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Dulya O, Mikryukov V, Shchepkin DV, Pent M, Tamm H, Guazzini M, Panagos P, Jones A, Orgiazzi A, Marroni F, Bahram M, Tedersoo L. A trait-based ecological perspective on the soil microbial antibiotic-related genetic machinery. ENVIRONMENT INTERNATIONAL 2024; 190:108917. [PMID: 39089094 DOI: 10.1016/j.envint.2024.108917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/24/2024] [Accepted: 07/25/2024] [Indexed: 08/03/2024]
Abstract
Antibiotic resistance crisis dictates the need for resistance monitoring and the search for new antibiotics. The development of monitoring protocols is hindered by the great diversity of resistance factors, while the "streetlight effect" denies the possibility of discovering novel drugs based on existing databases. In this study, we address these challenges using high-throughput environmental screening viewed from a trait-based ecological perspective. Through an in-depth analysis of the metagenomes of 658 topsoil samples spanning Europe, we explored the distribution of 241 prokaryotic and fungal genes responsible for producing metabolites with antibiotic properties and 485 antibiotic resistance genes. We analyzed the diversity of these gene collections at different levels and modeled the distribution of each gene across environmental gradients. Our analyses revealed several nonparallel distribution patterns of the genes encoding sequential steps of enzymatic pathways synthesizing large antibiotic groups, pointing to gaps in existing databases and suggesting potential for discovering new analogues of known antibiotics. We show that agricultural activity caused a continental-scale homogenization of microbial antibiotic-related machinery, emphasizing the importance of maintaining indigenous ecosystems within the landscape mosaic. Based on the relationships between the proportion of the genes in the metagenomes with the main predictors (soil pH, land cover type, climate temperature and humidity), we illustrate how the properties of chemical structures dictate the distribution of the genes responsible for their synthesis across environments. With this understanding, we propose general principles to facilitate the discovery of antibiotics, including principally new ones, establish abundance baselines for antibiotic resistance genes, and predict their dissemination.
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Affiliation(s)
- Olesya Dulya
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia; Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia.
| | - Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia; Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia.
| | - Daniil V Shchepkin
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia.
| | - Mari Pent
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia.
| | - Heidi Tamm
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia.
| | - Massimo Guazzini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy.
| | - Panos Panagos
- European Commission, Joint Research Centre (JRC), Ispra, Province of Varese 21027, Italy.
| | - Arwyn Jones
- European Commission, Joint Research Centre (JRC), Ispra, Province of Varese 21027, Italy.
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre (JRC), Ispra, Province of Varese 21027, Italy; European Dynamics, Brussels B-1000, Belgium.
| | - Fabio Marroni
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy.
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 50409, Estonia; Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden; Department of Agroecology, Aarhus University, Forsøgsvej 1 4200, Slagelse, Denmark.
| | - Leho Tedersoo
- Center of Mycology and Microbiology, University of Tartu, Tartu 50409, Estonia.
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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Hariharan P, Sudhahar CG, Chou SH, Chin DH. Lipid Bilayer-Assisted Release of an Enediyne Antibiotic from Neocarzinostatin Chromoprotein. Biochemistry 2010; 49:7722-32. [DOI: 10.1021/bi100735v] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Parameswaran Hariharan
- Department of Chemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | | | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Der-Hang Chin
- Department of Chemistry, National Chung Hsing University, Taichung 40227, Taiwan, ROC
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Sudhahar CG, Chin DH. Aponeocarzinostatin—A superior drug carrier exhibiting unusually high endurance against denaturants. Bioorg Med Chem 2006; 14:3543-52. [PMID: 16458518 DOI: 10.1016/j.bmc.2006.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Revised: 01/06/2006] [Accepted: 01/06/2006] [Indexed: 11/28/2022]
Abstract
The enediyne antitumor antibiotic chromoproteins are very potent in causing DNA damages. During the drug delivery time course, the stability of the carrier protein becomes an important concern. To simulate conceivably offensive environment in biological contexts, such as cell membrane, we studied structural endurance of aponeocarzinostatin against several denaturants by circular dichroism and nuclear magnetic resonance spectroscopy. For comparison, we also examined proteins known to be stable and similar in size to aponeocarzinostatin. The results highlight the unusual structural stability of aponeocarzinostatin against chemical denaturants, suggesting the potential of aponeocarzinostatin as an inherently superior carrier in drug delivery systems.
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Jayachithra K, Kumar TKS, Lu TJ, Yu C, Chin DH. Cold instability of aponeocarzinostatin and its stabilization by labile chromophore. Biophys J 2005; 88:4252-61. [PMID: 15821162 PMCID: PMC1305655 DOI: 10.1529/biophysj.104.051722] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Accepted: 03/22/2005] [Indexed: 11/18/2022] Open
Abstract
The conformational stability of aponeocarzinostatin, an all-beta-sheet protein with 113 amino-acid residues, is investigated by thermal-induced equilibrium unfolding between pH 2.0 and 10.0 with and without urea. At room temperature, the protein is stable in a pH range of 4.0-10.0, whereas the stability of the protein drastically decreases below pH 4.0. The thermal unfolding of aponeocarzinostatin is reversible and follows a two-state mechanism. By two-dimensional unfolding studies, the enthalpy change, heat capacity change, and free energy change for unfolding of the protein are estimated. Circular dichroism profiles suggest that this protein undergoes both heat- and cold-induced unfolding. The ellipticity changes at far- and near-UV circular dichroism suggest that the tertiary structure is disrupted but the secondary structure remains folded at low temperatures. Interestingly, the labile enediyne chromophore, which is highly stabilized by the protein, is able to protect the protein against cold-induced unfolding, but not the heat-induced unfolding.
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Affiliation(s)
- Kandaswamy Jayachithra
- Department of Chemistry, National Chung Hsing University, Taichung, Taiwan, Republic of China
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Tanaka T, Fukuda-Ishisaka S, Hirama M, Otani T. Solution structures of C-1027 apoprotein and its complex with the aromatized chromophore. J Mol Biol 2001; 309:267-83. [PMID: 11491295 DOI: 10.1006/jmbi.2001.4621] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
C-1027 is one of the most potent antitumor antibiotic chromoproteins, and is a 1:1 complex of an enediyne chromophore having DNA-cleaving ability and a carrier apoprotein. The three-dimensional solution structures of the 110 residue (10.5 kDa) C-1027 apoprotein and its complex with the aromatized chromophore have been determined separately by homonuclear two-dimensional nuclear magnetic resonance methods. The apoprotein is mainly composed of three antiparallel beta-sheets: four-stranded beta-sheet (43-45, 52-54; 30-38; 92-94; 104-106), three-stranded beta-sheet (4-6; 17-22; 61-66), and two-stranded beta-sheet (70-72; 83-85). The overall structure of the apoprotein is very similar to those of other chromoprotein apoproteins, such as neocarzinostatin and kedarcidin. A hydrophobic pocket with approximate dimensions of 14 A x 12 A x 8 A is formed by the four-stranded beta-sheet and the three loops (39-42; 75-79; 97-100). The holoprotein (complex form with the aromatized chromophore) structure reveals that the aromatized chromophore is bound to the hydrophobic pocket found in the apoprotein. The benzodihydropentalene core of the chromophore is located in the center of the pocket and other substituents (beta-tyrosine, benzoxazine, and aminosugar moieties) are arranged around the core. Major binding interactions between the apoprotein and the chromophore are likely the hydrophobic contacts between the core of the chromophore and the hydrophobic side-chains of the pocket-forming residues, which is supplemented by salt bridges and/or hydrogen bonds. Based on the holoprotein structure, we propose possible mechanisms for the stabilization and the release of chromophore by the apoprotein.
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Affiliation(s)
- T Tanaka
- Institute of Applied Biochemistry, University of Tsukuba, Ibaraki, Japan.
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Takahashi K, Tanaka T, Suzuki T, Hirama M. Synthesis and binding of simple neocarzinostatin chromophore analogues to the apoprotein. Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)80621-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Tanaka T, Hirama M, Fujita KI, Imajo S, Ishiguro M. Solution structure of the antitumour antibiotic neocarzinostatin, a chromophore–protein complex. ACTA ACUST UNITED AC 1993. [DOI: 10.1039/c39930001205] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Takahashi K, Suzuki T, Hirama M. A simple and efficient synthesis of the naphthoate moiety of neocarzinostatin chromophore. Tetrahedron Lett 1992. [DOI: 10.1016/s0040-4039(00)61324-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Tanaka T, Hirama M, Ueno M, Imajo S, Ishisuro M, Mizugaki M, Edo K, Komatsu H. Proton NMR studies on the chromophore binding structure in neocarzinostatin complex. Tetrahedron Lett 1991. [DOI: 10.1016/s0040-4039(00)79715-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ozawa S, Inaba M. Kinetic analysis of the in vitro cell-killing action of neocarzinostatin. Cancer Chemother Pharmacol 1989; 23:279-82. [PMID: 2523252 DOI: 10.1007/bf00292404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The relationship between the drug concentration and exposure time of neocarzinostatin (NCS) for a definite cell-killing effect was kinetically analyzed, taking into consideration its loss in biological activity during incubation. Its cell-killing activity was determined by a colony-forming inhibition assay, which was conducted at room temperature (25 degrees C) for 0.5-30 min exposure and at 37 degrees C for 5 min - 96 h exposure. Drug degradation at both temperatures was also investigated by bioassay. NCS lost its biological activity much faster at 37 degrees C than at 25 degrees C and the rate of loss in activity was higher at the lower initial concentration. Thus, the initial NCS concentrations necessary for 90% cell kill corresponding to each exposure time and a drug degradation constant were applied to a mathematical equation for the cell-killing effect of cell-cycle-phase-nonspecific agents. As a result, the curves for IC90-exposure time relationships predicted from drug degradation constants for 37 degrees C and 25 degrees C were fairly well fitted to the respective experimental data. These results indicate that the cell-killing action of NCS can be expressed by this mathematical equation with scrutiny of drug degradation and is dependent on the concentration-time product (C x T).
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Affiliation(s)
- S Ozawa
- Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo
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