Antimicrobial silver targets glyceraldehyde-3-phosphate dehydrogenase in glycolysis of <i>E. coli</i>

Wang, Haibo; Wang, Minji; Yang, Xinming; Xu, Xiaohan; Hao, Quan; Yan, Aixin; Hu, Maogui; Łobiński, Ryszard; Li, Hongyan; Sun, Hongzhe

doi:10.1039/c9sc02032b

Cited by 48 publications

(40 citation statements)

References 55 publications

(66 reference statements)

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“…Surprisingly, the presence of NAD + eliminated the positive electron density near the Cys149. This change also stabilized the secondary structure of the alpha helix, which recovered its commonly observed conformation [33,34,38,39]. However, we could not build the NAD + moiety due to its low occupancy (0.7); this data might be in agreement with previous studies in which the affinity towards NAD + is decreased for the oxidized enzyme [48].…”

Section: Discussionsupporting

confidence: 90%

“…Interestingly, soaking the crystals with NAD + highly reduces the presence of the large electron density around Cys149 and stabilizes the secondary structure of the alpha helix in only one conformation (Figure 4a,b). All residues recovered the conformation previously reported in other EcG3PDH models [33,34,38,39].…”

Section: Double Conformation Of the Helix (Residues 206-214)supporting

confidence: 79%

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A Novel Substrate-Binding Site in the X-ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion

2019

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Escherichia coli (E. coli), one of the most frequently used host for the expression of recombinant proteins, is often affected by the toxic effect of the exogenous proteins that is required to express. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a multi-functional protein that has been used as a control marker for basal function and it is known to undergo cysteine oxidation under different types of cellular stress. Here, we report the 3D structure of the endogenous GAPDH purified from stressed E. coli cells expressing a eukaryotic protein. The structure was solved at 1.64 Å using single-wavelength anomalous dispersion (SAD) phasing with a selenium-modified enzyme. Interestingly, each GAPDH monomer contains a molecule of glyceraldehyde-3 phosphate in a non-previously identified site. Furthermore, the catalytic Cys149 is covalently attached to a ~300 Da molecule, possibly glutathione. This modification alters the conformation of an adjacent alpha helix in the catalytic domain, right opposite to the NAD+ binding site. The conformation of the alpha helix is stabilized after soaking the crystals with NAD+. These results exemplify the effects that the overexpression of an exogenous protein has over the host proteins and sheds light on the structural changes that large oxidant molecules on the catalytic cysteine produce for the GAPDH enzyme.

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Section: Discussionsupporting

confidence: 90%

Section: Double Conformation Of the Helix (Residues 206-214)supporting

confidence: 79%

A Novel Substrate-Binding Site in the X-ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion

2019

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“…[40][41][42] Furthermore, new advances have revealed detailed information on possible modes of action for silver-based antimicrobial compounds. 43,44 Silver itself is known to be an antimicrobial agent, with varying activity depending on form (salts vs. nanoparticles vs. colloidal forms), so analysis of activity of silver complexes is complicated by this inherent activity. 45,46 Altogether, our data support the published literature and highlights that silver compounds are a proven starting point for preparation of new potential antibiotic compounds.…”

Section: 5%mentioning

confidence: 99%

Metal complexes as a promising source for new antibiotics

et al. 2020

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“…A possible hypothesis to explain this variation could be the downregulation of the glycolytic conversion of glucose to pyruvate, which is consistent with the observed significant reduction in pyruvate excretion. An early work has shown that silver ions could inactivate yeast hexokinase due to binding with protein thiol groups, while a recent metallomics work has highlighted glycolytic enzymes as primary targets of ionic silver in E. coli . Additionally, similar findings, namely decreased activities of hexokinase and enolase, have been recently reported in mouse macrophages exposed to AgNPs .…”

Section: Discussionmentioning

confidence: 75%

Macrophage Metabolomics Reveals Differential Metabolic Responses to Subtoxic Levels of Silver Nanoparticles and Ionic Silver

et al. 2020

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This study employed NMR metabolomics to characterize macrophage responses to subtoxic concentrations of silver nanoparticles (AgNPs ca. 30 nm) and ionic silver (Ag + ), with a view to further elucidate their immunomodulatory activity at the cell metabolism level. Exposure to AgNPs caused RAW 264.7 macrophages to decrease intracellular glucose utilization, possibly due to interference with glycolytic enzymes, and to reprogram the TCA cycle towards anaplerotic fueling and production of anti-inflammatory metabolites (e.g. itaconate and creatine). Moreover, AgNPs-exposed cells were able to control the levels [a] Dr. 1867of reactive oxygen/nitrogen species (ROS/RNS), likely through upregulation of glutathione synthesis. On the other hand, macrophages exposed to Ag + at equivalent subtoxic concentrations showed reduced metabolic activity, lower ability to counterbalance ROS/RNS and alterations in membrane-related lipids. Overall, the metabolomics approach hereby employed provided novel insights into the differential effects of AgNPs and Ag + , which help explain the lower toxic potential of nanosilver than silver ions.ter. Moreover, since the release of silver ions from AgNPs has been highlighted as a main driver of AgNPs toxicity, [23] the metabolic effects of ionic silver (administered as AgNO 3 ), at inhibi-Joana Carrola graduated in Chemistry from the University of Porto, and obtained her PhD in Nanosciences and Nanotechnology, in 2017, from the University of Aveiro. Her PhD research focused on silver nanoparticles metabolism in mammalian cells. She is an expert in metabolomics, with interests in the study of drugs and nanomaterials metabolism.Verónica Bastos obtained her PhD in Biology studying nanotoxicity in in vitro cell cultures at the University of Aveiro, 2016. She is currently a Researcher in a project studying upconversion nanoparticles for multimodal therapy of melanoma at CESAM, Biology department of University of Aveiro. Her main research interests are related to nanotoxicity, nanobiomedicine and cancer therapy, ecotoxicology and human health. Ana Luísa Daniel-da-Silva graduated in Chemical Engineering by Instituto Superior Técnico (Lisbon, Portugal) in 2000 and obtained her PhD degree in Materials Science from the University of Alicante (Spain) in 2005. Since 2009 she is researcher at CICECO-Portugal. Her research focuses on the development of functional nanoparticles and nanocomposites for applications in nanomedicine, bionanotechnology and water remediation. and a member of CICECO-Aveiro Institute of Materials. Her main research interests are: 1) NMR metabolomics of biological systems (biofluids, intact tissues, tissue/material systems, cell cultures) subjected to disease, therapeutics, toxicological or environmental stresses for identification of novel biomarkers; 2) Metabolomic testing of novel biomaterials with applications in biodegradable implants, drug delivery or localized cell recognition; 3) Development of spectroscopy-based methods for food quality control.Conceição Santos is a Full Profes...

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Antimicrobial silver targets glyceraldehyde-3-phosphate dehydrogenase in glycolysis of E. coli

Abstract: We report for the first time that antimicrobial Ag+ targets the glycolytic pathway through inhibiting the key enzyme of GAPDH.

Cited by 48 publications

References 55 publications

A Novel Substrate-Binding Site in the X-ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion

A Novel Substrate-Binding Site in the X-ray Structure of an Oxidized E. coli Glyceraldehyde 3-Phosphate Dehydrogenase Elucidated by Single-Wavelength Anomalous Dispersion

Metal complexes as a promising source for new antibiotics

Macrophage Metabolomics Reveals Differential Metabolic Responses to Subtoxic Levels of Silver Nanoparticles and Ionic Silver

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