scholarly journals Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli

Antioxidants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 861
Author(s):  
Hao Chen ◽  
Jessica Wilson ◽  
Carson Ercanbrack ◽  
Hannah Smith ◽  
Qinglei Gan ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Resistance Genes ◽  
Stress Responses ◽  
Host Cells ◽  
E Coli ◽  
Oxidizing Agents ◽  
Genome Wide ◽  
A Genome ◽  
Basic Studies ◽  
Oxidative Stress Responses

The use of oxidizing agents is one of the most favorable approaches to kill bacteria in daily life. However, bacteria have been evolving to survive in the presence of different oxidizing agents. In this study, we aimed to obtain a comprehensive list of genes whose expression can make Escherichiacoli cells resistant to different oxidizing agents. For this purpose, we utilized the ASKA library and performed a genome-wide screening of ~4200 E. coli genes. Hydrogen peroxide (H2O2) and hypochlorite (HOCl) were tested as representative oxidizing agents in this study. To further validate our screening results, we used different E. coli strains as host cells to express or inactivate selected resistance genes individually. More than 100 genes obtained in this screening were not known to associate with oxidative stress responses before. Thus, this study is expected to facilitate both basic studies on oxidative stress and the development of antibacterial agents.

scholarly journals The Arabidopsis mediator complex subunit 8 regulates oxidative stress responses

2021 ◽  
Author(s):  
Huaming He ◽  
Jordi Denecker ◽  
Katrien Van Der Kelen ◽  
Patrick Willems ◽  
Robin Pottie ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Salicylic Acid ◽  
Jasmonic Acid ◽  
Stress Responses ◽  
Negative Regulator ◽  
Mediator Complex ◽  
Defense Gene Expression ◽  
A Genome ◽  
Oxidative Stress Responses

Abstract Signaling events triggered by hydrogen peroxide (H2O2) regulate plant growth and defense by orchestrating a genome-wide transcriptional reprogramming. However, the specific mechanisms that govern H2O2-dependent gene expression are still poorly understood. Here, we identify the Arabidopsis Mediator complex subunit MED8 as a regulator of H2O2 responses. The introduction of the med8 mutation in a constitutive oxidative stress genetic background (catalase-deficient, cat2) was associated with enhanced activation of the salicylic acid pathway and accelerated cell death. Interestingly, med8 seedlings were more tolerant to oxidative stress generated by the herbicide methyl viologen (MV) and exhibited transcriptional hyperactivation of defense signaling, in particular salicylic acid- and jasmonic acid-related pathways. The med8-triggered tolerance to MV was manipulated by the introduction of secondary mutations in salicylic acid and jasmonic acid pathways. In addition, analysis of the Mediator interactome revealed interactions with components involved in mRNA processing and microRNA biogenesis, hence expanding the role of Mediator beyond transcription. Notably, MED8 interacted with the transcriptional regulator NEGATIVE ON TATA-LESS, NOT2, to control the expression of H2O2-inducible genes and stress responses. Our work establishes MED8 as a component regulating oxidative stress responses and demonstrates that it acts as a negative regulator of H2O2-driven activation of defense gene expression.

scholarly journals Biological links between nanoparticle biosynthesis and stress responses in bacteria

2018 ◽  
Vol 3 (4) ◽  
pp. 44-69
Author(s):  
Angela Chen ◽  
Benjamin K. Keitz ◽  
Lydia M. Contreras
Keyword(s):  
Oxidative Stress ◽  
Resistance Genes ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Metal Resistance ◽  
Reduction Mechanisms ◽  
Nanoparticle Morphology ◽  
Nanoparticle Biosynthesis ◽  
Oxidative Stress Responses

There is rising interest in nanoparticle biosynthesis using bacteria due to the potential for applications in bioremediation, catalysis, or as antimicrobials. However, biosynthesis remains limited by the inability to control nanoparticle morphology and size due to the lack of knowledge regarding explicit molecular mechanisms. Due to their importance in nanoparticle biosynthesis and as antimicrobials, we focus our discussion on silver, gold, and copper nanoparticles. We discuss recent efforts to elucidate reduction mechanisms that have identified generic enzymes and metal resistance genes as strong candidates to facilitate nanoparticle biosynthesis. Although it is known that these enzymes and genes play significant roles in maintaining bacterial homeostasis, there are few reports discussing this topic. Thus, we discuss examples of how metal resistance genes are conserved across bacteria and have been shown to be important for both nanoparticle biosynthesis and processes such as virulence or oxidative stress responses. Overall, this review highlights biological connections between nanoparticle biosynthesis and stress responses by examining the role of reductases and metal resistance genes in both processes. This understanding provides a greater role for nanoparticle biosynthesis in bacteria and could enable a systems biology level of control over nanoparticle biosynthesis.

Dynamic aqueous transformations of lithium cobalt oxide nanoparticle induce distinct oxidative stress responses of B. subtilis

2021 ◽  
Author(s):  
Metti K. Gari ◽  
Paul Lemke ◽  
Kelly H. Lu ◽  
Elizabeth D. Laudadio ◽  
Austin H. Henke ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Cobalt Oxide ◽  
Stress Responses ◽  
Lithium Ion ◽  
Model Organisms ◽  
Lithium Cobalt Oxide ◽  
Oxygen Species ◽  
Oxide Nanoparticle ◽  
Oxidative Stress Responses ◽  
Lithium Cobalt

Lithium cobalt oxide (LiCoO2), an example of nanoscale transition metal oxide and a widely commercialized cathode material in lithium ion batteries, has been shown to induce oxidative stress and generate intracellular reactive oxygen species (ROS) in model organisms.

Clade III cytokinin response factors share common roles in response to oxidative stress responses linked to cytokinin synthesis

2021 ◽  
Vol 72 (8) ◽  
pp. 3294-3306
Author(s):  
Ariel M Hughes ◽  
H Tucker Hallmark ◽  
Lenka Plačková ◽  
Ondrej Novák ◽  
Aaron M Rashotte
Keyword(s):  
Oxidative Stress ◽  
Transcription Factors ◽  
Stress Response ◽  
Stress Responses ◽  
Oxidative Stress Response ◽  
Response Factors ◽  
Ontology Term ◽  
Regulated Expression ◽  
Cytokinin Response ◽  
Oxidative Stress Responses

Abstract Cytokinin response factors (CRFs) are transcription factors that are involved in cytokinin (CK) response, as well as being linked to abiotic stress tolerance. In particular, oxidative stress responses are activated by Clade III CRF members, such as AtCRF6. Here we explored the relationships between Clade III CRFs and oxidative stress. Transcriptomic responses to oxidative stress were determined in two Clade III transcription factors, Arabidopsis AtCRF5 and tomato SlCRF5. AtCRF5 was required for regulated expression of >240 genes that are involved in oxidative stress response. Similarly, SlCRF5 was involved in the regulated expression of nearly 420 oxidative stress response genes. Similarities in gene regulation by these Clade III members in response to oxidative stress were observed between Arabidopsis and tomato, as indicated by Gene Ontology term enrichment. CK levels were also changed in response to oxidative stress in both species. These changes were regulated by Clade III CRFs. Taken together, these findings suggest that Clade III CRFs play a role in oxidative stress response as well as having roles in CK signaling.

scholarly journals Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Kingshuk Mukherjee ◽  
Massimiliano Rossi ◽  
Leena Salmela ◽  
Christina Boucher
Keyword(s):  
Single Molecule ◽  
De Bruijn Graph ◽  
Anabas Testudineus ◽  
E Coli ◽  
Genome Wide ◽  
A Genome ◽  
De Bruijn ◽  
Optical Maps ◽  
Definition Of ◽  
Numeric Representation

AbstractGenome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there are very few choices for assembling Rmap data. There exists only one publicly-available non-proprietary method for assembly and one proprietary software that is available via an executable. Furthermore, the publicly-available method, by Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006), follows the overlap-layout-consensus (OLC) paradigm, and therefore, is unable to scale for relatively large genomes. The algorithm behind the proprietary method, Bionano Genomics’ Solve, is largely unknown. In this paper, we extend the definition of bi-labels in the paired de Bruijn graph to the context of optical mapping data, and present the first de Bruijn graph based method for Rmap assembly. We implement our approach, which we refer to as rmapper, and compare its performance against the assembler of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) and Solve by Bionano Genomics on data from three genomes: E. coli, human, and climbing perch fish (Anabas Testudineus). Our method was able to successfully run on all three genomes. The method of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) only successfully ran on E. coli. Moreover, on the human genome rmapper was at least 130 times faster than Bionano Solve, used five times less memory and produced the highest genome fraction with zero mis-assemblies. Our software, rmapper is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/Rmapper.

scholarly journals Analysis of the proteins targeted by CDSP32, a plastidic thioredoxin participating in oxidative stress responses

2004 ◽  
Vol 41 (1) ◽  
pp. 31-42 ◽  
Author(s):  
Pascal Rey ◽  
Stéphan Cuiné ◽  
Françoise Eymery ◽  
Jérome Garin ◽  
Magali Court ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Stress Responses ◽  
Oxidative Stress Responses

Rhamnolipids induce oxidative stress responses in cherry tomato fruit toAlternaria alternata

2015 ◽  
Vol 72 (8) ◽  
pp. 1500-1507 ◽  
Author(s):  
Fujie Yan ◽  
Hao Hu ◽  
Laifeng Lu ◽  
Xiaodong Zheng
Keyword(s):  
Oxidative Stress ◽  
Stress Responses ◽  
Tomato Fruit ◽  
Cherry Tomato ◽  
Oxidative Stress Responses
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