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Pai H, Liu Y, Zhang C, Su J, Lu W. Effects of the pleiotropic regulator DasR on lincomycin production in Streptomyces lincolnensis. Appl Microbiol Biotechnol 2024; 108:373. [PMID: 38878095 PMCID: PMC11180011 DOI: 10.1007/s00253-024-13201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 06/19/2024]
Abstract
The lincoamide antibiotic lincomycin, derived from Streptomyces lincolnensis, is widely used for the treatment of infections caused by gram-positive bacteria. As a common global regulatory factor of GntR family, DasR usually exists as a regulatory factor that negatively regulates antibiotic synthesis in Streptomyces. However, the regulatory effect of DasR on lincomycin biosynthesis in S. lincolnensis has not been thoroughly investigated. The present study demonstrates that DasR functions as a positive regulator of lincomycin biosynthesis in S. lincolnensis, and its overexpression strain OdasR exhibits a remarkable 7.97-fold increase in lincomycin production compared to the wild-type strain. The effects of DasR overexpression could be attenuated by the addition of GlcNAc in the medium in S. lincolnensis. Combined with transcriptome sequencing and RT-qPCR results, it was found that most structural genes in GlcNAc metabolism and central carbon metabolism were up-regulated, but the lincomycin biosynthetic gene cluster (lmb) were down-regulated after dasR knock-out. However, DasR binding were detected with the DasR responsive elements (dre) of genes involved in GlcNAc metabolism pathway through electrophoretic mobility shift assay, while they were not observed in the lmb. These findings will provide novel insights for the genetic manipulation of S. lincolnensis to enhance lincomycin production. KEY POINTS: • DasR is a positive regulator that promotes lincomycin synthesis and does not affect spore production • DasR promotes lincomycin production through indirect regulation • DasR correlates with nutrient perception in S. lincolnensis.
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Affiliation(s)
- Huihui Pai
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Yiying Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
| | - Chuanbo Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, PR China
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, PR China
| | - Jianyu Su
- Key Laboratory of the Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Yinchuan, 750021, China.
- College of Life Science, Ningxia University, Yinchuan, 750021, Ningxia, China.
| | - Wenyu Lu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China.
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, PR China.
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, PR China.
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2
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Li C, Urem M, Du C, Zhang L, van Wezel GP. Systems-wide analysis of the ROK-family regulatory gene rokL6 and its role in the control of glucosamine toxicity in Streptomyces coelicolor. Appl Environ Microbiol 2023; 89:e0167423. [PMID: 37982622 PMCID: PMC10734537 DOI: 10.1128/aem.01674-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Central metabolism plays a key role in the control of growth and antibiotic production in streptomycetes. Specifically, aminosugars act as signaling molecules that affect development and antibiotic production, via metabolic interference with the global repressor DasR. While aminosugar metabolism directly connects to other major metabolic routes such as glycolysis and cell wall synthesis, several important aspects of their metabolism are yet unresolved. Accumulation of N-acetylglucosamine 6-phosphate or glucosamine 6-phosphate is lethal to many bacteria, a yet unresolved phenomenon referred to as "aminosugar sensitivity." We made use of this concept by selecting for suppressors in genes related to glucosamine toxicity in nagB mutants, which showed that the gene pair of rok-family regulatory gene rokL6 and major facilitator superfamily transporter gene sco1448 forms a cryptic rescue mechanism. Inactivation of rokL6 resulted in the expression of sco1448, which then prevents the toxicity of amino sugar-derived metabolites in Streptomyces. The systems biology of RokL6 and its transcriptional control of sco1448 shed new light on aminosugar metabolism in streptomycetes and on the response of bacteria to aminosugar toxicity.
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Affiliation(s)
- Chao Li
- Molecular Biotechnology, Leiden University, Leiden, the Netherlands
| | - Mia Urem
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Chao Du
- Molecular Biotechnology, Leiden University, Leiden, the Netherlands
| | - Le Zhang
- Molecular Biotechnology, Leiden University, Leiden, the Netherlands
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Wu W, Kang Y, Hou B, Ye J, Wang R, Wu H, Zhang H. Characterization of a TetR-type positive regulator AtrA for lincomycin production in Streptomyces lincolnensis. Biosci Biotechnol Biochem 2023; 87:786-795. [DOI: doi.org/10.1093/bbb/zbad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Abstract
ABSTRACT
AtrA belongs to the TetR family and has been well characterized for its roles in antibiotic biosynthesis regulation. Here, we identified an AtrA homolog (AtrA-lin) in Streptomyces lincolnensis. Disruption of atrA-lin resulted in reduced lincomycin production, whereas the complement restored the lincomycin production level to that of the wild-type. In addition, atrA-lin disruption did not affect cell growth and morphological differentiation. Furthermore, atrA-lin disruption hindered the transcription of regulatory gene lmbU, structural genes lmbA and lmbW inside the lincomycin biosynthesis gene cluster, and 2 other regulatory genes, adpA and bldA. Completement of atrA-lin restored the transcription of these genes to varying degrees. Notably, we found that AtrA-lin directly binds to the promoter region of lmbU. Collectively, AtrA-lin positively modulated lincomycin production via both pathway-specific and global regulators. This study offers further insights into the functional diversity of AtrA homologs and the mechanism of lincomycin biosynthesis regulation.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Yajing Kang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai , China
- Department of Applied Biology, East China University of Science and Technology , Shanghai , China
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4
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Fischer SW, Titgemeyer F. Protective Cultures in Food Products: From Science to Market. Foods 2023; 12:foods12071541. [PMID: 37048362 PMCID: PMC10094266 DOI: 10.3390/foods12071541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023] Open
Abstract
An ultimate goal in food production is to guarantee food safety and security. Fermented food products benefit from the intrinsic capabilities of the applied starter cultures as they produce organic acids and bactericidal compounds such as hydrogen peroxide that hamper most food pathogens. In addition, highly potent small peptides, bacteriocins, are being expelled to exert antibiotic effects. Based on ongoing scientific efforts, there is a growing market of food products to which protective cultures are added exclusively for food safety and for prolonged shelf life. In this regard, most genera from the order Lactobacillales play a prominent role. Here, we give an overview on protective cultures in food products. We summarize the mode of actions of antibacterial mechanisms. We display the strategies for the isolation and characterization of protective cultures in order to have them market-ready. A survey of the growing market reveals promising perspectives. Finally, a comprehensive chapter discusses the current legislation issues concerning protective cultures, leading to the conclusion that the application of protective cultures is superior to the usage of defined bacteriocins regarding simplicity, economic costs, and thus usage in less-developed countries. We believe that further discovery of bacteria to be implemented in food preservation will significantly contribute to customer's food safety and food security, badly needed to feed world's growing population but also for food waste reduction in order to save substantial amounts of greenhouse gas emissions.
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Affiliation(s)
- Sebastian W Fischer
- Department of Food, Nutrition and Facilities, FH Muenster, Correnstr. 25, 48149 Münster, Germany
| | - Fritz Titgemeyer
- Department of Food, Nutrition and Facilities, FH Muenster, Correnstr. 25, 48149 Münster, Germany
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Mitra S, Dhar R, Sen R. Designer bacterial cell factories for improved production of commercially valuable non-ribosomal peptides. Biotechnol Adv 2022; 60:108023. [PMID: 35872292 DOI: 10.1016/j.biotechadv.2022.108023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 11/27/2022]
Abstract
Non-ribosomal peptides have gained significant attention as secondary metabolites of high commercial importance. This group houses a diverse range of bioactive compounds, ranging from biosurfactants to antimicrobial and cytotoxic agents. However, low yield of synthesis by bacteria and excessive losses during purification hinders the industrial-scale production of non-ribosomal peptides, and subsequently limits their widespread applicability. While isolation of efficient producer strains and optimization of bioprocesses have been extensively used to enhance yield, further improvement can be made by optimization of the microbial strain using the tools and techniques of metabolic engineering, synthetic biology, systems biology, and adaptive laboratory evolution. These techniques, which directly target the genome of producer strains, aim to redirect carbon and nitrogen fluxes of the metabolic network towards the desired product, bypass the feedback inhibition and repression mechanisms that limit the maximum productivity of the strain, and even extend the substrate range of the cell for synthesis of the target product. The present review takes a comprehensive look into the biosynthesis of bacterial NRPs, how the same is regulated by the cell, and dives deep into the strategies that have been undertaken for enhancing the yield of NRPs, while also providing a perspective on other potential strategies that can allow for further yield improvement. Furthermore, this review provides the reader with a holistic perspective on the design of cellular factories of NRP production, starting from general techniques performed in the laboratory to the computational techniques that help a biochemical engineer model and subsequently strategize the architectural plan.
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Affiliation(s)
- Sayak Mitra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Riddhiman Dhar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
| | - Ramkrishna Sen
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
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Duhsaki L, Mukherjee S, Rani TS, Madhuprakash J. Genome analysis of Streptomyces sp. UH6 revealed the presence of potential chitinolytic machinery crucial for chitosan production. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:431-442. [PMID: 34192819 DOI: 10.1111/1758-2229.12986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 06/19/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Chitosan and its derivatives have numerous applications in wastewater treatment as bio-coagulants, flocculants and bio-adsorbents against both particulate and dissolved pollutants. Chitinolytic bacteria secrete an array of enzymes, which play crucial role in chitin to chitosan conversion. Consequently, there is a growing demand for identification and characterization of novel bacterial isolates with potential implications in chitosan production. We describe genomic features of the new isolate Streptomyces sp. UH6. Analysis of the 6.51 Mb genome revealed the GC content as 71.95% and presence of 6990 coding sequences of which 63% were functionally annotated. Further, we identified two possible chitin-utilization pathways, which employ secreted enzymes like lytic polysaccharide monooxygenases and family-18 glycoside hydrolases (GHs). More importantly, the genome has six family-4 polysaccharide deacetylases with probable role in chitin to chitosan conversion, as well as two chitosanases belonging to GH46 and GH75 families. In addition, the gene clusters, dasABC and ngcEFG coding for transporters, which mediate the uptake of N,N'-diacetylchitobiose and N-acetyl-d-glucosamine were identified. Several genes responsible for hydrolysis of other polysaccharides and fermentation of sugars were also identified. Taken together, the phylogenetic and genomic analyses suggest that the isolate Streptomyces sp. UH6 secretes potential chitin-active enzymes responsible for chitin to chitosan conversion.
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Affiliation(s)
- Lal Duhsaki
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
| | - Saumashish Mukherjee
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
| | | | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, India
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Ruiz-Villafán B, Cruz-Bautista R, Manzo-Ruiz M, Passari AK, Villarreal-Gómez K, Rodríguez-Sanoja R, Sánchez S. Carbon catabolite regulation of secondary metabolite formation, an old but not well-established regulatory system. Microb Biotechnol 2021; 15:1058-1072. [PMID: 33675560 PMCID: PMC8966007 DOI: 10.1111/1751-7915.13791] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/28/2022] Open
Abstract
Secondary microbial metabolites have various functions for the producer microorganisms, which allow them to interact and survive in adverse environments. In addition to these functions, other biological activities may have clinical relevance, as diverse as antimicrobial, anticancer and hypocholesterolaemic effects. These metabolites are usually formed during the idiophase of growth and have a wide diversity in their chemical structures. Their synthesis is under the impact of the type and concentration of the culture media nutrients. Some of the molecular mechanisms that affect the synthesis of secondary metabolites in bacteria (Gram‐positive and negative) and fungi are partially known. Moreover, all microorganisms have their peculiarities in the control mechanisms of carbon sources, even those belonging to the same genus. This regulatory knowledge is necessary to establish culture conditions and manipulation methods for genetic improvement and product fermentation. As the carbon source is one of the essential nutritional factors for antibiotic production, its study has been imperative both at the industrial and research levels. This review aims to draw the utmost recent advances performed to clarify the molecular mechanisms of the negative effect exerted by the carbon source on the secondary metabolite formation, emphasizing those found in Streptomyces, one of the genera most profitable antibiotic producers.
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Affiliation(s)
- Beatriz Ruiz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Rodrigo Cruz-Bautista
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Monserrat Manzo-Ruiz
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Ajit Kumar Passari
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Karen Villarreal-Gómez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CdMx, México City, 04510, México
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8
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Nóbile ML, Stricker AM, Iribarren AM, Lewkowicz ES. Streptomyces griseus: A new biocatalyst with N-oxygenase activity. J Biotechnol 2020; 327:36-42. [PMID: 33373628 DOI: 10.1016/j.jbiotec.2020.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/21/2022]
Abstract
Aromatic nitro compounds are key building blocks for many industrial syntheses and are also components of explosives, drugs and pesticides. Due to the environmentally unfriendly experimental conditions involved in their chemical syntheses, industrial processes would benefit from the use of biocatalysts. Among potentially useful enzymes, N-oxygenases, whose role is to oxygenate primary amines, are becoming relevant. These enzymes are involved in different secondary metabolic pathways in Streptomyces and in few other bacteria, forming part of the enzyme pools implicated in antibiotic synthesis. In this work, a group of Streptomyces strains, whose biomass was obtained from simple and novel culture media, were identified as new sources of N-oxygenase activity. Furthermore, the use of unspecific metabolic stimulation strategies allowed substantial improvements in the activity of whole cells as biocatalysts. It is remarkable the 6 to 50-fold increase in nitro compound yields compared to the biotransformation under standard conditions when Streptomyces griseus was the biocatalyst. In addition, biocatalyst substrate acceptance was studied in order to determine the biocatalytic potential of this enzyme.
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Affiliation(s)
- Matías L Nóbile
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina.
| | - Abigail M Stricker
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, LBB, Roque Sáenz Peña 352, Quilmes, 1876, Argentina
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Sulheim S, Kumelj T, van Dissel D, Salehzadeh-Yazdi A, Du C, van Wezel GP, Nieselt K, Almaas E, Wentzel A, Kerkhoven EJ. Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. iScience 2020; 23:101525. [PMID: 32942174 PMCID: PMC7501462 DOI: 10.1016/j.isci.2020.101525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/19/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Many biosynthetic gene clusters (BGCs) require heterologous expression to realize their genetic potential, including silent and metagenomic BGCs. Although the engineered Streptomyces coelicolor M1152 is a widely used host for heterologous expression of BGCs, a systemic understanding of how its genetic modifications affect the metabolism is lacking and limiting further development. We performed a comparative analysis of M1152 and its ancestor M145, connecting information from proteomics, transcriptomics, and cultivation data into a comprehensive picture of the metabolic differences between these strains. Instrumental to this comparison was the application of an improved consensus genome-scale metabolic model (GEM) of S. coelicolor. Although many metabolic patterns are retained in M1152, we find that this strain suffers from oxidative stress, possibly caused by increased oxidative metabolism. Furthermore, precursor availability is likely not limiting polyketide production, implying that other strategies could be beneficial for further development of S. coelicolor for heterologous production of novel compounds.
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Affiliation(s)
- Snorre Sulheim
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7034 Trondheim, Norway
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Tjaša Kumelj
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Dino van Dissel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7034 Trondheim, Norway
| | - Ali Salehzadeh-Yazdi
- Department of Systems Biology and Bioinformatics, Faculty of Computer Science and Electrical Engineering, University of Rostock, 18057 Rostock, Germany
| | - Chao Du
- Microbial Biotechnology, Institute of Biology, Leiden University, 2300 Leiden, the Netherlands
| | - Gilles P. van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, 2300 Leiden, the Netherlands
| | - Kay Nieselt
- Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, 72070 Tübingen, Germany
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and General Practice, NTNU - Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7034 Trondheim, Norway
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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Chen H, Cui J, Wang P, Wang X, Wen J. Enhancement of bleomycin production in Streptomyces verticillus through global metabolic regulation of N-acetylglucosamine and assisted metabolic profiling analysis. Microb Cell Fact 2020; 19:32. [PMID: 32054531 PMCID: PMC7017467 DOI: 10.1186/s12934-020-01301-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/05/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Bleomycin is a broad-spectrum glycopeptide antitumor antibiotic produced by Streptomyces verticillus. Clinically, the mixture of bleomycin A2 and bleomycin B2 is widely used in combination with other drugs for the treatment of various cancers. As a secondary metabolite, the biosynthesis of bleomycin is precisely controlled by the complex extra-/intracellular regulation mechanisms, it is imperative to investigate the global metabolic and regulatory system involved in bleomycin biosynthesis for increasing bleomycin production. RESULTS N-acetylglucosamine (GlcNAc), the vital signaling molecule controlling the onset of development and antibiotic synthesis in Streptomyces, was found to increase the yields of bleomycins significantly in chemically defined medium. To mine the gene information relevant to GlcNAc metabolism, the DNA sequences of dasR-dasA-dasBCD-nagB and nagKA in S. verticillus were determined by chromosome walking. From the results of Real time fluorescence quantitative PCR (RT-qPCR) and electrophoretic mobility shift assays (EMSAs), the repression of the expression of nagB and nagKA by the global regulator DasR was released under induction with GlcNAc. The relief of blmT expression repression by BlmR was the main reason for increased bleomycin production. DasR, however, could not directly affect the expression of the pathway-specific repressor BlmR in the bleomycins gene cluster. With at the beginning of bleomycin synthesis, the supply of the specific precursor GDP-mannose played the key role in bleomycin production. Genetic engineering of the GDP-mannose synthesis pathway indicated that phosphomannose isomerase (ManA) and phosphomannomutase (ManB) were key enzymes for bleomycins synthesis. Here, the blmT, manA and manB co-expression strain OBlmT/ManAB was constructed. Based on GlcNAc regulation and assisted metabolic profiling analysis, the yields of bleomycin A2 and B2 were ultimately increased to 61.79 and 36.9 mg/L, respectively. CONCLUSIONS Under GlcNAc induction, the elevated production of bleomycins was mainly associated with the alleviation of the inhibition of BlmT, so blmT and specific precursor synthesis pathways were genetically engineered for bleomycins production improvement. Combination with subsequent metabolomics analysis not only effectively increased the bleomycin yield, but also extended the utilization of chitin-derived substrates in microbial-based antibiotic production.
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Affiliation(s)
- Hong Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Jiaqi Cui
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Pan Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Xin Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
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11
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AveI, an AtrA homolog of Streptomyces avermitilis, controls avermectin and oligomycin production, melanogenesis, and morphological differentiation. Appl Microbiol Biotechnol 2019; 103:8459-8472. [PMID: 31422450 DOI: 10.1007/s00253-019-10062-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/21/2019] [Accepted: 07/24/2019] [Indexed: 01/22/2023]
Abstract
Streptomyces avermitilis is well known as the producer of anthelmintic agent avermectins, which are widely used in agriculture, veterinary medicine, and human medicine. aveI encodes a TetR-family regulator, which is the homolog of AtrA. It was reported that deletion of aveI caused enhanced avermectin production. In this study, we investigated the regulatory function of the AveI in S. avermitilis. By binding to the 15-nt palindromic sequence in the promoter regions, AveI directly regulates at least 35 genes. AveI represses avermectin production by directly regulating the transcription of the cluster-situated regulator gene aveR and structural genes aveA1, aveA3, and aveD. AveI represses oligomycin production by repressing the CSR gene olmRII and structural genes olmC. AveI activates melanin biosynthesis by activating the expression of melC1C2 operon. AveI activates morphological differentiation by activating the expression of ssgR and ssgD genes, repressing the expression of wblI gene. Besides, AveI regulates many genes involved in primary metabolism, including substrates transport, the metabolism of amino acids, lipids, and carbohydrates. Therefore, AveI functions as a global regulator in S. avermitilis, controls not only secondary metabolism and morphological differentiation, but also primary metabolism.
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Vollmer B, Steblau N, Ladwig N, Mayer C, Macek B, Mitousis L, Sigle S, Walter A, Wohlleben W, Muth G. Role of the Streptomyces spore wall synthesizing complex SSSC in differentiation of Streptomyces coelicolor A3(2). Int J Med Microbiol 2019; 309:151327. [PMID: 31324525 DOI: 10.1016/j.ijmm.2019.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 07/02/2019] [Accepted: 07/07/2019] [Indexed: 10/26/2022] Open
Abstract
A crucial stage of the Streptomyces life cycle is the sporulation septation, a process were dozens of cross walls are synchronously formed in the aerial hyphae in a highly coordinated manner. This process includes the remodeling of the spore envelopes to make Streptomyces spores resistant to detrimental environmental conditions. Sporulation septation and the synthesis of the thickened spore envelope in S. coelicolor A3(2) involves the Streptomyces spore wall synthesizing complex SSSC. The SSSC is a multi-protein complex including proteins directing peptidoglycan synthesis (MreBCD, PBP2, Sfr, RodZ) and cell wall glycopolymer synthesis (PdtA). It also includes two eukaryotic like serin/threonine protein kinases (eSTPK), PkaI and PkaH, which were shown to phosphorylate MreC. Since unbalancing phosphorylation activity by either deleting eSTPK genes or by expressing a second copy of an eSTPK gene affected proper sporulation, a model was developed, in which the activity of the SSSC is controlled by protein phosphorylation.
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Affiliation(s)
- B Vollmer
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - N Steblau
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - N Ladwig
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - C Mayer
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - B Macek
- Proteome Center Tuebingen, Interfakultaeres Institut für Zellbiologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - L Mitousis
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - S Sigle
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - A Walter
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - W Wohlleben
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany
| | - G Muth
- Interfakultaeres Institut für Mikrobiologie und Infektionsmedizin Tuebingen IMIT, Mikrobiologie/Biotechnologie, Eberhard Karls Universitaet Tuebingen, Auf der Morgenstelle 28, 72076, Tuebingen, Germany.
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13
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van der Heul HU, Bilyk BL, McDowall KJ, Seipke RF, van Wezel GP. Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era. Nat Prod Rep 2019; 35:575-604. [PMID: 29721572 DOI: 10.1039/c8np00012c] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.
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14
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Zheng Y, Sun CF, Fu Y, Chen XA, Li YQ, Mao XM. Dual regulation between the two-component system PhoRP and AdpA regulates antibiotic production in Streptomyces. J Ind Microbiol Biotechnol 2019; 46:725-737. [PMID: 30712141 DOI: 10.1007/s10295-018-02127-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/19/2018] [Indexed: 01/03/2023]
Abstract
Antibiotic production during secondary metabolism in Streptomyces spp. is elaborately controlled by multiple environmental signals and intracellular cascades. These include the two-component system PhoRP responding to phosphate starvation and a conserved signaling pathway mediated by the pleiotropic regulator AdpA. However, little information exists about how these two pathways work together for secondary metabolite production of Streptomyces. Herein, we report the dual regulation from the phosphate starvation-responsive regulator PhoP and AdpA on atrA promoter (atrAp) for the production of daptomycin, an antibiotic produced by Streptomyces roseosporus. We found that PhoP directly binds to atrAp, positively regulates atrA expression and thus daptomycin production. We also observed positive auto-regulation of phoRP expression during fermentation for daptomycin production. Moreover, partial overlap between PhoP- and AdpA-binding sites on atrAp was observed, which results in partial competitive binding between these two regulators. This partial overlapping and competition between PhoP and AdpA was further confirmed by mutations and binding assays. In summary, our findings have revealed dual regulation of PhoP and AdpA on the same promoter for antibiotic production in Streptomyces. This mechanism would be beneficial to further environment-responsive fermentation optimization for antibiotic production.
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Affiliation(s)
- Yang Zheng
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Chen-Fan Sun
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Yu Fu
- School of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China.
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China.
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15
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Ordóñez-Robles M, Rodríguez-García A, Martín JF. Genome-wide transcriptome response of Streptomyces tsukubaensis to N-acetylglucosamine: effect on tacrolimus biosynthesis. Microbiol Res 2018; 217:14-22. [DOI: 10.1016/j.micres.2018.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/04/2018] [Accepted: 08/29/2018] [Indexed: 11/29/2022]
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16
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Cloning and Expression of the Chitinase Encoded by ChiKJ406136 from Streptomyces Sampsonii (Millard & Burr) Waksman KJ40 and Its Antifungal Effect. FORESTS 2018. [DOI: 10.3390/f9110699] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The present study demonstrated that the chitinase gene ChiKJ406136 of Streptomyces sampsonii (Millard & Burr) Waksman KJ40 could be cloned using a PCR protocol and expressed in Escherichia coli (Migula) Castellani & Chalmers BL21 (DE3), and the recombinant protein had antifungal effect on four forest pathogens (Cylindrocladium scoparium Morgan, Cryphonectria parasitica (Murrill) Barr, Neofusicoccum parvum Crous, and Fusarium oxysporum Schl.) and also had the biological control effects on Eucalyptus robusta Smith leaf blight, Castanea mollissima BL. blight, Juglans regia L. blight and J. regia root rot. The results showed that ChiKJ406136 was efficiently expressed and a 48 kilodalton (kDa) recombinant protein was obtained. No significant change in protein production was observed in the presence of different concentrations of IPTG (isopropyl-b-D-thio-galactoside). The purified protein yield was greatest in the 150 mmol/L imidazole elution fraction, and the chitinase activities of the crude protein and purified protein solutions were 0.045 and 0.033 U/mL, respectively. The antifungal effects indicated that mycelial cells of the four fungi were disrupted, and the control effects of the chitinase on four forest diseases showed significant differences among the undiluted 10- and 20-fold dilutions and the control. The undiluted solution exhibited best effect. The results of this study provide a foundation for the use of S. sampsonii as a biocontrol agent and provides a new source for the chitinase gene, providing a theoretical basis for its application.
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17
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Iinuma C, Saito A, Ohnuma T, Tenconi E, Rosu A, Colson S, Mizutani Y, Liu F, Świątek-Połatyńska M, van Wezel GP, Rigali S, Fujii T, Miyashita K. NgcE Sco Acts as a Lower-Affinity Binding Protein of an ABC Transporter for the Uptake of N,N'-Diacetylchitobiose in Streptomyces coelicolor A3(2). Microbes Environ 2018; 33:272-281. [PMID: 30089751 PMCID: PMC6167110 DOI: 10.1264/jsme2.me17172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In the model species Streptomyces coelicolor A3(2), the uptake of chitin-degradation byproducts, mainly N,N′- diacetylchitobiose ([GlcNAc]2) and N-acetylglucosamine (GlcNAc), is performed by the ATP-binding cassette (ABC) transporter DasABC-MsiK and the sugar-phosphotransferase system (PTS), respectively. Studies on the S. coelicolor chromosome have suggested the occurrence of additional uptake systems of GlcNAc-related compounds, including the SCO6005–7 cluster, which is orthologous to the ABC transporter NgcEFG of S. olivaceoviridis. However, despite conserved synteny between the clusters in S. coelicolor and S. olivaceoviridis, homology between them is low, with only 35% of residues being identical between NgcE proteins, suggesting different binding specificities. Isothermal titration calorimetry experiments revealed that recombinant NgcESco interacts with GlcNAc and (GlcNAc)2, with Kd values (1.15 and 1.53 μM, respectively) that were higher than those of NgcE of S. olivaceoviridis (8.3 and 29 nM, respectively). The disruption of ngcESco delayed (GlcNAc)2 consumption, but did not affect GlcNAc consumption ability. The ngcESco-dasA double mutation severely decreased the ability to consume (GlcNAc)2 and abolished the induction of chitinase production in the presence of (GlcNAc)2, but did not affect the GlcNAc consumption rate. The results of these biochemical and reverse genetic analyses indicate that NgcESco acts as a (GlcNAc)2- binding protein of the ABC transporter NgcEFGSco-MsiK. Transcriptional and biochemical analyses of gene regulation demonstrated that the ngcESco gene was slightly induced by GlcNAc, (GlcNAc)2, and chitin, but repressed by DasR. Therefore, a model was proposed for the induction of the chitinolytic system and import of (GlcNAc)2, in which (GlcNAc)2 generated from chitin by chitinase produced leakily, is mainly transported via NgcEFG-MsiK and induces the expression of chitinase genes and dasABCD.
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Affiliation(s)
- Chiharu Iinuma
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University
| | - Akihiro Saito
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University.,Department of Materials and Life Science, Shizuoka Institute of Science and Technology
| | | | - Elodie Tenconi
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
| | - Adeline Rosu
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
| | - Séverine Colson
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
| | - Yuuki Mizutani
- Department of Materials and Life Science, Shizuoka Institute of Science and Technology
| | - Feng Liu
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University
| | | | | | - Sébastien Rigali
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
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18
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Cao ZL, Tan TT, Zhang YL, Han L, Hou XY, Ma HY, Cai J. NagR Bt Is a Pleiotropic and Dual Transcriptional Regulator in Bacillus thuringiensis. Front Microbiol 2018; 9:1899. [PMID: 30254611 PMCID: PMC6141813 DOI: 10.3389/fmicb.2018.01899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
NagR, belonging to the GntR/HutC family, is a negative regulator that directly represses the nagP and nagAB genes, which are involved in GlcNAc transport and utilization in Bacillus subtilis. Our previous work confirmed that the chitinase B gene (chiB) of Bacillus thuringiensis strain Bti75 is also negatively controlled by YvoABt, the ortholog of NagR from B. subtilis. In this work, we investigated its regulatory network in Bti75 and found that YvoABt is an N-acetylglucosamine utilization regulator primarily involved in GlcNAc catabolism; therefore YvoABt is renamed as NagRBt. The RNA-seq data revealed that 27 genes were upregulated and 14 genes were downregulated in the ΔnagR mutant compared with the wild-type strain. The regulon (exponential phase) was characterized by RNA-seq, bioinformatics software, electrophoretic mobility shift assays, and quantitative real-time reverse transcription PCR. In the Bti75 genome, 19 genes that were directly regulated and 30 genes that were indirectly regulated by NagRBt were identified. We compiled in silico, in vitro, and in vivo evidence that NagRBt behaves as a repressor and activator to directly or indirectly influence major biological processes involved in amino sugar metabolism, nucleotide metabolism, fatty acid metabolism, phosphotransferase system, and the Embden-Meyerhof-Parnas pathway.
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Affiliation(s)
- Zhang-Lei Cao
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Tong-Tong Tan
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yan-Li Zhang
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Lu Han
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiao-Yue Hou
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Hui-Yong Ma
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jun Cai
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
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19
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Planckaert S, Jourdan S, Francis IM, Deflandre B, Rigali S, Devreese B. Proteomic Response to Thaxtomin Phytotoxin Elicitor Cellobiose and to Deletion of Cellulose Utilization Regulator CebR in Streptomyces scabies. J Proteome Res 2018; 17:3837-3852. [DOI: 10.1021/acs.jproteome.8b00528] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sören Planckaert
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Samuel Jourdan
- InBioS − Center for Protein Engineering, University of Liège, Institut de Chimie, B-4000 Liège, Belgium
| | - Isolde M. Francis
- Department of Biology, California State University Bakersfield, Bakersfield, California 93311-1022, United States
| | - Benoit Deflandre
- InBioS − Center for Protein Engineering, University of Liège, Institut de Chimie, B-4000 Liège, Belgium
| | - Sébastien Rigali
- InBioS − Center for Protein Engineering, University of Liège, Institut de Chimie, B-4000 Liège, Belgium
| | - Bart Devreese
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
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20
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Du C, van Wezel GP. Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline. Proteomics 2018; 18:e1700332. [PMID: 29708658 PMCID: PMC6175363 DOI: 10.1002/pmic.201700332] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/09/2018] [Indexed: 12/23/2022]
Abstract
Natural products (NPs) are a major source of compounds for medical, agricultural, and biotechnological industries. Many of these compounds are of microbial origin, and, in particular, from Actinobacteria or filamentous fungi. To successfully identify novel compounds that correlate to a bioactivity of interest, or discover new enzymes with desired functions, systematic multiomics approaches have been developed over the years. Bioinformatics tools harness the rapidly expanding wealth of genome sequence information, revealing previously unsuspected biosynthetic diversity. Varying growth conditions or application of elicitors are applied to activate cryptic biosynthetic gene clusters, and metabolomics provide detailed insights into the NPs they specify. Combining these technologies with proteomics-based approaches to profile the biosynthetic enzymes provides scientists with insights into the full biosynthetic potential of microorganisms. The proteomics approaches include enrichment strategies such as employing activity-based probes designed by chemical biology, as well as unbiased (quantitative) proteomics methods. In this review, the opportunities and challenges in microbial NP research are discussed, and, in particular, the application of proteomics to link biosynthetic enzymes to the molecules they produce, and vice versa.
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Affiliation(s)
- Chao Du
- Microbial Biotechnology & Health Programme Institute of BiologyLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - Gilles P. van Wezel
- Microbial Biotechnology & Health Programme Institute of BiologyLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
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21
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Current strategies to induce secondary metabolites from microbial biosynthetic cryptic gene clusters. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1351-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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22
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Daniel-Ivad M, Pimentel-Elardo S, Nodwell JR. Control of Specialized Metabolism by Signaling and Transcriptional Regulation: Opportunities for New Platforms for Drug Discovery? Annu Rev Microbiol 2018; 72:25-48. [PMID: 29799791 DOI: 10.1146/annurev-micro-022618-042458] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Specialized metabolites are bacterially produced small molecules that have an extraordinary diversity of important biological activities. They are useful as biochemical probes of living systems, and they have been adapted for use as drugs for human afflictions ranging from infectious diseases to cancer. The biosynthetic genes for these molecules are controlled by a dense network of regulatory mechanisms: Cell-cell signaling and nutrient sensing are conspicuous features of this network. While many components of these mechanisms have been identified, important questions about their biological roles remain shrouded in mystery. In addition to identifying new molecules and solving their mechanisms of action (a central preoccupation in this field), we suggest that addressing questions of quorum sensing versus diffusion sensing and identifying the dominant nutritional and environmental cues for specialized metabolism are important directions for research.
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Affiliation(s)
- M Daniel-Ivad
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
| | - S Pimentel-Elardo
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
| | - J R Nodwell
- Department of Biochemistry, University of Toronto, Ontario M5G 1M1, Canada;
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23
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Romero-Rodríguez A, Maldonado-Carmona N, Ruiz-Villafán B, Koirala N, Rocha D, Sánchez S. Interplay between carbon, nitrogen and phosphate utilization in the control of secondary metabolite production in Streptomyces. Antonie van Leeuwenhoek 2018; 111:761-781. [PMID: 29605896 DOI: 10.1007/s10482-018-1073-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 03/21/2018] [Indexed: 12/21/2022]
Abstract
Streptomyces species are a wide and diverse source of many therapeutic agents (antimicrobials, antineoplastic and antioxidants, to name a few) and represent an important source of compounds with potential applications in medicine. The effect of nitrogen, phosphate and carbon on the production of secondary metabolites has long been observed, but it was not until recently that the molecular mechanisms on which these effects rely were ascertained. In addition to the specific macronutrient regulatory mechanisms, there is a complex network of interactions between these mechanisms influencing secondary metabolism. In this article, we review the recent advances in our understanding of the molecular mechanisms of regulation exerted by nitrogen, phosphate and carbon sources, as well as the effects of their interconnections, on the synthesis of secondary metabolites by members of the genus Streptomyces.
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Affiliation(s)
- Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico.
| | - Nidia Maldonado-Carmona
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Beatriz Ruiz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Niranjan Koirala
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Diana Rocha
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer circuito Exterior de Ciudad Universitaria, 04510, Mexico City, Mexico
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24
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Lee BR, Bhatia SK, Song HS, Kim J, Kim W, Park HY, Yoon JJ, Park SH, Hwang D, Kim BG, Yang YH. The role of NdgR in glycerol metabolism in Streptomyces coelicolor. Bioprocess Biosyst Eng 2017; 40:1573-1580. [PMID: 28730324 DOI: 10.1007/s00449-017-1813-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/13/2017] [Indexed: 01/23/2023]
Abstract
Streptomyces, which produces many pharmaceutical antibiotics and anticancer agents, is a genus of soil-dwelling bacteria with numerous regulators that control both primary and secondary metabolism. NdgR is highly conserved in Streptomyces spp. and is known to be involved in antibiotic production, tolerance against shock and physical stress, nitrogen metabolism, leucine metabolism, and N-acetylglucosamine metabolism. As another function of NdgR, we report the involvement of NdgR in glycerol metabolism in S. coelicolor. Initially, a glycerol utilization operon containing gylCABX was found to be up-regulated in an ndgR deletion mutant (BG11) grown in N-acetylglucosamine solid minimal media compared with wild-type strain (M145). BG11 produced more antibiotics with a small amount of glycerol and increased glycerol utilization, yielding higher concentrations of lactate and acetate per cell. Moreover, fatty acid production was also changed in BG11 to produce longer chain fatty acids, phenolic compounds, alkanes, and fatty alcohols. Using a gel retardation assay, NdgR was found to bind the upstream region of gylC, working as a repressor. NdgR is a second regulator of a glycerol utilization operon, for which only one regulator, GylR was previously known.
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Affiliation(s)
- Bo-Rahm Lee
- Department of Microbial Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Microbial Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea
- Institute for Ubiquitous Information Technology and Applications (UBITA), Konkuk University, Seoul, 143-701, Republic of Korea
| | - Hun-Suk Song
- Department of Microbial Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea
| | - Junyoung Kim
- Department of Microbial Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea
| | - Wooseong Kim
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI, USA
| | - Hyung-Yeon Park
- Department of Microbial Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea
| | - Jeong-Jun Yoon
- Intelligent Sustainable Materials R&D Group, Korea Institute of Industrial Technology (KITECH), Chungnam, 31056, Republic of Korea
| | - Sung-Hee Park
- School of Chemical and Biological Engineering, Seoul National University, Kwanak-gu, Seoul, 151-742, Republic of Korea
| | - Daehee Hwang
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
- Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Kwanak-gu, Seoul, 151-742, Republic of Korea
| | - Yung-Hun Yang
- Department of Microbial Engineering, College of Engineering, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea.
- Institute for Ubiquitous Information Technology and Applications (UBITA), Konkuk University, Seoul, 143-701, Republic of Korea.
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van der Meij A, Worsley SF, Hutchings MI, van Wezel GP. Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev 2017; 41:392-416. [DOI: 10.1093/femsre/fux005] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/02/2017] [Indexed: 12/13/2022] Open
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Afzal M, Shafeeq S, Manzoor I, Henriques-Normark B, Kuipers OP. N-acetylglucosamine-Mediated Expression of nagA and nagB in Streptococcus pneumoniae. Front Cell Infect Microbiol 2016; 6:158. [PMID: 27900287 PMCID: PMC5110562 DOI: 10.3389/fcimb.2016.00158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 11/02/2016] [Indexed: 11/13/2022] Open
Abstract
In this study, we have explored the transcriptomic response of Streptococcus pneumoniae D39 to N-acetylglucosamine (NAG). Transcriptome comparison of S. pneumoniae D39 wild-type grown in chemically defined medium (CDM) in the presence of 0.5% NAG to that grown in the presence of 0.5% glucose revealed elevated expression of many genes/operons, including nagA, nagB, manLMN, and nanP. We have further confirmed the NAG-dependent expression of nagA, nagB, manLMN, and nanP by β-galactosidase assays. nagA, nagB and glmS are putatively regulated by a transcriptional regulator NagR. We predicted the operator site of NagR (dre site) in PnagA, PnagB, and PglmS, which was further confirmed by mutating the predicted dre site in the respective promoters (nagA, nagB, and glmS). Growth comparison of ΔnagA, ΔnagB, and ΔglmS with the D39 wild-type demonstrates that nagA and nagB are essential for S. pneumoniae D39 to grow in the presence of NAG as a sole carbon source. Furthermore, deletion of ccpA shows that CcpA has no effect on the expression of nagA, nagB, and glmS in the presence of NAG in S. pneumoniae.
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Affiliation(s)
- Muhammad Afzal
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands; Department of Bioinformatics and Biotechnology, Government College UniversityFaisalabad, Pakistan
| | - Sulman Shafeeq
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Stockholm, Sweden
| | - Irfan Manzoor
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands; Department of Bioinformatics and Biotechnology, Government College UniversityFaisalabad, Pakistan
| | | | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
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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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28
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Substrate Inhibition of VanA by d-Alanine Reduces Vancomycin Resistance in a VanX-Dependent Manner. Antimicrob Agents Chemother 2016; 60:4930-9. [PMID: 27270282 DOI: 10.1128/aac.00276-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
The increasing resistance of clinical pathogens against the glycopeptide antibiotic vancomycin, a last-resort drug against infections with Gram-positive pathogens, is a major problem in the nosocomial environment. Vancomycin inhibits peptidoglycan synthesis by binding to the d-Ala-d-Ala terminal dipeptide moiety of the cell wall precursor lipid II. Plasmid-transferable resistance is conferred by modification of the terminal dipeptide into the vancomycin-insensitive variant d-Ala-d-Lac, which is produced by VanA. Here we show that exogenous d-Ala competes with d-Lac as a substrate for VanA, increasing the ratio of wild-type to mutant dipeptide, an effect that was augmented by several orders of magnitude in the absence of the d-Ala-d-Ala peptidase VanX. Liquid chromatography-mass spectrometry (LC-MS) analysis showed that high concentrations of d-Ala led to the production of a significant amount of wild-type cell wall precursors, while vanX-null mutants produced primarily wild-type precursors. This enhanced the efficacy of vancomycin in the vancomycin-resistant model organism Streptomyces coelicolor, and the susceptibility of vancomycin-resistant clinical isolates of Enterococcus faecium (VRE) increased by up to 100-fold. The enhanced vancomycin sensitivity of S. coelicolor cells correlated directly to increased binding of the antibiotic to the cell wall. Our work offers new perspectives for the treatment of diseases associated with vancomycin-resistant pathogens and for the development of drugs that target vancomycin resistance.
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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: 929] [Impact Index Per Article: 116.1] [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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Wu C, Medema MH, Läkamp RM, Zhang L, Dorrestein PC, Choi YH, van Wezel GP. Leucanicidin and Endophenasides Result from Methyl-Rhamnosylation by the Same Tailoring Enzymes in Kitasatospora sp. MBT66. ACS Chem Biol 2016; 11:478-90. [PMID: 26675041 DOI: 10.1021/acschembio.5b00801] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The increasing bacterial multidrug resistance necessitates novel drug-discovery efforts. One way to obtain novel chemistry is glycosylation, which is prevalent in nature, with high diversity in both the sugar moieties and the targeted aglycones. Kitasatospora sp. MBT66 produces endophenaside antibiotics, which is a family of (methyl-)rhamnosylated phenazines. Here we show that this strain also produces the plecomacrolide leucanicidin (1), which is derived from bafilomycin A1 by glycosylation with the same methyl-rhamnosyl moiety as present in the endophenasides. Immediately adjacent to the baf genes for bafilomycin biosynthesis lie leuA and leuB, which encode a sugar-O-methyltransferase and a glycosyltransferase, respectively. LeuA and LeuB are the only enzymes encoded by the genome of Kitasatospora sp. MBT66 that are candidates for the methyl-rhamnosylation of natural products, and mutation of leuB abolished glycosylation of both families of natural products. Thus, LeuA and -B mediate the post-PKS methyl-rhamnosylation of bafilomycin A1 to leucanicidin and of phenazines to endophenasides, showing surprising promiscuity by tolerating both macrolide and phenazine skeletons as the substrates. Detailed metabolic analysis by MS/MS based molecular networking facilitated the characterization of nine novel phenazine glycosides 6-8, 16, and 22-26, whereby compounds 23 and 24 represent an unprecedented tautomeric glyceride phenazine, further enriching the structural diversity of endophenasides.
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Affiliation(s)
- Changsheng Wu
- Molecular
Biotechnology, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE Leiden, The Netherlands
- Natural
Products Laboratory, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE Leiden, The Netherlands
| | - Marnix H. Medema
- Bioinformatics
Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Rianne M. Läkamp
- Molecular
Biotechnology, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE Leiden, The Netherlands
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0751, United States
| | - Le Zhang
- Molecular
Biotechnology, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE Leiden, The Netherlands
| | - Pieter C. Dorrestein
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman
Drive, La Jolla, California 92093-0751, United States
| | - Young Hae Choi
- Natural
Products Laboratory, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE Leiden, The Netherlands
| | - Gilles P. van Wezel
- Molecular
Biotechnology, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE 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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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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Metabolic profiling as a tool for prioritizing antimicrobial compounds. J Ind Microbiol Biotechnol 2015; 43:299-312. [PMID: 26335567 PMCID: PMC4752588 DOI: 10.1007/s10295-015-1666-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 07/25/2015] [Indexed: 11/29/2022]
Abstract
Metabolomics is an analytical technique that allows scientists to globally profile low molecular weight metabolites between samples in a medium- or high-throughput environment. Different biological samples are statistically analyzed and correlated to a bioactivity of interest, highlighting differentially produced compounds as potential biomarkers. Here, we review NMR- and MS-based metabolomics as technologies to facilitate the identification of novel antimicrobial natural products from microbial sources. Approaches to elicit the production of poorly expressed (cryptic) molecules are thereby a key to allow statistical analysis of samples to identify bioactive markers, while connection of compounds to their biosynthetic gene cluster is a determining step in elucidating the biosynthetic pathway and allows downstream process optimization and upscaling. The review focuses on approaches built around NMR-based metabolomics, which enables efficient dereplication and guided fractionation of (antimicrobial) compounds.
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Liao CH, Xu Y, Rigali S, Ye BC. DasR is a pleiotropic regulator required for antibiotic production, pigment biosynthesis, and morphological development in Saccharopolyspora erythraea. Appl Microbiol Biotechnol 2015; 99:10215-24. [DOI: 10.1007/s00253-015-6892-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/25/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
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36
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Tenconi E, Urem M, Świątek-Połatyńska MA, Titgemeyer F, Muller YA, van Wezel GP, Rigali S. Multiple allosteric effectors control the affinity of DasR for its target sites. Biochem Biophys Res Commun 2015; 464:324-9. [PMID: 26123391 DOI: 10.1016/j.bbrc.2015.06.152] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 06/24/2015] [Indexed: 01/10/2023]
Abstract
The global transcriptional regulator DasR connects N-acetylglucosamine (GlcNAc) utilization to the onset of morphological and chemical differentiation in the model actinomycete Streptomyces coelicolor. Previous work revealed that glucosamine-6-phosphate (GlcN-6P) acts as an allosteric effector which disables binding by DasR to its operator sites (called dre, for DasR responsive element) and allows derepression of DasR-controlled/GlcNAc-dependent genes. To unveil the mechanism by which DasR controls S. coelicolor development, we performed a series of electromobility shift assays with histidine-tagged DasR protein, which suggested that N-acetylglucosamine-6-phosphate (GlcNAc-6P) could also inhibit the formation of DasR-dre complexes and perhaps even more efficiently than GlcN-6P. The possibility that GlcNAc-6P is indeed an efficient allosteric effector of DasR was further confirmed by the high and constitutive activity of the DasR-repressed nagKA promoter in the nagA mutant, which lacks GlcNAc-6P deaminase activity and therefore accumulates GlcNAc-6P. In addition, we also observed that high concentrations of organic or inorganic phosphate enhanced binding of DasR to its recognition site, suggesting that the metabolic status of the cell could determine the selectivity of DasR in vivo, and hence its effect on the expression of its regulon.
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Affiliation(s)
- Elodie Tenconi
- Center for Protein Engineering, Institut de chimie B6a, University of Liège, B-4000 Liège, Belgium
| | - Mia Urem
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Magdalena A Świątek-Połatyńska
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Fritz Titgemeyer
- Department of Oecotrophologie, Münster University of Applied Sciences, Corrensstr. 25, 48149 Münster, Germany
| | - Yves A Muller
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestrasse 91, D-91052 Erlangen, Germany
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Sébastien Rigali
- Center for Protein Engineering, Institut de chimie B6a, University of Liège, B-4000 Liège, Belgium.
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Kim SH, Traag BA, Hasan AH, McDowall KJ, Kim BG, van Wezel GP. Transcriptional analysis of the cell division-related ssg genes in Streptomyces coelicolor reveals direct control of ssgR by AtrA. Antonie van Leeuwenhoek 2015; 108:201-13. [PMID: 26002075 PMCID: PMC4457907 DOI: 10.1007/s10482-015-0479-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/11/2015] [Indexed: 11/26/2022]
Abstract
SsgA-like proteins are a family of actinomycete-specific regulatory proteins that control cell division and spore maturation in streptomycetes. SsgA and SsgB together activate sporulation-specific cell division by controlling the localization of FtsZ. Here we report the identification of novel regulators that control the transcription of the ssgA-like genes. Transcriptional regulators controlling ssg gene expression were identified using a DNA-affinity capture assay. Supporting transcriptional and DNA binding studies showed that the ssgA activator gene ssgR is controlled by the TetR-family regulator AtrA, while the γ-butyrolactone-responsive AdpA (SCO2792) and SlbR (SCO0608) and the metabolic regulator Rok7B7 (SCO6008) were identified as candidate regulators for the cell division genes ssgA, ssgB and ssgG. Transcription of the cell division gene ssgB depended on the sporulation genes whiA and whiH, while ssgR, ssgA and ssgD were transcribed independently of the whi genes. Our work sheds new light on the mechanisms by which sporulation-specific cell division is controlled in Streptomyces.
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Affiliation(s)
- Songhee H. Kim
- />School of Chemical and Biological Engineering and Institute of Molecular Biology and Genetics, Seoul National University, Kwanak-gu, Seoul, 151-744 Korea
| | - Bjørn A. Traag
- />Bayer CropScience LP, Biologics, 890 Embarcadero Drive, West Sacramento, CA 95605 USA
| | - Ayad H. Hasan
- />Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT UK
| | - Kenneth J. McDowall
- />Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT UK
| | - Byung-Gee Kim
- />School of Chemical and Biological Engineering and Institute of Molecular Biology and Genetics, Seoul National University, Kwanak-gu, Seoul, 151-744 Korea
| | - Gilles P. van Wezel
- />Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
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38
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Wang W, Tian J, Li L, Ge M, Zhu H, Zheng G, Huang H, Ruan L, Jiang W, Lu Y. Identification of two novel regulatory genes involved in pristinamycin biosynthesis and elucidation of the mechanism for AtrA-p-mediated regulation in Streptomyces pristinaespiralis. Appl Microbiol Biotechnol 2015; 99:7151-64. [PMID: 25957493 DOI: 10.1007/s00253-015-6638-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/19/2015] [Accepted: 04/22/2015] [Indexed: 11/25/2022]
Abstract
In this study, using a transposon-based strategy, two novel regulatory genes were identified as being involved in the biosynthesis of both pristinamycin I (PI) and II (PII) in Streptomyces pristinaespiralis, including a TetR-family regulatory gene atrA-p (SSDG_00466) and an orphan histidine kinase gene SSDG_02492. The mechanism by which AtrA-p exerted a positive role in pristinamycin production was elucidated. We showed that deletion of atrA-p resulted in a delayed production of both PI and PII as well as reduced PII production. Transcriptional analysis integrated with electrophoretic mobility shift assays (EMSAs) demonstrated that AtrA-p played a positive role in pristinamycin production by directly activating the transcription of two cluster-situated regulatory genes, spbR and papR5, which encode a γ-butyrolactone receptor protein and a TetR-family repressor, respectively. The precise AtrA-p-binding sites upstream of these two targets were determined, which allowed the identification of a relatively conserved binding motif comprising two 5-nt inverted repeats separated by a variable 5-nt sequence (5'-GGAAT-n5-ATTCC-3') possibly required for the regulation of AtrA-like regulators in Streptomyces. Base substitutions of the AtrA-p-binding sites on the genome caused similar decreases in spbR and papR5 transcription as those observed in ∆atrA-p. Taken together, herein, a novel mechanism for AtrA-dependent regulation of antibiotic biosynthesis was revealed in S. pristinaespiralis, which is distinct from those of its homologs, AtrA-c from Streptomyces coelicolor, AtrA-g from Streptomyces griseus, and AtrA from Streptomyces roseosporus that perform their effects in antibiotic biosynthesis directly via pathway-specific activator genes or the biosynthetic structural genes.
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Affiliation(s)
- Wenfang Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, People's Republic of China
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Li X, Yu T, He Q, McDowall KJ, Jiang B, Jiang Z, Wu L, Li G, Li Q, Wang S, Shi Y, Wang L, Hong B. Binding of a biosynthetic intermediate to AtrA modulates the production of lidamycin by Streptomyces globisporus. Mol Microbiol 2015; 96:1257-71. [PMID: 25786547 DOI: 10.1111/mmi.13004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2015] [Indexed: 11/30/2022]
Abstract
The control of secondary production in streptomycetes involves the funneling of environmental and physiological signals to the cluster-situated (transcriptional) regulators (CSRs) of the biosynthetic genes. For some systems, the binding of biosynthetic products to the CSR has been shown to provide negative feedback. Here we show for the production of lidamycin (C-1027), a clinically relevant antitumor agent, by Streptomyces globisporus that negative feedback can extend to a point higher in the regulatory cascade. We show that the DNA-binding activity of the S. globisporus orthologue of AtrA, which was initially described as a transcriptional activator of actinorhodin biosynthesis in S. coelicolor, is inhibited by the binding of heptaene, a biosynthetic intermediate of lidamycin. Additional experiments described here show that S. globisporus AtrA binds in vivo as well as in vitro to the promoter region of the gene encoding SgcR1, one of the CSRs of lidamycin production. The feedback to the pleiotropic regulator AtrA is likely to provide a mechanism for coordinating the production of lidamycin with that of other secondary metabolites. The activity of AtrA is also regulated by actinorhodin. As AtrA is evolutionarily conserved, negative feedback of the type described here may be widespread within the streptomycetes.
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Affiliation(s)
- Xingxing Li
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Tengfei Yu
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qing He
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Kenneth J McDowall
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Bingya Jiang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Zhibo Jiang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Linzhuan Wu
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Guangwei Li
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qinglian Li
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Songmei Wang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yuanyuan Shi
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Lifei Wang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Bin Hong
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
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Świątek-Połatyńska MA, Bucca G, Laing E, Gubbens J, Titgemeyer F, Smith CP, Rigali S, van Wezel GP. Genome-wide analysis of in vivo binding of the master regulator DasR in Streptomyces coelicolor identifies novel non-canonical targets. PLoS One 2015; 10:e0122479. [PMID: 25875084 PMCID: PMC4398421 DOI: 10.1371/journal.pone.0122479] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 02/22/2015] [Indexed: 11/30/2022] Open
Abstract
Streptomycetes produce a wealth of natural products, including over half of all known antibiotics. It was previously demonstrated that N-acetylglucosamine and secondary metabolism are closely entwined in streptomycetes. Here we show that DNA recognition by the N-acetylglucosamine-responsive regulator DasR is growth-phase dependent, and that DasR can bind to sites in the S. coelicolor genome that have no obvious resemblance to previously identified DasR-responsive elements. Thus, the regulon of DasR extends well beyond what was previously predicted and includes a large number of genes with functions far removed from N-acetylglucosamine metabolism, such as genes for small RNAs and DNA transposases. Conversely, the DasR regulon during vegetative growth largely correlates to the presence of canonical DasR-responsive elements. The changes in DasR binding in vivo following N-acetylglucosamine induction were studied in detail and a possible molecular mechanism by which the influence of DasR is extended is discussed. Discussion of DasR binding was further informed by a parallel transcriptome analysis of the respective cultures. Evidence is provided that DasR binds directly to the promoters of all genes encoding pathway-specific regulators of antibiotic production in S. coelicolor, thereby providing an exquisitely simple link between nutritional control and secondary metabolism.
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Affiliation(s)
| | - Giselda Bucca
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Emma Laing
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Jacob Gubbens
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Fritz Titgemeyer
- Department of Oecotrophologie, Münster University of Applied Sciences, Corrensstr. 25, 48149 Münster, Germany
| | - Colin P. Smith
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Sébastien Rigali
- Centre for Protein Engineering, Université de Liège, Institut de Chimie B6a, Sart-Tilman, B-4000 Liège, Belgium
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
- * E-mail:
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Lambert S, Traxler MF, Craig M, Maciejewska M, Ongena M, van Wezel GP, Kolter R, Rigali S. Altered desferrioxamine-mediated iron utilization is a common trait of bald mutants of Streptomyces coelicolor. Metallomics 2015; 6:1390-9. [PMID: 24788337 DOI: 10.1039/c4mt00068d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Streptomyces coelicolor is an important model organism for developmental studies of filamentous GC-rich actinobacteria. The genetic characterization of mutants of S. coelicolor blocked at the vegetative mycelium stage, the so-called bald (bld) mutants that are unable to erect spore-forming aerial hyphae, has opened the way to discovering the molecular basis of development in actinomycetes. Desferrioxamine (DFO) production and import of ferrioxamines (FO; iron-complexed DFO) are key to triggering morphogenesis of S. coelicolor and we show here that growth of S. coelicolor on the reference medium for Streptomyces developmental studies is fully dependent on DFO biosynthesis. UPLC-ESI-MS analysis revealed that all bld mutants tested are affected in DFO biosynthesis, with bldA, bldJ, and ptsH mutants severely impaired in DFO production, while bldF, bldK, crr and ptsI mutants overproduce DFO. Morphogenesis of bldK and bldJ mutants was recovered by supplying exogenous iron. Transcript analysis showed that the bldJ mutant is impaired in expression of genes involved in the uptake of FO, whereas transcription of genes involved in both DFO biosynthesis and FO uptake is increased in bldK mutants. Our study allows proposing altered DFO production and/or FO uptake as a novel phenotypic marker of many S. coelicolor bld mutants, and strengthens the role of siderophores and iron acquisition in morphological development of actinomycetes.
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Affiliation(s)
- Stéphany Lambert
- Centre for Protein Engineering, University of Liège, Institut de Chimie B6a, B-4000 Liège, Belgium.
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van Dissel D, Claessen D, van Wezel GP. Morphogenesis of Streptomyces in submerged cultures. ADVANCES IN APPLIED MICROBIOLOGY 2014; 89:1-45. [PMID: 25131399 DOI: 10.1016/b978-0-12-800259-9.00001-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Members of the genus Streptomyces are mycelial bacteria that undergo a complex multicellular life cycle and propagate via sporulation. Streptomycetes are important industrial microorganisms, as they produce a plethora of medically relevant natural products, including the majority of clinically important antibiotics, as well as a wide range of enzymes with industrial application. While development of Streptomyces in surface-grown cultures is well studied, relatively little is known of the parameters that determine morphogenesis in submerged cultures. Here, growth is characterized by the formation of mycelial networks and pellets. From the perspective of industrial fermentations, such mycelial growth is unattractive, as it is associated with slow growth, heterogeneous cultures, and high viscosity. Here, we review the current insights into the genetic and environmental factors that determine mycelial growth and morphology in liquid-grown cultures. The genetic factors include cell-matrix proteins and extracellular polymers, morphoproteins with specific roles in liquid-culture morphogenesis, with the SsgA-like proteins as well-studied examples, and programmed cell death. Environmental factors refer in particular to those dictated by process engineering, such as growth media and reactor set-up. These insights are then integrated to provide perspectives as to how this knowledge can be applied to improve streptomycetes for industrial applications.
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Affiliation(s)
- Dino van Dissel
- Molecular Biotechnology, Institute Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute Biology Leiden, Leiden University, Leiden, The Netherlands.
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute Biology Leiden, Leiden University, Leiden, The Netherlands.
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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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Liao C, Rigali S, Cassani CL, Marcellin E, Nielsen LK, Ye BC. Control of chitin and N-acetylglucosamine utilization in Saccharopolyspora erythraea. MICROBIOLOGY-SGM 2014; 160:1914-1928. [PMID: 25009237 DOI: 10.1099/mic.0.078261-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chitin degradation and subsequent N-acetylglucosamine (GlcNAc) catabolism is thought to be a common trait of a large majority of actinomycetes. Utilization of aminosugars had been poorly investigated outside the model strain Streptomyces coelicolor A3(2), and we examined here the genetic setting of the erythromycin producer Saccharopolyspora erythraea for GlcNAc and chitin utilization, as well as the transcriptional control thereof. Sacch. erythraea efficiently utilize GlcNAc most likely via the phosphotransferase system (PTS(GlcNAc)); however, this strain is not able to grow when chitin or N,N'-diacetylchitobiose [(GlcNAc)2] is the sole nutrient source, despite a predicted extensive chitinolytic system (chi genes). The inability of Sacch. erythraea to utilize chitin and (GlcNAc)2 is probably because of the loss of genes encoding the DasABC transporter for (GlcNAc)2 import, and genes for intracellular degradation of (GlcNAc)2 by β-N-acetylglucosaminidases. Transcription analyses revealed that in Sacch. erythraea all putative chi and GlcNAc utilization genes are repressed by DasR, whereas in Strep. coelicolor DasR displayed either activating or repressing functions whether it targets genes involved in the polymer degradation or genes for GlcNAc dimer and monomer utilization, respectively. A transcriptomic analysis further showed that GlcNAc not only activates the transcription of GlcNAc catabolism genes but also activates chi gene expression, as opposed to the previously reported GlcNAc-mediated catabolite repression in Strep. coelicolor. Finally, synteny exploration revealed an identical genetic background for chitin utilization in other rare actinomycetes, which suggests that screening procedures that used only the chitin-based protocol for selective isolation of antibiotic-producing actinomycetes could have missed the isolation of many industrially promising strains.
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Affiliation(s)
- Chengheng Liao
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Sébastien Rigali
- Centre for Protein Engineering, Institut de Chimie B6a, B-4000 Liège, Belgium
| | - Cuauhtemoc Licona Cassani
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Queensland 4072, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lars Keld Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Queensland 4072, Australia
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, PR China
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Zhu H, Swierstra J, Wu C, Girard G, Choi YH, van Wamel W, Sandiford SK, van Wezel GP. Eliciting antibiotics active against the ESKAPE pathogens in a collection of actinomycetes isolated from mountain soils. MICROBIOLOGY-SGM 2014; 160:1714-1725. [PMID: 24794971 DOI: 10.1099/mic.0.078295-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The rapid emergence of multidrug-resistant (MDR) bacterial pathogens poses a major threat for human health. In recent years, genome sequencing has unveiled many poorly expressed antibiotic clusters in actinomycetes. Here, we report a well-defined ecological collection of >800 actinomycetes obtained from sites in the Himalaya and Qinling mountains, and we used these in a concept study to see how efficiently antibiotics can be elicited against MDR pathogens isolated recently from the clinic. Using 40 different growth conditions, 96 actinomycetes were identified - predominantly Streptomyces - that produced antibiotics with efficacy against the MDR clinical isolates referred to as ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and/or Enterobacter cloacae. Antimicrobial activities that fluctuated strongly with growth conditions were correlated with specific compounds, including borrelidin, resistomycin, carbomethoxy-phenazine, and 6,7,8- and 5,6,8-trimethoxy-3-methylisocoumarin, of which the latter was not described previously. Our work provided insights into the potential of actinomycetes as producers of drugs with efficacy against clinical isolates that have emerged recently and also underlined the importance of targeting a specific pathogen.
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Affiliation(s)
- Hua Zhu
- Molecular Biotechnology, Institute of Biology, Molecular Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jasper Swierstra
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Centre, 's Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Changsheng Wu
- Molecular Biotechnology, Institute of Biology, Molecular Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Geneviève Girard
- Molecular Biotechnology, Institute of Biology, Molecular Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Willem van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Centre, 's Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Stephanie K Sandiford
- Molecular Biotechnology, Institute of Biology, Molecular Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Molecular Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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Matano C, Uhde A, Youn JW, Maeda T, Clermont L, Marin K, Krämer R, Wendisch VF, Seibold GM. Engineering of Corynebacterium glutamicum for growth and L-lysine and lycopene production from N-acetyl-glucosamine. Appl Microbiol Biotechnol 2014; 98:5633-43. [PMID: 24668244 DOI: 10.1007/s00253-014-5676-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/05/2014] [Accepted: 03/06/2014] [Indexed: 11/27/2022]
Abstract
Sustainable supply of feedstock has become a key issue in process development in microbial biotechnology. The workhorse of industrial amino acid production Corynebacterium glutamicum has been engineered towards utilization of alternative carbon sources. Utilization of the chitin-derived aminosugar N-acetyl-glucosamine (GlcNAc) for both cultivation and production with C. glutamicum has hitherto not been investigated. Albeit this organism harbors the enzymes N-acetylglucosamine-6-phosphatedeacetylase and glucosamine-6P deaminase of GlcNAc metabolism (encoded by nagA and nagB, respectively) growth of C. glutamicum with GlcNAc as substrate was not observed. This was attributed to the lack of a functional system for GlcNAc uptake. Of the 17 type strains of the genus Corynebacterium tested here for their ability to grow with GlcNAc, only Corynebacterium glycinophilum DSM45794 was able to utilize this substrate. Complementation studies with a GlcNAc-uptake deficient Escherichia coli strain revealed that C. glycinophilum possesses a nagE-encoded EII permease for GlcNAc uptake. Heterologous expression of the C. glycinophilum nagE in C. glutamicum indeed enabled uptake of GlcNAc. For efficient GlcNac utilization in C. glutamicum, improved expression of nagE with concurrent overexpression of the endogenous nagA and nagB genes was found to be necessary. Based on this strategy, C. glutamicum strains for the efficient production of the amino acid L-lysine as well as the carotenoid lycopene from GlcNAc as sole substrate were constructed.
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Affiliation(s)
- Christian Matano
- Faculty of Biology and CeBiTec, Bielefeld University, 33501, Bielefeld, Germany
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47
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Rabyk MV, Ostash BO, Fedorenko VO. Gene networks regulating secondary metabolism in actinomycetes: Pleiotropic regulators. CYTOL GENET+ 2014. [DOI: 10.3103/s0095452714010083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Dual substrate specificity of an N-acetylglucosamine phosphotransferase system in Clostridium beijerinckii. Appl Environ Microbiol 2013; 79:6712-8. [PMID: 23995920 DOI: 10.1128/aem.01866-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The solventogenic clostridia have a considerable capacity to ferment carbohydrate substrates with the production of acetone and butanol, making them attractive organisms for the conversion of waste materials to valuable products. In common with other anaerobes, the clostridia show a marked dependence on the phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) to accumulate sugars and sugar derivatives. In this study, we demonstrate that extracts of Clostridium beijerinckii grown on N-acetylglucosamine (GlcNAc) exhibit PTS activity for the amino sugar. The PTS encoded by the divergent genes cbe4532 (encoding the IIC and IIB domains) and cbe4533 (encoding a IIA domain) was shown to transport and phosphorylate GlcNAc and also glucose. When the genes were recombined in series under the control of the lac promoter in pUC18 and transformed into a phosphotransferase mutant (nagE) of Escherichia coli lacking GlcNAc PTS activity, the ability to take up and ferment GlcNAc was restored, and extracts of the transformant showed PEP-dependent phosphorylation of GlcNAc. The gene products also complemented an E. coli mutant lacking glucose PTS activity but were unable to complement the same strain for PTS-dependent mannose utilization. Both GlcNAc and glucose induced the expression of cbe4532 and cbe4533 in C. beijerinckii, and consistent with this observation, extracts of cells grown on glucose exhibited PTS activity for GlcNAc, and glucose did not strongly repress utilization of GlcNAc by growing cells. On the basis of the phylogeny and function of the encoded PTS, we propose that the genes cbe4532 and cbe4533 should be designated nagE and nagF, respectively.
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Zhu H, Sandiford SK, van Wezel GP. Triggers and cues that activate antibiotic production by actinomycetes. J Ind Microbiol Biotechnol 2013; 41:371-86. [PMID: 23907251 DOI: 10.1007/s10295-013-1309-z] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/30/2013] [Indexed: 12/24/2022]
Abstract
Actinomycetes are a rich source of natural products, and these mycelial bacteria produce the majority of the known antibiotics. The increasing difficulty to find new drugs via high-throughput screening has led to a decline in antibiotic research, while infectious diseases associated with multidrug resistance are spreading rapidly. Here we review new approaches and ideas that are currently being developed to increase our chances of finding novel antimicrobials, with focus on genetic, chemical, and ecological methods to elicit the expression of biosynthetic gene clusters. The genome sequencing revolution identified numerous gene clusters for natural products in actinomycetes, associated with a potentially huge reservoir of unknown molecules, and prioritizing them is a major challenge for in silico screening-based approaches. Some antibiotics are likely only expressed under very specific conditions, such as interaction with other microbes, which explains the renewed interest in soil and marine ecology. The identification of new gene clusters, as well as chemical elicitors and culturing conditions that activate their expression, should allow scientists to reinforce their efforts to find the necessary novel antimicrobial drugs.
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Affiliation(s)
- Hua Zhu
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
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50
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Liu G, Chater KF, Chandra G, Niu G, Tan H. Molecular regulation of antibiotic biosynthesis in streptomyces. Microbiol Mol Biol Rev 2013; 77:112-43. [PMID: 23471619 PMCID: PMC3591988 DOI: 10.1128/mmbr.00054-12] [Citation(s) in RCA: 496] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Streptomycetes are the most abundant source of antibiotics. Typically, each species produces several antibiotics, with the profile being species specific. Streptomyces coelicolor, the model species, produces at least five different antibiotics. We review the regulation of antibiotic biosynthesis in S. coelicolor and other, nonmodel streptomycetes in the light of recent studies. The biosynthesis of each antibiotic is specified by a large gene cluster, usually including regulatory genes (cluster-situated regulators [CSRs]). These are the main point of connection with a plethora of generally conserved regulatory systems that monitor the organism's physiology, developmental state, population density, and environment to determine the onset and level of production of each antibiotic. Some CSRs may also be sensitive to the levels of different kinds of ligands, including products of the pathway itself, products of other antibiotic pathways in the same organism, and specialized regulatory small molecules such as gamma-butyrolactones. These interactions can result in self-reinforcing feed-forward circuitry and complex cross talk between pathways. The physiological signals and regulatory mechanisms may be of practical importance for the activation of the many cryptic secondary metabolic gene cluster pathways revealed by recent sequencing of numerous Streptomyces genomes.
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Affiliation(s)
- Gang Liu
- State Key Laboratory of Microbial Resources
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Keith F. Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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