RNase E cleavage shapes the transcriptome ofRhodobacter sphaeroidesand strongly impacts phototrophic growth

Bacteria adapt to changing environmental conditions by rapid changes in their transcriptome. This is achieved not only by adjusting rates of transcription but also by processing and degradation of RNAs. We applied TIER-Seq (transiently inactivating an endoribonuclease followed by RNA-Seq) for the transcriptome-wide identification of RNase E cleavage sites and of 5′ RNA ends, which are enriched when RNase E activity is reduced inRhodobacter sphaeroides. These results reveal the importance of RNase E for the maturation and turnover of mRNAs, rRNAs, and sRNAs in this guanine-cytosine-rich α-proteobacterium, some of the latter have well-described functions in the oxidative stress response. In agreement with this, a role of RNase E in the oxidative stress response is demonstrated. A remarkably strong phenotype of a mutant with reduced RNase E activity was observed regarding the formation of photosynthetic complexes and phototrophic growth, whereas there was no effect on chemotrophic growth.

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Meta-Analysis of Oxidative Transcriptomes in Insects

Antioxidants ◽

10.3390/antiox10030345 ◽

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.

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Role of ALADIN in Human Adrenocortical Cells for Oxidative Stress Response and Steroidogenesis

PLoS ONE ◽

10.1371/journal.pone.0124582 ◽

2015 ◽

Vol 10 (4) ◽

pp. e0124582 ◽

Cited By ~ 27

Author(s):

Ramona Jühlen ◽

Jan Idkowiak ◽

Angela E. Taylor ◽

Barbara Kind ◽

Wiebke Arlt ◽

...

Keyword(s):

Oxidative Stress ◽

Stress Response ◽

Oxidative Stress Response ◽

Adrenocortical Cells

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The role of CSA and CSB protein in the oxidative stress response

Mechanisms of Ageing and Development ◽

10.1016/j.mad.2013.03.006 ◽

2013 ◽

Vol 134 (5-6) ◽

pp. 261-269 ◽

Cited By ~ 21

Author(s):

Mariarosaria D’Errico ◽

Barbara Pascucci ◽

Egidio Iorio ◽

Bennett Van Houten ◽

Eugenia Dogliotti

Keyword(s):

Oxidative Stress ◽

Stress Response ◽

Oxidative Stress Response

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TrmB, a tRNA m7G46 methyltransferase, plays a role in hydrogen peroxide resistance and positively modulates the translation of katA and katB mRNAs in Pseudomonas aeruginosa

Nucleic Acids Research ◽

10.1093/nar/gkz702 ◽

2019 ◽

Vol 47 (17) ◽

pp. 9271-9281 ◽

Cited By ~ 5

Author(s):

Narumon Thongdee ◽

Juthamas Jaroensuk ◽

Sopapan Atichartpongkul ◽

Jurairat Chittrakanwong ◽

Kamonchanok Chooyoung ◽

...

Keyword(s):

Oxidative Stress ◽

Pseudomonas Aeruginosa ◽

Stress Response ◽

Translational Regulation ◽

Cellular Response ◽

Oxidative Stress Response ◽

Translation Efficiency ◽

Trna Modification ◽

Negative Effect

Abstract Cellular response to oxidative stress is a crucial mechanism that promotes the survival of Pseudomonas aeruginosa during infection. However, the translational regulation of oxidative stress response remains largely unknown. Here, we reveal a tRNA modification-mediated translational response to H2O2 in P. aeruginosa. We demonstrated that the P. aeruginosa trmB gene encodes a tRNA guanine (46)-N7-methyltransferase that catalyzes the formation of m7G46 in the tRNA variable loop. Twenty-three tRNA substrates of TrmB with a guanosine residue at position 46 were identified, including 11 novel tRNA substrates. We showed that loss of trmB had a strong negative effect on the translation of Phe- and Asp-enriched mRNAs. The trmB-mediated m7G modification modulated the expression of the catalase genes katA and katB, which are enriched with Phe/Asp codons at the translational level. In response to H2O2 exposure, the level of m7G modification increased, consistent with the increased translation efficiency of Phe- and Asp-enriched mRNAs. Inactivation of trmB led to decreased KatA and KatB protein abundance and decreased catalase activity, resulting in H2O2-sensitive phenotype. Taken together, our observations reveal a novel role of m7G46 tRNA modification in oxidative stress response through translational regulation of Phe- and Asp-enriched genes, such as katA and katB.

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Role of actin depolymerizing factor cofilin in Aspergillus fumigatus oxidative stress response and pathogenesis

Current Genetics ◽

10.1007/s00294-017-0777-5 ◽

2017 ◽

Vol 64 (3) ◽

pp. 619-634 ◽

Cited By ~ 3

Author(s):

Xiaodong Jia ◽

Xi Zhang ◽

Yingsong Hu ◽

Mandong Hu ◽

Shuguang Tian ◽

...

Keyword(s):

Oxidative Stress ◽

Stress Response ◽

Aspergillus Fumigatus ◽

Oxidative Stress Response ◽

Actin Depolymerizing Factor

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The role of Yap1p and Skn7p-mediated oxidative stress response in the defence ofSaccharomyces cerevisiae against singlet oxygen

Yeast ◽

10.1002/yea.1392 ◽

2006 ◽

Vol 23 (10) ◽

pp. 741-750 ◽

Cited By ~ 25

Author(s):

Katrin Brombacher ◽

Beat B. Fischer ◽

Karin Rüfenacht ◽

Rik I. L. Eggen

Keyword(s):

Oxidative Stress ◽

Stress Response ◽

Singlet Oxygen ◽

Oxidative Stress Response

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

10.1101/092007 ◽

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.

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The copper chaperone CcsA coupling with superoxide dismutase SodA mediates oxidative stress response in Aspergillus fumigatus

Applied and Environmental Microbiology ◽

10.1128/aem.01013-21 ◽

2021 ◽

Author(s):

Wenlong Du ◽

Pengfei Zhai ◽

Shuai Liu ◽

Yuanwei Zhang ◽

Ling Lu

Keyword(s):

Oxidative Stress ◽

Reactive Oxygen Species ◽

Stress Response ◽

Aspergillus Fumigatus ◽

Fungal Pathogens ◽

Oxidative Stress Response ◽

Superoxide Dismutases ◽

Oxygen Species ◽

Oxidative Response

Superoxide dismutases (SODs) are important metalloenzymes that protect fungal pathogens against the toxic effects of reactive oxygen species (ROS) generated by host defense mechanisms during the infection process. The activation of Cu/Zn-SOD1 is found to be dependent on its c haperone Ccs1 ( c opper c haperone for S OD1). However, the role of Ccs1 ortholog in the human pathogen Aspergillus fumigatus and how these SODs coordinate to mediate oxidative stress response remain elusive. Here, we demonstrated that A. fumigatus CcsA, a Saccharomyces cerevisiae Ccs1 ortholog, is required for cells in response to oxidative response and the activation of Sod1. Deletion of ccsA resulted in increased ROS accumulation and enhanced sensitivity to oxidative stress due to loss of SodA activity. Molecular characterization of CcsA revealed that the conserved CXC motif is required not only for the physical interaction with SodA but also for the oxidative stress adaption. Notably, addition of Mn 2+ or overexpression of cytoplasmic Mn-SodC could rescue the defects of the ccsA or sodA deletion mutant, indicating the important role of Mn 2+ and Mn-SodC in ROS detoxification; however, deletion of CcsA-SodA complex could not affect A. fumigatus virulence. Collectively, our findings demonstrate that CcsA functions as a Cu/Zn-Sod1 chaperone that participates in the adaptation to oxidative stress in A. fumigatus and provide a better understanding of the CcsA-SodA complex-mediated oxidative stress response in filamentous fungi. IMPORTANCE Reactive oxygen species (ROS) produced by phagocytes have been reported to participate in the killing of fungal pathogens. Superoxide dismutases (SODs) are considered to be the first defense line against superoxide anions. Characterizing the regulatory mechanisms of SOD activation is important for understanding how fungi adapt to oxidative stress in hosts. Our findings demonstrated that CcsA functions as a SodA chaperone in A. fumigatus and that the conserved CXC motif within CcsA is required for its interaction with SodA and the CcsA-SodA-mediated oxidative response. These data may provide new insights into how fungal pathogens adapt to oxidative stress via the CcsA-SodA complex.

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