scholarly journals Insights Into Mechanism of the Naphthalene-Enhanced Biodegradation of Phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Hao Cao ◽  
Xinyu Zhang ◽  
Shuangyan Wang ◽  
Jiading Liu ◽  
Dongfei Han ◽  
...  
Keyword(s):  
Metabolic Regulation ◽  
Physiological Activity ◽  
Degradation Process ◽  
Underlying Mechanism ◽  
Absolute Quantification ◽  
Joint Analysis ◽  
Enhanced Biodegradation ◽  
Polycyclic Aromatic ◽  
Major Bottleneck ◽  
Isobaric Tags

The existence of polycyclic aromatic hydrocarbons (PAHs) in contaminated environment is multifarious. At present, studies of metabolic regulation focus on the degradation process of single PAH. The global metabolic regulatory mechanisms of microorganisms facing coexisting PAHs are poorly understood, which is the major bottleneck for efficient bioremediation of PAHs pollution. Naphthalene (NAP) significantly enhanced the biodegradation of phenanthrene (PHE) by Pseudomonas sp. SL-6. To explore the underlying mechanism, isobaric tags for relative and absolute quantification (iTRAQ) labeled quantitative proteomics was used to characterize the differentially expressed proteins of SL-6 cultured with PHE or NAP + PHE as carbon source. Through joint analysis of proteome and genome, unique proteins were identified and quantified. The up-regulated proteins mainly concentrated in PAH catabolism, Transporters and Electron transfer carriers. In the process, the regulator NahR, activated by salicylate (intermediate of NAP-biodegradation), up-regulates degradation enzymes (NahABCDE and SalABCDEFGH), which enhances the biodegradation of PHE and accumulation of toxic intermediate–1-hydroxy-2-naphthoic acid (1H2Na); 1H2Na stimulates the expression of ABC transporter, which maintains intracellular physiological activity by excreting 1H2Na; the up-regulation of cytochrome C promotes the above process running smoothly. Salicylate works as a trigger that stimulates cell to respond globally. The conjecture was verified at transcriptional and metabolic levels. These new insights contribute to improving the overall understanding of PAHs-biodegradation processes under complex natural conditions, and promoting the application of microbial remediation technology for PAHs pollution.

scholarly journals S6K1 Is Indispensible for Stress-Induced Microtubule Acetylation and Autophagic Flux

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 929
Author(s):  
Aleksandra Hać ◽  
Karolina Pierzynowska ◽  
Anna Herman-Antosiewicz
Keyword(s):  
Degradation Process ◽  
Underlying Mechanism ◽  
Stress Conditions ◽  
Autophagic Flux ◽  
Ratiometric Fluorescence ◽  
Mouse Embryonic Fibroblasts ◽  
Double Knockout ◽  
Embryonic Fibroblasts ◽  
Microtubule Network ◽  
Tubulin Acetylation

Autophagy is a specific macromolecule and organelle degradation process. The target macromolecule or organelle is first enclosed in an autophagosome, and then delivered along acetylated microtubules to the lysosome. Autophagy is triggered by stress and largely contributes to cell survival. We have previously shown that S6K1 kinase is essential for autophagic flux under stress conditions. Here, we aimed to elucidate the underlying mechanism of S6K1 involvement in autophagy. We stimulated autophagy in S6K1/2 double-knockout mouse embryonic fibroblasts by exposing them to different stress conditions. Transient gene overexpression or silencing, immunoblotting, immunofluorescence, flow cytometry, and ratiometric fluorescence analyses revealed that the perturbation of autophagic flux in S6K1-deficient cells did not stem from impaired lysosomal function. Instead, the absence of S6K1 abolished stress-induced tubulin acetylation and disrupted the acetylated microtubule network, in turn impairing the autophagosome-lysosome fusion. S6K1 overexpression restored tubulin acetylation and autophagic flux in stressed S6K1/2-deficient cells. Similar effect of S6K1 status was observed in prostate cancer cells. Furthermore, overexpression of an acetylation-mimicking, but not acetylation-resistant, tubulin variant effectively restored autophagic flux in stressed S6K1/2-deficient cells. Collectively, S6K1 controls tubulin acetylation, hence contributing to the autophagic flux induced by different stress conditions and in different cells.

scholarly journals The role of γ-aminobutyric acid in aluminum stress tolerance in a woody plant, Liriodendron chinense × tulipifera

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Pengkai Wang ◽  
Yini Dong ◽  
Liming Zhu ◽  
Zhaodong Hao ◽  
LingFeng Hu ◽  
...  
Keyword(s):  
Woody Plant ◽  
Underlying Mechanism ◽  
Absolute Quantification ◽  
Aminobutyric Acid ◽  
Gamma Aminobutyric Acid ◽  
Aluminum Stress ◽  
Inhibitory Neurotransmitter ◽  
Al Stress ◽  
Protein Ubiquitination ◽  
Liriodendron Chinense

AbstractThe aluminum (Al) cation Al3+ in acidic soil shows severe rhizotoxicity that inhibits plant growth and development. Most woody plants adapted to acidic soils have evolved specific strategies against Al3+ toxicity, but the underlying mechanism remains elusive. The four-carbon amino acid gamma-aminobutyric acid (GABA) has been well studied in mammals as an inhibitory neurotransmitter; GABA also controls many physiological responses during environmental or biotic stress. The woody plant hybrid Liriodendron (L. chinense × tulipifera) is widely cultivated in China as a horticultural tree and provides high-quality timber; studying its adaptation to high Al stress is important for harnessing its ecological and economic potential. Here, we performed quantitative iTRAQ (isobaric tags for relative and absolute quantification) to study how protein expression is altered in hybrid Liriodendron leaves subjected to Al stress. Hybrid Liriodendron shows differential accumulation of several proteins related to cell wall biosynthesis, sugar and proline metabolism, antioxidant activity, cell autophagy, protein ubiquitination degradation, and anion transport in response to Al damage. We observed that Al stress upregulated glutamate decarboxylase (GAD) and its activity, leading to increased GABA biosynthesis. Additional GABA synergistically increased Al-induced antioxidant enzyme activity to efficiently scavenge ROS, enhanced proline biosynthesis, and upregulated the expression of MATE1/2, which subsequently promoted the efflux of citrate for chelation of Al3+. We also showed similar effects of GABA on enhanced Al3+ tolerance in Arabidopsis. Thus, our findings suggest a function of GABA signaling in enhancing hybrid Liriodendron tolerance to Al stress through promoting organic acid transport and sustaining the cellular redox and osmotic balance.

scholarly journals iTRAQ-Based Proteomics Analysis of Autophagy-Mediated Responses against MeJA in Laticifers of Euphorbia kansui L.

2019 ◽  
Vol 20 (15) ◽  
pp. 3770
Author(s):  
Fang ◽  
Yao ◽  
Zhang ◽  
Tian ◽  
Wang ◽  
...  
Keyword(s):  
Developmental Process ◽  
Cysteine Proteinase ◽  
Defense Responses ◽  
Absolute Quantification ◽  
Pcr Analysis ◽  
Control Group ◽  
Proteomics Analysis ◽  
Meja Treatment ◽  
Euphorbia Kansui ◽  
Isobaric Tags

Autophagy is a well-defined catabolic mechanism whereby cytoplasmic materials are engulfed into a structure termed the autophagosome. Methyl jasmonate (MeJA), a plant hormone, mediates diverse developmental process and defense responses which induce a variety of metabolites. In plants, little is known about autophagy-mediated responses against MeJA. In this study, we used high-throughput comparative proteomics to identify proteins of latex in the laticifers. The isobaric tags for relative and absolute quantification (iTRAQ) MS/MS proteomics were performed, and 298 proteins among MeJA treated groups and the control group of Euphorbia kansui were identified. It is interesting to note that 29 significant differentially expressed proteins were identified and their associations with autophagy and ROS pathway were verified for several selected proteins as follows: α-L-fucosidase, β-galactosidase, cysteine proteinase, and Cu/Zn superoxide dismutase. Quantitative real-time PCR analysis of the selected genes confirmed the fact that MeJA might enhance the expression of some genes related to autophagy. The western blotting and immunofluorescence results of ATG8 and ATG18a which are two important proteins for the formation of autophagosomes also demonstrated that MeJA could promote autophagy at the protein level. Using the electron microscope, we observed an increase in autophagosomes after MeJA treatment. These results indicated that MeJA might promote autophagy in E. kansui laticifers; and it was speculated that MeJA mediated autophagy through two possible ways: the increase of ROS induces ATG8 accumulation and then aotophagosome formation, and MeJA promotes ATG18 accumulation and then autophagosome formation. Taken together, our results provide several novel insights for understanding the mechanism between autophagy and MeJA treatment. However, the specific mechanism remains to be further studied in the future.

scholarly journals Comparative Proteomic Analysis of Dipsacus asperoides Roots from Different Habitats in China

Molecules ◽  
2020 ◽  
Vol 25 (16) ◽  
pp. 3605
Author(s):  
Haijun Jin ◽  
Hua Yu ◽  
Haixia Wang ◽  
Jia Zhang
Keyword(s):  
Proteomic Analysis ◽  
Absolute Quantification ◽  
Pcr Analysis ◽  
Allene Oxide ◽  
Allene Oxide Cyclase ◽  
Protein Levels ◽  
Depth Analysis ◽  
Differential Proteins ◽  
Isobaric Tags

Dipsacus asperoides is a kind of Chinese herbal medicine with beneficial health properties. To date, the quality of D. asperoides from different habitats has shown significant differences. However, the molecular differences in D. asperoides from different habitats are still unknown. The aim of this study was to investigate the differences in protein levels of D. asperoides from different habitats. Isobaric tags for relative and absolute quantification (iTRAQ) and 2DLC/MS/MS were used to detect statistically significant changes in D. asperoides from different habitats. Through proteomic analysis, a total of 2149 proteins were identified, of which 42 important differentially expressed proteins were screened. Through in-depth analysis of differential proteins, the protein metabolism energy and carbohydrate metabolism of D. asperoides from Hubei Province were strong, but their antioxidant capacity was weak. We found that three proteins, UTP-glucose-1-phosphate uridylyltransferase, allene oxide cyclase, and isopentyl diphosphate isomerase 2, may be the key proteins involved in dipsacus saponin VI synthesis. Eight proteins were found in D. asperoides in response to environmental stress from different habitats. Quantitative real-time PCR analysis confirmed the accuracy and authenticity of the proteomic analysis. The results of this study may provide the basic information for exploring the cause of differences in secondary metabolites in different habitats of D. asperoides and the protein mechanism governing differences in quality.

Enhanced Biodegradation of Aniline under Anoxic Condition

2011 ◽  
Vol 356-360 ◽  
pp. 25-30 ◽  
Author(s):  
Jin You Shen ◽  
Chao Zhang ◽  
Xiu Yun Sun ◽  
Jian Sheng Li ◽  
Lian Jun Wang
Keyword(s):  
Performance Analysis ◽  
Benzene Ring ◽  
Organic Pollutants ◽  
Degradation Rate ◽  
Removal Rate ◽  
Degradation Process ◽  
Anoxic Condition ◽  
Aerobic Degradation ◽  
Industrial Wastewaters ◽  
Enhanced Biodegradation

Recalcitrant and toxic organic pollutants such as aniline from numerous industrial wastewaters can not be efficiently removed using the conventional methods. This study reported a concept for mineralization of aniline in an anoxic reactor, where enhanced biodegradation of aniline were achieved under anoxic conditions. The results indicated that with the presence of nitrate, the degradation rate of aniline was greatly improved compared with the absence of nitrate. From the UV-vis adsorption spectra, COD analysis and denitrification performance analysis, it could be inferred that the cleavage of benzene ring of aniline occurred, aniline could be mineralization by microorganisms under the anoxic condition. However, aniline removal rate was lower compared to aerobic degradation process, and thus needs a significant improvement.

scholarly journals Quantitative proteomic analysis of G-protein signalling inStagonospora nodorumusing isobaric tags for relative and absolute quantification

PROTEOMICS ◽  
2010 ◽  
Vol 10 (1) ◽  
pp. 38-47 ◽  
Author(s):  
Tammy Casey ◽  
Peter S. Solomon ◽  
Scott Bringans ◽  
Kar-Chun Tan ◽  
Richard P. Oliver ◽  
...  
Keyword(s):  
G Protein ◽  
Proteomic Analysis ◽  
Absolute Quantification ◽  
Quantitative Proteomic Analysis ◽  
G Protein Signalling ◽  
Isobaric Tags

scholarly journals Monocyte Proteomics Reveals Involvement of Phosphorylated HSP27 in the Pathogenesis of Osteoporosis

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Bhavna Daswani ◽  
Manoj Kumar Gupta ◽  
Shubhangi Gavali ◽  
Meena Desai ◽  
Gajanan J. Sathe ◽  
...  
Keyword(s):  
Absolute Quantification ◽  
Osteoclast Formation ◽  
Mineral Density ◽  
Monocyte Migration ◽  
Receptor Activator ◽  
Lower Chamber ◽  
Isobaric Tags ◽  
First Time ◽  
Upper Chamber ◽  
Increased Susceptibility

Peripheral monocytes, precursors of osteoclasts, have emerged as important candidates for identifying proteins relevant to osteoporosis, a condition characterized by low Bone Mineral Density (BMD) and increased susceptibility for fractures. We employed 4-plex iTRAQ (isobaric tags for relative and absolute quantification) coupled with LC-MS/MS (liquid chromatography coupled with tandem mass spectrometry) to identify differentially expressed monocyte proteins from premenopausal and postmenopausal women with low versus high BMD. Of 1801 proteins identified, 45 were differentially abundant in low versus high BMD, with heat shock protein 27 (HSP27) distinctly upregulated in low BMD condition in both premenopausal and postmenopausal categories. Validation in individual samples (n=80) using intracellular ELISA confirmed that total HSP27 (tHSP27) as well as phosphorylated HSP27 (pHSP27) was elevated in low BMD condition in both categories (P<0.05). Further, using transwell assays, pHSP27, when placed in the upper chamber, could increase monocyte migration (P<0.0001) and this was additive in combination with RANKL (receptor activator ofNFkBligand) placed in the lower chamber (P=0.05). Effect of pHSP27 in monocyte migration towards bone milieu can result in increased osteoclast formation and thus contribute to pathogenesis of osteoporosis. Overall, this study reveals for the first time a novel link between monocyte HSP27 and BMD.

scholarly journals The essential function of IL-33 in metabolic regulation

2020 ◽  
Vol 52 (7) ◽  
pp. 768-775 ◽  
Author(s):  
Wenping Li ◽  
Yiyuan Li ◽  
Jin Jin
Keyword(s):  
Metabolic Regulation ◽  
Underlying Mechanism ◽  
Lymphoid Cells ◽  
Regulatory Function ◽  
Current Evidence ◽  
Metabolic Processes ◽  
Interleukin 33 ◽  
Health And Disease ◽  
Essential Function ◽  
Group 2

Abstract Interleukin-33 (IL-33) is produced by various types of cells under physical or pathological conditions. As a multifunctional partner in health and disease, current evidence reveals that IL-33 also participates in several metabolic processes. IL-33 has been proven to contribute to regulating the activity of ST2+ group 2 innate lymphoid cells and regulatory T cells in adipose, which leads to the shift of insulin sensitivity and glucose clearance in glucose metabolism, thermogenesis, and adipocyte beiging in adipose metabolism. In this review, we briefly summarize the biological characteristics of Il-33 and discuss its regulatory function in glucose and adipose metabolism. By clarifying the underlying mechanism of IL-33, we highlight the crosstalk between immune response and metabolic processes mediated by IL-33.

scholarly journals iTRAQ-Based Comparative Proteomics Analysis of Urolithiasis Rats Induced by Ethylene Glycol

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Yanan Cao ◽  
Bin Duan ◽  
Xiaowei Gao ◽  
E. Wang ◽  
Zhitao Dong
Keyword(s):  
Ethylene Glycol ◽  
Kidney Stones ◽  
Enrichment Analysis ◽  
Absolute Quantification ◽  
Rat Models ◽  
Protein Protein Interaction ◽  
Parallel Reaction Monitoring ◽  
High Prevalence ◽  
Isobaric Tags ◽  
And Control

Nephrolithiasis is a frequent chronic urological condition with a high prevalence and recurrence rate. Proteomics studies on urolithiasis rat models are highly important in characterizing the pathophysiology of kidney stones and identifying potential approaches for preventing and treating kidney stones. The isobaric tags for relative and absolute quantification (iTRAQ) were performed to identify differentially expressed proteins (DEPs) in the kidney between urolithiasis rats and control rats. The results showed that 127 DEPs (85 upregulated and 42 downregulated) were identified in urolithiasis and control rats. The functions of DEPs were predicted by Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein–protein interaction (PPI) network analysis. The expression of four upregulated proteins (Tagln, Akr1c9, Spp1, and Fbn1) and four downregulated proteins (Hbb, Epb42, Hmgcs2, and Ca1) were validated by parallel reaction monitoring (PRM). Proteomics studies of ethylene glycol-induced urolithiasis rat models using iTRAQ and PRM helped to elucidate the molecular mechanism governing nephrolithiasis and to identify candidate proteins for the treatment of kidney stones.

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