151
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Baral D, Dvorak BI, Admiraal D, Jia S, Zhang C, Li X. Tracking the Sources of Antibiotic Resistance Genes in an Urban Stream during Wet Weather using Shotgun Metagenomic Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:9033-9044. [PMID: 30020774 DOI: 10.1021/acs.est.8b01219] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Stormwater runoff has been known to cause increases in bacterial loadings in urban streams. However, little is known about its impacts on antibiotic resistance genes (ARGs) in urban watersheds. This study was performed to characterize the ARG composition of various environmental compartments of an urban watershed and to quantify their contributions of microbes and ARGs to an urban stream under wet weather conditions. Shotgun metagenomic results showed that the ARG abundance in wet weather flow was significantly higher than in base flow. Multidrug resistance genes were the most common ARG type across environmental samples. Vancomycin resistance genes were abundant in embankment soil and street sweeping samples. Analyses using SourceTracker estimated storm drain outfall water to be the biggest contributor of microbes (54-57%) and ARGs (82-88%) in the urban stream during wet weather flows. Furthermore, results on street sweepings showed that wash-off from streets was the biggest known contributor of microbes (41-45%) and ARGs (92-96%) in storm drain outfall water. Pantoea and Pseudomonas were associated with the highest numbers of ARGs and were most abundant in stormwater-related samples. Results from this study can advance our knowledge about ARGs in urban streams, an important medium linking environmental ARGs to the general public.
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Affiliation(s)
- Darshan Baral
- Department of Civil Engineering , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - Bruce I Dvorak
- Department of Civil Engineering , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - David Admiraal
- Department of Civil Engineering , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - Shangang Jia
- School of Biological Sciences , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - Chi Zhang
- School of Biological Sciences , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - Xu Li
- Department of Civil Engineering , University of Nebraska , Lincoln , Nebraska 68588 , United States
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152
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Shin JH, Eom H, Song WJ, Rho M. Integrative metagenomic and biochemical studies on rifamycin ADP-ribosyltransferases discovered in the sediment microbiome. Sci Rep 2018; 8:12143. [PMID: 30108275 PMCID: PMC6092378 DOI: 10.1038/s41598-018-30547-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/30/2018] [Indexed: 11/23/2022] Open
Abstract
Antibiotic resistance is a serious and growing threat to human health. The environmental microbiome is a rich reservoir of resistomes, offering opportunities to discover new antibiotic resistance genes. Here we demonstrate an integrative approach of utilizing gene sequence and protein structural information to characterize unidentified genes that are responsible for the resistance to the action of rifamycin antibiotic rifampin, a first-line antimicrobial agent to treat tuberculosis. Biochemical characterization of four environmental metagenomic proteins indicates that they are adenosine diphosphate (ADP)-ribosyltransferases and effective in the development of resistance to FDA-approved rifamycins. Our analysis suggests that even a single residue with low sequence conservation plays an important role in regulating the degrees of antibiotic resistance. In addition to advancing our understanding of antibiotic resistomes, this work demonstrates the importance of an integrative approach to discover new metagenomic genes and decipher their biochemical functions.
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Affiliation(s)
- Jae Hong Shin
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea
| | - Hyunuk Eom
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Woon Ju Song
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea.
| | - Mina Rho
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea.
- Department of Biomedical Informatics, Hanyang University, Seoul, Korea.
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153
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Tanno K, Maejima K, Miyazaki A, Koinuma H, Iwabuchi N, Kitazawa Y, Nijo T, Hashimoto M, Yamaji Y, Namba S. Comprehensive screening of antimicrobials to control phytoplasma diseases using an in vitro plant-phytoplasma co-culture system. MICROBIOLOGY-SGM 2018; 164:1048-1058. [PMID: 29952745 DOI: 10.1099/mic.0.000681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Phytoplasmas are plant-pathogenic bacteria that infect many important crops and cause serious economic losses worldwide. However, owing to an inability to culture phytoplasmas, screening of antimicrobials on media is difficult. The only antimicrobials being used to control phytoplasmas are tetracycline-class antibiotics. In this study, we developed an accurate and efficient screening method to evaluate the effects of antimicrobials using an in vitro plant-phytoplasma co-culture system. We tested 40 antimicrobials, in addition to tetracycline, and four of these (doxycycline, chloramphenicol, thiamphenicol and rifampicin) decreased the accumulation of 'Candidatus (Ca.) Phytoplasma asteris'. The phytoplasma was eliminated from infected plants by the application of both tetracycline and rifampicin. We also compared nucleotide sequences of rRNAs and amino acid sequences of proteins targeted by antimicrobials between phytoplasmas and other bacteria. Since antimicrobial target sequences were conserved among various phytoplasma species, the antimicrobials that decreased accumulation of 'Ca. P. asteris' may also have been effective against other phytoplasma species. These approaches will provide new strategies for phytoplasma disease management.
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Affiliation(s)
- Kazuyuki Tanno
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akio Miyazaki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroaki Koinuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takamichi Nijo
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masayoshi Hashimoto
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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154
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Qi F, Lei C, Li F, Zhang X, Wang J, Zhang W, Fan Z, Li W, Tang GL, Xiao Y, Zhao G, Li S. Deciphering the late steps of rifamycin biosynthesis. Nat Commun 2018; 9:2342. [PMID: 29904078 PMCID: PMC6002545 DOI: 10.1038/s41467-018-04772-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/12/2018] [Indexed: 12/12/2022] Open
Abstract
Rifamycin-derived drugs, including rifampin, rifabutin, rifapentine, and rifaximin, have long been used as first-line therapies for the treatment of tuberculosis and other deadly infections. However, the late steps leading to the biosynthesis of the industrially important rifamycin SV and B remain largely unknown. Here, we characterize a network of reactions underlying the biosynthesis of rifamycin SV, S, L, O, and B. The two-subunit transketolase Rif15 and the cytochrome P450 enzyme Rif16 are found to mediate, respectively, a unique C–O bond formation in rifamycin L and an atypical P450 ester-to-ether transformation from rifamycin L to B. Both reactions showcase interesting chemistries for these two widespread and well-studied enzyme families. The enzymes Rif15 and Rif16 are involved in the late steps of the biosynthesis of rifamycins, a group of antibiotics. Here, the authors characterized these two proteins and found that they catalyse unusual biochemical reactions.
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Affiliation(s)
- Feifei Qi
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Chao Lei
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Fengwei Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Xingwang Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Jin Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Zhen Fan
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Youli Xiao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China.
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155
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Xiao YS, Zhang B, Zhang M, Guo ZK, Deng XZ, Shi J, Li W, Jiao RH, Tan RX, Ge HM. Rifamorpholines A-E, potential antibiotics from locust-associated actinobacteria Amycolatopsis sp. Hca4. Org Biomol Chem 2018; 15:3909-3916. [PMID: 28422262 DOI: 10.1039/c7ob00614d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cultivation of locust associated rare actinobacteria, Amycolatopsis sp. HCa4, has provided five unusual macrolactams rifamorpholines A-E. Their structures were determined by interpretation of spectroscopic and crystallographic data. Rifamorpholines A-E possess an unprecedented 5/6/6/6 ring chromophore, representing a new subclass of rifamycin antibiotics. The biosynthetic pathway for compounds 1-5 involves a key 1,6-cyclization for the formation of the morpholine ring. Compounds 2 and 4 showed potent activities against methicillin-resistant Staphylococcus aureus (MRSA) with MICs of 4.0 and 8.0 μM, respectively.
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Affiliation(s)
- Yong Sheng Xiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210046, China.
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156
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Recent therapeutic approaches for the management of tuberculosis: Challenges and opportunities. Biomed Pharmacother 2018; 99:735-745. [DOI: 10.1016/j.biopha.2018.01.115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 11/19/2022] Open
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157
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Wang J, Li W, Wang H, Lu C. Pentaketide Ansamycin Microansamycins A-I from Micromonospora sp. Reveal Diverse Post-PKS Modifications. Org Lett 2018; 20:1058-1061. [PMID: 29412682 DOI: 10.1021/acs.orglett.7b04018] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Overexpression of the pathway-specific positive regulator gene mas13 activated the cryptic gene cluster mas, resulting in the isolation of nine novel pentaketide ansamycins, namely, microansamycins A-I (1-9). These results not only revealed a biosynthetic gene cluster of pentaketide ansamycins for the first time but also presented an unprecedented scenario of diverse post-PKS modifications in ansamycin biosynthesis.
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Affiliation(s)
- Jianxiong Wang
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , Jinan, Shandong 250012, China
| | - Wen Li
- State Key Laboratory of Microbial Technology, Shandong University , Jinan, Shandong 250100, China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology, Shandong University , Jinan, Shandong 250100, China
| | - Chunhua Lu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , Jinan, Shandong 250012, China
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158
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The 'gifted' actinomycete Streptomyces leeuwenhoekii. Antonie van Leeuwenhoek 2018; 111:1433-1448. [PMID: 29397490 DOI: 10.1007/s10482-018-1034-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/28/2018] [Indexed: 10/18/2022]
Abstract
Streptomyces leeuwenhoekii strains C34T, C38, C58 and C79 were isolated from a soil sample collected from the Chaxa Lagoon, located in the Salar de Atacama in northern Chile. These streptomycetes produce a variety of new specialised metabolites with antibiotic, anti-cancer and anti-inflammatory activities. Moreover, genome mining performed on two of these strains has revealed the presence of biosynthetic gene clusters with the potential to produce new specialised metabolites. This review focusses on this new clade of Streptomyces strains, summarises the literature and presents new information on strain C34T.
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159
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Liu L, Pan J, Wang Z, Yan X, Yang D, Zhu X, Shen B, Duan Y, Huang Y. Ribosome engineering and fermentation optimization leads to overproduction of tiancimycin A, a new enediyne natural product from Streptomyces sp. CB03234. J Ind Microbiol Biotechnol 2018; 45:141-151. [PMID: 29396746 DOI: 10.1007/s10295-018-2014-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022]
Abstract
Tiancimycin (TNM) A, a recently discovered enediyne natural product from Streptomyces sp. CB03234, showed rapid and complete killing of cancer cells and could be used as a payload in antibody drug conjugates. The low yield of TNM A in the wild-type strain promoted us to use ribosome engineering and fermentation optimization for its yield improvement. The Streptomyces sp. CB03234-R-16 mutant strain with a L422P mutation in RpoB, the RNA polymerase β-subunit, was obtained from the rifamycin-resistant screening. After fermentation optimization, the titers of TNM A in Streptomyces sp. CB03234-R-16 reached to 22.5 ± 3.1 mg L-1 in shaking flasks, and 13 ± 1 mg L-1 in 15 L fermentors, which were at least 40-fold higher than that in the wild-type strain (~ 0.3 mg L-1). Quantitative real-time RT-PCR revealed markedly enhanced expression of key genes encoding TNM A biosynthetic enzymes and regulators in Streptomyces sp. CB03234-R-16. Our study should greatly facilitate the future efforts to develop TNM A into a clinical anticancer drug.
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Affiliation(s)
- Ling Liu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Jian Pan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Zilong Wang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xiaohui Yan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Dong Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China.,Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, Hunan, China
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.,Natural Products Library Initiative, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China. .,Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, Hunan, China. .,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410011, Hunan, China.
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, Hunan, China. .,Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410011, Hunan, China.
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160
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Işık K, Gençbay T, Topkara AR, Sarıcaoğlu S, Saygın H, Ay H, Çetin D, Güven K, Şahin N. Amycolatopsis cappadoca sp. nov., isolated from soil. Antonie van Leeuwenhoek 2018; 111:1175-1182. [PMID: 29383462 DOI: 10.1007/s10482-018-1023-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/23/2018] [Indexed: 01/06/2023]
Abstract
An Amycolatopsis strain, designated AG28T, isolated from a soil sample collected from Acıgöl, Kapadokya, Turkey, was examined using a polyphasic taxonomic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence showed that the strain is closely related to the type strains of Amycolatopsis deserti GY024T (97.1%), Amycolatopsis taiwanensis 0345 M-7T (96.9%) and Amycolatopsis pigmentata TT00-43T (96.9%). Strain AG28T was found to have chemotaxonomic and phylogenetic properties consistent with its classification in the genus Amycolatopsis. The strain was found to contain meso-diaminopimelic acid as the diagnostic diamino acid. The whole cell sugars identified were rhamnose, ribose, arabinose and galactose. The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was identified as MK-9(H4). Major fatty acids (> 10%) were identified as iso-C15:0, iso-C16:0 and iso-C16:0 2OH. Consequently, on the basis of the data from this polyphasic study, it is proposed that strain AG28T represents a novel Amycolatopsis species for which the name Amycolatopsis cappadoca sp. nov. is proposed. The type strain is AG28T (= KCTC 39884T = DSM 104280T).
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Affiliation(s)
- Kamil Işık
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Samsun, Turkey.
| | - Talha Gençbay
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Ahmet Rıdvan Topkara
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Salih Sarıcaoğlu
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Hayrettin Saygın
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey
| | - Demet Çetin
- Division of Science Education, Department of Mathematics and Science Education, Gazi University, 06500, Ankara, Turkey
| | - Kıymet Güven
- Department of Biology, Faculty of Science, Anadolu University, 26470, Eskisehir, Turkey
| | - Nevzat Şahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Samsun, Turkey
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161
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Lei C, Wang J, Liu Y, Liu X, Zhao G, Wang J. A feedback regulatory model for RifQ-mediated repression of rifamycin export in Amycolatopsis mediterranei. Microb Cell Fact 2018; 17:14. [PMID: 29375035 PMCID: PMC5787919 DOI: 10.1186/s12934-018-0863-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Due to the important role of rifamycin in curing tuberculosis infection, the study on rifamycin has never been stopped. Although RifZ, which locates within the rifamycin biosynthetic cluster, has recently been characterized as a pathway-specific regulator for rifamycin biosynthesis, little is known about the regulation of rifamycin export. RESULTS In this work, we proved that the expression of the rifamycin efflux pump (RifP) was regulated by RifQ, a TetR-family transcriptional regulator. Deletion of rifQ had little impact on bacterial growth, but resulted in improved rifamycin production, which was consistent with the reverse transcription PCR results that RifQ negatively regulated rifP's transcription. With electrophoretic mobility shift assay and DNase I Footprinting assay, RifQ was found to directly bind to the promoter region of rifP, and a typical inverted repeat was identified within the RifQ-protected sequences. The transcription initiation site of rifP was further characterized and found to be upstream of the RifQ binding sites, well explaining the RifQ-mediated repression of rifP's transcription in vivo. Moreover, rifamycin B (the end product of rifamycin biosynthesis) remarkably decreased the DNA binding affinity of RifQ, which led to derepression of rifamycin export, reducing the intracellular concentration of rifamycin B as well as its toxicity against the host. CONCLUSIONS Here, we proved that the export of rifamycin B was repressed by RifQ in Amycolatopsis mediterranei, and the RifQ-mediated repression could be specifically relieved by rifamycin B, the end product of rifamycin biosynthesis, based on which a feedback model was proposed for regulation of rifamycin export. With the findings here, one could improve the antibiotic yield by simply inactivating the negative regulator of the antibiotic transporter.
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Affiliation(s)
- Chao Lei
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
| | - Jingzhi Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
| | - Yuanyuan Liu
- Shanghai Tolo Biotechnology Company Limited, Shanghai, 200233, China
| | - Xinqiang Liu
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.,Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Jin Wang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.
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162
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Sun C, Zhang C, Qin X, Wei X, Liu Q, Li Q, Ju J. Genome mining of Streptomyces olivaceus SCSIO T05: Discovery of olimycins A and B and assignment of absolute configurations. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.11.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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163
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Steffen R, Jiang ZD, Gracias Garcia ML, Araujo P, Stiess M, Nacak T, Greinwald R, DuPont HL. Rifamycin SV-MMX® for treatment of travellers' diarrhea: equally effective as ciprofloxacin and not associated with the acquisition of multi-drug resistant bacteria. J Travel Med 2018; 25:5193265. [PMID: 30462260 PMCID: PMC6331114 DOI: 10.1093/jtm/tay116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/16/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND The novel oral antibiotic formulation Rifamycin SV-MMX®, with a targeted delivery to the distal small bowel and colon, was superior to placebo in treating travellers' diarrhea (TD) in a previous study. Thus, a study was designed to compare this poorly absorbed antibiotic with the systemic agent ciprofloxacin. METHODS In a randomized double-blind phase 3 study (ERASE), the efficacy and safety of Rifamycin SV-MMX® 400 mg twice daily (RIF-MMX) was compared with ciprofloxacin 500 mg twice daily in the oral treatment of TD. Overall, 835 international visitors to India, Guatemala or Ecuador with acute TD were randomized to receive a 3-day treatment with RIF-MMX (n = 420) or ciprofloxacin (n = 415). Primary endpoint was time to last unformed stool (TLUS), after which clinical cure was declared. Stools samples for microbiological evaluation were collected at the baseline visit and the end of treatment visit. RESULTS Median TLUS in the RIF-MMX group was 42.8 h versus 36.8 h in the ciprofloxacin group indicating non-inferiority of RIF-MMX to ciprofloxacin (P = 0.0035). Secondary efficacy endpoint results including clinical cure rate, treatment failure rate, requirement of rescue therapy as well as microbiological eradication rate confirmed those of the primary analysis indicating equal efficacy for both compounds. While patients receiving ciprofloxacin showed a significant increase of Extended Spectrum Beta Lactamase Producing-Escherichia coli (ESBL-E. Coli) colonization rates after 3-days treatment (6.9%), rates did not increase in patients receiving RIF-MMX (-0.3%). Both drugs were well-tolerated and safe. CONCLUSION The novel multi-matrix formulation of the broad-spectrum, poorly absorbed antibiotic Rifamycin SV was found non-inferior to the systemic antibiotic ciprofloxacin in the oral treatment of non-dysenteric TD with the advantage of a lower risk of ESBL-E. Coli acquisition.
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Affiliation(s)
- Robert Steffen
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, WHO Collaborating Centre for Travellers' Health, University of Zurich, Zurich, Switzerland.,Division of Epidemiology, Human Genetics & Environmental Sciences and Center for Infectious Diseases, University of Texas School of Public Health, Houston, TX, USA
| | - Zhi-Dong Jiang
- Division of Epidemiology, Human Genetics & Environmental Sciences and Center for Infectious Diseases, University of Texas School of Public Health, Houston, TX, USA
| | | | - Prithi Araujo
- Medical Department, NUSI Wockhardt Hospital, Cuncolim, Margao, Goa, India
| | - Michael Stiess
- Research and Development, Dr Falk Pharma GmbH, Freiburg, Germany
| | - Tanju Nacak
- Research and Development, Dr Falk Pharma GmbH, Freiburg, Germany
| | - Roland Greinwald
- Research and Development, Dr Falk Pharma GmbH, Freiburg, Germany
| | - Herbert L DuPont
- Division of Epidemiology, Human Genetics & Environmental Sciences and Center for Infectious Diseases, University of Texas School of Public Health, Houston, TX, USA
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164
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 DOI: 10.3389/fmicb.2018.02928/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 05/20/2023] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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165
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Wi YM, Greenwood-Quaintance KE, Brinkman CL, Lee JYH, Howden BP, Patel R. Rifampicin resistance in Staphylococcus epidermidis: molecular characterisation and fitness cost of rpoB mutations. Int J Antimicrob Agents 2017; 51:670-677. [PMID: 29287710 DOI: 10.1016/j.ijantimicag.2017.12.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/07/2017] [Accepted: 12/16/2017] [Indexed: 11/26/2022]
Abstract
The molecular mechanisms and characteristics of rifampicin (RIF) resistance in Staphylococcus epidermidis are poorly characterised, even though S. epidermidis is one of the most common nosocomial pathogens associated with indwelling medical device-related infections. The aim of this study was to investigate the evolution of RIF resistance and to characterise the associated molecular mechanisms in S. epidermidis. RIF-resistant mutants from two RIF-susceptible S. epidermidis strains (RP62A and IDRL-8883) were selected through in vitro and in vivo exposure to RIF. A total of 16 colonies with an RP62A background and 63 colonies with an IDRL-8883 background were analysed for rpoB mutations. The fitness of RIF-susceptible and isogenic RIF-resistant strains was assessed using a paired competition assay and by comparing generation times. All mutations detected were in cluster I of rpoB. The following five amino acid substitutions were selected in vitro: Asp471→Asn; Asp471→Gly; Asp471→Val; Ser486→Tyr; and His481→Tyr. The following three amino acid substitutions were selected in vivo: His481→Tyr; Gln468→Lys; and Ser486→Phe. Asp471→Asn and Asp471→Gly changes were associated with susceptible minimal inhibitory concentrations (MICs). In vitro competition assays revealed that all RIF-resistant mutants other than Ser486→Tyr and Ser486→Phe had a relative fitness of <1.0. His481→Tyr mutations had their own specific fitness costs and effects on growth rate, irrespective of strain background. In conclusion, the current study presents molecular characterisations and fitness costs of several rpoB mutations in S. epidermidis.
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Affiliation(s)
- Yu Mi Wi
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Division of Infectious Diseases, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University, Changwon, Republic of Korea
| | | | - Cassandra L Brinkman
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jean Y H Lee
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
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166
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Liu Y, Chen X, Li Z, Xu W, Tao W, Wu J, Yang J, Deng Z, Sun Y. Functional Analysis of Cytochrome P450s Involved in Streptovaricin Biosynthesis and Generation of Anti-MRSA Analogues. ACS Chem Biol 2017; 12:2589-2597. [PMID: 28858479 DOI: 10.1021/acschembio.7b00467] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The streptovaricins, chemically related to the rifamycins, are highly effective antibacterial agents, particularly against mycobacteria. Herein, a bioassay-guided investigation of Streptomyces spectabilis CCTCC M2017417 has led to the characterization of streptovaricins as potent compounds against methicillin-resistant Staphylococcus aureus (MRSA). We identified the streptovaricin biosynthetic gene cluster from S. spectabilis CCTCC M2017417 based on genomic sequencing and bioinformatic analysis. Targeted in-frame deletion of five cytochrome P450 genes (stvP1-P5) resulted in the identification of four new streptovaricin analogues and revealed the functions of these genes as follows: stvP1, stvP4, and stvP5 are responsible for the hydroxylation of C-20, Me-24, and C-28, respectively. stvP2 is possibly involved in formation of the methylenedioxy bridge, and stvP3, a conserved gene found in the biosynthetic cluster for naphthalenic ansamycins, might be related to the formation of a naphthalene ring. Biochemical verification of the hydroxylase activity of StvP1, StvP4, and StvP5 was performed, and StvP1 showed unexpected biocatalytic specificity and promiscuity. More importantly, anti-MRSA studies of streptovaricins and derivatives revealed significant structure-activity relationships (SARs): The hydroxyl group at C-28 plays a vital role in antibacterial activity. The hydroxyl group at C-20 substantially enhances activity in the absence of the methoxycarbonyl side chain at C-24, which can increase the activity regardless of the presence of a hydroxyl group at C-20. The inner lactone ring between C-21 and C-24 shows a positive effect on activity. This work provides meaningful information on the SARs of streptovaricins and demonstrates the utility of the engineering of streptovaricins to yield novel anti-MRSA molecules.
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Affiliation(s)
- Yuanzhen Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Xu Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Zhengyuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Wei Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Weixin Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
| | - Jie Wu
- Renmin Hospital of Wuhan University, Wuhan 430060, People’s Republic of China
| | - Jian Yang
- Renmin Hospital of Wuhan University, Wuhan 430060, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, People’s Republic of China
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167
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Abstract
Natural products have served as powerful therapeutics against pathogenic bacteria since the golden age of antibiotics of the mid-20th century. However, the increasing frequency of antibiotic-resistant infections clearly demonstrates that new antibiotics are critical for modern medicine. Because combinatorial approaches have not yielded effective drugs, we propose that the development of new antibiotics around proven natural scaffolds is the best short-term solution to the rising crisis of antibiotic resistance. We analyze herein synthetic approaches aiming to reengineer natural products into potent antibiotics. Furthermore, we discuss approaches in modulating quorum sensing and biofilm formation as a nonlethal method, as well as narrow-spectrum pathogen-specific antibiotics, which are of interest given new insights into the implications of disrupting the microbiome.
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Affiliation(s)
- Sean E. Rossiter
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Madison H. Fletcher
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - William M. Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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168
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Catalytic Characteristics of New Antibacterials Based on Hexahistidine-Containing Organophosphorus Hydrolase. Catalysts 2017. [DOI: 10.3390/catal7090271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Catalytic characteristics of hexahistidine-containing organophosphorus hydrolase (His6-OPH) and its enzyme-polyelectrolyte complexes with poly-l-glutamic acid or poly-l-aspartic acid (His6-OPH/PLD50), hydrolyzing organophosphorous compounds, and N-acyl homoserine lactones were studied in the presence of various antibiotics (ampicillin, gentamicin, kanamycin, and rifampicin). The antibiotics at concentrations below 1 g·L−1 had a negligible inhibiting effect on the His6-OPH activity. Mixed inhibition of His6-OPH was established for higher antibiotic concentrations, and rifampicin was the most potent inhibitor. Stabilization of the His6-OPH activity was observed in the presence of antibiotics at a concentration of 0.2 g·L−1 during exposure at 25–41 °C. Molecular docking of antibiotics to the surface of His6-OPH dimer revealed the antibiotics binding both to the area near active centers of the enzyme subunits and to the region of contact between subunits of the dimer. Such interactions between antibiotics and His6-OPH were verified with Fourier-transform infrared (FTIR) spectroscopy. Considering all the results of the study, the combination of His6-OPH/PLD50 with β-lactam antibiotic ampicillin was established as the optimal one in terms of exhibition and persistence of maximal lactonase activity of the enzyme.
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169
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Alves MM, Bouchami O, Tavares A, Córdoba L, Santos CF, Miragaia M, de Fátima Montemor M. New Insights into Antibiofilm Effect of a Nanosized ZnO Coating against the Pathogenic Methicillin Resistant Staphylococcus aureus. ACS APPLIED MATERIALS & INTERFACES 2017; 9:28157-28167. [PMID: 28782933 DOI: 10.1021/acsami.7b02320] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
ZnO nanoparticles (NPs) are arising as promising novel antibiotics toward device-related infections. The surface functionalization of Zn, a novel resorbable biomaterial, with ZnO NPs could present an effective solution to overcome such a threat. In this sense, the antibacterial and antibiofilm activity of nano- and microsized ZnO coatings was studied against clinically relevant bacteria, methicillin resistant Staphylococcus aureus (MRSA). The bacterial viability of planktonic and biofilm cells together with the corresponding biofilm structures revealed that only the nanosized ZnO coating had an antibiofilm effect. To elucidate this effect, a novel approach was taken: preconditioning of bacteria with this ZnO coating followed by exposure to subinhibitory concentrations of antibiotics with well-known modes of actions. This approached revealed (i) a decreased biofilm formation in combination with gentamycin, targeting protein synthesis, and (ii) an increased biofilm formation in the presence of rifampicin and vancomycin, acting on RNA and cell wall biosynthesis, respectively. The increased bacteria resistance to these two antibiotics gave new insights into the antibiofilm effect of this nanosized ZnO coating. The synergistic effect observed for gentamycin opened new perspectives for the design of effective solutions against implant-related infections. During the in vitro degradation of this nanosized ZnO-coated Zn, a specific corrosion product, hopeite [Zn3(PO4)2], was depicted. Interestingly, the increased deposition of hopeite-derived compounds on MRSA cells surface seemed to be related to unhealthy and dead bacterial cells. This observation suggested that hopeite may well play a key role in this antibiofilm activity. The results obtained herein shed light on the possible antibacterial effect of a nanosized ZnO coating, and strengthened its antimicrobial (antibacterial and antifungal) potential, therefore providing a potentially effective material to overcome the growing trend of implant-related infections.
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Affiliation(s)
- Marta M Alves
- CQE, DEQ Instituto Superior Técnico, Universidade de Lisboa , Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Ons Bouchami
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Nova University (ITQB-NOVA) , 2780 Oeiras, Portugal
| | - Ana Tavares
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Nova University (ITQB-NOVA) , 2780 Oeiras, Portugal
| | - Laura Córdoba
- CQE, DEQ Instituto Superior Técnico, Universidade de Lisboa , Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Catarina F Santos
- CQE, DEQ Instituto Superior Técnico, Universidade de Lisboa , Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- EST Setúbal, DEM, Instituto Politécnico de Setúbal , Campus IPS, 2910 Setúbal, Portugal
| | - Maria Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Nova University (ITQB-NOVA) , 2780 Oeiras, Portugal
| | - Maria de Fátima Montemor
- CQE, DEQ Instituto Superior Técnico, Universidade de Lisboa , Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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170
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Alfarisi O, Alghamdi WA, Al-Shaer MH, Dooley KE, Peloquin CA. Rifampin vs. rifapentine: what is the preferred rifamycin for tuberculosis? Expert Rev Clin Pharmacol 2017; 10:1027-1036. [PMID: 28803492 DOI: 10.1080/17512433.2017.1366311] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION One-third of the world's population is infected with Mycobacterium tuberculosis (M.tb.). Latent tuberculosis infection (LTBI) can progress to tuberculosis disease, the leading cause of death by infection. Rifamycin antibiotics, like rifampin and rifapentine, have unique sterilizing activity against M.tb. What are the advantages of each for LTBI or tuberculosis treatment? Areas covered: We review studies assessing the pharmacokinetics (PK), pharmacodynamics (PD), drug interaction risk, safety, and efficacy of rifampin and rifapentine and provide basis for comparing them. Expert commentary: Rifampin has shorter half-life, higher MIC against M.tb, lower protein binding, and better distribution into cavitary contents than rifapentine. Drug interactions for the two drugs maybe similar in magnitude. For LTBI, rifapentine is effective as convenient, once-weekly, 12-week course of treatment. Rifampin is also effective for LTBI, but must be given daily for four months, therefore, drug interactions are more problematic. For drug-sensitive tuberculosis disease, rifampin remains the standard of care. Safety profile of rifampin is better-described; adverse events differ somewhat for the two drugs. The registered once-weekly rifapentine regimen is inadequate, but higher doses of either drugs may shorten the treatment duration required for effective management of TB. Results of clinical trials evaluating high-dose rifamycin regimens are eagerly awaited.
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Affiliation(s)
- Omamah Alfarisi
- a Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Wael A Alghamdi
- b Department of Pharmacotherapy and Translational Research , University of Florida, College of Pharmacy , Gainesville , FL , USA.,c Infectious Disease Pharmacokinetics Laboratory , University of Florida , Gainesville , FL , USA
| | - Mohammad H Al-Shaer
- b Department of Pharmacotherapy and Translational Research , University of Florida, College of Pharmacy , Gainesville , FL , USA.,c Infectious Disease Pharmacokinetics Laboratory , University of Florida , Gainesville , FL , USA
| | - Kelly E Dooley
- a Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Charles A Peloquin
- b Department of Pharmacotherapy and Translational Research , University of Florida, College of Pharmacy , Gainesville , FL , USA.,c Infectious Disease Pharmacokinetics Laboratory , University of Florida , Gainesville , FL , USA
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171
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Jensen PA, Zhu Z, van Opijnen T. Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria. Cell Rep 2017; 20:1705-1716. [PMID: 28813680 PMCID: PMC5584877 DOI: 10.1016/j.celrep.2017.07.062] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/28/2017] [Accepted: 07/23/2017] [Indexed: 01/19/2023] Open
Abstract
Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude. Moreover, a gene expression meta-analysis reveals that genes with large fitness changes during stress have low transcriptional variation across hundreds of other conditions, and vice versa. Our work suggests that cellular responses can be understood through network models that incorporate regulatory and genetic relationships, which could aid drug target predictions and genetic network engineering.
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Affiliation(s)
- Paul A Jensen
- Biology Department, Boston College, Chestnut Hill, MA, USA.
| | - Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, USA.
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172
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Lin SW, Lin CJ, Yang JC. Rifamycin SV MMX for the treatment of traveler’s diarrhea. Expert Opin Pharmacother 2017; 18:1269-1277. [DOI: 10.1080/14656566.2017.1353079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Shu-Wen Lin
- Graduate Institute of Clinical Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Pharmacy, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Jung Lin
- Graduate Institute of Clinical Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jyh-Chin Yang
- Department of Internal Medicine, Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
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173
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Bactericidal activity of alpha-bromocinnamaldehyde against persisters in Escherichia coli. PLoS One 2017; 12:e0182122. [PMID: 28750057 PMCID: PMC5531548 DOI: 10.1371/journal.pone.0182122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 07/12/2017] [Indexed: 12/18/2022] Open
Abstract
Persisters are tolerant to multiple antibiotics, and widely distributed in bacteria, fungi, parasites, and even cancerous human cell populations, leading to recurrent infections and relapse after therapy. In this study, we investigated the potential of cinnamaldehyde and its derivatives to eradicate persisters in Escherichia coli. The results showed that 200 μg/ml of alpha-bromocinnamaldehyde (Br-CA) was capable of killing all E. coli cells during the exponential phase. Considering the heterogeneous nature of persisters, multiple types of persisters were induced and exposed to Br-CA. Our results indicated that no cells in the ppGpp-overproducing strain or TisB-overexpressing strain survived the treatment of Br-CA although considerable amounts of persisters to ampicillin (Amp) and ciprofloxacin (Cip) were induced. Chemical induction by carbonyl cyanide m-chlorophenylhydrazone (CCCP) led to the formation of more than 10% persister to Amp and Cip in the entire population, and Br-CA still completely eradicated them. In addition, the cells in the stationary phase, which are usually highly recalcitrant to antibiotics treatment, were also completely eradicated by 400 μg/ml of Br-CA. Further studies showed that neither thiourea (hydroxyl-radical scavenger) nor DPTA (Fe3+ chelator to block the hydroxyl-radical) affected the bactericidal efficiency of the Br-CA to kill E. coli, indicating a ROS-independent bactericidal mechanism. Taken together, we concluded that Br-CA compound has a novel bactericidal mechanism and the potential to mitigate antibiotics resistance crisis.
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174
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Abstract
Emergence of resistance among the most important bacterial pathogens is recognized as a major public health threat affecting humans worldwide. Multidrug-resistant organisms have not only emerged in the hospital environment but are now often identified in community settings, suggesting that reservoirs of antibiotic-resistant bacteria are present outside the hospital. The bacterial response to the antibiotic "attack" is the prime example of bacterial adaptation and the pinnacle of evolution. "Survival of the fittest" is a consequence of an immense genetic plasticity of bacterial pathogens that trigger specific responses that result in mutational adaptations, acquisition of genetic material, or alteration of gene expression producing resistance to virtually all antibiotics currently available in clinical practice. Therefore, understanding the biochemical and genetic basis of resistance is of paramount importance to design strategies to curtail the emergence and spread of resistance and to devise innovative therapeutic approaches against multidrug-resistant organisms. In this chapter, we will describe in detail the major mechanisms of antibiotic resistance encountered in clinical practice, providing specific examples in relevant bacterial pathogens.
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175
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Angiolini L, Agnes M, Cohen B, Yannakopoulou K, Douhal A. Formation, characterization and pH dependence of rifampicin: heptakis(2,6-di-O-methyl)-β-cyclodextrin complexes. Int J Pharm 2017; 531:668-675. [PMID: 28596140 DOI: 10.1016/j.ijpharm.2017.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/17/2017] [Accepted: 06/05/2017] [Indexed: 01/22/2023]
Abstract
Rifampicin (Rif) is a broad spectrum antibiotic used as a first line agent in the treatment of mycobacterial infections. However, its low solubility and reduced stability in water limit its bioavailability, thus requiring the use of complex formulations. Here, we present a systematic study of Rif in complex with a methylated cyclodextrin, heptakis(2,6-di-O-methyl)-β-cyclodextrin (DIMEB), in phosphate buffer using a combination of nuclear magnetic resonance (NMR) and steady-state UV-vis spectroscopic methods. An increase in the stability and solubility of Rif in complex with DIMEB was observed in buffered solutions (phosphate, PBS). At neutral pH the presence of three distinguishable binding sites was revealed, demonstrating that DIMEB forms predominantly a stable 1:1 (K∼3000M-1) complex at the piperazine site of Rif, while at acidic pH the binding constant decreases significantly (K∼400M-1) due to protonation of the piperazine, thus inducing a release of Rif. The reported results provide new and relevant information for the stability and solubility of Rif in aqueous solution when forming a complex with DIMEB. Furthermore they contribute to clarify Rif interactions with cyclodextrin carriers, thus providing the basis for the development of new methylated cyclodextrin that can efficiently encapsulate and deliver Rif and derivatives of its family.
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Affiliation(s)
- Lorenzo Angiolini
- Departamento de Química Física, Facultad de Ciencias del Medio Ambiente y Bioquímica and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Marco Agnes
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", Patr. Grigoriou E' & 27 Neapoleos str., 15341, Agia Paraskevi, Greece
| | - Boiko Cohen
- Departamento de Química Física, Facultad de Ciencias del Medio Ambiente y Bioquímica and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain
| | - Konstantina Yannakopoulou
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", Patr. Grigoriou E' & 27 Neapoleos str., 15341, Agia Paraskevi, Greece.
| | - Abderrazzak Douhal
- Departamento de Química Física, Facultad de Ciencias del Medio Ambiente y Bioquímica and INAMOL, Universidad de Castilla-La Mancha, Avenida Carlos III, S/N, 45071 Toledo, Spain.
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176
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Vélez JR, Cameron M, Rodríguez-Lecompte JC, Xia F, Heider LC, Saab M, McClure JT, Sánchez J. Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds. Front Vet Sci 2017; 4:63. [PMID: 28589129 PMCID: PMC5438997 DOI: 10.3389/fvets.2017.00063] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/19/2017] [Indexed: 11/20/2022] Open
Abstract
The objectives of this study are to determine the occurrence of antimicrobial resistance (AMR) genes using whole-genome sequence (WGS) of Streptococcus uberis (S. uberis) and Streptococcus dysgalactiae (S. dysgalactiae) isolates, recovered from dairy cows in the Canadian Maritime Provinces. A secondary objective included the exploration of the association between phenotypic AMR and the genomic characteristics (genome size, guanine–cytosine content, and occurrence of unique gene sequences). Initially, 91 isolates were sequenced, and of these isolates, 89 were assembled. Furthermore, 16 isolates were excluded due to larger than expected genomic sizes (>2.3 bp × 1,000 bp). In the final analysis, 73 were used with complete WGS and minimum inhibitory concentration records, which were part of the previous phenotypic AMR study, representing 18 dairy herds from the Maritime region of Canada (1). A total of 23 unique AMR gene sequences were found in the bacterial genomes, with a mean number of 8.1 (minimum: 5; maximum: 13) per genome. Overall, there were 10 AMR genes [ANT(6), TEM-127, TEM-163, TEM-89, TEM-95, Linb, Lnub, Ermb, Ermc, and TetS] present only in S. uberis genomes and 2 genes unique (EF-TU and TEM-71) to the S. dysgalactiae genomes; 11 AMR genes [APH(3′), TEM-1, TEM-136, TEM-157, TEM-47, TetM, bl2b, gyrA, parE, phoP, and rpoB] were found in both bacterial species. Two-way tabulations showed association between the phenotypic susceptibility to lincosamides and the presence of linB (P = 0.002) and lnuB (P < 0.001) genes and the between the presence of tetM (P = 0.015) and tetS (P = 0.064) genes and phenotypic resistance to tetracyclines only for the S. uberis isolates. The logistic model showed that the odds of resistance (to any of the phenotypically tested antimicrobials) was 4.35 times higher when there were >11 AMR genes present in the genome, compared with <7 AMR genes (P < 0.001). The odds of resistance was lower for S. dysgalactiae than S. uberis (P = 0.031). When the within-herd somatic cell count was >250,000 cells/mL, a trend toward higher odds of resistance compared with the baseline category of <150,000 cells/mL was observed. When the isolate corresponded to a post-mastitis sample, there were lower odds of resistance when compared with non-clinical isolates (P = 0.01). The results of this study showed the strength of associations between phenotypic AMR resistance of both mastitis pathogens and their genotypic resistome and other epidemiological characteristics.
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Affiliation(s)
- Julián Reyes Vélez
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Marguerite Cameron
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Juan Carlos Rodríguez-Lecompte
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Fangfang Xia
- Mathematics and Computer Science Division, Argonne National Laboratory, Chicago, IL, USA
| | - Luke C Heider
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Matthew Saab
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada.,Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - J Trenton McClure
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Javier Sánchez
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
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177
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Klahn P, Brönstrup M. Bifunctional antimicrobial conjugates and hybrid antimicrobials. Nat Prod Rep 2017; 34:832-885. [PMID: 28530279 DOI: 10.1039/c7np00006e] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to the end of 2016Novel antimicrobial drugs are continuously needed to counteract bacterial resistance development. An innovative molecular design strategy for novel antibiotic drugs is based on the hybridization of an antibiotic with a second functional entity. Such conjugates can be grouped into two major categories. In the first category (antimicrobial hybrids), both functional elements of the hybrid exert antimicrobial activity. Due to the dual targeting, resistance development can be significantly impaired, the pharmacokinetic properties can be superior compared to combination therapies with the single antibiotics, and the antibacterial potency is often enhanced in a synergistic manner. In the second category (antimicrobial conjugates), one functional moiety controls the accumulation of the other part of the conjugate, e.g. by mediating an active transport into the bacterial cell or blocking the efflux. This approach is mostly applied to translocate compounds across the cell envelope of Gram-negative bacteria through membrane-embedded transporters (e.g. siderophore transporters) that provide nutrition and signalling compounds to the cell. Such 'Trojan Horse' approaches can expand the antibacterial activity of compounds against Gram-negative pathogens, or offer new options for natural products that could not be developed as standalone antibiotics, e.g. due to their toxicity.
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Affiliation(s)
- P Klahn
- Department for Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany. and Institute for Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.
| | - M Brönstrup
- Department for Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
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178
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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179
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Abstract
The enzymology of 135 assembly lines containing primarily cis-acyltransferase modules is comprehensively analyzed, with greater attention paid to less common phenomena. Diverse online transformations, in which the substrate and/or product of the reaction is an acyl chain bound to an acyl carrier protein, are classified so that unusual reactions can be compared and underlying assembly-line logic can emerge. As a complement to the chemistry surrounding the loading, extension, and offloading of assembly lines that construct primarily polyketide products, structural aspects of the assembly-line machinery itself are considered. This review of assembly-line phenomena, covering the literature up to 2017, should thus be informative to the modular polyketide synthase novice and expert alike.
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Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
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180
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Gallagher KA, Wanger G, Henderson J, Llorente M, Hughes CC, Jensen PR. Ecological implications of hypoxia-triggered shifts in secondary metabolism. Environ Microbiol 2017; 19:2182-2191. [PMID: 28205416 DOI: 10.1111/1462-2920.13700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 02/10/2017] [Indexed: 11/28/2022]
Abstract
Members of the actinomycete genus Streptomyces are non-motile, filamentous bacteria that are well-known for the production of biomedically relevant secondary metabolites. While considered obligate aerobes, little is known about how these bacteria respond to periods of reduced oxygen availability in their natural habitats, which include soils and ocean sediments. Here, we provide evidence that the marine streptomycete strain CNQ-525 can reduce MnO2 via a diffusible mechanism. We investigated the effects of hypoxia on secondary metabolite production and observed a shift away from the antibiotic napyradiomycin towards 8-amino-flaviolin, an intermediate in the napyradiomycin biosynthetic pathway. We purified 8-amino-flaviolin and demonstrated that it is reversibly redox-active (midpoint potential -474.5 mV), indicating that it has the potential to function as an endogenous extracellular electron shuttle. This study provides evidence that environmentally triggered changes in secondary metabolite production may provide clues to the ecological functions of specific compounds, and that Gram-positive bacteria considered to be obligate aerobes may play previously unrecognized roles in biogeochemical cycling through mechanisms that include extracellular electron shuttling.
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Affiliation(s)
- Kelley A Gallagher
- Scripps Institution of Oceanography, Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
| | - Greg Wanger
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jane Henderson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Mark Llorente
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Chambers C Hughes
- Scripps Institution of Oceanography, Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Scripps Institution of Oceanography, Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, USA
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181
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Synthesis Characterization and Biological Activities of Coordination Compounds of 4-Hydroxy-3-nitro-2 H-chromen-2-one and Its Aminoethanoic Acid and Pyrrolidine-2-carboxylic Acid Mixed Ligand Complexes. Bioinorg Chem Appl 2017; 2017:6426747. [PMID: 28270743 PMCID: PMC5320075 DOI: 10.1155/2017/6426747] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 11/27/2016] [Indexed: 11/17/2022] Open
Abstract
Coordination compounds of 4-hydroxy-3-nitro-2H-chromen-2-one and their mixed ligand complexes with aminoethanoic acid and pyrrolidine-2-carboxylic acid were synthesized by the reaction of Cu(II) and Zn(II) salts in molar ratio 1 : 2 for the coumarin complexes and 1 : 1 : 1 for the mixed ligand complexes, in basic media. The compounds formed were characterized using infrared, Uv-vis spectrophotometric analyses, mass spectrometry, magnetic susceptibility measurements, and EDX analyses. It was concluded that 4-hydroxy-3-nitro-2H-chromen-2-one coordinated as a monobasic ligand for all the complexes; it also coordinated via the carbonyl moiety in the case of the Cu(II) mixed ligand complexes. Similarly it was proposed that the amino acids also coordinated in a bidentate fashion via their amino nitrogen and carboxylate oxygen atoms. The synthesized compounds were screened for their antimicrobial and cytotoxic activities. The complexes exhibited marginal antimicrobial activity but good cytotoxic activity.
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182
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Zarins-Tutt JS, Abraham ER, Bailey CS, Goss RJM. Bluegenics: Bioactive Natural Products of Medicinal Relevance and Approaches to Their Diversification. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 55:159-186. [PMID: 28238038 DOI: 10.1007/978-3-319-51284-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Nature provides a valuable resource of medicinally relevant compounds, with many antimicrobial and antitumor agents entering clinical trials being derived from natural products. The generation of analogues of these bioactive natural products is important in order to gain a greater understanding of structure activity relationships; probing the mechanism of action, as well as to optimise the natural product's bioactivity and bioavailability. This chapter critically examines different approaches to generating natural products and their analogues, exploring the way in which synthetic and biosynthetic approaches may be blended together to enable expeditious access to new designer natural products.
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Affiliation(s)
| | - Emily R Abraham
- School of Chemistry, University of St Andrews, St Andrews, Scotland, UK
| | | | - Rebecca J M Goss
- School of Chemistry, University of St Andrews, St Andrews, Scotland, UK.
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183
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Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities. Appl Environ Microbiol 2017; 83:AEM.02676-16. [PMID: 27986719 DOI: 10.1128/aem.02676-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/07/2016] [Indexed: 02/06/2023] Open
Abstract
Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. IMPORTANCE Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments.
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184
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Fomogne-Fodjo MCY, Ndinteh DT, Olivier DK, Kempgens P, van Vuuren S, Krause RWM. Secondary metabolites from Tetracera potatoria stem bark with anti-mycobacterial activity. JOURNAL OF ETHNOPHARMACOLOGY 2017; 195:238-245. [PMID: 27864111 DOI: 10.1016/j.jep.2016.11.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/25/2016] [Accepted: 11/13/2016] [Indexed: 06/06/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Tetracera potatoria Afzel. Exg. Don (Dilleniaceae) is a medicinal plant used traditionally in Africa for the treatment of tuberculosis related ailments and respiratory infections. The antibacterial activity of the medium polar extracts of T. potatoria leaves and stem bark was recently reported against Mycobacterium smegmatis (MIC 25µg/mL) and M. aurum (65µg/mL), two fast-growing Mycobacterium strains used as model micro-organisms for the more pathogenic strain Mycobacterium tuberculosis (Fomogne-Fodjo et al., 2014). The aim of this study was consequently to isolate the compounds possibly contributing to this activity, and which may therefore be promising precursors to be used for the development of novel anti-TB drugs. MATERIALS AND METHODS T. potatoria medium polar extract [MeOH/DCM (1:1, v/v)] was fractionated sequentially with petroleum ether to which EtOAC and MeOH were gradually added to increase the polarity. The examination of T. potatoria extract and its fractions was guided by bioassays for anti-mycobacterial activity against M. smegmatis (ATCC 23246) and M. aurum (NCTC 10437) using the minimum inhibitory concentration (MIC) method. All the isolated compounds were structurally elucidated using spectroscopic techniques and evaluated for their anti-mycobacterial activity. RESULTS Two novel secondary metabolites (1, 2) named tetraceranoate and N-hydroxy imidate-tetracerane, together with five known compounds [β-stigmasterol (3), stigmast-5-en-3β-yl acetate (4), betulinic acid (5), betulin (6) and lupeol (7)] were isolated and identified. Tetraceranoate exhibited the best activity against M. smegmatis with a minimum inhibitory concentration (MIC) of 7.8µg/mL, while β-stigmasterol, betulinic acid and betulin showed appreciable anti-mycobacterial activity against both strains (MIC 15µg/mL). CONCLUSION Seven compounds were isolated from the medium polar extract [MeOH/DCM (1:1, v/v)] of T. potatoria stem bark. Only tetraceranoate one of the isolated compounds showed antibacterial activity against M. smegmatis having efficacy as high as rifampicin (one of a three drug regimen recommended in the initial phase short-course anti-tuberculosis therapy). Thus, tetraceranoate might be an interesting target for systematic testing of anti-TB treatment and management. This research supports the use of T. potatoria in African traditional medicine for the treatment of tuberculosis related symptoms.
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Affiliation(s)
- M C Y Fomogne-Fodjo
- Department of Chemistry, Rhodes University, PO Box 94, Grahamstown 6140, South Africa.
| | - D T Ndinteh
- Department of Applied Chemistry, University of Johannesburg, PO Box 17011, Doornfontein, Johannesburg 2028, South Africa
| | - D K Olivier
- Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, South Africa
| | - P Kempgens
- Department of Chemistry, Rhodes University, PO Box 94, Grahamstown 6140, South Africa
| | - S van Vuuren
- Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown 2193, South Africa
| | - R W M Krause
- Department of Chemistry, Rhodes University, PO Box 94, Grahamstown 6140, South Africa.
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185
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Ammermann J, Schmidt T, Donner J, Reck M, Dalton M, Stumpp N, Stiesch M, Wagner-Döbler I, Kirschning A. The carolactam strategy is ineffective: synthesis and biological evaluation of carolactam. Org Biomol Chem 2017; 15:8553-8558. [DOI: 10.1039/c7ob02060k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The lactam analogue of carolacton was prepared which has lost biofilm inhibitory activity towards Streptococcus mutans.
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Affiliation(s)
- Jonas Ammermann
- Institute of Organic Chemistry and Center of Biomolecular Drug Research (BMWZ)
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Thomas Schmidt
- Institute of Organic Chemistry and Center of Biomolecular Drug Research (BMWZ)
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Jannik Donner
- Helmholtz-Center for Infection Research
- Department of Microbial Communication
- 38124 Braunschweig
- Germany
| | - Michael Reck
- Helmholtz-Center for Infection Research
- Department of Microbial Communication
- 38124 Braunschweig
- Germany
| | - Marly Dalton
- Department of Prosthetic Dentistry and Biomedical Materials Science
- Hannover Medical School
- 30625 Hannover
- Germany
| | - Nico Stumpp
- Department of Prosthetic Dentistry and Biomedical Materials Science
- Hannover Medical School
- 30625 Hannover
- Germany
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science
- Hannover Medical School
- 30625 Hannover
- Germany
| | - Irene Wagner-Döbler
- Helmholtz-Center for Infection Research
- Department of Microbial Communication
- 38124 Braunschweig
- Germany
| | - Andreas Kirschning
- Institute of Organic Chemistry and Center of Biomolecular Drug Research (BMWZ)
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
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186
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Zhang Z, Zhang J, Song R, Guo Z, Wang H, Zhu J, Lu C, Shen Y. Ansavaricins A–E: five new streptovaricin derivatives from Streptomyces sp. S012. RSC Adv 2017. [DOI: 10.1039/c6ra27405f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Five new polyketides of the ansamycin class, named ansavaricins A–E (1–5), together with three known streptovaricins 6–8, were isolated from the Streptomyces sp. S012 strain.
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Affiliation(s)
- Zhiqiang Zhang
- Key Laboratory of Chemical Biology
- Ministry of Education
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
| | - Juanli Zhang
- Department of Pharmacy
- Xijing Hospital
- The Fourth Military Medical University
- Xi'an
- P. R. China
| | - Rentai Song
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan
- P. R. China
| | - Zhixing Guo
- Key Laboratory of Chemical Biology
- Ministry of Education
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan
- P. R. China
| | - Jing Zhu
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan
- P. R. China
| | - Chunhua Lu
- Key Laboratory of Chemical Biology
- Ministry of Education
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
| | - Yuemao Shen
- Key Laboratory of Chemical Biology
- Ministry of Education
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
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187
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Zhang Z, Wu X, Song R, Zhang J, Wang H, Zhu J, Lu C, Shen Y. Ansavaricins F–I, new DNA topoisomerase inhibitors produced by Streptomyces sp. S012. RSC Adv 2017. [DOI: 10.1039/c7ra00961e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Ansamycins are a family of macrolactams characterized by an aromatic chromophore with an aliphatic chain (ansa chain) connected back to a nonadjacent position through an amide bond.
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Affiliation(s)
- Zhiqiang Zhang
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
- P. R. China
| | - Xingkang Wu
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
- P. R. China
| | - Rentai Song
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan
- P. R. China
| | - Juanli Zhang
- Department of Pharmacy
- Xijing Hospital
- The Fourth Military Medical University
- Xi'an
- P. R. China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan
- P. R. China
| | - Jing Zhu
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan
- P. R. China
| | - Chunhua Lu
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
- P. R. China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
- P. R. China
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188
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Abstract
Neoansamycins D–I with unusual extender units and diverse post-PKS modifications were isolated from the Streptomyces sp. SR201nam1OE strain.
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Affiliation(s)
- Mengyujie Liu
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
- P. R. China
| | - Chunhua Lu
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
- P. R. China
| | - Ruocong Tang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan
- P. R. China
| | - Shanren Li
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
- P. R. China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology
- Shandong University
- Jinan
- P. R. China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology (Ministry of Education)
- School of Pharmaceutical Sciences
- Shandong University
- Jinan
- P. R. China
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189
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Scharf NT, Molodtsov V, Kontos A, Murakami KS, Garcia GA. Novel Chemical Scaffolds for Inhibition of Rifamycin-Resistant RNA Polymerase Discovered from High-Throughput Screening. SLAS DISCOVERY 2016; 22:287-297. [PMID: 28027449 DOI: 10.1177/2472555216679994] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Rifampin has been a cornerstone of tuberculosis (TB) treatment since its introduction. The rise of multidrug-resistant and extensively drug-resistant TB makes the development of novel therapeutics effective against these strains an urgent need. Site-specific mutations in the target enzyme of rifampin, RNA polymerase (RNAP) comprises the majority (~97%) of rifamycin-resistant (RifR) strains of Mycobacterium tuberculosis (MTB). To identify novel inhibitors of bacterial RNAP, an in vitro plasmid-based transcription assay that uses malachite green (MG) to detect transcribed RNA containing MG aptamers was developed. This assay was optimized in a 384-well plate format and used to screen 150,000 compounds against an Escherichia coli homolog of the most clinically relevant RifR RNAP (βS531L) containing a mutation (β'V408G) that compensates for the fitness defect of this RifR mutant. Following confirmation and concentration-response studies, 10 compounds were identified with similar in vitro inhibition values across a panel of wild-type and RifR E. coli and MTB RNAPs. Four compounds identified from the screen are active against MTB in culture at concentrations below 200 µM. Initial follow-up has resulted in the elimination of one scaffold due to potential pan-assay interference.
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Affiliation(s)
- Nathan T Scharf
- 1 Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Vadim Molodtsov
- 2 Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Arrin Kontos
- 1 Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Katsuhiko S Murakami
- 2 Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - George A Garcia
- 1 Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
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190
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Kamala K, Sivaperumal P. Biomedical Applications of Enzymes From Marine Actinobacteria. ADVANCES IN FOOD AND NUTRITION RESEARCH 2016; 80:107-123. [PMID: 28215321 DOI: 10.1016/bs.afnr.2016.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Marine microbial enzyme technologies have progressed significantly in the last few decades for different applications. Among the various microorganisms, marine actinobacterial enzymes have significant active properties, which could allow them to be biocatalysts with tremendous bioactive metabolites. Moreover, marine actinobacteria have been considered as biofactories, since their enzymes fulfill biomedical and industrial needs. In this chapter, the marine actinobacteria and their enzymes' uses in biological activities and biomedical applications are described.
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Affiliation(s)
- K Kamala
- Center for Environmental Nuclear Research, Directorate of Research, SRM University, Kattankulathur, India.
| | - P Sivaperumal
- Center for Environmental Nuclear Research, Directorate of Research, SRM University, Kattankulathur, India
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191
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Patil R, Bhand S, Konkimalla VB, Banerjee P, Ugale B, Chadar D, Saha SK, Praharaj PP, Nagaraja C, Chakrovarty D, Salunke-Gawali S. Molecular association of 2-( n -alkylamino)-1,4-naphthoquinone derivatives: Electrochemical, DFT studies and antiproliferative activity against leukemia cell lines. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.06.075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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192
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Mechanisms of β-amino acid incorporation in polyketide macrolactam biosynthesis. Curr Opin Chem Biol 2016; 35:58-64. [DOI: 10.1016/j.cbpa.2016.08.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/30/2016] [Accepted: 08/26/2016] [Indexed: 12/11/2022]
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193
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Liu LK, Abdelwahab H, Martin Del Campo JS, Mehra-Chaudhary R, Sobrado P, Tanner JJ. The Structure of the Antibiotic Deactivating, N-hydroxylating Rifampicin Monooxygenase. J Biol Chem 2016; 291:21553-21562. [PMID: 27557658 PMCID: PMC5076826 DOI: 10.1074/jbc.m116.745315] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/22/2016] [Indexed: 11/06/2022] Open
Abstract
Rifampicin monooxygenase (RIFMO) catalyzes the N-hydroxylation of the natural product antibiotic rifampicin (RIF) to 2'-N-hydroxy-4-oxo-rifampicin, a metabolite with much lower antimicrobial activity. RIFMO shares moderate sequence similarity with well characterized flavoprotein monooxygenases, but the protein has not been isolated and characterized at the molecular level. Herein, we report crystal structures of RIFMO from Nocardia farcinica, the determination of the oligomeric state in solution with small angle x-ray scattering, and the spectrophotometric characterization of substrate binding. The structure identifies RIFMO as a class A flavoprotein monooxygenase and is similar in fold and quaternary structure to MtmOIV and OxyS, which are enzymes in the mithramycin and oxytetracycline biosynthetic pathways, respectively. RIFMO is distinguished from other class A flavoprotein monooxygenases by its unique middle domain, which is involved in binding RIF. Small angle x-ray scattering analysis shows that RIFMO dimerizes via the FAD-binding domain to form a bell-shaped homodimer in solution with a maximal dimension of 110 Å. RIF binding was monitored using absorbance at 525 nm to determine a dissociation constant of 13 μm Steady-state oxygen consumption assays show that NADPH efficiently reduces the FAD only when RIF is present, implying that RIF binds before NADPH in the catalytic scheme. The 1.8 Å resolution structure of RIFMO complexed with RIF represents the precatalytic conformation that occurs before formation of the ternary E-RIF-NADPH complex. The RIF naphthoquinone blocks access to the FAD N5 atom, implying that large conformational changes are required for NADPH to reduce the FAD. A model for these conformational changes is proposed.
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Affiliation(s)
- Li-Kai Liu
- From the Departments of Biochemistry and
| | - Heba Abdelwahab
- the Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, and
- the Department of Chemistry, Faculty of Science, Damietta University, Damietta 34517, Egypt
| | | | | | - Pablo Sobrado
- the Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, and
| | - John J Tanner
- From the Departments of Biochemistry and
- Chemistry and
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194
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Aminov R. History of antimicrobial drug discovery: Major classes and health impact. Biochem Pharmacol 2016; 133:4-19. [PMID: 27720719 DOI: 10.1016/j.bcp.2016.10.001] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/04/2016] [Indexed: 12/12/2022]
Abstract
The introduction of antibiotics into clinical practice revolutionized the treatment and management of infectious diseases. Before the introduction of antibiotics, these diseases were the leading cause of morbidity and mortality in human populations. This review presents a brief history of discovery of the main antimicrobial classes (arsphenamines, β-lactams, sulphonamides, polypeptides, aminoglycosides, tetracyclines, amphenicols, lipopeptides, macrolides, oxazolidinones, glycopeptides, streptogramins, ansamycins, quinolones, and lincosamides) that have changed the landscape of contemporary medicine. Given within a historical timeline context, the review discusses how the introduction of certain antimicrobial classes affected the morbidity and mortality rates due to bacterial infectious diseases in human populations. Problems of resistance to antibiotics of different classes are also extensively discussed.
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Affiliation(s)
- Rustam Aminov
- School of Medicine and Dentistry, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom.
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195
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van Opijnen T, Dedrick S, Bento J. Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome. PLoS Pathog 2016; 12:e1005869. [PMID: 27607357 PMCID: PMC5015961 DOI: 10.1371/journal.ppat.1005869] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/15/2016] [Indexed: 11/19/2022] Open
Abstract
The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.
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Affiliation(s)
- Tim van Opijnen
- Boston College, Biology Department, Chestnut Hill, Massachusetts, United States of America
| | - Sandra Dedrick
- Boston College, Biology Department, Chestnut Hill, Massachusetts, United States of America
| | - José Bento
- Boston College, Computer Science Department, Massachusetts, United States of America
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196
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Kumari R, Singh P, Lal R. Genetics and Genomics of the Genus Amycolatopsis. Indian J Microbiol 2016; 56:233-46. [PMID: 27407288 PMCID: PMC4920768 DOI: 10.1007/s12088-016-0590-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/23/2016] [Indexed: 02/06/2023] Open
Abstract
Actinobacteria are gram-positive filamentous bacteria which contains some of the most deadly human pathogens (Mycobacterium tuberculosis, M. leprae, Corynebacterium diphtheriae, Nocardia farcinica), plant pathogens (Streptomyces scabies, Leifsonia xyli) along with organisms that produces antibiotic (Streptomycetes, Amycolatopsis, Salinospora). Interestingly, these bacteria are equipped with an extraordinary capability of producing antibiotics and other metabolites which have medicinal properties. With the advent of inexpensive genome sequencing techniques and their clinical importance, many genomes of Actinobacteria have been successfully sequenced. These days, with the constant increasing number of drug-resistant bacteria, the urgent need for discovering new antibiotics has emerged as a major scientific challenge. And, unfortunately the traditional method of screening bacterial strains for the production of antibiotics has decreased leading to a paradigm shift in the planning and execution of discovery of novel biosynthetic gene clusters via genome mining process. The entire focus has shifted to the evaluation of genetic capacity of organisms for metabolite production and activation of cryptic gene clusters. This has been made possible only due to the availability of genome sequencing and has been augmented by genomic studies and new biotechnological approaches. Through this article, we present the analysis of the genomes of species belonging to the genus Amycolatopsis, sequenced till date with a focus on completely sequenced genomes and their application for further studies.
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Affiliation(s)
- Rashmi Kumari
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Priya Singh
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
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197
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Abstract
INTRODUCTION There is a growing need for new antibacterial agents, but success in development of antibiotics in recent years has been limited. This has led researchers to investigate novel approaches to finding compounds that are effective against multi-drug resistant bacteria, and that delay onset of resistance. One such strategy has been to link antibiotics to produce hybrids designed to overcome resistance mechanisms. AREAS COVERED The concept of dual-acting hybrid antibiotics was introduced and reviewed in this journal in 2010. In the present review the authors sought to discover how clinical candidates described had progressed, and to examine how the field has developed. In three sections the authors cover the clinical progress of hybrid antibiotics, novel agents produced from hybridisation of two or more small-molecule antibiotics, and novel agents produced from hybridisation of antibiotics with small-molecules that have complementary activity. EXPERT OPINION Many key questions regarding dual-acting hybrid antibiotics remain to be answered, and the proposed benefits of this approach are yet to be demonstrated. While Cadazolid in particular continues to progress in the clinic, suggesting that there is promise in hybridisation through covalent linkage, it may be that properties other than antibacterial activity are key when choosing a partner molecule.
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Affiliation(s)
| | - Ian A Yule
- a Medicinal Chemistry , Evotec (UK) Ltd , Abingdon , UK
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198
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Feng Y, Liu J, Carrasco YP, MacMillan JB, De Brabander JK. Rifamycin Biosynthetic Congeners: Isolation and Total Synthesis of Rifsaliniketal and Total Synthesis of Salinisporamycin and Saliniketals A and B. J Am Chem Soc 2016; 138:7130-42. [DOI: 10.1021/jacs.6b03248] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yu Feng
- Department of Biochemistry and ‡Harold C. Simmons Comprehensive
Cancer Center, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry
Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Jun Liu
- Department of Biochemistry and ‡Harold C. Simmons Comprehensive
Cancer Center, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry
Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Yazmin P. Carrasco
- Department of Biochemistry and ‡Harold C. Simmons Comprehensive
Cancer Center, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry
Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - John B. MacMillan
- Department of Biochemistry and ‡Harold C. Simmons Comprehensive
Cancer Center, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry
Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Jef K. De Brabander
- Department of Biochemistry and ‡Harold C. Simmons Comprehensive
Cancer Center, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry
Hines Boulevard, Dallas, Texas 75390-9038, United States
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199
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Application of rifampicin as a chiral selector for enantioresolution of basic drugs using capillary electrophoresis. J Chromatogr A 2016; 1453:138-42. [PMID: 27240943 DOI: 10.1016/j.chroma.2016.05.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/13/2016] [Accepted: 05/15/2016] [Indexed: 11/21/2022]
Abstract
Rifampicin, a member of rifamycin sub-class of antibiotics which belongs to the naphthalenic ansamycin class of antibiotics, has a characteristic ansa structure, i.e., a ring structure or chromophore spanned by an aliphatic chain. The present work was designed to evaluate its potential as a chiral selector (CS) as its structure consisting of nine stereogenic centers, an aromatic moiety and several functional groups (i.e., one imine, one amide, one acetoxy residue, two aliphatic hydroxyl and three phenolic hydroxyl groups) was expected to instigate multiple enantioselective interactions, namely, hydrogen bonding and inclusion complexation with chiral analytes, and therefore resulting in efficient enantioseparations. Systematic experiments were performed to investigate the effects of concentration of CS, composition of background electrolyte (BGE) and applied voltage on chiral separation. Enantiomers of propranolol and metoprolol were baseline resolved using a BGE consisting of 20mM CS and 50/50 (v/v) iso-propanol/phosphate buffer (100mM, pH 7.0) whereas for enantiomers of sertraline, a BGE consisting of 23mM CS and 40/60 (v/v) iso-propanol/phosphate buffer (100mM, pH 7.0) resulted in baseline resolutions.
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200
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Korsak D, Krawczyk-Balska A. Rifampicin- and Rifabutin-Resistant Listeria monocytogenes Strains Isolated from Food Products Carry Mutations in rpoB Gene. Foodborne Pathog Dis 2016; 13:363-8. [PMID: 27105395 DOI: 10.1089/fpd.2015.2103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aim of this study was to investigate the mechanism of rifampicin resistance in Listeria monocytogenes strains isolated from different types of food and the impact of specific mutations in the rpoB gene on susceptibility to different antimicrobial agents and on fitness cost. Fifteen spontaneous rifampicin-resistant strains were selected. The DNA regions corresponding to clusters I-II, III, and N-terminal end of the rpoB gene of Escherichia coli were amplified and sequenced, leading to the identification of 10 different substitutions, nine of which (Ser466Pro, Gln470Lys Asp473Asn, Gly479Asp, His483Tyr/Arg/Asp, Arg486His, and Leu490Pro) were located in cluster I and one (Pro521Leu) in cluster II. From among these mutations, substitutions at positions 466, 470, 486, 490, and 521 have not been described for L. monocytogenes. Only substitutions at positions 470, 479, 483, and 486 lead to resistance to very high concentrations of rifampicin (minimum inhibitory concentration [MIC] ≥256 μg/mL) and rifabutin (MIC 128 μg/mL). Furthermore, mutations at positions 473, 490, and 521 had different effects on susceptibility to rifampicin compared to other bacterial species. A correlation between rifampicin resistance and susceptibility to a wide range of antimicrobials was determined. Substitutions in RpoB did not change the susceptibility of the mutants to different antimicrobials. The fitness of the mutants was assessed by paired competition experiments. Mutations at positions 470 and 479 were not associated with a reduction in fitness level. There was no correlation between the MIC of rifampicin and fitness cost. The risk of transmission of resistant strains through the food chain highlights the need for monitoring resistance, identifying mutant organisms, their genotypes, and their altered phenotypes to understand their dissemination.
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Affiliation(s)
- Dorota Korsak
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw , Warsaw, Poland
| | - Agata Krawczyk-Balska
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw , Warsaw, Poland
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