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Xiao W, Gao Z, Liu T, Zhong W, Jiang S, He M, Fu F, Li G, Su D, Guo J, Shan Y. Lemon essential oil nanoemulsions: Potential natural inhibitors against Escherichia coli. Food Microbiol 2024; 119:104459. [PMID: 38225037 DOI: 10.1016/j.fm.2023.104459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/17/2024]
Abstract
Lemon essential oil (LEO) is a common natural antibacterial substance, and encapsulating LEO into nanoemulsions (NEs) can improve their stability and broaden its application. Our study aimed to investigate the bacterial inhibitory effect of LEO-NEs against Escherichia coli (E. coli). Results showed that the minimum inhibitory concentration (MIC) of LEO-NEs was 6.25 mg/mL, and the time-kill curve showed that E. coli were significantly killed by LEO-NEs after 5 h of treatment at 1MIC. Flow-cytometry analysis showed that LEO-NEs adversely affected the cell-membrane depolarisation, cell-membrane integrity, and efflux pump function of E. coli. Confocal laser scanning microscopy demonstrated that 8MIC of LEO-NEs induced changes in the cell-membrane permeability and cell-wall integrity of E. coli. Proteomic results suggested that the mode of action LEO-NEs against E. coli was to enhance bacterial chemotaxis and significantly inhibit ribosomal assembly. They may also affect butyric acid, ascorbic acid and aldehyde metabolism, and sulphur-relay system pathways. In conclusion, LEO-NEs had potential application as a natural antibacterial agent for the control of E. coli in the food industry.
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Affiliation(s)
- Wenbin Xiao
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, Hunan Province, China; Hunan Agriculture Product Processing Institute, Dongting Laboratory, International Joint Lab on Fruits &Vegetables Processing, Quality and Safety, Hunan Provincial Key Laboratory of Fruits &Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan Province, China
| | - Zhipeng Gao
- Fisheries College, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Ting Liu
- Hunan Agriculture Product Processing Institute, Dongting Laboratory, International Joint Lab on Fruits &Vegetables Processing, Quality and Safety, Hunan Provincial Key Laboratory of Fruits &Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan Province, China
| | - Weiming Zhong
- Fisheries College, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Sifan Jiang
- Fisheries College, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Mingwang He
- Fisheries College, Hunan Agricultural University, Changsha, 410128, Hunan Province, China
| | - Fuhua Fu
- Hunan Agriculture Product Processing Institute, Dongting Laboratory, International Joint Lab on Fruits &Vegetables Processing, Quality and Safety, Hunan Provincial Key Laboratory of Fruits &Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan Province, China
| | - Gaoyang Li
- Hunan Agriculture Product Processing Institute, Dongting Laboratory, International Joint Lab on Fruits &Vegetables Processing, Quality and Safety, Hunan Provincial Key Laboratory of Fruits &Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan Province, China
| | - Donglin Su
- Hunan Agriculture Product Processing Institute, Dongting Laboratory, International Joint Lab on Fruits &Vegetables Processing, Quality and Safety, Hunan Provincial Key Laboratory of Fruits &Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan Province, China
| | - Jiajing Guo
- Hunan Agriculture Product Processing Institute, Dongting Laboratory, International Joint Lab on Fruits &Vegetables Processing, Quality and Safety, Hunan Provincial Key Laboratory of Fruits &Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan Province, China.
| | - Yang Shan
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, Hunan Province, China; Hunan Agriculture Product Processing Institute, Dongting Laboratory, International Joint Lab on Fruits &Vegetables Processing, Quality and Safety, Hunan Provincial Key Laboratory of Fruits &Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan Province, China.
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Zorrilla S, Mónico A, Duarte S, Rivas G, Pérez-Sala D, Pajares MA. Integrated approaches to unravel the impact of protein lipoxidation on macromolecular interactions. Free Radic Biol Med 2019; 144:203-217. [PMID: 30991143 DOI: 10.1016/j.freeradbiomed.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 12/13/2022]
Abstract
Protein modification by lipid derived reactive species, or lipoxidation, is increased during oxidative stress, a common feature observed in many pathological conditions. Biochemical and functional consequences of lipoxidation include changes in the conformation and assembly of the target proteins, altered recognition of ligands and/or cofactors, changes in the interactions with DNA or in protein-protein interactions, modifications in membrane partitioning and binding and/or subcellular localization. These changes may impact, directly or indirectly, signaling pathways involved in the activation of cell defense mechanisms, but when these are overwhelmed they may lead to pathological outcomes. Mass spectrometry provides state of the art approaches for the identification and characterization of lipoxidized proteins/residues and the modifying species. Nevertheless, understanding the complexity of the functional effects of protein lipoxidation requires the use of additional methodologies. Herein, biochemical and biophysical methods used to detect and measure functional effects of protein lipoxidation at different levels of complexity, from in vitro and reconstituted cell-like systems to cells, are reviewed, focusing especially on macromolecular interactions. Knowledge generated through innovative and complementary technologies will contribute to comprehend the role of lipoxidation in pathophysiology and, ultimately, its potential as target for therapeutic intervention.
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Affiliation(s)
- Silvia Zorrilla
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Andreia Mónico
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Sofia Duarte
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Germán Rivas
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Dolores Pérez-Sala
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - María A Pajares
- Dept. of Structural and Chemical Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
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Mangeol P, Bizebard T, Chiaruttini C, Dreyfus M, Springer M, Bockelmann U. Probing ribosomal protein-RNA interactions with an external force. Proc Natl Acad Sci U S A 2011; 108:18272-6. [PMID: 22025688 DOI: 10.1073/pnas.1107121108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosomal (r-) RNA adopts a well-defined structure within the ribosome, but the role of r-proteins in stabilizing this structure is poorly understood. To address this issue, we use optical tweezers to unfold RNA fragments in the presence or absence of r-proteins. Here, we focus on Escherichia coli r-protein L20, whose globular C-terminal domain (L20C) recognizes an irregular stem in domain II of 23S rRNA. L20C also binds its own mRNA and represses its translation; binding occurs at two different sites--i.e., a pseudoknot and an irregular stem. We find that L20C makes rRNA and mRNA fragments encompassing its binding sites more resistant to mechanical unfolding. The regions of increased resistance correspond within two base pairs to the binding sites identified by conventional methods. While stabilizing specific RNA structures, L20C does not accelerate their formation from alternate conformations--i.e., it acts as a clamp but not as a chaperone. In the ribosome, L20C contacts only one side of its target stem but interacts with both strands, explaining its clamping effect. Other r-proteins bind rRNA similarly, suggesting that several rRNA structures are stabilized by "one-side" clamping.
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Bekesi A, Pukancsik M, Haasz P, Felfoldi L, Leveles I, Muha V, Hunyadi-Gulyas E, Erdei A, Medzihradszky KF, Vertessy BG. Association of RNA with the uracil-DNA-degrading factor has major conformational effects and is potentially involved in protein folding. FEBS J 2010; 278:295-315. [PMID: 21134127 DOI: 10.1111/j.1742-4658.2010.07951.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, a novel uracil-DNA-degrading factor protein (UDE) was identified in Drosophila melanogaster, with homologues only in pupating insects. Its unique uracil-DNA-degrading activity and a potential domain organization pattern have been described. UDE seems to be the first representative of a new protein family with unique enzyme activity that has a putative role in insect development. In addition, UDE may also serve as potential tool in molecular biological applications. Owing to lack of homology with other proteins with known structure and/or function, de novo data are required for a detailed characterization of UDE structure and function. Here, experimental evidence is provided that recombinant protein is present in two distinct conformers. One of these contains a significant amount of RNA strongly bound to the protein, influencing its conformation. Detailed biophysical characterization of the two distinct conformational states (termed UDE and RNA-UDE) revealed essential differences. UDE cannot be converted into RNA-UDE by addition of the same RNA, implying putatively joint processes of RNA binding and protein folding in this conformational species. By real-time PCR and sequencing after random cloning, the bound RNA pool was shown to consist of UDE mRNA and the two ribosomal RNAs, also suggesting cotranslational RNA-assisted folding. This finding, on the one hand, might open a way to obtain a conformationally homogeneous UDE preparation, promoting successful crystallization; on the other hand, it might imply a further molecular function of the protein. In fact, RNA-dependent complexation of UDE was also demonstrated in a fruit fly pupal extract, suggesting physiological relevance of RNA binding of this DNA-processing enzyme.
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Affiliation(s)
- Angela Bekesi
- Institute of Enzymology, Biological Research Centre, Hungarian Academy of Sciences, Budapest, Hungary.
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Abstract
RNA binding proteins are capable of regulating translation initiation by a variety of mechanisms. Although the vast majority of these regulatory mechanisms involve translational repression, one example of translational activation has been characterized in detail. The RNA recognition targets of these regulatory proteins exhibit a wide range in structural complexity, with some proteins recognizing complex pseudoknot structures and others binding to simple RNA hairpins and/or short repeated single-stranded sequences. In some instances the bound protein directly competes with ribosome binding, and in other instances the bound protein promotes formation of an RNA structure that inhibits ribosome binding. Examples also exist in which the bound protein traps the ribosome in a complex that is incapable of initiating translation.
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Affiliation(s)
- Paul Babitzke
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M; Harvard FlyBase curators., Berkeley Drosophila Genome Project. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007; 450:219-32. [PMID: 17994088 DOI: 10.1038/nature06340] [Citation(s) in RCA: 462] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2007] [Accepted: 10/04/2007] [Indexed: 12/25/2022]
Abstract
Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.
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