Proteome Analysis of Isolated Podocytes Reveals Stress Responses in Glomerular Sclerosis

BackgroundUnderstanding podocyte-specific responses to injury at a systems level is difficult because injury leads to podocyte loss or an increase of extracellular matrix, altering glomerular cellular composition. Finding a window into early podocyte injury might help identify molecular pathways involved in the podocyte stress response.MethodsWe developed an approach to apply proteome analysis to very small samples of purified podocyte fractions. To examine podocytes in early disease states in FSGS mouse models, we used podocyte fractions isolated from individual mice after chemical induction of glomerular disease (with Doxorubicin or LPS). We also applied single-glomerular proteome analysis to tissue from patients with FSGS.ResultsTranscriptome and proteome analysis of glomeruli from patients with FSGS revealed an underrepresentation of podocyte-specific genes and proteins in late-stage disease. Proteome analysis of purified podocyte fractions from FSGS mouse models showed an early stress response that includes perturbations of metabolic, mechanical, and proteostasis proteins. Additional analysis revealed a high correlation between the amount of proteinuria and expression levels of the mechanosensor protein Filamin-B. Increased expression of Filamin-B in podocytes in biopsy samples from patients with FSGS, in single glomeruli from proteinuric rats, and in podocytes undergoing mechanical stress suggests that this protein has a role in detrimental stress responses. In Drosophila, nephrocytes with reduced filamin homolog Cher displayed altered filtration capacity, but exhibited no change in slit diaphragm structure.ConclusionsWe identified conserved mechanisms of the podocyte stress response through ultrasensitive proteome analysis of human glomerular FSGS tissue and purified native mouse podocytes during early disease stages. This approach enables systematic comparisons of large-scale proteomics data and phenotype-to-protein correlation.

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Transcriptomic and Proteomic Analysis of Drought Stress Response in Opium Poppy Plants during the First Week of Germination

Plants ◽

10.3390/plants10091878 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1878

Author(s):

Kristýna Kundrátová ◽

Martin Bartas ◽

Petr Pečinka ◽

Ondřej Hejna ◽

Andrea Rychlá ◽

...

Keyword(s):

Drought Stress ◽

Stress Response ◽

Stress Responses ◽

Proteomic Analysis ◽

Large Scale ◽

Crop Yields ◽

Opium Poppy ◽

Metabolic Pathway Analysis ◽

Ubiquitin E3 Ligase ◽

Key Genes

Water deficiency is one of the most significant abiotic stresses that negatively affects growth and reduces crop yields worldwide. Most research is focused on model plants and/or crops which are most agriculturally important. In this research, drought stress was applied to two drought stress contrasting varieties of Papaver somniferum (the opium poppy), a non-model plant species, during the first week of its germination, which differ in responses to drought stress. After sowing, the poppy seedlings were immediately subjected to drought stress for 7 days. We conducted a large-scale transcriptomic and proteomic analysis for drought stress response. At first, we found that the transcriptomic and proteomic profiles significantly differ. However, the most significant findings are the identification of key genes and proteins with significantly different expressions relating to drought stress, e.g., the heat-shock protein family, dehydration responsive element-binding transcription factors, ubiquitin E3 ligase, and others. In addition, metabolic pathway analysis showed that these genes and proteins were part of several biosynthetic pathways most significantly related to photosynthetic processes, and oxidative stress responses. A future study will focus on a detailed analysis of key genes and the development of selection markers for the determination of drought-resistant varieties and the breeding of new resistant lineages.

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Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat

Frontiers in Plant Science ◽

10.3389/fpls.2020.600278 ◽

2021 ◽

Vol 11 ◽

Cited By ~ 1

Author(s):

Arindam Ghatak ◽

Palak Chaturvedi ◽

Gert Bachmann ◽

Luis Valledor ◽

Živa Ramšak ◽

...

Keyword(s):

Drought Stress ◽

Pearl Millet ◽

Stress Responses ◽

Root Morphology ◽

Large Scale ◽

Foxtail Millet ◽

Proteome Analysis ◽

Specific Marker ◽

Stay Green ◽

Drought Tolerant

Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress responses in drought-tolerant and susceptible genotypes of pearl millet and wheat. These chosen genotypes are widely used in breeding and farming practices. The physiological responses demonstrated large differences in the regulation of root morphology and photosynthetic machinery, revealing a stay-green phenotype in pearl millet. Subsequent tissue-specific proteome analysis of leaves, roots and seeds led to the identification of 12,558 proteins in pearl millet and wheat under well-watered and stress conditions. To allow for this comparative proteome analysis and to provide a platform for future functional proteomics studies we performed a systematic phylogenetic analysis of all orthologues in pearl millet, wheat, foxtail millet, sorghum, barley, brachypodium, rice, maize, Arabidopsis, and soybean. In summary, we define (i) a stay-green proteome signature in the drought-tolerant pearl millet phenotype and (ii) differential senescence proteome signatures in contrasting wheat phenotypes not capable of coping with similar drought stress. These different responses have a significant effect on yield and grain filling processes reflected by the harvest index. Proteome signatures related to root morphology and seed yield demonstrated the unexpected intra- and interspecies-specific biochemical plasticity for stress adaptation for both pearl millet and wheat genotypes. These quantitative reference data provide tissue- and phenotype-specific marker proteins of stress defense mechanisms which are not predictable from the genome sequence itself and have potential value for marker-assisted breeding beyond genome assisted breeding.

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Aneuploidy-induced proteotoxic stress can be effectively tolerated without dosage compensation, genetic mutations, or stress responses

BMC Biology ◽

10.1186/s12915-020-00852-x ◽

2020 ◽

Vol 18 (1) ◽

Author(s):

Katherine E. Larrimore ◽

Natalia S. Barattin-Voynova ◽

David W. Reid ◽

Davis T. W. Ng

Keyword(s):

Stress Response ◽

Dosage Compensation ◽

Stress Responses ◽

Large Scale ◽

Protein Biosynthesis ◽

Yeast Cells ◽

Genetic Mutations ◽

Protein Homeostasis ◽

Proteotoxic Stress ◽

Multiple Drugs

Abstract Background The protein homeostasis (proteostasis) network maintains balanced protein synthesis, folding, transport, and degradation within a cell. Failure to maintain proteostasis is associated with aging and disease, leading to concerted efforts to study how the network responds to various proteotoxic stresses. This is often accomplished using ectopic overexpression of well-characterized, model misfolded protein substrates. However, how cells tolerate large-scale, diverse burden to the proteostasis network is not understood. Aneuploidy, the state of imbalanced chromosome content, adversely affects the proteostasis network by dysregulating the expression of hundreds of proteins simultaneously. Using aneuploid haploid yeast cells as a model, we address whether cells can tolerate large-scale, diverse challenges to the proteostasis network. Results Here we characterize several aneuploid Saccharomyces cerevisiae strains isolated from a collection of stable, randomly generated yeast aneuploid cells. These strains exhibit robust growth and resistance to multiple drugs which induce various forms of proteotoxic stress. Whole genome re-sequencing of the strains revealed this was not the result of genetic mutations, and transcriptome profiling combined with ribosome footprinting showed that genes are expressed and translated in accordance to chromosome copy number. In some strains, various facets of the proteostasis network are mildly upregulated without chronic activation of environmental stress response or heat shock response pathways. No severe defects were observed in the degradation of misfolded proteins, using model misfolded substrates of endoplasmic reticulum-associated degradation or cytosolic quality control pathways, and protein biosynthesis capacity was not impaired. Conclusions We show that yeast strains of some karyotypes in the genetic background studied here can tolerate the large aneuploidy-associated burden to the proteostasis machinery without genetic changes, dosage compensation, or activation of canonical stress response pathways. We suggest that proteotoxic stress, while common, is not always an obligate consequence of aneuploidy, but rather certain karyotypes and genetic backgrounds may be able to tolerate the excess protein burden placed on the protein homeostasis machinery. This may help clarify how cancer cells are paradoxically both highly aneuploid and highly proliferative at the same time.

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Quantitative Proteomic Analysis of Castor (Ricinus communis L.) Seeds During Early Imbibition Provided Novel Insights into Cold Stress Response

International Journal of Molecular Sciences ◽

10.3390/ijms20020355 ◽

2019 ◽

Vol 20 (2) ◽

pp. 355 ◽

Cited By ~ 3

Author(s):

Xiaoyu Wang ◽

Min Li ◽

Xuming Liu ◽

Lixue Zhang ◽

Qiong Duan ◽

...

Keyword(s):

Fatty Acid ◽

Stress Response ◽

Cold Stress ◽

Cold Tolerance ◽

Stress Responses ◽

Fatty Acid Biosynthesis ◽

Ricinus Communis ◽

Seedling Emergence ◽

Proteomics Data ◽

Castor Seeds

Early planting is one of the strategies used to increase grain yield in temperate regions. However, poor cold tolerance in castor inhibits seed germination, resulting in lower seedling emergence and biomass. Here, the elite castor variety Tongbi 5 was used to identify the differential abundance protein species (DAPS) between cold stress (4 °C) and control conditions (30 °C) imbibed seeds. As a result, 127 DAPS were identified according to isobaric tag for relative and absolute quantification (iTRAQ) strategy. These DAPS were mainly involved in carbohydrate and energy metabolism, translation and posttranslational modification, stress response, lipid transport and metabolism, and signal transduction. Enzyme-linked immunosorbent assays (ELISA) demonstrated that the quantitative proteomics data collected here were reliable. This study provided some invaluable insights into the cold stress responses of early imbibed castor seeds: (1) up-accumulation of all DAPS involved in translation might confer cold tolerance by promoting protein synthesis; (2) stress-related proteins probably protect the cell against damage caused by cold stress; (3) up-accumulation of key DAPS associated with fatty acid biosynthesis might facilitate resistance or adaptation of imbibed castor seeds to cold stress by the increased content of unsaturated fatty acid (UFA). The data has been deposited to the ProteomeXchange with identifier PXD010043.

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Covariability of Surface Wind and Stress Responses to Sea Surface Temperature Fronts

Journal of Climate ◽

10.1175/jcli-d-11-00230.1 ◽

2012 ◽

Vol 25 (17) ◽

pp. 5916-5942 ◽

Cited By ~ 63

Author(s):

Larry W. O’Neill ◽

Dudley B. Chelton ◽

Steven K. Esbensen

Keyword(s):

Stress Response ◽

Surface Temperature ◽

Sea Surface Temperature ◽

Stress Responses ◽

Large Scale ◽

Surface Wind ◽

Nonlinear Function ◽

Algebraic Manipulation ◽

Sea Surface ◽

Earth Observing System

Abstract The responses of surface wind and wind stress to spatial variations of sea surface temperature (SST) are investigated using satellite observations of the surface wind from the Quick Scatterometer (QuikSCAT) and SST from the Advanced Microwave Scanning Radiometer on the Advanced Microwave Scanning Radiometer for Earth Observing System (EOS) (AMSR-E) Aqua satellite. This analysis considers the 7-yr period June 2002–May 2009 during which both instruments were operating. Attention is focused in the Kuroshio, North and South Atlantic, and Agulhas Return Current regions. Since scatterometer wind stresses are computed solely as a nonlinear function of the scatterometer-derived 10-m equivalent neutral wind speed (ENW), qualitatively similar responses of the stress and ENW to SST are expected. However, the responses are found to be more complicated on the oceanic mesoscale. First, the stress and ENW are both approximately linearly related to SST, despite a nonlinear relationship between them. Second, the stress response to SST is 2 to 5 times stronger during winter compared to summer, while the ENW response to SST exhibits relatively little seasonal variability. Finally, the stress response to SST can be strong in regions where the ENW response is weak and vice versa. A straightforward algebraic manipulation shows that the stress perturbations are directly proportional to the ENW perturbations multiplied by a nonlinear function of the ambient large-scale ENW. This proportionality explains why both the stress and ENW depend linearly on the mesoscale SST perturbations, while the dependence of the stress perturbations on the ambient large-scale ENW explains both the seasonal pulsing and the geographic variability of the stress response to SST compared with the less variable ENW response.

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Critical review: involvement of endoplasmic reticulum stress in the aetiology of Alzheimer's disease

Open Biology ◽

10.1098/rsob.180024 ◽

2018 ◽

Vol 8 (4) ◽

pp. 180024 ◽

Cited By ~ 31

Author(s):

Shoko Hashimoto ◽

Takaomi C. Saido

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Endoplasmic Reticulum ◽

Stress Response ◽

Er Stress ◽

Mouse Models ◽

Stress Responses ◽

Molecular Mechanisms ◽

Neuronal Cell ◽

Er Stress Response

The endoplasmic reticulum (ER) stress response is regarded as an important process in the aetiology of Alzheimer's disease (AD). The accumulation of pathogenic misfolded proteins and the disruption of intracellular calcium (Ca 2+ ) signalling are considered to be fundamental mechanisms that underlie the induction of ER stress, leading to neuronal cell death. Indeed, a number of studies have proposed molecular mechanisms linking ER stress to AD pathogenesis based on results from in vitro systems and AD mouse models. However, stress responsivity was largely different between each mouse model, even though all of these models display AD-related pathologies. While several reports have shown elevated ER stress responses in amyloid precursor protein (APP) and presenilin 1 (PS1) double-transgenic (Tg) AD mouse models, we and other groups, in contrast, observed no such ER stress response in APP-single-Tg or App -knockin mice. Therefore, it is debatable whether the ER stress observed in APP and PS1 double-Tg mice is due to AD pathology. From these findings, the roles of ER stress in AD pathogenesis needs to be carefully addressed in future studies. In this review, we summarize research detailing the relationship between ER stress and AD, and analyse the results in detail.

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Podocyte proteome analysis reveals stress responses in glomerular sclerosis

The FASEB Journal ◽

10.1096/fasebj.2020.34.s1.06045 ◽

2020 ◽

Vol 34 (S1) ◽

pp. 1-1

Author(s):

Sybille Koehler ◽

Paul Brinkkoetter ◽

Markus M. Rinschen

Keyword(s):

Stress Responses ◽

Proteome Analysis ◽

Glomerular Sclerosis

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Flavonoids: Potential Candidates for the Treatment of Neurodegenerative Disorders

Biomedicines ◽

10.3390/biomedicines9020099 ◽

2021 ◽

Vol 9 (2) ◽

pp. 99

Author(s):

Shweta Devi ◽

Vijay Kumar ◽

Sandeep Kumar Singh ◽

Ashish Kant Dubey ◽

Jong-Joo Kim

Keyword(s):

Stress Response ◽

Stress Responses ◽

Neurodegenerative Disorders ◽

Cell Damage ◽

Cellular Stress ◽

Clinical Manifestations ◽

Cellular Stress Response ◽

Dramatic Rise ◽

Cellular Stress Responses

Neurodegenerative disorders, such as Parkinson’s disease (PD), Alzheimer’s disease (AD), Amyotrophic lateral sclerosis (ALS), and Huntington’s disease (HD), are the most concerning disorders due to the lack of effective therapy and dramatic rise in affected cases. Although these disorders have diverse clinical manifestations, they all share a common cellular stress response. These cellular stress responses including neuroinflammation, oxidative stress, proteotoxicity, and endoplasmic reticulum (ER)-stress, which combats with stress conditions. Environmental stress/toxicity weakened the cellular stress response which results in cell damage. Small molecules, such as flavonoids, could reduce cellular stress and have gained much attention in recent years. Evidence has shown the potential use of flavonoids in several ways, such as antioxidants, anti-inflammatory, and anti-apoptotic, yet their mechanism is still elusive. This review provides an insight into the potential role of flavonoids against cellular stress response that prevent the pathogenesis of neurodegenerative disorders.

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Efficacy and Underlying Mechanism of Acupuncture in the Treatment of Posttraumatic Stress Disorder: A Systematic Review of Animal Studies

Journal of Clinical Medicine ◽

10.3390/jcm10081575 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1575

Author(s):

Chan-Young Kwon ◽

Boram Lee ◽

Sang-Ho Kim

Keyword(s):

Posttraumatic Stress Disorder ◽

Posttraumatic Stress ◽

Stress Responses ◽

Methodological Quality ◽

Animal Studies ◽

Large Scale ◽

Stress Disorder ◽

Spatial Learning And Memory ◽

Expectancy Effects ◽

Therapeutic Mechanisms

Acupuncture is a nonpharmacological intervention that can be useful in the clinical management of posttraumatic stress disorder (PTSD), especially in situations with a lack of medical resources, including large-scale PTSD events such as disasters. Some clinical studies have reported the clinical effect of acupuncture in improving PTSD symptoms, but the underlying therapeutic mechanism has yet to be explored. Therefore, this review summarized the underlying therapeutic mechanisms of acupuncture in animal PTSD models. A comprehensive search was conducted in 14 electronic databases, and two independent researchers performed study selection, data extraction, and the methodological quality assessment. Twenty-four relevant studies were included in this review and summarized according to the proposed main mechanisms. In behavioral evaluation, acupuncture, including manual acupuncture and electro-acupuncture, reduced anxiety and fear responses and weakened fear conditioning, improved sleep architecture, reduced depressive symptoms, and alleviated disturbance of spatial learning and memory of PTSD animal models. The therapeutic mechanisms of acupuncture proposed in the included studies could be classified into two categories: (1) regulation of stress responses in the neuroendocrine system and (2) promotion of neuroprotection, neurogenesis, and synaptic plasticity in several brain areas. However, the methodological quality of the included animal studies was not high enough to produce robust evidence. In addition, mechanistic studies on specific aspects of acupuncture that may affect PTSD, including expectancy effects, in human PTSD subjects are also needed.

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Environmental Conditions Modulate the Transcriptomic Response of Both Caulobacter crescentus Morphotypes to Cu Stress

Microorganisms ◽

10.3390/microorganisms9061116 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1116

Author(s):

Laurens Maertens ◽

Pauline Cherry ◽

Françoise Tilquin ◽

Rob Van Houdt ◽

Jean-Yves Matroule

Keyword(s):

Oxidative Stress ◽

Stress Response ◽

Stress Responses ◽

Caulobacter Crescentus ◽

Oxidative Stress Response ◽

Transport Systems ◽

Transcriptomic Response ◽

Swarmer Cell ◽

Cu Stress ◽

Cellular Environment

Bacteria encounter elevated copper (Cu) concentrations in multiple environments, varying from mining wastes to antimicrobial applications of copper. As the role of the environment in the bacterial response to Cu ion exposure remains elusive, we used a tagRNA-seq approach to elucidate the disparate responses of two morphotypes of Caulobacter crescentus NA1000 to moderate Cu stress in a complex rich (PYE) medium and a defined poor (M2G) medium. The transcriptome was more responsive in M2G, where we observed an extensive oxidative stress response and reconfiguration of the proteome, as well as the induction of metal resistance clusters. In PYE, little evidence was found for an oxidative stress response, but several transport systems were differentially expressed, and an increased need for histidine was apparent. These results show that the Cu stress response is strongly dependent on the cellular environment. In addition, induction of the extracytoplasmic function sigma factor SigF and its regulon was shared by the Cu stress responses in both media, and its central role was confirmed by the phenotypic screening of a sigF::Tn5 mutant. In both media, stalked cells were more responsive to Cu stress than swarmer cells, and a stronger basal expression of several cell protection systems was noted, indicating that the swarmer cell is inherently more Cu resistant. Our approach also allowed for detecting several new transcription start sites, putatively indicating small regulatory RNAs, and additional levels of Cu-responsive regulation.

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