51
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Pait IGU, Kitani S, Roslan FW, Ulanova D, Arai M, Ikeda H, Nihira T. Discovery of a new diol-containing polyketide by heterologous expression of a silent biosynthetic gene cluster from Streptomyces lavendulae FRI-5. J Ind Microbiol Biotechnol 2017; 45:77-87. [PMID: 29255990 DOI: 10.1007/s10295-017-1997-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 12/09/2017] [Indexed: 11/29/2022]
Abstract
The genome of streptomycetes has the ability to produce many novel and potentially useful bioactive compounds, but most of which are not produced under standard laboratory cultivation conditions and are referred to as silent/cryptic secondary metabolites. Streptomyces lavendulae FRI-5 produces several types of bioactive compounds. However, this strain may also have the potential to biosynthesize more useful secondary metabolites. Here, we activated a silent biosynthetic gene cluster of an uncharacterized compound from S. lavendulae FRI-5 using heterologous expression. The engineered strain carrying the silent gene cluster produced compound 5, which was undetectable in the culture broth of S. lavendulae FRI-5. Using various spectroscopic analyses, we elucidated the chemical structure of compound 5 (named lavendiol) as a new diol-containing polyketide. The proposed assembly line of lavendiol shows a unique biosynthetic mechanism for polyketide compounds. The results of this study suggest the possibility of discovering more silent useful compounds from streptomycetes by genome mining and heterologous expression.
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Affiliation(s)
- Ivy Grace Umadhay Pait
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shigeru Kitani
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Farah Wahidah Roslan
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Dana Ulanova
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Marine Resource Science, Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takuya Nihira
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,MU-OU Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Rama VI Rd, Bangkok, 10400, Thailand.
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52
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Čihák M, Kameník Z, Šmídová K, Bergman N, Benada O, Kofroňová O, Petříčková K, Bobek J. Secondary Metabolites Produced during the Germination of Streptomyces coelicolor. Front Microbiol 2017; 8:2495. [PMID: 29326665 PMCID: PMC5733532 DOI: 10.3389/fmicb.2017.02495] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/30/2017] [Indexed: 11/16/2022] Open
Abstract
Spore awakening is a series of actions that starts with purely physical processes and continues via the launching of gene expression and metabolic activities, eventually achieving a vegetative phase of growth. In spore-forming microorganisms, the germination process is controlled by intra- and inter-species communication. However, in the Streptomyces clade, which is capable of developing a plethora of valuable compounds, the chemical signals produced during germination have not been systematically studied before. Our previously published data revealed that several secondary metabolite biosynthetic genes are expressed during germination. Therefore, we focus here on the secondary metabolite production during this developmental stage. Using high-performance liquid chromatography-mass spectrometry, we found that the sesquiterpenoid antibiotic albaflavenone, the polyketide germicidin A, and chalcone are produced during germination of the model streptomycete, S. coelicolor. Interestingly, the last two compounds revealed an inhibitory effect on the germination process. The secondary metabolites originating from the early stage of microbial growth may coordinate the development of the producer (quorum sensing) and/or play a role in competitive microflora repression (quorum quenching) in their nature environments.
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Affiliation(s)
- Matouš Čihák
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia
| | - Zdeněk Kameník
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Klára Šmídová
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia.,Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Natalie Bergman
- Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
| | - Oldřich Benada
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia.,Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
| | - Olga Kofroňová
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Kateřina Petříčková
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia
| | - Jan Bobek
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia.,Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia.,Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
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53
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Novakova R, Núñez LE, Homerova D, Knirschova R, Feckova L, Rezuchova B, Sevcikova B, Menéndez N, Morís F, Cortés J, Kormanec J. Increased heterologous production of the antitumoral polyketide mithramycin A by engineered Streptomyces lividans TK24 strains. Appl Microbiol Biotechnol 2017; 102:857-869. [DOI: 10.1007/s00253-017-8642-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 12/15/2022]
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54
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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: 164] [Impact Index Per Article: 23.4] [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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55
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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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56
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Suroto DA, Kitani S, Miyamoto KT, Sakihama Y, Arai M, Ikeda H, Nihira T. Activation of cryptic phthoxazolin A production in Streptomyces avermitilis by the disruption of autoregulator-receptor homologue AvaR3. J Biosci Bioeng 2017; 124:611-617. [PMID: 28728974 DOI: 10.1016/j.jbiosc.2017.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/08/2017] [Accepted: 06/26/2017] [Indexed: 11/28/2022]
Abstract
The genomes of actinomycetes encode many cryptic novel/useful bioactive compounds, but access to these cryptic secondary metabolites remains limited. Streptomyces avermitilis predominantly produces three polyketide antibiotics (avermectin, filipin, and oligomycin) but has the potential to produce more secondary metabolites based on the number of cryptic biosynthetic gene clusters. Here, we extensively investigated the metabolite profiles of a gene disruptant of AvaR3 (an autoregulator receptor homologue), which is involved in the pleiotropic regulation of antibiotic production and cell morphology. Unlike the wild-type strain, the avaR3 mutant accumulated compound 3 in the culture. The chemical structure of compound 3 was elucidated on the basis of various spectroscopic analyses, and was identified as phthoxazolin A, a cellulose synthesis inhibitor. Bioassays demonstrated that compound 3 exerts growth inhibitory activity against a broad range of plant pathogenic oomycetes. Moreover, unlike avermectin production, phthoxazolin A (3) production was negatively controlled by avenolide, a new type of autoregulator in streptomycetes, through the function of AvaR3. These results suggest that the genetic manipulation of autoregulator receptor homologues would be a valuable tool for the discovery of cryptic bioactive compounds.
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Affiliation(s)
- Dian Anggraini Suroto
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigeru Kitani
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kiyoko T Miyamoto
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuko Sakihama
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Takuya Nihira
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; MU-OU Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok 10400, Thailand.
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57
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Sun YQ, Busche T, Rückert C, Paulus C, Rebets Y, Novakova R, Kalinowski J, Luzhetskyy A, Kormanec J, Sekurova ON, Zotchev SB. Development of a Biosensor Concept to Detect the Production of Cluster-Specific Secondary Metabolites. ACS Synth Biol 2017; 6:1026-1033. [PMID: 28221784 DOI: 10.1021/acssynbio.6b00353] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genome mining of actinomycete bacteria aims at the discovery of novel bioactive secondary metabolites that can be developed into drugs. A new repressor-based biosensor to detect activated secondary metabolite biosynthesis gene clusters in Streptomyces was developed. Biosynthetic gene clusters for undecylprodigiosin and coelimycin in the genome of Streptomyces lividans TK24, which encoded TetR-like repressors and appeared to be almost "silent" based on the RNA-seq data, were chosen for the proof-of-principle studies. The bpsA reporter gene for indigoidine synthetase was placed under control of the promotor/operator regions presumed to be controlled by the cluster-associated TetR-like repressors. While the biosensor for undecylprodigiosin turned out to be nonfunctional, the coelimycin biosensor was shown to perform as expected, turning on biosynthesis of indigoidine in response to the concomitant production of coelimycin. The developed reporter system concept can be applied to those cryptic gene clusters that encode metabolite-sensing repressors to speed up discovery of novel bioactive compounds in Streptomyces.
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Affiliation(s)
- Yi-Qian Sun
- Department
of Biotechnology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
- The
Department of Laboratory Medicine, Children’s and Women’s
Health (LBK), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Tobias Busche
- Center
for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Christian Rückert
- Center
for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Constanze Paulus
- Helmholtz Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, 66123 Saarbrücken, Germany
- Universität des Saarlandes, Pharmaceutical Biotechnology, 66123 Saarbrücken, Germany
| | - Yuriy Rebets
- Helmholtz Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, 66123 Saarbrücken, Germany
| | - Renata Novakova
- Institute
of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Jörn Kalinowski
- Center
for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, 66123 Saarbrücken, Germany
- Universität des Saarlandes, Pharmaceutical Biotechnology, 66123 Saarbrücken, Germany
| | - Jan Kormanec
- Institute
of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Olga N. Sekurova
- Department
of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
| | - Sergey B. Zotchev
- Department
of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
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58
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Millan-Oropeza A, Henry C, Blein-Nicolas M, Aubert-Frambourg A, Moussa F, Bleton J, Virolle MJ. Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans. J Proteome Res 2017; 16:2597-2613. [DOI: 10.1021/acs.jproteome.7b00163] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Aaron Millan-Oropeza
- Institute
for
Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud,
Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Céline Henry
- Micalis Institute,
INRA, PAPPSO, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Mélisande Blein-Nicolas
- Génétique
Quantitative et Évolution (GQE) - Le Moulon, INRA, Univ Paris-Sud,
CNRS, AgroParisTech, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Anne Aubert-Frambourg
- Micalis Institute,
INRA, PAPPSO, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Fathi Moussa
- Lip(Sys)2, LETIAM (formerly included in
EA4041 Groupe de Chimie Analytique
de Paris-Sud), Univ. Paris-Sud, Université Paris-Saclay, IUT
d’Orsay, Plateau de Moulon, F-91400 Orsay, France
| | - Jean Bleton
- Lip(Sys)2, LETIAM (formerly included in
EA4041 Groupe de Chimie Analytique
de Paris-Sud), Univ. Paris-Sud, Université Paris-Saclay, IUT
d’Orsay, Plateau de Moulon, F-91400 Orsay, France
| | - Marie-Jöelle Virolle
- Institute
for
Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud,
Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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59
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Hill P, Heberlig GW, Boddy CN. Sampling Terrestrial Environments for Bacterial Polyketides. Molecules 2017; 22:E707. [PMID: 28468277 PMCID: PMC6154731 DOI: 10.3390/molecules22050707] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
Bacterial polyketides are highly biologically active molecules that are frequently used as drugs, particularly as antibiotics and anticancer agents, thus the discovery of new polyketides is of major interest. Since the 1980s discovery of polyketides has slowed dramatically due in large part to the repeated rediscovery of known compounds. While recent scientific and technical advances have improved our ability to discover new polyketides, one key area has been under addressed, namely the distribution of polyketide-producing bacteria in the environment. Identifying environments where producing bacteria are abundant and diverse should improve our ability to discover (bioprospect) new polyketides. This review summarizes for the bioprospector the state-of-the-field in terrestrial microbial ecology. It provides insight into the scientific and technical challenges limiting the application of microbial ecology discoveries for bioprospecting and summarizes key developments in the field that will enable more effective bioprospecting. The major recent efforts by researchers to sample new environments for polyketide discovery is also reviewed and key emerging environments such as insect associated bacteria, desert soils, disease suppressive soils, and caves are highlighted. Finally strategies for taking and characterizing terrestrial samples to help maximize discovery efforts are proposed and the inclusion of non-actinomycetal bacteria in any terrestrial discovery strategy is recommended.
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Affiliation(s)
- Patrick Hill
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Graham W Heberlig
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Christopher N Boddy
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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60
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 356] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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61
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Abstract
The enzymology of 135 assembly lines containing primarily cis-acyltransferase modules is comprehensively analyzed, with greater attention paid to less common phenomena. Diverse online transformations, in which the substrate and/or product of the reaction is an acyl chain bound to an acyl carrier protein, are classified so that unusual reactions can be compared and underlying assembly-line logic can emerge. As a complement to the chemistry surrounding the loading, extension, and offloading of assembly lines that construct primarily polyketide products, structural aspects of the assembly-line machinery itself are considered. This review of assembly-line phenomena, covering the literature up to 2017, should thus be informative to the modular polyketide synthase novice and expert alike.
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Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
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62
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Ye S, Molloy B, Braña AF, Zabala D, Olano C, Cortés J, Morís F, Salas JA, Méndez C. Identification by Genome Mining of a Type I Polyketide Gene Cluster from Streptomyces argillaceus Involved in the Biosynthesis of Pyridine and Piperidine Alkaloids Argimycins P. Front Microbiol 2017; 8:194. [PMID: 28239372 PMCID: PMC5300972 DOI: 10.3389/fmicb.2017.00194] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/26/2017] [Indexed: 12/21/2022] Open
Abstract
Genome mining of the mithramycin producer Streptomyces argillaceus ATCC 12956 revealed 31 gene clusters for the biosynthesis of secondary metabolites, and allowed to predict the encoded products for 11 of these clusters. Cluster 18 (renamed cluster arp) corresponded to a type I polyketide gene cluster related to the previously described coelimycin P1 and streptazone gene clusters. The arp cluster consists of fourteen genes, including genes coding for putative regulatory proteins (a SARP-like transcriptional activator and a TetR-like transcriptional repressor), genes coding for structural proteins (three PKSs, one aminotransferase, two dehydrogenases, two cyclases, one imine reductase, a type II thioesterase, and a flavin reductase), and one gene coding for a hypothetical protein. Identification of encoded compounds by this cluster was achieved by combining several strategies: (i) inactivation of the type I PKS gene arpPIII; (ii) inactivation of the putative TetR-transcriptional repressor arpRII; (iii) cultivation of strains in different production media; and (iv) using engineered strains with higher intracellular concentration of malonyl-CoA. This has allowed identifying six new alkaloid compounds named argimycins P, which were purified and structurally characterized by mass spectrometry and nuclear magnetic resonance spectroscopy. Some argimycins P showed a piperidine ring with a polyene side chain (argimycin PIX); others contain also a fused five-membered ring (argimycins PIV-PVI). Argimycins PI-PII showed a pyridine ring instead, and an additional N-acetylcysteinyl moiety. These compounds seem to play a negative role in growth and colony differentiation in S. argillaceus, and some of them show weak antibiotic activity. A pathway for the biosynthesis of argimycins P is proposed, based on the analysis of proposed enzyme functions and on the structure of compounds encoded by the arp cluster.
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Affiliation(s)
- Suhui Ye
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
| | - Brian Molloy
- 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
| | - Daniel Zabala
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
| | | | | | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo Oviedo, Spain
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63
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Peng H, Wei E, Wang J, Zhang Y, Cheng L, Ma H, Deng Z, Qu X. Deciphering Piperidine Formation in Polyketide-Derived Indolizidines Reveals a Thioester Reduction, Transamination, and Unusual Imine Reduction Process. ACS Chem Biol 2016; 11:3278-3283. [PMID: 27791349 DOI: 10.1021/acschembio.6b00875] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Piperidine and indolizidine are two basic units of alkaloids that are frequently observed in natural and synthetic compounds. Their biosynthesis in natural products is highly conserved and mostly derived from the incorporation of lysine cyclization products. Through in vitro reconstitution, we herein identified a novel pathway involving a group of polyketide-derived indolizidines, which comprises the processes of tandem two-electron thioester reduction, transamination, and imine reduction to convert acyl carrier protein (ACP)-tethered polyketide chains into the piperidine moieties of their indolizidine scaffolds. The enzymes that catalyze the imine reduction are distinct from previous known imine reductases, which have a fold of acyl-CoA dehydrogenase but do not require flavin for reduction. Our results not only provide a new way for the biosynthesis of the basic units of alkaloids but also show a novel class of imine reductases that may benefit the fields of biocatalysis and biomanufacturing.
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Affiliation(s)
- Haidong Peng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, 185
Donghu Road, Wuhan 430071, China
| | - Erman Wei
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, 185
Donghu Road, Wuhan 430071, China
| | - Jiali Wang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, 185
Donghu Road, Wuhan 430071, China
| | - Yanan Zhang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, 185
Donghu Road, Wuhan 430071, China
| | - Lin Cheng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, 185
Donghu Road, Wuhan 430071, China
| | - Hongmin Ma
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, 185
Donghu Road, Wuhan 430071, China
| | - Zixin Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, 185
Donghu Road, Wuhan 430071, China
| | - Xudong Qu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry
of Education, School of Pharmaceutical Sciences, Wuhan University, 185
Donghu Road, Wuhan 430071, China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), 200 North Zhongshan Road, Nanjing 210009, China
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Kuo J, Lynch SR, Liu CW, Xiao X, Khosla C. Partial In Vitro Reconstitution of an Orphan Polyketide Synthase Associated with Clinical Cases of Nocardiosis. ACS Chem Biol 2016; 11:2636-41. [PMID: 27384917 DOI: 10.1021/acschembio.6b00489] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although a few well-characterized polyketide synthases (PKSs) have been functionally reconstituted in vitro from purified protein components, the use of this strategy to decode "orphan" assembly line PKSs has not been described. To begin investigating a PKS found only in Nocardia strains associated with clinical cases of nocardiosis, we reconstituted in vitro its five terminal catalytic modules. In the presence of octanoyl-CoA, malonyl-CoA, NADPH, and S-adenosyl methionine, this pentamodular PKS system yielded unprecedented octaketide and heptaketide products whose structures were partially elucidated using mass spectrometry and NMR spectroscopy. The PKS has several notable features, including a "split, stuttering" module and a terminal reductive release mechanism. Our findings pave the way for further analysis of this unusual biosynthetic gene cluster whose natural product may enhance the infectivity of its producer strains in human hosts.
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Affiliation(s)
- James Kuo
- Department of Chemical Engineering, ‡Department of Chemistry, §Stanford Magnetic
Resonance Laboratory, and ∥Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Stephen R. Lynch
- Department of Chemical Engineering, ‡Department of Chemistry, §Stanford Magnetic
Resonance Laboratory, and ∥Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Corey W. Liu
- Department of Chemical Engineering, ‡Department of Chemistry, §Stanford Magnetic
Resonance Laboratory, and ∥Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Xirui Xiao
- Department of Chemical Engineering, ‡Department of Chemistry, §Stanford Magnetic
Resonance Laboratory, and ∥Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Chaitan Khosla
- Department of Chemical Engineering, ‡Department of Chemistry, §Stanford Magnetic
Resonance Laboratory, and ∥Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
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65
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Awodi UR, Ronan JL, Masschelein J, de Los Santos ELC, Challis GL. Thioester reduction and aldehyde transamination are universal steps in actinobacterial polyketide alkaloid biosynthesis. Chem Sci 2016; 8:411-415. [PMID: 28451186 PMCID: PMC5365063 DOI: 10.1039/c6sc02803a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/21/2016] [Indexed: 11/21/2022] Open
Abstract
Actinobacteria produce a variety of polyketide alkaloids with unusual structures. Recently, it was shown that a type I modular polyketide synthase (PKS) is involved in the assembly of coelimycin P1, a polyketide alkaloid produced by Streptomyces coelicolor M145. However, the mechanisms for converting the product of the PKS to coelimycin P1 remain to be elucidated. Here we show that the C-terminal thioester reductase (TR) domain of the PKS and an ω-transaminase are responsible for release of the polyketide chain as an aldehyde and its subsequent reductive amination. Bioinformatics analyses identified numerous gene clusters in actinobacterial genomes that encode modular PKSs with a C-terminal TR domain and a homolog of the ω-transaminase. These are predicted to direct the biosynthesis of both known and novel polyketide alkaloids, suggesting that reductive chain release and transamination constitutes a conserved mechanism for the biosynthesis of such metabolites.
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Affiliation(s)
- U R Awodi
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - J L Ronan
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - J Masschelein
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - E L C de Los Santos
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
| | - G L Challis
- Department of Chemistry , University of Warwick , Gibbet Hill Road , Coventry , CV4 7AL , UK .
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66
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Urem M, Świątek-Połatyńska MA, Rigali S, van Wezel GP. Intertwining nutrient-sensory networks and the control of antibiotic production inStreptomyces. Mol Microbiol 2016; 102:183-195. [DOI: 10.1111/mmi.13464] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Mia Urem
- Molecular Biotechnology, Institute of Biology, Leiden University; Sylviusweg 72 Leiden 2333BE The Netherlands
| | - Magdalena A. Świątek-Połatyńska
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Strasse 10 Marburg 35043 Germany
| | - Sébastien Rigali
- InBioS, Centre for Protein Engineering; University of Liège; Liège B-4000 Belgium
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University; Sylviusweg 72 Leiden 2333BE The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW); Droevendaalsesteeg 10 Wageningen 6708 PB The Netherlands
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Romero-Rodríguez A, Ruiz-Villafán B, Tierrafría VH, Rodríguez-Sanoja R, Sánchez S. Carbon Catabolite Regulation of Secondary Metabolite Formation and Morphological Differentiation in Streptomyces coelicolor. Appl Biochem Biotechnol 2016; 180:1152-1166. [PMID: 27372741 DOI: 10.1007/s12010-016-2158-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022]
Abstract
In the genus Streptomyces, carbon utilization is of significant importance for the expression of genes involved in morphological differentiation and antibiotic production. However, there is little information about the mechanism involved in these effects. In the present work, it was found that glucose exerted a suppressive effect on the Streptomyces coelicolor actinorhodin (Act) and undecylprodigiosin (Red) production, as well as in its morphological differentiation. Accordingly, using a high-density microarray approach in S. coelicolor grown under glucose repression, at early growth stages, a negative effect was exerted on the transcription of genes involved in Act and Red production, when compared with non-repressive conditions. Seven genes of Act and at least ten genes of Red production were down-regulated by glucose. Stronger repression was observed on the initial steps of antibiotics formation. On the contrary, the coelimycin P1 cluster was up-regulated by glucose. Regarding differentiation, no sporulation was observed in the presence of glucose and expression of a set of genes of the bld cascade was repressed as well as chaplins and rodlins genes. Finally, a series of transcriptional regulators involved in both processes were up- or down-regulated by glucose. This is the first global transcriptomic approach performed to understand the molecular basis of the glucose effect on the synthesis of secondary metabolism and differentiation in the genus Streptomyces. The results of this study are opening new avenues for further exploration.
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Affiliation(s)
- A Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Cd. de Mexico, Mexico
| | - B Ruiz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Cd. de Mexico, Mexico
| | - V H Tierrafría
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Cd. de Mexico, Mexico
| | - R Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Cd. de Mexico, Mexico
| | - S Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Cd. de Mexico, Mexico.
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Ordóñez-Robles M, Rodríguez-García A, Martín JF. Target genes of the Streptomyces tsukubaensis FkbN regulator include most of the tacrolimus biosynthesis genes, a phosphopantetheinyl transferase and other PKS genes. Appl Microbiol Biotechnol 2016; 100:8091-103. [PMID: 27357227 DOI: 10.1007/s00253-016-7696-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/15/2016] [Accepted: 06/17/2016] [Indexed: 01/01/2023]
Abstract
Tacrolimus (FK506) is a 23-membered macrolide immunosuppressant used in current clinics. Understanding how the tacrolimus biosynthetic gene cluster is regulated is important to increase its industrial production. Here, we analysed the effect of the disruption of fkbN (encoding a LAL-type positive transcriptional regulator) on the whole transcriptome of the tacrolimus producer Streptomyces tsukubaensis using microarray technology. Transcription of fkbN in the wild type strain increases from 70 h of cultivation reaching a maximum at 89 h, prior to the onset of tacrolimus biosynthesis. Disruption of fkbN in S. tsukubaensis does not affect growth but prevents tacrolimus biosynthesis. Inactivation of fkbN reduces the transcription of most of the fkb cluster genes, including some all (for allylmalonyl-CoA biosynthesis) genes but does not affect expression of allMNPOS or fkbR (encoding a LysR-type regulator). Disruption of fkbN does not suppress transcription of the cistron tcs6-fkbQ-fkbN; thus, FkbN self-regulates only weakly its own expression. Interestingly, inactivation of FkbN downregulates the transcription of a 4'-phosphopantetheinyl transferase coding gene, which product is involved in tacrolimus biosynthesis, and upregulates the transcription of a gene cluster containing a cpkA orthologous gene, which encodes a PKS involved in coelimycin P1 biosynthesis in Streptomyces coelicolor. We propose an information theory-based model for FkbN binding sequences. The consensus FkbN binding sequence consists of 14 nucleotides with dyad symmetry containing two conserved inverted repeats of 7 nt each. This FkbN target sequence is present in the promoters of FkbN-regulated genes.
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Affiliation(s)
- María Ordóñez-Robles
- Área de Microbiología, Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, 24071, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, León, 24006, Spain
| | - Antonio Rodríguez-García
- Área de Microbiología, Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, 24071, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, León, 24006, Spain
| | - Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, 24071, Spain.
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Chen S, Zheng G, Zhu H, He H, Chen L, Zhang W, Jiang W, Lu Y. Roles of two-component system AfsQ1/Q2 in regulating biosynthesis of the yellow-pigmented coelimycin P2 inStreptomyces coelicolor. FEMS Microbiol Lett 2016; 363:fnw160. [DOI: 10.1093/femsle/fnw160] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2016] [Indexed: 12/23/2022] Open
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Niu G, Chater KF, Tian Y, Zhang J, Tan H. Specialised metabolites regulating antibiotic biosynthesis in Streptomyces spp. FEMS Microbiol Rev 2016; 40:554-73. [PMID: 27288284 DOI: 10.1093/femsre/fuw012] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2016] [Indexed: 12/11/2022] Open
Abstract
Streptomyces bacteria are the major source of antibiotics and other secondary metabolites. Various environmental and physiological conditions affect the onset and level of production of each antibiotic by influencing concentrations of the ligands for conserved global regulatory proteins. In addition, as reviewed here, well-known autoregulators such as γ-butyrolactones, themselves products of secondary metabolism, accumulate late in growth to concentrations allowing their effective interaction with cognate binding proteins, in a necessary prelude to antibiotic biosynthesis. Most autoregulator binding proteins target the conserved global regulatory gene adpA, and/or regulatory genes for 'cluster-situated regulators' (CSRs) linked to antibiotic biosynthetic gene clusters. It now appears that some CSRs bind intermediates and end products of antibiotic biosynthesis, with regulatory effects interwoven with those of autoregulators. These ligands can exert cross-pathway effects within producers of more than one antibiotic, and when excreted into the extracellular environment may have population-wide effects on production, and mediate interactions with neighbouring microorganisms in natural communities, influencing speciation. Greater understanding of these autoregulatory and cross-regulatory activities may aid the discovery of new signalling molecules and their use in activating cryptic antibiotic biosynthetic pathways.
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Affiliation(s)
- Guoqing Niu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Keith F Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Yuqing Tian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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71
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Romero-Rodríguez A, Rocha D, Ruiz-Villafan B, Tierrafría V, Rodríguez-Sanoja R, Segura-González D, Sánchez S. Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor. BMC Microbiol 2016; 16:77. [PMID: 27121083 PMCID: PMC4848846 DOI: 10.1186/s12866-016-0690-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 04/14/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND In the genus Streptomyces, one of the most remarkable control mechanisms of physiological processes is carbon catabolite repression (CCR). This mechanism regulates the expression of genes involved in the uptake and utilization of alternative carbon sources. CCR also affects the synthesis of secondary metabolites and morphological differentiation. Even when the outcome effect of CCR in different bacteria is the same, their essential mechanisms can be quite different. In several streptomycetes glucose kinase (Glk) represents the main glucose phosphorylating enzyme and has been regarded as a regulatory protein in CCR. To evaluate the paradigmatic model proposed for CCR in Streptomyces, a high-density microarray approach was applied to Streptomyces coelicolor M145, under repressed and non-repressed conditions. The transcriptomic study was extended to assess the ScGlk role in this model by comparing the transcriptomic profile of S. coelicolor M145 with that of a ∆glk mutant derived from the wild-type strain, complemented with a heterologous glk gene from Zymomonas mobilis (Zmglk), insensitive to CCR but able to grow in glucose (ScoZm strain). RESULTS Microarray experiments revealed that glucose influenced the expression of 651 genes. Interestingly, even when the ScGlk protein does not have DNA binding domains and the glycolytic flux was restored by a heterologous glucokinase, the ScGlk replacement modified the expression of 134 genes. From these, 91 were also affected by glucose while 43 appeared to be under the control of ScGlk. This work identified the expression of S. coelicolor genes involved in primary metabolism that were influenced by glucose and/or ScGlk. Aside from describing the metabolic pathways influenced by glucose and/or ScGlk, several unexplored transcriptional regulators involved in the CCR mechanism were disclosed. CONCLUSIONS The transcriptome of a classical model of CCR was studied in S. coelicolor to differentiate between the effects due to glucose or ScGlk in this regulatory mechanism. Glucose elicited important metabolic and transcriptional changes in this microorganism. While its entry and flow through glycolysis and pentose phosphate pathway were stimulated, the gluconeogenesis was inhibited. Glucose also triggered the CCR by repressing transporter systems and the transcription of enzymes required for secondary carbon sources utilization. Our results confirm and update the agar model of the CCR in Streptomyces and its dependence on the ScGlk per se. Surprisingly, the expected regulatory function of ScGlk was not found to be as global as thought before (only 43 out of 779 genes were affected), although may be accompanied or coordinated by other transcriptional regulators. Aside from describing the metabolic pathways influenced by glucose and/or ScGlk, several unexplored transcriptional regulators involved in the CCR mechanism were disclosed. These findings offer new opportunities to study and understand the CCR in S. coelicolor by increasing the number of known glucose and ScGlk -regulated pathways and a new set of putative regulatory proteins possibly involved or controlling the CCR.
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Affiliation(s)
- Alba Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico
| | - Diana Rocha
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico
| | - Beatriz Ruiz-Villafan
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico
| | - Víctor Tierrafría
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico
| | - Romina Rodríguez-Sanoja
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico
| | - Daniel Segura-González
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ave. Universidad 2001, Cuernavaca, Mor. 62210, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico.
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Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk HP, Clément C, Ouhdouch Y, van Wezel GP. Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev 2016; 80:1-43. [PMID: 26609051 PMCID: PMC4711186 DOI: 10.1128/mmbr.00019-15] [Citation(s) in RCA: 947] [Impact Index Per Article: 118.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.
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Affiliation(s)
- Essaid Ait Barka
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Parul Vatsa
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Lisa Sanchez
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Nathalie Gaveau-Vaillant
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Cedric Jacquard
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christophe Clément
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Yder Ouhdouch
- Faculté de Sciences Semlalia, Université Cadi Ayyad, Laboratoire de Biologie et de Biotechnologie des Microorganismes, Marrakesh, Morocco
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Sylvius Laboratories, Leiden University, Leiden, The Netherlands
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Yu L, Gao W, Li S, Pan Y, Liu G. GntR family regulator SCO6256 is involved in antibiotic production and conditionally regulates the transcription of myo-inositol catabolic genes in Streptomyces coelicolor A3(2). MICROBIOLOGY-SGM 2016; 162:537-551. [PMID: 26744083 DOI: 10.1099/mic.0.000235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
SCO6256 belongs to the GntR family and shows 74% identity with SCO6974, which is the repressor of myo-inositol catabolism in Streptomyces coelicolor A3(2). Disruption of SCO6256 significantly enhanced the transcription of myo-inositol catabolic genes in R2YE medium. The purified recombinant SCO6256 directly bound to the upstream regions of SCO2727, SCO6978 and SCO6985, as well as its encoding gene. Footprinting assays demonstrated that SCO6256 bound to the same sites in the myo-inositol catabolic gene cluster as SCO6974. The expression of SCO6256 was repressed by SCO6974 in minimal medium with myo-inositol as the carbon source, but not in R2YE medium. Glutathione-S-transferase pull-down assays demonstrated that SCO6974 and SCO6256 interacted with each other; and both of the proteins controlled the transcription of myo-inositol catabolic genes in R2YE medium. These results indicated SCO6256 regulates the transcription of myo-inositol catabolic genes in coordination with SCO6974 in R2YE medium. In addition, SCO6256 negatively regulated the production of actinorhodin and calcium-dependent antibiotic via control of the transcription of actII-ORF4 and cdaR. SCO6256 bound to the upstream region of cdaR and the binding sequence was proved to be TTTCGGCACGCAGACAT, which was further confirmed through base substitution. Four putative targets (SCO2652, SCO4034, SCO4237 and SCO6377) of SCO6256 were found by screening the genome sequence of Strep. coelicolor A3(2) based on the conserved binding motif, and confirmed by transcriptional analysis and electrophoretic mobility shift assays. These results revealed that SCO6256 is involved in the regulation of myo-inositol catabolic gene transcription and antibiotic production in Strep. coelicolor A3(2).
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Affiliation(s)
- Lingjun Yu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,University of the Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wenyan Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuxian Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuanyuan Pan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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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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75
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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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76
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Rinkel J, Dickschat JS. Recent highlights in biosynthesis research using stable isotopes. Beilstein J Org Chem 2015; 11:2493-508. [PMID: 26734097 PMCID: PMC4685789 DOI: 10.3762/bjoc.11.271] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/23/2015] [Indexed: 02/03/2023] Open
Abstract
The long and successful history of isotopic labeling experiments within natural products research has both changed and deepened our understanding of biosynthesis. As demonstrated in this article, the usage of isotopes is not at all old-fashioned, but continues to give important insights into biosynthetic pathways of secondary metabolites. This review with 85 cited references is structured by separate discussions of compounds from different classes including polyketides, non-ribosomal peptides, their hybrids, terpenoids, and aromatic compounds formed via the shikimate pathway. The text does not aim at a comprehensive overview, but instead a selection of recent important examples of isotope usage within biosynthetic studies is presented, with a special emphasis on mechanistic surprises.
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Affiliation(s)
- Jan Rinkel
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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77
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Li X, Wang J, Li S, Ji J, Wang W, Yang K. ScbR- and ScbR2-mediated signal transduction networks coordinate complex physiological responses in Streptomyces coelicolor. Sci Rep 2015; 5:14831. [PMID: 26442964 PMCID: PMC4595836 DOI: 10.1038/srep14831] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/07/2015] [Indexed: 12/21/2022] Open
Abstract
In model organism Streptomyces coelicolor, γ-butyrolactones (GBLs) and antibiotics were recognized as signalling molecules playing fundamental roles in intra- and interspecies communications. To dissect the GBL and antibiotic signalling networks systematically, the in vivo targets of their respective receptors ScbR and ScbR2 were identified on a genome scale by ChIP-seq. These identified targets encompass many that are known to play important roles in diverse cellular processes (e.g. gap1, pyk2, afsK, nagE2, cdaR, cprA, cprB, absA1, actII-orf4, redZ, atrA, rpsL and sigR), and they formed regulatory cascades, sub-networks and feedforward loops to elaborately control key metabolite processes, including primary and secondary metabolism, morphological differentiation and stress response. Moreover, interplay among ScbR, ScbR2 and other regulators revealed intricate cross talks between signalling pathways triggered by GBLs, antibiotics, nutrient availability and stress. Our work provides a global view on the specific responses that could be triggered by GBL and antibiotic signals in S. coelicolor, among which the main echo was the change of production profile of endogenous antibiotics and antibiotic signals manifested a role to enhance bacterial stress tolerance as well, shedding new light on GBL and antibiotic signalling networks widespread among streptomycetes.
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Affiliation(s)
- Xiao Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Juan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Shanshan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Junjie Ji
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Keqian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
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78
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Barajas JF, Phelan RM, Schaub AJ, Kliewer JT, Kelly PJ, Jackson DR, Luo R, Keasling JD, Tsai SC. Comprehensive Structural and Biochemical Analysis of the Terminal Myxalamid Reductase Domain for the Engineered Production of Primary Alcohols. ACTA ACUST UNITED AC 2015; 22:1018-29. [PMID: 26235055 DOI: 10.1016/j.chembiol.2015.06.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/05/2015] [Accepted: 06/22/2015] [Indexed: 01/22/2023]
Abstract
The terminal reductase (R) domain from the non-ribosomal peptide synthetase (NRPS) module MxaA in Stigmatella aurantiaca Sga15 catalyzes a non-processive four-electron reduction to produce the myxalamide family of secondary metabolites. Despite widespread use in nature, a lack of structural and mechanistic information concerning reductive release from polyketide synthase (PKS) and NRPS assembly lines principally limits our ability to redesign R domains with altered or improved activity. Here we report crystal structures for MxaA R, both in the absence and, for the first time, in the presence of the NADPH cofactor. Molecular dynamics simulations were employed to provide a deeper understanding of this domain and further identify residues critical for structural integrity, substrate binding, and catalysis. Aggregate computational and structural findings provided a basis for mechanistic investigations and, in the process, delivered a rationally altered variant with improved activity toward highly reduced substrates.
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Affiliation(s)
- Jesus F Barajas
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Ryan M Phelan
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA
| | - Andrew J Schaub
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jaclyn T Kliewer
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Peter J Kelly
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - David R Jackson
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Jay D Keasling
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA; Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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79
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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: 615] [Impact Index Per Article: 68.3] [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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80
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Traxler MF, Kolter R. Natural products in soil microbe interactions and evolution. Nat Prod Rep 2015; 32:956-70. [DOI: 10.1039/c5np00013k] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gram positive bacteria from the soil have historically been a deep source of useful natural products. This article considers how natural products may mediate microbial interactions in the soil environment.
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Affiliation(s)
- Matthew F. Traxler
- Dept. of Plant and Microbial Biology
- University of California at Berkeley
- Berkeley
- USA
| | - Roberto Kolter
- Dept. of Microbiology and Immunobiology
- Harvard Medical School
- Boston
- USA
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81
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A reinvigorated era of bacterial secondary metabolite discovery. Curr Opin Chem Biol 2014; 24:104-11. [PMID: 25461728 DOI: 10.1016/j.cbpa.2014.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 10/23/2014] [Indexed: 11/20/2022]
Abstract
Secondary metabolite discovery from bacteria has become increasingly successful in the last decade due to the advancement of integrated genetic-based, spectrometric-based and informatics-based techniques. Microbes and their unique metabolic outputs have been widely studied since the beginning of modern medicine; however, it is well known that the current repertoire of secondary metabolites, or more commonly natural products, is incomplete and the understanding of natural product-mediated intracellular dialog is in its infancy. Here, we highlight the present state of bacterial metabolomics including compound discovery approaches and new strategies for probing the role of these molecules within communication networks.
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82
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Production of specialized metabolites by Streptomyces coelicolor A3(2). ADVANCES IN APPLIED MICROBIOLOGY 2014; 89:217-66. [PMID: 25131404 DOI: 10.1016/b978-0-12-800259-9.00006-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The actinomycetes are well-known bioactive natural product producers, comprising the Streptomycetes, the richest drug-prolific family in all kingdoms, producing therapeutic compounds for the areas of infection, cancer, circulation, and immunity. Completion and annotation of many actinomycete genomes has highlighted further how proficient these bacteria are in specialized metabolism, which have been largely underexploited in traditional screening programs. The genome sequence of the model strain Streptomyces coelicolor A3(2), and subsequent development of genomics-driven approaches to understand its large specialized metabolome, has been key in unlocking the high potential of specialized metabolites for natural product genomics-based drug discovery. This review discusses systematically the biochemistry and genetics of each of the specialized metabolites of S. coelicolor and describes metabolite transport processes for excretion and complex regulatory patterns controlling biosynthesis.
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83
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Recent advances in genome-based polyketide discovery. Curr Opin Biotechnol 2014; 29:107-15. [DOI: 10.1016/j.copbio.2014.03.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/11/2014] [Accepted: 03/14/2014] [Indexed: 11/27/2022]
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84
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Kotowska M, Pawlik K. Roles of type II thioesterases and their application for secondary metabolite yield improvement. Appl Microbiol Biotechnol 2014; 98:7735-46. [PMID: 25081554 PMCID: PMC4147253 DOI: 10.1007/s00253-014-5952-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 12/31/2022]
Abstract
A large number of antibiotics and other industrially important microbial secondary metabolites are synthesized by polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). These multienzymatic complexes provide an enormous flexibility in formation of diverse chemical structures from simple substrates, such as carboxylic acids and amino acids. Modular PKSs and NRPSs, often referred to as megasynthases, have brought about a special interest due to the colinearity between enzymatic domains in the proteins working as an “assembly line” and the chain elongation and modification steps. Extensive efforts toward modified compound biosynthesis by changing organization of PKS and NRPS domains in a combinatorial manner laid good grounds for rational design of new structures and their controllable biosynthesis as proposed by the synthetic biology approach. Despite undeniable progress made in this field, the yield of such “unnatural” natural products is often not satisfactory. Here, we focus on type II thioesterases (TEIIs)—discrete hydrolytic enzymes often encoded within PKS and NRPS gene clusters which can be used to enhance product yield. We review diverse roles of TEIIs (removal of aberrant residues blocking the megasynthase, participation in substrate selection, intermediate, and product release) and discuss their application in new biosynthetic systems utilizing PKS and NRPS parts.
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Affiliation(s)
- Magdalena Kotowska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Rudolfa Weigla 12, 53-114, Wroclaw, Poland,
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85
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Cook C, Martin L, Bastow R. Opportunities in plant synthetic biology. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1921-6. [PMID: 24502956 DOI: 10.1093/jxb/eru013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.
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Affiliation(s)
- Charis Cook
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
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86
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Heterologous expression of natural product biosynthetic gene clusters in Streptomyces coelicolor: from genome mining to manipulation of biosynthetic pathways. ACTA ACUST UNITED AC 2014; 41:425-31. [DOI: 10.1007/s10295-013-1348-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/12/2013] [Indexed: 12/22/2022]
Abstract
Abstract
Heterologous gene expression is one of the main strategies used to access the full biosynthetic potential of actinomycetes, as well as to study the metabolic pathways of natural product biosynthesis and to create unnatural pathways. Streptomyces coelicolor A3(2) is the most studied member of the actinomycetes, bacteria renowned for their prolific capacity to synthesize a wide range of biologically active specialized metabolites. We review here the use of strains of this species for the heterologous production of structurally diverse actinomycete natural products.
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87
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Nett M. Genome mining: concept and strategies for natural product discovery. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2014; 99:199-245. [PMID: 25296440 DOI: 10.1007/978-3-319-04900-7_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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88
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Two-component systems in Streptomyces: key regulators of antibiotic complex pathways. Microb Cell Fact 2013; 12:127. [PMID: 24354561 PMCID: PMC3881020 DOI: 10.1186/1475-2859-12-127] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/16/2013] [Indexed: 01/16/2023] Open
Abstract
Streptomyces, the main antibiotic-producing bacteria, responds to changing environmental conditions through a complex sensing mechanism and two-component systems (TCSs) play a crucial role in this extraordinary "sensing" device.Moreover, TCSs are involved in the biosynthetic control of a wide range of secondary metabolites, among them commercial antibiotics. Increased knowledge about TCSs can be a powerful asset in the manipulation of bacteria through genetic engineering with a view to obtaining higher efficiencies in secondary metabolite production. In this review we summarise the available information about Streptomyces TCSs, focusing specifically on their connections to antibiotic production.
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89
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Challis GL. Exploitation of the Streptomyces coelicolor A3(2) genome sequence for discovery of new natural products and biosynthetic pathways. J Ind Microbiol Biotechnol 2013; 41:219-32. [PMID: 24322202 DOI: 10.1007/s10295-013-1383-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 11/15/2013] [Indexed: 11/28/2022]
Abstract
Streptomyces, and related genera of Actinobacteria, are renowned for their ability to produce antibiotics and other bioactive natural products with a wide range of applications in medicine and agriculture. Streptomyces coelicolor A3(2) is a model organism that has been used for more than five decades to study the genetic and biochemical basis for the production of bioactive metabolites. In 2002, the complete genome sequence of S. coelicolor was published. This greatly accelerated progress in understanding the biosynthesis of metabolites known or suspected to be produced by S. coelicolor and revealed that streptomycetes have far greater potential to produce bioactive natural products than suggested by classical bioassay-guided isolation studies. In this article, efforts to exploit the S. coelicolor genome sequence for the discovery of novel natural products and biosynthetic pathways are summarized.
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Affiliation(s)
- Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK,
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90
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Aigle B, Lautru S, Spiteller D, Dickschat JS, Challis GL, Leblond P, Pernodet JL. Genome mining of Streptomyces ambofaciens. J Ind Microbiol Biotechnol 2013; 41:251-63. [PMID: 24258629 DOI: 10.1007/s10295-013-1379-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/30/2013] [Indexed: 02/04/2023]
Abstract
Since the discovery of the streptomycin produced by Streptomyces griseus in the middle of the last century, members of this bacterial genus have been largely exploited for the production of secondary metabolites with wide uses in medicine and in agriculture. They have even been recognized as one of the most prolific producers of natural products among microorganisms. With the onset of the genomic era, it became evident that these microorganisms still represent a major source for the discovery of novel secondary metabolites. This was highlighted with the complete genome sequencing of Streptomyces coelicolor A3(2) which revealed an unexpected potential of this organism to synthesize natural products undetected until then by classical screening methods. Since then, analysis of sequenced genomes from numerous Streptomyces species has shown that a single species can carry more than 30 secondary metabolite gene clusters, reinforcing the idea that the biosynthetic potential of this bacterial genus is far from being fully exploited. This review highlights our knowledge on the potential of Streptomyces ambofaciens ATCC 23877 to synthesize natural products. This industrial strain was known for decades to only produce the drug spiramycin and another antibacterial compound, congocidine. Mining of its genome allowed the identification of 23 clusters potentially involved in the production of other secondary metabolites. Studies of some of these clusters resulted in the characterization of novel compounds and of previously known compounds but never characterized in this Streptomyces species. In addition, genome mining revealed that secondary metabolite gene clusters of phylogenetically closely related Streptomyces are mainly species-specific.
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Affiliation(s)
- Bertrand Aigle
- Université de Lorraine, Dynamique des Génomes et Adaptation Microbienne, UMR 1128, 54506, Vandœuvre-lès-Nancy, France,
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91
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GouR, a TetR family transcriptional regulator, coordinates the biosynthesis and export of gougerotin in Streptomyces graminearus. Appl Environ Microbiol 2013; 80:714-22. [PMID: 24242236 DOI: 10.1128/aem.03003-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Gougerotin is a peptidyl nucleoside antibiotic. It functions as a specific inhibitor of protein synthesis by binding ribosomal peptidyl transferase and exhibits a broad spectrum of biological activities. gouR, situated in the gougerotin biosynthetic gene cluster, encodes a TetR family transcriptional regulatory protein. Gene disruption and genetic complementation revealed that gouR plays an important role in the biosynthesis of gougerotin. Transcriptional analysis suggested that GouR represses the transcription of the gouL-to-gouB operon consisting of 11 structural genes and activates the transcription of the major facilitator superfamily (MFS) transporter gene (gouM). Electrophoresis mobility shift assays (EMSAs) and DNase I footprinting experiments showed that GouR has specific DNA-binding activity for the promoter regions of gouL, gouM, and gouR. Our data suggested that GouR modulates gougerotin production by coordinating its biosynthesis and export in Streptomyces graminearus.
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92
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Rebets Y, Brötz E, Tokovenko B, Luzhetskyy A. Actinomycetes biosynthetic potential: how to bridge in silico and in vivo? J Ind Microbiol Biotechnol 2013; 41:387-402. [PMID: 24127068 DOI: 10.1007/s10295-013-1352-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
Abstract
Actinomycetes genome sequencing and bioinformatic analyses revealed a large number of "cryptic" gene clusters coding for secondary metabolism. These gene clusters have the potential to increase the chemical diversity of natural products. Indeed, reexamination of well-characterized actinomycetes strains revealed a variety of hidden treasures. Growing information about this metabolic diversity has promoted further development of strategies to discover novel biologically active compounds produced by actinomycetes. This new task for actinomycetes genetics requires the development and use of new approaches and tools. Application of synthetic biology approaches led to the development of a set of strategies and tools to satisfy these new requirements. In this review, we discuss strategies and methods to discover small molecules produced by these fascinating bacteria and also discuss a variety of genetic instruments and regulatory elements used to activate secondary metabolism cryptic genes for the overproduction of these metabolites.
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Affiliation(s)
- Yuriy Rebets
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus, Building C2.3, Saarbrücken, 66123, Germany
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93
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Moody MJ, Young RA, Jones SE, Elliot MA. Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria. BMC Genomics 2013; 14:558. [PMID: 23947565 PMCID: PMC3765725 DOI: 10.1186/1471-2164-14-558] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/13/2013] [Indexed: 12/11/2022] Open
Abstract
Background Non-coding RNAs (ncRNAs) are key regulatory elements that control a wide range of cellular processes in all bacteria in which they have been studied. Taking advantage of recent technological innovations, we set out to fully explore the ncRNA potential of the multicellular, antibiotic-producing Streptomyces bacteria. Results Using a comparative RNA sequencing analysis of three divergent model streptomycetes (S. coelicolor, S. avermitilis and S. venezuelae), we discovered hundreds of novel cis-antisense RNAs and intergenic small RNAs (sRNAs). We identified a ubiquitous antisense RNA species that arose from the overlapping transcription of convergently-oriented genes; we termed these RNA species ‘cutoRNAs’, for convergent untranslated overlapping RNAs. Conservation between different classes of ncRNAs varied greatly, with sRNAs being more conserved than antisense RNAs. Many species-specific ncRNAs, including many distinct cutoRNA pairs, were located within antibiotic biosynthetic clusters, including the actinorhodin, undecylprodigiosin, and coelimycin clusters of S. coelicolor, the chloramphenicol cluster of S. venezuelae, and the avermectin cluster of S. avermitilis. Conclusions These findings indicate that ncRNAs, including a novel class of antisense RNA, may exert a previously unrecognized level of regulatory control over antibiotic production in these bacteria. Collectively, this work has dramatically expanded the ncRNA repertoire of three Streptomyces species and has established a critical foundation from which to investigate ncRNA function in this medically and industrially important bacterial genus.
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Affiliation(s)
- Matthew J Moody
- Department of Biology and Michael G, DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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94
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Lian W, Upadhyaya P, Rhodes CA, Liu Y, Pei D. Screening bicyclic peptide libraries for protein-protein interaction inhibitors: discovery of a tumor necrosis factor-α antagonist. J Am Chem Soc 2013; 135:11990-5. [PMID: 23865589 PMCID: PMC3856571 DOI: 10.1021/ja405106u] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions represent a new class of exciting but challenging drug targets, because their large, flat binding sites lack well-defined pockets for small molecules to bind. We report here a methodology for chemical synthesis and screening of large combinatorial libraries of bicyclic peptides displayed on rigid small-molecule scaffolds. With planar trimesic acid as the scaffold, the resulting bicyclic peptides are effective for binding to protein surfaces such as the interfaces of protein-protein interactions. Screening of a bicyclic peptide library against tumor necrosis factor-α (TNFα) identified a potent antagonist that inhibits the TNFα-TNFα receptor interaction and protects cells from TNFα-induced cell death. Bicyclic peptides of this type may provide a general solution for inhibition of protein-protein interactions.
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Affiliation(s)
- Wenlong Lian
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
| | - Punit Upadhyaya
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
| | - Curran A. Rhodes
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
| | - Yusen Liu
- Center for Perinatal Research, The Research Institute at Nationwide Children’s Hospital, Department of Pediatrics, The Ohio State University College of Medicine, 700 Children’s Drive, Columbus, OH 43205, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
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95
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Abstract
Well-characterized promoters are essential tools for metabolic engineering and synthetic biology. In Streptomyces coelicolor, the native kasOp is a temporally expressed promoter strictly controlled by two regulators, ScbR and ScbR2. In this work, first, kasOp was engineered to remove a common binding site of ScbR and ScbR2 upstream of its core region, thus generating a stronger promoter, kasOp3. Second, another ScbR binding site internal to the kasOp3 core promoter region was abolished by random mutation and screening of the mutant library to obtain the strongest promoter, kasOp* (where the asterisk is used to distinguish the engineered promoter from the native promoter). The activities of kasOp* were compared with those of two known strong promoters, ermEp* and SF14p, in three Streptomyces species. kasOp* showed the highest activity at the transcription and protein levels in all three hosts. Furthermore, relative to ermEp* and SF14p, kasOp* was shown to confer the highest actinorhodin production level when used to drive the expression of actII-ORF4 in S. coelicolor. Therefore, kasOp* is a simple and well-defined strong promoter useful for gene overexpression in streptomycetes.
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96
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Craney A, Ahmed S, Nodwell J. Towards a new science of secondary metabolism. J Antibiot (Tokyo) 2013; 66:387-400. [PMID: 23612726 DOI: 10.1038/ja.2013.25] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/12/2013] [Accepted: 02/12/2013] [Indexed: 12/20/2022]
Abstract
Secondary metabolites are a reliable and very important source of medicinal compounds. While these molecules have been mined extensively, genome sequencing has suggested that there is a great deal of chemical diversity and bioactivity that remains to be discovered and characterized. A central challenge to the field is that many of the novel or poorly understood molecules are expressed at low levels in the laboratory-such molecules are often described as the 'cryptic' secondary metabolites. In this review, we will discuss evidence that research in this field has provided us with sufficient knowledge and tools to express and purify any secondary metabolite of interest. We will describe 'unselective' strategies that bring about global changes in secondary metabolite output as well as 'selective' strategies where a specific biosynthetic gene cluster of interest is manipulated to enhance the yield of a single product.
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Affiliation(s)
- Arryn Craney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael Degroote Institute for Infectious Diseases Research, Hamilton, Ontario, Canada
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97
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Yagüe P, Rodríguez-García A, López-García MT, Martín JF, Rioseras B, Sánchez J, Manteca A. Transcriptomic analysis of Streptomyces coelicolor differentiation in solid sporulating cultures: first compartmentalized and second multinucleated mycelia have different and distinctive transcriptomes. PLoS One 2013; 8:e60665. [PMID: 23555999 PMCID: PMC3610822 DOI: 10.1371/journal.pone.0060665] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 03/01/2013] [Indexed: 11/18/2022] Open
Abstract
Streptomycetes are very important industrial bacteria, which produce two thirds of all clinically relevant secondary metabolites. They have a complex developmental-cycle in which an early compartmentalized mycelium (MI) differentiates to a multinucleated mycelium (MII) that grows inside the culture medium (substrate mycelium) until it starts to growth into the air (aerial mycelium) and ends up forming spores. Streptomyces developmental studies have focused mainly on the later stages of MII differentiation (aerial mycelium and sporulation), with regulation of pre-sporulation stages (MI/MII transition) essentially unknown. This work represents the first study of the Streptomyces MI transcriptome, analyzing how it differs from the MII transcriptome. We have used a very conservative experimental approach to fractionate MI from MII and quantify gene expressions. The expression of well characterized key developmental/metabolic genes involved in bioactive compound production (actinorhodin, undecylprodigiosin, calcium-dependent antibiotic, cpk, geosmin) or hydrophobic cover formation-sporulation (bld, whi, wbl, rdl, chp, ram) was correlated with MII differentiation. Additionally, 122 genes conserved in the Streptomyces genus, whose biological function had not been previously characterized, were found to be differentially expressed (more than 4-fold) in MI or MII. These genes encoded for putative regulatory proteins (transcriptional regulators, kinases), as well as hypothetical proteins. Knowledge about differences between the MI (vegetative) and MII (reproductive) transcriptomes represents a huge advance in Streptomyces biology that will make future experiments possible aimed at characterizing the biochemical pathways controlling pre-sporulation developmental stages and activation of secondary metabolism in Streptomyces.
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Affiliation(s)
- Paula Yagüe
- Área de Microbiología, Departamento de Biología Funcional and Instituto Universitario de Biotecnología de Asturias (IUBA), Universidad de Oviedo, Oviedo, Spain
| | | | - María T. López-García
- Área de Microbiología, Departamento de Biología Funcional and Instituto Universitario de Biotecnología de Asturias (IUBA), Universidad de Oviedo, Oviedo, Spain
| | - Juan F. Martín
- Instituto de Biotecnología de León (INBIOTEC), León, Spain
| | - Beatriz Rioseras
- Área de Microbiología, Departamento de Biología Funcional and Instituto Universitario de Biotecnología de Asturias (IUBA), Universidad de Oviedo, Oviedo, Spain
| | - Jesús Sánchez
- Área de Microbiología, Departamento de Biología Funcional and Instituto Universitario de Biotecnología de Asturias (IUBA), Universidad de Oviedo, Oviedo, Spain
| | - Angel Manteca
- Área de Microbiología, Departamento de Biología Funcional and Instituto Universitario de Biotecnología de Asturias (IUBA), Universidad de Oviedo, Oviedo, Spain
- * E-mail:
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98
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Dunbar KL, Mitchell DA. Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis. ACS Chem Biol 2013; 8:473-87. [PMID: 23286465 DOI: 10.1021/cb3005325] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature's synthetic potential is revealed. This Review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions.
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Affiliation(s)
- Kyle L. Dunbar
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
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99
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Antimicrobial drug resistance affects broad changes in metabolomic phenotype in addition to secondary metabolism. Proc Natl Acad Sci U S A 2013; 110:2336-41. [PMID: 23341601 DOI: 10.1073/pnas.1218524110] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria develop resistance to many classes of antibiotics vertically, by engendering mutations in genes encoding transcriptional and translational apparatus. These severe adaptations affect global transcription, translation, and the correspondingly affected metabolism. Here, we characterize metabolome scale changes in transcriptional and translational mutants in a genomically characterized Nocardiopsis, a soil-derived actinomycete, in stationary phase. Analysis of ultra-performance liquid chromatography-ion mobility-mass spectrometry metabolomic features from a cohort of streptomycin- and rifampicin-resistant mutants grown in the absence of antibiotics exhibits clear metabolomic speciation, and loadings analysis catalogs a marked change in metabolic phenotype. Consistent with derepression, up to 311 features are observed in antibiotic-resistant mutants that are not detected in their progenitors. Mutants demonstrate changes in primary metabolism, such as modulation of fatty acid composition and the increased production of the osmoprotectant ectoine, in addition to the presence of abundant emergent potential secondary metabolites. Isolation of three of these metabolites followed by structure elucidation demonstrates them to be an unusual polyketide family with a previously uncharacterized xanthene framework resulting from sequential oxidative carbon skeletal rearrangements. Designated as "mutaxanthenes," this family can be correlated to a type II polyketide gene cluster in the producing organism. Taken together, these data suggest that biosynthetic pathway derepression is a general consequence of some antibiotic resistance mutations.
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100
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