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Contaldo U, Savant-Aira D, Vergnes A, Becam J, Biaso F, Ilbert M, Aussel L, Ezraty B, Lojou E, Mazurenko I. Methionine-rich domains emerge as facilitators of copper recruitment in detoxification systems. Proc Natl Acad Sci U S A 2024; 121:e2402862121. [PMID: 39378088 DOI: 10.1073/pnas.2402862121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 09/01/2024] [Indexed: 10/10/2024] Open
Abstract
Copper homeostasis mechanisms are critical for bacterial resistance to copper-induced stress. The Escherichia coli multicopper oxidase copper efflux oxidase (CueO) is part of the copper detoxification system in aerobic conditions. CueO contains a methionine-rich (Met-rich) domain believed to interact with copper, but its exact function and the importance of related copper-binding sites remain unclear. This study investigates these open questions by employing a multimodal and multiscale approach. Through the design of various E. coli CueO (EcCueO) variants with altered copper-coordinating residues and domain deletions, we employ biological, biochemical, and physico-chemical approaches to unravel in vitro CueO catalytic properties and in vivo copper resistance. Strong correlation between the different methods enables evaluation of EcCueO variants' activity as a function of Cu+ availability. Our findings demonstrate the Met-rich domain is not essential for cuprous oxidation, but it facilitates Cu+ recruitment from strongly chelated forms, acting as transient copper binding domain thanks to multiple methionines. They also indicate that the Cu6/7 copper-binding sites previously observed within the Met-rich domain play a negligible role. Meanwhile, Cu5, located at the interface with the Met-rich domain, emerges as the primary and sole substrate-binding active site for cuprous oxidation. The Cu5 coordination sphere strongly affects the enzyme activity and the in vivo copper resistance. This study provides insights into the nuanced role of CueO Met-rich domain, enabling the functions of copper-binding sites and the entire domain itself to be decoupled. This paves the way for a deeper understanding of Met-rich domains in the context of bacterial copper homeostasis.
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Affiliation(s)
- Umberto Contaldo
- Aix Marseille University, CNRS, BIP - UMR 7281, IMM - FR3479, 13402 Marseille, France
| | - Dylan Savant-Aira
- Aix Marseille University, CNRS, BIP - UMR 7281, IMM - FR3479, 13402 Marseille, France
| | - Alexandra Vergnes
- Aix Marseille University, CNRS, LCB - UMR 7283, IMM - FR3479, 13402 Marseille, France
| | - Jérôme Becam
- Aix Marseille University, CNRS, LCB - UMR 7283, IMM - FR3479, 13402 Marseille, France
| | - Frédéric Biaso
- Aix Marseille University, CNRS, BIP - UMR 7281, IMM - FR3479, 13402 Marseille, France
| | - Marianne Ilbert
- Aix Marseille University, CNRS, BIP - UMR 7281, IMM - FR3479, 13402 Marseille, France
| | - Laurent Aussel
- Aix Marseille University, CNRS, LCB - UMR 7283, IMM - FR3479, 13402 Marseille, France
| | - Benjamin Ezraty
- Aix Marseille University, CNRS, LCB - UMR 7283, IMM - FR3479, 13402 Marseille, France
| | - Elisabeth Lojou
- Aix Marseille University, CNRS, BIP - UMR 7281, IMM - FR3479, 13402 Marseille, France
| | - Ievgen Mazurenko
- Aix Marseille University, CNRS, BIP - UMR 7281, IMM - FR3479, 13402 Marseille, France
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Otur Ç, Okay S, Konuksever Ö, Duyar O, Kaya Y, Kurt-Kızıldoğan A. Comprehensive characterization and resistome analysis of Antarctic Pseudomonas migulae strain CAS19. World J Microbiol Biotechnol 2024; 40:347. [PMID: 39397126 DOI: 10.1007/s11274-024-04153-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 09/30/2024] [Indexed: 10/15/2024]
Abstract
Although traditionally considered pristine, Antarctica faces an increasing threat of antibiotic resistance due to human intervention. Here, we obtained a bacterial isolate, the CAS19 strain, from a lake water sample from Ardley Island, Antarctica and characterized it comprehensively. The CAS19 was a psychrotrophic and neutrophilic/alkalitolerant bacterium thriving at temperatures from 15 to 33 °C and pH levels from 6.0 to 9.0. Besides the production of siderophore and indole acetic acid, it also exhibited proteolytic and lipolytic activities. It was identified as Pseudomonas migulae by multilocus (16S rRNA, gyrB, rpoB and rpoD) sequence analysis, and its genome was 6.5 Mbps in length, had 59% GC content, and contained 5,821 coding sequences. The CAS19 was resistant to several antibiotics, including trimethoprim, penicillin, vancomycin, and erythromycin, confirmed by RT-qPCR analysis, with a notable increase in dfr (63-fold), bla (461-fold), vanW (31.7-fold) and macA (24.7-fold) expressions upon antibiotic exposure. Additionally, CAS19 exhibited resistance to heavy metals with an order of Cr(III) = Cu(II) > Ni(II) > Zn(II) > Cd(II), and showed diesel fuel (5%) degradation capacity. Cold-related genes cspA_2 and cspD were overexpressed at 4 and 15 °C, consistent with the cold adaptation mechanism. In conclusion, for the first time an Antarctic P. migulae isolate has been characterized in detail, uncovering a rich resistome repertoir that might be associated with anthropogenic disturbances.
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Affiliation(s)
- Çiğdem Otur
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, 55139, Türkiye
| | - Sezer Okay
- Department of Vaccine Technology, Vaccine Institute, Hacettepe University, Ankara, 06230, Türkiye.
| | - Ömer Konuksever
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, 55139, Türkiye
| | - Oğuzhan Duyar
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, 55139, Türkiye
| | - Yılmaz Kaya
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, 55139, Türkiye
| | - Aslıhan Kurt-Kızıldoğan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, 55139, Türkiye.
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Ferrara F, Castagna T, Pantolini B, Campanardi MC, Roperti M, Grotto A, Fattori M, Dal Maso L, Carrara F, Zambarbieri G, Zovi A, Capuozzo M, Langella R. The challenge of antimicrobial resistance (AMR): current status and future prospects. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03318-x. [PMID: 39052061 DOI: 10.1007/s00210-024-03318-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
Antimicrobial resistance (AMR) represents a critical global threat, compromising the effectiveness of antibacterial drugs as bacteria adapt and survive exposure to many classes of these drugs. This phenomenon is primarily fueled by the widespread overuse and misuse of antibacterial drugs, exerting selective pressure on bacteria and promoting the emergence of multi-resistant strains. AMR poses a top-priority challenge to public health due to its widespread epidemiological and economic implications, exacerbated not only by the diminishing effectiveness of currently available antimicrobial agents but also by the limited development of genuinely effective new molecules. In addressing this issue, our research aimed to examine the scientific literature narrating the Italian situation in the common European context of combating AMR. We sought to delineate the current state of AMR and explore future prospects through an analysis of strategies to counter antibacterial drug resistance. Adopting the "One Health" model, our objective was to comprehensively engage diverse sectors, integrate various disciplines, and propose programs, policies, and regulations. This narrative review, based on PubMed research related to antibiotic resistance, emphasizes the urgent need for a coordinated and proactive approach at both national and European levels to mitigate the impact of AMR and pave the way for effective strategies to counter this global health challenge.
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Affiliation(s)
- Francesco Ferrara
- Pharmaceutical Department, Asl Napoli 3 Sud, Dell'amicizia Street 72, 80035, Nola, Naples, Italy.
| | - Tommaso Castagna
- Pharmacy Unit, ASST Di Lecco, Dell'Eremo Street 9/11, 23900, Lecco, Italy
| | | | | | - Martina Roperti
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, 20159, Milan, Italy
| | - Alessandra Grotto
- University of Milan, Festa del Perdono Street 7, 20122, Milan, Italy
| | - Martina Fattori
- Istituto Europeo Di Oncologia, Ripamonti Street 435, 20122, Milan, Italy
| | - Lucia Dal Maso
- Pharmaceutical Department, ASST Santi Paolo E Carlo, Antonio Rudinì Street 8, 20159, Milan, Italy
| | - Federica Carrara
- Pharmaceutical Department, Humanitas Gavazzeni, Mauro Gavazzeni Street 21, 24125, Bergamo, BG, Italy
| | - Giulia Zambarbieri
- Pharmaceutical Department, Humanitas Gavazzeni, Mauro Gavazzeni Street 21, 24125, Bergamo, BG, Italy
| | - Andrea Zovi
- Ministry of Health, Viale Giorgio Ribotta 5, 00144, Rome, Italy
| | - Maurizio Capuozzo
- Pharmaceutical Department, Asl Napoli 3 Sud, Dell'amicizia Street 72, 80035, Nola, Naples, Italy
| | - Roberto Langella
- Italian Society of Hospital Pharmacy (SIFO), SIFO Secretariat of the Lombardy Region, Via Carlo Farini, 81, 20159, Milan, Italy
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4
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Partipilo G, Bowman EK, Palmer EJ, Gao Y, Ridley RS, Alper HS, Keitz BK. Single-Cell Phenotyping of Extracellular Electron Transfer via Microdroplet Encapsulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598847. [PMID: 38915652 PMCID: PMC11195189 DOI: 10.1101/2024.06.13.598847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes. Studying this phenomenon in high-throughput is challenging since extracellular reduction cannot easily be traced back to its cell of origin within a mixed population. Here, we describe the development of a microdroplet emulsion system to enrich EET-capable organisms. We validated our system using the model electroactive organism S. oneidensis and describe the tooling of a benchtop microfluidic system for oxygen-limited processes. We demonstrated enrichment of EET-capable phenotypes from a mixed wild-type and EET-knockout population. As a proof-of-concept application, bacteria were collected from iron sedimentation from Town Lake (Austin, TX) and subjected to microdroplet enrichment. We observed an increase in EET-capable organisms in the sorted population that was distinct when compared to a population enriched in a bulk culture more closely akin to traditional techniques for discovering EET-capable bacteria. Finally, two bacterial species, C. sakazakii and V. fessus not previously shown to be electroactive, were further cultured and characterized for their ability to reduce channel conductance in an organic electrochemical transistor (OECT) and to reduce soluble Fe(III). We characterized two bacterial species not previously shown to exhibit electrogenic behavior. Our results demonstrate the utility of a microdroplet emulsions for identifying putative EET-capable bacteria and how this technology can be leveraged in tandem with existing methods.
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Affiliation(s)
- Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Emily K. Bowman
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, 78712
| | - Emma J. Palmer
- Civil, Architectural, and Environmental Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Yang Gao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Rodney S. Ridley
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Benjamin K. Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
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5
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Elsen S, Simon V, Attrée I. Cross-regulation and cross-talk of conserved and accessory two-component regulatory systems orchestrate Pseudomonas copper resistance. PLoS Genet 2024; 20:e1011325. [PMID: 38861577 PMCID: PMC11195947 DOI: 10.1371/journal.pgen.1011325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/24/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
Bacteria use diverse strategies and molecular machinery to maintain copper homeostasis and to cope with its toxic effects. Some genetic elements providing copper resistance are acquired by horizontal gene transfer; however, little is known about how they are controlled and integrated into the central regulatory network. Here, we studied two copper-responsive systems in a clinical isolate of Pseudomonas paraeruginosa and deciphered the regulatory and cross-regulation mechanisms. To do so, we combined mutagenesis, transcriptional fusion analyses and copper sensitivity phenotypes. Our results showed that the accessory CusRS two-component system (TCS) responds to copper and activates both its own expression and that of the adjacent nine-gene operon (the pcoA2 operon) to provide resistance to elevated levels of extracellular copper. The same locus was also found to be regulated by two core-genome-encoded TCSs-the copper-responsive CopRS and the zinc-responsive CzcRS. Although the target palindromic sequence-ATTCATnnATGTAAT-is the same for the three response regulators, transcriptional outcomes differ. Thus, depending on the operon/regulator pair, binding can result in different activation levels (from none to high), with the systems demonstrating considerable plasticity. Unexpectedly, although the classical CusRS and the noncanonical CopRS TCSs rely on distinct signaling mechanisms (kinase-based vs. phosphatase-based), we discovered cross-talk in the absence of the cognate sensory kinases. This cross-talk occurred between the proteins of these two otherwise independent systems. The cusRS-pcoA2 locus is part of an Integrative and Conjugative Element and was found in other Pseudomonas strains where its expression could provide copper resistance under appropriate conditions. The results presented here illustrate how acquired genetic elements can become part of endogenous regulatory networks, providing a physiological advantage. They also highlight the potential for broader effects of accessory regulatory proteins through interference with core regulatory proteins.
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Affiliation(s)
- Sylvie Elsen
- University Grenoble Alpes, Institute of Structural Biology, UMR5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| | - Victor Simon
- University Grenoble Alpes, Institute of Structural Biology, UMR5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| | - Ina Attrée
- University Grenoble Alpes, Institute of Structural Biology, UMR5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
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6
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Behzadinasab S, Williams MD, Falkinham Iii JO, Ducker WA. Antimicrobial mechanism of cuprous oxide (Cu 2O) coatings. J Colloid Interface Sci 2023; 652:1867-1877. [PMID: 37688933 DOI: 10.1016/j.jcis.2023.08.136] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023]
Abstract
Some very effective antimicrobial coatings exploit copper or cuprous oxide (Cu2O) as the active agent. The aim of this study is to determine which species is the active antimicrobial - dissolved ions, the Cu2O solid, or reactive oxygen species. Copper ions were leached from Cu2O into various solutions and the leachate tested for both dissolved copper and the efficacy in killing Pseudomonas aeruginosa. The concentration of copper species leached from Cu2O into aqueous solution varied greatly with the composition of the aqueous solution. For a range of solution buffers, killing of P. aeruginosa was highly correlated with the concentration of copper in the leachate. Further, 10 µL bacterial suspension droplets were placed on Cu2O coatings, with or without a polymer barrier layer, and tested for bacterial kill. Killing occurred without contact between bacterium and solid, demonstrating that contact with Cu2O is not necessary. We therefore conclude that soluble copper species are the antimicrobial agent, and that the most potent species is Cu+. The solid quickly raises and sustains the concentration of soluble copper species near the bacterium. Killing via soluble copper ions rather than contact should allow copper coatings to kill bacteria even when fouled, which is an important practical consideration.
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Affiliation(s)
- Saeed Behzadinasab
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA; Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Myra D Williams
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
| | | | - William A Ducker
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, 24061, USA; Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA, 24061, USA.
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7
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Igbaria-Jaber Y, Hofmann L, Gevorkyan-Airapetov L, Shenberger Y, Ruthstein S. Revealing the DNA Binding Modes of CsoR by EPR Spectroscopy. ACS OMEGA 2023; 8:39886-39895. [PMID: 37901548 PMCID: PMC10601412 DOI: 10.1021/acsomega.3c06336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/31/2023]
Abstract
In pathogens, a unique class of metalloregulator proteins, called gene regulatory proteins, sense specific metal ions that initiate gene transcription of proteins that export metal ions from the cell, thereby preventing toxicity and cell death. CsoR is a metalloregulator protein found in various bacterial systems that "sense" Cu(I) ions with high affinity. Upon copper binding, CsoR dissociates from the DNA promoter region, resulting in initiation of gene transcription. Crystal structures of CsoR in the presence and absence of Cu(I) from various bacterial systems have been reported, suggesting either a dimeric or tetrameric structure of these helical proteins. However, structural information about the CsoR-DNA complex is missing. Here, we applied electron paramagnetic resonance (EPR) spectroscopy to follow the conformational and dynamical changes that Mycobacterium tuberculosis CsoR undergoes upon DNA binding in solution. We showed that the quaternary structure is predominantly dimeric in solution, and only minor conformational and dynamical changes occur in the DNA bound state. Also, labeling of the unresolved C- terminus revealed no significant change in dynamics upon DNA binding. These observations are unique, since for other bacterial copper metalloregulators, such as the MerR and CopY families, major conformational changes were observed upon DNA binding, indicating a different mode of action for this protein family.
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Affiliation(s)
- Yasmin Igbaria-Jaber
- Department of Chemistry and the Institute
of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Lukas Hofmann
- Department of Chemistry and the Institute
of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry and the Institute
of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yulia Shenberger
- Department of Chemistry and the Institute
of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Sharon Ruthstein
- Department of Chemistry and the Institute
of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 52900, Israel
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8
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Skvortsov AN, Ilyechova EY, Puchkova LV. Chemical background of silver nanoparticles interfering with mammalian copper metabolism. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131093. [PMID: 36905906 DOI: 10.1016/j.jhazmat.2023.131093] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
The rapidly increasing application of silver nanoparticles (AgNPs) boosts their release into the environment, which raises a reasonable alarm for ecologists and health specialists. This is manifested as increased research devoted to the influence of AgNPs on physiological and cellular processes in various model systems, including mammals. The topic of the present paper is the ability of silver to interfere with copper metabolism, the potential health effects of this interference, and the danger of low silver concentrations to humans. The chemical properties of ionic and nanoparticle silver, supporting the possibility of silver release by AgNPs in extracellular and intracellular compartments of mammals, are discussed. The possibility of justified use of silver for the treatment of some severe diseases, including tumors and viral infections, based on the specific molecular mechanisms of the decrease in copper status by silver ions released from AgNPs is also discussed.
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Affiliation(s)
- Alexey N Skvortsov
- Graduate School of Biomedical Systems and Technologies, Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia; Laboratory of Molecular Biology of Stem Cells, Institute of Cytology of the Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | - Ekaterina Yu Ilyechova
- Graduate School of Biomedical Systems and Technologies, Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia; Department of Molecular Genetics, Institute of Experimental Medicine of the Russian Academy of Sciences, Saint Petersburg 197376, Russia; Research Center of Advanced Functional Materials and Laser Communication Systems (RC AFMLCS), ITMO University, Saint Petersburg 197101, Russia.
| | - Ludmila V Puchkova
- Graduate School of Biomedical Systems and Technologies, Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia; Department of Molecular Genetics, Institute of Experimental Medicine of the Russian Academy of Sciences, Saint Petersburg 197376, Russia; Research Center of Advanced Functional Materials and Laser Communication Systems (RC AFMLCS), ITMO University, Saint Petersburg 197101, Russia
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9
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Wang S, Zhang K, Zhang Q, Li Y, Yin Y, Liu W, An S, Zhang R, Zhang Z. Pseudomonas aeruginosa Y12 play positive roles regulating larval gut communities when housefly encountered copper stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 258:114978. [PMID: 37150108 DOI: 10.1016/j.ecoenv.2023.114978] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/25/2023] [Accepted: 05/01/2023] [Indexed: 05/09/2023]
Abstract
Heavy metal contamination has become a global concern that threatens the lives of animals and insects throughout the food chain. Pseudomonas is a commonly found genus of bacteria that colonizes the intestines of insects and constitutes a necessary part of the insect gut microbiota. This research analyzed the influence of different concentrations of Cu2+ on housefly larval development, gut microbial structure and antioxidant defense system, and investigated the regulatory mechanism of P. aeruginosa Y12 on the gut microbiota when houseflies were exposed to Cu2+. We found that adding Cu2+ to the larval diet inhibited larval growth, while the mixed addition of P. aeruginosa Y12 and Cu2+ to the diet reduced the inhibitory effects of Cu2+ on larval growth. Oral administration of Cu2+ significantly changed the gut community structure and increased larval gut bacterial diversity. In vitro analysis revealed that P. aeruginosa Y12 showed Cu2+ adsorption effects and increased Cu2+ aggregation. The mixed addition of low concentrations of P. aeruginosa Y12 and Cu2+ to the larval diet caused a dynamic shift in the gut microbiota and resulted in a novel gut community structure with an increase in beneficial bacteria and a decrease in pathogenic bacteria. Furthermore, P. aeruginosa Y12 treatment influenced the activity of antioxidant enzymes in housefly larvae, indicating that the addition of P. aeruginosa Y12 to the larval diet could further influence the antioxidant system through P. aeruginosa Y12-Cu2+ interactions. In conclusion, our research revealed that intestinal flora dysbiosis was the essential reason why copper inhibits housefly larval growth. However, proper supplementation with P. aeruginosa Y12 played positive roles in regulating larval gut communities and protecting insects from toxic heavy metals.
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Affiliation(s)
- Shumin Wang
- School of Life Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Kexin Zhang
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Qian Zhang
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Ying Li
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Yansong Yin
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Wenjuan Liu
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Sha An
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China
| | - Ruiling Zhang
- School of Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China.
| | - Zhong Zhang
- School of Life Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian 271016, Shandong, China; Weifang Medical University, Weifang 261021, Shandong, China.
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10
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Gajera G, Henriksen N, Cox B, Kothari V. Identification of anti-pathogenic activity among in silico predicted small-molecule inhibitors of Pseudomonas aeruginosa LasR or nitric oxide reductase (NOR). Drug Target Insights 2023; 17:101-109. [PMID: 37811195 PMCID: PMC10551673 DOI: 10.33393/dti.2023.2638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Antibiotic-resistant Pseudomonas aeruginosa strains cause considerable morbidity and mortality globally. Identification of novel targets in this notorious pathogen is urgently warranted to facilitate discovery of new anti-pathogenic agents against it. This study attempted to identify small-molecule inhibitors of two important proteins LasR and nitric oxide reductase (NOR) in P. aeruginosa. 'Las' system can be said to be the 'master' regulator of quorum sensing in P. aeruginosa, whose receptor protein is LasR. Similarly, NOR is crucial to detoxification of reactive nitrogen species. Methods In silico identification of potential LasR or NOR inhibitors was attempted through a virtual screening platform AtomNet® to obtain a final subset of <100 top scoring compounds. These compounds were evaluated for their in vivo anti-pathogenic activity by challenging the model host Caenorhabditis elegans with P. aeruginosa in the presence or absence of test compounds. Survival of the worm population in 24-well assay plates was monitored over a period of 5 days microscopically. Results Of the 96 predicted LasR inhibitors, 11 exhibited anti-Pseudomonas activity (23%-96% inhibition of bacterial virulence as per third-day end-point) at 25-50 µg/mL. Of the 85 predicted NOR inhibitors, 8 exhibited anti-Pseudomonas activity (40%-85% inhibition of bacterial virulence as per second-day end-point) at 25-50 µg/mL. Conclusion Further investigation on molecular mode of action of compounds found active in this study is warranted. Virtual screening can be said to be a useful tool in narrowing down the list of compounds requiring actual wet-lab screening, saving considerable time and efforts for drug discovery.
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Affiliation(s)
- Gemini Gajera
- Institute of Science, Nirma University, Ahmedabad - India
| | | | - Bryan Cox
- Atomwise Inc, San Francisco, CA - USA
| | - Vijay Kothari
- Institute of Science, Nirma University, Ahmedabad - India
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11
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Marcelo GA, Galhano J, Duarte MP, Kurutos A, Capelo-Martínez JL, Lodeiro C, Oliveira E. Functional Cyanine-Based PVA:PVP Polymers as Antimicrobial Tools toward Food and Health-Care Bacterial Infections. Macromol Biosci 2022; 22:e2200244. [PMID: 36004698 DOI: 10.1002/mabi.202200244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/22/2022] [Indexed: 01/15/2023]
Abstract
The rising of multidrug-resistant bacteria and their associated proliferation as harmful microorganisms boosts the creation of new antibacterial surfaces and biomaterials with applications ranging from health to food packing. Herein, low-cost antibacterial PVA:PVP copolymers containing cyanine derivatives (1, 2, and 3) and their respective Cu2+ complexes are successfully obtained and tested against Gram-negative and Gram-positive bacteria. The possible application in food packing is addressed by covering the surface of typical paper mockups with the doped polymers. All dye-doped polymers present a broad-spectrum antibacterial effect against Gram-positive bacteria, especially for Bacillus cereus (B. cereus), Staphylococcus aureus (S. aureus), and methicillin-resistant S. aureus (MRSA) strains, with PVA:PVP@3 and PVA:PVP@3-Cu being the most effective. Moreover, polymers containing cyanine derivatives present interesting inhibition effects against Pseudomonas aeruginosa (P. aeruginosa), where the production of its characteristic blue/green virulent pigment is not observed. Of the coated paper mockups, PVA:PVP:paper@2 and PVA:PVP:paper@2-Cu are most effective against B. cereus and S. aureus, while PVA:PVP:paper@3 and PVA:PVP:paper@3-Cu are most effective against the MRSA strain. In these formulations, direct contact inhibition mechanisms appear to be more significant than diffusional mechanisms, due to cyanine release hindrance, making them very interesting and versatile platforms for medical and food applications.
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Affiliation(s)
- Gonçalo A Marcelo
- BIOSCOPE Research Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, Caparica, 2829-516, Portugal
| | - Joana Galhano
- BIOSCOPE Research Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, Caparica, 2829-516, Portugal
| | - Maria Paula Duarte
- Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, 2829-516, Portugal
| | - Atanas Kurutos
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev str., bl. 9, Sofia, 1113, Bulgaria
| | - Jose Luis Capelo-Martínez
- BIOSCOPE Research Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, Caparica, 2829-516, Portugal.,PROTEOMASS Scientific Society. Rua dos Inventores. Madam Parque, Caparica Campus, Caparica, 2829-516, Portugal
| | - Carlos Lodeiro
- BIOSCOPE Research Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, Caparica, 2829-516, Portugal.,PROTEOMASS Scientific Society. Rua dos Inventores. Madam Parque, Caparica Campus, Caparica, 2829-516, Portugal
| | - Elisabete Oliveira
- BIOSCOPE Research Group, LAQV-REQUIMTE, Chemistry Department, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, Caparica, 2829-516, Portugal.,PROTEOMASS Scientific Society. Rua dos Inventores. Madam Parque, Caparica Campus, Caparica, 2829-516, Portugal
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Deng S, Tu Y, Fu L, Liu J, Jia L. A label-free biosensor for selective detection of Gram-negative bacteria based on the oxidase-like activity of cupric oxide nanoparticles. Mikrochim Acta 2022; 189:471. [DOI: 10.1007/s00604-022-05571-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/03/2022] [Indexed: 11/27/2022]
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13
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de Oliveira HL, Dias GM, Neves BC. Genome sequence of Pseudomonas aeruginosa PA1-Petro—A role model of environmental adaptation and a potential biotechnological tool. Heliyon 2022; 8:e11566. [DOI: 10.1016/j.heliyon.2022.e11566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/12/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
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Hofmann L, Mandato A, Saxena S, Ruthstein S. The use of EPR spectroscopy to study transcription mechanisms. Biophys Rev 2022; 14:1141-1159. [PMID: 36345280 PMCID: PMC9636360 DOI: 10.1007/s12551-022-01004-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 02/08/2023] Open
Abstract
Electron paramagnetic resonance (EPR) spectroscopy has become a promising structural biology tool to resolve complex and dynamic biological mechanisms in-vitro and in-cell. Here, we focus on the advantages of continuous wave (CW) and pulsed EPR distance measurements to resolve transcription processes and protein-DNA interaction. The wide range of spin-labeling approaches that can be used to follow structural changes in both protein and DNA render EPR a powerful method to study protein-DNA interactions and structure-function relationships in other macromolecular complexes. EPR-derived data goes well beyond static structural information and thus serves as the method of choice if dynamic insight is needed. Herein, we describe the conceptual details of the theory and the methodology and illustrate the use of EPR to study the protein-DNA interaction of the copper-sensitive transcription factor, CueR.
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Affiliation(s)
- L. Hofmann
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat-Gan, Israel
| | - A. Mandato
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA USA
| | - S. Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA USA
| | - S. Ruthstein
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat-Gan, Israel
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Yakobov I, Mandato A, Hofmann L, Singewald K, Shenberger Y, Gevorkyan‐Airapetov L, Saxena S, Ruthstein S. Allostery-driven changes in dynamics regulate the activation of bacterial copper transcription factor. Protein Sci 2022; 31:e4309. [PMID: 35481642 PMCID: PMC9004249 DOI: 10.1002/pro.4309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 12/27/2022]
Abstract
Metalloregulators bind and respond to metal ions by regulating the transcription of metal homeostasis genes. Copper efflux regulator (CueR) is a copper-responsive metalloregulator that is found in numerous Gram-negative bacteria. Upon Cu(I) coordination, CueR initiates transcription by bending the bound DNA promoter regions facilitating interaction with RNA polymerase. The structure of Escherichia coli CueR in presence of DNA and metal ion has been reported using X-ray crystallography and cryo-EM, providing information about the mechanism of action. However, the specific role of copper in controlling this transcription mechanism remains elusive. Herein, we use room temperature electron paramagnetic resonance (EPR) experiments to follow allosterically driven dynamical changes in E. coli CueR induced by Cu(I) binding. We suggest that more than one Cu(I) ion binds per CueR monomer, leading to changes in site-specific dynamics at the Cu(I) binding domain and at the distant DNA binding site. Interestingly, Cu(I) binding leads to an increase in dynamics about 27 Å away at the DNA binding domain. These changes in the dynamics of the DNA binding domain are important for exact coordination with the DNA. Thus, Cu(I) binding is critical to initiate a series of conformational changes that regulate and initiate gene transcription. BROAD AUDIENCE STATEMENT: The dynamics of metal transcription factors as a function of metal and DNA binding are complex. In this study, we use EPR spectroscopy to measure dynamical changes of Escherichia coli CueR as a function of copper and DNA binding. We show that copper controls the activation of the transcription processes by initiation a series of dynamical changes over the protein.
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Affiliation(s)
- Idan Yakobov
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of exact sciencesBar Ilan UniversityRamat‐GanIsrael
| | - Alysia Mandato
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Lukas Hofmann
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of exact sciencesBar Ilan UniversityRamat‐GanIsrael
| | - Kevin Singewald
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Yulia Shenberger
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of exact sciencesBar Ilan UniversityRamat‐GanIsrael
| | - Lada Gevorkyan‐Airapetov
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of exact sciencesBar Ilan UniversityRamat‐GanIsrael
| | - Sunil Saxena
- Department of ChemistryUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Sharon Ruthstein
- Department of Chemistry and the Institute of Nanotechnology & Advanced Materials, Faculty of exact sciencesBar Ilan UniversityRamat‐GanIsrael
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The Advantages of EPR Spectroscopy in Exploring Diamagnetic Metal Ion Binding and Transfer Mechanisms in Biological Systems. MAGNETOCHEMISTRY 2021. [DOI: 10.3390/magnetochemistry8010003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy has emerged as an ideal biophysical tool to study complex biological processes. EPR spectroscopy can follow minor conformational changes in various proteins as a function of ligand or protein binding or interactions with high resolution and sensitivity. Resolving cellular mechanisms, involving small ligand binding or metal ion transfer, is not trivial and cannot be studied using conventional biophysical tools. In recent years, our group has been using EPR spectroscopy to study the mechanism underlying copper ion transfer in eukaryotic and prokaryotic systems. This mini-review focuses on our achievements following copper metal coordination in the diamagnetic oxidation state, Cu(I), between biomolecules. We discuss the conformational changes induced in proteins upon Cu(I) binding, as well as the conformational changes induced in two proteins involved in Cu(I) transfer. We also consider how EPR spectroscopy, together with other biophysical and computational tools, can identify the Cu(I)-binding sites. This work describes the advantages of EPR spectroscopy for studying biological processes that involve small ligand binding and transfer between intracellular proteins.
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Biotechnological approaches in agriculture and environmental management - bacterium Kocuria rhizophila 14ASP as heavy metal and salt- tolerant plant growth- promoting strain. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00826-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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