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Wang R, Nji Wandi B, Schwartz N, Hecht J, Ponomareva L, Paige K, West A, Desanti K, Nguyen J, Niemi J, Thorson JS, Shaaban KA, Metsä-Ketelä M, Nybo SE. Diverse Combinatorial Biosynthesis Strategies for C-H Functionalization of Anthracyclinones. ACS Synth Biol 2024; 13:1523-1536. [PMID: 38662967 PMCID: PMC11101304 DOI: 10.1021/acssynbio.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/18/2024]
Abstract
Streptomyces spp. are "nature's antibiotic factories" that produce valuable bioactive metabolites, such as the cytotoxic anthracycline polyketides. While the anthracyclines have hundreds of natural and chemically synthesized analogues, much of the chemical diversity stems from enzymatic modifications to the saccharide chains and, to a lesser extent, from alterations to the core scaffold. Previous work has resulted in the generation of a BioBricks synthetic biology toolbox in Streptomyces coelicolor M1152ΔmatAB that could produce aklavinone, 9-epi-aklavinone, auramycinone, and nogalamycinone. In this work, we extended the platform to generate oxidatively modified analogues via two crucial strategies. (i) We swapped the ketoreductase and first-ring cyclase enzymes for the aromatase cyclase from the mithramycin biosynthetic pathway in our polyketide synthase (PKS) cassettes to generate 2-hydroxylated analogues. (ii) Next, we engineered several multioxygenase cassettes to catalyze 11-hydroxylation, 1-hydroxylation, 10-hydroxylation, 10-decarboxylation, and 4-hydroxyl regioisomerization. We also developed improved plasmid vectors and S. coelicolor M1152ΔmatAB expression hosts to produce anthracyclinones. This work sets the stage for the combinatorial biosynthesis of bespoke anthracyclines using recombinant Streptomyces spp. hosts.
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Affiliation(s)
- Rongbin Wang
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Benjamin Nji Wandi
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Nora Schwartz
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Jacob Hecht
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Larissa Ponomareva
- Center
for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Kendall Paige
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Alexis West
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Kathryn Desanti
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Jennifer Nguyen
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
| | - Jarmo Niemi
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Jon S. Thorson
- Center
for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Khaled A. Shaaban
- Center
for Pharmaceutical Research and Innovation, Department of Pharmaceutical Sciences,
College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Mikko Metsä-Ketelä
- Department
of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - S. Eric Nybo
- Department
of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, Michigan 49307, United States
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2
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Vojnovic S, Aleksic I, Ilic-Tomic T, Stevanovic M, Nikodinovic-Runic J. Bacillus and Streptomyces spp. as hosts for production of industrially relevant enzymes. Appl Microbiol Biotechnol 2024; 108:185. [PMID: 38289383 PMCID: PMC10827964 DOI: 10.1007/s00253-023-12900-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 02/01/2024]
Abstract
The application of enzymes is expanding across diverse industries due to their nontoxic and biodegradable characteristics. Another advantage is their cost-effectiveness, reflected in reduced processing time, water, and energy consumption. Although Gram-positive bacteria, Bacillus, and Streptomyces spp. are successfully used for production of industrially relevant enzymes, they still lag far behind Escherichia coli as hosts for recombinant protein production. Generally, proteins secreted by Bacillus and Streptomyces hosts are released into the culture medium; their native conformation is preserved and easier recovery process enabled. Given the resilience of both hosts in harsh environmental conditions and their spore-forming capability, a deeper understanding and broader use of Bacillus and Streptomyces as expression hosts could significantly enhance the robustness of industrial bioprocesses. This mini-review aims to compare two expression hosts, emphasizing their specific advantages in industrial surroundings such are chemical, detergent, textile, food, animal feed, leather, and paper industries. The homologous sources, heterologous hosts, and molecular tools used for the production of recombinant proteins in these hosts are discussed. The potential to use both hosts as biocatalysts is also evaluated. Undoubtedly, Bacillus and Streptomyces spp. as production hosts possess the potential to take on a more substantial role, providing superior (bio-based) process robustness and flexibility. KEY POINTS: • Bacillus and Streptomyces spp. as robust hosts for enzyme production. • Industrially relevant enzyme groups for production in alternative hosts highlighted. • Molecular biology techniques are enabling easier utilization of both hosts.
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Affiliation(s)
- Sandra Vojnovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia.
| | - Ivana Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia
| | - Tatjana Ilic-Tomic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia
| | - Jasmina Nikodinovic-Runic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade 152, Serbia.
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3
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Cuebas‐Irizarry MF, Grunden AM. Streptomyces spp. as biocatalyst sources in pulp and paper and textile industries: Biodegradation, bioconversion and valorization of waste. Microb Biotechnol 2024; 17:e14258. [PMID: 37017414 PMCID: PMC10832569 DOI: 10.1111/1751-7915.14258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Complex polymers represent a challenge for remediating environmental pollution and an opportunity for microbial-catalysed conversion to generate valorized chemicals. Members of the genus Streptomyces are of interest because of their potential use in biotechnological applications. Their versatility makes them excellent sources of biocatalysts for environmentally responsible bioconversion, as they have a broad substrate range and are active over a wide range of pH and temperature. Most Streptomyces studies have focused on the isolation of strains, recombinant work and enzyme characterization for evaluating their potential for biotechnological application. This review discusses reports of Streptomyces-based technologies for use in the textile and pulp-milling industry and describes the challenges and recent advances aimed at achieving better biodegradation methods featuring these microbial catalysts. The principal points to be discussed are (1) Streptomyces' enzymes for use in dye decolorization and lignocellulosic biodegradation, (2) biotechnological processes for textile and pulp and paper waste treatment and (3) challenges and advances for textile and pulp and paper effluent treatment.
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Affiliation(s)
- Mara F. Cuebas‐Irizarry
- Department of Plant and Microbial BiologyNorth Carolina State UniversityPlant Sciences Building Rm 2323, 840 Oval DrRaleighNorth Carolina27606USA
| | - Amy M. Grunden
- Department of Plant and Microbial BiologyNorth Carolina State UniversityPlant Sciences Building Rm 2323, 840 Oval DrRaleighNorth Carolina27606USA
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4
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Lin CY, Ru Y, Jin Y, Lin Q, Zhao GR. PAS domain containing regulator SLCG_7083 involved in morphological development and glucose utilization in Streptomyces lincolnensis. Microb Cell Fact 2023; 22:257. [PMID: 38093313 PMCID: PMC10717218 DOI: 10.1186/s12934-023-02263-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Streptomyces lincolnensis is well known for producing the clinically important antimicrobial agent lincomycin. The synthetic and regulatory mechanisms on lincomycin biosynthesis have been deeply explored in recent years. However, the regulation involved in primary metabolism have not been fully addressed. RESULTS SLCG_7083 protein contains a Per-Arnt-Sim (PAS) domain at the N-terminus, whose homologous proteins are highly distributed in Streptomyces. The inactivation of the SLCG_7083 gene indicated that SLCG_7083 promotes glucose utilization, slows mycelial growth and affects sporulation in S. lincolnensis. Comparative transcriptomic analysis further revealed that SLCG_7083 represses eight genes involved in sporulation, cell division and lipid metabolism, and activates two genes involved in carbon metabolism. CONCLUSIONS SLCG_7083 is a PAS domain-containing regulator on morphological development and glucose utilization in S. lincolnensis. Our results first revealed the regulatory function of SLCG_7083, and shed new light on the transcriptional effects of SLCG_7083-like family proteins in Streptomyces.
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Affiliation(s)
- Chun-Yan Lin
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, China
| | - Yixian Ru
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, China
| | - Yanchao Jin
- College of Environmental and Resource Sciences, Fujian Normal University, Fuzhou, Fujian, 350117, China
| | - Qi Lin
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou, 350108, China.
| | - Guang-Rong Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China.
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China.
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen, 518055, China.
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5
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De Wannemaeker L, Bervoets I, De Mey M. Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools. Biotechnol Adv 2022; 60:108028. [PMID: 36031082 DOI: 10.1016/j.biotechadv.2022.108028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/02/2022]
Abstract
Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.
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Affiliation(s)
- Lien De Wannemaeker
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Indra Bervoets
- Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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Genetic and Biochemical Characterization of Halogenation and Drug Transportation Genes Encoded in the Albofungin Biosynthetic Gene Cluster. Appl Environ Microbiol 2022; 88:e0080622. [PMID: 36000868 PMCID: PMC9469721 DOI: 10.1128/aem.00806-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Albofungin, a hexacyclic aromatic natural product, exhibits broad-spectrum antimicrobial activity. Its biosynthesis, regulation, and resistance remain elusive. Here, we report the albofungin (abf) biosynthetic gene cluster (BGC) from its producing strain Streptomyces tumemacerans JCM5050. The nascent abf BGC encodes 70 putative genes, including regulators, transporters, type II polyketide synthases (PKSs), oxidoreductase, and tailoring enzymes. To validate the intactness and functionality of the BGC, we developed an Escherichia coli-Streptomyces shuttle bacterial artificial chromosome system, whereby the abf BGC was integrated into the genome of a nonproducing host via heterologous conjugation, wherefrom albofungin can be produced, confirming that the BGC is in effect. We then delimited the boundaries of the BGC by means of in vitro CRISPR-Cas9 DNA editing, concluding a minimal but essential 60-kb abf BGC ranging from orfL to abf58. The orfA gene encoding a reduced flavin adenine dinucleotide (FADH2)-dependent halogenase was examined and is capable of transforming albofungin to halogen-substituted congeners in vivo and in vitro. The orfL gene encoding a transporter was examined in vivo. The presence/absence of orfA or orfL demonstrated that the MIC of albofungin is subject to alteration when an extracellular polysaccharide intercellular adhesin was formed. Despite that halogenation of albofungin somewhat increases binding affinity to transglycosylase (TGase), albofungin with/without a halogen substituent manifests similar in vitro antimicrobial activity. Halogenation, however, limits overall dissemination and effectiveness given a high secretion rate, weak membrane permeability, and high hydrophobicity of the resulting products, whereby the functions of orfA and orfL are correlated with drug detoxification/resistance for the first time. IMPORTANCE Albofungin, a natural product produced from Streptomycetes, exhibits bioactivities against bacteria, fungi, and tumor cells. The biosynthetic logic, regulations, and resistance of albofungin remain yet to be addressed. Herein, the minimal albofungin (abf) biosynthetic gene cluster (BGC) from the producing strain Streptomyces tumemacerans JCM5050 was precisely delimited using the Escherichia coli-Streptomyces shuttle bacterial artificial chromosome system, of which the gene essentiality was established in vivo and in vitro. Next, we characterized two genes orfA and orfL encoded in the abf BGC, which act as a reduced flavin adenine dinucleotide (FADH2)-dependent halogenase and an albofungin-congeners transporter, respectively. While each testing microorganism exhibited different sensitivities to albofungins, the MIC values of albofungins against testing strains with/without orfA and/or orfL were subject to considerable changes. Halogen-substituted albofungins mediated by OrfA manifested overall compromised dissemination and effectiveness, revealing for the first time that two functionally distinct proteins OrfA and OrfL are associated together, exerting a novel “belt and braces” mechanism in antimicrobial detoxification/resistance.
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7
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Single cell mutant selection for metabolic engineering of actinomycetes. Metab Eng 2022; 73:124-133. [PMID: 35809806 DOI: 10.1016/j.ymben.2022.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/31/2022] [Accepted: 07/01/2022] [Indexed: 11/23/2022]
Abstract
Actinomycetes are important producers of pharmaceuticals and industrial enzymes. However, wild type strains require laborious development prior to industrial usage. Here we present a generally applicable reporter-guided metabolic engineering tool based on random mutagenesis, selective pressure, and single-cell sorting. We developed fluorescence-activated cell sorting (FACS) methodology capable of reproducibly identifying high-performing individual cells from a mutant population directly from liquid cultures. Actinomycetes are an important source of catabolic enzymes, where product yields determine industrial viability. We demonstrate 5-fold yield improvement with an industrial cholesterol oxidase ChoD producer Streptomyces lavendulae to 20.4 U g-1 in three rounds. Strain development is traditionally followed by production medium optimization, which is a time-consuming multi-parameter problem that may require hard to source ingredients. Ultra-high throughput screening allowed us to circumvent medium optimization and we identified high ChoD yield production strains directly from mutant libraries grown under preset culture conditions. Genome-mining based drug discovery is a promising source of bioactive compounds, which is complicated by the observation that target metabolic pathways may be silent under laboratory conditions. We demonstrate our technology for drug discovery by activating a silent mutaxanthene metabolic pathway in Amycolatopsis. We apply the method for industrial strain development and increase mutaxanthene yields 9-fold to 99 mg l-1 in a second round of mutant selection. In summary, the ability to screen tens of millions of mutants in a single cell format offers broad applicability for metabolic engineering of actinomycetes for activation of silent metabolic pathways and to increase yields of proteins and natural products.
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8
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Salama S, Habib MH, Hatti-Kaul R, Gaber Y. Reviewing a plethora of oxidative-type reactions catalyzed by whole cells of Streptomyces species. RSC Adv 2022; 12:6974-7001. [PMID: 35424663 PMCID: PMC8982256 DOI: 10.1039/d1ra08816e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/17/2022] [Indexed: 11/21/2022] Open
Abstract
Selective oxidation reactions represent a challenging task for conventional organic chemistry. Whole-cell biocatalysis provides a very convenient, easy to apply method to carry out different selective oxidation reactions including chemo-, regio-, and enantio-selective reactions. Streptomyces species are important biocatalysts as they can catalyze these selective reactions very efficiently owing to the wide diversity of enzymes and enzymatic cascades in their cell niche. In this review, we present and analyze most of the examples reported to date of oxidative reactions catalyzed by Streptomyces species as whole-cell biocatalysts. We discuss 33 different Streptomyces species and strains and the role they play in different oxidative reactions over the past five decades. The oxidative reactions have been classified into seven categories that include: hydroxylation of steroids/non-steroids, asymmetric sulfoxidations, oxidation of aldehydes, multi-step oxidations, oxidative cleavage, and N-oxidations. The role played by Streptomyces species as recombinant hosts catalyzing bio-oxidations has also been highlighted.
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Affiliation(s)
- Sara Salama
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University Beni-Suef 62517 Egypt
| | - Mohamed H Habib
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University Sweden
| | - Yasser Gaber
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University Beni-Suef 62511 Egypt
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Mutah University Al-Karak 61710 Jordan
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9
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Sharma A, Balda S, Capalash N, Sharma P. Engineering multifunctional enzymes for agro-biomass utilization. BIORESOURCE TECHNOLOGY 2022; 347:126706. [PMID: 35033642 DOI: 10.1016/j.biortech.2022.126706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Lignocellulosic biomass is a plentiful renewable resource that can be converted into a wide range of high-value-added industrial products. However, the complexity of its structural integrity is one of the major constraints and requires combinations of different fibrolytic enzymes for the cost-effective, industrially and environmentally feasible transformation. An interesting approach is constructing multifunctional enzymes, either in a single polypeptide or by joining multiple domains with linkers and performing diverse reactions simultaneously, in a single host. The production of such chimera proteins multiplies the advantages of different enzymatic reactions in a single setup, in lesser time, at lower production cost and with desirable and improved catalytic activities. This review embodies the various domain-tailoring and extracellular secretion strategies, possible solutions to their challenges, and efforts to experimentally connect different catalytic activities in a single host, as well as their applications.
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Affiliation(s)
- Aarjoo Sharma
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjeev Balda
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Prince Sharma
- Department of Microbiology, Panjab University, Chandigarh, India.
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10
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Hwang S, Lee Y, Kim JH, Kim G, Kim H, Kim W, Cho S, Palsson BO, Cho BK. Streptomyces as Microbial Chassis for Heterologous Protein Expression. Front Bioeng Biotechnol 2022; 9:804295. [PMID: 34993191 PMCID: PMC8724576 DOI: 10.3389/fbioe.2021.804295] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/30/2021] [Indexed: 12/29/2022] Open
Abstract
Heterologous production of recombinant proteins is gaining increasing interest in biotechnology with respect to productivity, scalability, and wide applicability. The members of genus Streptomyces have been proposed as remarkable hosts for heterologous production due to their versatile nature of expressing various secondary metabolite biosynthetic gene clusters and secretory enzymes. However, there are several issues that limit their use, including low yield, difficulty in genetic manipulation, and their complex cellular features. In this review, we summarize rational engineering approaches to optimizing the heterologous production of secondary metabolites and recombinant proteins in Streptomyces species in terms of genetic tool development and chassis construction. Further perspectives on the development of optimal Streptomyces chassis by the design-build-test-learn cycle in systems are suggested, which may increase the availability of secondary metabolites and recombinant proteins.
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Affiliation(s)
- Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Gahyeon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Hyeseong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Innovative Biomaterials Research Center, KAIST Institutes, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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11
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Purification and Characterization of Strong Simultaneous Enzyme Production of Protease and α-Amylase from an Extremophile-Bacillus sp. FW2 and Its Possibility in Food Waste Degradation. FERMENTATION 2021. [DOI: 10.3390/fermentation8010012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Microbial enzymes such as protease and amylase are valuable enzymes with various applications, widely investigated for their applications in degradation of organic waste, biofuel industries, agricultural, pharmaceuticals, chemistry, and biotechnology. In particular, extremophiles play an important role in biorefinery due to their novel metabolic products such as high value catalytic enzymes that are active even under harsh environmental conditions. Due to their potentials and very broad activities, this study isolated, investigated, and characterized the protease- and amylase-producing bacterial strain FW2 that was isolated from food waste. Strain FW2 belongs to the genus Bacillus and was found to be closest to Bacillus amyloliquefaciens DSM 7T with a similarity of 99.86%. This strain was able to degrade organic compounds at temperatures from −6 °C to 75 °C (but weak at 80 °C) under a wide pH range (4.5–12) and high-salinity conditions up to 35% NaCl. Maximum enzyme production was obtained at 1200 ± 23.4 U/mL for protease and 2400 ± 45.8 U/mL for amylase for 4 days at pH 7–7.5, 40–45 °C, and 0–10% NaCl. SDS-PAGE analysis showed that the molecular weights of purified protease were 28 kDa and 44 kDa, corresponding to alkaline protease (AprM) and neutral protease (NprM), respectively, and molecular weight of α-amylase was 55 kDa. Degradation food waste was determined after 15 days, observing a 69% of volume decrease. A potential commercial extremozyme-producing bacteria such as strain FW2 may be a promising contributor to waste degradation under extreme environmental conditions.
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12
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Ijoma GN, Heri SM, Matambo TS, Tekere M. Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi. J Fungi (Basel) 2021; 7:700. [PMID: 34575737 PMCID: PMC8464691 DOI: 10.3390/jof7090700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. This review aims to provide a detailed overview of the necessary steps employed in both qualitative and quantitative research using the omics technologies that are pertinent to fungi characterisation. This stems from the understanding that data provided from the functional characterisation of fungi and their metabolites is important towards the techno-economic feasibility of large-scale production of biological products. The review further describes how the functional gaps left by genomics, internal transcribe spacer (ITS) regions are addressed by transcriptomics and the various techniques and platforms utilised, including quantitive reverse transcription polymerase chain reaction (RT-qPCR), hybridisation techniques, and RNA-seq, and the insights such data provide on the effect of environmental changes on fungal enzyme production from an expressional standpoint. The review also offers information on the many available bioinformatics tools of analysis necessary for the analysis of the overwhelming data synonymous with the omics approach to fungal characterisation.
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Affiliation(s)
- Grace N. Ijoma
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Sylvie M. Heri
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Tonderayi S. Matambo
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Memory Tekere
- Department of Environmental Science, College of Agricultural and Environmental Science, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa;
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13
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Marasinghe SD, Jo E, Hettiarachchi SA, Lee Y, Eom TY, Gang Y, Kang YH, Oh C. Characterization of glycoside hydrolase family 11 xylanase from Streptomyces sp. strain J103; its synergetic effect with acetyl xylan esterase and enhancement of enzymatic hydrolysis of lignocellulosic biomass. Microb Cell Fact 2021; 20:129. [PMID: 34238305 PMCID: PMC8265113 DOI: 10.1186/s12934-021-01619-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/25/2021] [Indexed: 11/18/2022] Open
Abstract
Background Xylanase-containing enzyme cocktails are used on an industrial scale to convert xylan into value-added products, as they hydrolyse the β-1,4-glycosidic linkages between xylopyranosyl residues. In the present study, we focused on xynS1, the glycoside hydrolase (GH) 11 xylanase gene derived from the Streptomyces sp. strain J103, which can mediate XynS1 protein synthesis and lignocellulosic material hydrolysis. Results xynS1 has an open reading frame with 693 base pairs that encodes a protein with 230 amino acids. The predicted molecular weight and isoelectric point of the protein were 24.47 kDa and 7.92, respectively. The gene was cloned into the pET-11a expression vector and expressed in Escherichia coli BL21(DE3). Recombinant XynS1 (rXynS1) was purified via His-tag affinity column chromatography. rXynS1 exhibited optimal activity at a pH of 5.0 and temperature of 55 °C. Thermal stability was in the temperature range of 50–55 °C. The estimated Km and Vmax values were 51.4 mg/mL and 898.2 U/mg, respectively. One millimolar of Mn2+ and Na+ ions stimulated the activity of rXynS1 by up to 209% and 122.4%, respectively, and 1 mM Co2+ and Ni2+ acted as inhibitors of the enzyme. The mixture of rXynS1, originates from Streptomyces sp. strain J103 and acetyl xylan esterase (AXE), originating from the marine bacterium Ochrovirga pacifica, enhanced the xylan degradation by 2.27-fold, compared to the activity of rXynS1 alone when Mn2+ was used in the reaction mixture; this reflected the ability of both enzymes to hydrolyse the xylan structure. The use of an enzyme cocktail of rXynS1, AXE, and commercial cellulase (Celluclast® 1.5 L) for the hydrolysis of lignocellulosic biomass was more effective than that of commercial cellulase alone, thereby increasing the relative activity 2.3 fold. Conclusion The supplementation of rXynS1 with AXE enhanced the xylan degradation process via the de-esterification of acetyl groups in the xylan structure. Synergetic action of rXynS1 with commercial cellulase improved the hydrolysis of pre-treated lignocellulosic biomass; thus, rXynS1 could potentially be used in several industrial applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01619-x.
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Affiliation(s)
- Svini Dileepa Marasinghe
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Eunyoung Jo
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Sachithra Amarin Hettiarachchi
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.,Department of Fisheries and Aquaculture, Faculty of Fisheries and Marine Sciences and Technology, University of Ruhuna, Matara, Sri Lanka
| | - Youngdeuk Lee
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea
| | - Tae-Yang Eom
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yehui Gang
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yoon-Hyeok Kang
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea.,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chulhong Oh
- Korea Institute of Ocean Science and Technology, 2670, Iljudong-ro, Gujwa-eup, Jeju, Republic of Korea. .,Department of Ocean Science, University of Science and Technology, (34113) 217, Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea.
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14
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Kuhl M, Rückert C, Gläser L, Beganovic S, Luzhetskyy A, Kalinowski J, Wittmann C. Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development. Biotechnol Bioeng 2021; 118:3076-3093. [PMID: 33974270 DOI: 10.1002/bit.27818] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/17/2021] [Accepted: 04/30/2021] [Indexed: 11/09/2022]
Abstract
Actinobacteria provide a rich spectrum of bioactive natural products and therefore display an invaluable source towards commercially valuable pharmaceuticals and agrochemicals. Here, we studied the use of inorganic talc microparticles (hydrous magnesium silicate, 3MgO·4SiO2 ·H2 O, 10 µm) as a general supplement to enhance natural product formation in this important class of bacteria. Added to cultures of recombinant Streptomyces lividans, talc enhanced production of the macrocyclic peptide antibiotic bottromycin A2 and its methylated derivative Met-bottromycin A2 up to 109 mg L-1 , the highest titer reported so far. Hereby, the microparticles fundamentally affected metabolism. With 10 g L-1 talc, S. lividans grew to 40% smaller pellets and, using RNA sequencing, revealed accelerated morphogenesis and aging, indicated by early upregulation of developmental regulator genes such as ssgA, ssgB, wblA, sigN, and bldN. Furthermore, the microparticles re-balanced the expression of individual bottromycin cluster genes, resulting in a higher macrocyclization efficiency at the level of BotAH and correspondingly lower levels of non-cyclized shunt by-products, driving the production of mature bottromycin. Testing a variety of Streptomyces species, talc addition resulted in up to 13-fold higher titers for the RiPPs bottromycin and cinnamycin, the alkaloid undecylprodigiosin, the polyketide pamamycin, the tetracycline-type oxytetracycline, and the anthramycin-analogs usabamycins. Moreover, talc addition boosted production in other actinobacteria, outside of the genus of Streptomyces: vancomycin (Amycolatopsis japonicum DSM 44213), teicoplanin (Actinoplanes teichomyceticus ATCC 31121), and the angucyclinone-type antibiotic simocyclinone (Kitasatospora sp.). For teicoplanin, the microparticles were even crucial to activate production. Taken together, the use of talc was beneficial in 75% of all tested cases and optimized natural and heterologous hosts forming the substance of interest with clusters under native and synthetic control. Given its simplicity and broad benefits, microparticle-supplementation appears as an enabling technology in natural product research of these most important microbes.
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Affiliation(s)
- Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
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15
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Mrudulakumari Vasudevan U, Lee OK, Lee EY. Alginate derived functional oligosaccharides: Recent developments, barriers, and future outlooks. Carbohydr Polym 2021; 267:118158. [PMID: 34119132 DOI: 10.1016/j.carbpol.2021.118158] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Alginate is a biopolymer used extensively in the food, pharmaceutical, and chemical industries. Alginate oligosaccharides (AOS) derived from alginate exhibit superior biological activities and therapeutic potential. Alginate lyases with characteristic substrate specificity can facilitate the production of a broad array of AOS with precise structure and functionality. By adopting innovative analytical tools in conjunction with focused clinical studies, the structure-bioactivity relationship of a number of AOS has been brought to light. This review covers fundamental aspects and recent developments in AOS research. Enzymatic and microbial processes involved in AOS production from brown algae and sequential steps involved in AOS structure elucidation are outlined. Biological mechanisms underlying the health benefits of AOS and their potential industrial and therapeutic applications are elaborated. Withal, various challenges in AOS research are traced out, and future directions, specifically on recombinant systems for AOS preparation, are delineated to further widen the horizon of these exceptional oligosaccharides.
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Affiliation(s)
- Ushasree Mrudulakumari Vasudevan
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Ok Kyung Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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16
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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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17
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Sidar A, Albuquerque ED, Voshol GP, Ram AFJ, Vijgenboom E, Punt PJ. Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms. Front Bioeng Biotechnol 2020; 8:871. [PMID: 32850729 PMCID: PMC7410926 DOI: 10.3389/fbioe.2020.00871] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.
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Affiliation(s)
- Andika Sidar
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Department of Food Science and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Erica D Albuquerque
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Sun Pharmaceutical Industries Europe BV., Hoofddorp, Netherlands
| | - Gerben P Voshol
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
| | - Arthur F J Ram
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Erik Vijgenboom
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Peter J Punt
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
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18
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Exploration of cryptic organic photosensitive compound as Zincphyrin IV in Streptomyces venezuelae ATCC 15439. Appl Microbiol Biotechnol 2019; 104:713-724. [PMID: 31820068 DOI: 10.1007/s00253-019-10262-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/07/2019] [Accepted: 11/19/2019] [Indexed: 12/30/2022]
Abstract
Zincphyrin IV is a potential organic photosensitizer which is of significant interest for applications in biomedicine, materials science, agriculture (as insecticide), and chemistry. Most studies on Zincphyrin are focused on Zincphyrin III while biosynthesis and application of Zincphyrin IV is comparatively less explored. In this study, we explored Zincphyrin IV production in Streptomyces venezuelae ATCC 15439 through combination of morphology engineering and "One strain many compounds" approach. The morphology engineering followed by change in culture medium led to activation of cryptic Zincphyrin IV biosynthetic pathway in S. venezuelae with subsequent detection of Zincphyrin IV. Morphology engineering applied in S. venezuelae increased the biomass from 7.17 to 10.5 mg/mL after 48 h of culture. Moreover, morphology of engineered strain examined by SEM showed reduced branching and fragmentation of mycelia. The distinct change in color of culture broth visually demonstrated the activation of the cryptic biosynthetic pathway in S. venezuelae. The production of Zincphyrin IV was found to be initiated after overexpression ssgA, resulting in the increase in titer from 4.21 to 7.54 μg/mL. Furthermore, Zincphyrin IV demonstrated photodynamic antibacterial activity against Bacillus subtilis and photodynamic anticancer activity against human ovarian carcinoma cell lines.
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19
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Rahmani N, Kahar P, Lisdiyanti P, Lee J, Prasetya B, Ogino C, Kondo A. GH-10 and GH-11 Endo-1,4-β-xylanase enzymes from Kitasatospora sp. produce xylose and xylooligosaccharides from sugarcane bagasse with no xylose inhibition. BIORESOURCE TECHNOLOGY 2019; 272:315-325. [PMID: 30384206 DOI: 10.1016/j.biortech.2018.10.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 05/10/2023]
Abstract
A novel strategy for the low-cost, high-yield co-production of xylose and xylooligosaccharides together with no xylose inhibition was developed using a novel heterologous expression of XYN10Ks_480 endo-1,4-β-xylanase with a ricin-type β-trefoil type of domain and XYN11Ks_480 endo-1,4-β-xylanase with a CBM 2 superfamily from the Kitasatospora sp in an actinomycetes expression system. Xylose is the main building block for hemicellulose xylan. Our findings demonstrated high levels of expression and catalytic activity for XYN10Ks_480 during hydrolysis of the extracted xylan of bagasse, and three types of xylan-based substrates were used to produce xylose and xylooligosaccharides. However, hydrolysis by XYN11Ks_480 produced xylooligosaccharides without xylose formation. This study demonstrated how integrating sodium hypochlorite-extracted xylan and enzymatic hydrolysis could provide an alternative strategy for the generation of XOS from lignocellulosic material.
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Affiliation(s)
- Nanik Rahmani
- Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong Science Center. Jl. Raya Bogor Km. 46, Cibinong 16911, West Java, Indonesia
| | - Prihardi Kahar
- Department of Chemical and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Puspita Lisdiyanti
- Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong Science Center. Jl. Raya Bogor Km. 46, Cibinong 16911, West Java, Indonesia
| | - Jaemin Lee
- Department of Chemical and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Bambang Prasetya
- Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong Science Center. Jl. Raya Bogor Km. 46, Cibinong 16911, West Java, Indonesia; National Standardization Agency of Indonesia, Gedung I BPPT Jl. M.H. Thamrin No. 8, Kebun Sirih, Jakarta 10340, Indonesia
| | - Chiaki Ogino
- Department of Chemical and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
| | - Akihiko Kondo
- Department of Chemical and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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20
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Daniels W, Bouvin J, Busche T, Rückert C, Simoens K, Karamanou S, Van Mellaert L, Friðjónsson ÓH, Nicolai B, Economou A, Kalinowski J, Anné J, Bernaerts K. Transcriptomic and fluxomic changes in Streptomyces lividans producing heterologous protein. Microb Cell Fact 2018; 17:198. [PMID: 30577858 PMCID: PMC6302529 DOI: 10.1186/s12934-018-1040-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/26/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Gram-positive Streptomyces lividans TK24 is an attractive host for heterologous protein production because of its high capability to secrete proteins-which favors correct folding and facilitates downstream processing-as well as its acceptance of methylated DNA and its low endogeneous protease activity. However, current inconsistencies in protein yields urge for a deeper understanding of the burden of heterologous protein production on the cell. In the current study, transcriptomics and [Formula: see text]-based fluxomics were exploited to uncover gene expression and metabolic flux changes associated with heterologous protein production. The Rhodothermus marinus thermostable cellulase A (CelA)-previously shown to be successfully overexpressed in S. lividans-was taken as an example protein. RESULTS RNA-seq and [Formula: see text]-based metabolic flux analysis were performed on a CelA-producing and an empty-plasmid strain under the same conditions. Differential gene expression, followed by cluster analysis based on co-expression and co-localization, identified transcriptomic responses related to secretion-induced stress and DNA damage. Furthermore, the OsdR regulon (previously associated with hypoxia, oxidative stress, intercellular signaling, and morphological development) was consistently upregulated in the CelA-producing strain and exhibited co-expression with isoenzymes from the pentose phosphate pathway linked to secondary metabolism. Increased expression of these isoenzymes matches to increased fluxes in the pentose phosphate pathway. Additionally, flux maps of the central carbon metabolism show increased flux through the tricarboxylic acid cycle in the CelA-producing strain. Redirection of fluxes in the CelA-producing strain leads to higher production of NADPH, which can only partly be attributed to increased secretion. CONCLUSIONS Transcriptomic and fluxomic changes uncover potential new leads for targeted strain improvement strategies which may ease the secretion stress and metabolic burden associated with heterologous protein synthesis and secretion, and may help create a more consistently performing S. lividans strain. Yet, links to secondary metabolism and redox balancing should be further investigated to fully understand the S. lividans metabolome under heterologous protein production.
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Affiliation(s)
- Wouter Daniels
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Jeroen Bouvin
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Kenneth Simoens
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Lieve Van Mellaert
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | | | - Bart Nicolai
- Division of Mechatronics, Biostatistics and Sensors (MeBioS), Department of Biosystems (BIOSYST), KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jozef Anné
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, box 1037, 3000, Leuven, Belgium
| | - Kristel Bernaerts
- Department of Chemical Engineering, Bio- and Chemical Systems Technology, Reactor Engineering and Safety Section, KU Leuven, Celestijnenlaan 200F, box 2424, 3001, Leuven, Belgium.
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21
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Rebets Y, Tsolis KC, Guðmundsdóttir EE, Koepff J, Wawiernia B, Busche T, Bleidt A, Horbal L, Myronovskyi M, Ahmed Y, Wiechert W, Rückert C, Hamed MB, Bilyk B, Anné J, Friðjónsson Ó, Kalinowski J, Oldiges M, Economou A, Luzhetskyy A. Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions. Front Microbiol 2018; 9:3033. [PMID: 30619125 PMCID: PMC6295645 DOI: 10.3389/fmicb.2018.03033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/23/2018] [Indexed: 12/15/2022] Open
Abstract
Alternative sigma factors control numerous aspects of bacterial life, including adaptation to physiological stresses, morphological development, persistence states and virulence. This is especially true for the physiologically complex actinobacteria. Here we report the development of a robust gene deletions system for Streptomyces lividans TK24 based on a BAC library combined with the λ-Red recombination technique. The developed system was validated by systematically deleting the most highly expressed genes encoding alternative sigma factors and several other regulatory genes within the chromosome of S. lividans TK24. To demonstrate the possibility of large scale genomic manipulations, the major part of the undecylprodigiosin gene cluster was deleted as well. The resulting mutant strains were characterized in terms of morphology, growth parameters, secondary metabolites production and response to thiol-oxidation and cell-wall stresses. Deletion of SLIV_12645 gene encoding S. coelicolor SigR1 ortholog has the most prominent phenotypic effect, resulted in overproduction of actinorhodin and coelichelin P1 and increased sensitivity to diamide. The secreted proteome analysis of SLIV_12645 mutant revealed SigR1 influence on trafficking of proteins involved in cell wall biogenesis and refactoring. The reported here gene deletion system will further facilitate work on S. lividans strain improvement as a host for either secondary metabolites or protein production and will contribute to basic research in streptomycetes physiology, morphological development, secondary metabolism. On the other hand, the systematic deletion of sigma factors encoding genes demonstrates the complexity and conservation of regulatory processes conducted by sigma factors in streptomycetes.
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Affiliation(s)
- Yuriy Rebets
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | | | | | - Joachim Koepff
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | | | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Arne Bleidt
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Liliya Horbal
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Yousra Ahmed
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Mohamed B. Hamed
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Molecular Biology, National Research Centre, Giza, Egypt
| | - Bohdan Bilyk
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Jozef Anné
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
- Actinobacteria Metabolic Engineering Group, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
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22
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Engineering diverse eubacteria promoters for robust Gene expression in Streptomyces lividans. J Biotechnol 2018; 289:93-102. [PMID: 30481545 DOI: 10.1016/j.jbiotec.2018.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/13/2018] [Accepted: 11/20/2018] [Indexed: 11/23/2022]
Abstract
Due to the lack of powerful gene regulation elements, the engineering development of Streptomyces is often limited. Here, we disclosed that the heterologous σ70 -dependent promoters, which have been reported as inefficient tools for gene expression in Streptomyces, could be efficiently recognized by Streptomyces housekeeping factor σhrdB. Therefore, an effective strategy was developed to engineer these promoters for robust gene expression in Streptomyces by fusing them with optimized 5'-untranslation regions (5'-UTRs). As a proof of concept, the widely used Ptac in E. coli was engineered by fusing its core promoter region with the 5'-UTRR15 from a relatively powerful Streptomyces promoter PkasO*R15 and resulted in Ptac*, the activity of which was 8.1-fold that of Ptac and 1.7-fold that of PkasO*R15 in S. lividans TK24. Next, the 5'-UTRR15 was optimized by randomizing the ribosome binding site (RBS). Based on the base biases of those RBSs with higher activity, eight artificial RBSs were rationally designed, and the optimal resulting promoter Ptac*RBS3 showed about 2.1, 3.6, and 17.6 times the activity of Ptac*, PkasO*R15, and Ptac, respectively, demonstrating that the heterologous Ptac was converted into a type of robust Streptomyces promoters. This study thus greatly expands promoter diversity for the engineering of Streptomyces.
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23
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Koepff J, Sachs CC, Wiechert W, Kohlheyer D, Nöh K, Oldiges M, Grünberger A. Germination and Growth Analysis of Streptomyces lividans at the Single-Cell Level Under Varying Medium Compositions. Front Microbiol 2018; 9:2680. [PMID: 30524383 PMCID: PMC6262040 DOI: 10.3389/fmicb.2018.02680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/19/2018] [Indexed: 01/27/2023] Open
Abstract
Quantitative single-cell cultivation has provided fundamental contributions to our understanding of heterogeneity among industrially used microorganisms. Filamentous growing Streptomyces species are emerging platform organisms for industrial production processes, but their exploitation is still limited due to often reported high batch-to-batch variations and unexpected growth and production differences. Population heterogeneity is suspected to be one responsible factor, which is so far not systematically investigated at the single-cell level. Novel microfluidic single-cell cultivation devices offer promising solutions to investigate these phenomena. In this study, we investigated the germination and growth behavior of Streptomyces lividans TK24 under varying medium compositions on different complexity levels (i.e., mycelial growth, hyphal growth and tip elongation) on single-cell level. Our analysis reveals a remarkable stability within growth and germination of spores and early mycelium development when exposed to constant and defined environments. We show that spores undergo long metabolic adaptation processes of up to > 30 h to adjust to new medium conditions, rather than using a "persister" strategy as a possibility to cope with rapidly changing environments. Due to this uniform behavior, we conclude that S. lividans can be cultivated quite robustly under constant environmental conditions as provided by microfluidic cultivation approaches. Failure and non-reproducible cultivations are thus most likely to be found in less controllable larger-scale cultivation workflows and as a result of environmental gradients within large-scale cultivations.
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Affiliation(s)
- Joachim Koepff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christian Carsten Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology, RWTH Aachen University – Aachener Verfahrenstechnik, Aachen, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Microscale Bioengineering, RWTH Aachen University – Aachener Verfahrenstechnik, Aachen, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany
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24
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Santamaría RI, Sevillano L, Martín J, Genilloud O, González I, Díaz M. The XRE-DUF397 Protein Pair, Scr1 and Scr2, Acts as a Strong Positive Regulator of Antibiotic Production in Streptomyces. Front Microbiol 2018; 9:2791. [PMID: 30524403 PMCID: PMC6262351 DOI: 10.3389/fmicb.2018.02791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/30/2018] [Indexed: 12/18/2022] Open
Abstract
The xenobiotic response element (XRE) transcription factors belong to a regulator family frequently found in Streptomyces that are often followed by small proteins with a DUF397 domain. In fact, the pair XRE-DUF397 has been proposed to comprise toxin–antitoxin (TA) type II systems. In this work, we demonstrate that one of these putative TA-systems, encoded by the genes SCO4441 and SCO4442 of Streptomyces coelicolor, and denominated Scr1/Scr2 (which stands for S. coelicolorregulator), does not behave as a toxin–antitoxin system under the conditions used as was originally expected. Instead the pair Scr1/Scr2 acts as a strong positive regulator of endogenous antibiotic production in S. coelicolor. The analysis of the 19 Streptomyces strains tested determined that overexpression of the pair Scr1/Scr2 drastically induces the production of antibiotics not only in S. coelicolor, but also in Streptomyces lividans, Streptomyces peucetius, Streptomyces steffisburgensis and Streptomyces sp. CA-240608. Our work also shows that Scr1 needs Scr2 to exert positive regulation on antibiotic production.
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Affiliation(s)
- Ramón I Santamaría
- Instituto de Biología Funcional y Genómica, Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Laura Sevillano
- Instituto de Biología Funcional y Genómica, Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Granada, Spain
| | - Ignacio González
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Granada, Spain
| | - Margarita Díaz
- Instituto de Biología Funcional y Genómica, Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
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25
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Wang L, Zhao S, Chen XX, Deng QP, Li CX, Feng JX. Secretory overproduction of a raw starch-degrading glucoamylase in Penicillium oxalicum using strong promoter and signal peptide. Appl Microbiol Biotechnol 2018; 102:9291-9301. [PMID: 30155751 DOI: 10.1007/s00253-018-9307-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 07/27/2018] [Accepted: 08/02/2018] [Indexed: 02/05/2023]
Abstract
Raw starch-degrading enzymes (RSDEs) are capable of directly degrading raw starch granules below the gelatinization temperature of starch, which may significantly reduce the cost of starch-based biorefining. However, low yields of natural RSDEs from filamentous fungi limit their industrial application. In this study, transcriptomic and secretomic profiling was employed to screen strongest promoters and signal peptides for use in overexpression of a RSDE gene in Penicillium oxalicum. Top five strong promoters and three signal peptides were detected. Using a green fluorescent protein (GFP) as the reporter, the inducible promoter pPoxEgCel5B of an endoglucanase gene PoxEgCel5B and the signal peptide spPoxGA15A of a raw starch-degrading glucoamylase PoxGA15A were respectively identified as driving the highest GFP production in P. oxalicum. PoxGA15A-overexpressed P. oxalicum strain OXPoxGA15A, which was constructed based on both pPoxEgCel5B and spPoxGA15A, produced significantly higher amounts of recombinant PoxGA15A than the parental strain ∆PoxKu70. Furthermore, crude enzyme from the OXPoxGA15A strain exhibited high activities towards raw starch from cassava, potato, and uncooked soluble starch. Specifically, raw cassava starch-degrading enzyme activity reached 241.6 U/mL in the OXPoxGA15A, which was 3.4-fold higher than that of the ∆PoxKu70. This work provides a feasible method for hyperproduction of RSDEs in P. oxalicum.
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Affiliation(s)
- Long Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China.
| | - Xing-Xiang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Qiao-Ping Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, People's Republic of China.
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26
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Spasic J, Mandic M, Radivojevic J, Jeremic S, Vasiljevic B, Nikodinovic-Runic J, Djokic L. Biocatalytic potential of Streptomyces spp. isolates from rhizosphere of plants and mycorrhizosphere of fungi. Biotechnol Appl Biochem 2018; 65:822-833. [PMID: 29797672 DOI: 10.1002/bab.1664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/10/2018] [Indexed: 11/09/2022]
Abstract
Biocatalytic potential of Streptomyces strains isolated from the rhizosphere of plants and from mycorrhizosphere of fungi has been investigated. A total of 118 Streptomyces isolates were selected and functionally screened for 10 different biotechnologically important enzymatic activities: hydrolase (cellulase, cutinase, gelatinase, lipase, protease, polyhydroxyalkanoate (PHA) depolymerase), phenol oxidase and peroxidase (laccase, tyrosinase, and lignin peroxidase), and aminotransferase. Out of 118 tested Streptomyces spp., 90% showed at least one enzymatic activity. The most abundant were enzymes involved in the biomass degradation, as the production of cutinase, cellulase, and lignin peroxidase were detected in 31%, 40%, and 48% of the isolates, respectively. The improved specific activities of lipase (isolates BV315 and BV100) and tyrosinase (isolates BV87 and BV88) were shown in comparison with the industrially relevant activities of Pseudomonas strains. Plant rhizosphere soils were more prolific source of Streptomyces strains with biocatalytic potential in comparison with mycorrhizosphere soils. Overall, 284 enzyme activities among 118 Streptomyces isolates have been detected. This is the first comprehensive screening of Streptomyces isolates from rhizosphere and mycorrhizosphere soils for novel biocatalysts, showing that specific environmental habitats, such as rhizosphere soils, are "treasure troves" of Streptomyces with biocatalytic potential.
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Affiliation(s)
- Jelena Spasic
- Institute of Molecular Genetics and Genetic Engineering , University of Belgrade, Belgrade, Serbia
| | - Mina Mandic
- Institute of Molecular Genetics and Genetic Engineering , University of Belgrade, Belgrade, Serbia
| | - Jelena Radivojevic
- Institute of Molecular Genetics and Genetic Engineering , University of Belgrade, Belgrade, Serbia
| | - Sanja Jeremic
- Institute of Molecular Genetics and Genetic Engineering , University of Belgrade, Belgrade, Serbia
| | - Branka Vasiljevic
- Institute of Molecular Genetics and Genetic Engineering , University of Belgrade, Belgrade, Serbia
| | | | - Lidija Djokic
- Institute of Molecular Genetics and Genetic Engineering , University of Belgrade, Belgrade, Serbia
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27
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Streptomyces spp. in the biocatalysis toolbox. Appl Microbiol Biotechnol 2018; 102:3513-3536. [PMID: 29502181 DOI: 10.1007/s00253-018-8884-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/17/2018] [Accepted: 02/19/2018] [Indexed: 02/07/2023]
Abstract
About 20,100 research publications dated 2000-2017 were recovered searching the PubMed and Web of Science databases for Streptomyces, which are the richest known source of bioactive molecules. However, these bacteria with versatile metabolism are powerful suppliers of biocatalytic tools (enzymes) for advanced biotechnological applications such as green chemical transformations and biopharmaceutical and biofuel production. The recent technological advances, especially in DNA sequencing coupled with computational tools for protein functional and structural prediction, and the improved access to microbial diversity enabled the easier access to enzymes and the ability to engineer them to suit a wider range of biotechnological processes. The major driver behind a dramatic increase in the utilization of biocatalysis is sustainable development and the shift toward bioeconomy that will, in accordance to the UN policy agenda "Bioeconomy to 2030," become a global effort in the near future. Streptomyces spp. already play a significant role among industrial microorganisms. The intention of this minireview is to highlight the presence of Streptomyces in the toolbox of biocatalysis and to give an overview of the most important advances in novel biocatalyst discovery and applications. Judging by the steady increase in a number of recent references (228 for the 2000-2017 period), it is clear that biocatalysts from Streptomyces spp. hold promises in terms of valuable properties and applicative industrial potential.
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28
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Kashiwagi N, Ogino C, Kondo A. Production of chemicals and proteins using biomass-derived substrates from a Streptomyces host. BIORESOURCE TECHNOLOGY 2017; 245:1655-1663. [PMID: 28651868 DOI: 10.1016/j.biortech.2017.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
Bioproduction using microbes from biomass feedstocks is of interest in regards to environmental problems and cost reduction. Streptomyces as an industrial microorganism plays an important role in the production of useful secondary metabolites for various applications. This strain also secretes a wide range of extracellular enzymes which degrade various biopolymers in nature, and it consumes these degrading substrates as nutrients. Hence, Streptomyces can be employed as a cell factory for the conversion of biomass-derived substrates into various products. This review focuses on the following two points: (1) Streptomyces as a producer of enzymes for degrading biomass-derived polysaccharides and polymers; and, (2) wild-type and engineered strains of Streptomyces as a host for chemical production from biomass-derived substrates.
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Affiliation(s)
- Norimasa Kashiwagi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan.
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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29
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Sevillano L, Díaz M, Santamaría RI. Development of an antibiotic marker-free platform for heterologous protein production in Streptomyces. Microb Cell Fact 2017; 16:164. [PMID: 28950904 PMCID: PMC5615484 DOI: 10.1186/s12934-017-0781-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/20/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The industrial use of enzymes produced by microorganisms is continuously growing due to the need for sustainable solutions. Nevertheless, many of the plasmids used for recombinant production of proteins in bacteria are based on the use of antibiotic resistance genes as selection markers. The safety concerns and legal requirements surrounding the increased use of antibiotic resistance genes have made the development of new antibiotic-free approaches essential. RESULTS In this work, a system completely free of antibiotic resistance genes and useful for the production of high yields of proteins in Streptomyces is described. This system is based on the separation of the two components of the yefM/yoeBsl (antitoxin/toxin) operon; the toxin (yoeBsl) gene, responsible for host death, is integrated into the genome and the antitoxin gene (yefMsl), which inactivates the toxin, is located in the expression plasmid. To develop this system, the toxin gene was integrated into the genome of a strain lacking the complete operon, and the antibiotic resistance gene integrated along with the toxin was eliminated by Cre recombinase to generate a final host strain free of any antibiotic resistance marker. In the same way, the antibiotic resistance gene from the final expression plasmid was removed by Dre recombinase. The usefulness of this system was analysed by checking the production of two hydrolases from different Streptomyces. Production of both proteins, with potential industrial use, was high and stable over time after strain storage and after serial subcultures. These results support the robustness and stability of the positive selection system developed. CONCLUSIONS The total absence of antibiotic resistance genes makes this system a powerful tool for using Streptomyces as a host to produce proteins at the industrial level. This work is the first Streptomyces antibiotic marker-free system to be described. Graphical abstract Antibiotic marker-free platform for protein expression in Streptomyces. The antitoxin gene present in the expression plasmid counteracts the effect of the toxin gene in the genome. In absence of the expression plasmid, the toxin causes cell death ensuring that only plasmid-containing cells persist.
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Affiliation(s)
- Laura Sevillano
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, C/Zacarías González no 2, 37007, Salamanca, Spain
| | - Margarita Díaz
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, C/Zacarías González no 2, 37007, Salamanca, Spain.
| | - Ramón I Santamaría
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, C/Zacarías González no 2, 37007, Salamanca, Spain.
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30
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Protein Secretion in Gram-Positive Bacteria: From Multiple Pathways to Biotechnology. Curr Top Microbiol Immunol 2017; 404:267-308. [PMID: 27885530 DOI: 10.1007/82_2016_49] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A number of Gram-positive bacteria are important players in industry as producers of a diverse array of economically interesting metabolites and proteins. As discussed in this overview, several Gram-positive bacteria are valuable hosts for the production of heterologous proteins. In contrast to Gram-negative bacteria, proteins secreted by Gram-positive bacteria are released into the culture medium where conditions for correct folding are more appropriate, thus facilitating the isolation and purification of active proteins. Although seven different protein secretion pathways have been identified in Gram-positive bacteria, the majority of heterologous proteins are produced via the general secretion or Sec pathway. Not all proteins are equally well secreted, because heterologous protein production often faces bottlenecks including hampered secretion, susceptibility to proteases, secretion stress, and metabolic burden. These bottlenecks are associated with reduced yields leading to non-marketable products. In this chapter, besides a general overview of the different protein secretion pathways, possible hurdles that may hinder efficient protein secretion are described and attempts to improve yield are discussed including modification of components of the Sec pathway. Attention is also paid to omics-based approaches that may offer a more rational approach to optimize production of heterologous proteins.
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31
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Jia H, Zhang L, Wang T, Han J, Tang H, Zhang L. Development of a CRISPR/Cas9-mediated gene-editing tool in Streptomyces rimosus. Microbiology (Reading) 2017; 163:1148-1155. [DOI: 10.1099/mic.0.000501] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Haiyan Jia
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, PR China
| | - Longmei Zhang
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, PR China
| | - Tongtong Wang
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, PR China
| | - Jin Han
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, PR China
| | - Hui Tang
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, PR China
| | - Liping Zhang
- Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province; Key Laboratory of Microbial Diversity Research and Application of Hebei Province; Key Discipline of Biological Engineering of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, PR China
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32
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Koepff J, Keller M, Tsolis KC, Busche T, Rückert C, Hamed MB, Anné J, Kalinowski J, Wiechert W, Economou A, Oldiges M. Fast and reliable strain characterization of Streptomyces lividans
through micro-scale cultivation. Biotechnol Bioeng 2017; 114:2011-2022. [DOI: 10.1002/bit.26321] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/15/2017] [Accepted: 04/17/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Joachim Koepff
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
| | - Matthias Keller
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
| | - Konstantinos C. Tsolis
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld University; Bielefeld Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld University; Bielefeld Germany
| | - Mohamed B. Hamed
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
- Department of Molecular Biology Department; The National Research Centre, Dokki; Giza Egypt
| | - Jozef Anné
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
| | - Joern Kalinowski
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld University; Bielefeld Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
| | - Marco Oldiges
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
- Institute of Biotechnology; RWTH Aachen University; Worringer Weg 3 52074 Aachen Germany
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