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Xue Y, Zhou Z, Feng F, Zhao H, Tan S, Li J, Wu S, Ju Z, He S, Ding L. Genomic Analysis of Kitasatospora setae to Explore Its Biosynthetic Potential Regarding Secondary Metabolites. Antibiotics (Basel) 2024; 13:459. [PMID: 38786187 PMCID: PMC11117518 DOI: 10.3390/antibiotics13050459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Actinomycetes have long been recognized as important sources of clinical antibiotics. However, the exploration of rare actinomycetes, despite their potential for producing bioactive molecules, has remained relatively limited compared to the extensively studied Streptomyces genus. The extensive investigation of Streptomyces species and their natural products has led to a diminished probability of discovering novel bioactive compounds from this group. Consequently, our research focus has shifted towards less explored actinomycetes, beyond Streptomyces, with particular emphasis on Kitasatospora setae (K. setae). The genome of K. setae was annotated and analyzed through whole-genome sequencing using multiple bio-informatics tools, revealing an 8.6 Mbp genome with a 74.42% G + C content. AntiSMASH analysis identified 40 putative biosynthetic gene clusters (BGCs), approximately half of which were recessive and unknown. Additionally, metabolomic mining utilizing mass spectrometry demonstrated the potential for this rare actinomycete to generate numerous bioactive compounds such as glycosides and macrolides, with bafilomycin being the major compound produced. Collectively, genomics- and metabolomics-based techniques confirmed K. setae's potential as a bioactive secondary metabolite producer that is worthy of further exploration.
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Affiliation(s)
- Yutong Xue
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
| | - Zhiyan Zhou
- School of Pharmacy, Ningbo University, Ningbo 315211, China;
| | - Fangjian Feng
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
| | - Hang Zhao
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
| | - Shuangling Tan
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
| | - Jinling Li
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
| | - Sitong Wu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (S.W.); (Z.J.)
| | - Zhiran Ju
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (S.W.); (Z.J.)
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
- School of Pharmacy, Ningbo University, Ningbo 315211, China;
| | - Lijian Ding
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315211, China; (Y.X.); (F.F.); (H.Z.); (S.T.); (J.L.)
- School of Pharmacy, Ningbo University, Ningbo 315211, China;
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Rebets Y, Kormanec J, Lutzhetskyy A, Bernaerts K, Anné J. Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Its Subsequent Fermentation for Optimized Production. Methods Mol Biol 2023; 2555:213-260. [PMID: 36306090 DOI: 10.1007/978-1-0716-2795-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The choice of an expression system for the metagenomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the Gram-negative bacterium Escherichia coli as a host for metagenomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40% of the enzymatic activities may be readily recovered by random cloning in E. coli. To recover some of the remaining 60%, alternative cloning hosts such as Streptomyces spp. have been used. Streptomycetes are high-GC Gram-positive bacteria belonging to the Actinomycetales and they have been studied extensively for more than 25 years as an alternative expression system. They are extremely well suited for the expression of DNA from other actinomycetes and genomes of high GC content. Furthermore, due to its high innate, extracellular secretion capacity, Streptomyces can be a better system than E. coli for the production of many extracellular proteins. In this article, an overview is given about the materials and methods for growth and successful expression and secretion of heterologous proteins from diverse origin using Streptomyces lividans as a host. More in detail, an overview is given about the protocols of transformation, type of plasmids used and of vectors useful for integration of DNA into the host chromosome, and accompanying cloning strategies. In addition, various control elements for gene expression including synthetic promoters are discussed, and methods to compare their strength are described. Stable and efficient marker-less integration of the gene of interest under the control of the promoter of choice into S. lividans chromosome via homologous recombination using pAMR23A-based system will be explained. Finally, a basic protocol for bench-top bioreactor experiments which can form the start in the production process optimization and up-scaling will be provided.
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Affiliation(s)
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andriy Lutzhetskyy
- Department of Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), University of Saarland, Saarbrücken, Germany
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety Division, KU Leuven, Leuven, Belgium
| | - Jozef Anné
- Department of Microbiology, Immunology and Transplantation, lab. Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.
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Chetri SPK, Rahman Z, Thomas L, Lal R, Gour T, Agarwal LK, Vashishtha A, Kumar S, Kumar G, Kumar R, Sharma K. Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives. J Basic Microbiol 2022; 62:764-778. [PMID: 35638879 DOI: 10.1002/jobm.202200043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/17/2022] [Accepted: 05/14/2022] [Indexed: 11/05/2022]
Abstract
Nitrogen occurs as inert and inaccessible dinitrogen gaseous form (N2 ) in the atmosphere. Biological nitrogen fixation is a chief process that makes this dinitrogen (N2 ) accessible and bioavailable in the form of ammonium (NH4 + ) ions. The key organisms to fix nitrogen are certain prokaryotes, called diazotrophs either in the free-living form or establishing significant mutual relationships with a variety of plants. On such examples is ~95-100 MY old incomparable symbiosis between dicotyledonous trees and a unique actinobacterial diazotroph in diverse ecosystems. In this association, the root of the certain dicotyledonous tree (~25 genera and 225 species) belonging to three different taxonomic orders, Fagales, Cucurbitales, and Rosales (FaCuRo) known as actinorhizal trees can host a diazotroph, Frankia of order Frankiales. Frankia is gram-positive, branched, filamentous, sporulating, and free-living soil actinobacterium. It resides in the specialized, multilobed, and coralloid organs (lateral roots but without caps), the root nodules of actinorhizal tress. This review aims to provide systematic information on the distribution and the phylogenetic diversity of hosts from FaCuRo and their micro-endosymbionts (Frankia spp.), colonization mechanisms, and signaling pathways. We also aim to provide details on developmental and physiological imperatives for gene regulation and functional genomics of symbiosis, phenomenal restoration ecology, influences of contemporary global climatic changes, and anthropogenic impacts on plant-Frankia interactions for the functioning of ecosystems and the biosphere.
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Affiliation(s)
| | - Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, New Delhi, Delhi, India
| | - Lebin Thomas
- Department of Botany, Hansraj College, University of Delhi, New Delhi, Delhi, India
| | - Ratan Lal
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Tripti Gour
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Lokesh Kumar Agarwal
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Akanksha Vashishtha
- Department of Plant Protection, CCS University, Meerut, Uttar Pradesh, India
| | - Sachin Kumar
- Department of Botany, Shri Venkateshwara College, University of Delhi, New Delhi, Delhi, India
| | - Gaurav Kumar
- Department of Environmental Studies, PGDAV College, University of Delhi, New Delhi, Delhi, India
| | - Rajesh Kumar
- Department of Botany, Hindu College, University of Delhi, New Delhi, Delhi, India
| | - Kuldeep Sharma
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
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Makitrynskyy R, Tsypik O, Bechthold A. Genetic Engineering of Streptomyces ghanaensis ATCC14672 for Improved Production of Moenomycins. Microorganisms 2021; 10:microorganisms10010030. [PMID: 35056478 PMCID: PMC8778134 DOI: 10.3390/microorganisms10010030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 01/11/2023] Open
Abstract
Streptomycetes are soil-dwelling multicellular microorganisms famous for their unprecedented ability to synthesize numerous bioactive natural products (NPs). In addition to their rich arsenal of secondary metabolites, Streptomyces are characterized by complex morphological differentiation. Mostly, industrial production of NPs is done by submerged fermentation, where streptomycetes grow as a vegetative mycelium forming pellets. Often, suboptimal growth peculiarities are the major bottleneck for industrial exploitation. In this work, we employed genetic engineering approaches to improve the production of moenomycins (Mm) in Streptomyces ghanaensis, the only known natural direct inhibitors of bacterial peptidoglycan glycosyltransferses. We showed that in vivo elimination of binding sites for the pleiotropic regulator AdpA in the oriC region strongly influences growth and positively correlates with Mm accumulation. Additionally, a marker- and “scar”-less deletion of moeH5, encoding an amidotransferase from the Mm gene cluster, significantly narrows down the Mm production spectrum. Strikingly, antibiotic titers were strongly enhanced by the elimination of the pleiotropic regulatory gene wblA, involved in the late steps of morphogenesis. Altogether, we generated Mm overproducers with optimized growth parameters, which are useful for further genome engineering and chemoenzymatic generation of novel Mm derivatives. Analogously, such a scheme can be applied to other Streptomyces spp.
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Droplet-based microfluidic platform for high-throughput screening of Streptomyces. Commun Biol 2021; 4:647. [PMID: 34059751 PMCID: PMC8166820 DOI: 10.1038/s42003-021-02186-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
Streptomyces are one of the most important industrial microorganisms for the production of proteins and small-molecule drugs. Previously reported flow cytometry-based screening methods can only screen spores or protoplasts released from mycelium, which do not represent the filamentous stationary phase Streptomyces used in industrial cultivation. Here we show a droplet-based microfluidic platform to facilitate more relevant, reliable and rapid screening of Streptomyces mycelium, and achieved an enrichment ratio of up to 334.2. Using this platform, we rapidly characterized a series of native and heterologous constitutive promoters in Streptomyces lividans 66 in droplets, and efficiently screened out a set of engineered promoter variants with desired strengths from two synthetic promoter libraries. We also successfully screened out several hyperproducers of cellulases from a random S. lividans 66 mutant library, which had 69.2–111.4% greater cellulase production than the wild type. Our method provides a fast, simple, and powerful solution for the industrial engineering and screening of Streptomyces in more industry-relevant conditions. Streptomyces are an important filamentous bacterium genus in industry, but most of the high-throughput techniques so far can only separate spores or protoplasts. Tu et al. develop an encapsulating method that allows screening of Streptomyces in the filamentous, stationary phase.
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Berini F, Marinelli F, Binda E. Streptomycetes: Attractive Hosts for Recombinant Protein Production. Front Microbiol 2020; 11:1958. [PMID: 32973711 PMCID: PMC7468451 DOI: 10.3389/fmicb.2020.01958] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/24/2020] [Indexed: 01/28/2023] Open
Abstract
Enzymes are increasingly applied as biocatalysts for fulfilling industrial needs in a variety of applications and there is a bursting of interest for novel therapeutic proteins. Consequently, developing appropriate expression platforms for efficiently producing such recombinant proteins represents a crucial challenge. It is nowadays widely accepted that an ideal ‘universal microbial host’ for heterologous protein expression does not exist. Indeed, the first-choice microbes, as Escherichia coli or yeasts, possess known intrinsic limitations that inevitably restrict their applications. In this scenario, bacteria belonging to the Streptomyces genus need to be considered with more attention as promising, alternative, and versatile platforms for recombinant protein production. This is due to their peculiar features, first-of-all their natural attitude to secrete proteins in the extracellular milieu. Additionally, streptomycetes are considered robust and scalable industrial strains and a wide range of tools for their genetic manipulation is nowadays available. This mini-review includes an overview of recombinant protein production in streptomycetes, covering nearly 100 cases of heterologous proteins expressed in these Gram-positives from the 1980s to December 2019. We investigated homologous sources, heterologous hosts, and molecular tools (promoters/vectors/signal peptides) used for the expression of these recombinant proteins. We reported on their final cellular localization and yield. Thus, this analysis might represent a useful source of information, showing pros and cons of using streptomycetes as platform for recombinant protein production and paving the way for their more extensive use in future as alternative heterologous hosts.
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Affiliation(s)
- Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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van Bergeijk DA, Terlouw BR, Medema MH, van Wezel GP. Ecology and genomics of Actinobacteria: new concepts for natural product discovery. Nat Rev Microbiol 2020; 18:546-558. [DOI: 10.1038/s41579-020-0379-y] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 01/09/2023]
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Vicente RL, Marín S, Valverde JR, Palomino C, Mellado RP, Gullón S. Functional identification of a Streptomyces lividans FKBP-like protein involved in the folding of overproduced secreted proteins. Open Biol 2019; 9:190201. [PMID: 31662098 PMCID: PMC6833217 DOI: 10.1098/rsob.190201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/01/2019] [Indexed: 01/21/2023] Open
Abstract
Some bacterial peptidyl-prolyl cis/trans isomerases (PPIases) are involved in secretory protein folding after the translocation step. Streptomyces lividans has been used as a host for engineering extracellular overproduction of homologous and heterologous proteins in industrial applications. Although the mechanisms governing the major secretory pathway (Sec route) and the minor secretory pathway (Tat route) are reasonably well described, the function of proteins responsible for the extracellular secretory protein folding is not characterized as yet. We have characterized a Tat-dependent S. lividans FK506-binding protein-like lipoprotein (FKBP) that has PPIase activity. A mutant in the sli-fkbp gene induces a secretion stress response and affects secretion and activity of the Sec-dependent protein α-amylase. Additionally, propagation in high copy number of the sli-fkbp gene has a positive effect on the activity of both the overproduced α-amylase and the overproduced Tat-dependent agarase, both containing proline cis isomers. Targeted proteomic analyses showed that a relevant group of secreted proteins in S. lividans TK21 are affected by Sli-FKBP, revealing a wide substrate range. The results obtained indicate that, regardless of the secretory route used by proteins in S. lividans, adjusting the expression of sli-fkbp may facilitate folding of dependent proteins when engineering Streptomyces strains for the overproduction of homologous or heterologous secretory proteins.
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Affiliation(s)
- R. L. Vicente
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain
| | - S. Marín
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain
| | - J. R. Valverde
- Scientific Computing Service, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain
| | - C. Palomino
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain
| | - R. P. Mellado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain
| | - S. Gullón
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049 Madrid, Spain
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Djinni I, Defant A, Kecha M, Mancini I. Actinobacteria Derived from Algerian Ecosystems as a Prominent Source of Antimicrobial Molecules. Antibiotics (Basel) 2019; 8:E172. [PMID: 31581466 PMCID: PMC6963827 DOI: 10.3390/antibiotics8040172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 01/19/2023] Open
Abstract
Actinobacteria, in particular "rare actinobacteria" isolated from extreme ecosystems, remain the most inexhaustible source of novel antimicrobials, offering a chance to discover new bioactive metabolites. This is the first overview on actinobacteria isolated in Algeria since 2002 to date with the aim to present their potential in producing bioactive secondary metabolites. Twenty-nine new species and one novel genus have been isolated, mainly from the Saharan soil and palm groves, where 37.93% of the most abundant genera belong to Saccharothrix and Actinopolyspora. Several of these strains were found to produce antibiotics and antifungal metabolites, including 17 new molecules among the 50 structures reported, and some of these antibacterial metabolites have shown interesting antitumor activities. A series of approaches used to enhance the production of bioactive compounds is also presented as the manipulation of culture media by both classical methods and modeling designs through statistical strategies and the associations with diverse organisms and strains. Focusing on the Algerian natural sources of antimicrobial metabolites, this work is a representative example of the potential of a closely combined study on biology and chemistry of natural products.
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Affiliation(s)
- Ibtissem Djinni
- Laboratoire de Microbiologie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia 06000, Algeria.
- Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, Trento 38123, Italy.
| | - Andrea Defant
- Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, Trento 38123, Italy.
| | - Mouloud Kecha
- Laboratoire de Microbiologie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia 06000, Algeria.
| | - Ines Mancini
- Bioorganic Chemistry Laboratory, Department of Physics, University of Trento, Trento 38123, Italy.
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Pham JV, Yilma MA, Feliz A, Majid MT, Maffetone N, Walker JR, Kim E, Cho HJ, Reynolds JM, Song MC, Park SR, Yoon YJ. A Review of the Microbial Production of Bioactive Natural Products and Biologics. Front Microbiol 2019; 10:1404. [PMID: 31281299 PMCID: PMC6596283 DOI: 10.3389/fmicb.2019.01404] [Citation(s) in RCA: 244] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/04/2019] [Indexed: 12/24/2022] Open
Abstract
A variety of organisms, such as bacteria, fungi, and plants, produce secondary metabolites, also known as natural products. Natural products have been a prolific source and an inspiration for numerous medical agents with widely divergent chemical structures and biological activities, including antimicrobial, immunosuppressive, anticancer, and anti-inflammatory activities, many of which have been developed as treatments and have potential therapeutic applications for human diseases. Aside from natural products, the recent development of recombinant DNA technology has sparked the development of a wide array of biopharmaceutical products, such as recombinant proteins, offering significant advances in treating a broad spectrum of medical illnesses and conditions. Herein, we will introduce the structures and diverse biological activities of natural products and recombinant proteins that have been exploited as valuable molecules in medicine, agriculture and insect control. In addition, we will explore past and ongoing efforts along with achievements in the development of robust and promising microorganisms as cell factories to produce biologically active molecules. Furthermore, we will review multi-disciplinary and comprehensive engineering approaches directed at improving yields of microbial production of natural products and proteins and generating novel molecules. Throughout this article, we will suggest ways in which microbial-derived biologically active molecular entities and their analogs could continue to inspire the development of new therapeutic agents in academia and industry.
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Affiliation(s)
- Janette V. Pham
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Mariamawit A. Yilma
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Adriana Feliz
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Murtadha T. Majid
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Nicholas Maffetone
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Jorge R. Walker
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Eunji Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
| | - Hyo Je Cho
- School of Life Sciences and Biotechnology, Kyungpook National University, Daegu, South Korea
| | - Jared M. Reynolds
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
| | - Sung Ryeol Park
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Baruch S. Blumberg Institute, Doylestown, PA, United States
- Natural Products Discovery Institute, Doylestown, PA, United States
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, South Korea
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Zhan W, Yao J, Tang K, Li Y, Guo Y, Wang X. Characterization of Two Toxin-Antitoxin Systems in Deep-Sea Streptomyces sp. SCSIO 02999. Mar Drugs 2019; 17:md17040211. [PMID: 30987346 PMCID: PMC6521030 DOI: 10.3390/md17040211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/26/2019] [Accepted: 04/01/2019] [Indexed: 12/20/2022] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitous and abundant genetic elements in bacteria and archaea. Most previous TA studies have focused on commensal and pathogenic bacteria, but have rarely focused on marine bacteria, especially those isolated from the deep sea. Here, we identified and characterized three putative TA pairs in the deep-sea-derived Streptomyces sp. strain SCSIO 02999. Our results showed that Orf5461/Orf5462 and Orf2769/Orf2770 are bona fide TA pairs. We provide several lines of evidence to demonstrate that Orf5461 and Orf5462 constitute a type-II TA pair that are homologous to the YoeB/YefM TA pair from Escherichia coli. Although YoeB from SCSIO 02999 was toxic to an E. coli host, the homologous YefM antitoxin from SCSIO 02999 did not neutralize the toxic effect of YoeB from E. coli. For the Orf2769/Orf2770 TA pair, Orf2769 overexpression caused significant cell elongation and could lead to cell death in E. coli, and the neighboring Orf2770 could neutralize the toxic effect of Orf2769. However, no homologous toxin or antitoxin was found for this pair, and no direct interaction was found between Orf2769 and Orf2770. These results suggest that Orf2769 and Orf2770 may constitute a novel TA pair. Thus, deep-sea bacteria harbor typical and novel TA pairs. The biochemical and physiological functions of different TAs in deep-sea bacteria warrant further investigation.
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Affiliation(s)
- Waner Zhan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Yangmei Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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Hamed MB, Vrancken K, Bilyk B, Koepff J, Novakova R, van Mellaert L, Oldiges M, Luzhetskyy A, Kormanec J, Anné J, Karamanou S, Economou A. Monitoring Protein Secretion in Streptomyces Using Fluorescent Proteins. Front Microbiol 2018; 9:3019. [PMID: 30581427 PMCID: PMC6292873 DOI: 10.3389/fmicb.2018.03019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/22/2018] [Indexed: 01/25/2023] Open
Abstract
Fluorescent proteins are a major cell biology tool to analyze protein sub-cellular topology. Here we have applied this technology to study protein secretion in the Gram-positive bacterium Streptomyces lividans TK24, a widely used host for heterologous protein secretion biotechnology. Green and monomeric red fluorescent proteins were fused behind Sec (SPSec) or Tat (SPTat) signal peptides to direct them through the respective export pathway. Significant secretion of fluorescent eGFP and mRFP was observed exclusively through the Tat and Sec pathways, respectively. Plasmid over-expression was compared to a chromosomally integrated spSec-mRFP gene to allow monitoring secretion under high and low level synthesis in various media. Fluorimetric detection of SPSec-mRFP recorded folded states, while immuno-staining detected even non-folded topological intermediates. Secretion of SPSec-mRFP is unexpectedly complex, is regulated independently of cell growth phase and is influenced by the growth regime. At low level synthesis, highly efficient secretion occurs until it is turned off and secretory preforms accumulate. At high level synthesis, the secretory pathway overflows and proteins are driven to folding and subsequent degradation. High-level synthesis of heterologous secretory proteins, whether secretion competent or not, has a drastic effect on the endogenous secretome, depending on their secretion efficiency. These findings lay the foundations of dissecting how protein targeting and secretion are regulated by the interplay between the metabolome, secretion factors and stress responses in the S. lividans model.
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Affiliation(s)
- Mohamed Belal Hamed
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Molecular Biology Department, National Research Centre, Dokki, Egypt
| | - Kristof Vrancken
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Joachim Koepff
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Renata Novakova
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lieve van Mellaert
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Andriy Luzhetskyy
- Helmholtz-Zentrum für Infektionsforschung GmbH, Braunschweig, Germany
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jozef Anné
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
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13
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Iinuma C, Saito A, Ohnuma T, Tenconi E, Rosu A, Colson S, Mizutani Y, Liu F, Świątek-Połatyńska M, van Wezel GP, Rigali S, Fujii T, Miyashita K. NgcE Sco Acts as a Lower-Affinity Binding Protein of an ABC Transporter for the Uptake of N,N'-Diacetylchitobiose in Streptomyces coelicolor A3(2). Microbes Environ 2018; 33:272-281. [PMID: 30089751 PMCID: PMC6167110 DOI: 10.1264/jsme2.me17172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In the model species Streptomyces coelicolor A3(2), the uptake of chitin-degradation byproducts, mainly N,N′- diacetylchitobiose ([GlcNAc]2) and N-acetylglucosamine (GlcNAc), is performed by the ATP-binding cassette (ABC) transporter DasABC-MsiK and the sugar-phosphotransferase system (PTS), respectively. Studies on the S. coelicolor chromosome have suggested the occurrence of additional uptake systems of GlcNAc-related compounds, including the SCO6005–7 cluster, which is orthologous to the ABC transporter NgcEFG of S. olivaceoviridis. However, despite conserved synteny between the clusters in S. coelicolor and S. olivaceoviridis, homology between them is low, with only 35% of residues being identical between NgcE proteins, suggesting different binding specificities. Isothermal titration calorimetry experiments revealed that recombinant NgcESco interacts with GlcNAc and (GlcNAc)2, with Kd values (1.15 and 1.53 μM, respectively) that were higher than those of NgcE of S. olivaceoviridis (8.3 and 29 nM, respectively). The disruption of ngcESco delayed (GlcNAc)2 consumption, but did not affect GlcNAc consumption ability. The ngcESco-dasA double mutation severely decreased the ability to consume (GlcNAc)2 and abolished the induction of chitinase production in the presence of (GlcNAc)2, but did not affect the GlcNAc consumption rate. The results of these biochemical and reverse genetic analyses indicate that NgcESco acts as a (GlcNAc)2- binding protein of the ABC transporter NgcEFGSco-MsiK. Transcriptional and biochemical analyses of gene regulation demonstrated that the ngcESco gene was slightly induced by GlcNAc, (GlcNAc)2, and chitin, but repressed by DasR. Therefore, a model was proposed for the induction of the chitinolytic system and import of (GlcNAc)2, in which (GlcNAc)2 generated from chitin by chitinase produced leakily, is mainly transported via NgcEFG-MsiK and induces the expression of chitinase genes and dasABCD.
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Affiliation(s)
- Chiharu Iinuma
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University
| | - Akihiro Saito
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University.,Department of Materials and Life Science, Shizuoka Institute of Science and Technology
| | | | - Elodie Tenconi
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
| | - Adeline Rosu
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
| | - Séverine Colson
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
| | - Yuuki Mizutani
- Department of Materials and Life Science, Shizuoka Institute of Science and Technology
| | - Feng Liu
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University
| | | | | | - Sébastien Rigali
- InBioS-Center for Protein Engineering, Institut de Chimie B6a, University of Liège
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14
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Noguchi Y, Kashiwagi N, Uzura A, Ogino C, Kondo A, Ikeda H, Sota M. Development of a strictly regulated xylose-induced expression system in Streptomyces. Microb Cell Fact 2018; 17:151. [PMID: 30241528 PMCID: PMC6149001 DOI: 10.1186/s12934-018-0991-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
Background Genetic tools including constitutive and inducible promoters have been developed over the last few decades for strain engineering in Streptomyces. Inducible promoters are useful for controlling gene expression, however only a limited number are applicable to Streptomyces. The aim of this study is to develop a controllable protein expression system based on an inducible promoter using sugar inducer, which has not yet been widely applied in Streptomyces. Results To determine a candidate promoter, inducible protein expression was first examined in Streptomyces avermitilis MA-4680 using various carbon sources. Xylose isomerase (xylA) promoter derived from xylose (xyl) operon was selected due to strong expression of xylose isomerase (XylA) in the presence of d-xylose. Next, a xylose-inducible protein expression system was constructed by investigating heterologous protein expression (chitobiase as a model protein) driven by the xylA promoter in Streptomyces lividans. Chitobiase activity was detected at high levels in S. lividans strain harboring an expression vector with xylA promoter (pXC), under both xylose-induced and non-induced conditions. Thus, S. avermitilis xylR gene, which encodes a putative repressor of xyl operon, was introduced into constructed vectors in order to control protein expression by d-xylose. Among strains constructed in the study, XCPR strain harboring pXCPR vector exhibited strict regulation of protein expression. Chitobiase activity in the XCPR strain was observed to be 24 times higher under xylose-induced conditions than that under non-induced conditions. Conclusion In this study, a strictly regulated protein expression system was developed based on a xylose-induced system. As far as we could ascertain, this is the first report of engineered inducible protein expression in Streptomyces by means of a xylose-induced system. This system might be applicable for controllable expression of toxic products or in the field of synthetic biology using Streptomyces strains. Electronic supplementary material The online version of this article (10.1186/s12934-018-0991-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuji Noguchi
- Nagase R&D Center, Nagase & Co., Ltd., 2-2-3 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
| | - Norimasa Kashiwagi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Atsuko Uzura
- Nagase R&D Center, Nagase & Co., Ltd., 2-2-3 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Haruo Ikeda
- Laboratory of Microbial Engineering, Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Masahiro Sota
- Nagase R&D Center, Nagase & Co., Ltd., 2-2-3 Murotani, Nishi-ku, Kobe, Hyogo, 651-2241, Japan
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15
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Zacchetti B, Smits P, Claessen D. Dynamics of Pellet Fragmentation and Aggregation in Liquid-Grown Cultures of Streptomyces lividans. Front Microbiol 2018; 9:943. [PMID: 29867851 PMCID: PMC5958208 DOI: 10.3389/fmicb.2018.00943] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/23/2018] [Indexed: 11/20/2022] Open
Abstract
Streptomycetes are extensively used for the production of valuable products, including various antibiotics and industrial enzymes. The preferred way to grow these bacteria in industrial settings is in large-scale fermenters. Growth of streptomycetes under these conditions is characterized by the formation of complex mycelial particles, called pellets. While the process of pellet formation is well characterized, little is known about their disintegration. Here, we use a qualitative and quantitative approach to show that pellet fragmentation in Streptomyces lividans is initiated when cultures enter the stationary phase, which coincides with a remarkable change in pellet architecture. Unlike young pellets, aging pellets have a less dense appearance and are characterized by the appearance of filaments protruding from their outer edges. These morphological changes are accompanied by a dramatic increase in the number of mycelial fragments in the culture broth. In the presence of fresh nutrients, these fragments are able to aggregate with other small fragments, but not with disintegrating pellets, to form new mycelial particles. Altogether, our work indicates that fragmentation might represent an escape mechanism from the environmental stress caused by nutrient scarcity, with striking similarities to the disassembly of bacterial biofilms.
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Affiliation(s)
- Boris Zacchetti
- Microbial Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Paul Smits
- Microbial Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Dennis Claessen
- Microbial Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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16
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Zacchetti B, Andrianos A, van Dissel D, de Ruiter E, van Wezel GP, Claessen D. Microencapsulation extends mycelial viability of Streptomyces lividans 66 and increases enzyme production. BMC Biotechnol 2018. [PMID: 29530017 PMCID: PMC5848461 DOI: 10.1186/s12896-018-0425-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Filamentous bacteria of the genus Streptomyces produce a large arsenal of industrially relevant antibiotics and enzymes. The industrial production of these molecules occurs in large fermenters, where many streptomycetes form dense mycelial networks called pellets. Pellets are characterized by slow growth and inefficient nutrient transfer and therefore regarded as undesirable from the perspective of productivity. Although non-pelleting strains have increased growth rates, their morphology also leads to a dramatic increase in the viscosity of the culture broth, which negatively impacts the process dynamics. RESULTS Here, we applied immobilization of Streptomyces lividans 66 using alginate as semi-solid matrix. This alginate-mediated micro-encapsulation increased the production of the extracellular enzyme tyrosinase more than three-fold. The increased production was accompanied by extended viability of the mycelium and a dramatic reduction in the release of intracellular proteins into the culture broth. CONCLUSIONS Our data demonstrate the utility of micro-encapsulation as a powerful technique to achieve higher yields and lower downstream-processing costs of streptomycetes.
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Affiliation(s)
- Boris Zacchetti
- Microbial Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | | | - Dino van Dissel
- Microbial Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Evelien de Ruiter
- Microbial Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Gilles P van Wezel
- Microbial Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Dennis Claessen
- Microbial Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands.
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17
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van Dissel D, Willemse J, Zacchetti B, Claessen D, Pier GB, van Wezel GP. Production of poly-β-1,6-N-acetylglucosamine by MatAB is required for hyphal aggregation and hydrophilic surface adhesion by Streptomyces. MICROBIAL CELL 2018; 5:269-279. [PMID: 29850464 PMCID: PMC5972031 DOI: 10.15698/mic2018.06.635] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Streptomycetes are multicellular filamentous microorganisms, and major producers of industrial enzymes and bioactive compounds such as antibiotics and anticancer drugs. The mycelial lifestyle plays an important role in the productivity during industrial fermentations. The hyphae of liquid-grown streptomycetes can self-aggregate into pellets, which hampers their industrial exploitation. Here we show that the Mat complex, which is required for pellet formation, catalyzes the synthesis of extracellular poly-β-1,6-N-acetylglucosamine (PNAG) in the model organisms Streptomyces coelicolor and Streptomyces lividans. Extracellular accumulation of PNAG allows Streptomyces to attach to hydrophilic surfaces, while attachment to hydrophobic surfaces requires a cellulase-degradable extracellular polymer (EPS) produced by CslA. Over-expression of matAB was sufficient to restore pellet formation to cslA null mutants of S. lividans. The two EPS systems together increase the robustness of mycelial pellets. These new insights allow better control of liquid-culture morphology of streptomycetes, which may be harnessed to improve growth and industrial exploitation of these highly versatile natural product and enzyme producers.
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Affiliation(s)
- Dino van Dissel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Boris Zacchetti
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gerald B Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
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18
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Morphology-driven downscaling of Streptomyces lividans to micro-cultivation. Antonie van Leeuwenhoek 2017; 111:457-469. [PMID: 29094245 PMCID: PMC5816114 DOI: 10.1007/s10482-017-0967-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/19/2017] [Indexed: 11/20/2022]
Abstract
Actinobacteria are prolific producers of secondary metabolites and industrially relevant enzymes. Growth of these mycelial micro-organisms in small culture volumes is challenging due to their complex morphology. Since morphology and production are typically linked, scaling down culture volumes requires better control over morphogenesis. In larger scale platforms, ranging from shake flasks to bioreactors, the hydrodynamics play an important role in shaping the morphology and determining product formation. Here, we report on the effects of agitation on the mycelial morphology of Streptomyces lividans grown in microtitre plates. Our work shows that at the appropriate agitation rates cultures can be scaled down to volumes as small as 100 µl while maintaining the same morphology as seen in larger scale platforms. Using image analysis and principal component analysis we compared the morphologies of the cultures; when agitated at 1400–1600 rpm the mycelial morphology in micro-cultures was similar to that obtained in shake flasks, while product formation was also maintained. Our study shows that the morphology of actinobacteria in micro-cultures can be controlled in a similar manner as in larger scale cultures by carefully controlling the mixing rate. This could facilitate high-throughput screening and upscaling.
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19
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van der Meij A, Worsley SF, Hutchings MI, van Wezel GP. Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev 2017; 41:392-416. [DOI: 10.1093/femsre/fux005] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/02/2017] [Indexed: 12/13/2022] Open
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20
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Rebets Y, Kormanec J, Luzhetskyy A, Bernaerts K, Anné J. Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Subsequent Fermentation for Optimized Production. Methods Mol Biol 2017; 1539:99-144. [PMID: 27900687 DOI: 10.1007/978-1-4939-6691-2_8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The choice of an expression system for the metagenomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the gram-negative bacterium Escherichia coli as a host for metagenomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40 % of the enzymatic activities may be readily recovered by random cloning in E. coli. To recover some of the remaining 60 %, alternative cloning hosts such as Streptomyces spp. have been used. Streptomycetes are high-GC gram-positive bacteria belonging to the Actinomycetales and they have been studied extensively for more than 15 years as an alternative expression system. They are extremely well suited for the expression of DNA from other actinomycetes and genomes of high GC content. Furthermore, due to its high innate, extracellular secretion capacity, Streptomyces can be a better system than E. coli for the production of many extracellular proteins. In this article an overview is given about the materials and methods for growth and successful expression and secretion of heterologous proteins from diverse origin using Streptomyces lividans has a host. More in detail, an overview is given about the protocols of transformation, type of plasmids used and of vectors useful for integration of DNA into the host chromosome, and accompanying cloning strategies. In addition, various control elements for gene expression including synthetic promoters are discussed, and methods to compare their strength are described. Integration of the gene of interest under the control of the promoter of choice into S. lividans chromosome via homologous recombination using pAMR4-based system is explained. Finally a basic protocol for benchtop bioreactor experiments which can form the start in the production process optimization and upscaling is provided.
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Affiliation(s)
- Yuriy Rebets
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), University of Saarland, Saarbrücken, Germany
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andriy Luzhetskyy
- Actinobacteria Metabolic Engineering Group, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), University of Saarland, Saarbrücken, Germany
- Department of Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Kristel Bernaerts
- Department of Chemical Engineering, KU Leuven (University of Leuven), Leuven, Belgium
| | - Jozef Anné
- Lab. Molecular Bacteriology, Department Microbiology and Immunology, Rega Institute, KU Leuven (University of Leuven), Box 1037, Herestraat 49, B-3000, Leuven, Belgium.
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21
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Affiliation(s)
- Oksana Bilyk
- Helmholtz Institute for Pharmaceutical Research; Actinobacteria Metabolic Engineering Group; Universitätscampus E8 66123 Saarbrücken Germany
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research; Actinobacteria Metabolic Engineering Group; Universitätscampus E8 66123 Saarbrücken Germany
- University of Saarland; Department of Pharmaceutical Biotechnology; UdS Campus C2.366123 Saarbrücken Germany
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22
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Petrus MLC, Vijgenboom E, Chaplin AK, Worrall JAR, van Wezel GP, Claessen D. The DyP-type peroxidase DtpA is a Tat-substrate required for GlxA maturation and morphogenesis in Streptomyces. Open Biol 2016; 6:150149. [PMID: 26740586 PMCID: PMC4736821 DOI: 10.1098/rsob.150149] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The filamentous bacterium Streptomyces lividans depends on the radical copper oxidase GlxA for the formation of reproductive aerial structures and, in liquid environments, for the formation of pellets. Incorporation of copper into the active site is essential for the formation of a cross-linked tyrosyl-cysteine cofactor, which is needed for enzymatic activity. In this study, we show a crucial link between GlxA maturation and a group of copper-related proteins including the chaperone Sco and a novel DyP-type peroxidase hereinafter called DtpA. Under copper-limiting conditions, the sco and dtpA deletion mutants are blocked in aerial growth and pellet formation, similarly to a glxA mutant. Western blot analysis showed that GlxA maturation is perturbed in the sco and dtpA mutants, but both maturation and morphology can by rescued by increasing the bioavailability of copper. DtpA acts as a peroxidase in the presence of GlxA and is a substrate for the twin-arginine translocation (Tat) translocation pathway. In agreement, the maturation status of GlxA is also perturbed in tat mutants, which can be compensated for by the addition of copper, thereby partially restoring their morphological defects. Our data support a model wherein a copper-trafficking pathway and Tat-dependent secretion of DtpA link to the GlxA-dependent morphogenesis pathway.
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Affiliation(s)
- Marloes L C Petrus
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Erik Vijgenboom
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Amanda K Chaplin
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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23
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Fujiwara R, Noda S, Tanaka T, Kondo A. Styrene production from a biomass-derived carbon source using a coculture system of phenylalanine ammonia lyase and phenylacrylic acid decarboxylase-expressing Streptomyces lividans transformants. J Biosci Bioeng 2016; 122:730-735. [PMID: 27405271 DOI: 10.1016/j.jbiosc.2016.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/16/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
To produce styrene from a biomass-derived carbon source, Streptomyces lividans was adopted as a host strain. The gene encoding ferulic acid decarboxylase from Saccharomyces cerevisiae (FDC1) was introduced into S. lividans, and the resulting S. lividans transformant successfully expressed FDC1 and converted trans-cinnamic acid (CA) to styrene. A key factor in styrene production using microbes is the recovery of volatile styrene. In the present study, we selected polystyrene resin beads XRD-4 as the absorbent agent to recover styrene produced using S. lividans transformants, which enabled recovery of styrene from the culture broth. For styrene production from biomass-derived carbon sources, S. lividans/FDC1 was cultured together with S. lividans/p-encP, which we previously reported as a CA-producing S. lividans strain. This coculture system combined with the recovery of styrene using XAD-4 allowed the production of styrene from glucose, cellobiose, or xylo-oligosaccharide, respectively.
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Affiliation(s)
- Ryosuke Fujiwara
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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24
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Zacchetti B, Willemse J, Recter B, van Dissel D, van Wezel GP, Wösten HAB, Claessen D. Aggregation of germlings is a major contributing factor towards mycelial heterogeneity of Streptomyces. Sci Rep 2016; 6:27045. [PMID: 27244565 PMCID: PMC4886682 DOI: 10.1038/srep27045] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/13/2016] [Indexed: 12/22/2022] Open
Abstract
Streptomycetes are filamentous bacteria that produce numerous valuable compounds, including the majority of clinically used antibiotics. At an industrial scale, most of these compounds are produced in bioreactors. Growth of streptomycetes under these conditions is characterized by the formation of complex mycelial particles, whose sizes follow a bimodal distribution. Given the correlation between specific productivity and morphology, this size heterogeneity poses a potential drawback in industry. Recent work indicates that mycelial morphology is controlled by a number of genes that encode proteins required for the synthesis of cell surface-associated glycans. Using a quantifiable system based on fluorescent markers, we here show that these glycans mediate aggregation between germlings and young mycelia, yielding mycelial particles that originate from many different individuals. We also demonstrate that at later time points aggregation between distinct particles is no longer detectable. Notably, the absence of the corresponding glycan synthases yields mycelia that are homogeneous in size, identifying mycelial aggregation as a driving factor towards size heterogeneity. Given that aggregation is widespread within streptomycetes and can also occur between different Streptomyces strains, our work paves the way to improve Streptomyces as a cell factory for the production of known metabolites, but possibly also to discover new ones.
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Affiliation(s)
- Boris Zacchetti
- Microbial Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Joost Willemse
- Microbial Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Brand Recter
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dino van Dissel
- Microbial Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Gilles P. van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - H. A. B. Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dennis Claessen
- Microbial Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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Chaplin AK, Wilson MT, Hough MA, Svistunenko DA, Hemsworth GR, Walton PH, Vijgenboom E, Worrall JAR. Heterogeneity in the Histidine-brace Copper Coordination Sphere in Auxiliary Activity Family 10 (AA10) Lytic Polysaccharide Monooxygenases. J Biol Chem 2016; 291:12838-12850. [PMID: 27129229 DOI: 10.1074/jbc.m116.722447] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 12/23/2022] Open
Abstract
Copper-dependent lytic polysaccharide monooxygenases (LPMOs) are enzymes that oxidatively deconstruct polysaccharides. The active site copper in LPMOs is coordinated by a histidine-brace. This utilizes the amino group and side chain of the N-terminal His residue with the side chain of a second His residue to create a T-shaped arrangement of nitrogen ligands. We report a structural, kinetic, and thermodynamic appraisal of copper binding to the histidine-brace in an auxiliary activity family 10 (AA10) LPMO from Streptomyces lividans (SliLPMO10E). Unexpectedly, we discovered the existence of two apo-SliLPMO10E species in solution that can each bind copper at a single site with distinct kinetic and thermodynamic (exothermic and endothermic) properties. The experimental EPR spectrum of copper-bound SliLPMO10E requires the simulation of two different line shapes, implying two different copper-bound species, indicative of three and two nitrogen ligands coordinating the copper. Amino group coordination was probed through the creation of an N-terminal extension variant (SliLPMO10E-Ext). The kinetics and thermodynamics of copper binding to SliLPMO10E-Ext are in accord with copper binding to one of the apo-forms in the wild-type protein, suggesting that amino group coordination is absent in the two-nitrogen coordinate form of SliLPMO10E. Copper binding to SliLPMO10B was also investigated, and again it revealed the presence of two apo-forms with kinetics and stoichiometry of copper binding identical to that of SliLPMO10E. Our findings highlight that heterogeneity exists in the active site copper coordination sphere of LPMOs that may have implications for the mechanism of loading copper in the cell.
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Affiliation(s)
- Amanda K Chaplin
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Michael T Wilson
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Michael A Hough
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Dimitri A Svistunenko
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Glyn R Hemsworth
- the Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, and
| | - Paul H Walton
- the Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, and
| | - Erik Vijgenboom
- the Molecular Biotechnology, Institute of Biology, Sylvius Laboratory, Leiden University, P. O. Box 9505, 2300RA Leiden, The Netherlands
| | - Jonathan A R Worrall
- From the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom,.
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Sevillano L, Vijgenboom E, van Wezel GP, Díaz M, Santamaría RI. New approaches to achieve high level enzyme production in Streptomyces lividans. Microb Cell Fact 2016; 15:28. [PMID: 26846788 PMCID: PMC4743123 DOI: 10.1186/s12934-016-0425-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/19/2016] [Indexed: 11/29/2022] Open
Abstract
Background Actinomycetes are saprophytic soil bacteria, and a rich source of industrial enzymes. While some of these enzymes can be produced using well-characterized production platforms such as Escherichia coli or Bacillus subtilis,Streptomyces lividans may be the preferred host for proper folding and efficient secretion of active enzymes. A combination of promoters, signal peptides and hosts were tested in order to obtain the best protein expression in this actinomycete. The xylanase, Xys1, from S. halstedii, the α-amylase, Amy, from S. griseus and the small laccase, SLAC, from S. coelicolor were used as reporters. Results The promoters xysAp from S. halstedii JM8 and pstSp from S. lividans were the most efficient among those tested. An improvement of 17 % was obtained in xylanase activity when the signal peptide of the α-amylase protein (Amy) of S. griseus IMRU3570 was used to direct its secretion. Enhanced expression of SsgA, a protein that plays a role in processes that require cell-wall remodelling, resulted in a improvement of 40 and 70 % of xylanase and amylase production, respectively. Deletion of genes SLI7232 and SLI4452 encoding putative repressors of xysAp provided improvement of production up to 70 % in the SLI7232 deletion strain. However, full derepression of this promoter activity was not obtained under the conditions assayed. Conclusions Streptomyces lividans is a frequently used platform for industrial enzyme production and a rational strain-development approach delivered significant improvement of protein production by this host. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0425-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Sevillano
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, C/Zacarías González nº 2, 37007, Salamanca, Spain.
| | - Erik Vijgenboom
- Molecular Biotechnology, IBL, Sylvius Laboratory, Leiden University, Leiden, The Netherlands.
| | - Gilles P van Wezel
- Molecular Biotechnology, IBL, Sylvius Laboratory, Leiden University, Leiden, The Netherlands.
| | - Margarita Díaz
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, C/Zacarías González nº 2, 37007, Salamanca, Spain.
| | - Ramón I Santamaría
- Instituto de Biología Funcional y Genómica/Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, C/Zacarías González nº 2, 37007, Salamanca, Spain.
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Bouvin J, Cajot S, D’Huys PJ, Ampofo-Asiama J, Anné J, Van Impe J, Geeraerd A, Bernaerts K. Multi-objective experimental design for 13 C-based metabolic flux analysis. Math Biosci 2015; 268:22-30. [DOI: 10.1016/j.mbs.2015.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/15/2015] [Accepted: 08/01/2015] [Indexed: 01/30/2023]
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Gullón S, Marín S, Mellado RP. Overproduction of a Model Sec- and Tat-Dependent Secretory Protein Elicits Different Cellular Responses in Streptomyces lividans. PLoS One 2015. [PMID: 26200356 PMCID: PMC4511581 DOI: 10.1371/journal.pone.0133645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Streptomyces lividans is considered an efficient host for the secretory production of homologous and heterologous proteins. To identify possible bottlenecks in the protein production process, a comparative transcriptomic approach was adopted to study cellular responses during the overproduction of a Sec-dependent model protein (alpha-amylase) and a Tat-dependent model protein (agarase) in Streptomyces lividans. The overproduction of the model secretory proteins via the Sec or the Tat route in S. lividans does elicit a different major cell response in the bacterium. The stringent response is a bacterial response to nutrients’ depletion, which naturally occurs at late times of the bacterial cell growth. While the induction of the stringent response at the exponential phase of growth may limit overall productivity in the case of the Tat route, the induction of that response does not take place in the case of the Sec route, which comparatively is an advantage in secretory protein production processes. Hence, this study identifies a potential major drawback in the secretory protein production process depending on the secretory route, and provides clues to improving S. lividans as a protein production host.
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Affiliation(s)
- Sonia Gullón
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049, Madrid, Spain
| | - Silvia Marín
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049, Madrid, Spain
| | - Rafael P. Mellado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), c/Darwin 3, 28049, Madrid, Spain
- * E-mail:
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van Dissel D, Claessen D, Roth M, van Wezel GP. A novel locus for mycelial aggregation forms a gateway to improved Streptomyces cell factories. Microb Cell Fact 2015; 14:44. [PMID: 25889360 PMCID: PMC4391728 DOI: 10.1186/s12934-015-0224-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/09/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Streptomycetes produce a plethora of natural products including antibiotics and anticancer drugs, as well as many industrial enzymes. Their mycelial life style is a major bottleneck for industrial exploitation and over decades strain improvement programs have selected production strains with better growth properties. Uncovering the nature of the underlying mutations should allow the ready transfer of desirable traits to other production hosts. RESULTS Here we report that the mat gene cluster, which was identified through reverse engineering of a non-pelleting mutant selected in a chemostat, is key to pellet formation of Streptomyces lividans. Deletion of matA or matB, which encode putative polysaccharide synthases, effects mycelial metamorphosis, with very small and open mycelia. Growth rate and productivity of the matAB null mutant were increased by over 60% as compared to the wild-type strain. CONCLUSION Here, we present a way to counteract pellet formation by streptomycetes, which is one of the major bottlenecks in their industrial application. The mat locus is an ideal target for rational strain design approaches aimed at improving streptomycetes as industrial production hosts.
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Affiliation(s)
- Dino van Dissel
- Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300RA, Leiden, The Netherlands.
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300RA, Leiden, The Netherlands.
| | - Martin Roth
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Adolf-Reichwein-Str. 23, 07745, Jena, Germany.
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, PO Box 9505, 2300RA, Leiden, The Netherlands.
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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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31
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The role of volumetric power input in the growth, morphology, and production of a recombinant glycoprotein by Streptomyces lividans in shake flasks. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2014.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Function and evolution of two forms of SecDF homologs in Streptomyces coelicolor. PLoS One 2014; 9:e105237. [PMID: 25140821 PMCID: PMC4139356 DOI: 10.1371/journal.pone.0105237] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 07/19/2014] [Indexed: 01/08/2023] Open
Abstract
The general secretion (Sec) pathway plays a prominent role in bacterial protein export, and the accessory component SecDF has been shown to improve transportation efficiency. Inspection of Streptomyces coelicolor genome reveals the unexpected presence of two different forms of secDF homologous genes: one in fused form (secDF) and the other in separated form (secD and secF). However, the functional role of two SecDF homologs in S. coelicolor has not yet been determined. Transcriptional analysis of secDF homologs reveals that these genes are constitutively expressed. However, the transcript levels of secD and secF are much higher than that of secDF in S. coelicolor. Deletion of secDF or/and secD/secF in S. coelicolor did result in reduced secretion efficiency of Xylanase A and Amylase C, suggesting that they may have redundant functions for Sec-dependent translocation pathway. Moreover, our results also indicate that SecD/SecF plays a more prominent role than SecDF in protein translocation. Evolutionary analysis suggests that the fused and separated SecDF homologs in Streptomyces may have disparate evolutionary ancestries. SecD/SecF may be originated from vertical transmission of existing components from ancestor of Streptomyces species. However, SecDF may be derived from bacterial ancestors through horizontal gene transfer. Alternately, it is also plausible that SecDF may have arisen through additional gene duplication and fusion events. The acquisition of a second copy may confer a selective benefit to Streptomyces by enhancing protein transport capacity. Taken together, our results provide new insights into the potential biological function and evolutionary aspects of the prokaryotic SecDF complex.
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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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Miyazaki T, Noda S, Tanaka T, Kondo A. Hyper secretion of Thermobifida fusca β-glucosidase via a Tat-dependent signal peptide using Streptomyces lividans. Microb Cell Fact 2013; 12:88. [PMID: 24083334 PMCID: PMC3850917 DOI: 10.1186/1475-2859-12-88] [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: 07/02/2013] [Accepted: 09/28/2013] [Indexed: 12/02/2022] Open
Abstract
Background Protein production as secretory-form is a powerful tool in industrial enzyme production due to the simple purification procedure. Streptomyces lividans is a versatile host for secretory production of useful proteins. In order to expand the amount of secreted protein, signal peptide sequences, which encourage protein secretion from inside cell to extracellular environment, are one of the most significant factors. In this study, we focused on Streptomyces lividans as a host strain to secrete useful proteins, and screened for signal peptides from the biomass-degradation enzymes derived from Thermobifida fusca YX and S. lividans. Results Three candidate signal peptides were isolated and evaluated for their protein secretion ability using β-glucosidase derived from T. fusca YX, which is a non-secreted protein, as a model protein. Using S. lividans xylanase C signal peptide, the amount of produced the β-glucosidase reached 10 times as much as that when using Streptomyces cinnamoneus phospholipase D signal peptide, which was identified as a versatile signal peptide in our previous report. In addition, the introduction of the β-glucosidase fused to xylanase C signal peptide using two kinds of plasmid, pUC702 and pTYM18, led to further protein secretion, and the maximal level of produced the β-glucosidase increased up to 17 times (1.1 g/l) compared to using only pUC702 carrying the β-glucosidase fused to S. cinnamoneus phospholipase D signal peptide. Conclusion In the present study, we focused on signal peptide sequences derived from biomass degradation enzymes, which are usually secreted into the culture supernatant, and screened for signal peptides leading to effective protein secretion. Using the signal peptides, the hyper-protein secretion system was successfully demonstrated for the cytoplasmic β-glucosidase.
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Affiliation(s)
- Takaya Miyazaki
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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Recent advances in recombinant protein expression by Corynebacterium, Brevibacterium, and Streptomyces: from transcription and translation regulation to secretion pathway selection. Appl Microbiol Biotechnol 2013; 97:9597-608. [PMID: 24068337 DOI: 10.1007/s00253-013-5250-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 09/03/2013] [Accepted: 09/05/2013] [Indexed: 12/14/2022]
Abstract
Gram-positive bacteria are widely used to produce recombinant proteins, amino acids, organic acids, higher alcohols, and polymers. Many proteins have been expressed in Gram-positive hosts such as Corynebacterium, Brevibacterium, and Streptomyces. The favorable and advantageous characteristics (e.g., high secretion capacity and efficient production of metabolic products) of these species have increased the biotechnological applications of bacteria. However, owing to multiplicity from genes encoding the proteins and expression hosts, the expression of recombinant proteins is limited in Gram-positive bacteria. Because there is a very recent review about protein expression in Bacillus subtilis, here we summarize recent strategies for efficient expression of recombinant proteins in the other three typical Gram-positive bacteria (Corynebacterium, Brevibacterium, and Streptomyces) and discuss future prospects. We hope that this review will contribute to the development of recombinant protein expression in Corynebacterium, Brevibacterium, and Streptomyces.
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Sevillano L, Díaz M, Santamaría RI. Stable expression plasmids for Streptomyces based on a toxin-antitoxin system. Microb Cell Fact 2013; 12:39. [PMID: 23617558 PMCID: PMC3655019 DOI: 10.1186/1475-2859-12-39] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/22/2013] [Indexed: 11/10/2022] Open
Abstract
Background Bacteria included in the genus Streptomyces exhibit several attractive characteristics that make them adequate hosts for the heterologous expression of proteins. One of them is that some of its species have a high secretion capacity and hence the protein of interest could be released to the culture supernatant, facilitating downstream processing. To date, all the expression vectors described for these bacteria contain antibiotic resistance genes as selection markers. However, the use of antibiotics to produce proteins at industrial level is currently becoming more restricted owing to the possibility of contamination of the final product. In this report, we describe the use of the S. lividans yefM/yoeBsl toxin-antitoxin system to develop a stable plasmid expression system. Results In order to use the yefM/yoeBsl system to stabilize expression plasmids in Streptomyces, a S. lividans mutant strain that contained only the toxin gene (yoeBsl) in its genome and the antitoxin gene (yefMsl) located in a temperature-sensitive plasmid was constructed and used as host. This strain was transformed with an expression plasmid harbouring both the antitoxin gene and the gene encoding the protein of interest. Thus, after elimination of the temperature-sensitive plasmid, only cells with the expression plasmid were able to survive. On using this system, two proteins - an α-amylase from S. griseus and a xylanase from S. halstedii - were overproduced without the addition of antibiotic to the culture medium. The production of both proteins was high, even after long incubations (8 days), and after serial subcultures, confirming the stability of the plasmids without antibiotic selection. Conclusions This is the first report that describes the use of a toxin-antitoxin system to maintain high -copy plasmids in Streptomyces. This finding could be a valuable tool for using Streptomyces as a host to produce proteins at the industrial and pharmaceutical levels without the use of antibiotics in the production step.
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Affiliation(s)
- Laura Sevillano
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca 37007, Spain
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Vertès AA. Protein Secretion Systems of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Analysis of two distinct mycelial populations in liquid-grown Streptomyces cultures using a flow cytometry-based proteomics approach. Appl Microbiol Biotechnol 2012; 96:1301-12. [PMID: 23070651 DOI: 10.1007/s00253-012-4490-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 09/30/2012] [Accepted: 10/01/2012] [Indexed: 12/23/2022]
Abstract
Streptomycetes are proficient producers of enzymes and antibiotics. When grown in bioreactors, these filamentous microorganisms form mycelial pellets that consist of interconnected hyphae. We here employed a flow cytometry approach designed for large particles (COPAS) and demonstrate that liquid-grown Streptomyces cultures consist of two distinct populations of pellets. One population consists of mycelia with a constant mean diameter of approximately 260 μm, whereas the other population contains larger mycelia whose diameter depends on the strain, the age of the culture, and medium composition. Quantitative proteomics analysis revealed that 37 proteins differed in abundance between the two populations of pellets. Stress-related proteins and biosynthetic proteins for production of the calcium-dependent antibiotic were more abundant in the population of large mycelia, while proteins involved in DNA topology, modification, or degradation were overrepresented in the population of small mycelia. Deletion of genes for the cellulose synthase-like protein CslA and the chaplins affected the average size of the population of large pellets but not that of small pellets. Considering the fact that the production of enzymes and metabolites depends on pellet size, these results provide new leads toward rational strain design of Streptomyces strains tailored for industrial fermentations.
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Bacterial expression systems for recombinant protein production: E. coli and beyond. Biotechnol Adv 2012; 30:1102-7. [DOI: 10.1016/j.biotechadv.2011.09.013] [Citation(s) in RCA: 255] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 09/07/2011] [Accepted: 09/17/2011] [Indexed: 11/17/2022]
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Abstract
Background Streptomycetes are filamentous soil-dwelling bacteria. They are best known as the
producers of a great variety of natural products such as antibiotics, antifungals,
antiparasitics, and anticancer agents and the decomposers of organic substances
for carbon recycling. They are also model organisms for the studies of gene
regulatory networks, morphological differentiation, and stress response. The
availability of sets of genomes from closely related Streptomyces strains
makes it possible to assess the mechanisms underlying genome plasticity and
systems adaptation. Results We present the results of a comprehensive analysis of the genomes of five
Streptomyces species with distinct phenotypes. These streptomycetes
have a pan-genome comprised of 17,362 orthologous families which includes 3,096
components in the core genome, 5,066 components in the dispensable genome, and
9,200 components that are uniquely present in only one species. The core genome
makes up about 33%-45% of each genome repertoire. It contains important genes for
Streptomyces biology including those involved in gene regulation,
secretion, secondary metabolism and morphological differentiation. Abundant
duplicate genes have been identified, with 4%-11% of the whole genomes composed of
lineage-specific expansions (LSEs), suggesting that frequent gene duplication or
lateral gene transfer events play a role in shaping the genome diversification
within this genus. Two patterns of expansion, single gene expansion and chromosome
block expansion are observed, representing different scales of duplication. Conclusions Our results provide a catalog of genome components and their potential functional
roles in gene regulatory networks and metabolic networks. The core genome
components reveal the minimum requirement for streptomycetes to sustain a
successful lifecycle in the soil environment, reflecting the effects of both
genome evolution and environmental stress acting upon the expressed phenotypes. A
better understanding of the LSE gene families will, on the other hand, bring a
wealth of new insights into the mechanisms underlying strain-specific phenotypes,
such as the production of novel antibiotics, pathogenesis, and adaptive response
to environmental challenges.
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Affiliation(s)
- Zhan Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
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D'Huys PJ, Lule I, Vercammen D, Anné J, Van Impe JF, Bernaerts K. Genome-scale metabolic flux analysis of Streptomyces lividans growing on a complex medium. J Biotechnol 2012; 161:1-13. [PMID: 22641041 DOI: 10.1016/j.jbiotec.2012.04.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 04/09/2012] [Accepted: 04/23/2012] [Indexed: 11/27/2022]
Abstract
Constraint-based metabolic modeling comprises various excellent tools to assess experimentally observed phenotypic behavior of micro-organisms in terms of intracellular metabolic fluxes. In combination with genome-scale metabolic networks, micro-organisms can be investigated in much more detail and under more complex environmental conditions. Although complex media are ubiquitously applied in industrial fermentations and are often a prerequisite for high protein secretion yields, such multi-component conditions are seldom investigated using genome-scale flux analysis. In this paper, a systematic and integrative approach is presented to determine metabolic fluxes in Streptomyces lividans TK24 grown on a nutritious and complex medium. Genome-scale flux balance analysis and randomized sampling of the solution space are combined to extract maximum information from exometabolome profiles. It is shown that biomass maximization cannot predict the observed metabolite production pattern as such. Although this cellular objective commonly applies to batch fermentation data, both input and output constraints are required to reproduce the measured biomass production rate. Rich media hence not necessarily lead to maximum biomass growth. To eventually identify a unique intracellular flux vector, a hierarchical optimization of cellular objectives is adopted. Out of various tested secondary objectives, maximization of the ATP yield per flux unit returns the closest agreement with the maximum frequency in flux histograms. This unique flux estimation is hence considered as a reasonable approximation for the biological fluxes. Flux maps for different growth phases show no active oxidative part of the pentose phosphate pathway, but NADPH generation in the TCA cycle and NADPH transdehydrogenase activity are most important in fulfilling the NADPH balance. Amino acids contribute to biomass growth by augmenting the pool of available amino acids and by boosting the TCA cycle, particularly when using glutamate and aspartate. Depletion of glutamate and aspartate causes a distinct shift in fluxes of the central carbon and nitrogen metabolism. In the current work, hurdles encountered in flux analysis at a genome-scale level are addressed using hierarchical flux balance analysis and uniform sampling of the constrained solution space. This general framework can now be adopted in further studies of S. lividans, e.g., as a host for heterologous protein production.
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Affiliation(s)
- Pieter-Jan D'Huys
- Chemical and Biochemical Process Technology and Control Section, Department of Chemical Engineering, Katholieke Universiteit Leuven, W. de Croylaan 46, B-3001 Leuven, Belgium
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Recombinant protein production and streptomycetes. J Biotechnol 2012; 158:159-67. [DOI: 10.1016/j.jbiotec.2011.06.028] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 06/17/2011] [Accepted: 06/22/2011] [Indexed: 11/21/2022]
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Noda S, Miyazaki T, Tanaka T, Ogino C, Kondo A. Production of Streptoverticillium cinnamoneum transglutaminase and cinnamic acid by recombinant Streptomyces lividans cultured on biomass-derived carbon sources. BIORESOURCE TECHNOLOGY 2012; 104:648-651. [PMID: 22115528 DOI: 10.1016/j.biortech.2011.10.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 09/20/2011] [Accepted: 10/12/2011] [Indexed: 05/31/2023]
Abstract
Transglutaminase from Streptoverticillium cinnamoneum (StvcMTG) was produced using recombinant Streptomyces lividans. When grown on glycerol and xylose as sole carbon sources, S. lividans/StvcMTG produced 360 and 530 mg of StvcMTG per liter, respectively. With starch and xylan, the strain produced 230 and 400mg of StvcMTG per liter, respectively. Recombinant S. lividans/encP, which expresses phenylalanine ammonia lyase from Streptomyces maritimus, produced 160 mg/L of cinnamic acid from cellulose. These results show that S. lividans can assimilate various carbon sources and produce useful compounds in desirable quantities.
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Affiliation(s)
- Shuhei Noda
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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Zhou Z, Gu J, Du YL, Li YQ, Wang Y. The -omics Era- Toward a Systems-Level Understanding of Streptomyces. Curr Genomics 2011; 12:404-16. [PMID: 22379394 PMCID: PMC3178909 DOI: 10.2174/138920211797248556] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 06/28/2011] [Accepted: 07/03/2011] [Indexed: 11/22/2022] Open
Abstract
Streptomyces is a group of soil bacteria of medicinal, economic, ecological, and industrial importance. It is renowned for its complex biology in gene regulation, antibiotic production, morphological differentiation, and stress response. In this review, we provide an overview of the recent advances in Streptomyces biology inspired by -omics based high throughput technologies. In this post-genomic era, vast amounts of data have been integrated to provide significant new insights into the fundamental mechanisms of system control and regulation dynamics of Streptomyces.
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Affiliation(s)
- Zhan Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P.R. China
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Jianying Gu
- Department of Biology, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
| | - Yi-Ling Du
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P.R. China
| | - Yong-Quan Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058, P.R. China
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
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Properties of CsnR, the transcriptional repressor of the chitosanase gene, csnA, of Streptomyces lividans. J Bacteriol 2011; 193:2441-50. [PMID: 21441516 DOI: 10.1128/jb.01476-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A palindromic sequence is present in the intergenic region preceding the chitosanase gene csnA (SSPG_06922) of Streptomyces lividans TK24. This sequence was also found in front of putative chitosanase genes in several other actinomycete genomes and upstream genes encoding putative transcriptional regulators of the ROK family, including csnR (SSPG_04872) in S. lividans. The latter was examined as a possible transcriptional regulator (CsnR) of chitosanase gene expression. In vitro, purified CsnR bound strongly to the palindromic sequences of the csnA and csnR genes (equilibrium dissociation constant [K(D)] = 0.032 and 0.040 nM, respectively). Binding was impaired in the presence of chitosan oligosaccharides and d-glucosamine, and chitosan dimer was found to be the best effector, as determined by an equilibrium competition experiment and 50% inhibitory concentration (IC(50)) determination, while glucose, N-acetyl-glucosamine, and galactosamine had no effect. In vivo, comparison of the S. lividans wild type and ΔCsnR strains using β-lactamase reporter genes showed that CsnR represses the expression of csnA and of its own gene, which was confirmed by quantitative PCR (qPCR). CsnR is localized at the beginning of a gene cluster, possibly an operon, the organization of which is conserved through many actinomycete genomes. The CsnR-mediated chitosanase regulation mechanism seems to be widespread among actinomycetes.
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Mellado RP. Summing up particular features of protein secretion in Streptomyces lividans. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0709-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Zhu Y, Wang L, Du Y, Wang S, Yu T, Hong B. Heterologous expression of human interleukin-6 in Streptomyces lividans TK24 using novel secretory expression vectors. Biotechnol Lett 2010; 33:253-61. [DOI: 10.1007/s10529-010-0428-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Accepted: 09/23/2010] [Indexed: 11/24/2022]
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D'Huys PJ, Lule I, Van Hove S, Vercammen D, Wouters C, Bernaerts K, Anné J, Van Impe JFM. Amino acid uptake profiling of wild type and recombinant Streptomyces lividans TK24 batch fermentations. J Biotechnol 2010; 152:132-43. [PMID: 20797416 DOI: 10.1016/j.jbiotec.2010.08.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 08/12/2010] [Accepted: 08/17/2010] [Indexed: 11/19/2022]
Abstract
Streptomyces lividans is considered an interesting host for the secretory production of heterologous proteins. To obtain a good secretion yield of heterologous proteins, the availability of suitable nitrogen sources in the medium is required. Often, undefined mixtures of amino acids are used to improve protein yields. However, the understanding of amino acid utilization as well as their contribution to the heterologous protein synthesis is poor. In this paper, amino acid utilization by wild type and recombinant S. lividans TK24 growing on a minimal medium supplemented with casamino acids is profiled by intensive analysis of the exometabolome (metabolic footprint) as a function of time. Dynamics of biomass, substrates, by-products and heterologous protein are characterized, analyzed and compared. As an exemplary protein mouse Tumor Necrosis Factor Alpha (mTNF-α) is considered. Results unveil preferential glutamate and aspartate assimilation, together with glucose and ammonium, but the associated high biomass growth rate is unfavorable for protein production. Excretion of organic acids as well as alanine is observed. Pyruvate and alanine overflow point at an imbalance between carbon and nitrogen catabolism and biosynthetic fluxes. Lactate secretion is probably related to clump formation. Heterologous protein production induces a slowdown in growth, denser clump formation and a shift in metabolism, as reflected in the altered substrate requirements and overflow pattern. Besides glutamate and aspartate, most amino acids are catabolized, however, their exact contribution in heterologous protein production could not be seized from macroscopic quantities. The metabolic footprints presented in this paper provide a first insight into the impact and relevance of amino acids on biomass growth and protein production. Type and availability of substrates together with biomass growth rate and morphology affect the protein secretion efficiency and should be optimally controlled, e.g., by appropriate medium formulation and substrate dosing. Overflow metabolism as well as high biomass growth rates must be avoided because they reduce protein yields. Further investigation of the intracellular metabolic fluxes should be conducted to fully unravel and identify ways to relieve the metabolic burden of plasmid maintenance and heterologous protein production and to prevent overflow.
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Affiliation(s)
- Pieter-Jan D'Huys
- Chemical and Biochemical Process Technology and Control Section (BioTeC), Department of Chemical Engineering, Katholieke Universiteit Leuven, Willem de Croylaan 46, B-3001 Leuven, Belgium
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Sinsereekul N, Wangkam T, Thamchaipenet A, Srikhirin T, Eurwilaichitr L, Champreda V. Recombinant expression of BTA hydrolase in Streptomyces rimosus and catalytic analysis on polyesters by surface plasmon resonance. Appl Microbiol Biotechnol 2010; 86:1775-84. [PMID: 20174792 DOI: 10.1007/s00253-010-2465-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 01/20/2010] [Accepted: 01/21/2010] [Indexed: 11/28/2022]
Abstract
A recombinant polyester-degrading hydrolase from Thermobifida sp. BCC23166 targeting on aliphatic-aromatic copolyester (rTfH) was produced in Streptomyces rimosus R7. rTfH was expressed by induction with thiostrepton as a C-terminal His(6) fusion from the native gene sequence under the control of tipA promoter and purified from the culture supernatant to high homogeneity by a single step affinity purification on Ni-Sepharose matrix. The enzyme worked optimally at 50-55 degrees C and showed esterase activity on C3-C16 p-nitrophenyl alkanoates with a specific activity of 76.5 U/mg on p-nitrophenyl palmitate. Study of rTfH catalysis on surface degradation of polyester films using surface plasmon resonance analysis revealed that the degradation rates were in the order of poly-epsilon-caprolactone > Ecoflex > polyhydroxybutyrate. Efficient hydrolysis of Ecoflex by rTfH was observed in mild alkaline conditions, with the highest activity at pH 8.0 and ionic strength at 250 mM sodium chloride, with the maximal specific activity of 0.79 mg(-1)min(-1)mg(-1) protein. Under the optimal conditions, rTfH showed a remarkable 110-time higher specific activity on Ecoflex in comparison to a lipase from Thermomyces lanuginosus, while less difference in degradation efficiency of the two enzymes was observed on the aliphatic polyesters, suggesting greater specificities of rTfH to the aliphatic-aromatic copolyester. This study demonstrated the use of streptomycetes as an alternative expression system for production of the multi-polyester-degrading enzyme of actinomycete origin and provided insights on its catalytic properties on surface degradation contributing to further biotechnological application of this enzyme.
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Affiliation(s)
- Nitat Sinsereekul
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
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Vrancken K, Van Mellaert L, Anné J. Cloning and expression vectors for a Gram-positive host, Streptomyces lividans. Methods Mol Biol 2010; 668:97-107. [PMID: 20830558 DOI: 10.1007/978-1-60761-823-2_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The choice of an expression system for the meta-genomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the Gram-negative bacterium Escherichia coli as a host for the meta-genomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40% of the enzymatic activities may be readily recovered by random cloning in E. coli (Gabor et al., Environ Microbiol 6:879-886, 2004). To recover some of the remaining 60%, alternative cloning hosts such as Streptomyces spp. have been used (Lorenz and Eck, Nat Rev Microbiol 3:510-516, 2005). Streptomycetes are high-GC Gram-positive bacteria that belong to the Actinomycetales, and they have been studied extensively in the last 10 years as an alternative expression system (reviewed in Vrancken and Anné, Future Microbiol 4:181-188, 2009). Streptomyces is extremely well suited for the expression of DNA from other actinomycetes and genomes of high GC content (Wang et al., Org Lett 2:2401-2404, 2000). Furthermore, due to its high innate secretion capacity, it can be a superior system than E. coli for the production of many extra-cellular proteins.
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Affiliation(s)
- Kristof Vrancken
- Department of Microbiology and Immunology, Rega Institute for Medical Research, K.U. Leuven, Leuven, Belgium
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