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Fedorenko V, Genilloud O, Horbal L, Marcone GL, Marinelli F, Paitan Y, Ron EZ. Antibacterial Discovery and Development: From Gene to Product and Back. BIOMED RESEARCH INTERNATIONAL 2015; 2015:591349. [PMID: 26339625 PMCID: PMC4538407 DOI: 10.1155/2015/591349] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/30/2014] [Accepted: 01/13/2015] [Indexed: 12/23/2022]
Abstract
Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement.
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Affiliation(s)
- Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences Technology Park, 18016 Granada, Spain
| | - Liliya Horbal
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano, and University of Insubria, 21100 Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano, and University of Insubria, 21100 Varese, Italy
| | - Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, 44281 Kfar Saba, Israel
| | - Eliora Z. Ron
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 6997801 Tel Aviv, Israel
- Galilee Research Institute (MIGAL), 11016 Kiryat Shmona, Israel
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202
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Socially mediated induction and suppression of antibiosis during bacterial coexistence. Proc Natl Acad Sci U S A 2015. [PMID: 26216986 DOI: 10.1073/pnas.1504076112] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Despite their importance for humans, there is little consensus on the function of antibiotics in nature for the bacteria that produce them. Classical explanations suggest that bacteria use antibiotics as weapons to kill or inhibit competitors, whereas a recent alternative hypothesis states that antibiotics are signals that coordinate cooperative social interactions between coexisting bacteria. Here we distinguish these hypotheses in the prolific antibiotic-producing genus Streptomyces and provide strong evidence that antibiotics are weapons whose expression is significantly influenced by social and competitive interactions between competing strains. We show that cells induce facultative responses to cues produced by competitors by (i) increasing their own antibiotic production, thereby decreasing costs associated with constitutive synthesis of these expensive products, and (ii) by suppressing antibiotic production in competitors, thereby reducing direct threats to themselves. These results thus show that although antibiotic production is profoundly social, it is emphatically not cooperative. Using computer simulations, we next show that these facultative strategies can facilitate the maintenance of biodiversity in a community context by converting lethal interactions between neighboring colonies to neutral interactions where neither strain excludes the other. Thus, just as bacteriocins can lead to increased diversity via rock-paper-scissors dynamics, so too can antibiotics via elicitation and suppression. Our results reveal that social interactions are crucial for understanding antibiosis and bacterial community dynamics, and highlight the potential of interbacterial interactions for novel drug discovery by eliciting pathways that mediate interference competition.
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203
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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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204
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Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 2015; 13:509-23. [PMID: 26119570 DOI: 10.1038/nrmicro3496] [Citation(s) in RCA: 601] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities and a wide variety of applications in medicine and agriculture, such as the treatment of infectious diseases and cancer, and the prevention of crop damage. Genomics has revealed that many microorganisms have far greater potential to produce specialized metabolites than was thought from classic bioactivity screens; however, realizing this potential has been hampered by the fact that many specialized metabolite biosynthetic gene clusters (BGCs) are not expressed in laboratory cultures. In this Review, we discuss the strategies that have been developed in bacteria and fungi to identify and induce the expression of such silent BGCs, and we briefly summarize methods for the isolation and structural characterization of their metabolic products.
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205
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Romero-Rodríguez A, Robledo-Casados I, Sánchez S. An overview on transcriptional regulators in Streptomyces. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1017-39. [PMID: 26093238 DOI: 10.1016/j.bbagrm.2015.06.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 12/19/2022]
Abstract
Streptomyces are Gram-positive microorganisms able to adapt and respond to different environmental conditions. It is the largest genus of Actinobacteria comprising over 900 species. During their lifetime, these microorganisms are able to differentiate, produce aerial mycelia and secondary metabolites. All of these processes are controlled by subtle and precise regulatory systems. Regulation at the transcriptional initiation level is probably the most common for metabolic adaptation in bacteria. In this mechanism, the major players are proteins named transcription factors (TFs), capable of binding DNA in order to repress or activate the transcription of specific genes. Some of the TFs exert their action just like activators or repressors, whereas others can function in both manners, depending on the target promoter. Generally, TFs achieve their effects by using one- or two-component systems, linking a specific type of environmental stimulus to a transcriptional response. After DNA sequencing, many streptomycetes have been found to have chromosomes ranging between 6 and 12Mb in size, with high GC content (around 70%). They encode for approximately 7000 to 10,000 genes, 50 to 100 pseudogenes and a large set (around 12% of the total chromosome) of regulatory genes, organized in networks, controlling gene expression in these bacteria. Among the sequenced streptomycetes reported up to now, the number of transcription factors ranges from 471 to 1101. Among these, 315 to 691 correspond to transcriptional regulators and 31 to 76 are sigma factors. The aim of this work is to give a state of the art overview on transcription factors in the genus Streptomyces.
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Affiliation(s)
- Alba Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Ivonne Robledo-Casados
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F. 04510, Mexico.
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206
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Increasing Avermectin Production in Streptomyces avermitilis by Manipulating the Expression of a Novel TetR-Family Regulator and Its Target Gene Product. Appl Environ Microbiol 2015; 81:5157-73. [PMID: 26002902 DOI: 10.1128/aem.00868-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/18/2015] [Indexed: 11/20/2022] Open
Abstract
Avermectins produced by Streptomyces avermitilis are commercially important anthelmintic agents. The detailed regulatory mechanisms of avermectin biosynthesis remain unclear. Here, we identified SAV3619, a TetR-family transcriptional regulator designated AveT, to be an activator for both avermectin production and morphological differentiation in S. avermitilis. AveT was shown to indirectly stimulate avermectin production by affecting transcription of the cluster-situated activator gene aveR. AveT directly repressed transcription of its own gene (aveT), adjacent gene pepD2 (sav_3620), sav_7490 (designated aveM), and sav_7491 by binding to an 18-bp perfect palindromic sequence (CGAAACGKTKYCGTTTCG, where K is T or G and Y is T or C and where the underlining indicates inverted repeats) within their promoter regions. aveM (which encodes a putative transmembrane efflux protein belonging to the major facilitator superfamily [MFS]), the important target gene of AveT, had a striking negative effect on avermectin production and morphological differentiation. Overexpression of aveT and deletion of aveM in wild-type and industrial strains of S. avermitilis led to clear increases in the levels of avermectin production. In vitro gel-shift assays suggested that C-5-O-B1, the late pathway precursor of avermectin B1, acts as an AveT ligand. Taken together, our findings indicate positive-feedback regulation of aveT expression and avermectin production by a late pathway intermediate and provide the basis for an efficient strategy to increase avermectin production in S. avermitilis by manipulation of AveT and its target gene product, AveM.
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207
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Ahmad MS, Yasser MM, Sholkamy EN, Ali AM, Mehanni MM. Anticancer activity of biostabilized selenium nanorods synthesized by Streptomyces bikiniensis strain Ess_amA-1. Int J Nanomedicine 2015; 10:3389-401. [PMID: 26005349 PMCID: PMC4428361 DOI: 10.2147/ijn.s82707] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Selenium is an important component of human diet and a number of studies have declared its chemopreventive and therapeutic properties against cancer. However, very limited studies have been conducted about the properties of selenium nanostructured materials in comparison to other well-studied selenospecies. Here, we have shown that the anticancer property of biostabilized selenium nanorods (SeNrs) synthesized by applying a novel strain Ess_amA-1 of Streptomyces bikiniensis. The strain was grown aerobically with selenium dioxide and produced stable SeNrs with average particle size of 17 nm. The optical, structural, morphological, elemental, and functional characterizations of the SeNrs were carried out using techniques such as UV-vis spectrophotometry, transmission electron microscopy, energy dispersive X-ray spectrometry, and Fourier transform infrared spectrophotometry, respectively. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay revealed that the biosynthesized SeNrs induces cell death of Hep-G2 and MCF-7 human cancer cells. The lethal dose (LD50%) of SeNrs on Hep-G2 and MCF-7 cells was recorded at 75.96 μg/mL and 61.86 μg/mL, respectively. It can be concluded that S. bikiniensis strain Ess_amA-1 could be used as renewable bioresources of biosynthesis of anticancer SeNrs. A hypothetical mechanism for anticancer activity of SeNrs is also proposed.
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Affiliation(s)
- Maged Sayed Ahmad
- Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef, Egypt
| | - Manal Mohamed Yasser
- Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef, Egypt
| | - Essam Nageh Sholkamy
- Department of Botany, Faculty of Science, University of Beni-Suef, Beni-Suef, Egypt
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ali Mohamed Ali
- Department of Botany and Microbiology, College of Science, Minia University, El-Minia, Egypt
- Department of Biological Sciences, College of Science, King Faisal University, Saudi Arabia
| | - Magda Mohamed Mehanni
- Department of Botany and Microbiology, College of Science, Minia University, El-Minia, Egypt
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208
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Li X, Yu T, He Q, McDowall KJ, Jiang B, Jiang Z, Wu L, Li G, Li Q, Wang S, Shi Y, Wang L, Hong B. Binding of a biosynthetic intermediate to AtrA modulates the production of lidamycin by Streptomyces globisporus. Mol Microbiol 2015; 96:1257-71. [PMID: 25786547 DOI: 10.1111/mmi.13004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2015] [Indexed: 11/30/2022]
Abstract
The control of secondary production in streptomycetes involves the funneling of environmental and physiological signals to the cluster-situated (transcriptional) regulators (CSRs) of the biosynthetic genes. For some systems, the binding of biosynthetic products to the CSR has been shown to provide negative feedback. Here we show for the production of lidamycin (C-1027), a clinically relevant antitumor agent, by Streptomyces globisporus that negative feedback can extend to a point higher in the regulatory cascade. We show that the DNA-binding activity of the S. globisporus orthologue of AtrA, which was initially described as a transcriptional activator of actinorhodin biosynthesis in S. coelicolor, is inhibited by the binding of heptaene, a biosynthetic intermediate of lidamycin. Additional experiments described here show that S. globisporus AtrA binds in vivo as well as in vitro to the promoter region of the gene encoding SgcR1, one of the CSRs of lidamycin production. The feedback to the pleiotropic regulator AtrA is likely to provide a mechanism for coordinating the production of lidamycin with that of other secondary metabolites. The activity of AtrA is also regulated by actinorhodin. As AtrA is evolutionarily conserved, negative feedback of the type described here may be widespread within the streptomycetes.
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Affiliation(s)
- Xingxing Li
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Tengfei Yu
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qing He
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Kenneth J McDowall
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Bingya Jiang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Zhibo Jiang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Linzhuan Wu
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Guangwei Li
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qinglian Li
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Songmei Wang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yuanyuan Shi
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Lifei Wang
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Bin Hong
- The Key Laboratory of Biotechnology of Antibiotics of Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
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209
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Phelan RM, Sekurova ON, Keasling JD, Zotchev SB. Engineering terpene biosynthesis in Streptomyces for production of the advanced biofuel precursor bisabolene. ACS Synth Biol 2015; 4:393-9. [PMID: 25006988 DOI: 10.1021/sb5002517] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The past decade has witnessed a large influx of research toward the creation of sustainable, biologically derived fuels. While significant effort has been exerted to improve production capacity in common hosts, such as Escherichia coli or Saccharomyces cerevisiae, studies concerning alternate microbes comparatively lag. In an effort to expand the breadth of characterized hosts for fuel production, we map the terpene biosynthetic pathway in a model actinobacterium, Streptomyces venezuelae, and further alter secondary metabolism to afford the advanced biofuel precursor bisabolene. Leveraging information gained from study of the native isoprenoid pathway, we were able to increase bisabolene titer nearly 5-fold over the base production strain, more than 2 orders of magnitude greater than the combined terpene yield in the wild-type host. We also explored production on carbon sources of varying complexity to, notably, define this host as one able to perform consolidated bioprocessing.
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Affiliation(s)
- Ryan M. Phelan
- Joint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, California 94608, United States
| | - Olga N. Sekurova
- Department
of Biotechnology, Norwegian University of Science and Technology, Sem Saelands vei 6/8, 7491 Trondheim, Norway
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, California 94608, United States
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720 United States
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 United States
| | - Sergey B. Zotchev
- Department
of Biotechnology, Norwegian University of Science and Technology, Sem Saelands vei 6/8, 7491 Trondheim, Norway
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210
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Świątek-Połatyńska MA, Bucca G, Laing E, Gubbens J, Titgemeyer F, Smith CP, Rigali S, van Wezel GP. Genome-wide analysis of in vivo binding of the master regulator DasR in Streptomyces coelicolor identifies novel non-canonical targets. PLoS One 2015; 10:e0122479. [PMID: 25875084 PMCID: PMC4398421 DOI: 10.1371/journal.pone.0122479] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 02/22/2015] [Indexed: 11/30/2022] Open
Abstract
Streptomycetes produce a wealth of natural products, including over half of all known antibiotics. It was previously demonstrated that N-acetylglucosamine and secondary metabolism are closely entwined in streptomycetes. Here we show that DNA recognition by the N-acetylglucosamine-responsive regulator DasR is growth-phase dependent, and that DasR can bind to sites in the S. coelicolor genome that have no obvious resemblance to previously identified DasR-responsive elements. Thus, the regulon of DasR extends well beyond what was previously predicted and includes a large number of genes with functions far removed from N-acetylglucosamine metabolism, such as genes for small RNAs and DNA transposases. Conversely, the DasR regulon during vegetative growth largely correlates to the presence of canonical DasR-responsive elements. The changes in DasR binding in vivo following N-acetylglucosamine induction were studied in detail and a possible molecular mechanism by which the influence of DasR is extended is discussed. Discussion of DasR binding was further informed by a parallel transcriptome analysis of the respective cultures. Evidence is provided that DasR binds directly to the promoters of all genes encoding pathway-specific regulators of antibiotic production in S. coelicolor, thereby providing an exquisitely simple link between nutritional control and secondary metabolism.
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Affiliation(s)
| | - Giselda Bucca
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Emma Laing
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Jacob Gubbens
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Fritz Titgemeyer
- Department of Oecotrophologie, Münster University of Applied Sciences, Corrensstr. 25, 48149 Münster, Germany
| | - Colin P. Smith
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
| | - Sébastien Rigali
- Centre for Protein Engineering, Université de Liège, Institut de Chimie B6a, Sart-Tilman, B-4000 Liège, Belgium
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
- * E-mail:
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211
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Lambert S, Traxler MF, Craig M, Maciejewska M, Ongena M, van Wezel GP, Kolter R, Rigali S. Altered desferrioxamine-mediated iron utilization is a common trait of bald mutants of Streptomyces coelicolor. Metallomics 2015; 6:1390-9. [PMID: 24788337 DOI: 10.1039/c4mt00068d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Streptomyces coelicolor is an important model organism for developmental studies of filamentous GC-rich actinobacteria. The genetic characterization of mutants of S. coelicolor blocked at the vegetative mycelium stage, the so-called bald (bld) mutants that are unable to erect spore-forming aerial hyphae, has opened the way to discovering the molecular basis of development in actinomycetes. Desferrioxamine (DFO) production and import of ferrioxamines (FO; iron-complexed DFO) are key to triggering morphogenesis of S. coelicolor and we show here that growth of S. coelicolor on the reference medium for Streptomyces developmental studies is fully dependent on DFO biosynthesis. UPLC-ESI-MS analysis revealed that all bld mutants tested are affected in DFO biosynthesis, with bldA, bldJ, and ptsH mutants severely impaired in DFO production, while bldF, bldK, crr and ptsI mutants overproduce DFO. Morphogenesis of bldK and bldJ mutants was recovered by supplying exogenous iron. Transcript analysis showed that the bldJ mutant is impaired in expression of genes involved in the uptake of FO, whereas transcription of genes involved in both DFO biosynthesis and FO uptake is increased in bldK mutants. Our study allows proposing altered DFO production and/or FO uptake as a novel phenotypic marker of many S. coelicolor bld mutants, and strengthens the role of siderophores and iron acquisition in morphological development of actinomycetes.
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Affiliation(s)
- Stéphany Lambert
- Centre for Protein Engineering, University of Liège, Institut de Chimie B6a, B-4000 Liège, Belgium.
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212
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Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea. Appl Microbiol Biotechnol 2015; 99:5939-50. [PMID: 25820602 DOI: 10.1007/s00253-015-6547-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/05/2015] [Accepted: 03/15/2015] [Indexed: 10/23/2022]
Abstract
Phenazines represent a large group of nitrogen-containing heterocyclic compounds produced by the diverse group of bacteria including actinobacteria. In this study, a total of 197 actinobacterial strains were isolated from seven different marine sponge species in the South China Sea using five different culture media. Eighty-seven morphologically different actinobacterial strains were selected and grouped into 13 genera, including Actinoalloteichus, Kocuria, Micrococcus, Micromonospora, Mycobacterium, Nocardiopsis, Prauserella, Rhodococcus, Saccharopolyspora, Salinispora, Serinicoccus, and Streptomyces by the phylogenetic analysis of 16S rRNA gene. Based on the screening of phzE genes, ten strains, including five Streptomyces, two Nocardiopsis, one Salinispora, one Micrococcus, and one Serinicoccus were found to be potential for phenazine production. The level of phzE gene expression was highly expressed in Nocardiopsis sp. 13-33-15, 13-12-13, and Serinicoccus sp. 13-12-4 on the fifth day of fermentation. Finally, 1,6-dihydroxy phenazine (1) from Nocardiopsis sp. 13-33-15 and 13-12-13, and 1,6-dimethoxy phenazine (2) from Nocardiopsis sp. 13-33-15 were isolated and identified successfully based on ESI-MS and NMR analysis. The compounds 1 and 2 showed antibacterial activity against Bacillus mycoides SJ14, Staphylococcus aureus SJ51, Escherichia coli SJ42, and Micrococcus luteus SJ47. This study suggests that the integrated approach of gene screening and chemical analysis is an effective strategy to find the target compounds and lays the basis for the production of phenazine from the sponge-associated actinobacteria.
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213
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A MarR Family Transcriptional Regulator, DptR3, Activates Daptomycin Biosynthesis and Morphological Differentiation in Streptomyces roseosporus. Appl Environ Microbiol 2015; 81:3753-65. [PMID: 25819953 DOI: 10.1128/aem.00057-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/19/2015] [Indexed: 11/20/2022] Open
Abstract
Daptomycin produced by Streptomyces roseosporus is an important lipopeptide antibiotic used to treat human infections caused by Gram-positive pathogenic bacteria, including drug-resistant strains. The genetic basis for regulatory mechanisms of daptomycin production is poorly known. Here, we characterized the dptR3 gene, which encodes a MarR family transcriptional regulator located adjacent to the known daptomycin biosynthetic (dpt) genes. Deletion of dptR3 reduced daptomycin production significantly and delayed aerial mycelium formation and sporulation on solid media. Dissection of the mechanism underlying the function of DptR3 in daptomycin production revealed that it stimulates daptomycin production indirectly by altering the transcription of dpt structural genes. DptR3 directly activated the transcription of its own gene, dptR3, but repressed the transcription of the adjacent, divergent gene orf16 (which encodes a putative ABC transporter ATP-binding protein). A 66-nucleotide DptR3-binding site in the intergenic region of dptR3-orf16 was determined by DNase I footprinting, and the palindromic sequence TCATTGTTACCTATGCTCACAATGA (underlining indicates inverted repeats) in the protected region was found to be essential for DptR3 binding. orf16, the major target gene of DptR3, exerted a positive effect on daptomycin biosynthesis. Our findings indicate that DptR3 functions as a global regulator that positively controls daptomycin production and morphological development in S. roseosporus.
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214
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Tyc O, Wolf AB, Garbeva P. The effect of phylogenetically different bacteria on the fitness of Pseudomonas fluorescens in sand microcosms. PLoS One 2015; 10:e0119838. [PMID: 25774766 PMCID: PMC4361692 DOI: 10.1371/journal.pone.0119838] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/19/2015] [Indexed: 12/13/2022] Open
Abstract
In most environments many microorganisms live in close vicinity and can interact in various ways. Recent studies suggest that bacteria are able to sense and respond to the presence of neighbouring bacteria in the environment and alter their response accordingly. This ability might be an important strategy in complex habitats such as soils, with great implications for shaping the microbial community structure. Here, we used a sand microcosm approach to investigate how Pseudomonas fluorescens Pf0-1 responds to the presence of monocultures or mixtures of two phylogenetically different bacteria, a Gram-negative (Pedobacter sp. V48) and a Gram-positive (Bacillus sp. V102) under two nutrient conditions. Results revealed that under both nutrient poor and nutrient rich conditions confrontation with the Gram-positive Bacillus sp. V102 strain led to significant lower cell numbers of Pseudomonas fluorescens Pf0-1, whereas confrontation with the Gram-negative Pedobacter sp. V48 strain did not affect the growth of Pseudomonas fluorescens Pf0-1. However, when Pseudomonas fluorescens Pf0-1 was confronted with the mixture of both strains, no significant effect on the growth of Pseudomonas fluorescens Pf0-1 was observed. Quantitative real-time PCR data showed up-regulation of genes involved in the production of a broad-spectrum antibiotic in Pseudomonas fluorescens Pf0-1 when confronted with Pedobacter sp. V48, but not in the presence of Bacillus sp. V102. The results provide evidence that the performance of bacteria in soil depends strongly on the identity of neighbouring bacteria and that inter-specific interactions are an important factor in determining microbial community structure.
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Affiliation(s)
- Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB, Wageningen, the Netherlands
- * E-mail:
| | - Alexandra B. Wolf
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB, Wageningen, the Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB, Wageningen, the Netherlands
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215
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Tan GY, Peng Y, Lu C, Bai L, Zhong JJ. Engineering validamycin production by tandem deletion of γ-butyrolactone receptor genes in Streptomyces hygroscopicus 5008. Metab Eng 2015; 28:74-81. [DOI: 10.1016/j.ymben.2014.12.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/31/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
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216
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Structural diversity and possible functional roles of free fatty acids of the novel soil isolate Streptomyces sp. NP10. Appl Microbiol Biotechnol 2015; 99:4815-33. [DOI: 10.1007/s00253-014-6364-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 12/22/2014] [Accepted: 12/24/2014] [Indexed: 02/07/2023]
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217
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Sang Y, Blecha F. Alternatives to antibiotics in animal agriculture: an ecoimmunological view. Pathogens 2014; 4:1-19. [PMID: 25551290 PMCID: PMC4384068 DOI: 10.3390/pathogens4010001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 12/24/2014] [Indexed: 12/13/2022] Open
Abstract
Ecological immunology (or ecoimmunology) is a new discipline in animal health and immunology that extends immunologists’ views into a natural context where animals and humans have co-evolved. Antibiotic resistance and tolerance (ART) in bacteria are manifested in antibiosis-surviving subsets of resisters and persisters. ART has emerged though natural evolutionary consequences enriched by human nosocomial and agricultural practices, in particular, wide use of antibiotics that overwhelms other ecological and immunological interactions. Most previous reviews of antibiotic resistance focus on resisters but overlook persisters, although both are fundamental to bacteria survival through antibiosis. Here, we discuss resisters and persisters together to contrast the distinct ecological responses of persisters during antibiotic stress and propose different regimens to eradicate persisters. Our intention is not only to provide an ecoimmunological interpretation, but also to use an ecoimmunological system to categorize available alternatives and promote the discovery of prospective approaches to relieve ART problems within the general scope of improving animal health. Thus, we will categorize available alternatives to antibiotics and envision applications of ecoimmunological tenets to promote related studies in animal production.
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Affiliation(s)
- Yongming Sang
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Frank Blecha
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
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218
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Uncovering the cultivable microbial diversity of costa rican beetles and its ability to break down plant cell wall components. PLoS One 2014; 9:e113303. [PMID: 25411842 PMCID: PMC4239062 DOI: 10.1371/journal.pone.0113303] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 10/27/2014] [Indexed: 11/19/2022] Open
Abstract
Coleopterans are the most diverse insect order described to date. These organisms have acquired an array of survival mechanisms through their evolution, including highly efficient digestive systems. Therefore, the coleopteran intestinal microbiota constitutes an important source of novel plant cell wall-degrading enzymes with potential biotechnological applications. We isolated and described the cultivable fungi, actinomycetes and aerobic eubacteria associated with the gut of larvae and adults from six different beetle families colonizing decomposing logs in protected Costa Rican ecosystems. We obtained 611 isolates and performed phylogenetic analyses using the ITS region (fungi) and 16S rDNA (bacteria). The majority of fungal isolates belonged to the order Hypocreales (26% of 169 total), while the majority of actinomycetes belonged to the genus Streptomyces (86% of 241 total). Finally, we isolated 201 bacteria spanning 19 different families belonging into four phyla: Firmicutes, α, β and γ-proteobacteria. Subsequently, we focused on microbes isolated from Passalid beetles to test their ability to degrade plant cell wall polymers. Highest scores in these assays were achieved by a fungal isolate (Anthostomella sp.), two Streptomyces and one Bacillus bacterial isolates. Our study demonstrates that Costa Rican beetles harbor several types of cultivable microbes, some of which may be involved in symbiotic relationships that enable the insect to digest complex polymers such as lignocellulose.
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219
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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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220
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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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221
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Tyc O, van den Berg M, Gerards S, van Veen JA, Raaijmakers JM, de Boer W, Garbeva P. Impact of interspecific interactions on antimicrobial activity among soil bacteria. Front Microbiol 2014; 5:567. [PMID: 25389421 PMCID: PMC4211544 DOI: 10.3389/fmicb.2014.00567] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/08/2014] [Indexed: 11/13/2022] Open
Abstract
Certain bacterial species produce antimicrobial compounds only in the presence of a competing species. However, little is known on the frequency of interaction-mediated induction of antibiotic compound production in natural communities of soil bacteria. Here we developed a high-throughput method to screen for the production of antimicrobial activity by monocultures and pair-wise combinations of 146 phylogenetically different bacteria isolated from similar soil habitats. Growth responses of two human pathogenic model organisms, Escherichia coli WA321 and Staphylococcus aureus 533R4, were used to monitor antimicrobial activity. From all isolates, 33% showed antimicrobial activity only in monoculture and 42% showed activity only when tested in interactions. More bacterial isolates were active against S. aureus than against E. coli. The frequency of interaction-mediated induction of antimicrobial activity was 6% (154 interactions out of 2798) indicating that only a limited set of species combinations showed such activity. The screening revealed also interaction-mediated suppression of antimicrobial activity for 22% of all combinations tested. Whereas all patterns of antimicrobial activity (non-induced production, induced production and suppression) were seen for various bacterial classes, interaction-mediated induction of antimicrobial activity was more frequent for combinations of Flavobacteria and alpha- Proteobacteria. The results of our study give a first indication on the frequency of interference competitive interactions in natural soil bacterial communities which may forms a basis for selection of bacterial groups that are promising for the discovery of novel, cryptic antibiotics.
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Affiliation(s)
- Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Marlies van den Berg
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Saskia Gerards
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Department of Soil Quality, Wageningen University and Research Centre Wageningen, Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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222
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Baltz RH. Combinatorial biosynthesis of cyclic lipopeptide antibiotics: a model for synthetic biology to accelerate the evolution of secondary metabolite biosynthetic pathways. ACS Synth Biol 2014; 3:748-58. [PMID: 23654258 DOI: 10.1021/sb3000673] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are giant multi-enzymes that carry out sequencial assembly line couplings of amino acids to generate linear or cyclic peptides. NRPSs are composed of repeating enzyme domains with modular organization to activate and couple specific amino acids in a particular order. From a synthetic biology perspective, they can be considered as peptide assembly machines composed of devices to couple fatty acids to l-amino acids, l-amino acids to l-amino acids, and d-amino acids to l-amino acids. The coupling devices are composed of specific parts that contain two or more enzyme domains that can be exchanged combinatorially to generate novel peptide assembly machines to produce novel peptides. The potent lipopeptide antibiotics daptomycin and A54145E have identical cyclic depsipeptide ring structures and stereochemistry but have divergent amino acid sequences. As their biosynthetic gene clusters are derived from an ancient ancestral lipopetide pathway, these lipopeptides provided an attractive model to develop combinatorial biosynthesis to generate antibiotics superior to daptomycin. These studies on combinatorial biosynthesis have helped generate guidelines for the successful assembly of NRPS parts and devices that can be used to generate novel lipopeptide structures and have established a basis for future synthetic biology studies to further develop combinatorial biosynthesis as a robust approach to natural product drug discovery.
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Affiliation(s)
- Richard H. Baltz
- CognoGen Biotechnology Consulting, 6438 North Olney Street, Indianapolis,
Indiana 46220, United States
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223
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Giardina A, Alduina R, Gallo G, Monciardini P, Sosio M, Puglia AM. Inorganic phosphate is a trigger factor for Microbispora sp. ATCC-PTA-5024 growth and NAI-107 production. Microb Cell Fact 2014; 13:133. [PMID: 25300322 PMCID: PMC4203916 DOI: 10.1186/s12934-014-0133-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 09/01/2014] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND NAI-107, produced by the actinomycete Microbispora sp. ATCC-PTA-5024, is a promising lantibiotic active against Gram-positive bacteria and currently in late preclinical-phase. Lantibiotics (lanthionine-containing antibiotics) are ribosomally synthesized and post-translationally modified peptides (RiPPs), encoded by structural genes as precursor peptides. The biosynthesis of biologically active compounds is developmentally controlled and it depends upon a variety of environmental stimuli and conditions. Inorganic phosphate (Pi) usually negatively regulates biologically-active molecule production in Actinomycetes, while it has been reported to have a positive control on lantibiotic production in Firmicutes strains. So far, no information is available concerning the Pi effect on lantibiotic biosynthesis in Actinomycetes. RESULTS After having developed a suitable defined medium, Pi-limiting conditions were established and confirmed by quantitative analysis of polyphosphate accumulation and of expression of selected Pho regulon genes, involved in the Pi-limitation stress response. Then, the effect of Pi on Microbispora growth and NAI-107 biosynthesis was investigated in a defined medium containing increasing Pi amounts. Altogether, our analyses revealed that phosphate is necessary for growth and positively influences both growth and NAI-107 production up to a concentration of 5 mM. Higher Pi concentrations were not found to further stimulate Microbispora growth and NAI-107 production. CONCLUSION These results, on one hand, enlarge the knowledge on Microbispora physiology, and, on the other one, could be helpful to develop a robust and economically feasible production process of NAI-107 as a drug for human use.
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Affiliation(s)
- Anna Giardina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze - Bd. 16, 90128, Palermo, Italy.
| | - Rosa Alduina
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze - Bd. 16, 90128, Palermo, Italy.
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze - Bd. 16, 90128, Palermo, Italy.
| | - Paolo Monciardini
- Naicons S.r.l., Viale Ortles 22/4, 20139, Milan, Italy. .,KtedoGen S.r.l., Viale Ortles 22/4, 20139, Milan, Italy.
| | - Margherita Sosio
- Naicons S.r.l., Viale Ortles 22/4, 20139, Milan, Italy. .,KtedoGen S.r.l., Viale Ortles 22/4, 20139, Milan, Italy.
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze - Bd. 16, 90128, Palermo, Italy.
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224
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Romero DA, Hasan AH, Lin YF, Kime L, Ruiz-Larrabeiti O, Urem M, Bucca G, Mamanova L, Laing EE, van Wezel GP, Smith CP, Kaberdin VR, McDowall KJ. A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing. Mol Microbiol 2014; 94:963-987. [PMID: 25266672 PMCID: PMC4681348 DOI: 10.1111/mmi.12810] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2014] [Indexed: 12/12/2022]
Abstract
Streptomyces coelicolor is a model for studying bacteria renowned as the foremost source of natural products used clinically. Post-genomic studies have revealed complex patterns of gene expression and links to growth, morphological development and individual genes. However, the underlying regulation remains largely obscure, but undoubtedly involves steps after transcription initiation. Here we identify sites involved in RNA processing and degradation as well as transcription within a nucleotide-resolution map of the transcriptional landscape. This was achieved by combining RNA-sequencing approaches suited to the analysis of GC-rich organisms. Escherichia coli was analysed in parallel to validate the methodology and allow comparison. Previously, sites of RNA processing and degradation had not been mapped on a transcriptome-wide scale for E. coli. Through examples, we show the value of our approach and data sets. This includes the identification of new layers of transcriptional complexity associated with several key regulators of secondary metabolism and morphological development in S. coelicolor and the identification of host-encoded leaderless mRNA and rRNA processing associated with the generation of specialized ribosomes in E. coli. New regulatory small RNAs were identified for both organisms. Overall the results illustrate the diversity in mechanisms used by different bacterial groups to facilitate and regulate gene expression.
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Affiliation(s)
- David A Romero
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Ayad H Hasan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Yu-fei Lin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Louise Kime
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
| | - Olatz Ruiz-Larrabeiti
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHULeioa, Spain
| | - Mia Urem
- Institute of Biology, Sylvius Laboratories, Leiden UniversityLeiden, NL-2300 RA, The Netherlands
| | - Giselda Bucca
- Department of Microbial & Cellular Sciences, Faculty of Health & Medical Sciences, University of SurreyGuildford, GU2 7XH, UK
| | - Lira Mamanova
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusHinxton, Cambridge, CB10 1SA, UK
| | - Emma E Laing
- Department of Microbial & Cellular Sciences, Faculty of Health & Medical Sciences, University of SurreyGuildford, GU2 7XH, UK
| | - Gilles P van Wezel
- Institute of Biology, Sylvius Laboratories, Leiden UniversityLeiden, NL-2300 RA, The Netherlands
| | - Colin P Smith
- Department of Microbial & Cellular Sciences, Faculty of Health & Medical Sciences, University of SurreyGuildford, GU2 7XH, UK
| | - Vladimir R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHULeioa, Spain
- IKERBASQUE, Basque Foundation for Science48011, Bilbao, Spain
| | - Kenneth J McDowall
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
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225
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WblAch, a pivotal activator of natamycin biosynthesis and morphological differentiation in Streptomyces chattanoogensis L10, is positively regulated by AdpAch. Appl Environ Microbiol 2014; 80:6879-87. [PMID: 25172865 DOI: 10.1128/aem.01849-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Detailed mechanisms of WhiB-like (Wbl) proteins involved in antibiotic biosynthesis and morphological differentiation are poorly understood. Here, we characterize the role of WblAch, a Streptomyces chattanoogensis L10 protein belonging to this superfamily. Based on DNA microarray data and verified by real-time quantitative PCR (qRT-PCR), the expression of wblAch was shown to be positively regulated by AdpAch. Gel retardation assays and DNase I footprinting experiments showed that AdpAch has specific DNA-binding activity for the promoter region of wblAch. Gene disruption and genetic complementation revealed that WblAch acts in a positive manner to regulate natamycin production. When wblAch was overexpressed in the wild-type strain, the natamycin yield was increased by ∼30%. This provides a strategy to generate improved strains for natamycin production. Moreover, transcriptional analysis showed that the expression levels of whi genes (including whiA, whiB, whiH, and whiI) were severely depressed in the ΔwblAch mutant, suggesting that WblAch plays a part in morphological differentiation by influencing the expression of the whi genes.
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226
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Zou Z, Du D, Zhang Y, Zhang J, Niu G, Tan H. A γ-butyrolactone-sensing activator/repressor, JadR3, controls a regulatory mini-network for jadomycin biosynthesis. Mol Microbiol 2014; 94:490-505. [PMID: 25116816 DOI: 10.1111/mmi.12752] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2014] [Indexed: 01/12/2023]
Abstract
Two regulatory genes, jadR2 and jadR3, in the jadomycin (jad) biosynthetic gene cluster of Streptomyces venezuelae encode homologues of γ-butyrolactone receptor. JadR2 was previously shown to be a pseudo γ-butyrolactone receptor. jadR3 is situated at the upstream of jadW123 encoding putative enzymes for γ-butyrolactone biosynthesis. Disruption of jadR3 resulted in markedly decreased production of jadomycin. Transcriptional analysis revealed that JadR3 represses jadW1, jadR2 and jadR3 but activates jadR1, the key activator gene for jadomycin biosynthesis. DNase I footprinting showed that JadR3 has four binding sites in the intergenic regions of jadR2-jadR1 and jadR3-jadW1. A JadR3 interactive molecule, SVB1, was purified from a large-scale fermentation and its structure found to be the same as SCB3, a γ-butyrolactone from Streptomyces coelicolor, and was absent from a jadW123 mutant lacking jadomycin production. Addition of SVB1 or extract from S. coelicolor to the mutant restored jadomycin production. Overall, our results revealed that the association of JadR3 and SVB1 plays an important role in controlling a regulatory mini-network governing jadomycin biosynthesis, providing new insights into the ways in which γ-butyrolactone/receptor systems modulate antibiotic biosynthesis in Streptomyces.
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Affiliation(s)
- Zhengzhong Zou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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227
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Horbal L, Kobylyanskyy A, Truman AW, Zaburranyi N, Ostash B, Luzhetskyy A, Marinelli F, Fedorenko V. The pathway-specific regulatory genes, tei15* and tei16*, are the master switches of teicoplanin production in Actinoplanes teichomyceticus. Appl Microbiol Biotechnol 2014; 98:9295-309. [PMID: 25104028 DOI: 10.1007/s00253-014-5969-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 12/01/2022]
Abstract
Pathogenic antibiotic-resistant bacteria are an unprecedented threat to health care worldwide. The range of antibiotics active against these bacteria is narrow; it includes teicoplanin, a "last resort" drug, which is produced by the filamentous actinomycete Actinoplanes teichomyceticus. In this report, we determine the functions of tei15* and tei16*, pathway-specific regulatory genes that code for StrR- and LuxR-type transcriptional factors, respectively. The products of these genes are master switches of teicoplanin biosynthesis, since their inactivation completely abolished antibiotic production. We show that Tei15* positively regulates the transcription of at least 17 genes in the cluster, whereas the targets of Tei16* still remain unknown. Integration of tei15* or tei16* under the control of the aminoglycoside resistance gene aac(3)IV promoter into attBϕC31 site of the A. teichomyceticus chromosome increased teicoplanin productivity to nearly 1 g/L in TM1 industrial medium. The expression of these genes from the moderate copy number episomal vector pKC1139 led to 3-4 g/L teicoplanin, while under the same conditions, wild type produced approximately 100 mg/L. This shows that a significant increase in teicoplanin production can be achieved by a single step of genetic manipulation of the wild-type strain by increasing the expression of the tei regulatory genes. This confirms that natural product yields can be increased using rational engineering once suitable genetic tools have been developed. We propose that this new technology for teicoplanin overproduction might now be transferred to industrial mutants of A. teichomyceticus.
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Affiliation(s)
- Liliya Horbal
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv, Ukraine
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228
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Recent advances in biochemistry and biotechnological synthesis of avermectins and their derivatives. Appl Microbiol Biotechnol 2014; 98:7747-59. [DOI: 10.1007/s00253-014-5926-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/29/2014] [Accepted: 07/01/2014] [Indexed: 10/24/2022]
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229
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Bignell DRD, Francis IM, Fyans JK, Loria R. Thaxtomin A production and virulence are controlled by several bld gene global regulators in Streptomyces scabies. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:875-85. [PMID: 24678834 DOI: 10.1094/mpmi-02-14-0037-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Streptomyces scabies is the main causative agent of common scab disease, which leads to significant annual losses to potato growers worldwide. The main virulence factor produced by S. scabies is a phytotoxic secondary metabolite called thaxtomin A, which functions as a cellulose synthesis inhibitor. Thaxtomin A production is controlled by the cluster-situated regulator TxtR, which activates expression of the thaxtomin biosynthetic genes in response to cello-oligosaccharides. Here, we demonstrate that at least five additional regulatory genes are required for wild-type levels of thaxtomin A production and plant pathogenicity in S. scabies. These regulatory genes belong to the bld gene family of global regulators that control secondary metabolism or morphological differentiation in Streptomyces spp. Quantitative reverse-transcriptase polymerase chain reaction showed that expression of the thaxtomin biosynthetic genes was significantly downregulated in all five bld mutants and, in four of these mutants, this downregulation was attributed to the reduction in expression of txtR. Furthermore, all of the mutants displayed reduced expression of other known or predicted virulence genes, suggesting that the bld genes may function as global regulators of virulence gene expression in S. scabies.
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230
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Novel and tightly regulated resorcinol and cumate-inducible expression systems for Streptomyces and other actinobacteria. Appl Microbiol Biotechnol 2014; 98:8641-55. [DOI: 10.1007/s00253-014-5918-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/24/2014] [Accepted: 06/25/2014] [Indexed: 01/07/2023]
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231
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Charlop-Powers Z, Milshteyn A, Brady SF. Metagenomic small molecule discovery methods. Curr Opin Microbiol 2014; 19:70-75. [PMID: 25000402 DOI: 10.1016/j.mib.2014.05.021] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/10/2014] [Accepted: 05/28/2014] [Indexed: 12/18/2022]
Abstract
Metagenomic approaches to natural product discovery provide the means to harvest bioactive small molecules synthesized by environmental bacteria without the requirement of first culturing these organisms. Advances in sequencing technologies and general metagenomic methods are beginning to provide the tools necessary to unlock the unexplored biosynthetic potential encoded by the genomes of uncultured environmental bacteria. Here, we highlight recent advances in sequence-based and functional-based metagenomic approaches that promise to facilitate antibiotic discovery from diverse environmental microbiomes.
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Affiliation(s)
- Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States.
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232
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Analysis of novel kitasatosporae reveals significant evolutionary changes in conserved developmental genes between Kitasatospora and Streptomyces. Antonie van Leeuwenhoek 2014; 106:365-80. [DOI: 10.1007/s10482-014-0209-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 05/30/2014] [Indexed: 12/17/2022]
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233
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GlnR-mediated regulation of nitrogen metabolism in the actinomycete Saccharopolyspora erythraea. Appl Microbiol Biotechnol 2014; 98:7935-48. [PMID: 24931311 DOI: 10.1007/s00253-014-5878-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/22/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
Abstract
Nitrogen source sensing, uptake, and assimilation are central for growth and development of microorganisms which requires the participation of a global control of nitrogen metabolism-associated genes at the transcriptional level. In soil-dwelling antibiotic-producing actinomycetes, this role is played by GlnR, an OmpR family regulator. In this work, we demonstrate that SACE_7101 is the ortholog of actinomycetes' GlnR global regulators in the erythromycin producer Saccharopolyspora erythraea. Indeed, the chromosomal deletion of SACE_7101 severely affects the viability of S. erythraea when inoculated in minimal media supplemented with NaNO3, NaNO2, NH4Cl, glutamine, or glutamate as sole nitrogen source. Combination of in silico prediction of cis-acting elements, subsequent in vitro (through gel shift assays) and in vivo (real-time reverse transcription polymerase chain reaction) validations of the predicted target genes revealed a very large GlnR regulon aimed at adapting the nitrogen metabolism of S. erythraea. Indeed, enzymes/proteins involved in (i) uptake and assimilation of ammonium, (ii) transport and utilization of urea, (iii) nitrite/nitrate, (iv) glutamate/glutamine, (v) arginine metabolism, (vi) nitric oxide biosynthesis, and (vii) signal transduction associated with the nitrogen source supplied have at least one paralog gene which expression is controlled by GlnR. Our work highlights a GlnR-binding site consensus sequence (t/gna/cAC-n6-GaAAc) which is similar although not identical to the consensus sequences proposed for other actinomycetes. Finally, we discuss the distinct and common features of the GlnR-mediated transcriptional control of nitrogen metabolism between S. erythraea and the model organism Streptomyces coelicolor.
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234
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Genilloud O. The re-emerging role of microbial natural products in antibiotic discovery. Antonie Van Leeuwenhoek 2014; 106:173-88. [PMID: 24923558 DOI: 10.1007/s10482-014-0204-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/23/2014] [Indexed: 11/28/2022]
Abstract
New classes of antibacterial compounds are urgently needed to respond to the high frequency of occurrence of resistances to all major classes of known antibiotics. Microbial natural products have been for decades one of the most successful sources of drugs to treat infectious diseases but today, the emerging unmet clinical need poses completely new challenges to the discovery of novel candidates with the desired properties to be developed as antibiotics. While natural products discovery programs have been gradually abandoned by the big pharma, smaller biotechnology companies and research organizations are taking over the lead in the discovery of novel antibacterials. Recent years have seen new approaches and technologies being developed and integrated in a multidisciplinary effort to further exploit microbial resources and their biosynthetic potential as an untapped source of novel molecules. New strategies to isolate novel species thought to be uncultivable, and synthetic biology approaches ranging from genome mining of microbial strains for cryptic biosynthetic pathways to their heterologous expression have been emerging in combination with high throughput sequencing platforms, integrated bioinformatic analysis, and on-site analytical detection and dereplication tools for novel compounds. These different innovative approaches are defining a completely new framework that is setting the bases for the future discovery of novel chemical scaffolds that should foster a renewed interest in the identification of novel classes of natural product antibiotics from the microbial world.
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Affiliation(s)
- Olga Genilloud
- Fundación MEDINA, Avda Conocimiento 3, Parque Tecnológico Ciencias de la Salud, 18016, Granada, Spain,
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235
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Garbeva P, Hordijk C, Gerards S, de Boer W. Volatile-mediated interactions between phylogenetically different soil bacteria. Front Microbiol 2014; 5:289. [PMID: 24966854 PMCID: PMC4052926 DOI: 10.3389/fmicb.2014.00289] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/25/2014] [Indexed: 12/01/2022] Open
Abstract
There is increasing evidence that organic volatiles play an important role in interactions between micro-organisms in the porous soil matrix. Here we report that volatile compounds emitted by different soil bacteria can affect the growth, antibiotic production and gene expression of the soil bacterium Pseudomonas fluorescens Pf0–1. We applied a novel cultivation approach that mimics the natural nutritional heterogeneity in soil in which P. fluorescens grown on nutrient-limited agar was exposed to volatiles produced by 4 phylogenetically different bacterial isolates (Collimonas pratensis, Serratia plymuthica, Paenibacillus sp., and Pedobacter sp.) growing in sand containing artificial root exudates. Contrary to our expectation, the produced volatiles stimulated rather than inhibited the growth of P. fluorescens. A genome-wide, microarray-based analysis revealed that volatiles of all four bacterial strains affected gene expression of P. fluorescens, but with a different pattern of gene expression for each strain. Based on the annotation of the differently expressed genes, bacterial volatiles appear to induce a chemotactic motility response in P. fluorescens, but also an oxidative stress response. A more detailed study revealed that volatiles produced by C. pratensis triggered, antimicrobial secondary metabolite production in P. fluorescens. Our results indicate that bacterial volatiles can have an important role in communication, trophic - and antagonistic interactions within the soil bacterial community.
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Affiliation(s)
- Paolina Garbeva
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Cornelis Hordijk
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Saskia Gerards
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Wietse de Boer
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Department of Soil Quality, Wageningen University and Research Centre Wageningen, Netherlands
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236
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Two adjacent and similar TetR family transcriptional regulator genes, SAV577 and SAV576, co-regulate avermectin production in Streptomyces avermitilis. PLoS One 2014; 9:e99224. [PMID: 24915523 PMCID: PMC4051647 DOI: 10.1371/journal.pone.0099224] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/13/2014] [Indexed: 12/02/2022] Open
Abstract
Streptomyces avermitilis is an important bacterial species used for industrial production of avermectins, a family of broad-spectrum anthelmintic agents. We previously identified the protein SAV576, a TetR family transcriptional regulator (TFR), as a downregulator of avermectin biosynthesis that acts by controlling transcription of its major target gene SAV575 (which encodes cytochrome P450/NADPH-ferrihemoprotein reductase) and ave genes. SAV577, another TFR gene, encodes a SAV577 protein that displays high amino acid homology with SAV576. In this study, we examined the effect of SAV577 on avermectin production and the relationships between SAV576 and SAV577. SAV577 downregulated avermectin biosynthesis indirectly, similarly to SAV576. SAV576 and SAV577 both directly repressed SAV575 transcription, and reciprocally repressed each other's expression. SAV575 transcription levels in various S. avermitilis strains were correlated with avermectin production levels. DNase I footprinting and electrophoretic mobility shift assays indicated that SAV576 and SAV577 compete for the same binding regions, and that DNA-binding affinity of SAV576 is much stronger than that of SAV577. GST pull-down assays revealed no direct interaction between the two proteins. Taken together, these findings suggest that SAV577 regulates avermectin production in S. avermitilis by a mechanism similar to that of SAV576, and that the role of SAV576 is dominant over that of SAV577. This is the first report of two adjacent and similar TFR genes that co-regulate antibiotic production in Streptomyces.
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237
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Unexpected extensive lysine acetylation in the trump-card antibiotic producer Streptomyces roseosporus revealed by proteome-wide profiling. J Proteomics 2014; 106:260-9. [DOI: 10.1016/j.jprot.2014.04.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/14/2014] [Accepted: 04/09/2014] [Indexed: 01/10/2023]
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238
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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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239
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Zhu H, Swierstra J, Wu C, Girard G, Choi YH, van Wamel W, Sandiford SK, van Wezel GP. Eliciting antibiotics active against the ESKAPE pathogens in a collection of actinomycetes isolated from mountain soils. MICROBIOLOGY-SGM 2014; 160:1714-1725. [PMID: 24794971 DOI: 10.1099/mic.0.078295-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The rapid emergence of multidrug-resistant (MDR) bacterial pathogens poses a major threat for human health. In recent years, genome sequencing has unveiled many poorly expressed antibiotic clusters in actinomycetes. Here, we report a well-defined ecological collection of >800 actinomycetes obtained from sites in the Himalaya and Qinling mountains, and we used these in a concept study to see how efficiently antibiotics can be elicited against MDR pathogens isolated recently from the clinic. Using 40 different growth conditions, 96 actinomycetes were identified - predominantly Streptomyces - that produced antibiotics with efficacy against the MDR clinical isolates referred to as ESKAPE pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and/or Enterobacter cloacae. Antimicrobial activities that fluctuated strongly with growth conditions were correlated with specific compounds, including borrelidin, resistomycin, carbomethoxy-phenazine, and 6,7,8- and 5,6,8-trimethoxy-3-methylisocoumarin, of which the latter was not described previously. Our work provided insights into the potential of actinomycetes as producers of drugs with efficacy against clinical isolates that have emerged recently and also underlined the importance of targeting a specific pathogen.
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Affiliation(s)
- Hua Zhu
- Molecular Biotechnology, Institute of Biology, Molecular Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jasper Swierstra
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Centre, 's Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Changsheng Wu
- Molecular Biotechnology, Institute of Biology, Molecular Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Geneviève Girard
- Molecular Biotechnology, Institute of Biology, Molecular Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Willem van Wamel
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Centre, 's Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Stephanie K Sandiford
- Molecular Biotechnology, Institute of Biology, Molecular Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Molecular Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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240
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Gene clustering in plant specialized metabolism. Curr Opin Biotechnol 2014; 26:91-9. [DOI: 10.1016/j.copbio.2013.10.009] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/22/2013] [Accepted: 10/23/2013] [Indexed: 11/21/2022]
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241
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Braña AF, Rodríguez M, Pahari P, Rohr J, García LA, Blanco G. Activation and silencing of secondary metabolites in Streptomyces albus and Streptomyces lividans after transformation with cosmids containing the thienamycin gene cluster from Streptomyces cattleya. Arch Microbiol 2014; 196:345-55. [PMID: 24633227 DOI: 10.1007/s00203-014-0977-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 02/17/2014] [Accepted: 03/04/2014] [Indexed: 01/09/2023]
Abstract
Activation and silencing of antibiotic production was achieved in Streptomyces albus J1074 and Streptomyces lividans TK21 after introduction of genes within the thienamycin cluster from S. cattleya. Dramatic phenotypic and metabolic changes, involving activation of multiple silent secondary metabolites and silencing of others normally produced, were found in recombinant strains harbouring the thienamycin cluster in comparison to the parental strains. In S. albus, ultra-performance liquid chromatography purification and NMR structural elucidation revealed the identity of four structurally related activated compounds: the antibiotics paulomycins A, B and the paulomenols A and B. Four volatile compounds whose biosynthesis was switched off were identified by gas chromatography-mass spectrometry analyses and databases comparison as pyrazines; including tetramethylpyrazine, a compound with important clinical applications to our knowledge never reported to be produced by Streptomyces. In addition, this work revealed the potential of S. albus to produce many others secondary metabolites normally obtained from plants, including compounds of medical relevance as dihydro-β-agarofuran and of interest in perfume industry as β-patchoulene, suggesting that it might be an alternative model for their industrial production. In S. lividans, actinorhodins production was strongly activated in the recombinant strains whereas undecylprodigiosins were significantly reduced. Activation of cryptic metabolites in Streptomyces species might represent an alternative approach for pharmaceutical drug discovery.
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Affiliation(s)
- Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006, Oviedo, Spain
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242
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Rabyk MV, Ostash BO, Fedorenko VO. Gene networks regulating secondary metabolism in actinomycetes: Pleiotropic regulators. CYTOL GENET+ 2014. [DOI: 10.3103/s0095452714010083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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243
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Petrus MLC, van Veluw GJ, Wösten HAB, Claessen D. Sorting of Streptomyces cell pellets using a complex object parametric analyzer and sorter. J Vis Exp 2014:e51178. [PMID: 24561666 PMCID: PMC4123467 DOI: 10.3791/51178] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Streptomycetes are filamentous soil bacteria that are used in industry for the production of enzymes and antibiotics. When grown in bioreactors, these organisms form networks of interconnected hyphae, known as pellets, which are heterogeneous in size. Here we describe a method to analyze and sort mycelial pellets using a Complex Object Parametric Analyzer and Sorter (COPAS). Detailed instructions are given for the use of the instrument and the basic statistical analysis of the data. We furthermore describe how pellets can be sorted according to user-defined settings, which enables downstream processing such as the analysis of the RNA or protein content. Using this methodology the mechanism underlying heterogeneous growth can be tackled. This will be instrumental for improving streptomycetes as a cell factory, considering the fact that productivity correlates with pellet size.
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Affiliation(s)
| | - G Jerre van Veluw
- Microbiology, Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University
| | - Han A B Wösten
- Microbiology, Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University
| | - Dennis Claessen
- Microbial Biotechnology, Institute Biology Leiden, Leiden University;
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244
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Deciphering the regulon of Streptomyces coelicolor AbrC3, a positive response regulator of antibiotic production. Appl Environ Microbiol 2014; 80:2417-28. [PMID: 24509929 DOI: 10.1128/aem.03378-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The atypical two-component system (TCS) AbrC1/C2/C3 (encoded by SCO4598, SCO4597, and SCO4596), comprising two histidine kinases (HKs) and a response regulator (RR), is crucial for antibiotic production in Streptomyces coelicolor and for morphological differentiation under certain nutritional conditions. In this study, we demonstrate that deletion of the RR-encoding gene, abrC3 (SCO4596), results in a dramatic decrease in actinorhodin (ACT) and undecylprodiginine (RED) production and delays morphological development. In contrast, the overexpression of abrC3 in the parent strain leads to a 33% increase in ACT production in liquid medium. Transcriptomic analysis and chromatin immunoprecipitation with microarray technology (ChIP-chip) analysis of the ΔabrC3 mutant and the parent strain revealed that AbrC3 directly controls ACT production by binding to the actII-ORF4 promoter region; this was independently verified by in vitro DNA-binding assays. This binding is dependent on the sequence 5'-GAASGSGRMS-3'. In contrast, the regulation of RED production is not due to direct binding of AbrC3 to either the redZ or redD promoter region. This study also revealed other members of the AbrC3 regulon: AbrC3 is a positive autoregulator which also binds to the promoter regions of SCO0736, bdtA (SCO3328), absR1 (SCO6992), and SCO6809. The direct targets share the 10-base consensus binding sequence and may be responsible for some of the phenotypes of the ΔabrC3 mutant. The identification of the AbrC3 regulon as part of the complex regulatory network governing antibiotic production widens our knowledge regarding TCS involvement in control of antibiotic synthesis and may contribute to the rational design of new hyperproducer host strains through genetic manipulation of such systems.
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245
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Ostash B, Shashkov A, Streshinskaya G, Tul'skaya E, Baryshnikova L, Dmitrenok A, Dacyuk Y, Fedorenko V. Identification of Streptomyces coelicolor M145 genomic region involved in biosynthesis of teichulosonic acid-cell wall glycopolymer. Folia Microbiol (Praha) 2014; 59:355-60. [PMID: 24526589 DOI: 10.1007/s12223-014-0306-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 01/19/2014] [Indexed: 11/30/2022]
Abstract
The cell wall of the model actinomycete Streptomyces coelicolor M145 has recently been shown to contain the novel glycopolymer teichulosonic acid. The major building block of this polymer is 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (Kdn), suggesting initial clues about the genetic control of biosynthesis of this cell wall component. Here, through genome mining and gene knockouts, we demonstrate that the sco4879-sco4882 genomic region of S. coelicolor M145 is necessary for biosynthesis of teichulosonic acid. Specifically, mutants carrying individual knockouts of sco4879, sco4880 and sco4881 genes do not produce Kdn-containing glycopolymer and instead accumulate the minor cell wall component poly(diglycosyl 1-phosphate). Our studies provide evidence that this region is at least partly responsible for biosynthesis of Kdn, whereas flanking genes might control the other steps of teichulosonic acid formation.
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Affiliation(s)
- Bohdan Ostash
- Department of Genetics and Biotechnology, Ivan Franko National University, Lviv, 4 Hrushevskoho st, Lviv, 79005, Ukraine
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246
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Genome-wide analysis of the regulation of pimaricin production in Streptomyces natalensis by reactive oxygen species. Appl Microbiol Biotechnol 2014; 98:2231-41. [PMID: 24413916 DOI: 10.1007/s00253-013-5455-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 12/20/2022]
Abstract
To investigate the molecular mechanisms that interplay between oxygen metabolism and secondary metabolism in Streptomyces natalensis, we compared the transcriptomes of the strains CAM.02 (ΔsodF), pimaricin under-producer phenotype, and CAM.04 (ΔahpCD), pimaricin over-producer phenotype, with that of the wild type at late exponential and stationary growth phases. Microarray data interpretation was supported by characterization of the mutant strains regarding enzymatic activities, phosphate uptake, oxygen consumption and pimaricin production.Both mutant strains presented a delay in the transcription activation of the PhoRP system and pimaricin biosynthetic gene cluster that correlated with the delayed inorganic phosphate (Pi) depletion in the medium and late onset of pimaricin production, respectively. The carbon flux of both mutants was also altered: a re-direction from glycolysis to the pentose phosphate pathway (PPP) in early exponential phase followed by a transcriptional activation of both pathways in subsequent growth phases was observed. Mutant behavior diverged at the respiratory chain/tricarboxylic acid cycle (TCA) and the branched chain amino acid (BCAA) metabolism. CAM.02 (ΔsodF) presented an impaired TCA cycle and an inhibition of the BCAA biosynthesis and degradation pathways. Conversely, CAM.04 (ΔahpCD) presented a global activation of BCAA metabolism.The results highlight the cellular NADPH/NADH ratio and the availability of biosynthetic precursors via the BCAA metabolism as the main pimaricin biosynthetic bottlenecks under oxidative stress conditions. Furthermore, new evidences are provided regarding a crosstalk between phosphate metabolism and oxidative stress in Streptomyces.
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247
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Anné J, Vrancken K, Van Mellaert L, Van Impe J, Bernaerts K. Protein secretion biotechnology in Gram-positive bacteria with special emphasis on Streptomyces lividans. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1750-61. [PMID: 24412306 DOI: 10.1016/j.bbamcr.2013.12.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/26/2013] [Accepted: 12/31/2013] [Indexed: 02/07/2023]
Abstract
Proteins secreted by Gram-positive bacteria are released into the culture medium with the obvious benefit that they usually retain their native conformation. This property makes these host cells potentially interesting for the production of recombinant proteins, as one can take full profit of established protocols for the purification of active proteins. Several state-of-the-art strategies to increase the yield of the secreted proteins will be discussed, using Streptomyces lividans as an example and compared with approaches used in some other host cells. It will be shown that approaches such as increasing expression and translation levels, choice of secretion pathway and modulation of proteins thereof, avoiding stress responses by changing expression levels of specific (stress) proteins, can be helpful to boost production yield. In addition, the potential of multi-omics approaches as a tool to understand the genetic background and metabolic fluxes in the host cell and to seek for new targets for strain and protein secretion improvement is discussed. It will be shown that S. lividans, along with other Gram-positive host cells, certainly plays a role as a production host for recombinant proteins in an economically viable way. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Jozef Anné
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Kristof Vrancken
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Lieve Van Mellaert
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Jan Van Impe
- Chemical and Biochemical Process Technology and Control Section (BioTeC), Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 box 2423, B-3001 Leuven, Belgium.
| | - Kristel Bernaerts
- Chemical and Biochemical Process Technology and Control Section (BioTeC), Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 box 2423, B-3001 Leuven, Belgium.
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Claessen D, Rozen DE, Kuipers OP, Søgaard-Andersen L, van Wezel GP. Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies. Nat Rev Microbiol 2014; 12:115-24. [PMID: 24384602 DOI: 10.1038/nrmicro3178] [Citation(s) in RCA: 275] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although bacteria frequently live as unicellular organisms, many spend at least part of their lives in complex communities, and some have adopted truly multicellular lifestyles and have abandoned unicellular growth. These transitions to multicellularity have occurred independently several times for various ecological reasons, resulting in a broad range of phenotypes. In this Review, we discuss the strategies that are used by bacteria to form and grow in multicellular structures that have hallmark features of multicellularity, including morphological differentiation, programmed cell death and patterning. In addition, we examine the evolutionary and ecological factors that lead to the wide range of coordinated multicellular behaviours that are observed in bacteria.
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Affiliation(s)
- Dennis Claessen
- 1] Molecular Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, P.O. Box 9502, 2300 RA Leiden, The Netherlands. [2]
| | - Daniel E Rozen
- 1] Molecular Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, P.O. Box 9502, 2300 RA Leiden, The Netherlands. [2]
| | - Oscar P Kuipers
- 1] Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Linnaeusborg, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. [2] Kluyver Center for Genomics of Industrial Fermentation, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Klymyshin DO, Honchar MA, Stafanyshyn OM, Fedorenko VO. A gene cloning system for the aranciamycin producer strain Streptomyces echinatus Lv 22. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714020118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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250
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Koning RI, Celler K, Willemse J, Bos E, van Wezel GP, Koster AJ. Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces. Methods Cell Biol 2014; 124:217-39. [PMID: 25287843 DOI: 10.1016/b978-0-12-801075-4.00010-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Light microscopy and electron microscopy are complementary techniques that in a correlative approach enable identification and targeting of fluorescently labeled structures in situ for three-dimensional imaging at nanometer resolution. Correlative imaging allows electron microscopic images to be positioned in a broader temporal and spatial context. We employed cryo-correlative light and electron microscopy (cryo-CLEM), combining cryo-fluorescence light microscopy and cryo-electron tomography, on vitrified Streptomyces bacteria to study cell division. Streptomycetes are mycelial bacteria that grow as long hyphae and reproduce via sporulation. On solid media, Streptomyces subsequently form distinct aerial mycelia where cell division leads to the formation of unigenomic spores which separate and disperse to form new colonies. In liquid media, only vegetative hyphae are present divided by noncell separating crosswalls. Their multicellular life style makes them exciting model systems for the study of bacterial development and cell division. Complex intracellular structures have been visualized with transmission electron microscopy. Here, we describe the methods for cryo-CLEM that we applied for studying Streptomyces. These methods include cell growth, fluorescent labeling, cryo-fixation by vitrification, cryo-light microscopy using a Linkam cryo-stage, image overlay and relocation, cryo-electron tomography using a Titan Krios, and tomographic reconstruction. Additionally, methods for segmentation, volume rendering, and visualization of the correlative data are described.
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Affiliation(s)
- Roman I Koning
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
| | - Katherine Celler
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, The Netherlands
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, The Netherlands
| | - Erik Bos
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology Leiden, Leiden University, PO Box 9505, Leiden, The Netherlands
| | - Abraham J Koster
- Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
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