1
|
Chen S, Rao M, Jin W, Hu M, Chen D, Ge M, Mao W, Qian X. Metabolomic analysis in Amycolatopsis keratiniphila disrupted the competing ECO0501 pathway for enhancing the accumulation of vancomycin. World J Microbiol Biotechnol 2024; 40:297. [PMID: 39126539 DOI: 10.1007/s11274-024-04105-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Vancomycin is a clinically important glycopeptide antibiotic against Gram-positive pathogenic bacteria, especially methicillin-resistant Staphylococcus aureus. In the mutant strain of Amycolatopsis keratiniphila HCCB10007 Δeco-cds4-27, the production of ECO-0501 was disrupted, but enhanced vancomycin yield by 55% was observed compared with the original strain of A. keratiniphila HCCB10007. To gain insights into the mechanism of the enhanced production of vancomycin in the mutant strain, comparative metabolomics analyses were performed between the mutant strain and the original strain, A. keratiniphila HCCB10007 via GC-TOF-MS and UPLC-HRMS. The results of PCA and OPLS-DA revealed a significant distinction of the intracellular metabolites between the two strains during the fermentation process. 64 intracellular metabolites, which involved in amino acids, fatty acids and central carbon metabolism, were identified as differential metabolites. The high-yield mutant strain maintained high levels of glucose-1-phosphate and glucose-6-phosphate and they declined with the increases of vancomycin production. Particularly, a strong association of fatty acids accumulation as well as 3,5-dihydroxyphenylacetic acid and non-proteinogenic amino acid 3,5-dihydroxyphenylglycine (Dpg) with enhancement of vancomycin production was observed in the high-yield mutant strain, indicating that the consumption of fatty acid pools might be beneficial for giving rise to 3,5-dihydroxyphenylacetic acid and Dpg which further lead to improve vancomycin production. In addition, the lower levels of glyoxylic acid and lactic acid and the higher levels of sulfur amino acids might be beneficial for improving vancomycin production. These findings proposed more advanced elucidation of metabolomic characteristics in the high-yield strain for vancomycin production and could provide potential strategies to enhance the vancomycin production.
Collapse
Affiliation(s)
- Shuo Chen
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Min Rao
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
- Zhejiang Pharmaceutical Co., Ltd, Shaoxing, China
| | - Wenxiang Jin
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
| | - Mengyi Hu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Daijie Chen
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Mei Ge
- Shanghai Laiyi Center for Biopharmaceutical R&D, Shanghai, China
- Zhejiang Pharmaceutical Co., Ltd, Shaoxing, China
| | - Wenwei Mao
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
| | - Xiuping Qian
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
2
|
Żywicka A, Ciecholewska-Juśko D, Drozd R, Rakoczy R, Konopacki M, Kordas M, Junka A, Migdał P, Fijałkowski K. Preparation of Komagataeibacter xylinus Inoculum for Bacterial Cellulose Biosynthesis Using Magnetically Assisted External-Loop Airlift Bioreactor. Polymers (Basel) 2021; 13:polym13223950. [PMID: 34833249 PMCID: PMC8623894 DOI: 10.3390/polym13223950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 01/26/2023] Open
Abstract
The aim of this study was to demonstrate the applicability of a novel magnetically assisted external-loop airlift bioreactor (EL-ALB), equipped with rotating magnetic field (RMF) generators for the preparation of Komagataeibacterxylinus inoculum during three-cycle repeated fed-batch cultures, further used for bacterial cellulose (BC) production. The fermentation carried out in the RMF-assisted EL-ALB allowed to obtain an inoculum of more than 200× higher cellular density compared to classical methods of inoculum preparation. The inoculum obtained in the RMF-assisted EL-ALB was characterized by a high and stable metabolic activity during repeated batch fermentation process. The application of the RMF-assisted EL-ALB for K. xylinus inoculum production did not induce the formation of cellulose-deficient mutants. It was also confirmed that the ability of K. xylinus to produce BC was at the same level (7.26 g/L of dry mass), regardless of inoculum age. Additionally, the BC obtained from the inoculum produced in the RMF-assisted EL-ALB was characterized by reproducible water-related properties, mechanical strength, nano-fibrillar structure and total crystallinity index. The lack of any negative impact of inoculum preparation method using RMF-assisted EL-ALB on BC properties is of paramount value for its future applications, including use as a biomaterial in tissue engineering, wound healing, and drug delivery, where especially BC liquid capacity, nanostructure, crystallinity, and mechanical properties play essential roles.
Collapse
Affiliation(s)
- Anna Żywicka
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów Ave. 45, 70-311 Szczecin, Poland; (D.C.-J.); (R.D.)
- Correspondence: (A.Ż.); (K.F.); Tel.: +48-91-449-6709 (A.Ż.); +48-91-449-6714 (K.F.)
| | - Daria Ciecholewska-Juśko
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów Ave. 45, 70-311 Szczecin, Poland; (D.C.-J.); (R.D.)
| | - Radosław Drozd
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów Ave. 45, 70-311 Szczecin, Poland; (D.C.-J.); (R.D.)
| | - Rafał Rakoczy
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology in Szczecin, Piastów Ave. 42, 71-065 Szczecin, Poland; (R.R.); (M.K.); (M.K.)
| | - Maciej Konopacki
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology in Szczecin, Piastów Ave. 42, 71-065 Szczecin, Poland; (R.R.); (M.K.); (M.K.)
| | - Marian Kordas
- Department of Chemical and Process Engineering, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology in Szczecin, Piastów Ave. 42, 71-065 Szczecin, Poland; (R.R.); (M.K.); (M.K.)
| | - Adam Junka
- Department of Pharmaceutical Microbiology and Parasitology, Faculty of Pharmacy, Medical University of Wroclaw, Borowska 211a, 50-534 Wrocław, Poland;
| | - Paweł Migdał
- Department of Environment, Hygiene and Animal Welfare, Faculty of Biology and Animal Science, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 38C, 51-630 Wrocław, Poland;
| | - Karol Fijałkowski
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów Ave. 45, 70-311 Szczecin, Poland; (D.C.-J.); (R.D.)
- Correspondence: (A.Ż.); (K.F.); Tel.: +48-91-449-6709 (A.Ż.); +48-91-449-6714 (K.F.)
| |
Collapse
|
3
|
Grenade NL, Howe GW, Ross AC. The convergence of bacterial natural products from evolutionarily distinct pathways. Curr Opin Biotechnol 2020; 69:17-25. [PMID: 33296737 DOI: 10.1016/j.copbio.2020.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/21/2020] [Accepted: 10/05/2020] [Indexed: 10/22/2022]
Abstract
As bacteria readily convert simple starting materials into a diverse array of complex molecules with useful bioactivities, these microorganisms and their biosynthetic machinery represent attractive alternatives to traditional chemical syntheses. While the well-documented divergent evolution of biosynthesis has allowed bacteria to explore wide swaths of natural product chemical space, the convergent evolution of these pathways remains a comparably rare phenomenon. The emergence of similar phenotypes within disparate genetic contexts provides a unique opportunity to probe the limitations of natural selection and the predictability and reproducibility of evolution under different constraints. Here, we report several recent examples of functional and structural convergence of bacterial natural products, as well as intra- and inter-domain convergence of bacterial biosynthetic machinery. While the genetic underpinnings of biosynthetic pathway evolution are of fundamental interest, the evolutionary constraints exemplified by phenotypic convergence also have immediate implications for efforts to engineer microorganisms for therapeutic small molecule production.
Collapse
Affiliation(s)
- Neil L Grenade
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Graeme W Howe
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
| |
Collapse
|
4
|
Davis K, Gkotsi DS, Smith DRM, Goss RJM, Caputi L, O’Connor SE. Nicotiana benthamiana as a Transient Expression Host to Produce Auxin Analogs. FRONTIERS IN PLANT SCIENCE 2020; 11:581675. [PMID: 33329644 PMCID: PMC7714751 DOI: 10.3389/fpls.2020.581675] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/26/2020] [Indexed: 05/29/2023]
Abstract
Plant secondary metabolites have applications for the food, biofuel, and pharmaceutical industries. Recent advances in pathway elucidation and host expression systems now allow metabolic engineering of plant metabolic pathways to produce "new-to-nature" derivatives with novel biological activities, thereby amplifying the range of industrial uses for plant metabolites. Here we use a transient expression system in the model plant Nicotiana benthamiana to reconstitute the two-step plant-derived biosynthetic pathway for auxin (indole acetic acid) to achieve accumulation up to 500 ng/g fresh mass (FM). By expressing these plant-derived enzymes in combination with either bacterial halogenases and alternative substrates, we can produce both natural and new-to-nature halogenated auxin derivatives up to 990 ng/g FM. Proteins from the auxin synthesis pathway, tryptophan aminotransferases (TARs) and flavin-dependent monooxygenases (YUCs), could be transiently expressed in combination with four separate bacterial halogenases to generate halogenated auxin derivatives. Brominated auxin derivatives could also be observed after infiltration of the transfected N. benthamiana with potassium bromide and the halogenases. Finally, the production of additional auxin derivatives could also be achieved by co-infiltration of TAR and YUC genes with various tryptophan analogs. Given the emerging importance of transient expression in N. benthamiana for industrial scale protein and product expression, this work provides insight into the capacity of N. benthamiana to interface bacterial genes and synthetic substrates to produce novel halogenated metabolites.
Collapse
Affiliation(s)
- Katharine Davis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Danai S. Gkotsi
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Duncan R. M. Smith
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| |
Collapse
|
5
|
Hu D, Sun C, Jin T, Fan G, Mok KM, Li K, Lee SMY. Exploring the Potential of Antibiotic Production From Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis. Front Microbiol 2020; 11:1540. [PMID: 32922368 PMCID: PMC7375171 DOI: 10.3389/fmicb.2020.01540] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/12/2020] [Indexed: 11/26/2022] Open
Abstract
Actinobacteria are well recognized for their production of structurally diverse bioactive secondary metabolites, but the rare actinobacterial genera have been underexploited for such potential. To search for new sources of active compounds, an experiment combining genomic analysis and tandem mass spectrometry (MS/MS) screening was designed to isolate and characterize actinobacterial strains from a mangrove environment in Macau. Fourteen actinobacterial strains were isolated from the collected samples. Partial 16S sequences indicated that they were from six genera, including Brevibacterium, Curtobacterium, Kineococcus, Micromonospora, Mycobacterium, and Streptomyces. The isolate sp.01 showing 99.28% sequence similarity with a reference rare actinobacterial species Micromonospora aurantiaca ATCC 27029T was selected for whole genome sequencing. Organization of its gene clusters for secondary metabolite biosynthesis revealed 21 clusters encoded to antibiotic production, which is higher than other Micromonospora species. Of the genome-predicted antibiotics, kanamycin was found through guided MS/MS analysis producible by the M. aurantiaca strain for the first time. The present study highlighted that genomic analysis combined with MS/MS screening is a promising method to discover potential of antibiotic production from rare actinobacteria.
Collapse
Affiliation(s)
- Dini Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Chenghang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Jin
- Beijing Genomics Institute, Shenzhen, China
| | | | - Kai Meng Mok
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Kai Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| |
Collapse
|
6
|
Zhang L, Liu L, Wang KF, Xu L, Zhou L, Wang W, Li C, Xu Z, Shi T, Chen H, Li Y, Xu H, Yang X, Zhu Z, Chen B, Li D, Zhan G, Zhang SL, Zhang LX, Tan GY. Phosphate limitation increases coenzyme Q 10 production in industrial Rhodobacter sphaeroides HY01. Synth Syst Biotechnol 2019; 4:212-219. [PMID: 31890925 PMCID: PMC6909082 DOI: 10.1016/j.synbio.2019.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/02/2022] Open
Abstract
Coenzyme Q10 (CoQ10) is an important component of the respiratory chain in humans and some bacteria. As a high-value-added nutraceutical antioxidant, CoQ10 has excellent capacity to prevent cardiovascular disease. The content of CoQ10 in the industrial Rhodobacter sphaeroides HY01 is hundreds of folds higher than normal physiological levels. In this study, we found that overexpression or optimization of the synthetic pathway failed CoQ10 overproduction in the HY01 strain. Moreover, under phosphate- limited conditions (decreased phosphate or in the absence of inorganic phosphate addition), CoQ10 production increased significantly by 12% to220 mg/L, biomass decreased by 12%, and the CoQ10 productivity of unit cells increased by 27%. In subsequent fed-batch fermentation, CoQ10 production reached 272 mg/L in the shake-flask fermentation and 1.95 g/L in a 100-L bioreactor under phosphate limitation. Furthermore, to understand the mechanism associated with CoQ10 overproduction under phosphate- limited conditions, the comparatve transcriptome analysis was performed. These results indicated that phosphate limitation combined with glucose fed-batch fermentation represented an effective strategy for CoQ10 production in the HY01. Phosphate limitation induced a pleiotropic effect on cell metabolism, and that improved CoQ10 biosynthesis efficiency was possibly related to the disturbance of energy metabolism and redox potential.
Collapse
Affiliation(s)
- Lu Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Leshi Liu
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Ke-Feng Wang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Lan Xu
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), No.1 Beichen West Road, Beijing, 100101, China
| | - Liming Zhou
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), No.1 Beichen West Road, Beijing, 100101, China
| | - Chuan Li
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Zheng Xu
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), No.1 Beichen West Road, Beijing, 100101, China
| | - Tong Shi
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Haihong Chen
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Yuanhang Li
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Hui Xu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - XiuLiang Yang
- Shandong Jincheng Bio-Pharmaceutical Co., Ltd, No. 117 Qixing River Road, Zibo, 255130, China
| | - Zhichun Zhu
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Biqin Chen
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Dan Li
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Guanghuang Zhan
- Inner Mongolia Kingdomway Pharmaceutical Co., Ltd, Tuoketuo Power Industrial Park, Hohhot, 010206, China
| | - Si-Liang Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Li-Xin Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering (SKLBE), And School of Biotechnology, East China University of Science and Technology (ECUST), No. 130 Meilong Road, Shanghai, 200237, China
| |
Collapse
|
7
|
A Review on the Feedstocks for the Sustainable Production of Bioactive Compounds in Biorefineries. SUSTAINABILITY 2019. [DOI: 10.3390/su11236765] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since 2015, the sustainable development goals of the United Nations established a route map to achieve a sustainable society, pushing the industry to aim for sustainable processes. Biorefineries have been studied as the technological scheme to process integrally renewable resources. The so-called “bioactive” compounds (BACs) have been of high interest, given their high added value and potential application in pharmaceutics and health, among others. However, there are still elements to be addressed to consider them as economic drivers of sustainable processes. First, BACs can be produced from many sources and it is important to identify feedstocks for this purpose. Second, a sustainable production process should also consider valorizing the remaining components. Finally, feedstock availability plays an important role in affecting the process scale, logistics, and feasibility. This work consists of a review on the feedstocks for the sustainable production of BACs in biorefineries, covering the type of BAC, composition, and availability. Some example biorefineries are proposed using wheat straw, hemp and grapevine shoots. As a main conclusion, multiple raw materials have the potential to obtain BACs that can become economic drivers of biorefineries. This is an interesting outlook, as the integral use of the feedstocks may not only allow obtaining different types of BACs, but also other fiber products and energy for the process self-supply.
Collapse
|
8
|
Gao H, Murugesan B, Hoßbach J, Evans SK, Stark WM, Smith MCM. Integrating vectors for genetic studies in the rare Actinomycete Amycolatopsis marina. BMC Biotechnol 2019; 19:32. [PMID: 31164159 PMCID: PMC6549336 DOI: 10.1186/s12896-019-0521-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 04/30/2019] [Indexed: 11/15/2022] Open
Abstract
Background Few natural product pathways from rare Actinomycetes have been studied due to the difficulty in applying molecular approaches in these genetically intractable organisms. In this study, we sought to identify more integrating vectors, using phage int/attP loci, that would efficiently integrate site-specifically in the rare Actinomycete, Amycolatopsis marina DSM45569. Results Analysis of the genome of A. marina DSM45569 indicated the presence of attB-like sequences for TG1 and R4 integrases. The TG1 and R4 attBs were active in in vitro recombination assays with their cognate purified integrases and attP loci. Integrating vectors containing either the TG1 or R4 int/attP loci yielded exconjugants in conjugation assays from Escherichia coli to A. marina DSM45569. Site-specific recombination of the plasmids into the host TG1 or R4 attB sites was confirmed by sequencing. Conclusions The homologous TG1 and R4 attB sites within the genus Amycolatopsis have been identified. The results indicate that vectors based on TG1 and R4 integrases could be widely applicable in this genus.
Collapse
Affiliation(s)
- Hong Gao
- Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK. .,Present address: School of Science, Engineering & Design, Teesside University, Middlesbrough, TS1 3BX, UK.
| | - Buvani Murugesan
- Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| | - Janina Hoßbach
- Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| | - Stephanie K Evans
- Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| | - W Marshall Stark
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Margaret C M Smith
- Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Menon BRK, Latham J, Dunstan MS, Brandenburger E, Klemstein U, Leys D, Karthikeyan C, Greaney MF, Shepherd SA, Micklefield J. Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes. Org Biomol Chem 2018; 14:9354-9361. [PMID: 27714222 DOI: 10.1039/c6ob01861k] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Flavin-dependent halogenase (Fl-Hal) enzymes have been shown to halogenate a range of synthetic as well as natural aromatic compounds. The exquisite regioselectively of Fl-Hal enzymes can provide halogenated building blocks which are inaccessible using standard halogenation chemistries. Consequently, Fl-Hal are potentially useful biocatalysts for the chemoenzymatic synthesis of pharmaceuticals and other valuable products, which are derived from haloaromatic precursors. However, the application of Fl-Hal enzymes, in vitro, has been hampered by their poor catalytic activity and lack of stability. To overcome these issues, we identified a thermophilic tryptophan halogenase (Th-Hal), which has significantly improved catalytic activity and stability, compared with other Fl-Hal characterised to date. When used in combination with a thermostable flavin reductase, Th-Hal can efficiently halogenate a number of aromatic substrates. X-ray crystal structures of Th-Hal, and the reductase partner (Th-Fre), provide insights into the factors that contribute to enzyme stability, which could guide the discovery and engineering of more robust and productive halogenase biocatalysts.
Collapse
Affiliation(s)
- Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Jonathan Latham
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Mark S Dunstan
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Eileen Brandenburger
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Ulrike Klemstein
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - David Leys
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Chinnan Karthikeyan
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Michael F Greaney
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| |
Collapse
|
11
|
Old and new glycopeptide antibiotics: From product to gene and back in the post-genomic era. Biotechnol Adv 2018; 36:534-554. [PMID: 29454983 DOI: 10.1016/j.biotechadv.2018.02.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/22/2018] [Accepted: 02/14/2018] [Indexed: 02/05/2023]
Abstract
Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by multi-drug resistant Gram-positive pathogens. First-generation glycopeptides (vancomycin and teicoplanin) are produced by soil-dwelling actinomycetes. Second-generation glycopeptides (dalbavancin, oritavancin, and telavancin) are semi-synthetic derivatives of the progenitor natural products. Herein, we cover past and present biotechnological approaches for searching for and producing old and new glycopeptide antibiotics. We review the strategies adopted to increase microbial production (from classical strain improvement to rational genetic engineering), and the recent progress in genome mining, chemoenzymatic derivatization, and combinatorial biosynthesis for expanding glycopeptide chemical diversity and tackling the never-ceasing evolution of antibiotic resistance.
Collapse
|
12
|
Lee Y, Phat C, Hong SC. Structural diversity of marine cyclic peptides and their molecular mechanisms for anticancer, antibacterial, antifungal, and other clinical applications. Peptides 2017; 95:94-105. [PMID: 28610952 DOI: 10.1016/j.peptides.2017.06.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 06/06/2017] [Accepted: 06/06/2017] [Indexed: 01/28/2023]
Abstract
Many cyclic peptides and analogues derived from marine sources are known to possess biological properties, including anticancer, antitumor, antibacterial, antifungal, antiparasitic, anti-inflammation, anti-proliferative, anti-hypertensive, cytotoxic, and antibiotic properties. These compounds demonstrate different activities and modes of action according to their structure such as cyclic oligopeptide, cyclic lipopeptide, cyclic glycopeptide and cyclic depsipeptide. The recent advances in application of the above-mentioned cyclic peptides were reported in dolastatins, soblidotin, didemnin B, aplidine, salinosporamide A, kahalalide F and bryostatin 1 and they are currently in clinical trials. These cyclic peptides are possible novel drugs discovered and developed from marine origin. Literature data concerning the potential properties of marine cyclic peptides were reviewed here, and the structural diversity and biological activities of marine cyclic peptides are discussed in relation to the molecular mechanisms of these marine cyclic peptides.
Collapse
Affiliation(s)
- Yeji Lee
- College of Medicine, Korea University, Seoul, Republic of Korea
| | - Chanvorleak Phat
- School of Food Science and Technology, Chung-Ang University, Anseong-Si, Gyeonggi-Do, Republic of Korea
| | - Soon-Cheol Hong
- College of Medicine, Korea University, Seoul, Republic of Korea.
| |
Collapse
|
13
|
Genome Sequence of the Vancomycin-Producing Amycolatopsis orientalis subsp. orientalis Strain KCTC 9412T. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00408-13. [PMID: 23814036 PMCID: PMC3695432 DOI: 10.1128/genomea.00408-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Amycolatopsis orientalis is the producer of vancomycin, a glycopeptide antibiotic that is used for the treatment of serious infections with Gram-positive bacteria. Here we present the next-generation sequencing (NGS)-based 9.06-Mb draft genome sequence of the type strain Amycolatopsis orientalis subsp. orientalis KCTC 9412 (DSM 40040; ATCC 19795).
Collapse
|
14
|
Pathak TP, Miller SJ. Chemical tailoring of teicoplanin with site-selective reactions. J Am Chem Soc 2013; 135:8415-22. [PMID: 23692563 DOI: 10.1021/ja4038998] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Semisynthesis of natural product derivatives combines the power of fermentation with orthogonal chemical reactions. Yet, chemical modification of complex structures represents an unmet challenge, as poor selectivity often undermines efficiency. The complex antibiotic teicoplanin eradicates bacterial infections. However, as resistance emerges, the demand for improved analogues grows. We have discovered chemical reactions that achieve site-selective alteration of teicoplanin. Utilizing peptide-based additives that alter reaction selectivities, certain bromo-teicoplanins are accessible. These new compounds are also scaffolds for selective cross-coupling reactions, enabling further molecular diversification. These studies enable two-step access to glycopeptide analogues not available through either biosynthesis or rapid total chemical synthesis alone. The new compounds exhibit a spectrum of activities, revealing that selective chemical alteration of teicoplanin may lead to analogues with attenuated or enhanced antibacterial properties, in particular against vancomycin- and teicoplanin-resistant strains.
Collapse
Affiliation(s)
- Tejas P Pathak
- Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
| | | |
Collapse
|
15
|
Zeng X, Wang S, Jing K, Zhang Z, Lu Y. Use of biodiesel-derived crude glycerol for vancomycin production byAmycolatopsis orientalisXMU-VS01. Eng Life Sci 2012. [DOI: 10.1002/elsc.201200062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Xianhai Zeng
- Department of Chemical and Biochemical Engineering; College of Chemistry and Chemical Engineering; Xiamen University; Xiamen; P. R. China
| | - Sili Wang
- Faculty of Blood; the First Affiliated Hospital of Xiamen University; Xiamen; P. R. China
| | - Keju Jing
- Department of Chemical and Biochemical Engineering; College of Chemistry and Chemical Engineering; Xiamen University; Xiamen; P. R. China
| | - Zhixiang Zhang
- Department of Chemical and Biochemical Engineering; College of Chemistry and Chemical Engineering; Xiamen University; Xiamen; P. R. China
| | | |
Collapse
|
16
|
Fowler BS, Laemmerhold KM, Miller SJ. Catalytic site-selective thiocarbonylations and deoxygenations of vancomycin reveal hydroxyl-dependent conformational effects. J Am Chem Soc 2012; 134:9755-61. [PMID: 22621706 PMCID: PMC3374881 DOI: 10.1021/ja302692j] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We have examined peptide-based catalysts for the site-selective thiocarbonylation of a protected form of vancomycin. Several catalysts were identified that either enhanced or altered the inherent selectivity profile exhibited by the substrate. Two catalysts, one identified through screening and another through rational design, were demonstrated to be effective on 0.50-g scale. Deoxygenations led ultimately to two new deoxy-vancomycin derivatives, and surprising conformational consequences of deoxygenation were revealed for one of the new compounds. These effects were mirrored in the biological activities of the new analogues and support a structural role for certain hydroxyls in the native structure.
Collapse
Affiliation(s)
- Brandon S. Fowler
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107
| | - Kai M. Laemmerhold
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107
| |
Collapse
|
17
|
Ponder C, Overcash M. Cradle-to-gate life cycle inventory of vancomycin hydrochloride. THE SCIENCE OF THE TOTAL ENVIRONMENT 2010; 408:1331-1337. [PMID: 19942254 DOI: 10.1016/j.scitotenv.2009.10.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 10/10/2009] [Accepted: 10/20/2009] [Indexed: 05/28/2023]
Abstract
A life cycle analysis on the cradle-to-gate production of vancomycin hydrochloride, which begins at natural resource extraction and spans through factory (gate) production, not only shows all inputs, outputs, and energy usage to manufacture the product and all related supply chain chemicals, but can highlight where process changes would have the greatest impact on raw material and energy consumption and emissions. Vancomycin hydrochloride is produced by a low-yield fermentation process that accounts for 47% of the total cradle-to-gate energy. The fermentation step consumes the most raw materials and energy cradle-to-gate. Over 75% of the total cradle-to-gate energy consumption is due to steam use; sterilization within fermentation is the largest user of steam. Aeration and agitation in the fermentation vessels use 65% of the cradle-to-gate electrical energy. To reduce raw materials, energy consumption, and the associated environmental footprint of producing vancomycin hydrochloride, other sterilization methods, fermentation media, nutrient sources, or synthetic manufacture should be investigated. The reported vancomycin hydrochloride life cycle inventory is a part of a larger life cycle study of the environmental consequences of the introduction of biocide-coated medical textiles for the prevention of MRSA (methicillin-resistant Staphylococcus aureus) nosocomial infections.
Collapse
Affiliation(s)
- Celia Ponder
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | | |
Collapse
|
18
|
Actinomycetes scale-up for the production of the antibacterial, nocathiacin. Biotechnol Prog 2009; 25:176-88. [DOI: 10.1002/btpr.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|