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Cruz-Bautista R, Zelarayan-Agüero A, Ruiz-Villafán B, Escalante-Lozada A, Rodríguez-Sanoja R, Sánchez S. An overview of the two-component system GarR/GarS role on antibiotic production in Streptomyces coelicolor. Appl Microbiol Biotechnol 2024; 108:306. [PMID: 38656376 PMCID: PMC11043171 DOI: 10.1007/s00253-024-13136-z] [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: 01/09/2024] [Revised: 03/23/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
The Streptomyces genus comprises Gram-positive bacteria known to produce over two-thirds of the antibiotics used in medical practice. The biosynthesis of these secondary metabolites is highly regulated and influenced by a range of nutrients present in the growth medium. In Streptomyces coelicolor, glucose inhibits the production of actinorhodin (ACT) and undecylprodigiosin (RED) by a process known as carbon catabolite repression (CCR). However, the mechanism mediated by this carbon source still needs to be understood. It has been observed that glucose alters the transcriptomic profile of this actinobacteria, modifying different transcriptional regulators, including some of the one- and two-component systems (TCSs). Under glucose repression, the expression of one of these TCSs SCO6162/SCO6163 was negatively affected. We aimed to study the role of this TCS on secondary metabolite formation to define its influence in this general regulatory process and likely establish its relationship with other transcriptional regulators affecting antibiotic biosynthesis in the Streptomyces genus. In this work, in silico predictions suggested that this TCS can regulate the production of the secondary metabolites ACT and RED by transcriptional regulation and protein-protein interactions of the transcriptional factors (TFs) with other TCSs. These predictions were supported by experimental procedures such as deletion and complementation of the TFs and qPCR experiments. Our results suggest that in the presence of glucose, the TCS SCO6162/SCO6163, named GarR/GarS, is an important negative regulator of the ACT and RED production in S. coelicolor. KEY POINTS: • GarR/GarS is a TCS with domains for signal transduction and response regulation • GarR/GarS is an essential negative regulator of the ACT and RED production • GarR/GarS putatively interacts with and regulates activators of ACT and RED.
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Affiliation(s)
- Rodrigo Cruz-Bautista
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Augusto Zelarayan-Agüero
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Beatriz Ruiz-Villafán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Adelfo Escalante-Lozada
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ave. Universidad 2001, 62210, Cuernavaca, Mexico
| | - Romina Rodríguez-Sanoja
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico.
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Tatta ER, Imchen M, Moopantakath J, Kumavath R. Bioprospecting of microbial enzymes: current trends in industry and healthcare. Appl Microbiol Biotechnol 2022; 106:1813-1835. [PMID: 35254498 DOI: 10.1007/s00253-022-11859-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/15/2022] [Accepted: 02/26/2022] [Indexed: 12/13/2022]
Abstract
Microbial enzymes have an indispensable role in producing foods, pharmaceuticals, and other commercial goods. Many novel enzymes have been reported from all domains of life, such as plants, microbes, and animals. Nonetheless, industrially desirable enzymes of microbial origin are limited. This review article discusses the classifications, applications, sources, and challenges of most demanded industrial enzymes such as pectinases, cellulase, lipase, and protease. In addition, the production of novel enzymes through protein engineering technologies such as directed evolution, rational, and de novo design, for the improvement of existing industrial enzymes is also explored. We have also explored the role of metagenomics, nanotechnology, OMICs, and machine learning approaches in the bioprospecting of novel enzymes. Overall, this review covers the basics of biocatalysts in industrial and healthcare applications and provides an overview of existing microbial enzyme optimization tools. KEY POINTS: • Microbial bioactive molecules are vital for therapeutic and industrial applications. • High-throughput OMIC is the most proficient approach for novel enzyme discovery. • Comprehensive databases and efficient machine learning models are the need of the hour to fast forward de novo enzyme design and discovery.
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Affiliation(s)
- Eswar Rao Tatta
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (PO.), Kasaragod, Kerala, 671320, India.
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Diana RM, Monserrat MR, Alba RR, Beatriz RV, Romina RS, Sergio SE. Dissecting the role of the two Streptomyces peucetius var. caesius glucokinases in the sensitivity to carbon catabolite repression. J Ind Microbiol Biotechnol 2021; 48:6349106. [PMID: 34383077 PMCID: PMC8788730 DOI: 10.1093/jimb/kuab047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022]
Abstract
Streptomyces peucetius var. caesius, the doxorubicin-producing strain, has two glucokinases (Glk) for glucose phosphorylation. One of them (ATP-Glk) uses adenosine triphosphate as its phosphate source, and the other one uses polyphosphate (PP). Glk regulates the carbon catabolite repression (CCR) process, as well as glucose utilization. However, in the streptomycetes, the specific role of each one of the Glks in these processes is unknown. With the use of PP- and ATP-Glk null mutants, we aimed to establish their respective role in glucose metabolism and their possible implication in the CCR. Our results supported that in S. peucetius var. caesius, both Glks allowed this strain to grow in different glucose concentrations. PP-Glk seems to be the main enzyme for glucose metabolism, and ATP-Glk is the only one involved in the CCR process affecting the levels of α-amylase and anthracycline production. Besides, analysis of Glk activities in the parental strain and the mutants revealed ATP-Glk as an enzyme negatively affected by high glucose concentrations. Although ATP-Glk utilizes only ATP as the substrate for glucose phosphorylation, probably PP-Glk can use either ATP or polyphosphate. Finally, a possible connection between both Glks may exist from the regulatory point of view.
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Affiliation(s)
- Rocha-Mendoza Diana
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México. Ciudad de México, CDMX, 04510. México
| | - Manzo-Ruiz Monserrat
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México. Ciudad de México, CDMX, 04510. México
| | - Romero-Rodríguez Alba
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México. Ciudad de México, CDMX, 04510. México
| | - Ruiz-Villafán Beatriz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México. Ciudad de México, CDMX, 04510. México
| | - Rodríguez-Sanoja Romina
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México. Ciudad de México, CDMX, 04510. México
| | - Sánchez-Esquivel Sergio
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México. Ciudad de México, CDMX, 04510. México
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Gläser L, Kuhl M, Stegmüller J, Rückert C, Myronovskyi M, Kalinowski J, Luzhetskyy A, Wittmann C. Superior production of heavy pamamycin derivatives using a bkdR deletion mutant of Streptomyces albus J1074/R2. Microb Cell Fact 2021; 20:111. [PMID: 34082758 PMCID: PMC8176718 DOI: 10.1186/s12934-021-01602-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Background Pamamycins are macrodiolides of polyketide origin which form a family of differently large homologues with molecular weights between 579 and 663. They offer promising biological activity against pathogenic fungi and gram-positive bacteria. Admittedly, production titers are very low, and pamamycins are typically formed as crude mixture of mainly smaller derivatives, leaving larger derivatives rather unexplored so far. Therefore, strategies that enable a more efficient production of pamamycins and provide increased fractions of the rare large derivatives are highly desired. Here we took a systems biology approach, integrating transcription profiling by RNA sequencing and intracellular metabolite analysis, to enhance pamamycin production in the heterologous host S. albus J1074/R2. Results Supplemented with l-valine, the recombinant producer S. albus J1074/R2 achieved a threefold increased pamamycin titer of 3.5 mg L−1 and elevated fractions of larger derivatives: Pam 649 was strongly increased, and Pam 663 was newly formed. These beneficial effects were driven by increased availability of intracellular CoA thioesters, the building blocks for the polyketide, resulting from l-valine catabolism. Unfavorably, l-valine impaired growth of the strain, repressed genes of mannitol uptake and glycolysis, and suppressed pamamycin formation, despite the biosynthetic gene cluster was transcriptionally activated, restricting production to the post l-valine phase. A deletion mutant of the transcriptional regulator bkdR, controlling a branched-chain amino acid dehydrogenase complex, revealed decoupled pamamycin biosynthesis. The regulator mutant accumulated the polyketide independent of the nutrient status. Supplemented with l-valine, the novel strain enabled the biosynthesis of pamamycin mixtures with up to 55% of the heavy derivatives Pam 635, Pam 649, and Pam 663: almost 20-fold more than the wild type. Conclusions Our findings open the door to provide rare heavy pamamycins at markedly increased efficiency and facilitate studies to assess their specific biological activities and explore this important polyketide further. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01602-6.
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Affiliation(s)
- Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Maksym Myronovskyi
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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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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Abstract
Bacteria secrete antibiotics to inhibit their competitors, but the presence of competitors can determine whether these toxins are produced. Here, we study the role of the competitive and resource environment on antibiotic production in Streptomyces, bacteria renowned for their production of antibiotics. One of the most important ways that bacteria compete for resources and space is by producing antibiotics that inhibit competitors. Because antibiotic production is costly, the biosynthetic gene clusters coordinating their synthesis are under strict regulatory control and often require “elicitors” to induce expression, including cues from competing strains. Although these cues are common, they are not produced by all competitors, and so the phenotypes causing induction remain unknown. By studying interactions between 24 antibiotic-producing strains of streptomycetes, we show that strains commonly inhibit each other’s growth and that this occurs more frequently if strains are closely related. Next, we show that antibiotic production is more likely to be induced by cues from strains that are closely related or that share secondary metabolite biosynthetic gene clusters (BGCs). Unexpectedly, antibiotic production is less likely to be induced by competitors that inhibit the growth of a focal strain, indicating that cell damage is not a general cue for induction. In addition to induction, antibiotic production often decreases in the presence of a competitor, although this response was not associated with genetic relatedness or overlap in BGCs. Finally, we show that resource limitation increases the chance that antibiotic production declines during competition. Our results reveal the importance of social cues and resource availability in the dynamics of interference competition in streptomycetes.
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Schniete JK, Selem-Mojica N, Birke AS, Cruz-Morales P, Hunter IS, Barona-Gomez F, Hoskisson PA. ActDES - a curated Actinobacterial Database for Evolutionary Studies. Microb Genom 2021; 7:mgen000498. [PMID: 33433310 PMCID: PMC8115908 DOI: 10.1099/mgen.0.000498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/06/2020] [Indexed: 12/25/2022] Open
Abstract
Actinobacteria is a large and diverse phylum of bacteria that contains medically and ecologically relevant organisms. Many members are valuable sources of bioactive natural products and chemical precursors that are exploited in the clinic and made using the enzyme pathways encoded in their complex genomes. Whilst the number of sequenced genomes has increased rapidly in the last 20 years, the large size, complexity and high G+C content of many actinobacterial genomes means that the sequences remain incomplete and consist of large numbers of contigs with poor annotation, which hinders large-scale comparative genomic and evolutionary studies. To enable greater understanding and exploitation of actinobacterial genomes, specialized genomic databases must be linked to high-quality genome sequences. Here, we provide a curated database of 612 high-quality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome re-annotation. Utilizing this database will provide researchers with a framework for evolutionary and metabolic studies, to enable a foundation for genome and metabolic engineering, to facilitate discovery of novel bioactive therapeutics and studies on gene family evolution. This article contains data hosted by Microreact.
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Affiliation(s)
- Jana K. Schniete
- Biology Department, Edge Hill University, St Helens Road, Ormskirk, Lancashire L39 4QP, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Libramiento Norte Carretera Leon Km 9.6, 36821 Irapuato, Guanajuato, México
| | - Anna S. Birke
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Libramiento Norte Carretera Leon Km 9.6, 36821 Irapuato, Guanajuato, México
| | - Iain S. Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Libramiento Norte Carretera Leon Km 9.6, 36821 Irapuato, Guanajuato, México
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
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The Onset of Tacrolimus Biosynthesis in Streptomyces tsukubaensis Is Dependent on the Intracellular Redox Status. Antibiotics (Basel) 2020; 9:antibiotics9100703. [PMID: 33076498 PMCID: PMC7602649 DOI: 10.3390/antibiotics9100703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 11/16/2022] Open
Abstract
The oxidative stress response is a key mechanism that microorganisms have to adapt to changeling environmental conditions. Adaptation is achieved by a fine-tuned molecular response that extends its influence to primary and secondary metabolism. In the past, the role of the intracellular redox status in the biosynthesis of tacrolimus in Streptomyces tsukubaensis has been briefly acknowledged. Here, we investigate the impact of the oxidative stress response on tacrolimus biosynthesis in S. tsukubaensis. Physiological characterization of S. tsukubaensis showed that the onset of tacrolimus biosynthesis coincided with the induction of catalase activity. In addition, tacrolimus displays antioxidant properties and thus a controlled redox environment would be beneficial for its biosynthesis. In addition, S. tsukubaensis ∆ahpC strain, a strain defective in the H2O2-scavenging enzyme AhpC, showed increased production of tacrolimus. Proteomic and transcriptomic studies revealed that the tacrolimus over-production phenotype was correlated with a metabolic rewiring leading to increased availability of tacrolimus biosynthetic precursors. Altogether, our results suggest that the carbon source, mainly used for cell growth, can trigger the production of tacrolimus by modulating the oxidative metabolism to favour a low oxidizing intracellular environment and redirecting the metabolic flux towards the increase availability of biosynthetic precursors.
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Crotonylation of key metabolic enzymes regulates carbon catabolite repression in Streptomyces roseosporus. Commun Biol 2020; 3:192. [PMID: 32332843 PMCID: PMC7181814 DOI: 10.1038/s42003-020-0924-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/31/2020] [Indexed: 12/22/2022] Open
Abstract
Due to the plethora natural products made by Streptomyces, the regulation of its metabolism are of great interest, whereas there is a lack of detailed understanding of the role of posttranslational modifications (PTM) beyond traditional transcriptional regulation. Herein with Streptomyces roseosporus as a model, we showed that crotonylation is widespread on key enzymes for various metabolic pathways, and sufficient crotonylation in primary metabolism and timely elimination in secondary metabolism are required for proper Streptomyces metabolism. Particularly, the glucose kinase Glk, a keyplayer of carbon catabolite repression (CCR) regulating bacterial metabolism, is identified reversibly crotonylated by the decrotonylase CobB and the crotonyl-transferase Kct1 to negatively control its activity. Furthermore, crotonylation positively regulates CCR for Streptomyces metabolism through modulation of the ratio of glucose uptake/Glk activity and utilization of carbon sources. Thus, our results revealed a regulatory mechanism that crotonylation globally regulates Streptomyces metabolism at least through positive modulation of CCR. Chen-Fan Sun et al. show that key enzymes in several metabolic pathways are crotonylated in Streptomyces roseosporus. This study suggests that crotonylation increases carbon catabolite repression by increasing glucose uptake while reducing the activity of glucose kinase.
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Schniete JK, Reumerman R, Kerr L, Tucker NP, Hunter IS, Herron PR, Hoskisson PA. Differential transcription of expanded gene families in central carbon metabolism of Streptomyces coelicolor A3(2). Access Microbiol 2020; 2:acmi000122. [PMID: 32974587 PMCID: PMC7494193 DOI: 10.1099/acmi.0.000122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 02/21/2020] [Indexed: 11/18/2022] Open
Abstract
Background Streptomycete bacteria are prolific producers of specialized metabolites, many of which have clinically relevant bioactivity. A striking feature of their genomes is the expansion of gene families that encode the same enzymatic function. Genes that undergo expansion events, either by horizontal gene transfer or duplication, can have a range of fates: genes can be lost, or they can undergo neo-functionalization or sub-functionalization. To test whether expanded gene families in Streptomyces exhibit differential expression, an RNA-Seq approach was used to examine cultures of wild-type Streptomyces coelicolor grown with either glucose or tween as the sole carbon source. Results RNA-Seq analysis showed that two-thirds of genes within expanded gene families show transcriptional differences when strains were grown on tween compared to glucose. In addition, expression of specialized metabolite gene clusters (actinorhodin, isorenieratane, coelichelin and a cryptic NRPS) was also influenced by carbon source. Conclusions Expression of genes encoding the same enzymatic function had transcriptional differences when grown on different carbon sources. This transcriptional divergence enables partitioning to function under different physiological conditions. These approaches can inform metabolic engineering of industrial Streptomyces strains and may help develop cultivation conditions to activate the so-called silent biosynthetic gene clusters.
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Affiliation(s)
- Jana K Schniete
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK.,Biology Department, Edge Hill University, St Helens Road, Ormskirk, Lancashire, L39 4QP, UK
| | | | - Leena Kerr
- Institute of Earth and Life Sciences, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS, UK
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Iain S Hunter
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Paul R Herron
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
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Fernández-Martínez LT, Hoskisson PA. Expanding, integrating, sensing and responding: the role of primary metabolism in specialised metabolite production. Curr Opin Microbiol 2019; 51:16-21. [DOI: 10.1016/j.mib.2019.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/22/2019] [Accepted: 03/12/2019] [Indexed: 01/30/2023]
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Multi-level regulation of coelimycin synthesis in Streptomyces coelicolor A3(2). Appl Microbiol Biotechnol 2019; 103:6423-6434. [PMID: 31250060 PMCID: PMC6667686 DOI: 10.1007/s00253-019-09975-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 11/03/2022]
Abstract
Despite being a yellow pigment visible to the human eye, coelimycin (CPK) remained to be an undiscovered secondary metabolite for over 50 years of Streptomyces research. Although the function of this polyketide is still unclear, we now know that its "cryptic" nature is attributed to a very complex and precise mechanism of cpk gene cluster regulation in the model actinomycete S. coelicolor A3(2). It responds to the stringent culture density and timing of the transition phase by the quorum-sensing butanolide system and to the specific nutrient availability/uptake signals mediated by the global (pleiotropic) regulators; many of which are two-component signal transduction systems. The final effectors of this regulation cascade are predicted to be two cluster-situated Streptomyces antibiotic regulatory proteins (SARPs) putatively activating the expression of type I polyketide synthase (PKS I) genes. After its synthesis, unstable, colorless antibiotic coelimycin A reacts with specific compounds in the medium losing its antibacterial properties and giving rise to yellow coelimycins P1 and P2. Here we review the current knowledge on coelimycin synthesis regulation in Streptomyces coelicolor A3(2). We focus on the regulatory feedback loop which interconnects the butanolide system with other cpk cluster-situated regulators. We also present the effects exerted on cpk genes expression by the global, pleiotropic regulators, and the regulatory connections between cpk and other biosynthetic gene clusters.
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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: 141] [Impact Index Per Article: 28.2] [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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Zhu XM, Zhang XX, Cheng RT, Yu HL, Yuan RS, Bu XL, Xu J, Ao P, Chen YC, Xu MJ. Dynamical modelling of secondary metabolism and metabolic switches in Streptomyces xiamenensis 318. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190418. [PMID: 31183155 PMCID: PMC6502367 DOI: 10.1098/rsos.190418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
The production of secondary metabolites, while important for bioengineering purposes, presents a paradox in itself. Though widely existing in plants and bacteria, they have no definite physiological roles. Yet in both native habitats and laboratories, their production appears robust and follows apparent metabolic switches. We show in this work that the enzyme-catalysed process may improve the metabolic stability of the cells. The latter can be responsible for the overall metabolic behaviours such as dynamic metabolic landscape, metabolic switches and robustness, which can in turn affect the genetic formation of the organism in question. Mangrove-derived Streptomyces xiamenensis 318, with a relatively compact genome for secondary metabolism, is used as a model organism in our investigation. Integrated studies via kinetic metabolic modelling, transcriptase measurements and metabolic profiling were performed on this strain. Our results demonstrate that the secondary metabolites increase the metabolic fitness of the organism via stabilizing the underlying metabolic network. And the fluxes directing to NADH, NADPH, acetyl-CoA and glutamate provide the key switches for the overall and secondary metabolism. The information may be helpful for improving the xiamenmycin production on the strain.
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Affiliation(s)
- Xiao-Mei Zhu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
- Shanghai Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai 200444, People's Republic of China
| | - Xing-Xing Zhang
- Shanghai Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai 200444, People's Republic of China
| | - Run-Tan Cheng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - He-Lin Yu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Ruo-Shi Yuan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Xu-Liang Bu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
- School of Oceanography, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Jun Xu
- School of Oceanography, State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Ping Ao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
- Shanghai Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai 200444, People's Republic of China
| | - Yong-Cong Chen
- Shanghai Center for Quantitative Life Sciences and Physics Department, Shanghai University, Shanghai 200444, People's Republic of China
| | - Min-Juan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
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15
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Daniels W, Bouvin J, Busche T, Rückert C, Simoens K, Karamanou S, Van Mellaert L, Friðjónsson ÓH, Nicolai B, Economou A, Kalinowski J, Anné J, Bernaerts K. Transcriptomic and fluxomic changes in Streptomyces lividans producing heterologous protein. Microb Cell Fact 2018; 17:198. [PMID: 30577858 PMCID: PMC6302529 DOI: 10.1186/s12934-018-1040-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/26/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Gram-positive Streptomyces lividans TK24 is an attractive host for heterologous protein production because of its high capability to secrete proteins-which favors correct folding and facilitates downstream processing-as well as its acceptance of methylated DNA and its low endogeneous protease activity. However, current inconsistencies in protein yields urge for a deeper understanding of the burden of heterologous protein production on the cell. In the current study, transcriptomics and [Formula: see text]-based fluxomics were exploited to uncover gene expression and metabolic flux changes associated with heterologous protein production. The Rhodothermus marinus thermostable cellulase A (CelA)-previously shown to be successfully overexpressed in S. lividans-was taken as an example protein. RESULTS RNA-seq and [Formula: see text]-based metabolic flux analysis were performed on a CelA-producing and an empty-plasmid strain under the same conditions. Differential gene expression, followed by cluster analysis based on co-expression and co-localization, identified transcriptomic responses related to secretion-induced stress and DNA damage. Furthermore, the OsdR regulon (previously associated with hypoxia, oxidative stress, intercellular signaling, and morphological development) was consistently upregulated in the CelA-producing strain and exhibited co-expression with isoenzymes from the pentose phosphate pathway linked to secondary metabolism. Increased expression of these isoenzymes matches to increased fluxes in the pentose phosphate pathway. Additionally, flux maps of the central carbon metabolism show increased flux through the tricarboxylic acid cycle in the CelA-producing strain. Redirection of fluxes in the CelA-producing strain leads to higher production of NADPH, which can only partly be attributed to increased secretion. CONCLUSIONS Transcriptomic and fluxomic changes uncover potential new leads for targeted strain improvement strategies which may ease the secretion stress and metabolic burden associated with heterologous protein synthesis and secretion, and may help create a more consistently performing S. lividans strain. Yet, links to secondary metabolism and redox balancing should be further investigated to fully understand the S. lividans metabolome under heterologous protein production.
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Affiliation(s)
- Wouter Daniels
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Jeroen Bouvin
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Kenneth Simoens
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Lieve Van Mellaert
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | | | - Bart Nicolai
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jozef Anné
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Kristel Bernaerts
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium.
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16
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Rioseras B, Shliaha PV, Gorshkov V, Yagüe P, López-García MT, Gonzalez-Quiñonez N, Kovalchuk S, Rogowska-Wrzesinska A, Jensen ON, Manteca A. Quantitative Proteome and Phosphoproteome Analyses of Streptomyces coelicolor Reveal Proteins and Phosphoproteins Modulating Differentiation and Secondary Metabolism. Mol Cell Proteomics 2018; 17:1591-1611. [PMID: 29784711 PMCID: PMC6072539 DOI: 10.1074/mcp.ra117.000515] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/15/2018] [Indexed: 02/03/2023] Open
Abstract
Streptomycetes are multicellular bacteria with complex developmental cycles. They are of biotechnological importance as they produce most bioactive compounds used in biomedicine, e.g. antibiotic, antitumoral and immunosupressor compounds. Streptomyces genomes encode many Ser/Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor We identified and quantified 3461 proteins corresponding to 44.3% of the S. coelicolor proteome across three developmental stages: vegetative hypha (first mycelium); secondary metabolite producing hyphae (second mycelium); and sporulating hyphae. A total of 1350 proteins exhibited more than 2-fold expression changes during the bacterial differentiation process. These proteins include 136 regulators (transcriptional regulators, transducers, Ser/Thr/Tyr kinases, signaling proteins), as well as 542 putative proteins with no clear homology to known proteins which are likely to play a role in differentiation and secondary metabolism. Phosphoproteomics revealed 85 unique protein phosphorylation sites, 58 of them differentially phosphorylated during differentiation. Computational analysis suggested that these regulated protein phosphorylation events are implicated in important cellular processes, including cell division, differentiation, regulation of secondary metabolism, transcription, protein synthesis, protein folding and stress responses. We discovered a novel regulated phosphorylation site in the key bacterial cell division protein FtsZ (pSer319) that modulates sporulation and regulates actinorhodin antibiotic production. We conclude that manipulation of distinct protein phosphorylation events may improve secondary metabolite production in industrial streptomycetes, including the activation of cryptic pathways during the screening for new secondary metabolites from streptomycetes.
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Affiliation(s)
- Beatriz Rioseras
- From the ‡Área de Microbiología, Departamento de Biología Funcional e IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Pavel V Shliaha
- §Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Vladimir Gorshkov
- §Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Paula Yagüe
- From the ‡Área de Microbiología, Departamento de Biología Funcional e IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - María T López-García
- From the ‡Área de Microbiología, Departamento de Biología Funcional e IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Nathaly Gonzalez-Quiñonez
- From the ‡Área de Microbiología, Departamento de Biología Funcional e IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Sergey Kovalchuk
- §Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Adelina Rogowska-Wrzesinska
- §Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Ole N Jensen
- §Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Angel Manteca
- From the ‡Área de Microbiología, Departamento de Biología Funcional e IUOPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain;
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17
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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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18
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Kashiwagi N, Ogino C, Kondo A. Production of chemicals and proteins using biomass-derived substrates from a Streptomyces host. BIORESOURCE TECHNOLOGY 2017; 245:1655-1663. [PMID: 28651868 DOI: 10.1016/j.biortech.2017.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
Bioproduction using microbes from biomass feedstocks is of interest in regards to environmental problems and cost reduction. Streptomyces as an industrial microorganism plays an important role in the production of useful secondary metabolites for various applications. This strain also secretes a wide range of extracellular enzymes which degrade various biopolymers in nature, and it consumes these degrading substrates as nutrients. Hence, Streptomyces can be employed as a cell factory for the conversion of biomass-derived substrates into various products. This review focuses on the following two points: (1) Streptomyces as a producer of enzymes for degrading biomass-derived polysaccharides and polymers; and, (2) wild-type and engineered strains of Streptomyces as a host for chemical production from biomass-derived substrates.
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Affiliation(s)
- Norimasa Kashiwagi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan.
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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19
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Gubbens J, Wu C, Zhu H, Filippov DV, Florea BI, Rigali S, Overkleeft HS, van Wezel GP. Intertwined Precursor Supply during Biosynthesis of the Catecholate-Hydroxamate Siderophores Qinichelins in Streptomyces sp. MBT76. ACS Chem Biol 2017; 12:2756-2766. [PMID: 28945067 PMCID: PMC5696649 DOI: 10.1021/acschembio.7b00597] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The explosive increase in genome sequencing and the advances in bioinformatic tools have revolutionized the rationale for natural product discovery from actinomycetes. In particular, this has revealed that actinomycete genomes contain numerous orphan gene clusters that have the potential to specify many yet unknown bioactive specialized metabolites, representing a huge unexploited pool of chemical diversity. Here, we describe the discovery of a novel group of catecholate-hydroxamate siderophores termed qinichelins (2-5) from Streptomyces sp. MBT76. Correlation between the metabolite levels and the protein expression profiles identified the biosynthetic gene cluster (named qch) most likely responsible for qinichelin biosynthesis. The structure of the molecules was elucidated by bioinformatics, mass spectrometry, and NMR. The genome of Streptomyces sp. MBT76 contains three gene clusters for the production of catecholate-peptide siderophores, including a separate cluster for the production of a shared catecholate precursor. In addition, an operon in the qch cluster was identified for the production of the ornithine precursor for qinichelins, independent of primary metabolism. This biosynthetic complexity provides new insights into the challenges scientists face when applying synthetic biology approaches for natural product discovery.
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Affiliation(s)
- Jacob Gubbens
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Changsheng Wu
- Molecular
Biotechnology, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE, Leiden, The Netherlands
| | - Hua Zhu
- Molecular
Biotechnology, Institute of Biology, Leiden University, Sylviusweg
72, 2333 BE, Leiden, The Netherlands
| | - Dmitri V. Filippov
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bogdan I. Florea
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Sébastien Rigali
- InBioS,
Centre for Protein Engineering, University of Liège, Liège, B-4000, Belgium
| | - Herman S. Overkleeft
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC 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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20
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Jones SE, Elliot MA. 'Exploring' the regulation of Streptomyces growth and development. Curr Opin Microbiol 2017; 42:25-30. [PMID: 29024914 DOI: 10.1016/j.mib.2017.09.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/06/2017] [Accepted: 09/14/2017] [Indexed: 12/14/2022]
Abstract
The Streptomyces life cycle encompasses three well-established developmental stages: vegetative hyphae, aerial hyphae and spores. Many regulators governing the transitions between these life cycle stages have been identified, and recent work is shedding light on their specific functions. A new discovery has shown Streptomyces can deviate from this classic life cycle through a process termed 'exploration', where cells rapidly traverse solid surfaces. Exploration does not require any of the traditional developmental regulators, and therefore provides an exciting new context in which to uncover novel developmental pathways. Here, we summarize our understanding of how Streptomyces exploration is controlled, and we speculate on how insight into classical regulation and stress response systems can inform future research into the regulation of exploratory growth.
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Affiliation(s)
- Stephanie E Jones
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1
| | - Marie A Elliot
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1.
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21
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Ordóñez-Robles M, Santos-Beneit F, Albillos SM, Liras P, Martín JF, Rodríguez-García A. Streptomyces tsukubaensis as a new model for carbon repression: transcriptomic response to tacrolimus repressing carbon sources. Appl Microbiol Biotechnol 2017; 101:8181-8195. [PMID: 28983826 DOI: 10.1007/s00253-017-8545-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 11/26/2022]
Abstract
In this work, we identified glucose and glycerol as tacrolimus repressing carbon sources in the important species Streptomyces tsukubaensis. A genome-wide analysis of the transcriptomic response to glucose and glycerol additions was performed using microarray technology. The transcriptional time series obtained allowed us to compare the transcriptomic profiling of S. tsukubaensis growing under tacrolimus producing and non-producing conditions. The analysis revealed important and different metabolic changes after the additions and a lack of transcriptional activation of the fkb cluster. In addition, we detected important differences in the transcriptional response to glucose between S. tsukubaensis and the model species Streptomyces coelicolor. A number of genes encoding key players of morphological and biochemical differentiation were strongly and permanently downregulated by the carbon sources. Finally, we identified several genes showing transcriptional profiles highly correlated to that of the tacrolimus biosynthetic pathway regulator FkbN that might be potential candidates for the improvement of tacrolimus production.
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Affiliation(s)
- María Ordóñez-Robles
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
| | - Fernando Santos-Beneit
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Silvia M Albillos
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
- Departamento de Biotecnología y Ciencia de los Alimentos, Facultad de Ciencias, Universidad de Burgos, 09001, Burgos, Spain
| | - Paloma Liras
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
| | - Juan F Martín
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain
| | - Antonio Rodríguez-García
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071, León, Spain.
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, 24006, León, Spain.
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22
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Romero-Rodríguez A, Rocha D, Ruiz-Villafán B, Guzmán-Trampe S, Maldonado-Carmona N, Vázquez-Hernández M, Zelarayán A, Rodríguez-Sanoja R, Sánchez S. Carbon catabolite regulation in Streptomyces: new insights and lessons learned. World J Microbiol Biotechnol 2017; 33:162. [PMID: 28770367 DOI: 10.1007/s11274-017-2328-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 07/30/2017] [Indexed: 11/25/2022]
Abstract
One of the most significant control mechanisms of the physiological processes in the genus Streptomyces is carbon catabolite repression (CCR). This mechanism controls the expression of genes involved in the uptake and utilization of alternative carbon sources in Streptomyces and is mostly independent of the phosphoenolpyruvate phosphotransferase system (PTS). CCR also affects morphological differentiation and the synthesis of secondary metabolites, although not all secondary metabolite genes are equally sensitive to the control by the carbon source. Even when the outcome effect of CCR in bacteria is the same, their essential mechanisms can be rather different. Although usually, glucose elicits this phenomenon, other rapidly metabolized carbon sources can also cause CCR. Multiple efforts have been put through to the understanding of the mechanism of CCR in this genus. However, a reasonable mechanism to explain the nature of this process in Streptomyces does not yet exist. Several examples of primary and secondary metabolites subject to CCR will be examined in this review. Additionally, recent advances in the metabolites and protein factors involved in the Streptomyces CCR, as well as their mechanisms will be described and discussed in this review.
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Affiliation(s)
- Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Diana Rocha
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Beatriz Ruiz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Silvia Guzmán-Trampe
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Nidia Maldonado-Carmona
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Melissa Vázquez-Hernández
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Augusto Zelarayán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior de Ciudad Universitaria, Mexico City, 04510, Mexico.
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23
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Millan-Oropeza A, Henry C, Blein-Nicolas M, Aubert-Frambourg A, Moussa F, Bleton J, Virolle MJ. Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans. J Proteome Res 2017; 16:2597-2613. [DOI: 10.1021/acs.jproteome.7b00163] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Aaron Millan-Oropeza
- Institute
for
Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud,
Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Céline Henry
- Micalis Institute,
INRA, PAPPSO, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Mélisande Blein-Nicolas
- Génétique
Quantitative et Évolution (GQE) - Le Moulon, INRA, Univ Paris-Sud,
CNRS, AgroParisTech, Université Paris-Saclay, F-91190 Gif-sur-Yvette, France
| | - Anne Aubert-Frambourg
- Micalis Institute,
INRA, PAPPSO, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Fathi Moussa
- Lip(Sys)2, LETIAM (formerly included in
EA4041 Groupe de Chimie Analytique
de Paris-Sud), Univ. Paris-Sud, Université Paris-Saclay, IUT
d’Orsay, Plateau de Moulon, F-91400 Orsay, France
| | - Jean Bleton
- Lip(Sys)2, LETIAM (formerly included in
EA4041 Groupe de Chimie Analytique
de Paris-Sud), Univ. Paris-Sud, Université Paris-Saclay, IUT
d’Orsay, Plateau de Moulon, F-91400 Orsay, France
| | - Marie-Jöelle Virolle
- Institute
for
Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud,
Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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24
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Gubbens J, Janus MM, Florea BI, Overkleeft HS, van Wezel GP. Identification of glucose kinase-dependent and -independent pathways for carbon control of primary metabolism, development and antibiotic production in Streptomyces coelicolor by quantitative proteomics. Mol Microbiol 2017. [PMID: 28631385 DOI: 10.1111/mmi.13714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Tierrafría VH, Licona-Cassani C, Maldonado-Carmona N, Romero-Rodríguez A, Centeno-Leija S, Marcellin E, Rodríguez-Sanoja R, Ruiz-Villafán B, Nielsen LK, Sánchez S. Deletion of the hypothetical protein SCO2127 of Streptomyces coelicolor allowed identification of a new regulator of actinorhodin production. Appl Microbiol Biotechnol 2016; 100:9229-9237. [PMID: 27604626 DOI: 10.1007/s00253-016-7811-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/10/2016] [Accepted: 08/26/2016] [Indexed: 01/19/2023]
Abstract
Although the specific function of SCO2127 remains elusive, it has been assumed that this hypothetical protein plays an important role in carbon catabolite regulation and therefore in antibiotic biosynthesis in Streptomyces coelicolor. To shed light on the functional relationship of SCO2127 to the biosynthesis of actinorhodin, a detailed analysis of the proteins differentially produced between the strain M145 and the Δsco2127 mutant of S. coelicolor was performed. The delayed morphological differentiation and impaired production of actinorhodin showed by the deletion strain were accompanied by increased abundance of gluconeogenic enzymes, as well as downregulation of both glycolysis and acetyl-CoA carboxylase. Repression of mycothiol biosynthetic enzymes was further observed in the absence of SCO2127, in addition to upregulation of hydroxyectoine biosynthetic enzymes and SCO0204, which controls nitrite formation. The data generated in this study reveal that the response regulator SCO0204 greatly contributes to prevent the formation of actinorhodin in the ∆sco2127 mutant, likely through the activation of some proteins associated with oxidative stress that include the nitrite producer SCO0216.
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Affiliation(s)
- Víctor H Tierrafría
- Instituto de Investigaciones Biomédicas. 3er Circuito Exterior s/n, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, Mexico
| | - Cuauhtemoc Licona-Cassani
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Brisbane, Australia
| | - Nidia Maldonado-Carmona
- Instituto de Investigaciones Biomédicas. 3er Circuito Exterior s/n, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, Mexico
| | - Alba Romero-Rodríguez
- Instituto de Investigaciones Biomédicas. 3er Circuito Exterior s/n, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, Mexico
| | - Sara Centeno-Leija
- Instituto de Investigaciones Biomédicas. 3er Circuito Exterior s/n, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, Mexico
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Brisbane, Australia
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas. 3er Circuito Exterior s/n, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, Mexico
| | - Beatriz Ruiz-Villafán
- Instituto de Investigaciones Biomédicas. 3er Circuito Exterior s/n, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, Mexico
| | - Lars K Nielsen
- Laboratorio de Bioingeniería, Universidad de Colima, Coquimatlán-, 28400, Colima, Mexico
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas. 3er Circuito Exterior s/n, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, Mexico.
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26
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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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27
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Romero-Rodríguez A, Ruiz-Villafán B, Tierrafría VH, Rodríguez-Sanoja R, Sánchez S. Carbon Catabolite Regulation of Secondary Metabolite Formation and Morphological Differentiation in Streptomyces coelicolor. Appl Biochem Biotechnol 2016; 180:1152-1166. [PMID: 27372741 DOI: 10.1007/s12010-016-2158-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022]
Abstract
In the genus Streptomyces, carbon utilization is of significant importance for the expression of genes involved in morphological differentiation and antibiotic production. However, there is little information about the mechanism involved in these effects. In the present work, it was found that glucose exerted a suppressive effect on the Streptomyces coelicolor actinorhodin (Act) and undecylprodigiosin (Red) production, as well as in its morphological differentiation. Accordingly, using a high-density microarray approach in S. coelicolor grown under glucose repression, at early growth stages, a negative effect was exerted on the transcription of genes involved in Act and Red production, when compared with non-repressive conditions. Seven genes of Act and at least ten genes of Red production were down-regulated by glucose. Stronger repression was observed on the initial steps of antibiotics formation. On the contrary, the coelimycin P1 cluster was up-regulated by glucose. Regarding differentiation, no sporulation was observed in the presence of glucose and expression of a set of genes of the bld cascade was repressed as well as chaplins and rodlins genes. Finally, a series of transcriptional regulators involved in both processes were up- or down-regulated by glucose. This is the first global transcriptomic approach performed to understand the molecular basis of the glucose effect on the synthesis of secondary metabolism and differentiation in the genus Streptomyces. The results of this study are opening new avenues for further exploration.
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Affiliation(s)
- A Romero-Rodríguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Cd. de Mexico, Mexico
| | - B Ruiz-Villafán
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Cd. de Mexico, Mexico
| | - V H Tierrafría
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Cd. de Mexico, Mexico
| | - R Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Cd. de Mexico, Mexico
| | - S Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Cd. de Mexico, Mexico.
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28
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Romero-Rodríguez A, Rocha D, Ruiz-Villafan B, Tierrafría V, Rodríguez-Sanoja R, Segura-González D, Sánchez S. Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor. BMC Microbiol 2016; 16:77. [PMID: 27121083 PMCID: PMC4848846 DOI: 10.1186/s12866-016-0690-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 04/14/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND In the genus Streptomyces, one of the most remarkable control mechanisms of physiological processes is carbon catabolite repression (CCR). This mechanism regulates the expression of genes involved in the uptake and utilization of alternative carbon sources. CCR also affects the synthesis of secondary metabolites and morphological differentiation. Even when the outcome effect of CCR in different bacteria is the same, their essential mechanisms can be quite different. In several streptomycetes glucose kinase (Glk) represents the main glucose phosphorylating enzyme and has been regarded as a regulatory protein in CCR. To evaluate the paradigmatic model proposed for CCR in Streptomyces, a high-density microarray approach was applied to Streptomyces coelicolor M145, under repressed and non-repressed conditions. The transcriptomic study was extended to assess the ScGlk role in this model by comparing the transcriptomic profile of S. coelicolor M145 with that of a ∆glk mutant derived from the wild-type strain, complemented with a heterologous glk gene from Zymomonas mobilis (Zmglk), insensitive to CCR but able to grow in glucose (ScoZm strain). RESULTS Microarray experiments revealed that glucose influenced the expression of 651 genes. Interestingly, even when the ScGlk protein does not have DNA binding domains and the glycolytic flux was restored by a heterologous glucokinase, the ScGlk replacement modified the expression of 134 genes. From these, 91 were also affected by glucose while 43 appeared to be under the control of ScGlk. This work identified the expression of S. coelicolor genes involved in primary metabolism that were influenced by glucose and/or ScGlk. Aside from describing the metabolic pathways influenced by glucose and/or ScGlk, several unexplored transcriptional regulators involved in the CCR mechanism were disclosed. CONCLUSIONS The transcriptome of a classical model of CCR was studied in S. coelicolor to differentiate between the effects due to glucose or ScGlk in this regulatory mechanism. Glucose elicited important metabolic and transcriptional changes in this microorganism. While its entry and flow through glycolysis and pentose phosphate pathway were stimulated, the gluconeogenesis was inhibited. Glucose also triggered the CCR by repressing transporter systems and the transcription of enzymes required for secondary carbon sources utilization. Our results confirm and update the agar model of the CCR in Streptomyces and its dependence on the ScGlk per se. Surprisingly, the expected regulatory function of ScGlk was not found to be as global as thought before (only 43 out of 779 genes were affected), although may be accompanied or coordinated by other transcriptional regulators. Aside from describing the metabolic pathways influenced by glucose and/or ScGlk, several unexplored transcriptional regulators involved in the CCR mechanism were disclosed. These findings offer new opportunities to study and understand the CCR in S. coelicolor by increasing the number of known glucose and ScGlk -regulated pathways and a new set of putative regulatory proteins possibly involved or controlling the CCR.
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Affiliation(s)
- Alba Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico
| | - Diana Rocha
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico
| | - Beatriz Ruiz-Villafan
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico
| | - Víctor Tierrafría
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico
| | - Romina Rodríguez-Sanoja
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico
| | - Daniel Segura-González
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Ave. Universidad 2001, Cuernavaca, Mor. 62210, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior s/n, Ciudad de Mexico, 04510, Mexico.
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29
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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: 915] [Impact Index Per Article: 114.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.
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Affiliation(s)
- Essaid Ait Barka
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Parul Vatsa
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Lisa Sanchez
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Nathalie Gaveau-Vaillant
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Cedric Jacquard
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christophe Clément
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Yder Ouhdouch
- Faculté de Sciences Semlalia, Université Cadi Ayyad, Laboratoire de Biologie et de Biotechnologie des Microorganismes, Marrakesh, Morocco
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Sylvius Laboratories, Leiden University, Leiden, The Netherlands
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30
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Nitrogen regulator GlnR controls uptake and utilization of non-phosphotransferase-system carbon sources in actinomycetes. Proc Natl Acad Sci U S A 2015; 112:15630-5. [PMID: 26644570 DOI: 10.1073/pnas.1508465112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The regulatory mechanisms underlying the uptake and utilization of multiple types of carbohydrates in actinomycetes remain poorly understood. In this study, we show that GlnR (central regulator of nitrogen metabolism) serves as a universal regulator of nitrogen metabolism and plays an important, previously unknown role in controlling the transport of non-phosphotransferase-system (PTS) carbon sources in actinomycetes. It was observed that GlnR can directly interact with the promoters of most (13 of 20) carbohydrate ATP-binding cassette (ABC) transporter loci and can activate the transcription of these genes in response to nitrogen availability in industrial, erythromycin-producing Saccharopolyspora erythraea. Deletion of the glnR gene resulted in severe growth retardation under the culture conditions used, with select ABC-transported carbohydrates (maltose, sorbitol, mannitol, cellobiose, trehalose, or mannose) used as the sole carbon source. Furthermore, we found that GlnR-mediated regulation of carbohydrate transport was highly conserved in actinomycetes. These results demonstrate that GlnR serves a role beyond nitrogen metabolism, mediating critical functions in carbon metabolism and crosstalk of nitrogen- and carbon-metabolism pathways in response to the nutritional states of cells. These findings provide insights into the molecular regulation of transport and metabolism of non-PTS carbohydrates and reveal potential applications for the cofermentation of biomass-derived sugars in the production of biofuels and bio-based chemicals.
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31
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Wu C, Du C, Gubbens J, Choi YH, van Wezel GP. Metabolomics-Driven Discovery of a Prenylated Isatin Antibiotic Produced by Streptomyces Species MBT28. JOURNAL OF NATURAL PRODUCTS 2015; 78:2355-2363. [PMID: 26438963 DOI: 10.1021/acs.jnatprod.5b00276] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Actinomycetes are a major source of antimicrobials, anticancer compounds, and other medically important products, and their genomes harbor extensive biosynthetic potential. Major challenges in the screening of these microorganisms are to activate the expression of cryptic biosynthetic gene clusters and the development of technologies for efficient dereplication of known molecules. Here we report the identification of a previously unidentified isatin-type antibiotic produced by Streptomyces sp. MBT28, following a strategy based on NMR-based metabolomics combined with the introduction of streptomycin resistance in the producer strain. NMR-guided isolation by tracking the target proton signal resulted in the characterization of 7-prenylisatin (1) with antimicrobial activity against Bacillus subtilis. The metabolite-guided genome mining of Streptomyces sp. MBT28 combined with proteomics identified a gene cluster with an indole prenyltransferase that catalyzes the conversion of tryptophan into 7-prenylisatin. This study underlines the applicability of NMR-based metabolomics in facilitating the discovery of novel antibiotics.
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Affiliation(s)
| | | | - Jacob Gubbens
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
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32
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Biochemistry and regulatory functions of bacterial glucose kinases. Arch Biochem Biophys 2015; 577-578:1-10. [DOI: 10.1016/j.abb.2015.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/30/2015] [Accepted: 05/02/2015] [Indexed: 11/19/2022]
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33
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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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34
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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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35
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Natural Product Proteomining, a Quantitative Proteomics Platform, Allows Rapid Discovery of Biosynthetic Gene Clusters for Different Classes of Natural Products. ACTA ACUST UNITED AC 2014; 21:707-18. [DOI: 10.1016/j.chembiol.2014.03.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 03/02/2014] [Accepted: 03/24/2014] [Indexed: 11/23/2022]
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36
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Characterization of Polyphosphate Glucokinase SCO5059 fromStreptomyces coelicolorA3(2). Biosci Biotechnol Biochem 2014; 77:2322-4. [DOI: 10.1271/bbb.130498] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Glucose kinases from Streptomyces peucetius var. caesius. Appl Microbiol Biotechnol 2014; 98:6061-71. [DOI: 10.1007/s00253-014-5662-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 11/26/2022]
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38
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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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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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The ROK family regulator Rok7B7 pleiotropically affects xylose utilization, carbon catabolite repression, and antibiotic production in streptomyces coelicolor. J Bacteriol 2013; 195:1236-48. [PMID: 23292782 DOI: 10.1128/jb.02191-12] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Members of the ROK family of proteins are mostly transcriptional regulators and kinases that generally relate to the control of primary metabolism, whereby its member glucose kinase acts as the central control protein in carbon control in Streptomyces. Here, we show that deletion of SCO6008 (rok7B7) strongly affects carbon catabolite repression (CCR), growth, and antibiotic production in Streptomyces coelicolor. Deletion of SCO7543 also affected antibiotic production, while no major changes were observed after deletion of the rok family genes SCO0794, SCO1060, SCO2846, SCO6566, or SCO6600. Global expression profiling of the rok7B7 mutant by proteomics and microarray analysis revealed strong upregulation of the xylose transporter operon xylFGH, which lies immediately downstream of rok7B7, consistent with the improved growth and delayed development of the mutant on xylose. The enhanced CCR, which was especially obvious on rich or xylose-containing media, correlated with elevated expression of glucose kinase and of the glucose transporter GlcP. In liquid-grown cultures, expression of the biosynthetic enzymes for production of prodigionines, siderophores, and calcium-dependent antibiotic (CDA) was enhanced in the mutant, and overproduction of prodigionines was corroborated by matrix-assisted laser desorption ionization-time-of-flight analysis. These data present Rok7B7 as a pleiotropic regulator of growth, CCR, and antibiotic production in Streptomyces.
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