying embryo implantation.

scholarly journals A study on regional differences in decidualization of the mouse uterus

Reproduction ◽  
2017 ◽  
Vol 153 (5) ◽  
pp. 645-653 ◽  
Author(s):  
Miao Zhao ◽  
Wen-Qian Zhang ◽  
Ji-Long Liu
Keyword(s):  
Differentially Expressed Genes ◽  
Regional Differences ◽  
Molecular Mechanisms ◽  
Cell Metabolism ◽  
Gene Expression Pattern ◽  
Differentially Expressed ◽  
Hub Genes ◽  
Promoter Regions ◽  
Mouse Uterus ◽  
Region Gene

Although regional differences in mouse decidualization have been recognized for decades, the molecular mechanisms remain understudied. In the present study, by using RNA-seq, we compared transcriptomic differences between the anti-mesometrial (AM) region and the mesometrial (M) region of mouse uterus on day 8 of pregnancy. A total of 1423 differentially expressed genes were identified, of which 811 genes were upregulated and 612 genes were downregulated in the AM region compared to those in the M region. Gene ontology analysis showed that upregulated genes were generally involved in cell metabolism and differentiation, whereas downregulated genes were associated with lymphocyte themes and immune response. Through network analysis, we identified a total of 6 hub genes. These hub genes are likely more important than other genes due to their key positions in the network. We also examined the promoter regions of differentially expressed genes for the enrichment of transcription factor-binding sites. In the end, we demonstrated that a similar regional gene expression pattern can be observed in the artificial decidualization model. Our study contributes to an increase in the knowledge on the molecular mechanisms underlying regional decidualization in mice.

scholarly journals The inducible response of the nematode Caenorhabditis elegans to members of its natural microbiome across development and adult life

2019 ◽  
Author(s):  
W Yang ◽  
C Petersen ◽  
B Pees ◽  
J Zimmermann ◽  
S Waschina ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Metabolic Network ◽  
Differentially Expressed Genes ◽  
Adult Life ◽  
Differentially Expressed ◽  
Promoter Regions ◽  
Data Set ◽  
C Elegans ◽  
Folate Biosynthesis ◽  
Transcriptome Response

AbstractThe biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiome affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematode C. elegans as a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiome. For this study, we focused on two isolates of the genus Ochrobactrum. These bacteria are known to be abundant in the nematode’s microbiome and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general and C. elegans-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiome members on the nematode’s dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes and the affected functions. Our analysis further identified a core set of 86 genes that consistently responded to the microbiome members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network for C. elegans. This analysis complemented the enrichment analyses by revealing an influence of the Ochrobactrum isolates on C. elegans energy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiome isolates on C. elegans life history and thereby provide a framework for further analysis of microbiome-mediated host functions.

Integrated computational analysis revealed hub genes in lung adenocarcinoma

2021 ◽  
Author(s):  
Muhammad Jamal ◽  
Abdul Saboor Khan ◽  
Hina Iqbal Bangash ◽  
Tian Xie ◽  
Tianbao Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Survival Analysis ◽  
Differentially Expressed Genes ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Normal Lung ◽  
Hub Genes ◽  
Altered Expression ◽  
Study Gene Expression

Abstract Background Lung cancer (LUCA) is the leading cause of cancer-related morbidities and mortalities globally. Despite the recent advancements in lung cancer research, understanding of the molecular mechanism underlying LUCA tumorigenesis and prognosis remains suboptimal. This study aims to identify the candidate biomarkers and therapeutic genes in lung cancer. Methods In this study, gene expression profiles of GSE30219, GSE33532, GSE32863 and GSE43458 were downloaded from GEO. The differentially expressed genes (DEGs) in LUAD tissue and normal lung tissue with a p-value < 0.05 and a |log fold change (FC)| >1.0 were identified by GEO2R. For functional enrichment analysis of these DEGs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed with KOBAS and DAVID tools. Next, the candidate hub genes were filtered out with Cytoscape using CytoHubba plugin. These hub genes were validated by (the Cancer Genome Atlas) TCGA-based gene expression analysis, protein-protein network interaction (PPI) analysis, survival analysis. Moreover, the expression of these genes in cancer and normal tissue was assessed in the Human Protein Atlas (HPA) database. In addition, miRNA network of the hub genes was constructed. Finally, DGIdb database was used to check the drug-targeting potentials of the hub genes. Results a total of 332 overlapping differentially expressed genes (DEGs) including 73 upregulated and 259 downregulated, respectively were identified. GO analysis revealed that the DEGs were principally regulating various cancer-associated functions and pathways. The module analysis revealed 55 hub genes in 4 modules. The survival analysis through Kaplan-Meier (KM) plotter indicated that the altered expression of these genes resulted in the poor overall survival (OS) of LUCA patients. Moreover, these genes show a differential expression on both protein and mRNA level in cancer patient compared to the normal. In addition, in addition, 6 potential microRNAs (miRNAs) interacting with hub genes were identified. Finally, a list of 117 therapeutic small molecules was tabulated that could facilitate LUCA treatment. Conclusions the findings of this study may help in the development of novel and reliable biomarkers for diagnosis, prognosis and therapeutic intervention for LUAD.

Effects of breaking up prolonged sitting on skeletal muscle gene expression

2013 ◽  
Vol 114 (4) ◽  
pp. 453-460 ◽  
Author(s):  
Celine Latouche ◽  
Jeremy B. M. Jowett ◽  
Andrew L. Carey ◽  
David A. Bertovic ◽  
Neville Owen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Carbohydrate Metabolism ◽  
Differentially Expressed Genes ◽  
Sedentary Time ◽  
Standardized Test ◽  
Differentially Expressed ◽  
Moderate Intensity ◽  
Altered Expression ◽  
Prolonged Sitting

Breaking up prolonged sitting has been beneficially associated with cardiometabolic risk markers in both observational and intervention studies. We aimed to define the acute transcriptional events induced in skeletal muscle by breaks in sedentary time. Overweight/obese adults participated in a randomized three-period, three-treatment crossover trial in an acute setting. The three 5-h interventions were performed in the postprandial state after a standardized test drink and included seated position with no activity and seated with 2-min bouts of light- or moderate-intensity treadmill walking every 20 min. Vastus lateralis biopsies were obtained in eight participants after each treatment, and gene expression was examined using microarrays validated with real-time quantitative PCR. There were 75 differentially expressed genes between the three conditions. Pathway analysis indicated the main biological functions affected were related to small-molecule biochemistry, cellular development, growth and proliferation, and carbohydrate metabolism. Interestingly, differentially expressed genes were also linked to cardiovascular disease. For example, relative to prolonged sitting, activity bouts increased expression of nicotamide N-methyltransferase, which modulates anti-inflammatory and anti-oxidative pathways and triglyceride metabolism. Activity bouts also altered expression of 10 genes involved in carbohydrate metabolism, including increased expression of dynein light chain, which may regulate translocation of the GLUT-4 glucose transporter. In addition, breaking up sedentary time reversed the effects of chronic inactivity on expression of some specific genes. This study provides insight into the muscle regulatory systems and molecular processes underlying the physiological benefits induced by interrupting prolonged sitting.

scholarly journals A comparison of transcriptomic profiles in endometrium during window of implantation between women with unexplained recurrent implantation failure and recurrent miscarriage

Reproduction ◽  
2017 ◽  
Vol 153 (6) ◽  
pp. 749-758 ◽  
Author(s):  
Jin Huang ◽  
Hao Qin ◽  
Yihua Yang ◽  
Xiaoyan Chen ◽  
Jiamiao Zhang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Recurrent Miscarriage ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Coagulation Cascade ◽  
Support Vector ◽  
Implantation Failure ◽  
Rna Seq ◽  
Recurrent Implantation Failure ◽  
Altered Expression

The endometrium becomes receptive to the embryo only in the mid-luteal phase, but not in the other stages of the menstrual cycle. Endometrial factors play an important role in implantation. Women with recurrent miscarriage and recurrent implantation failure have both been reported to have altered expression of receptivity markers during the window of implantation. We aimed to compare the gene expression profiles of the endometrium in the window of implantation among women with unexplained recurrent implantation failures (RIF) and unexplained recurrent miscarriages (RM) by RNA sequencing (RNA-Seq). In total 20 patients (9 RIF and 11 RM) were recruited. In addition 4 fertile subjects were included as reference. Endometrium samples were precisely timed on the 7th day after luteal hormone surge (LH + 7). All the 24 endometrium samples were extracted for total RNA. The transcriptome was determined by RNA-Seq in the first 14 RNA samples (5 RIF, 6 RM and 3 fertile). Differentially expressed genes between RM and RIF were validated by quantitative real-time PCR (qPCR) in all 24 RNA samples (9 RIF, 11 RM and 4 fertile). Transcriptomic profiles of RM and RIF, but not control samples, were separated from each other by principle component analysis (PCA) and support vector machine (SVM). Complementary and coagulation cascades pathway was significantly up-regulated in RIF while down-regulated in RM. Differentially expressed genes C3, C4, C4BP, DAF, DF and SERPING1 in complement and coagulation cascade pathway between RM and RIF were further validated by qPCR. This study compared endometrial transcriptome among patients with RIF and RM in the window of implantation; it identified differential molecular pathways in endometrium between RIF and RM, which potentially affect the implantation process.

Quorum sensing and the anaerobic regulator (ANR) control Polyhydroxyalkanoate (PHA) production in Pseudomonas chlororaphis PA23

2019 ◽  
Author(s):  
Nisha Mohanan ◽  
April Gislason ◽  
Parveen K Sharma ◽  
Akrm Ghergab ◽  
Jocelyn Plouffe ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Minimal Medium ◽  
Biocontrol Agent ◽  
Antifungal Compounds ◽  
Pseudomonas Chlororaphis ◽  
Promoter Regions ◽  
Consensus Sequences ◽  
Energy Sink ◽  
Pha Production

Abstract Pseudomonas chlororaphis PA23 is a biocontrol agent that, in addition to producing antifungal compounds, synthesizes polyhydroxyalkanoate (PHA) polymers as a carbon and energy sink. Quorum sensing (QS) and the anaerobic regulator (ANR) are required for PA23-mediated fungal suppression; however, the role of these regulators in PHA production is unknown. Strains lacking either QS or ANR accumulated less PHA polymers when propagated on Ramsay's Minimal Medium (RMM) with glucose or octanoate as the carbon source. In the AHL-deficient background, all six of the genes in the pha locus (phaC1, phaC2, phaZ, phaD, phaF, phaI) showed reduced expression in RMM-glucose, and all except phaC2 were repressed in RMM-octanoate. While changes in gene activity were observed in the anr mutant, they were less pronounced. Analysis of the promoter regions for QS- and ANR-binding consensus sequences revealed putative phz-boxes upstream of phaZ and phaI, but no anr-boxes were identified. Our findings indicate that altered pha gene expression likely contributes to the lower PHA accumulation in the QS- and ANR-deficient strains, which may be in part indirectly mediated. This study is the first to show that mcl-PHA production is under QS and ANR control.

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