scholarly journals A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction

2021 ◽  
Vol 2 ◽  
Author(s):  
Candice L. Swift ◽  
Nikola G. Malinov ◽  
Stephen J. Mondo ◽  
Asaf Salamov ◽  
Igor V. Grigoriev ◽  
...  
Keyword(s):  
Stress Response ◽  
Heat Shock ◽  
Stress Responses ◽  
Protein Trafficking ◽  
Anaerobic Fungi ◽  
Transcriptional Responses ◽  
Unfolded Protein ◽  
Catalytic Domains ◽  
Stress Response Genes ◽  
Stress Sensing

Anaerobic fungi are a potential biotechnology platform to produce biomass-degrading enzymes. Unlike model fungi such as yeasts, stress responses that are relevant during bioprocessing have not yet been established for anaerobic fungi. In this work, we characterize both the heat shock and unfolded protein responses of four strains of anaerobic fungi (Anaeromyces robustus, Caecomyces churrovis, Neocallimastix californiae, and Piromyces finnis). The inositol-requiring 1 (Ire1) stress sensor, which typically initiates the fungal UPR, was conserved in all four genomes. However, these genomes also encode putative transmembrane kinases with catalytic domains that are similar to the metazoan stress-sensing enzyme PKR-like endoplasmic reticulum kinase (PERK), although whether they function in the UPR of anaerobic fungi remains unclear. Furthermore, we characterized the global transcriptional responses of Anaeromyces robustus and Neocallimastix californiae to a transient heat shock. Both fungi exhibited the hallmarks of ER stress, including upregulation of genes with functions in protein folding, ER-associated degradation, and intracellular protein trafficking. Relative to other fungi, the genomes of Neocallimastigomycetes contained the greatest gene percentage of HSP20 and HSP70 chaperones, which may serve to stabilize their asparagine-rich genomes. Taken together, these results delineate the unique stress response of anaerobic fungi, which is an important step toward their development as a biotechnology platform to produce enzymes and valuable biomolecules.

scholarly journals Global Transcriptional Response of Bacillus subtilis to Heat Shock

2001 ◽  
Vol 183 (24) ◽  
pp. 7318-7328 ◽  
Author(s):  
John D. Helmann ◽  
Ming Fang Winston Wu ◽  
Phil A. Kobel ◽  
Francisco-Javier Gamo ◽  
Michael Wilson ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Stress Response ◽  
Heat Shock ◽  
Dna Sequences ◽  
Stress Responses ◽  
Transcriptional Response ◽  
Transcriptional Responses ◽  
General Stress Response ◽  
General Stress ◽  
Induced Genes

ABSTRACT In response to heat stress, Bacillus subtilisactivates the transcription of well over 100 different genes. Many of these genes are members of a general stress response regulon controlled by the secondary sigma factor, ςB, while others are under control of the HrcA or CtsR heat shock regulators. We have used DNA microarrays to monitor the global transcriptional response to heat shock. We find strong induction of known ςB-dependent genes with a characteristic rapid induction followed by a return to near prestimulus levels. The HrcA and CtsR regulons are also induced, but with somewhat slower kinetics. Analysis of DNA sequences proximal to newly identified heat-induced genes leads us to propose ∼70 additional members of the ςB regulon. We have also identified numerous heat-induced genes that are not members of known heat shock regulons. Notably, we observe very strong induction of arginine biosynthesis and transport operons. Induction of several genes was confirmed by quantitative reverse transcriptase PCR. In addition, the transcriptional responses measured by microarray hybridization compare favorably with the numerous previous studies of heat shock in this organism. Since many different conditions elicit both specific and general stress responses, knowledge of the heat-induced general stress response reported here will be helpful for interpreting future microarray studies of other stress responses.

scholarly journals BrPP5.2 Overexpression Confers Heat Shock Tolerance in Transgenic Brassica rapa through Inherent Chaperone Activity, Induced Glucosinolate Biosynthesis, and Differential Regulation of Abiotic Stress Response Genes

2021 ◽  
Vol 22 (12) ◽  
pp. 6437
Author(s):  
Muthusamy Muthusamy ◽  
Jonghee Kim ◽  
Sukhee Kim ◽  
Soyoung Park ◽  
Sooin Lee
Keyword(s):  
Heat Stress ◽  
Abiotic Stress ◽  
Stress Response ◽  
Heat Shock ◽  
Brassica Rapa ◽  
Stress Responses ◽  
Abiotic Stress Response ◽  
Glucosinolate Biosynthesis ◽  
Stress Response Genes ◽  
Transgenic Lines

Plant phosphoprotein phosphatases are ubiquitous and multifarious enzymes that respond to developmental requirements and stress signals through reversible dephosphorylation of target proteins. In this study, we investigated the hitherto unknown functions of Brassica rapa protein phosphatase 5.2 (BrPP5.2) by transgenic overexpression of B. rapa lines. The overexpression of BrPP5.2 in transgenic lines conferred heat shock tolerance in 65–89% of the young transgenic seedlings exposed to 46 °C for 25 min. The examination of purified recombinant BrPP5.2 at different molar ratios efficiently prevented the thermal aggregation of malate dehydrogenase at 42 °C, thus suggesting that BrPP5.2 has inherent chaperone activities. The transcriptomic dynamics of transgenic lines, as determined using RNA-seq, revealed that 997 and 1206 (FDR < 0.05, logFC ≥ 2) genes were up- and down-regulated, as compared to non-transgenic controls. Statistical enrichment analyses revealed abiotic stress response genes, including heat stress response (HSR), showed reduced expression in transgenic lines under optimal growth conditions. However, most of the HSR DEGs were upregulated under high temperature stress (37 °C/1 h) conditions. In addition, the glucosinolate biosynthesis gene expression and total glucosinolate content increased in the transgenic lines. These findings provide a new avenue related to BrPP5.2 downstream genes and their crucial metabolic and heat stress responses in plants.

scholarly journals Short- and Long-Term Transcriptomic Responses of Escherichia coli to Biocides: a Systems Analysis

2020 ◽  
Vol 86 (14) ◽  
Author(s):  
Beatriz Merchel Piovesan Pereira ◽  
Xiaokang Wang ◽  
Ilias Tagkopoulos
Keyword(s):  
Escherichia Coli ◽  
Stress Response ◽  
Stress Responses ◽  
Zinc Homeostasis ◽  
Cross Resistance ◽  
Transcriptional Responses ◽  
Systematic Analysis ◽  
Content Type ◽  
Short Term Exposure

ABSTRACT The mechanisms of the bacterial response to biocides are poorly understood, despite their broad application. To identify the genetic basis and pathways implicated in the biocide stress response, we exposed Escherichia coli populations to 10 ubiquitous biocides. By comparing the transcriptional responses between a short-term exposure (30 min) and a long-term exposure (8 to 12 h) to biocide stress, we established the common gene and pathway clusters that are implicated in general and biocide-specific stress responses. Our analysis revealed a temporal choreography, starting from the upregulation of chaperones to the subsequent repression of motility and chemotaxis pathways and the induction of an anaerobic pool of enzymes and biofilm regulators. A systematic analysis of the transcriptional data identified a zur-regulated gene cluster to be highly active in the stress response against sodium hypochlorite and peracetic acid, presenting a link between the biocide stress response and zinc homeostasis. Susceptibility assays with knockout mutants further validated our findings and provide clear targets for downstream investigation of the implicated mechanisms of action. IMPORTANCE Antiseptics and disinfectant products are of great importance to control and eliminate pathogens, especially in settings such as hospitals and the food industry. Such products are widely distributed and frequently poorly regulated. Occasional outbreaks have been associated with microbes resistant to such compounds, and researchers have indicated potential cross-resistance with antibiotics. Despite that, there are many gaps in knowledge about the bacterial stress response and the mechanisms of microbial resistance to antiseptics and disinfectants. We investigated the stress response of the bacterium Escherichia coli to 10 common disinfectant and antiseptic chemicals to shed light on the potential mechanisms of tolerance to such compounds.

scholarly journals Mammalian orthoreovirusinfection is enhanced in cells pre-treated with sodium arsenite

2019 ◽  
Author(s):  
Michael M. Lutz ◽  
Megan P. Worth ◽  
Meleana M. Hinchman ◽  
John S. L. Parker ◽  
Emily D. Ledgerwood
Keyword(s):  
Stress Response ◽  
Heat Shock ◽  
Protein Expression ◽  
Stress Responses ◽  
Sodium Arsenite ◽  
Integrated Stress Response ◽  
Reovirus Infection ◽  
Cellular Stress Responses ◽  
Pre Treatment ◽  
Reovirus Replication

ABSTRACTFollowing reovirus infection, cells activate stress responses that repress canonical cellular translation as a mechanism to limit production of progeny virions. This includes the formation of stress granules (SG) that sequester translationally-stalled cellular transcripts, translation initiation factors, ribosomal proteins, and RNA binding proteins until conditions improve and translation can resume. Work by others suggests that these cellular stress responses, which are part of the integrated stress response, may benefit rather than repress reovirus replication. In agreement with this, we report that stressing cells prior to infection with sodium arsenite (SA), a robust inducer of SG and activator of eIF2α kinases, enhanced viral protein expression, percent infectivity and viral titer in SA-treated cells compared to untreated cells. SA-mediated enhancement of reovirus replication was not strain-specific, but was cell-type specific. While pre-treatment of cells with SA offered the greatest enhancement, treatment of infected cultures as late as 4 h post infection resulted in an increase in the percent of cells infected. SA activates the HRI kinase, which phosphorylates eIF2α and subsequently induces SG formation. Other stresses, such as heat shock (HS) and osmotic shock also activate HRI. Heat shock of cells prior to reovirus infection readily induced SG in greater than 85% of cells. Although HS pre-treatment had no effect on the percentage of infected cells or viral yield, it did enhance viral protein expression. These data suggest that SA pre-treatment perturbs the cell in a way that is beneficial for reovirus and that neither HRI activation nor SG induction is sufficient for reovirus infection enhancement.SIGNIFICANCEAll viruses rely on the host translational machinery for the synthesis of viral proteins. In response to viral infection, cells activate the integrated stress response resulting in the phosphorylation of eIF2α and translation shutoff. Despite this, reovirus replicates to reduced titers in the absence of this response. In this work, we report that sodium arsenite activation of the integrated stress response prior to virus inoculation enhances virus infectivity, protein expression and titer. Together, these data suggest that modulation of conserved cellular stress responses can alter reovirus replication.

scholarly journals Combining auxin-induced degradation and RNAi screening identifies novel genes involved in lipid bilayer stress sensing in Caenorhabditis elegans

2020 ◽  
Author(s):  
Richard Venz ◽  
Anastasiia Korosteleva ◽  
Collin Y. Ewald
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Lipid Bilayer ◽  
Screening Strategy ◽  
Suppressor Genes ◽  
C Elegans ◽  
Unfolded Protein ◽  
Stress Sensing ◽  
The Unfolded Protein Response ◽  
Almost All

AbstractAlteration of the lipid composition of biological membranes interferes with their function and can cause tissue damage by triggering apoptosis. Upon lipid bilayer stress, the endoplasmic reticulum mounts a stress response that is similar to the unfolded protein response. However, only a few genes are known to regulate lipid bilayer stress. Here, we performed a suppressor screen that combined the auxin-inducible degradation (AID) system with conventional RNAi in C. elegans to identify members of the lipid bilayer stress response. AID-mediated knockdown of the mediator MDT-15, a protein required for the upregulation of fatty acid desaturases, caused activation of a lipid bilayer stress sensitive reporters. We screened through almost all C. elegans kinases and transcription factors using RNAi by feeding. We report the identification of 8 genes that have not been implicated previously with lipid bilayer stress before in C. elegans. These suppressor genes include skn-1/NRF1,2,3 and let-607/CREB3. Our candidate suppressor genes suggest a network of transcription factors and the integration of multiple tissues for a centralized lipotoxicity response in the intestine. Additionally, we propose and demonstrate the proof-of-concept for combining AID and RNAi as a new screening strategy.

scholarly journals Multilevel regulation of endoplasmic reticulum stress responses in plants: where old roads and new paths meet

2019 ◽  
Vol 71 (5) ◽  
pp. 1659-1667 ◽  
Author(s):  
Taiaba Afrin ◽  
Danish Diwan ◽  
Katrina Sahawneh ◽  
Karolina Pajerowska-Mukhtar
Keyword(s):  
Endoplasmic Reticulum ◽  
Stress Response ◽  
Er Stress ◽  
Stress Responses ◽  
Translational Control ◽  
Protein Quality ◽  
Unfolded Protein ◽  
Transcriptional Gene Regulation ◽  
The Unfolded Protein Response ◽  
Protein Response

Abstract The sessile lifestyle of plants requires them to cope with a multitude of stresses in situ. In response to diverse environmental and intracellular cues, plant cells respond by massive reprogramming of transcription and translation of stress response regulators, many of which rely on endoplasmic reticulum (ER) processing. This increased protein synthesis could exceed the capacity of precise protein quality control, leading to the accumulation of unfolded and/or misfolded proteins that triggers the unfolded protein response (UPR). Such cellular stress responses are multilayered and executed in different cellular compartments. Here, we will discuss the three main branches of UPR signaling in diverse eukaryotic systems, and describe various levels of ER stress response regulation that encompass transcriptional gene regulation by master transcription factors, post-transcriptional activities including cytoplasmic splicing, translational control, and multiple post-translational events such as peptide modifications and cleavage. In addition, we will discuss the roles of plant ER stress sensors in abiotic and biotic stress responses and speculate on the future prospects of engineering these signaling events for heightened stress tolerance.

scholarly journals PhyR Is Involved in the General Stress Response of Methylobacterium extorquens AM1

2007 ◽  
Vol 190 (3) ◽  
pp. 1027-1035 ◽  
Author(s):  
Benjamin Gourion ◽  
Anne Francez-Charlot ◽  
Julia A. Vorholt
Keyword(s):  
Stress Response ◽  
Heat Shock ◽  
Stress Responses ◽  
Target Genes ◽  
Stress Proteins ◽  
Plant Colonization ◽  
Methylobacterium Extorquens ◽  
General Stress Response ◽  
Amino Terminal ◽  
General Stress

ABSTRACTPhyR represents a novel alphaproteobacterial family of response regulators having a structure consisting of two domains; a predicted amino-terminal extracytoplasmic function (ECF) sigma factor-like domain and a carboxy-terminal receiver domain. PhyR was first described inMethylobacterium extorquensAM1, in which it has been shown to be essential for plant colonization, probably due to its suggested involvement in the regulation of a number of stress proteins. Here we investigated the PhyR regulon using microarray technology. We found that the PhyR regulon is rather large and that most of the 246 targets are under positive control. Mapping of transcriptional start sites revealed candidate promoters for PhyR-mediated regulation. One of these promoters, an ECF-type promoter, was identified upstream of one-third of the target genes by in silico analysis. Among the PhyR targets are genes predicted to be involved in multiple stress responses, includingkatE,osmC,htrA,dnaK,gloA,dps, anduvrA. The induction of these genes is consistent with our phenotypic analyses which revealed that PhyR is involved in resistance to heat shock and desiccation, as well as oxidative, UV, ethanol, and osmotic stresses, inM. extorquensAM1. The finding that PhyR is involved in the general stress response was further substantiated by the finding that carbon starvation induces protection against heat shock and that this protection is at least in part dependent on PhyR.

scholarly journals Cellular proteostasis decline in human senescence

2020 ◽  
Vol 117 (50) ◽  
pp. 31902-31913
Author(s):  
Niv Sabath ◽  
Flonia Levy-Adam ◽  
Amal Younis ◽  
Kinneret Rozales ◽  
Anatoly Meller ◽  
...  
Keyword(s):  
Nuclear Localization ◽  
Transcriptional Activation ◽  
Translational Regulation ◽  
Transcriptional Responses ◽  
Significant Deterioration ◽  
Unfolded Protein ◽  
Transcriptional Regulatory ◽  
Stress Sensing ◽  
Protein Response

Proteostasis collapse, the diminished ability to maintain protein homeostasis, has been established as a hallmark of nematode aging. However, whether proteostasis collapse occurs in humans has remained unclear. Here, we demonstrate that proteostasis decline is intrinsic to human senescence. Using transcriptome-wide characterization of gene expression, splicing, and translation, we found a significant deterioration in the transcriptional activation of the heat shock response in stressed senescent cells. Furthermore, phosphorylated HSF1 nuclear localization and distribution were impaired in senescence. Interestingly, alternative splicing regulation was also dampened. Surprisingly, we found a decoupling between different unfolded protein response (UPR) branches in stressed senescent cells. While young cells initiated UPR-related translational and transcriptional regulatory responses, senescent cells showed enhanced translational regulation and endoplasmic reticulum (ER) stress sensing; however, they were unable to trigger UPR-related transcriptional responses. This was accompanied by diminished ATF6 nuclear localization in stressed senescent cells. Finally, we found that proteasome function was impaired following heat stress in senescent cells, and did not recover upon return to normal temperature. Together, our data unraveled a deterioration in the ability to mount dynamic stress transcriptional programs upon human senescence with broad implications on proteostasis control and connected proteostasis decline to human aging.

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