scholarly journals Transcriptome analysis of Xanthomonas oryzae pv. oryzicola exposed to H2O2 reveals horizontal gene transfer contributes to its oxidative stress response

2019 ◽  
Author(s):  
Yuan Fang ◽  
Haoye Wang ◽  
Xia Liu ◽  
Yuchun Rao ◽  
Xin Dedong ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Time Series ◽  
Stress Response ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Oxidative Stress Response ◽  
Xanthomonas Oryzae ◽  
Gene Location ◽  
Rna Seq

AbstractXanthomonas oryzae pv. oryzicola (Xoc) is the causal agent of bacterial leaf streak in rice. It is known as one of the most severe seed-born bacterial diseases of rice, molecular role governing its interaction with rice is mostly still unexplored. To successfully invade rice, the survival of the Xoc is mandotarory following generating a specific response to its host’s oxidative stress condition. However, the response network of Xoc is still unknown. To address this question, we performed a time-series RNA-seq analysis on the Xoc response to H2O2. Overall, our RNA sequence analysis of Xoc revealed a significant global gene expression profile when it exposed to H2O2. The response of key genes was also noted that soxR triggers and regulates the Xoc oxidative stress response in the early stage of infection, gene expression kinetics among the time-series samples, namely for TonB-dependent receptors and the suf and pst operons. Moreover, a hypothetical protein (XOC_2868) showed significant differential expression following its mutant endorsed RNA-seq findings by clearly displaying a greater H2O2 sensitivity and decreased pathogenicity than the wild-type. Gene location and phylogeny analysis strongly suggests that this gene may have been horizontally transferred from a Burkholderiaceae ancestor. Our study not only provides a first glance of Xoc’s global response against oxidative stress, but it also reveals the impact of horizontal gene transfer in the evolutionary history of Xoc.

scholarly journals Meta-Analysis of Oxidative Transcriptomes in Insects

Antioxidants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 345
Author(s):  
Hidemasa Bono
Keyword(s):  
Oxidative Stress ◽  
Stress Response ◽  
Meta Analysis ◽  
Adherens Junction ◽  
Enrichment Analysis ◽  
Oxidative Stress Response ◽  
Insect Species ◽  
Rna Seq ◽  
Manual Curation ◽  
Analysis Workflow

Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data of Drosophila melanogaster were found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data of Caenorhabditis elegans were curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response.

Time series analysis of oxidative stress response patterns in HepG2: A toxicogenomics approach

Toxicology ◽  
2013 ◽  
Vol 306 ◽  
pp. 24-34 ◽  
Author(s):  
L. Deferme ◽  
J.J. Briedé ◽  
S.M.H. Claessen ◽  
D.G.J. Jennen ◽  
R. Cavill ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Time Series ◽  
Stress Response ◽  
Time Series Analysis ◽  
Oxidative Stress Response ◽  
Response Patterns ◽  
Series Analysis

Calcineurin Silencing in Dictyostelium discoideum Leads to Cellular Alterations Affecting Mitochondria, Gene Expression, and Oxidative Stress Response

Protist ◽  
2018 ◽  
Vol 169 (4) ◽  
pp. 584-602 ◽  
Author(s):  
Konstanze Kobel-Höller ◽  
Kevin Gley ◽  
Janina Jochinke ◽  
Kristina Heider ◽  
Verena Nadin Fritsch ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Stress Response ◽  
Dictyostelium Discoideum ◽  
Oxidative Stress Response ◽  
And Oxidative Stress ◽  
Cellular Alterations

scholarly journals Differential gene expression of granulosa cells after ovarian superstimulation in beef cattle

Reproduction ◽  
2013 ◽  
Vol 146 (2) ◽  
pp. 181-191 ◽  
Author(s):  
F C F Dias ◽  
M I R Khan ◽  
M A Sirard ◽  
G P Adams ◽  
J Singh
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Stress Response ◽  
Granulosa Cells ◽  
Rna Extraction ◽  
Oxidative Stress Response ◽  
Endoplasmic Reticulum Stress Response ◽  
Control Group ◽  
Matrix Remodeling ◽  
Upregulated Genes

Microarray analysis was used to compare the gene expression of granulosa cells from dominant follicles with that of those after superstimulatory treatment. Cows were allocated randomly to two groups (superstimulation and control, n=6/group). A new follicular wave was induced by ablation of follicles ≥5 mm in diameter, and a progesterone-releasing device controlled internal drug release (CIDR) was placed in the vagina. The superstimulation group was given eight doses of 25 mg FSH at 12-h intervals starting from the day of wave emergence (day 0), whereas the control group was not given FSH treatment. Both groups were given prostaglandin F2α twice, 12 h apart, on day 3 and the CIDR was removed at the second injection; 25 mg porcine luteinizing hormone (pLH) was given 24 h after CIDR removal, and cows were ovariectomized 24 h later. Granulosa cells were collected for RNA extraction, amplification, and microarray hybridization. A total of 190 genes were downregulated and 280 genes were upregulated. To validate the microarray results, five genes were selected for real-time PCR (NTS, FOS, THBS1, FN1, and IGF2). Expression of four genes increased significantly in the three different animals tested (NTS, FOS, THBS1, and FN1). The upregulated genes are related to matrix remodeling (i.e. tissue proliferation), disturbance of angiogenesis, apoptosis, and oxidative stress response. We conclude that superstimulation treatment i) results in granulosa cells that lag behind in maturation and differentiation (most of the upregulated genes are markers of the follicular growth stage), ii) activates genes involved with the NFE2L2 oxidative stress response and endoplasmic reticulum stress response, and iii) disturbs angiogenesis.

scholarly journals Understanding genetic changes underlying the molybdate resistance and the glutathione production inSaccharomyces cerevisiaewine strains using an evolution-based strategy

2016 ◽  
Author(s):  
Francesco Mezzetti ◽  
Justin C. Fay ◽  
Paolo Giudici ◽  
Luciana De Vero
Keyword(s):  
Oxidative Stress ◽  
Stress Response ◽  
Oxidative Stress Response ◽  
Selection Strategy ◽  
Rna Seq ◽  
Genetic Changes ◽  
Over Expression ◽  
Sexual Recombination ◽  
Wine Strain ◽  
The Relationship

AbstractIn this work we have investigated the genetic changes underlying the high glutathione (GSH) production showed by the evolvedSaccharomyces cerevisiaestrain UMCC 2581, selected in a molybdate-enriched environment after sexual recombination of the parental wine strain UMCC 855. To reach our goal, we first generated strains with the desired phenotype, and then we mapped changes underlying adaptation to molybdate by using a whole-genome sequencing. Moreover, we carried out the RNA-seq that allowed an accurate measurement of gene expression and an effective comparison between the transcriptional profiles of parental and evolved strains, in order to investigate the relationship between genotype and high GSH production phenotype.Among all genes evaluated only two genes,MED2andRIM15both related to oxidative stress response, presented new mutations in the UMCC 2581 strain sequence and were potentially related to the evolved phenotype.Regarding the expression of high GSH production phenotype, it included over-expression of amino acids permeases and precursor biosynthetic enzymes rather than the two GSH metabolic enzymes, whereas GSH production and metabolism, transporter activity, vacuolar detoxification and oxidative stress response enzymes were probably added resulting in the molybdate resistance phenotype. This work provides an example of a combination of an evolution-based strategy to successful obtain yeast strain with desired phenotype and inverse engineering approach to genetic characterize the evolved strain. The obtained genetic information could be useful for further optimization of the evolved strains and for providing an even more rapid approach to identify new strains, with a high GSH production, through a marked-assisted selection strategy.

scholarly journals Redox-Dependent Condensation Of the Mycobacterial Nucleoid By WhiB4

2017 ◽  
Author(s):  
Manbeena Chawla ◽  
Saurabh Mishra ◽  
Pankti Parikh ◽  
Mansi Mehta ◽  
Prashant Shukla ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Mycobacterium Tuberculosis ◽  
Stress Response ◽  
Redox Homeostasis ◽  
Oxidative Stress Response ◽  
Chromosomal Structure ◽  
Redox Sensor ◽  
Intracellular Redox

AbstractOxidative stress response in bacteria is generally mediated through coordination between the regulators of oxidant-remediation systems (e.g.OxyR, SoxR) and nucleoid condensation (e.g.Dps, Fis). However, these genetic factors are either absent or rendered nonfunctional in the human pathogenMycobacterium tuberculosis(Mtb). Therefore, howMtborganizes genome architecture and regulates gene expression to counterbalance oxidative imbalance during infection is not known. Here, we report that an intracellular redox-sensor, WhiB4, dynamically links genome condensation and oxidative stress response inMtb. Disruption of WhiB4 affects the expression of genes involved in maintaining redox homeostasis, central carbon metabolism (CCM), respiration, cell wall biogenesis, DNA repair and protein quality control under oxidative stress. Notably, disulfide-linked oligomerization of WhiB4 in response to oxidative stress activates the protein’s ability to condense DNAin vitroandin vivo. Further, overexpression of WhiB4 led to hypercondensation of nucleoids, redox imbalance and increased susceptibility to oxidative stress, whereas WhiB4 disruption reversed this effect. In accordance with the findingsin vitro, ChIP-Seq data demonstrated non-specific binding of WhiB4 to GC-rich regions of theMtbgenome. Lastly, data indicate that WhiB4 deletion affected the expression of only a fraction of genes preferentially bound by the protein, suggesting its indirect effect on gene expression. We propose that WhiB4 is a novel redox-dependent nucleoid condensing protein that structurally couplesMtb’sresponse to oxidative stress with genome organization and transcription.Significance StatementMycobacterium tuberculosis (Mtb)needs to adapt in response to oxidative stress encountered inside human phagocytes. In other bacteria, condensation state of nucleoids modulates gene expression to coordinate oxidative stress response. However, this relation remains elusive inMtb. We performed molecular dissection of a mechanism controlled by an intracellular redox sensor, WhiB4, in organizing both chromosomal structure and selective expression of adaptive traits to counter oxidative stress inMtb. Using high-resolution sequencing, transcriptomics, imaging, and redox biosensor, we describe how WhiB4 modulates nucleoid condensation, global gene expression, and redox-homeostasis. WhiB4 over-expression hypercondensed nucleoids and perturbed redox homeostasis whereas WhiB4 disruption had an opposite effect. Our study discovered an empirical role for WhiB4 in integrating redox signals with nucleoid condensation inMtb.

scholarly journals Rapamycin increases oxidative stress response gene expression in adult stem cells

Aging ◽  
2012 ◽  
Vol 4 (4) ◽  
pp. 279-289 ◽  
Author(s):  
Amber E. Kofman ◽  
Margeaux R. McGraw ◽  
Christopher J. Payne
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Stem Cells ◽  
Stress Response ◽  
Adult Stem Cells ◽  
Oxidative Stress Response ◽  
Response Gene ◽  
Stress Response Gene
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