101
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Choi SS, Katsuyama Y, Bai L, Deng Z, Ohnishi Y, Kim ES. Genome engineering for microbial natural product discovery. Curr Opin Microbiol 2018; 45:53-60. [PMID: 29510374 DOI: 10.1016/j.mib.2018.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 11/16/2022]
Abstract
The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach. Here, we describe recent developments in the MNP research paradigm, including microbial genome mining, NP BGC activation, and NP overproducing cell factory design.
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Affiliation(s)
- Si-Sun Choi
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, China
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea.
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102
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Kallifidas D, Jiang G, Ding Y, Luesch H. Rational engineering of Streptomyces albus J1074 for the overexpression of secondary metabolite gene clusters. Microb Cell Fact 2018; 17:25. [PMID: 29454348 PMCID: PMC5816538 DOI: 10.1186/s12934-018-0874-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 02/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome sequencing revealed that Streptomyces sp. can dedicate up to ~ 10% of their genomes for the biosynthesis of bioactive secondary metabolites. However, the majority of these biosynthetic gene clusters are only weakly expressed or not at all. Indeed, the biosynthesis of natural products is highly regulated through integrating multiple nutritional and environmental signals perceived by pleiotropic and pathway-specific transcriptional regulators. Although pathway-specific refactoring has been a proved, productive approach for the activation of individual gene clusters, the construction of a global super host strain by targeting pleiotropic-specific genes for the expression of multiple diverse gene clusters is an attractive approach. RESULTS Streptomyces albus J1074 is a gifted heterologous host. To further improve its secondary metabolite expression capability, we rationally engineered the host by targeting genes affecting NADPH availability, precursor flux, cell growth and biosynthetic gene transcriptional activation. These studies led to the activation of the native paulomycin pathway in engineered S. albus strains and importantly the upregulated expression of the heterologous actinorhodin gene cluster. CONCLUSIONS Rational engineering of Streptomyces albus J1074 yielded a series of mutants with improved capabilities for native and heterologous expression of secondary metabolite gene clusters.
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Affiliation(s)
- Dimitris Kallifidas
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610 USA
- Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610 USA
| | - Guangde Jiang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610 USA
- Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610 USA
| | - Yousong Ding
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610 USA
- Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610 USA
| | - Hendrik Luesch
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610 USA
- Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610 USA
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103
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Choudoir MJ, Pepe-Ranney C, Buckley DH. Diversification of Secondary Metabolite Biosynthetic Gene Clusters Coincides with Lineage Divergence in Streptomyces. Antibiotics (Basel) 2018; 7:E12. [PMID: 29438308 PMCID: PMC5872123 DOI: 10.3390/antibiotics7010012] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 11/16/2022] Open
Abstract
We have identified Streptomyces sister-taxa which share a recent common ancestor and nearly identical small subunit (SSU) rRNA gene sequences, but inhabit distinct geographic ranges demarcated by latitude and have sufficient genomic divergence to represent distinct species. Here, we explore the evolutionary dynamics of secondary metabolite biosynthetic gene clusters (SMGCs) following lineage divergence of these sister-taxa. These sister-taxa strains contained 310 distinct SMGCs belonging to 22 different gene cluster classes. While there was broad conservation of these 22 gene cluster classes among the genomes analyzed, each individual genome harbored a different number of gene clusters within each class. A total of nine SMGCs were conserved across nearly all strains, but the majority (57%) of SMGCs were strain-specific. We show that while each individual genome has a unique combination of SMGCs, this diversity displays lineage-level modularity. Overall, the northern-derived (NDR) clade had more SMGCs than the southern-derived (SDR) clade (40.7 ± 3.9 and 33.8 ± 3.9, mean and S.D., respectively). This difference in SMGC content corresponded with differences in the number of predicted open reading frames (ORFs) per genome (7775 ± 196 and 7093 ± 205, mean and S.D., respectively) such that the ratio of SMGC:ORF did not differ between sister-taxa genomes. We show that changes in SMGC diversity between the sister-taxa were driven primarily by gene acquisition and deletion events, and these changes were associated with an overall change in genome size which accompanied lineage divergence.
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Affiliation(s)
- Mallory J Choudoir
- School of Integrative Plant Science, Bradfield Hall 705, Cornell University, Ithaca, NY 14853, USA.
| | - Charles Pepe-Ranney
- School of Integrative Plant Science, Bradfield Hall 705, Cornell University, Ithaca, NY 14853, USA.
| | - Daniel H Buckley
- School of Integrative Plant Science, Bradfield Hall 705, Cornell University, Ithaca, NY 14853, USA.
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104
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Malmierca MG, González-Montes L, Pérez-Victoria I, Sialer C, Braña AF, García Salcedo R, Martín J, Reyes F, Méndez C, Olano C, Salas JA. Searching for Glycosylated Natural Products in Actinomycetes and Identification of Novel Macrolactams and Angucyclines. Front Microbiol 2018; 9:39. [PMID: 29441046 PMCID: PMC5797532 DOI: 10.3389/fmicb.2018.00039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/09/2018] [Indexed: 11/13/2022] Open
Abstract
Many bioactive natural products are glycosylated compounds in which the sugar components usually participate in interaction and molecular recognition of the cellular target. Therefore, the presence of sugar moieties is important, in some cases essential, for bioactivity. Searching for novel glycosylated bioactive compounds is an important aim in the field of the research for natural products from actinomycetes. A great majority of these sugar moieties belong to the 6-deoxyhexoses and share two common biosynthetic steps catalyzed by a NDP-D-glucose synthase (GS) and a NDP-D-glucose 4,6-dehydratase (DH). Based on this fact, seventy one Streptomyces strains isolated from the integument of ants of the Tribe Attini were screened for the presence of biosynthetic gene clusters (BGCs) for glycosylated compounds. Total DNAs were analyzed by PCR amplification using oligo primers for GSs and DHs and also for a NDP-D-glucose-2,3-dehydratases. Amplicons were used in gene disruption experiments to generate non-producing mutants in the corresponding clusters. Eleven mutants were obtained and comparative dereplication analyses between the wild type strains and the corresponding mutants allowed in some cases the identification of the compound coded by the corresponding cluster (lobophorins, vicenistatin, chromomycins and benzanthrins) and that of two novel macrolactams (sipanmycin A and B). Several strains did not show UPLC differential peaks between the wild type strain and mutant profiles. However, after genome sequencing of these strains, the activation of the expression of two clusters was achieved by using nutritional and genetic approaches leading to the identification of compounds of the cervimycins family and two novel members of the warkmycins family. Our work defines a useful strategy for the identification new glycosylated compounds by a combination of genome mining, gene inactivation experiments and the activation of silent biosynthetic clusters in Streptomyces strains.
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Affiliation(s)
- Mónica G Malmierca
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Lorena González-Montes
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | | | - Carlos Sialer
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Raúl García Salcedo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Jesús Martín
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Fernando Reyes
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Granada, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
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105
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Li L, Jiang W, Lu Y. New strategies and approaches for engineering biosynthetic gene clusters of microbial natural products. Biotechnol Adv 2017; 35:936-949. [DOI: 10.1016/j.biotechadv.2017.03.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/12/2017] [Accepted: 03/15/2017] [Indexed: 12/11/2022]
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106
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Quezada M, Licona-Cassani C, Cruz-Morales P, Salim AA, Marcellin E, Capon RJ, Barona-Gómez F. Diverse Cone-Snail Species Harbor Closely Related Streptomyces Species with Conserved Chemical and Genetic Profiles, Including Polycyclic Tetramic Acid Macrolactams. Front Microbiol 2017; 8:2305. [PMID: 29225593 PMCID: PMC5705629 DOI: 10.3389/fmicb.2017.02305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 11/08/2017] [Indexed: 12/30/2022] Open
Abstract
Streptomyces are Gram-positive bacteria that occupy diverse ecological niches including host-associations with animals and plants. Members of this genus are known for their overwhelming repertoire of natural products, which has been exploited for almost a century as a source of medicines and agrochemicals. Notwithstanding intense scientific and commercial interest in Streptomyces natural products, surprisingly little is known of the intra- and/or inter-species ecological roles played by these metabolites. In this report we describe the chemical structures, biological properties, and biosynthetic relationships between natural products produced by Streptomyces isolated from internal tissues of predatory Conus snails, collected from the Great Barrier Reef, Australia. Using chromatographic, spectroscopic and bioassays methodology, we demonstrate that Streptomyces isolated from five different Conus species produce identical chemical and antifungal profiles - comprising a suite of polycyclic tetramic acid macrolactams (PTMs). To investigate possible ecological (and evolutionary) relationships we used genome analyses to reveal a close taxonomic relationship with other sponge-derived and free-living PTM producing Streptomyces (i.e., Streptomyces albus). In-depth phylogenomic analysis of PTM biosynthetic gene clusters indicated PTM structure diversity was governed by a small repertoire of genetic elements, including discrete gene acquisition events involving dehydrogenases. Overall, our study shows a Streptomyces-Conus ecological relationship that is concomitant with specific PTM chemical profiles. We provide an evolutionary framework to explain this relationship, driven by anti-fungal properties that protect Conus snails from fungal pathogens.
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Affiliation(s)
- Michelle Quezada
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Cuauhtemoc Licona-Cassani
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico
| | - Angela A. Salim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Robert J. Capon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico
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107
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Robertsen HL, Weber T, Kim HU, Lee SY. Toward Systems Metabolic Engineering of Streptomycetes for Secondary Metabolites Production. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700465] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/20/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Helene Lunde Robertsen
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kongens Lyngby Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kongens Lyngby Denmark
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Korea Advanced Institute of Science and Technology (KAIST); Yuseong-gu Daejeon 306-701 Republic of Korea
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 Kongens Lyngby Denmark
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Korea Advanced Institute of Science and Technology (KAIST); Yuseong-gu Daejeon 306-701 Republic of Korea
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108
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Li G, Lou HX. Strategies to diversify natural products for drug discovery. Med Res Rev 2017; 38:1255-1294. [PMID: 29064108 DOI: 10.1002/med.21474] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/18/2017] [Accepted: 09/28/2017] [Indexed: 12/11/2022]
Abstract
Natural product libraries contain specialized metabolites derived from plants, animals, and microorganisms that play a pivotal role in drug discovery due to their immense structural diversity and wide variety of biological activities. The strategies to greatly extend natural product scaffolds through available biological and chemical approaches offer unique opportunities to access a new series of natural product analogues, enabling the construction of diverse natural product-like libraries. The affordability of these structurally diverse molecules has been a crucial step in accelerating drug discovery. This review provides an overview of various approaches to exploit the diversity of compounds for natural product-based drug development, drawing upon a series of examples to illustrate each strategy.
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Affiliation(s)
- Gang Li
- Department of Natural Medicine and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao, China
| | - Hong-Xiang Lou
- Department of Natural Medicine and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao, China.,Department of Natural Products Chemistry, Key Lab of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
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109
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Hoz JFDL, Méndez C, Salas JA, Olano C. Novel Bioactive Paulomycin Derivatives Produced by Streptomyces albus J1074. Molecules 2017; 22:molecules22101758. [PMID: 29057800 PMCID: PMC6151807 DOI: 10.3390/molecules22101758] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/11/2017] [Accepted: 10/17/2017] [Indexed: 12/16/2022] Open
Abstract
Four novel paulomycin derivatives have been isolated from S. albus J1074 grown in MFE culture medium. These compounds are structural analogs of antibiotics 273a2α and 273a2β containing a thiazole moiety, probably originated through an intramolecular Michael addition. The novel, thiazole, moiety-containing paulomycins show a lower antibiotic activity than paulomycins A and B against Gram-positive bacteria. However, two of them show an improved activity against Gram-negative bacteria. In addition, the four novel compounds are more stable in culture than paulomycins A and B. Thus, the presence of an N-acetyl-l-cysteine moiety linked to the carbon atom of the paulic acid isothiocyanate moiety, via a thioester bond, and the subsequent intramolecular cyclization of the paulic acid to generate a thiazole heterocycle confer to paulomycins a higher structural stability that otherwise will conduce to paulomycin degradation and into inactive paulomenols.
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Affiliation(s)
- Jorge Fernández-De la Hoz
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo (Asturias), Spain.
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo (Asturias), Spain.
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo (Asturias), Spain.
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo (Asturias), Spain.
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110
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Chen R, Zhang Q, Tan B, Zheng L, Li H, Zhu Y, Zhang C. Genome Mining and Activation of a Silent PKS/NRPS Gene Cluster Direct the Production of Totopotensamides. Org Lett 2017; 19:5697-5700. [PMID: 29019409 DOI: 10.1021/acs.orglett.7b02878] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A 92 kb silent hybrid polyketide and nonribosomal peptide gene cluster in marine-derived Streptomyces pactum SCSIO 02999 was activated by genetically manipulating the regulatory genes, including the knockout of two negative regulators (totR5 and totR3) and overexpression of a positive regulator totR1, to direct the production of the known totopotensamides (TPMs) A (1) and B (3) and a novel sulfonate-containing analogue TPM C (2). Inactivation of totG led to accumulation of TPM B (3) lacking the glycosyl moiety, which indicated TotG as a dedicated glycosyltransferase in the biosynthesis of 1 and 2.
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Affiliation(s)
- Ruidong Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Liujuan Zheng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Huixian Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , 164 West Xingang Road, Guangzhou 510301, China
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111
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Machado H, Tuttle RN, Jensen PR. Omics-based natural product discovery and the lexicon of genome mining. Curr Opin Microbiol 2017; 39:136-142. [PMID: 29175703 PMCID: PMC5732065 DOI: 10.1016/j.mib.2017.10.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/28/2017] [Indexed: 11/29/2022]
Abstract
Genome sequencing and the application of omic techniques are driving many important advances in the field of microbial natural products research. Despite these gains, there remain aspects of the natural product discovery pipeline where our knowledge remains poor. These include the extent to which biosynthetic gene clusters are transcriptionally active in native microbes, the temporal dynamics of transcription, translation, and natural product assembly, as well as the relationships between small molecule production and detection. Here we touch on a number of these concepts in the context of continuing efforts to unlock the natural product potential revealed in genome sequence data and discuss nomenclatural issues that warrant consideration as the field moves forward.
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Affiliation(s)
- Henrique Machado
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Robert N Tuttle
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA; Center for Microbiome Innovation, University of California, San Diego, USA.
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112
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Xu J, Zhang J, Zhuo J, Li Y, Tian Y, Tan H. Activation and mechanism of a cryptic oviedomycin gene cluster via the disruption of a global regulatory gene, adpA, in Streptomyces ansochromogenes. J Biol Chem 2017; 292:19708-19720. [PMID: 28972184 DOI: 10.1074/jbc.m117.809145] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 09/13/2017] [Indexed: 11/06/2022] Open
Abstract
Genome sequencing analysis has revealed at least 35 clusters of likely biosynthetic genes for secondary metabolites in Streptomyces ansochromogenes. Disruption of adpA encoding a global regulator (AdpA) resulted in the failure of nikkomycin production, whereas other antibacterial activities against Staphylococcus aureus, Bacillus cereus, and Bacillus subtilis were observed with the fermentation broth of ΔadpA but not with that of the wild-type strain. Transcriptional analysis showed that a cryptic gene cluster (pks7), which shows high identity with an oviedomycin biosynthetic gene cluster (ovm), was activated in ΔadpA. The corresponding product of pks7 was characterized as oviedomycin by MS and NMR spectroscopy. To understand the molecular mechanism of ovm activation, the roles of six regulatory genes situated in the ovm cluster were investigated. Among them, proteins encoded by co-transcribed genes ovmZ and ovmW are positive regulators of ovm AdpA directly represses the transcription of ovmZ and ovmW Co-overexpression of ovmZ and ovmW can relieve the repression of AdpA on ovm transcription and effectively activate oviedomycin biosynthesis. The promoter of ovmOI-ovmH is identified as the direct target of OvmZ and OvmW. This is the first report that AdpA can simultaneously activate nikkomycin biosynthesis but repress oviedomycin biosynthesis in one strain. Our findings provide an effective strategy that is able to activate cryptic secondary metabolite gene clusters by genetic manipulation of global regulatory genes.
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Affiliation(s)
- Jingjing Xu
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China and.,the University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Jihui Zhang
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China and
| | - Jiming Zhuo
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China and.,the University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yue Li
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China and
| | - Yuqing Tian
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China and .,the University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Huarong Tan
- From the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China and .,the University of the Chinese Academy of Sciences, Beijing 100039, China
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113
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Identification of butenolide regulatory system controlling secondary metabolism in Streptomyces albus J1074. Sci Rep 2017; 7:9784. [PMID: 28852167 PMCID: PMC5575351 DOI: 10.1038/s41598-017-10316-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/28/2017] [Indexed: 11/09/2022] Open
Abstract
A large majority of genome-encrypted chemical diversity in actinobacteria remains to be discovered, which is related to the low level of secondary metabolism genes expression. Here, we report the application of a reporter-guided screening strategy to activate cryptic polycyclic tetramate macrolactam gene clusters in Streptomyces albus J1074. The analysis of the S. albus transcriptome revealed an overall low level of secondary metabolism genes transcription. Combined with transposon mutagenesis, reporter-guided screening resulted in the selection of two S. albus strains with altered secondary metabolites production. Transposon insertion in the most prominent strain, S. albus ATGSal2P2::TN14, was mapped to the XNR_3174 gene encoding an unclassified transcriptional regulator. The mutant strain was found to produce the avenolide-like compound butenolide 4. The deletion of the gene encoding a putative acyl-CoA oxidase, an orthologue of the Streptomyces avermitilis avenolide biosynthesis enzyme, in the S. albus XNR_3174 mutant caused silencing of secondary metabolism. The homologues of XNR_3174 and the butenolide biosynthesis genes were found in the genomes of multiple Streptomyces species. This result leads us to believe that the discovered regulatory elements comprise a new condition-dependent system that controls secondary metabolism in actinobacteria and can be manipulated to activate cryptic biosynthetic pathways.
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Ceniceros A, Dijkhuizen L, Petrusma M, Medema MH. Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus. BMC Genomics 2017; 18:593. [PMID: 28793878 PMCID: PMC5550956 DOI: 10.1186/s12864-017-3966-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/27/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Bacteria of the genus Rhodococcus are well known for their ability to degrade a large range of organic compounds. Some rhodococci are free-living, saprophytic bacteria; others are animal and plant pathogens. Recently, several studies have shown that their genomes encode putative pathways for the synthesis of a large number of specialized metabolites that are likely to be involved in microbe-microbe and host-microbe interactions. To systematically explore the specialized metabolic potential of this genus, we here performed a comprehensive analysis of the biosynthetic coding capacity across publicly available rhododoccal genomes, and compared these with those of several Mycobacterium strains as well as that of their mutual close relative Amycolicicoccus subflavus. RESULTS Comparative genomic analysis shows that most predicted biosynthetic gene cluster families in these strains are clade-specific and lack any homology with gene clusters encoding the production of known natural products. Interestingly, many of these clusters appear to encode the biosynthesis of lipopeptides, which may play key roles in the diverse environments were rhodococci thrive, by acting as biosurfactants, pathogenicity factors or antimicrobials. We also identified several gene cluster families that are universally shared among all three genera, which therefore may have a more 'primary' role in their physiology. Inactivation of these clusters by mutagenesis might help to generate weaker strains that can be used as live vaccines. CONCLUSIONS The genus Rhodococcus thus provides an interesting target for natural product discovery, in view of its large and mostly uncharacterized biosynthetic repertoire, its relatively fast growth and the availability of effective genetic tools for its genomic modification.
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Affiliation(s)
- Ana Ceniceros
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.
| | - Mirjan Petrusma
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
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Thao NB, Kitani S, Nitta H, Tomioka T, Nihira T. Discovering potential Streptomyces hormone producers by using disruptants of essential biosynthetic genes as indicator strains. J Antibiot (Tokyo) 2017; 70:1004-1008. [PMID: 28951606 DOI: 10.1038/ja.2017.85] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/13/2017] [Accepted: 06/20/2017] [Indexed: 12/21/2022]
Abstract
Autoregulators are low-molecular-weight signaling compounds that control the production of many secondary metabolites in actinomycetes and have been referred to as 'Streptomyces hormones'. Here, potential producers of Streptomyces hormones were investigated in 40 Streptomyces and 11 endophytic actinomycetes. Production of γ-butyrolactone-type (IM-2, VB) and butenolide-type (avenolide) Streptomyces hormones was screened using Streptomyces lavendulae FRI-5 (ΔfarX), Streptomyces virginiae (ΔbarX) and Streptomyces avermitilis (Δaco), respectively. In these strains, essential biosynthetic genes for Streptomyces hormones were disrupted, enabling them to respond solely to the externally added hormones. The results showed that 20% of each of the investigated strains produced IM-2 and VB, confirming that γ-butyrolactone-type Streptomyces hormones are the most common in actinomycetes. Unlike the γ-butyrolactone type, butenolide-type Streptomyces hormones have been discovered in recent years, but their distribution has been unclear. Our finding that 24% of actinomycetes (12 of 51 strains) showed avenolide activity revealed for the first time that the butenolide-type Streptomyces hormone is also common in actinomycetes.
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Affiliation(s)
- Nguyen B Thao
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Shigeru Kitani
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Hiroko Nitta
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Toshiya Tomioka
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Takuya Nihira
- International Center for Biotechnology, Osaka University, Osaka, Japan.,Faculty of Science, MU-OU Collaborative Research Center for Bioscience and Biotechnology, Mahidol University, Bangkok, Thailand
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Xu F, Nazari B, Moon K, Bushin LB, Seyedsayamdost MR. Discovery of a Cryptic Antifungal Compound from Streptomyces albus J1074 Using High-Throughput Elicitor Screens. J Am Chem Soc 2017; 139:9203-9212. [PMID: 28590725 DOI: 10.1021/jacs.7b02716] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
An important unresolved issue in microbial secondary metabolite production is the abundance of biosynthetic gene clusters that are not expressed under typical laboratory growth conditions. These so-called silent or cryptic gene clusters are sources of new natural products, but how they are silenced, and how they may be rationally activated are areas of ongoing investigation. We recently devised a chemogenetic high-throughput screening approach ("HiTES") to discover small molecule elicitors of silent biosynthetic gene clusters. This method was successfully applied to a Gram-negative bacterium; it has yet to be implemented in the prolific antibiotic-producing streptomycetes. Herein we have developed a high-throughput transcriptional assay format in Streptomyces spp. by leveraging eGFP, inserted both at a neutral site and inside the biosynthetic cluster of interest, as a read-out for secondary metabolite synthesis. Using this approach, we successfully used HiTES to activate a silent gene cluster in Streptomyces albus J1074. Our results revealed the cytotoxins etoposide and ivermectin as potent inducers, allowing us to isolate and structurally characterize 14 novel small molecule products of the chosen cluster. One of these molecules is a novel antifungal, while several others inhibit a cysteine protease implicated in cancer. Studies addressing the mechanism of induction by the two elicitors led to the identification of a pathway-specific transcriptional repressor that silences the gene cluster under standard growth conditions. The successful application of HiTES will allow future interrogations of the biological regulation and chemical output of the countless silent gene clusters in Streptomyces spp.
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Affiliation(s)
- Fei Xu
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Behnam Nazari
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Kyuho Moon
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Leah B Bushin
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States.,Department of Molecular Biology, Princeton University , Princeton, New Jersey 08544, United States
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Losada AA, Méndez C, Salas JA, Olano C. Exploring the biocombinatorial potential of benzoxazoles: generation of novel caboxamycin derivatives. Microb Cell Fact 2017; 16:93. [PMID: 28545544 PMCID: PMC5445379 DOI: 10.1186/s12934-017-0709-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/23/2017] [Indexed: 11/10/2022] Open
Abstract
Background The biosynthesis pathway of benzoxazole compounds caboxamycin and nataxazole have been recently elucidated. Both compounds share one of their precursors, 3-hydroxyanthranilate (two units in the case of nataxazole). In addition, caboxamycin structure includes a salicylate moiety while 6-methylsalycilate is the third scaffold in nataxazole. Pathways cross-talk has been identified in caboxamycin producer Streptomyces sp. NTK937, between caboxamycin and enterobactin pathways, and nataxazole producer Streptomyces sp. Tü6176, between nataxazole and coelibactin pathways. These events represent a natural form of combinatorial biosynthesis. Results Eleven novel caboxamycin derivatives, and five putative novel derivatives, bearing distinct substitutions in the aryl ring have been generated. These compounds were produced by heterologous expression of several caboxamycin biosynthesis genes in Streptomyces albus J1074 (two compounds), by combinatorial biosynthesis in Streptomyces sp. NTK937 expressing nataxazole iterative polyketide synthase (two compounds) and by mutasynthesis using a nonproducing mutant of Streptomyces sp. NTK937 (12 compounds). Some of the compounds showed improved bioactive properties in comparison with caboxamycin. Conclusions In addition to the benzoxazoles naturally biosynthesized by the caboxamycin and nataxazole producers, a greater structural diversity can be generated by mutasynthesis and heterologous expression of benzoxazole biosynthesis genes, not only in the respective producer strains but also in non-benzoxazole producers such as S. albus strains. These results show that the production of a wide variety of benzoxazoles could be potentially achieved by the sole expression of cbxBCDE genes (or orthologs thereof), supplying an external source of salicylate-like compounds, or with the concomitant expression of other genes capable of synthesizing salicylates, such as cbxA or natPK. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0709-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Armando A Losada
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Asturias, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Asturias, Spain
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Asturias, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo, Asturias, Spain.
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Koshla O, Lopatniuk M, Rokytskyy I, Yushchuk O, Dacyuk Y, Fedorenko V, Luzhetskyy A, Ostash B. Properties of Streptomyces albus J1074 mutant deficient in tRNALeu UAA gene bldA. Arch Microbiol 2017; 199:1175-1183. [DOI: 10.1007/s00203-017-1389-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/06/2017] [Accepted: 05/16/2017] [Indexed: 11/28/2022]
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119
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Zhang MM, Wong FT, Wang Y, Luo S, Lim YH, Heng E, Yeo WL, Cobb RE, Enghiad B, Ang EL, Zhao H. CRISPR-Cas9 strategy for activation of silent Streptomyces biosynthetic gene clusters. Nat Chem Biol 2017; 13:nchembio.2341. [PMID: 28398287 PMCID: PMC5634907 DOI: 10.1038/nchembio.2341] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 01/13/2017] [Indexed: 02/02/2023]
Abstract
Here we report an efficient CRISPR-Cas9 knock-in strategy to activate silent biosynthetic gene clusters (BGCs) in streptomycetes. We applied this one-step strategy to activate multiple BGCs of different classes in five Streptomyces species and triggered the production of unique metabolites, including a novel pentangular type II polyketide in Streptomyces viridochromogenes. This potentially scalable strategy complements existing activation approaches and facilitates discovery efforts to uncover new compounds with interesting bioactivities.
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Affiliation(s)
- Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab, Biomedical Science Institutes, A*STAR, Singapore
| | - Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Shangwen Luo
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yee Hwee Lim
- Organic Chemistry, Institute of Chemical and Engineering Sciences, A*STAR, Singapore
| | - Elena Heng
- Molecular Engineering Lab, Biomedical Science Institutes, A*STAR, Singapore
| | - Wan Lin Yeo
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), Singapore
| | - Ryan E Cobb
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Behnam Enghiad
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), Singapore
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Zou X, Wang L, Li Z, Luo J, Wang Y, Deng Z, Du S, Chen S. Genome Engineering and Modification Toward Synthetic Biology for the Production of Antibiotics. Med Res Rev 2017; 38:229-260. [PMID: 28295439 DOI: 10.1002/med.21439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 01/06/2017] [Accepted: 01/14/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Xuan Zou
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Lianrong Wang
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
| | - Zhiqiang Li
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
| | - Jie Luo
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Yunfu Wang
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Zixin Deng
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
| | - Shiming Du
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
| | - Shi Chen
- Zhongnan Hospital, and Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; Wuhan Hubei 430071 China
- Taihe Hospital; Hubei University of Medicine; Shiyan Hubei China
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121
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Zhang MM, Qiao Y, Ang EL, Zhao H. Using natural products for drug discovery: the impact of the genomics era. Expert Opin Drug Discov 2017; 12:475-487. [PMID: 28277838 DOI: 10.1080/17460441.2017.1303478] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Evolutionarily selected over billions of years for their interactions with biomolecules, natural products have been and continue to be a major source of pharmaceuticals. In the 1990s, pharmaceutical companies scaled down their natural product discovery programs in favor of synthetic chemical libraries due to major challenges such as high rediscovery rates, challenging isolation, and low production titers. Propelled by advances in DNA sequencing and synthetic biology technologies, insights into microbial secondary metabolism provided have inspired a number of strategies to address these challenges. Areas covered: This review highlights the importance of genomics and metagenomics in natural product discovery, and provides an overview of the technical and conceptual advances that offer unprecedented access to molecules encoded by biosynthetic gene clusters. Expert opinion: Genomics and metagenomics revealed nature's remarkable biosynthetic potential and her vast chemical inventory that we can now prioritize and systematically mine for novel chemical scaffolds with desirable bioactivities. Coupled with synthetic biology and genome engineering technologies, significant progress has been made in identifying and predicting the chemical output of biosynthetic gene clusters, as well as in optimizing cluster expression in native and heterologous host systems for the production of pharmaceutically relevant metabolites and their derivatives.
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Affiliation(s)
- Mingzi M Zhang
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Yuan Qiao
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Ee Lui Ang
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Huimin Zhao
- a Metabolic Engineering Research Laboratory , Science and Engineering Institutes, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore.,b Department of Chemical and Biomolecular Engineering , University of Illinois at Urbana-Champaign , Urbana , IL , USA
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Studies on the Kinetics of Antibacterial Agent Production in Two Actinomycete Strains, F9 and Is5, Isolated from Soil Samples, Iran. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2017. [DOI: 10.1007/s40995-017-0171-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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123
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Tan GY, Liu T. Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria. Metab Eng 2017; 39:228-236. [DOI: 10.1016/j.ymben.2016.12.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/31/2016] [Accepted: 12/05/2016] [Indexed: 11/28/2022]
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Coordinate Regulation of Antimycin and Candicidin Biosynthesis. mSphere 2016; 1:mSphere00305-16. [PMID: 27981234 PMCID: PMC5143413 DOI: 10.1128/msphere.00305-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/11/2016] [Indexed: 12/14/2022] Open
Abstract
Natural products produced by members of the phylum Actinobacteria underpin many industrially and medically important compounds; however, the majority of the ~30 biosynthetic pathways harbored by an average species are not expressed in the laboratory. Understanding the diversity of regulatory strategies controlling the expression of these pathways is therefore critical if their biosynthetic potential is to be explored for new drug leads. Our findings reveal that the candicidin cluster-situated regulator FscRI coordinately controls the biosynthesis of both candicidin and antimycin, which is the first observation of cross-regulation of disparate biosynthetic gene clusters specifying unrelated natural products. We anticipate that this will emerge as a major strategy by which members of the phylum Actinobacteria coordinately produce natural products, which will advance our understanding of how the expression of secondary metabolism is controlled and will aid the pursuit of “silent” biosynthetic pathway activation. Streptomyces species produce an incredible array of high-value specialty chemicals and medicinal therapeutics. A single species typically harbors ~30 biosynthetic pathways, but only a few them are expressed in the laboratory; thus, poor understanding of how natural-product biosynthesis is regulated is a major bottleneck in drug discovery. Antimycins are a large family of anticancer compounds widely produced by Streptomyces species, and their regulation is atypical compared to that of most other natural products. Here we demonstrate that antimycin production by Streptomyces albus S4 is regulated by FscRI, a PAS-LuxR family cluster-situated regulator of the polyene antifungal agent candicidin. We report that heterologous production of antimycins by Streptomyces coelicolor is dependent on FscRI and show that FscRI activates the transcription of key biosynthetic genes. We also demonstrate through chromatin immunoprecipitation sequencing that FscRI regulation is direct, and we provide evidence that this regulation strategy is conserved and unique to short-form antimycin gene clusters. Our study provides direct in vivo evidence of the cross-regulation of disparate biosynthetic gene clusters specifying unrelated natural products and expands the paradigmatic understanding of the regulation of secondary metabolism. IMPORTANCE Natural products produced by members of the phylum Actinobacteria underpin many industrially and medically important compounds; however, the majority of the ~30 biosynthetic pathways harbored by an average species are not expressed in the laboratory. Understanding the diversity of regulatory strategies controlling the expression of these pathways is therefore critical if their biosynthetic potential is to be explored for new drug leads. Our findings reveal that the candicidin cluster-situated regulator FscRI coordinately controls the biosynthesis of both candicidin and antimycin, which is the first observation of cross-regulation of disparate biosynthetic gene clusters specifying unrelated natural products. We anticipate that this will emerge as a major strategy by which members of the phylum Actinobacteria coordinately produce natural products, which will advance our understanding of how the expression of secondary metabolism is controlled and will aid the pursuit of “silent” biosynthetic pathway activation.
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Saha S, Zhang W, Zhang G, Zhu Y, Chen Y, Liu W, Yuan C, Zhang Q, Zhang H, Zhang L, Zhang W, Zhang C. Activation and characterization of a cryptic gene cluster reveals a cyclization cascade for polycyclic tetramate macrolactams. Chem Sci 2016; 8:1607-1612. [PMID: 28451290 PMCID: PMC5361873 DOI: 10.1039/c6sc03875a] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/21/2016] [Indexed: 12/24/2022] Open
Abstract
We report the activation of a PTM gene cluster in marine-derived Streptomyces pactum, leading to the discovery of six new PTMs, the pactamides A-F.
Polycyclic tetramate macrolactams (PTMs) are a growing class of natural products and are derived from a hybrid polyketide synthase (PKS)/non-ribosomal peptide synthetase (NRPS) pathway. PTM biosynthetic gene clusters are conserved and widely distributed in bacteria, however, most of them remain silent. Herein we report the activation of a PTM gene cluster in marine-derived Streptomyces pactum SCSIO 02999 by promoter engineering and heterologous expression, leading to the discovery of six new PTMs, pactamides A–F (11–16), with potent cytotoxic activity upon several human cancer cell lines. In vivo gene disruption experiments and in vitro biochemical assays reveal a reductive cyclization cascade for polycycle formation, with reactions sequentially generating the 5, 5/5 and 5/5/6 carbocyclic ring systems, catalysed by the phytoene dehydrogenase PtmB2, the oxidoreductase PtmB1, and the alcohol dehydrogenase PtmC, respectively. Furthermore, PtmC was demonstrated as a bifunctional cyclase for catalyzing the formation of the inner five-membered ring in ikarugamycin. This study suggests the possibility of finding more bioactive PTMs by genome mining and discloses a general mechanism for the formation of 5/5/6-type carbocyclic rings in PTMs.
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Affiliation(s)
- Subhasish Saha
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Wenjun Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Guangtao Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China , Guangdong Institute of Microbiology , 100 Central Xianlie Road , Guangzhou 510070 , China
| | - Wei Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ; .,State Key Laboratory of Applied Microbiology Southern China , South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC) , China
| | - Chengshan Yuan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Qingbo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Haibo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ;
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China , Guangdong Institute of Microbiology , 100 Central Xianlie Road , Guangzhou 510070 , China
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology , Guangdong Key Laboratory of Marine Materia Medica , South China Sea Institute of Oceanology , Chinese Academy of Sciences , 164 West Xingang Road , Guangzhou 510301 , China . ; .,State Key Laboratory of Applied Microbiology Southern China , South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC) , China
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Zhang MM, Wang Y, Ang EL, Zhao H. Engineering microbial hosts for production of bacterial natural products. Nat Prod Rep 2016; 33:963-87. [PMID: 27072804 PMCID: PMC4963277 DOI: 10.1039/c6np00017g] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.
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Affiliation(s)
- Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
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127
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Generation of new compounds through unbalanced transcription of landomycin A cluster. Appl Microbiol Biotechnol 2016; 100:9175-9186. [DOI: 10.1007/s00253-016-7721-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 11/26/2022]
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128
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Insights into microbial cryptic gene activation and strain improvement: principle, application and technical aspects. J Antibiot (Tokyo) 2016; 70:25-40. [PMID: 27381522 DOI: 10.1038/ja.2016.82] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/22/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022]
Abstract
As bacteria and fungi have been found to contain genes encoding enzymes that synthesize a plethora of potential secondary metabolites, interest has grown in the activation of these cryptic pathways. Homologous and heterologous expression of these cryptic secondary metabolite-biosynthetic genes, often silent under ordinary laboratory fermentation conditions, may lead to the discovery of novel secondary metabolites. This review addresses current progress in the activation of these pathways, describing methods for activating silent genes. It especially focuses on genetic manipulation of transcription and translation (ribosome engineering), the utilization of elicitors, metabolism remodeling and co-cultivation. In particular, the principles and technical points of ribosome engineering and the significance of S-adenosylmethionine in bacterial physiology, especially secondary metabolism, are described in detail.
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129
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Maxson T, Mitchell DA. Targeted Treatment for Bacterial Infections: Prospects for Pathogen-Specific Antibiotics Coupled with Rapid Diagnostics. Tetrahedron 2016; 72:3609-3624. [PMID: 27429480 PMCID: PMC4941824 DOI: 10.1016/j.tet.2015.09.069] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Antibiotics are a cornerstone of modern medicine and have significantly reduced the burden of infectious diseases. However, commonly used broad-spectrum antibiotics can cause major collateral damage to the human microbiome, causing complications ranging from antibiotic-associated colitis to the rapid spread of resistance. Employing narrower spectrum antibiotics targeting specific pathogens may alleviate this predicament as well as provide additional tools to expand an antibiotic repertoire threatened by the inevitability of resistance. Improvements in clinical diagnosis will be required to effectively utilize pathogen-specific antibiotics and new molecular diagnostics are poised to fulfill this need. Here we review recent trends and the future prospects of deploying narrower spectrum antibiotics coupled with rapid diagnostics. Further, we discuss the theoretical advantages and limitations of this emerging approach to controlling bacterial infectious diseases.
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Affiliation(s)
- Tucker Maxson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Du D, Katsuyama Y, Onaka H, Fujie M, Satoh N, Shin-ya K, Ohnishi Y. Production of a Novel Amide-Containing Polyene by Activating a Cryptic Biosynthetic Gene Cluster inStreptomycessp. MSC090213JE08. Chembiochem 2016; 17:1464-71. [DOI: 10.1002/cbic.201600167] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Danyao Du
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Yohei Katsuyama
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Hiroyasu Onaka
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha, Onna-son Kunigami-gun Okinawa 904-0495 Japan
| | - Noriyuki Satoh
- Okinawa Institute of Science and Technology Graduate University; 1919-1 Tancha, Onna-son Kunigami-gun Okinawa 904-0495 Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST); 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan
| | - Yasuo Ohnishi
- Department of Biotechnology; Graduate School of Agricultural and Life Sciences; The University of Tokyo; 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
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131
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Shashkov AS, Streshinskaya GM, Tul'skaya EM, Senchenkova SN, Baryshnikova LM, Dmitrenok AS, Ostash BE, Fedorenko VA. Cell wall glycopolymers of Streptomyces albus, Streptomyces albidoflavus and Streptomyces pathocidini. Antonie van Leeuwenhoek 2016; 109:923-36. [PMID: 27055525 DOI: 10.1007/s10482-016-0691-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/28/2016] [Indexed: 11/25/2022]
Abstract
The cell wall glycopolymers of three strains of Streptomyces albus and the type strain of Streptomyces pathocidini were investigated. The structures of the glycopolymers were established using a combination of chemical and NMR spectroscopic methods. The cell wall of S. albus subsp. albus VKM Ac-35(T) was found to be comprised of three glycopolymers, viz. unsubstituted 1,5-poly(ribitol phosphate), 1,3-poly(glycerol phosphate) substituted with β-D-glucopyranose, and the major polymer, a 3-deoxy-D-glycero-D-galacto-non-2-ulosonic acid (Kdn)-teichulosonic acid: β-D-Glcp-(1 → 8)-α-Kdnp-(2[(→6)-β-D-Glcp-(1 → 8)-α-Kdnp-(2 →] n 6)-β-D-Glcp-(1 → 8)-β-Kdnp-(2-OH, where n ≥ 3. The cell walls of 'S. albus' J1074 and 'S. albus' R1-100 were found to contain three glycopolymers of identical structures, viz. unsubstituted 1,3- and 2,3-poly(glycerol phosphates), and the major polymer, a Kdn-teichulosonic acid with an unusual structure that has not been previously described: β-D-Galp-(1 → 9)-α-Kdnp-(2[(→3)-β-D-Galp-(1 → 9)-α-Kdnp-(2 →] n 3)-β-D-Galp-(1 → 9)-β-Kdnp-(2-OH, where n ~ 7-8. The cell wall of S. pathocidini (formerly S. albus subsp. pathocidicus) VKM Ac-598(T) was found to contain two glycopolymers, viz. 1,3-poly(glycerol phosphate) partially O-glycosylated with 2-acetamido-2-deoxy-α-D-glucopyranose and/or O-acylated with L-lysine, and a poly(diglycosyl 1-phosphate) of hitherto unknown structure: -6)-α-D-Glcp-(1 → 6)-α-D-GlcpNAc-(1-P-.
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Affiliation(s)
- Alexander S Shashkov
- ND Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia, 119991
| | - Galina M Streshinskaya
- School of Biology MV, Lomonosov Moscow State University, Vorob'evy gory 1 Stroenie 12, Moscow, Russia, 119991.
| | - Elena M Tul'skaya
- School of Biology MV, Lomonosov Moscow State University, Vorob'evy gory 1 Stroenie 12, Moscow, Russia, 119991
| | - Sophia N Senchenkova
- ND Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia, 119991
| | - Lidia M Baryshnikova
- All-Russian Collection of Microorganisms (VKM), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia, 142290
| | - Andrey S Dmitrenok
- ND Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, Russia, 119991
| | - Bohdan E Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
| | - Victor A Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, 79005, Ukraine
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132
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Caffrey P, De Poire E, Sheehan J, Sweeney P. Polyene macrolide biosynthesis in streptomycetes and related bacteria: recent advances from genome sequencing and experimental studies. Appl Microbiol Biotechnol 2016; 100:3893-908. [PMID: 27023916 DOI: 10.1007/s00253-016-7474-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 02/07/2023]
Abstract
The polyene macrolide group includes important antifungal drugs, to which resistance does not arise readily. Chemical and biological methods have been used in attempts to make polyene antibiotics with fewer toxic side effects. Genome sequencing of producer organisms is contributing to this endeavour, by providing access to new compounds and by enabling yield improvement for polyene analogues obtained by engineered biosynthesis. This recent work is also enhancing bioinformatic methods for deducing the structures of cryptic natural products from their biosynthetic enzymes. The stereostructure of candicidin D has recently been determined by NMR spectroscopy. Genes for the corresponding polyketide synthase have been uncovered in several different genomes. Analysis of this new information strengthens the view that protein sequence motifs can be used to predict double bond geometry in many polyketides.Chemical studies have shown that improved polyenes can be obtained by modifying the mycosamine sugar that is common to most of these compounds. Glycoengineered analogues might be produced by biosynthetic methods, but polyene glycosyltransferases show little tolerance for donors other than GDP-α-D-mycosamine. Genome sequencing has revealed extending glycosyltransferases that add a second sugar to the mycosamine of some polyenes. NppY of Pseudonocardia autotrophica uses UDP-N-acetyl-α-D-glucosamine as donor whereas PegA from Actinoplanes caeruleus uses GDP-α-D-mannose. These two enzymes show 51 % sequence identity and are also closely related to mycosaminyltransferases. These findings will assist attempts to construct glycosyltransferases that transfer alternative UDP- or (d)TDP-linked sugars to polyene macrolactones.
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Affiliation(s)
- Patrick Caffrey
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Eimear De Poire
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - James Sheehan
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul Sweeney
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
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133
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González A, Rodríguez M, Braña AF, Méndez C, Salas JA, Olano C. New insights into paulomycin biosynthesis pathway in Streptomyces albus J1074 and generation of novel derivatives by combinatorial biosynthesis. Microb Cell Fact 2016; 15:56. [PMID: 27001601 PMCID: PMC4802897 DOI: 10.1186/s12934-016-0452-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/09/2016] [Indexed: 12/16/2022] Open
Abstract
Background Streptomyces albus J1074 produces glycosylated antibiotics paulomycin A, B and E that derive from chorismate and contain an isothiocyanate residue in form of paulic acid. Paulomycins biosynthesis pathway involves two glycosyltransferases, three acyltransferases, enzymes required for paulic acid biosynthesis (in particular an aminotransferase and a sulfotransferase), and enzymes involved in the biosynthesis of two deoxysugar moieties: D-allose and L-paulomycose. Results Inactivation of genes encoding enzymes involved in deoxysugar biosynthesis, paulic acid biosynthesis, deoxysugar transfer, and acyl moieties transfer has allowed the identification of several biosynthetic intermediates and shunt products, derived from paulomycin intermediates, and to propose a refined version of the paulomycin biosynthesis pathway. Furthermore, several novel bioactive derivatives of paulomycins carrying modifications in the L-paulomycose moiety have been generated by combinatorial biosynthesis using different plasmids that direct the biosynthesis of alternative deoxyhexoses. Conclusions The paulomycins biosynthesis pathway has been defined by inactivation of genes encoding glycosyltransferases, acyltransferases and enzymes involved in paulic acid and L-paulomycose biosynthesis. These experiments have allowed the assignment of each of these genes to specific paulomycin biosynthesis steps based on characterization of products accumulated by the corresponding mutant strains. In addition, novel derivatives of paulomycin A and B containing L-paulomycose modified moieties were generated by combinatorial biosynthesis. The production of such derivatives shows that L-paulomycosyl glycosyltransferase Plm12 possesses a certain degree of flexibility for the transfer of different deoxysugars. In addition, the pyruvate dehydrogenase system form by Plm8 and Plm9 is also flexible to catalyze the attachment of a two-carbon side chain, derived from pyruvate, into both 2,6-dideoxyhexoses and 2,3,6-trideoxyhexoses. The activity of the novel paulomycin derivatives carrying modifications in the L-paulomycose moiety is lower than the original compounds pointing to some interesting structure–activity relationships. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0452-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aránzazu González
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo (Asturias), Spain
| | - Miriam Rodríguez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo (Asturias), Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo (Asturias), Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo (Asturias), Spain
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo (Asturias), Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/Julian Claveria s/n, 33006, Oviedo (Asturias), Spain.
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134
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Abstract
This review covers the literature published in 2014 for marine natural products (MNPs), with 1116 citations (753 for the period January to December 2014) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1378 in 456 papers for 2014), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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135
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Rasimus-Sahari S, Mikkola R, Andersson MA, Jestoi M, Salkinoja-Salonen M. Streptomyces strains producing mitochondriotoxic antimycin A found in cereal grains. Int J Food Microbiol 2016; 218:78-85. [DOI: 10.1016/j.ijfoodmicro.2015.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 11/06/2015] [Accepted: 11/14/2015] [Indexed: 01/28/2023]
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136
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DNA affinity capturing identifies new regulators of the heterologously expressed novobiocin gene cluster in Streptomyces coelicolor M512. Appl Microbiol Biotechnol 2016; 100:4495-509. [PMID: 26795961 DOI: 10.1007/s00253-016-7306-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
Abstract
Understanding the regulation of a heterologously expressed gene cluster in a host organism is crucial for activation of silent gene clusters or overproduction of the corresponding natural product. In this study, Streptomyces coelicolor M512(nov-BG1) containing the novobiocin biosynthetic gene cluster from Streptomyces niveus NCIMB 11891 was chosen as a model. An improved DNA affinity capturing assay (DACA), combined with semi-quantitative mass spectrometry, was used to identify proteins binding to the promoter regions of the novobiocin gene cluster. Altogether, 2475 proteins were identified in DACA studies with the promoter regions of the pathway-specific regulators novE (PnovE) and novG (PnovG), of the biosynthetic genes novH-W (PnovH) and of the vegetative σ-factor hrdB (PhrdB) as a negative control. A restrictive classification for specific binding reduced this number to 17 proteins. Twelve of them were captured by PnovH, among them, NovG, two were captured by PnovE, and three by PnovG. Unexpectedly some well-known regulatory proteins, such as the global regulators NdgR, AdpA, SlbR, and WhiA were captured in similar intensities by all four tested promoter regions. Of the 17 promoter-specific proteins, three were studied in more detail by deletion mutagenesis and by overexpression. Two of them, BxlRSc and BxlR2Sc, could be identified as positive regulators of novobiocin production in S. coelicolor M512. Deletion of a third gene, sco0460, resulted in reduced novobiocin production, while overexpression had no effect. Furthermore, binding of BxlRSc to PnovH and to its own promoter region was confirmed via surface plasmon resonance spectroscopy.
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137
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Zarins-Tutt JS, Barberi TT, Gao H, Mearns-Spragg A, Zhang L, Newman DJ, Goss RJM. Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating and upregulating the biosynthesis of bacterial cryptic or silent natural products. Nat Prod Rep 2016; 33:54-72. [DOI: 10.1039/c5np00111k] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Over the centuries, microbial secondary metabolites have played a central role in the treatment of human diseases and have revolutionised the pharmaceutical industry.
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Affiliation(s)
| | | | - Hong Gao
- School of Chemistry
- University of St Andrews
- St Andrews
- UK
| | | | - Lixin Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology
- Institute of Microbiology
- Chinese Academy of Sciences
- Beijing
- China
| | - David J. Newman
- Frederick National Laboratories for Cancer Research
- Natural Products Branch
- Frederick
- USA
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138
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Myronovskyi M, Luzhetskyy A. Native and engineered promoters in natural product discovery. Nat Prod Rep 2016; 33:1006-19. [DOI: 10.1039/c6np00002a] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transcriptional activation of biosynthetic gene clusters.
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Affiliation(s)
- Maksym Myronovskyi
- Helmholtz-Institute for Pharmaceutical Research Saarland
- 66123 Saarbrücken
- Germany
| | - Andriy Luzhetskyy
- Helmholtz-Institute for Pharmaceutical Research Saarland
- 66123 Saarbrücken
- Germany
- Department of Pharmaceutical Biotechnology
- Saarland University
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139
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Affiliation(s)
- Sarah E. O'Connor
- The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom;
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140
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Culture-independent discovery of natural products from soil metagenomes. J Ind Microbiol Biotechnol 2015; 43:129-41. [PMID: 26586404 DOI: 10.1007/s10295-015-1706-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 10/29/2015] [Indexed: 12/20/2022]
Abstract
Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or "metagenomic," methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth's microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.
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141
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Strain-level diversity of secondary metabolism in the biocontrol species Aneurinibacillus migulanus. Microbiol Res 2015; 182:116-24. [PMID: 26686620 DOI: 10.1016/j.micres.2015.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/01/2015] [Accepted: 10/22/2015] [Indexed: 12/24/2022]
Abstract
Aneurinibacillus migulanus strains Nagano and NCTC 7096 show potential in biocontrol against fungal and fungus-like plant pathogens, including a wide range of Ascomycota, Basidiomycota, and Oomycetes. Differences in terms of the range of pathogens that each strain inhibits, however, suggested that production of a single antibiotic cyclic peptide, gramicidin S (GS), by the two strains, is not the sole mechanism of inhibition. The availability of four sequenced genomes of Aneurinibacillus prompted us to apply genome mining techniques to identify the bioactive potential of A. migulanus and to provide insights into the secondary metabolite arsenal of the genus Aneurinibacillus. Up to eleven secondary metabolite biosynthetic gene clusters were present in the three Aneurinibacillus species. Biosynthetic gene clusters specifying bacteriocins, microcins, non-ribosomal peptides, polyketides, terpenes, phosphonates, lasso peptides and linaridins were identified. Chitinolytic potential and iron metabolism regulation were also investigated. With increasing numbers of biocontrol bacterial genomes being sequenced and mined, the use of approaches similar to those described in this paper will lead to an increase in the numbers of environmentally friendly natural products available to use against plant diseases.
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142
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Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes. J Ind Microbiol Biotechnol 2015; 43:343-70. [PMID: 26364200 DOI: 10.1007/s10295-015-1682-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/28/2015] [Indexed: 12/18/2022]
Abstract
Actinomycetes continue to be important sources for the discovery of secondary metabolites for applications in human medicine, animal health, and crop protection. With the maturation of actinomycete genome mining as a robust approach to identify new and novel cryptic secondary metabolite gene clusters, it is critical to continue developing methods to activate and enhance secondary metabolite biosynthesis for discovery, development, and large-scale manufacturing. This review covers recent reports on promising new approaches and further validations or technical improvements of existing approaches to strain improvement applicable to a wide range of Streptomyces species and other actinomycetes.
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143
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Beites T, Mendes MV. Chassis optimization as a cornerstone for the application of synthetic biology based strategies in microbial secondary metabolism. Front Microbiol 2015; 6:906. [PMID: 26441855 PMCID: PMC4563238 DOI: 10.3389/fmicb.2015.00906] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/19/2015] [Indexed: 02/06/2023] Open
Abstract
The increased number of bacterial genome sequencing projects has generated over the last years a large reservoir of genomic information. In silico analysis of this genomic data has renewed the interest in bacterial bioprospecting for bioactive compounds by unveiling novel biosynthetic gene clusters of unknown or uncharacterized metabolites. However, only a small fraction of those metabolites is produced under laboratory-controlled conditions; the remaining clusters represent a pool of novel metabolites that are waiting to be “awaken”. Activation of the biosynthetic gene clusters that present reduced or no expression (known as cryptic or silent clusters) by heterologous expression has emerged as a strategy for the identification and production of novel bioactive molecules. Synthetic biology, with engineering principles at its core, provides an excellent framework for the development of efficient heterologous systems for the expression of biosynthetic gene clusters. However, a common problem in its application is the host-interference problem, i.e., the unpredictable interactions between the device and the host that can hamper the desired output. Although an effort has been made to develop orthogonal devices, the most proficient way to overcome the host-interference problem is through genome simplification. In this review we present an overview on the strategies and tools used in the development of hosts/chassis for the heterologous expression of specialized metabolites biosynthetic gene clusters. Finally, we introduce the concept of specialized host as the next step of development of expression hosts.
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Affiliation(s)
- Tiago Beites
- I3S Instituto de Investigação e Inovação em Saúde, Universidade do Porto Porto, Portugal ; Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal
| | - Marta V Mendes
- I3S Instituto de Investigação e Inovação em Saúde, Universidade do Porto Porto, Portugal ; Instituto de Biologia Molecular e Celular, Universidade do Porto Porto, Portugal
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144
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Azman AS, Othman I, Velu SS, Chan KG, Lee LH. Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity. Front Microbiol 2015; 6:856. [PMID: 26347734 PMCID: PMC4542535 DOI: 10.3389/fmicb.2015.00856] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 08/06/2015] [Indexed: 11/13/2022] Open
Abstract
Actinobacteria are one of the most important and efficient groups of natural metabolite producers. The genus Streptomyces have been recognized as prolific producers of useful natural compounds as they produced more than half of the naturally-occurring antibiotics isolated to-date and continue as the primary source of new bioactive compounds. Lately, Streptomyces groups isolated from different environments produced the same types of compound, possibly due to frequent genetic exchanges between species. As a result, there is a dramatic increase in demand to look for new compounds which have pharmacological properties from another group of Actinobacteria, known as rare actinobacteria; which is isolated from special environments such as mangrove. Recently, mangrove ecosystem is becoming a hot spot for studies of bioactivities and the discovery of natural products. Many novel compounds discovered from the novel rare actinobacteria have been proven as potential new drugs in medical and pharmaceutical industries such as antibiotics, antimicrobials, antibacterials, anticancer, and antifungals. This review article highlights the latest studies on the discovery of natural compounds from the novel mangrove rare actinobacteria and provides insight on the impact of these findings.
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Affiliation(s)
- Adzzie-Shazleen Azman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
| | - Iekhsan Othman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
| | - Saraswati S Velu
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus Selangor, Malaysia
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145
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Liang ZX. The expanding roles of c-di-GMP in the biosynthesis of exopolysaccharides and secondary metabolites. Nat Prod Rep 2015; 32:663-83. [PMID: 25666534 DOI: 10.1039/c4np00086b] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The cyclic dinucleotide c-di-GMP has emerged in the last decade as a prevalent intracellular messenger that orchestrates the transition between the motile and sessile lifestyles of many bacterial species. The motile-to-sessile transition is often associated with the formation of extracellular matrix-encased biofilm, an organized community of bacterial cells that often contributes to antibiotic resistance and host-pathogen interaction. It is increasingly clear that c-di-GMP controls motility, biofilm formation and bacterial pathogenicity partially through regulating the production of exopolysaccharides (EPS) and small-molecule secondary metabolites. This review summarizes our current understanding of the regulation of EPS biosynthesis by c-di-GMP in a diversity of bacterial species and highlights the emerging role of c-di-GMP in the biosynthesis of small-molecule secondary metabolites.
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Affiliation(s)
- Zhao-Xun Liang
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637551.
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146
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Cano-Prieto C, Losada AA, Braña AF, Méndez C, Salas JA, Olano C. Crosstalk of Nataxazole Pathway with Chorismate-Derived Ionophore Biosynthesis Pathways in Streptomyces sp. Tü 6176. Chembiochem 2015; 16:1925-1932. [PMID: 26083234 DOI: 10.1002/cbic.201500261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Indexed: 11/12/2022]
Abstract
Streptomyces sp. Tü 6176, producer of cytotoxic benzoxazoles AJI9561, nataxazole, and 5-hydroxy-nataxazole, has been found to produce a fourth benzoxazole, UK-1. All derive from 3-hydroxy-anthranilate synthesized by the nataxazole biosynthesis machinery. However, biosynthesis of AJI9561, nataxazole, and 5-hydroxy-nataxazole requires 6-methylsalicylic acid also provided by nataxazole biosynthesis pathway, while biosynthesis of UK-1 utilizes salicylic acid produced by a salicylate synthase from the coelibactin biosynthesis pathway. This clearly suggests crosstalk between nataxazole and coelibactin pathways. Overproduction of UK-1 was obtained by growing a nataxazole non-producing mutant (lacking 6-methylsalicylate synthase, NatPK) in a zinc-deficient medium. Furthermore, Streptomyces sp. Tü 6176 also produces the siderophore enterobactin in an iron-free medium. Enterobactin production can be induced in an iron-independent manner by inactivating natAN, which encodes an anthranilate synthase involved in nataxazole production. The results indicate a close relationship between nataxazole, enterobactin and coelibactin pathways through the shikimate pathway, the source of their common precursor, chorismate.
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Affiliation(s)
- Carolina Cano-Prieto
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería, s/n, 33006 Oviedo (Spain)
| | - Armando A Losada
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería, s/n, 33006 Oviedo (Spain)
| | - Alfredo F Braña
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería, s/n, 33006 Oviedo (Spain)
| | - Carmen Méndez
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería, s/n, 33006 Oviedo (Spain)
| | - José A Salas
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería, s/n, 33006 Oviedo (Spain)
| | - Carlos Olano
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, C/ Julian Clavería, s/n, 33006 Oviedo (Spain)
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147
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Yeast homologous recombination-based promoter engineering for the activation of silent natural product biosynthetic gene clusters. Proc Natl Acad Sci U S A 2015; 112:8953-8. [PMID: 26150486 DOI: 10.1073/pnas.1507606112] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Large-scale sequencing of prokaryotic (meta)genomic DNA suggests that most bacterial natural product gene clusters are not expressed under common laboratory culture conditions. Silent gene clusters represent a promising resource for natural product discovery and the development of a new generation of therapeutics. Unfortunately, the characterization of molecules encoded by these clusters is hampered owing to our inability to express these gene clusters in the laboratory. To address this bottleneck, we have developed a promoter-engineering platform to transcriptionally activate silent gene clusters in a model heterologous host. Our approach uses yeast homologous recombination, an auxotrophy complementation-based yeast selection system and sequence orthogonal promoter cassettes to exchange all native promoters in silent gene clusters with constitutively active promoters. As part of this platform, we constructed and validated a set of bidirectional promoter cassettes consisting of orthogonal promoter sequences, Streptomyces ribosome binding sites, and yeast selectable marker genes. Using these tools we demonstrate the ability to simultaneously insert multiple promoter cassettes into a gene cluster, thereby expediting the reengineering process. We apply this method to model active and silent gene clusters (rebeccamycin and tetarimycin) and to the silent, cryptic pseudogene-containing, environmental DNA-derived Lzr gene cluster. Complete promoter refactoring and targeted gene exchange in this "dead" cluster led to the discovery of potent indolotryptoline antiproliferative agents, lazarimides A and B. This potentially scalable and cost-effective promoter reengineering platform should streamline the discovery of natural products from silent natural product biosynthetic gene clusters.
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148
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Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 2015; 13:509-23. [PMID: 26119570 DOI: 10.1038/nrmicro3496] [Citation(s) in RCA: 588] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities and a wide variety of applications in medicine and agriculture, such as the treatment of infectious diseases and cancer, and the prevention of crop damage. Genomics has revealed that many microorganisms have far greater potential to produce specialized metabolites than was thought from classic bioactivity screens; however, realizing this potential has been hampered by the fact that many specialized metabolite biosynthetic gene clusters (BGCs) are not expressed in laboratory cultures. In this Review, we discuss the strategies that have been developed in bacteria and fungi to identify and induce the expression of such silent BGCs, and we briefly summarize methods for the isolation and structural characterization of their metabolic products.
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149
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Cobb RE, Wang Y, Zhao H. High-efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 2015; 4:723-8. [PMID: 25458909 PMCID: PMC4459934 DOI: 10.1021/sb500351f] [Citation(s) in RCA: 393] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Actinobacteria,
particularly those of genus Streptomyces, remain
invaluable hosts for the discovery and engineering of natural
products and their cognate biosynthetic pathways. However, genetic
manipulation of these bacteria is often labor and time intensive.
Here, we present an engineered CRISPR/Cas system for rapid multiplex
genome editing of Streptomyces strains, demonstrating
targeted chromosomal deletions in three different Streptomyces species and of various sizes (ranging from 20 bp to 30 kb) with
efficiency ranging from 70 to 100%. The designed pCRISPomyces plasmids
are amenable to assembly of spacers and editing templates via Golden
Gate assembly and isothermal assembly (or traditional digestion/ligation),
respectively, allowing rapid plasmid construction to target any genomic
locus of interest. As such, the pCRISPomyces system represents a powerful
new tool for genome editing in Streptomyces.
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Affiliation(s)
- Ryan E. Cobb
- Department of Chemical and Biomolecular
Engineering, ‡Institute for Genomic Biology, §Departments of Chemistry,
Biochemistry and Bioengineering, Center for Biophysics and Computational
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yajie Wang
- Department of Chemical and Biomolecular
Engineering, ‡Institute for Genomic Biology, §Departments of Chemistry,
Biochemistry and Bioengineering, Center for Biophysics and Computational
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular
Engineering, ‡Institute for Genomic Biology, §Departments of Chemistry,
Biochemistry and Bioengineering, Center for Biophysics and Computational
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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150
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Abdelmohsen UR, Grkovic T, Balasubramanian S, Kamel MS, Quinn RJ, Hentschel U. Elicitation of secondary metabolism in actinomycetes. Biotechnol Adv 2015; 33:798-811. [PMID: 26087412 DOI: 10.1016/j.biotechadv.2015.06.003] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 05/29/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
Genomic sequence data have revealed the presence of a large fraction of putatively silent biosynthetic gene clusters in the genomes of actinomycetes that encode for secondary metabolites, which are not detected under standard fermentation conditions. This review focuses on the effects of biological (co-cultivation), chemical, as well as molecular elicitation on secondary metabolism in actinomycetes. Our review covers the literature until June 2014 and exemplifies the diversity of natural products that have been recovered by such approaches from the phylum Actinobacteria.
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Affiliation(s)
- Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany; Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt.
| | - Tanja Grkovic
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Srikkanth Balasubramanian
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
| | - Mohamed Salah Kamel
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
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