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Sood U, Müller M, Lan T, Garg G, Singhvi N, Hira P, Singh P, Nigam A, Verma M, Lata P, Kaur H, Kumar A, Rawat CD, Lal S, Aldrich C, Bechthold A, Lal R. Amycolatopsis mediterranei: A Sixty-Year Journey from Strain Isolation to Unlocking Its Potential of Rifamycin Analogue Production by Combinatorial Biosynthesis. JOURNAL OF NATURAL PRODUCTS 2024; 87:424-438. [PMID: 38289177 DOI: 10.1021/acs.jnatprod.3c00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Ever since the isolation of Amycolatopsis mediterranei in 1957, this strain has been the focus of research worldwide. In the last 60 years or more, our understanding of the taxonomy, development of cloning vectors and conjugation system, physiology, genetics, genomics, and biosynthetic pathway of rifamycin B production in A. mediterranei has substantially increased. In particular, the development of cloning vectors, transformation system, characterization of the rifamycin biosynthetic gene cluster, and the regulation of rifamycin B production by the pioneering work of Heinz Floss have made the rifamycin polyketide biosynthetic gene cluster (PKS) an attractive target for extensive genetic manipulations to produce rifamycin B analogues which could be effective against multi-drug-resistant tuberculosis. Additionally, a better understanding of the regulation of rifamycin B production and the application of newer genomics tools, including CRISPR-assisted genome editing systems, might prove useful to overcome the limitations associated with low production of rifamycin analogues.
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Affiliation(s)
- Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi-110007, India
| | - Moritz Müller
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Tian Lan
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Gauri Garg
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi-110007, India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, Uttarakhand 248007, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, Delhi-110003, India
| | - Priya Singh
- Department of Zoology, Maitreyi College, University of Delhi, Delhi-110003, India
| | - Aeshna Nigam
- Department of Zoology, Shivaji College, University of Delhi, Delhi-110027, India
| | - Mansi Verma
- Department of Zoology, Hansraj College, University of Delhi, Delhi-110007, India
| | - Pushp Lata
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Hardeep Kaur
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Abhilash Kumar
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi-110007, India
| | - Sukanya Lal
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
| | - Courtney Aldrich
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andreas Bechthold
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Rup Lal
- PhiXGen Private Limited, Gurugram, Haryana-122001, India
- Acharya Narendra Dev College, University of Delhi, Delhi-110019, India
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Fernández-López M, Sánchez-Reyes A, Barcelos C, Sidón-Ceseña K, Leite RB, Lago-Lestón A. Deep-Sea Sediments from the Southern Gulf of Mexico Harbor a Wide Diversity of PKS I Genes. Antibiotics (Basel) 2022; 11:antibiotics11070887. [PMID: 35884142 PMCID: PMC9311598 DOI: 10.3390/antibiotics11070887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022] Open
Abstract
The excessive use of antibiotics has triggered the appearance of new resistant strains, which is why great interest has been taken in the search for new bioactive compounds capable of overcoming this emergency in recent years. Massive sequencing tools have enabled the detection of new microorganisms that cannot be cultured in a laboratory, thus opening the door to the search for new biosynthetic genes. The great variety in oceanic environments in terms of pressure, salinity, temperature, and nutrients enables marine microorganisms to develop unique biochemical and physiological properties for their survival, enhancing the production of secondary metabolites that can vary from those produced by terrestrial microorganisms. We performed a search for type I PKS genes in metagenomes obtained from the marine sediments of the deep waters of the Gulf of Mexico using Hidden Markov Models. More than 2000 candidate genes were detected in the metagenomes that code for type I PKS domains, while biosynthetic pathways that may code for other secondary metabolites were also detected. Our research demonstrates the great potential use of the marine sediments of the Gulf of Mexico for identifying genes that code for new secondary metabolites.
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Affiliation(s)
- Maikel Fernández-López
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca 62209, Mexico;
| | - Ayixon Sánchez-Reyes
- CONACYT-Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Mexico;
| | - Clara Barcelos
- Posgrado de Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico; (C.B.); (K.S.-C.)
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
| | - Karla Sidón-Ceseña
- Posgrado de Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico; (C.B.); (K.S.-C.)
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
| | - Ricardo B. Leite
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal;
| | - Asunción Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
- Correspondence:
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Xu G, Zhang L, Liu X, Guan F, Xu Y, Yue H, Huang JQ, Chen J, Wu N, Tian J. Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome. BMC Genomics 2022; 23:37. [PMID: 34996356 PMCID: PMC8742384 DOI: 10.1186/s12864-021-08260-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/13/2021] [Indexed: 12/22/2022] Open
Abstract
Background Advances in DNA sequencing technologies have transformed our capacity to perform life science research, decipher the dynamics of complex soil microbial communities and exploit them for plant disease management. However, soil is a complex conglomerate, which makes functional metagenomics studies very challenging. Results Metagenomes were assembled by long-read (PacBio, PB), short-read (Illumina, IL), and mixture of PB and IL (PI) sequencing of soil DNA samples were compared. Ortholog analyses and functional annotation revealed that the PI approach significantly increased the contig length of the metagenomic sequences compared to IL and enlarged the gene pool compared to PB. The PI approach also offered comparable or higher species abundance than either PB or IL alone, and showed significant advantages for studying natural product biosynthetic genes in the soil microbiomes. Conclusion Our results provide an effective strategy for combining long and short-read DNA sequencing data to explore and distill the maximum information out of soil metagenomics. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08260-3.
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Affiliation(s)
- Guoshun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China.
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Haitao Yue
- Department of Biology and Biotechnology, Xinjiang University, 666 Shengli Road, Urumqi, 830046, People's Republic of China
| | - Jin-Qun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Jieyin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China.
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A Combinatorial Approach of High-Throughput Genomics and Mass Proteomics for Understanding the Regulation and Expression of Secondary Metabolite Production in Actinobacteria. mSystems 2021; 6:e0086221. [PMID: 34427500 PMCID: PMC8407205 DOI: 10.1128/msystems.00862-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Secondary metabolites produced by Actinobacteria are an important source of antibiotics, drugs, and antimicrobial peptides. However, the large genome size of actinobacteria with high gene coding density makes it difficult to understand the complex regulation of biosynthesis of such critically and economically important products. In the last few decades, apart from genomics sequences, high-throughput proteomics has proven beneficial to understand the key players regulating the expression pattern of secondary metabolite and antibiotic production in different experimental set-ups. In the past, we have been analyzing the genomics data and mass spectrometry-based proteomics to predict the regulation dynamics and crucial regulatory hubs in Actinobacteria. The multidirectional regulation and expression of the biosynthetic gene cluster responsible for the production of important metabolite take their cue from the other primary metabolism pathways with which they show intricate interactions in the interactome. The regulation occurs by not only the action and expression of the biosynthetic gene cluster but also the role of transcription factors and primary metabolic pathways. Using the key players of these interactomes, we can regulate the synthesis/production of these valuable peptides/metabolites. Simultaneously, the multi-omics approach has now opened new gateways in investigation, screening, and identification of naturally occurring antimicrobial peptides from actinobacteria which are beneficial for humans and also provide economic and industrial benefits to humankind.
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Singhvi N, Singh P, Prakash O, Gupta V, Lal S, Bechthold A, Singh Y, Singh RK, Lal R. Differential mass spectrometry-based proteome analyses unveil major regulatory hubs in rifamycin B production in Amycolatopsis mediterranei. J Proteomics 2021; 239:104168. [PMID: 33662614 DOI: 10.1016/j.jprot.2021.104168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 01/18/2023]
Abstract
Rifamycin B is produced by Amycolatopsis mediterranei S699 as a secondary metabolite. Its semi-synthetic derivatives have been used for curing tuberculosis caused by Mycobacterium tuberculosis. But the emergence of rifampicin-resistant strains required analogs of rifamycin B to be developed by rifamycin biosynthetic gene cluster manipulation. In 2014 genetic engineering of the rifamycin polyketide synthase gene cluster in S699 led to a mutant, A. mediterranei DCO#34, that produced 24-desmethylrifamycin B. Unfortunately, the productivity was strongly reduced to 20 mgL-1 as compared to 50 mgL-1 of rifamycin B. To understand the mechanisms leading to reduced productivity and rifamycin biosynthesis by A. mediterranei S699 during the early and late growth phase we performed a proteome study for wild type strain S699, mutant DCO#34, and the non-producer strain SCO2-2. Proteins identification and relative label-free quantification were performed by nLC-MS/MS. Data are available via ProteomeXchange with identifier PXD016416. Also, in-silico protein-protein interaction approach was used to determine the relationship between different structural and regulatory proteins involved in rifamycin biosynthesis. Our studies revealed RifA, RifK, RifL, Rif-Orf19 as the major regulatory hubs. Relative abundance expression values revealed that genes encoding RifC-RifI and the transporter RifP, down-regulated in DCO#34 and genes encoding RifR, RifZ, other regulatory proteins up-regulated. SIGNIFICANCE: The study is designed mainly to understand the underlying mechanisms of rifamycin biosynthesis in Amycolatopsis mediterranei. This resulted in the identification of regulatory hubs which play a crucial role in regulating secondary metabolism. It elucidates the complex mechanism of secondary metabolite biosynthesis and their conversion and extracellular transportation in temporal correlation with the different growth phases. The study also elucidated the mechanisms leading to reduced production of analog, 24-desmethylrifamycin B by the genetically modified strain DCO#34, derivatives of which have been found effective against rifampicin-resistant strains of Mycobacterium tuberculosis. These results can be useful while carrying out genetic manipulations to improve the strains of Amycolatopsis to produce better analogs/drugs and promote the eradication of TB. Thus, this study is contributing significantly to the growing knowledge in the field of the crucial drug, rifamycin B biosynthesis by an economically important bacterium Amycolatopsis mediterranei.
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Affiliation(s)
- Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Priya Singh
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Om Prakash
- National Centre for Microbial Resource-National Centre for Cell Sciences, Pune, Maharashtra 411007, India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Sukanya Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
| | - Andreas Bechthold
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, 79104 Freiburg, Germany
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Rakesh Kumar Singh
- Translational Science Laboratory, Florida State University, FL 32306, USA
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi 110007, India.
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Singhvi N, Gupta V, Singh P, Prakash O, Bechthold A, Singh Y, Lal R. Prediction of Transcription Factors and Their Involvement in Regulating Rifamycin Production in Amycolatopsis mediterranei S699. Indian J Microbiol 2020; 60:310-317. [PMID: 32655198 DOI: 10.1007/s12088-020-00868-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/03/2020] [Indexed: 12/16/2022] Open
Abstract
Amycolatopsis mediterranei S699 produces rifamycin B and successors of this strain are in use for the industrial production of rifamycin B. Semisynthetic derivatives of rifamycin B are used against Mycobacterium tuberculosis that causes tuberculosis. Although the rifamycin biosynthetic gene cluster was characterized two decades ago, the regulation of rifamycin B biosynthesis in Amycolatopsis mediterranei S699 is poorly understood. In this study, we analysed the genome and proteome of Amycolatopsis mediterranei S699 and identified 1102 transcription factors which comprise about 10% of the total genome. Using interactomics approaches we delineated 30 unique transcription factors directly involved in secondary metabolism that regulate rifamycin B biosynthesis. We also predict the role of RifN as hub in controlling the regulation of other genes involved in rifamycin biosynthesis. RifN is important for maintaining the integrity of the rifamycin-network. Thus, these transcription factor can be exploited to improve rifamycin B production in Amycolatopsis mediterranei S699.
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Affiliation(s)
- Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Priya Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: Acharya Narendra Dev College, University of Delhi, New Delhi, 110019 India
| | - Om Prakash
- National Centre for Cell Sciences, Pune, Maharashtra 411007 India
| | - Andreas Bechthold
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, 79104 Freiburg, Germany
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, New Delhi, 110033 India
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7
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Biosynthesis of Polyketides in Streptomyces. Microorganisms 2019; 7:microorganisms7050124. [PMID: 31064143 PMCID: PMC6560455 DOI: 10.3390/microorganisms7050124] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/24/2019] [Accepted: 04/27/2019] [Indexed: 12/12/2022] Open
Abstract
Polyketides are a large group of secondary metabolites that have notable variety in their structure and function. Polyketides exhibit a wide range of bioactivities such as antibacterial, antifungal, anticancer, antiviral, immune-suppressing, anti-cholesterol, and anti-inflammatory activity. Naturally, they are found in bacteria, fungi, plants, protists, insects, mollusks, and sponges. Streptomyces is a genus of Gram-positive bacteria that has a filamentous form like fungi. This genus is best known as one of the polyketides producers. Some examples of polyketides produced by Streptomyces are rapamycin, oleandomycin, actinorhodin, daunorubicin, and caprazamycin. Biosynthesis of polyketides involves a group of enzyme activities called polyketide synthases (PKSs). There are three types of PKSs (type I, type II, and type III) in Streptomyces responsible for producing polyketides. This paper focuses on the biosynthesis of polyketides in Streptomyces with three structurally-different types of PKSs.
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Elshobary ME, Becker MG, Kalichuk JL, Chan AC, Belmonte MF, Piercey-Normore MD. Tissue-specific localization of polyketide synthase and other associated genes in the lichen, Cladonia rangiferina, using laser microdissection. PHYTOCHEMISTRY 2018; 156:142-150. [PMID: 30296707 DOI: 10.1016/j.phytochem.2018.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 08/25/2018] [Accepted: 09/28/2018] [Indexed: 02/05/2023]
Abstract
The biosynthesis of two polyketides, atranorin and fumarprotocetraric acid, produced from a lichen-forming fungus, Cladonia rangiferina (L.) F. H. Wigg. was correlated with the expression of eight fungal genes (CrPKS1, CrPKS3, CrPKS16, Catalase (CAT), Sugar Transporter (MFsug), Dioxygenase (YQE1), C2H2 Transcription factor (C2H2), Transcription Factor PacC (PacC), which are thought to be involved in polyketide biosynthesis, and one algal gene, NAD-dependent deacetylase sirtuin 2 (AsNAD)), using laser microdissection (LMD). The differential gene expression levels within the thallus tissue layers demonstrate that the most active region for potential polyketide biosynthesis within the lichen is the outer apical region proximal to the photobiont but some expression also occurs in reproductive tissue. This is the first study using laser microdissection to explore gene expression of these nine genes and their location of expression; it provides a proof-of-concept for future experiments exploring tissue-specific gene expression within lichens; and it highlights the utility of LMD for use in lichen systems.
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Affiliation(s)
| | - Michael G Becker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Jenna L Kalichuk
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Ainsley C Chan
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - Michele D Piercey-Normore
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada; School of Science and the Environment, Memorial University of Newfoundland (Grenfell Campus), Corner Brook, NL, A2H 5G4, Canada.
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9
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Cuadrat RRC, Ionescu D, Dávila AMR, Grossart HP. Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics. Front Microbiol 2018. [PMID: 29515540 PMCID: PMC5826242 DOI: 10.3389/fmicb.2018.00251] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.
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Affiliation(s)
- Rafael R C Cuadrat
- Bioinformatics Core Facility, Max Plank Institute for Biology of Ageing, Köln, Germany.,Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Danny Ionescu
- Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Hans-Peter Grossart
- Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
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Cuadrat RRC, Cury JC, Dávila AMR. Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS. Int J Mol Sci 2015; 16:28285-95. [PMID: 26633360 PMCID: PMC4691048 DOI: 10.3390/ijms161226101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 11/23/2022] Open
Abstract
Marine environments harbor a wide range of microorganisms from the three domains of life. These microorganisms have great potential to enable discovery of new enzymes and bioactive compounds for industrial use. However, only ~1% of microorganisms from the environment can currently be identified through cultured isolates, limiting the discovery of new compounds. To overcome this limitation, a metagenomics approach has been widely adopted for biodiversity studies on samples from marine environments. In this study, we screened metagenomes in order to estimate the potential for new natural compound synthesis mediated by diversity in the Polyketide Synthase (PKS) and Nonribosomal Peptide Synthetase (NRPS) genes. The samples were collected from the Praia dos Anjos (Angel’s Beach) surface water—Arraial do Cabo (Rio de Janeiro state, Brazil), an environment affected by upwelling. In order to evaluate the potential for screening natural products in Arraial do Cabo samples, we used KS (keto-synthase) and C (condensation) domains (from PKS and NRPS, respectively) to build Hidden Markov Models (HMM) models. From both samples, a total of 84 KS and 46 C novel domain sequences were obtained, showing the potential of this environment for the discovery of new genes of biotechnological interest. These domains were classified by phylogenetic analysis and this was the first study conducted to screen PKS and NRPS genes in an upwelling affected sample
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Affiliation(s)
- Rafael R C Cuadrat
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Rio de Janeiro CEP 21040-360, Brazil.
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, OT Neuglobsow, Stechlin 16775, Germany.
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, Berlin 14195, Germany.
| | - Juliano C Cury
- Molecular Microbiology Laboratory, Federal University of São João del-Rei, Sete Lagoas Campus Rua Sétimo Moreira Martins 188, Itapoã II, Sete Lagoas CEP 35702-031, Brazil.
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Rio de Janeiro CEP 21040-360, Brazil.
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Nigam A, Almabruk KH, Saxena A, Yang J, Mukherjee U, Kaur H, Kohli P, Kumari R, Singh P, Zakharov LN, Singh Y, Mahmud T, Lal R. Modification of rifamycin polyketide backbone leads to improved drug activity against rifampicin-resistant Mycobacterium tuberculosis. J Biol Chem 2015; 289:21142-52. [PMID: 24923585 DOI: 10.1074/jbc.m114.572636] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rifamycin B, a product of Amycolatopsis mediterranei S699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and AIDS-related mycobacterial infections. However, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of Mycobacterium tuberculosis. As part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of module 2 of rapamycin polyketide synthase. The resulting mutants (rifAT6::rapAT2) of A. mediterranei S699 produced new rifamycin analogs, 24-desmethylrifamycin B and 24-desmethylrifamycin SV, which contained modification in the polyketide backbone. 24-Desmethylrifamycin B was then converted to 24-desmethylrifamycin S, whose structure was confirmed by MS, NMR, and X-ray crystallography. Subsequently, 24-desmethylrifamycin S was converted to 24-desmethylrifampicin, which showed excellent antibacterial activity against several rifampicin-resistant M. tuberculosis strains.
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Saxena A, Mukherjee U, Kumari R, Singh P, Lal R. Synthetic Biology in Action: Developing a Drug Against MDR-TB. Indian J Microbiol 2014; 54:369-75. [PMID: 25320433 PMCID: PMC4186943 DOI: 10.1007/s12088-014-0498-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 09/11/2014] [Indexed: 12/29/2022] Open
Abstract
The amalgamation of the research efforts of biologists, chemists and geneticists led by scientists at the Department of Zoology, University of Delhi has resulted in the development of a novel rifamycin derivative; 24-desmethylrifampicin, which is highly effective against multi-drug resistant (MDR) strains of Mycobacterium tuberculosis. The production of rifamycin analogue was facilitated by genetic-synthetic strategies that have opened an interdisciplinary route for the development of more such rifamycin analogues aiming at a better therapeutic potential. The results of this painstaking effort of nearly 25 years of a team of students and scientists led by Professor Rup Lal have been recently published in the Journal of Biological Chemistry (www.jbc.org/content/289/30/21142.long). This strategy can now find applications for developing newer rifamycin analogues that can be harnessed to overcome the problem of MDR, extensively drug resistant (XDR) and totally drug resistant (TDR) M. tuberculosis.
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Affiliation(s)
- Anjali Saxena
- Department of Zoology, University of Delhi, Delhi, Delhi 110007 India
| | - Udita Mukherjee
- Department of Zoology, University of Delhi, Delhi, Delhi 110007 India
| | - Rashmi Kumari
- Department of Zoology, University of Delhi, Delhi, Delhi 110007 India
| | - Priya Singh
- Department of Zoology, University of Delhi, Delhi, Delhi 110007 India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, Delhi 110007 India
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Draft Genome Sequence of Amycolatopsis mediterranei DSM 40773, a Tangible Antibiotic Producer. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00752-14. [PMID: 25081263 PMCID: PMC4118066 DOI: 10.1128/genomea.00752-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Amycolatopsis mediterranei DSM 40773 has been of special interest as successors of this strain are in use for the commercial production of rifamycin B. Here we present the draft genome sequence (~10 Mb) of this strain, which contains 108 contigs, 9,198 genes, and has a G+C content of 71.3%.
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Draft Genome Sequence of the Rifamycin Producer Amycolatopsis rifamycinica DSM 46095. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00662-14. [PMID: 24994803 PMCID: PMC4082003 DOI: 10.1128/genomea.00662-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Amycolatopsis rifamycinica DSM 46095 is an actinobacterium that produces rifamycin SV, an antibiotic used against Mycobacterium tuberculosis. Here, we present the draft genome of DSM 46095, which harbors a novel rifamycin polyketide biosynthetic gene cluster (rif PKS) that differed by 10% in nucleotide sequence from the already reported rif PKS cluster of Amycolatopsis mediterranei S699.
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15
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Whole genome sequence of the rifamycin B-producing strain Amycolatopsis mediterranei S699. J Bacteriol 2011; 193:5562-3. [PMID: 21914879 DOI: 10.1128/jb.05819-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Amycolatopsis mediterranei S699 is an actinomycete that produces an important antibiotic, rifamycin B. Semisynthetic derivatives of rifamycin B are used for the treatment of tuberculosis, leprosy, and AIDS-related mycobacterial infections. Here, we report the complete genome sequence (10.2 Mb) of A. mediterranei S699, with 9,575 predicted coding sequences.
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Mupirocin: biosynthesis, special features and applications of an antibiotic from a gram-negative bacterium. Appl Microbiol Biotechnol 2011; 90:11-21. [PMID: 21336932 DOI: 10.1007/s00253-011-3128-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 01/12/2011] [Accepted: 01/12/2011] [Indexed: 10/18/2022]
Abstract
Mupirocin is a polyketide antibiotic produced by Pseudomonas fluorescens. The biosynthetic cluster encodes 6 type I polyketide synthase multifunctional proteins and 29 single function proteins. The biosynthetic pathway belongs to the trans-AT group in which acyltransferase activity is provided by a separate polypeptide rather than in-cis as found in the original type I polyketide synthases. Special features of this group are in-cis methyltransferase domains and a trans-acting HMG-CoA synthase-cassette which insert α- and β- methyl groups respectively while enoyl reductase domains are absent from the condensing modules. In addition, for the mupirocin system, there is no obvious loading mechanism for initiation of the polyketide chain and many aspects of the pathway remain to be elucidated. Mupirocin inhibits isoleucyl-tRNA synthetase and has been used since 1985 to help prevent infection by methicillin-resistant Staphylococcus aureus, particularly within hospitals. Resistance to mupirocin was first detected in 1987 and high-level resistance in S. aureus is due to a plasmid-encoded second isoleucyl-tRNA synthetase, a more eukaryotic-like enzyme. Recent analysis of the biosynthetic pathway for thiomarinols from marine bacteria opens up possibilities to modify mupirocin so as to overcome this resistance.
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Wang X, Sa N, Tian PF, Tan TW. Classifying DNA assembly protocols for devising cellular architectures. Biotechnol Adv 2010; 29:156-63. [PMID: 21034806 DOI: 10.1016/j.biotechadv.2010.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Revised: 10/09/2010] [Accepted: 10/17/2010] [Indexed: 11/26/2022]
Abstract
DNA assembly is one of the most fundamental techniques in synthetic biology. Efficient methods can turn traditional DNA cloning into time-saving and higher efficiency practice, which is a foundation to accomplish the dreams of synthetic biologists for devising cellular architectures, reprogramming cellular behaviors, or creating synthetic cells. In this review, typical strategies of DNA assembly are discussed with special emphasis on the assembly of long and multiple DNA fragments into intact plasmids or assembled compositions. Constructively, all reported strategies were categorized into in vivo and in vitro types, and protocols are presented in a functional and practice-oriented way in order to portray the general nature of DNA assembly applications. Significantly, a five-step blueprint is proposed for devising cell architectures that produce valuable chemicals.
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Affiliation(s)
- Xi Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Beijing 100029, PR China
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Ruiz B, Chávez A, Forero A, García-Huante Y, Romero A, Sánchez M, Rocha D, Sánchez B, Rodríguez-Sanoja R, Sánchez S, Langley E. Production of microbial secondary metabolites: regulation by the carbon source. Crit Rev Microbiol 2010; 36:146-67. [PMID: 20210692 DOI: 10.3109/10408410903489576] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Microbial secondary metabolites are low molecular mass products, not essential for growth of the producing cultures, but very important for human health. They include antibiotics, antitumor agents, cholesterol-lowering drugs, and others. They have unusual structures and are usually formed during the late growth phase of the producing microorganisms. Its synthesis can be influenced greatly by manipulating the type and concentration of the nutrients formulating the culture media. Among these nutrients, the effect of the carbon sources has been the subject of continuous studies for both, industry and research groups. Different mechanisms have been described in bacteria and fungi to explain the negative carbon catabolite effects on secondary metabolite production. Their knowledge and manipulation have been useful either for setting fermentation conditions or for strain improvement. During the last years, important advances have been reported on these mechanisms at the biochemical and molecular levels. The aim of the present review is to describe these advances, giving special emphasis to those reported for the genus Streptomyces.
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Affiliation(s)
- Beatriz Ruiz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, México
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20
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Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 2009; 75:2046-56. [PMID: 19201974 DOI: 10.1128/aem.02294-08] [Citation(s) in RCA: 462] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.
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Hill AM. The biosynthesis, molecular genetics and enzymology of the polyketide-derived metabolites. Nat Prod Rep 2005; 23:256-320. [PMID: 16572230 DOI: 10.1039/b301028g] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This review covers the biosynthesis of aliphatic and aromatic polyketides as well as mixed polyketide/NRPS metabolites, and discusses the molecular genetics and enzymology of the proteins responsible for their formation.
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Abstract
We identified a polyketide synthase (PKS) gene, pksN, from a strain of Nectria haematococca by complementing a mutant unable to synthesize a red perithecial pigment. pksN encodes a 2,106-amino-acid polypeptide with conserved motifs characteristic of type I PKS enzymatic domains: beta-ketoacyl synthase, acyltransferase, duplicated acyl carrier proteins, and thioesterase. The pksN product groups with the Aspergillus nidulans WA-type PKSs involved in conidial pigmentation and melanin, bikaverin, and aflatoxin biosynthetic pathways. Inactivation of pksN did not cause any visible change in fungal growth, asexual sporulation, or ascospore formation, suggesting that it is involved in a specific developmental function. We propose that pksN encodes a novel PKS required for the perithecial red pigment biosynthesis.
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Affiliation(s)
- Stephane Graziani
- Institut de Génétique et Microbiologie, Université Paris-Sud, 91405 Orsay Cedex, France
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Dhingra G, Kumari R, Bala S, Majumdar S, Malhotra S, Sharma P, Lal S, Cullum J, Lal R. Development of cloning vectors and transformation methods for Amycolatopsis. J Ind Microbiol Biotechnol 2003; 30:195-204. [PMID: 12687493 DOI: 10.1007/s10295-003-0040-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2002] [Accepted: 01/08/2003] [Indexed: 10/23/2022]
Abstract
The genus Amycolatopsis is of industrial importance, as its species are known to produce commercial antibiotics. It belongs to the family Pseudonocardiaceae and has an eventful taxonomic history. Initially strains were identified as Streptomyces, then later as Nocardia. However, based on biochemical, morphological and molecular features, the genus Amycolatopsis, containing seventeen species, was created. The development of molecular genetic techniques for this group has been slow. The scarcity of molecular genetic tools including stable plasmids, antibiotic resistance markers, transposons, reporter genes, cloning vectors, and high efficiency transformation protocols has made progress slow, but efforts in the past decade have led to the development of cloning vectors and transformation methods for these organisms. Some of the cloning vectors have broad host range (pRL series) whereas others have limited host range (pMEA300 and pMEA100). The cloning vector pMEA300 has been completely sequenced, while only the minimal replicon (pA- rep) has been sequenced from pRL plasmids. Direct transformation of mycelia and electroporation are the most widely applicable methods for transforming species of Amycolatopsis. Conjugational transfer from Escherichia coli has been reported only in the species A. japonicum, and gene disruption and replacements using homologous recombination are now possible in some strains.
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Affiliation(s)
- Gauri Dhingra
- Molecular Biology Laboratory, University of Delhi, Department of Zoology, Delhi 110007, India
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Kaur H, Cortes J, Leadlay P, Lal R. Cloning and partial characterization of the putative rifamycin biosynthetic gene cluster from the actinomycete Amycolatopsis mediterranei DSM 46095. Microbiol Res 2002; 156:239-46. [PMID: 11716212 DOI: 10.1078/0944-5013-00108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The actinomycete Amycolatopsis mediterranei produces the commercially and medically important polyketide antibiotic rifamycin, which is widely used against mycobacterial infections. The rifamycin biosynthetic (rif) gene cluster has been isolated, cloned and characterized from A. mediterranei S699 and A. mediterranei LBGA 3136. However, there are several other strains of A. mediterranei which also produce rifamycins. In order to detect the variability in the rif gene cluster among these strains, several strains were screened by PCR amplification using oligonucleotide primers based on the published DNA sequence of the rif gene cluster and by using dEBS II (second component of deoxy-erythronolide biosynthase gene) as a gene probe. Out of eight strains of A. mediterranei selected for the study, seven of them showed the expected amplification of the DNA fragments whereas the amplified DNA pattern was different in strain A. mediterranei DSM 46095. This strain also showed striking differences in the banding pattern obtained after hybridization of its genomic DNA against the dEBS II probe. Initial cloning and characterization of the 4-kb DNA fragment from the strain DSM 46095, representing a part of the putative rifamycin biosynthetic cluster, revealed nearly 10% and 8% differences in the DNA and amino acid sequence, respectively, as compared to that of A. mediterranei S699 and A. mediterranei LBGA 3136. The entire rif gene cluster was later cloned on two cosmids from A. mediterranei DSM 46095. Based on the partial sequence analysis of the cluster and sequence comparison with the published sequence, it was deduced that among eight strains of A. mediterranei, only A. mediterranei DSM 46095 carries a novel rifamycin biosynthetic gene cluster.
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