Novel perspectives of environmental proteomics

Guo, Huiying; Wang, Lili; Deng, Ying; Ye, Jinshao

doi:10.1016/j.scitotenv.2021.147588

Cited by 10 publications

(5 citation statements)

References 102 publications

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“…The indirect enzyme extraction method and the efficiency at specific procedural points were determined for soils inoculated with A. oryzae cells or lysates. The enzyme quality was assessed for the presence of coextracted humic substances, which could interfere with downstream activity-based profiling ( Guo et al, 2021 ) or advanced mass spectro-scopic methods, including thermal shift assays ( Jafari et al, 2014 ; Savitski et al, 2014 ). Here, we compare our extraction efficiencies for enzyme activity and overall protein quality to other efforts in the literature and discuss other quality considerations when using soil extracted, active enzymes in downstream analysis.…”

Section: Discussionmentioning

confidence: 99%

“…While several studies have examined extracellular enzymes for their importance in nutrient (i.e., carbon and nitrogen) cycling, few studies have examined the extraction of active and intracellular enzymes involved in contaminant reduction. Intracellular proteins include highly specific and specialized enzymes critical for pollutant degradation, including perchlorate, an endocrine-disrupting compound ( Hutchison et al, 2013 ; Hutchison et al, 2017 ), and novel downstream proteomic processes require active enzymes ( Guo et al, 2021 ). Therefore, this study aimed to propose an indirect method of extracting active enzymes from soil using a model organism, Azospira oryzae , a known perchlorate-reducing and soil-relevant bacteria.…”

Section: Introductionmentioning

confidence: 99%

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Extraction of active, contaminant degrading enzymes from soil

Chacha

Tran

Scarlett

et al. 2023

Applied Soil Ecology

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Extraction of active, contaminant degrading enzymes from soil

Chacha

Tran

Scarlett

et al. 2023

Applied Soil Ecology

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“…The structural properties of proteins, as well as the physicochemical connections between effective proteins and pollutants, are thought to have a crucial role in the binding, absorption, and transformation of pollutants ( 120 ). The formation of adducts, alteration of phosphorylation status (Phorbol Esters), alteration of thiols, reactive oxygen species (ROS), and conversion of side chains to aldehyde or ketone groups are all examples of how environmental toxicants, medications, and diet interact with proteins ( 121 ).…”

Section: Understanding Omicsmentioning

confidence: 99%

“…One strategy for uncovering the mechanism of protein evolution under stress is to compare the proportion of individual amino acid residues in the functional protein sequence at different stages of environmental stress and then calculate the correlation between the proportions of amino acid residues and protein physicochemical properties ( 123 ). Another technique for investigating the evolutionary process is to analyze the mutation site and conservation sequence of proteins at various phases of environmental stress ( 120 ).…”

Section: Understanding Omicsmentioning

confidence: 99%

Climate change, human health, and the exposome: Utilizing OMIC technologies to navigate an era of uncertainty

Abdelzaher

Tawfik

Nour

et al. 2022

Front. Public Health

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Climate change is an anthropogenic phenomenon that is alarming scientists and non-scientists alike. The emission of greenhouse gases is causing the temperature of the earth to rise and this increase is accompanied by a multitude of climate change-induced environmental exposures with potential health impacts. Tracking human exposure has been a major research interest of scientists worldwide. This has led to the development of exposome studies that examine internal and external individual exposures over their lifetime and correlate them to health. The monitoring of health has also benefited from significant technological advances in the field of “omics” technologies that analyze physiological changes on the nucleic acid, protein, and metabolism levels, among others. In this review, we discuss various climate change-induced environmental exposures and their potential health implications. We also highlight the potential integration of the technological advancements in the fields of exposome tracking, climate monitoring, and omics technologies shedding light on important questions that need to be answered.

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“…Proteins are involved in almost all biochemical reactions that occur in a cell (Heyer et al 2017). Accordingly, the development of proteomics technologies to study all proteins in a species has opened new opportunities for elucidating the bacterial molecular mechanisms in response to speci c stress (Chen et al 2020;Guo et al 2021). In particular, comparative proteomics is a useful approach that allows the analysis of proteins expressed and repressed differently under normal conditions with respect to stressful conditions (Gao et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Proteomic analysis to unravel the biochemical mechanisms triggered by Bacillus toyonensis SFC 500-1E under chromium(VI) and phenol stress

et al. 2023

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Bacillus toyonensis SFC 500-1E is a member of the consortium SFC 500-1 able to remove Cr(VI) and simultaneously tolerate high phenol concentrations. In order to elucidate mechanisms utilized by this strain during the bioremediation process, the differential expression pattern of proteins was analyzed when it grew with or without Cr(VI) (10 mg/L) and Cr(VI)+phenol (10 and 300 mg/L), through two complementary proteomic approaches: gel-based (SDS-PAGE) and gel-free (nanoUPLC-ESI-MS/MS).A total of 400 differentially expressed proteins were identi ed, out of which 152 proteins were down-regulated under Cr(VI) and 205 up-regulated in the presence of Cr(VI)+phenol, suggesting the extra effort made by the strain to adapt itself and keep growing when phenol was added. The major metabolic pathways affected include carbohydrate and energetic metabolism, followed by lipid and amino acid metabolism. Particularly interesting were also ABC transporters and the iron-siderophore transporter as well as transcriptional regulators that can bind metals. Stressassociated global response involving the expression of thioredoxins, SOS response, and chaperones appears to be crucial for the survival of this strain under treatment with both contaminants. This research not only provided a deeper understanding of B. toyonensis SFC 500-1E metabolic role in Cr(VI) and phenol bioremediation process but also allowed us to complete an overview of the consortium SFC 500-1 behavior. This may contribute to an improvement in its use as a bioremediation strategy and also provides a baseline for further research.

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Novel perspectives of environmental proteomics

Cited by 10 publications

References 102 publications

Extraction of active, contaminant degrading enzymes from soil

Extraction of active, contaminant degrading enzymes from soil

Climate change, human health, and the exposome: Utilizing OMIC technologies to navigate an era of uncertainty

Proteomic analysis to unravel the biochemical mechanisms triggered by Bacillus toyonensis SFC 500-1E under chromium(VI) and phenol stress

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