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Karimian S, Farahmandzad N, Mohammadipanah F. Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria. World J Microbiol Biotechnol 2024; 40:65. [PMID: 38191749 DOI: 10.1007/s11274-023-03861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less than the detectable level. The non-genetic approaches including biological interactions, chemical agents, and physical stresses that can be used to awaken silenced pathways are compared in this paper. These non-genetic induction strategies often need screening approaches, including one strain many compounds (OSMAC), reporter-guided mutant selection, and high throughput elicitor screening (HiTES) have been developed. Different types of genetic manipulations applied in the induction of cryptic BGCs of Actinobacteria can be categorized as genome-wide pleiotropic and targeted approaches like manipulation of global regulatory systems, modulation of regulatory genes, ribosome and engineering of RNA polymerase or phosphopantheteine transferases. Targeted approaches including genome editing by CRISPR, mutation in transcription factors and modification of BGCs promoters, inactivation of the highly expressed biosynthetic pathways, deleting the suppressors or awakening the activators, heterologous expression, or refactoring of gene clusters can be applied for activation of pathways which are predicted to synthesize new bioactive structures in genome mining studies of Acinobacteria. In this review, the challenges and advantages of employing these approaches in induction of Actinobacteria BGCs are discussed. Further, novel natural products needed as drug for pharmaceutical industry or as biofertilizers in agricultural industry can be discovered even from known species of Actinobactera by the innovative approaches of metabolite biosynthesis elicitation.
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Affiliation(s)
- Sanaz Karimian
- Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran
| | - Navid Farahmandzad
- Department of Biosystems Engineering, Auburn university, Auburn, AL 36849, USA
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran.
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2
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Dinglasan JLN, Sword TT, Barker JW, Doktycz MJ, Bailey CB. Investigating and Optimizing the Lysate-Based Expression of Nonribosomal Peptide Synthetases Using a Reporter System. ACS Synth Biol 2023; 12:1447-1460. [PMID: 37039644 PMCID: PMC11236431 DOI: 10.1021/acssynbio.2c00658] [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] [Indexed: 04/12/2023]
Abstract
Lysate-based cell-free expression (CFE) systems are accessible platforms for expressing proteins that are difficult to synthesize in vivo, such as nonribosomal peptide synthetases (NRPSs). NRPSs are large (>100 kDa), modular enzyme complexes that synthesize bioactive peptide natural products. This synthetic process is analogous to transcription/translation (TX/TL) in lysates, resulting in potential resource competition between NRPS expression and NRPS activity in cell-free environments. Moreover, CFE conditions depend on the size and structure of the protein. Here, a reporter system for rapidly investigating and optimizing reaction environments for NRPS CFE is described. This strategy is demonstrated in E. coli lysate reactions using blue pigment synthetase A (BpsA), a model NRPS, carrying a C-terminal tetracysteine (TC) tag which forms a fluorescent complex with the biarsenical dye, FlAsH. A colorimetric assay was adapted for lysate reactions to detect the blue pigment product, indigoidine, of cell-free expressed BpsA-TC, confirming that the tagged enzyme is catalytically active. An optimized protocol for end point TC/FlAsH complex measurements in reactions enables quick comparisons of full-length BpsA-TC expressed under different reaction conditions, defining unique requirements for NRPS expression that are related to the protein's catalytic activity and size. Importantly, these protein-dependent CFE conditions enable higher indigoidine titer and improve the expression of other monomodular NRPSs. Notably, these conditions differ from those used for the expression of superfolder GFP (sfGFP), a common reporter for optimizing lysate-based CFE systems, indicating the necessity for tailored reporters to optimize expression for specific enzyme classes. The reporter system is anticipated to advance lysate-based CFE systems for complex enzyme synthesis, enabling natural product discovery.
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Affiliation(s)
- Jaime Lorenzo N Dinglasan
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - J William Barker
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
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Yang D, Eun H, Prabowo CPS. Metabolic Engineering and Synthetic Biology Approaches for the Heterologous Production of Aromatic Polyketides. Int J Mol Sci 2023; 24:8923. [PMID: 37240269 PMCID: PMC10219323 DOI: 10.3390/ijms24108923] [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: 04/18/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Polyketides are a diverse set of natural products with versatile applications as pharmaceuticals, nutraceuticals, and cosmetics, to name a few. Of several types of polyketides, aromatic polyketides comprising type II and III polyketides contain many chemicals important for human health such as antibiotics and anticancer agents. Most aromatic polyketides are produced from soil bacteria or plants, which are difficult to engineer and grow slowly in industrial settings. To this end, metabolic engineering and synthetic biology have been employed to efficiently engineer heterologous model microorganisms for enhanced production of important aromatic polyketides. In this review, we discuss the recent advancement in metabolic engineering and synthetic biology strategies for the production of type II and type III polyketides in model microorganisms. Future challenges and prospects of aromatic polyketide biosynthesis by synthetic biology and enzyme engineering approaches are also discussed.
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Affiliation(s)
- Dongsoo Yang
- Synthetic Biology and Enzyme Engineering Laboratory, Department of Chemical and Biological Engineering (BK21 Four), Korea University, Seoul 02481, Republic of Korea
| | - Hyunmin Eun
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Cindy Pricilia Surya Prabowo
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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4
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Winand L, Lernoud L, Meyners SA, Kuhr K, Hiller W, Nett M. Myxococcus xanthus as Host for the Production of Benzoxazoles. Chembiochem 2023; 24:e202200635. [PMID: 36484355 DOI: 10.1002/cbic.202200635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/09/2022] [Accepted: 12/09/2022] [Indexed: 12/13/2022]
Abstract
Benzoxazoles are important structural motifs in pharmaceutical drugs. Here, we present the heterologous production of 3-hydroxyanthranilate-derived benzoxazoles in the host bacterium Myxococcus xanthus following the expression of two genes from the nataxazole biosynthetic gene cluster of Streptomyces sp. Tü 6176. The M. xanthus expression strain achieved a benzoxazole titer of 114.6±7.4 mg L-1 upon precursor supplementation, which is superior to other bacterial production systems. Crosstalk between the heterologously expressed benzoxazole pathway and the endogenous myxochelin pathway led to the combinatorial biosynthesis of benzoxazoles featuring a 2,3-dihydroxybenzoic acid (2,3-DHBA) building block. Subsequent in vitro studies confirmed that this crosstalk is not only due to the availability of 2,3-DHBA in M. xanthus, rather, it is promoted by the adenylating enzyme MxcE from the myxochelin pathway, which contributes to the activation of aryl carboxylic acids and delivers them to benzoxazole biosynthesis.
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Affiliation(s)
- Lea Winand
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
| | - Lucia Lernoud
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
| | - Saskia Anna Meyners
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
| | - Katharina Kuhr
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, NMR Laboratory, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Str. 66, 44227, Dortmund, Germany
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Baldera-Aguayo PA, Lee A, Cornish VW. High-Titer Production of the Fungal Anhydrotetracycline, TAN-1612, in Engineered Yeasts. ACS Synth Biol 2022; 11:2429-2444. [PMID: 35699947 PMCID: PMC9480237 DOI: 10.1021/acssynbio.2c00116] [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] [Indexed: 12/30/2022]
Abstract
Antibiotic resistance is a growing global health threat, demanding urgent responses. Tetracyclines, a widely used antibiotic class, are increasingly succumbing to antibiotic resistance; generating novel analogues is therefore a top priority for public health. Fungal tetracyclines provide structural and enzymatic diversity for novel tetracycline analogue production in tractable heterologous hosts, like yeasts, to combat antibiotic-resistant pathogens. Here, we successfully engineered Saccharomyces cerevisiae (baker's yeast) and Saccharomyces boulardii (probiotic yeast) to produce the nonantibiotic fungal anhydrotetracycline, TAN-1612, in synthetic defined media─necessary for clean purifications─through heterologously expressing TAN-1612 genes mined from the fungus, Aspergillus niger ATCC 1015. This was accomplished via (i) a promoter library-based combinatorial pathway optimization of the biosynthetic TAN-1612 genes coexpressed with a putative TAN-1612 efflux pump, reducing TAN-1612 toxicity in yeasts while simultaneously increasing supernatant titers and (ii) the development of a medium-throughput UV-visible spectrophotometric assay that facilitates TAN-1612 combinatorial library screening. Through this multipronged approach, we optimized TAN-1612 production, yielding an over 450-fold increase compared to previously reported S. cerevisiae yields. TAN-1612 is an important tetracycline analogue precursor, and we thus present the first step toward generating novel tetracycline analogue therapeutics to combat current and emerging antibiotic resistance. We also report the first heterologous production of a fungal polyketide, like TAN-1612, in the probiotic S. boulardii. This highlights that engineered S. boulardii can biosynthesize complex natural products like tetracyclines, setting the stage to equip probiotic yeasts with synthetic therapeutic functionalities to generate living therapeutics or biocontrol agents for clinical and agricultural applications.
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Affiliation(s)
- Pedro A Baldera-Aguayo
- Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, New York 10032, United States
- Department of Chemistry, Columbia University, 550 W 120th Street, Northwest Corner Building 1206, New York, New York 10027, United States
| | - Arden Lee
- Department of Chemistry, Columbia University, 550 W 120th Street, Northwest Corner Building 1206, New York, New York 10027, United States
| | - Virginia W Cornish
- Department of Chemistry, Columbia University, 550 W 120th Street, Northwest Corner Building 1206, New York, New York 10027, United States
- Department of Systems Biology, Columbia University Irving Cancer Research Center, 1130 St. Nicholas Avenue, New York, New York 10032, United States
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Yang D, Jang WD, Lee SY. Production of Carminic Acid by Metabolically Engineered Escherichia coli. J Am Chem Soc 2021; 143:5364-5377. [PMID: 33797895 DOI: 10.1021/jacs.0c12406] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Carminic acid is an aromatic polyketide found in scale insects (i.e., Dactylopius coccus) and is a widely used natural red colorant. It has long been produced by the cumbersome farming of insects followed by multistep purification processes. Thus, there has been much interest in producing carminic acid by the fermentation of engineered bacteria. Here we report the complete biosynthesis of carminic acid from glucose in engineered Escherichia coli. We first optimized the type II polyketide synthase machinery from Photorhabdus luminescens, enabling a high-level production of flavokermesic acid upon coexpression of the cyclases ZhuI and ZhuJ from Streptomyces sp. R1128. To discover the enzymes responsible for the remaining two reactions (hydroxylation and C-glucosylation), biochemical reaction analyses were performed by testing enzyme candidates reported to perform similar reactions. The two identified enzymes, aklavinone 12-hydroxylase (DnrF) from Streptomyces peucetius and C-glucosyltransferase (GtCGT) from Gentiana triflora, could successfully perform hydroxylation and C-glucosylation of flavokermesic acid, respectively. Then, homology modeling and docking simulations were performed to enhance the activities of these two enzymes, leading to the generation of beneficial mutants with 2-5-fold enhanced conversion efficiencies. In addition, the GtCGT mutant was found to be a generally applicable C-glucosyltransferase in E. coli, as was showcased by the successful production of aloesin found in Aloe vera. Simple metabolic engineering followed by fed-batch fermentation resulted in 0.63 ± 0.02 mg/L of carminic acid production from glucose. The strategies described here will be useful for the design and construction of biosynthetic pathways involving unknown enzymes and consequently the production of diverse industrially important natural products.
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Affiliation(s)
- Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- BioProcess Engineering Research Center and BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Woo Dae Jang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- BioProcess Engineering Research Center and BioInformatics Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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Ma M, Welch RD, Garza AG. The σ 54 system directly regulates bacterial natural product genes. Sci Rep 2021; 11:4771. [PMID: 33637792 PMCID: PMC7910581 DOI: 10.1038/s41598-021-84057-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023] Open
Abstract
Bacterial-derived polyketide and non-ribosomal peptide natural products are crucial sources of therapeutics and yet little is known about the conditions that favor activation of natural product genes or the regulatory machinery controlling their transcription. Recent findings suggest that the σ54 system, which includes σ54-loaded RNA polymerase and transcriptional activators called enhancer binding proteins (EBPs), might be a common regulator of natural product genes. Here, we explored this idea by analyzing a selected group of putative σ54 promoters identified in Myxococcus xanthus natural product gene clusters. We show that mutations in putative σ54-RNA polymerase binding regions and in putative Nla28 EBP binding sites dramatically reduce in vivo promoter activities in growing and developing cells. We also show in vivo promoter activities are reduced in a nla28 mutant, that Nla28 binds to wild-type fragments of these promoters in vitro, and that in vitro binding is lost when the Nla28 binding sites are mutated. Together, our results indicate that M. xanthus uses σ54 promoters for transcription of at least some of its natural product genes. Interestingly, the vast majority of experimentally confirmed and putative σ54 promoters in M. xanthus natural product loci are located within genes and not in intergenic sequences.
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Affiliation(s)
- Muqing Ma
- grid.264484.80000 0001 2189 1568Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244 USA
| | - Roy D. Welch
- grid.264484.80000 0001 2189 1568Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244 USA
| | - Anthony G. Garza
- grid.264484.80000 0001 2189 1568Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244 USA
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Gao Y, Zhao Y, He X, Deng Z, Jiang M. Challenges of functional expression of complex polyketide biosynthetic gene clusters. Curr Opin Biotechnol 2021; 69:103-111. [PMID: 33422913 DOI: 10.1016/j.copbio.2020.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/27/2020] [Accepted: 12/02/2020] [Indexed: 11/28/2022]
Abstract
Polyketide natural products are valuable sources of bioactive molecules such as nutraceuticals and pharmaceuticals. The tremendous development of the genome sequence database revealed that the majority of the biosynthetic gene clusters (BGCs) are cryptic. Activation of these cryptic BGCs and identification of the related products is essential for finding more lead compounds for pharmaceuticals. On the other hand, 99% of microbes in nature cannot be cultured in regular conditions, which greatly hinders the efforts to explore their biosynthetic potentials. Expression of polyketide BGCs in heterologous hosts with better growth, good genetic characteristics, and amenable molecular tools is a robust approach to identify new polyketides and characterize their biosynthesis. This review outlines the challenges in the heterologous production of polyketide BGCs of bacterial origins.
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Affiliation(s)
- Yaojie Gao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Yuchun Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, PR China.
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Production and bioprocess optimization of antitumor Epothilone B analogue from Aspergillus fumigatus, endophyte of Catharanthus roseus, with response surface methodology. Enzyme Microb Technol 2020; 143:109718. [PMID: 33375978 DOI: 10.1016/j.enzmictec.2020.109718] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/23/2020] [Accepted: 11/22/2020] [Indexed: 11/23/2022]
Abstract
Epothilones are secondary metabolites produced by Sorangium cellulosum with powerful antiproliferative activity against tumor cells by stabilizing their microtubule arrays, arresting their cellular division at G2-M phase. Unfortunately, the lower yield of epothilone is the challenge for its higher accessibility, thus, searching for alternative sources with promising epothilone producing potency is the prospective. Endophytic fungi are the potential repertoire for bioactive metabolites, thus exploring the epothilone producing potency of endophytic fungi of medicinal plants was objective. Thirty-two fungal isolates were recovered from the tested medicinal plants and their potency to produced epothilone have been assessed using the TLC, HPLC and molecular markers epoA, epoC and epoK. Aspergillus fumigatus EFBL, an endophyte of Catharanthus roseus, was the potent epothilone producer (21.5 μg/g biomass) as revealed from the chromatographic analyses and PCR of molecular markers. The chemical identity of extracted epothilone was verified from the HPLC, NMR, FTIR and LC-MS analyses as epothilone B analogue. The putative epoA gene from A. fumigatus was amplified using RT-PCR with the conservative corresponding primers to the active-sites of S. cellulosum. The amplicons of epoA was 517 bp displayed 98 % similarity with A. fumigatus PKS-NRPS domains, and 40 % similarity with epoA of S. cellulosum. From the in silico analyses, Val506, Ala605 and Ser630 are the conservative amino acids of epoA protein of A. fumigatus and S. cellulosum. Epothilone B from A. fumigatus displayed a strong antiproliferative activity against HepG-2, MCF-7 and LS174 T as revealed from the IC50 values 6.4, 8.7 and 10.21 μM, respectively. The productivity of epothilone B from A. fumigatus was optimized by surface response methodology with Plackett-Burman and Faced Centered Central Composite. With the Plackett-Burman design, the yield of epothilone (54.4-60.1 μg/g biomass) by A. fumigatus was increased by about 2.8-3.0 folds comparing to non-optimized cultures (21.5 μg/ g biomass). From the FCCD design, sucrose, tryptone and incubation time being the highest significant variables medium components affecting the epothilone yield of A. fumigatus. This is the first report exploring the feasibility of endophytic fungi for epothilone producing potency, that could be a novel platform for industrial production of epothilone.
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Hussain A, Hassan QP, Shouche YS. New approaches for antituberculosis leads from Actinobacteria. Drug Discov Today 2020; 25:2335-2342. [PMID: 33069935 DOI: 10.1016/j.drudis.2020.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 09/11/2020] [Accepted: 10/09/2020] [Indexed: 12/31/2022]
Abstract
Bioactive metabolites derived from the phylum Actinobacteria represent many of the existing antimicrobial drugs. Compared with other bacterial pathogens, direct preliminary screening by diffusion assays is a limiting factor against Mycobacterium tuberculosis (Mtb) and different methodologies have been used to improve the search for new molecules. However, the concern remains that most of the previously discovered molecules replicate by conventional procedures. The combination of multidisciplinary approaches with new technologies could advance the discovery of new leads against Mtb like considering the unexplored Actinobacteria jointly with selective and integrative procedures.
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Affiliation(s)
- Aehtesham Hussain
- National Centre for Microbial Resource (NCMR) - National Centre for Cell Science (NCCS), Pune, Maharashtra 411021, India.
| | - Qazi Parvaiz Hassan
- Microbial Biotechnology Division, CSIR - Indian Institute of Integrative Medicine, Jammu & Kashmir 190005, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR) - National Centre for Cell Science (NCCS), Pune, Maharashtra 411021, India
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Yang D, Park SY, Park YS, Eun H, Lee SY. Metabolic Engineering of Escherichia coli for Natural Product Biosynthesis. Trends Biotechnol 2020; 38:745-765. [DOI: 10.1016/j.tibtech.2019.11.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 12/27/2022]
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12
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Boutin S, Dalpke AH. The Microbiome: A Reservoir to Discover New Antimicrobials Agents. Curr Top Med Chem 2020; 20:1291-1299. [DOI: 10.2174/1568026620666200320112731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/10/2020] [Accepted: 02/17/2020] [Indexed: 02/01/2023]
Abstract
Nature offered mankind the first golden era of discovery of novel antimicrobials based on
the ability of eukaryotes or micro-organisms to produce such compounds. The microbial world proved
to be a huge reservoir of such antimicrobial compounds which play important functional roles in every
environment. However, most of those organisms are still uncultivable in a classical way, and therefore,
the use of extended culture or DNA based methods (metagenomics) to discover novel compounds
promises usefulness. In the past decades, the advances in next-generation sequencing and bioinformatics
revealed the enormous diversity of the microbial worlds and the functional repertoire available for
studies. Thus, data-mining becomes of particular interest in the context of the increased need for new
antibiotics due to antimicrobial resistance and the rush in antimicrobial discovery. In this review, an
overview of principles will be presented to discover new natural compounds from the microbiome. We
describe culture-based and culture-independent (metagenomic) approaches that have been developed to
identify new antimicrobials and the input of those methods in the field as well as their limitations.
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Affiliation(s)
- Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Alexander H. Dalpke
- Institute of Medical Microbiology and Hygiene, Medical Faculty, Technische Universität Dresden, 01307 Dresden, Germany
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Wang J, Zhang R, Chen X, Sun X, Yan Y, Shen X, Yuan Q. Biosynthesis of aromatic polyketides in microorganisms using type II polyketide synthases. Microb Cell Fact 2020; 19:110. [PMID: 32448179 PMCID: PMC7247197 DOI: 10.1186/s12934-020-01367-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Aromatic polyketides have attractive biological activities and pharmacological properties. Different from other polyketides, aromatic polyketides are characterized by their polycyclic aromatic structure. The biosynthesis of aromatic polyketides is usually accomplished by the type II polyketide synthases (PKSs), which produce highly diverse polyketide chains by sequential condensation of the starter units with extender units, followed by reduction, cyclization, aromatization and tailoring reactions. Recently, significant progress has been made in characterization and engineering of type II PKSs to produce novel products and improve product titers. In this review, we briefly summarize the architectural organizations and genetic contributions of PKS genes to provide insight into the biosynthetic process. We then review the most recent progress in engineered biosynthesis of aromatic polyketides, with emphasis on generating novel molecular structures. We also discuss the current challenges and future perspectives in the rational engineering of type II PKSs for large scale production of aromatic polyketides.
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Affiliation(s)
- Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA, 30602, USA
| | - Xin Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA, 30602, USA
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
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14
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Liu X, Hua K, Liu D, Wu ZL, Wang Y, Zhang H, Deng Z, Pfeifer BA, Jiang M. Heterologous Biosynthesis of Type II Polyketide Products Using E. coli. ACS Chem Biol 2020; 15:1177-1183. [PMID: 31825590 DOI: 10.1021/acschembio.9b00827] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The heterologous biosynthesis of complex natural products has enabled access to polyketide, nonribosomal peptide, isoprenoid, and other compounds with wide-spanning societal value. Though several surrogate host systems exist, Escherichia coli is often a preferred choice due to its rapid growth kinetics and extensive molecular biology protocols. However, a persistent challenge to the utilization of E. coli has been the successful in vivo reconstitution of type II polyketide synthase (PKS) systems. In particular, gene expression of the ketosynthase (KS) components of the minimal PKS has consistently yielded insoluble protein products. In the following report, two type II PKS systems were functionally reconstituted in E. coli. The approach to do so relied upon the utilization of the native transcriptional coupling between the dimeric KS subunits, leading to soluble recombinant protein products and successful polyketide biosynthesis. Resulting strains produced 10 mg/L TW95c and 25 mg/L dehydrorabelomycin. Hence, the strategy offers a new option in the biosynthetic engineering efforts for the heterologous production of type II polyketide products using E. coli.
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Affiliation(s)
- Xiangyang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, People’s Republic of China
| | - Kangmin Hua
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, People’s Republic of China
| | - Dongxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, People’s Republic of China
| | - Zhen-Long Wu
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Ying Wang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Haoran Zhang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, People’s Republic of China
| | - Blaine A. Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14214, United States
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, People’s Republic of China
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15
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Fazal A, Thankachan D, Harris E, Seipke RF. A chromatogram-simplified Streptomyces albus host for heterologous production of natural products. Antonie Van Leeuwenhoek 2020; 113:511-520. [PMID: 31781915 PMCID: PMC7089911 DOI: 10.1007/s10482-019-01360-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022]
Abstract
Cloning natural product biosynthetic gene clusters from cultured or uncultured sources and their subsequent expression by genetically tractable heterologous hosts is an essential strategy for the elucidation and characterisation of novel microbial natural products. The availability of suitable expression hosts is a critical aspect of this workflow. In this work, we mutagenised five endogenous biosynthetic gene clusters from Streptomyces albus S4, which reduced the complexity of chemical extracts generated from the strain and eliminated antifungal and antibacterial bioactivity. We showed that the resulting quintuple mutant can express foreign biosynthetic gene clusters by heterologously producing actinorhodin, cinnamycin and prunustatin. We envisage that our strain will be a useful addition to the growing suite of heterologous expression hosts available for exploring microbial secondary metabolism.
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Affiliation(s)
- Asif Fazal
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Divya Thankachan
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Ellie Harris
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Ryan F Seipke
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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16
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Markina NM, Kotlobay AA, Tsarkova AS. Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts. Acta Naturae 2020; 12:28-39. [PMID: 32742725 PMCID: PMC7385092 DOI: 10.32607/actanaturae.10966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022] Open
Abstract
Heterologous pathways are linked series of biochemical reactions occurring in a host organism after the introduction of foreign genes. Incorporation of metabolic pathways into host organisms is a major strategy used to increase the production of valuable secondary metabolites. Unfortunately, simple introduction of the pathway genes into the heterologous host in most cases does not result in successful heterologous expression. Extensive modification of heterologous genes and the corresponding enzymes on many different levels is required to achieve high target metabolite production rates. This review summarizes the essential techniques used to create heterologous biochemical pathways, with a focus on the key challenges arising in the process and the major strategies for overcoming them.
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Affiliation(s)
- N. M. Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Planta LLC, Moscow, 121205 Russia
| | - A. A. Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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17
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Zhang JJ, Tang X, Moore BS. Genetic platforms for heterologous expression of microbial natural products. Nat Prod Rep 2019; 36:1313-1332. [PMID: 31197291 PMCID: PMC6750982 DOI: 10.1039/c9np00025a] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: 2005 up to 2019Natural products are of paramount importance in human medicine. Not only are most antibacterial and anticancer drugs derived directly from or inspired by natural products, many other branches of medicine, such as immunology, neurology, and cardiology, have similarly benefited from natural product-based drugs. Typically, the genetic material required to synthesize a microbial specialized product is arranged in a multigene biosynthetic gene cluster (BGC), which codes for proteins associated with molecule construction, regulation, and transport. The ability to connect natural product compounds to BGCs and vice versa, along with ever-increasing knowledge of biosynthetic machineries, has spawned the field of genomics-guided natural product genome mining for the rational discovery of new chemical entities. One significant challenge in the field of natural product genome mining is how to rapidly link orphan biosynthetic genes to their associated chemical products. This review highlights state-of-the-art genetic platforms to identify, interrogate, and engineer BGCs from diverse microbial sources, which can be broken into three stages: (1) cloning and isolation of genomic loci, (2) heterologous expression in a host organism, and (3) genetic manipulation of cloned pathways. In the future, we envision natural product genome mining will be rapidly accelerated by de novo DNA synthesis and refactoring of whole biosynthetic pathways in combination with systematic heterologous expression methodologies.
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Affiliation(s)
- Jia Jia Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Xiaoyu Tang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
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18
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Cummings M, Peters AD, Whitehead GFS, Menon BRK, Micklefield J, Webb SJ, Takano E. Assembling a plug-and-play production line for combinatorial biosynthesis of aromatic polyketides in Escherichia coli. PLoS Biol 2019; 17:e3000347. [PMID: 31318855 PMCID: PMC6638757 DOI: 10.1371/journal.pbio.3000347] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/14/2019] [Indexed: 11/19/2022] Open
Abstract
Polyketides are a class of specialised metabolites synthesised by both eukaryotes and prokaryotes. These chemically and structurally diverse molecules are heavily used in the clinic and include frontline antimicrobial and anticancer drugs such as erythromycin and doxorubicin. To replenish the clinicians' diminishing arsenal of bioactive molecules, a promising strategy aims at transferring polyketide biosynthetic pathways from their native producers into the biotechnologically desirable host Escherichia coli. This approach has been successful for type I modular polyketide synthases (PKSs); however, despite more than 3 decades of research, the large and important group of type II PKSs has until now been elusive in E. coli. Here, we report on a versatile polyketide biosynthesis pipeline, based on identification of E. coli-compatible type II PKSs. We successfully express 5 ketosynthase (KS) and chain length factor (CLF) pairs-e.g., from Photorhabdus luminescens TT01, Streptomyces resistomycificus, Streptoccocus sp. GMD2S, Pseudoalteromonas luteoviolacea, and Ktedonobacter racemifer-as soluble heterodimeric recombinant proteins in E. coli for the first time. We define the anthraquinone minimal PKS components and utilise this biosynthetic system to synthesise anthraquinones, dianthrones, and benzoisochromanequinones (BIQs). Furthermore, we demonstrate the tolerance and promiscuity of the anthraquinone heterologous biosynthetic pathway in E. coli to act as genetically applicable plug-and-play scaffold, showing it to function successfully when combined with enzymes from phylogenetically distant species, endophytic fungi and plants, which resulted in 2 new-to-nature compounds, neomedicamycin and neochaetomycin. This work enables plug-and-play combinatorial biosynthesis of aromatic polyketides using bacterial type II PKSs in E. coli, providing full access to its many advantages in terms of easy and fast genetic manipulation, accessibility for high-throughput robotics, and convenient biotechnological scale-up. Using the synthetic and systems biology toolbox, this plug-and-play biosynthetic platform can serve as an engine for the production of new and diversified bioactive polyketides in an automated, rapid, and versatile fashion.
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Affiliation(s)
- Matthew Cummings
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Anna D. Peters
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - George F. S. Whitehead
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Binuraj R. K. Menon
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
- Warwick Integrative Synthetic Biology Centre, WISB, School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Jason Micklefield
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Simon J. Webb
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Eriko Takano
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
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Liu B, Han L, Liu X, Wu J, Ma Q. Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1211-1218. [PMID: 29993815 DOI: 10.1109/tcbb.2018.2816032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sigma factor, as a unit of RNA polymerase holoenzyme, is a critical factor in the process of gene transcriptional regulation. It recognizes the specific DNA sites and brings the core enzyme of RNA polymerase to the upstream regions of target genes. Therefore, the prediction of the promoters for a particular sigma factor is essential for interpreting functional genomic data and observation. This paper develops a new method to predict sigma-54 promoters in bacterial genomes. The new method organically integrates motif finding and machine learning strategies to capture the intrinsic features of sigma-54 promoters. The experiments on E. coli benchmark test set show that our method has good capability to distinguish sigma-54 promoters from surrounding or randomly selected DNA sequences. The applications of the other three bacterial genomes indicate the potential robustness and applicative power of our method on a large number of bacterial genomes. The source code of our method can be freely downloaded at https://github.com/maqin2001/PromotePredictor.
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20
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Cook TB, Pfleger BF. Leveraging synthetic biology for producing bioactive polyketides and non-ribosomal peptides in bacterial heterologous hosts. MEDCHEMCOMM 2019; 10:668-681. [PMID: 31191858 PMCID: PMC6540960 DOI: 10.1039/c9md00055k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/06/2019] [Indexed: 12/14/2022]
Abstract
Bacteria have historically been a rich source of natural products (e.g. polyketides and non-ribosomal peptides) that possess medically-relevant activities. Despite extensive discovery programs in both industry and academia, a plethora of biosynthetic pathways remain uncharacterized and the corresponding molecular products untested for potential bioactivities. This knowledge gap comes in part from the fact that many putative natural product producers have not been cultured in conventional laboratory settings in which the corresponding products are produced at detectable levels. Next-generation sequencing technologies are further increasing the knowledge gap by obtaining metagenomic sequence information from complex communities where production of the desired compound cannot be isolated in the laboratory. For these reasons, many groups are turning to synthetic biology to produce putative natural products in heterologous hosts. This strategy depends on the ability to heterologously express putative biosynthetic gene clusters and produce relevant quantities of the corresponding products. Actinobacteria remain the most abundant source of natural products and the most promising heterologous hosts for natural product discovery and production. However, researchers are discovering more natural products from other groups of bacteria, such as myxobacteria and cyanobacteria. Therefore, phylogenetically similar heterologous hosts have become promising candidates for synthesizing these novel molecules. The downside of working with these microbes is the lack of well-characterized genetic tools for optimizing expression of gene clusters and product titers. This review examines heterologous expression of natural product gene clusters in terms of the motivations for this research, the traits desired in an ideal host, tools available to the field, and a survey of recent progress.
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Affiliation(s)
- Taylor B Cook
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Dr. Room 3629 , Madison , WI 53706 , USA .
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Dr. Room 3629 , Madison , WI 53706 , USA .
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21
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Cai D, Zhu J, Zhu S, Lu Y, Zhang B, Lu K, Li J, Ma X, Chen S. Metabolic Engineering of Main Transcription Factors in Carbon, Nitrogen, and Phosphorus Metabolisms for Enhanced Production of Bacitracin in Bacillus licheniformis. ACS Synth Biol 2019; 8:866-875. [PMID: 30865822 DOI: 10.1021/acssynbio.9b00005] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Primary metabolism plays a key role in the synthesis of secondary metabolite. In this study, the main transcription factors in carbon, nitrogen, and phosphorus metabolisms (CcpA, CcpC, CcpN, CodY, TnrA, GlnR, and PhoP) were engineered to improve bacitracin yield in Bacillus licheniformis DW2, an industrial strain for bacitracin production. First, our results demonstrated that deletions of ccpC and ccpN improved ATP and NADPH supplies, and the bacitracin yields were respectively increased by 14.02% and 16.06% compared with that of DW2, while it was decreased significantly in ccpA deficient strain DW2ΔccpA. Second, excessive branched chain amino acids (BCAAs) were accumulated in codY, tnrA, and glnR deletion strains DW2ΔcodY, DW2ΔtnrA, and DW2ΔglnR, which resulted in the nitrogen catabolite repressions and reductions of bacitracin yields. Moreover, overexpression of these regulators improved intracellular BCAA supplies, and further enhanced bacitracin yields by 14.17%, 12.98%, and 16.20%, respectively. Furthermore, our results confirmed that phosphate addition reduced bacitracin synthesis capability, and bacitracin yield was improved by 15.71% in gene phop deletion strain. On the contrary, overexpression of PhoP led to a 19.40% decrease of bacitracin yield. Finally, a combinatorial engineering of these above metabolic manipulations was applied, and bacitracin yield produced by the final strain DW2-CNCTGP (Simultaneously deleting ccpC, ccpN, phop and overexpressing glnR, codY, and tnrA in DW2) reached 1014.38 U/mL, increased by 35.72% compared to DW2, and this yield was the highest bacitracin yield currently reported. Taken together, this study implied that metabolic engineering of carbon, nitrogen, and phosphorus metabolism regulators is an efficient strategy to enhance bacitracin production, and provided a promising B. licheniformis strain for industrial production of bacitracin.
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Affiliation(s)
- Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Jiang Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Shan Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yu Lu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Bowen Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Kai Lu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Junhui Li
- Lifecome Biochemistry Co., Ltd., Nanping 353400, PR China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan 430062, PR China
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22
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Baral B, Akhgari A, Metsä-Ketelä M. Activation of microbial secondary metabolic pathways: Avenues and challenges. Synth Syst Biotechnol 2018; 3:163-178. [PMID: 30345402 PMCID: PMC6190515 DOI: 10.1016/j.synbio.2018.09.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 12/21/2022] Open
Abstract
Microbial natural products are a tremendous source of new bioactive chemical entities for drug discovery. Next generation sequencing has revealed an unprecedented genomic potential for production of secondary metabolites by diverse micro-organisms found in the environment and in the microbiota. Genome mining has further led to the discovery of numerous uncharacterized 'cryptic' metabolic pathways in the classical producers of natural products such as Actinobacteria and fungi. These biosynthetic gene clusters may code for improved biologically active metabolites, but harnessing the full genetic potential has been hindered by the observation that many of the pathways are 'silent' under laboratory conditions. Here we provide an overview of the various biotechnological methodologies, which can be divided to pleiotropic, biosynthetic gene cluster specific, and targeted genome-wide approaches that have been developed for the awakening of microbial secondary metabolic pathways.
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Affiliation(s)
| | | | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, FIN-20014, Turku, Finland
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23
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The evolving interface between synthetic biology and functional metagenomics. Nat Chem Biol 2018; 14:752-759. [DOI: 10.1038/s41589-018-0100-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 06/13/2018] [Indexed: 12/15/2022]
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Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
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Affiliation(s)
- Joachim J Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Maja Remškar
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
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25
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Chiara M, Placido A, Picardi E, Ceci LR, Horner DS, Pesole G. A-GAME: improving the assembly of pooled functional metagenomics sequence data. BMC Genomics 2018; 19:44. [PMID: 29329522 PMCID: PMC5767027 DOI: 10.1186/s12864-017-4369-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/08/2017] [Indexed: 02/06/2023] Open
Abstract
Background Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such “functional metagenomics” experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications. Results Here we present A-GAME (A GAlaxy suite for functional MEtagenomics), a web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. We illustrate the potential of A-GAME workflows using real functional metagenomics data, showing that they outperform alternative metagenomics assemblers. Dedicated tools available in A-GAME allow efficient analysis of pooled libraries and rapid identification of candidate genes, reducing sequencing costs and saving the need for laborious manual annotation. Conclusion In conclusion, we believe A-GAME will constitute a valuable resource for the functional metagenomics community. A-GAME is publicly available at http://beaconlab.it/agame Electronic supplementary material The online version of this article (10.1186/s12864-017-4369-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matteo Chiara
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Antonio Placido
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", via Orabona, 4, 70126, Bari, Italy
| | - Luigi Ruggiero Ceci
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy
| | - David Stephen Horner
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy. .,Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy.
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, Consiglio Nazionale delle Ricerche, via Amendola 165A, 70126, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", via Orabona, 4, 70126, Bari, Italy
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26
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Park SY, Yang D, Ha SH, Lee SY. Metabolic Engineering of Microorganisms for the Production of Natural Compounds. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700190] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seon Young Park
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Shin Hee Ha
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
- BioProcess Engineering Research Center; KAIST; Daejeon 34141 Republic of Korea
- BioInformatics Research Center; KAIST; Daejeon 34141 Republic of Korea
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Abstract
Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.
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Overexpression of the primary sigma factor gene sigA improved carotenoid production by Corynebacterium glutamicum: Application to production of β-carotene and the non-native linear C50 carotenoid bisanhydrobacterioruberin. Metab Eng Commun 2017; 4:1-11. [PMID: 29142827 PMCID: PMC5678898 DOI: 10.1016/j.meteno.2017.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/14/2016] [Accepted: 01/12/2017] [Indexed: 02/07/2023] Open
Abstract
Corynebacterium glutamicum shows yellow pigmentation due to biosynthesis of the C50 carotenoid decaprenoxanthin and its glycosides. This bacterium has been engineered for production of various non-native cyclic C40 and C50 carotenoids such as β-carotene, astaxanthin or sarcinaxanthin. In this study, the effect of modulating gene expression more broadly by overexpression of sigma factor genes on carotenoid production by C. glutamicum was characterized. Overexpression of the primary sigma factor gene sigA improved lycopene production by recombinant C. glutamicum up to 8-fold. In C. glutamicum wild type, overexpression of sigA led to 2-fold increased accumulation of the native carotenoid decaprenoxanthin in the stationary growth phase. Under these conditions, genes related to thiamine synthesis and aromatic compound degradation showed increased RNA levels and addition of thiamine and the aromatic iron chelator protocatechuic acid to the culture medium enhanced carotenoid production when sigA was overexpressed. Deletion of the gene for the alternative sigma factor SigB, which is expected to replace SigA in RNA polymerase holoenzymes during transition to the stationary growth phase, also increased carotenoid production. The strategy of sigA overexpression could be successfully transferred to production of the non-native carotenoids β-carotene and bisanhydrobacterioruberin (BABR). Production of the latter is the first demonstration that C. glutamicum may accumulate a non-native linear C50 carotenoid instead of the native cyclic C50 carotenoid decaprenoxanthin. Overexpression of the primary sigma factor gene sigA enhanced carotenoid production. Enhanced production of carotenoids in the absence of alternative sigma factor SigB. Production of the linear C50 carotenoid bisanhydrobacterioruberin established.
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29
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Recent progress in therapeutic natural product biosynthesis using Escherichia coli. Curr Opin Biotechnol 2016; 42:7-12. [DOI: 10.1016/j.copbio.2016.02.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 01/29/2023]
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30
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Adu-Oppong B, Gasparrini AJ, Dantas G. Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes. Ann N Y Acad Sci 2016; 1388:42-58. [PMID: 27768825 DOI: 10.1111/nyas.13257] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/16/2016] [Accepted: 08/22/2016] [Indexed: 02/07/2023]
Abstract
Microbial communities contain diverse bacteria that play important roles in every environment. Advances in sequencing and computational methodologies over the past decades have illuminated the phylogenetic and functional diversity of microbial communities from diverse habitats. Among the activities encoded in microbiomes are the abilities to synthesize and resist small molecules, yielding antimicrobial activity. These functions are of particular interest when viewed in light of the public health emergency posed by the increase in clinical antimicrobial resistance and the dwindling antimicrobial discovery and approval pipeline, and given the intimate ecological and evolutionary relationship between antimicrobial biosynthesis and resistance. Here, we review genomic and functional methods that have been developed for accessing the antimicrobial biosynthesis and resistance capacity of microbiomes and highlight outstanding examples of their applications.
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Affiliation(s)
- Boahemaa Adu-Oppong
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Andrew J Gasparrini
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri.,Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
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31
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Contemporary molecular tools in microbial ecology and their application to advancing biotechnology. Biotechnol Adv 2015; 33:1755-73. [DOI: 10.1016/j.biotechadv.2015.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/19/2015] [Accepted: 09/20/2015] [Indexed: 12/30/2022]
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32
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Culture-independent discovery of natural products from soil metagenomes. J Ind Microbiol Biotechnol 2015; 43:129-41. [PMID: 26586404 DOI: 10.1007/s10295-015-1706-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 10/29/2015] [Indexed: 12/20/2022]
Abstract
Bacterial natural products have proven to be invaluable starting points in the development of many currently used therapeutic agents. Unfortunately, traditional culture-based methods for natural product discovery have been deemphasized by pharmaceutical companies due in large part to high rediscovery rates. Culture-independent, or "metagenomic," methods, which rely on the heterologous expression of DNA extracted directly from environmental samples (eDNA), have the potential to provide access to metabolites encoded by a large fraction of the earth's microbial biosynthetic diversity. As soil is both ubiquitous and rich in bacterial diversity, it is an appealing starting point for culture-independent natural product discovery efforts. This review provides an overview of the history of soil metagenome-driven natural product discovery studies and elaborates on the recent development of new tools for sequence-based, high-throughput profiling of environmental samples used in discovering novel natural product biosynthetic gene clusters. We conclude with several examples of these new tools being employed to facilitate the recovery of novel secondary metabolite encoding gene clusters from soil metagenomes and the subsequent heterologous expression of these clusters to produce bioactive small molecules.
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Fedorenko V, Genilloud O, Horbal L, Marcone GL, Marinelli F, Paitan Y, Ron EZ. Antibacterial Discovery and Development: From Gene to Product and Back. BIOMED RESEARCH INTERNATIONAL 2015; 2015:591349. [PMID: 26339625 PMCID: PMC4538407 DOI: 10.1155/2015/591349] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/30/2014] [Accepted: 01/13/2015] [Indexed: 12/23/2022]
Abstract
Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement.
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Affiliation(s)
- Victor Fedorenko
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences Technology Park, 18016 Granada, Spain
| | - Liliya Horbal
- Department of Genetics and Biotechnology, Ivan Franko National University of Lviv, Lviv 79005, Ukraine
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano, and University of Insubria, 21100 Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano, and University of Insubria, 21100 Varese, Italy
| | - Yossi Paitan
- Clinical Microbiology Laboratory, Meir Medical Center, 44281 Kfar Saba, Israel
| | - Eliora Z. Ron
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 6997801 Tel Aviv, Israel
- Galilee Research Institute (MIGAL), 11016 Kiryat Shmona, Israel
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34
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Yang J, Xiong ZQ, Song SJ, Wang JF, Lv HJ, Wang Y. Improving heterologous polyketide production in Escherichia coli by transporter engineering. Appl Microbiol Biotechnol 2015; 99:8691-700. [DOI: 10.1007/s00253-015-6718-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/27/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
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35
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Krauser S, Hoffmann T, Heinzle E. Directed Multistep Biocatalysis for the Synthesis of the Polyketide Oxytetracycline in Permeabilized Cells of Escherichia coli. ACS Catal 2015. [DOI: 10.1021/cs501825u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Steffen Krauser
- Biochemical Engineering, Saarland University, Campus A1.5, 66123 Saarbrücken, Germany
| | - Thomas Hoffmann
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123 Saarbrücken, Germany
| | - Elmar Heinzle
- Biochemical Engineering, Saarland University, Campus A1.5, 66123 Saarbrücken, Germany
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36
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Harvey AL, Edrada-Ebel R, Quinn RJ. The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 2015; 14:111-29. [PMID: 25614221 DOI: 10.1038/nrd4510] [Citation(s) in RCA: 1520] [Impact Index Per Article: 168.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.
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Affiliation(s)
- Alan L Harvey
- 1] Research and Innovation Support, Dublin City University, Dublin 9, Ireland. [2] Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
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37
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Sun L, Zeng J, Zhang S, Gladwin T, Zhan J. Effects of exogenous nutrients on polyketide biosynthesis in Escherichia coli. Appl Microbiol Biotechnol 2014; 99:693-701. [PMID: 25411046 DOI: 10.1007/s00253-014-6212-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/05/2014] [Accepted: 11/03/2014] [Indexed: 10/24/2022]
Abstract
Heterologous hosts are important platforms for engineering natural product biosynthesis. Escherichia coli is such a host widely used for expression of various biosynthetic enzymes. While numerous studies have been focused on optimizing the expression conditions for desired functional proteins, this work describes how supplement of exogenous nutrients into the fermentation broth influences the formation of natural products in E. coli. A type III polyketide synthase gene stts from Streptomyces toxytricini NRRL 15443 was heterogeneously expressed in E. coli BL21(DE3). This enzyme uses five units of malonyl-CoA to generate a polyketide 1,3,6,8-tetrahydroxynaphthalene, which can be spontaneously oxidized into a red compound flaviolin. In this work, we manipulated the fermentation broth of E. coli BL21(DE3)/pET28a-stts by supplying different nutrients including glucose and sodium pyruvate at different concentrations, from which six flaviolin derivatives 1-6 were produced. While addition of glucose yielded the production of 1-4, supplement of sodium pyruvate into the induced broth of E. coli BL21(DE3)/pET28a-stts resulted in the synthesis of 5 and 6, suggesting that different nutrients may enable E. coli to generate different metabolites. These products were purified and structurally characterized based on the spectral data, among which 2-6 are novel compounds. These molecules were formed through addition of different moieties such as acetone and indole to the flaviolin scaffold. The concentrations of glucose and sodium pyruvate and incubation time affect the product profiles. This work demonstrates that supplement of nutrients can link certain intracellular metabolites to the engineered biosynthetic pathway to yield new products. It provides a new approach to biosynthesizing novel molecules in the commonly used heterologous host E. coli.
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Affiliation(s)
- Lei Sun
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA
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38
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Milshteyn A, Schneider JS, Brady SF. Mining the metabiome: identifying novel natural products from microbial communities. CHEMISTRY & BIOLOGY 2014; 21:1211-23. [PMID: 25237864 PMCID: PMC4171686 DOI: 10.1016/j.chembiol.2014.08.006] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 12/21/2022]
Abstract
Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review, we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of reinvigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities.
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Affiliation(s)
- Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jessica S Schneider
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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39
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Tripathi L, Zhang Y, Lin Z. Bacterial sigma factors as targets for engineered or synthetic transcriptional control. Front Bioeng Biotechnol 2014; 2:33. [PMID: 25232540 PMCID: PMC4153023 DOI: 10.3389/fbioe.2014.00033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 08/20/2014] [Indexed: 11/20/2022] Open
Abstract
Sigma (σ) factors are the predominant constituents of transcription regulation in bacteria. σ Factors recruit the core RNA polymerase to recognize promoters with specific DNA sequences. Recently, engineering of transcriptional regulators has become a significant tool for strain engineering. The present review summarizes the recent advances in σ factor based engineering or synthetic design. The manipulation of σ factors presents insights into the bacterial stress tolerance and metabolite productivity. We envision more synthetic design based on σ factors that can be used to tune the regulatory network of bacteria.
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Affiliation(s)
- Lakshmi Tripathi
- Department of Chemical Engineering, Tsinghua University , Beijing , China
| | - Yan Zhang
- Department of Chemical Engineering, Tsinghua University , Beijing , China
| | - Zhanglin Lin
- Department of Chemical Engineering, Tsinghua University , Beijing , China
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40
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Charlop-Powers Z, Milshteyn A, Brady SF. Metagenomic small molecule discovery methods. Curr Opin Microbiol 2014; 19:70-75. [PMID: 25000402 DOI: 10.1016/j.mib.2014.05.021] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/10/2014] [Accepted: 05/28/2014] [Indexed: 12/18/2022]
Abstract
Metagenomic approaches to natural product discovery provide the means to harvest bioactive small molecules synthesized by environmental bacteria without the requirement of first culturing these organisms. Advances in sequencing technologies and general metagenomic methods are beginning to provide the tools necessary to unlock the unexplored biosynthetic potential encoded by the genomes of uncultured environmental bacteria. Here, we highlight recent advances in sequence-based and functional-based metagenomic approaches that promise to facilitate antibiotic discovery from diverse environmental microbiomes.
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Affiliation(s)
- Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States.
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41
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Kang Z, Zhang C, Zhang J, Jin P, Zhang J, Du G, Chen J. Small RNA regulators in bacteria: powerful tools for metabolic engineering and synthetic biology. Appl Microbiol Biotechnol 2014; 98:3413-24. [DOI: 10.1007/s00253-014-5569-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 12/17/2022]
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42
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Boddy CN. Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides. ACTA ACUST UNITED AC 2014; 41:443-50. [DOI: 10.1007/s10295-013-1368-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/14/2013] [Indexed: 12/12/2022]
Abstract
Abstract
Microbial natural products have played a key role in the development of clinical agents in nearly all therapeutic areas. Recent advances in genome sequencing have revealed that there is an incredible wealth of new polyketide and non-ribosomal peptide natural product diversity to be mined from genetic data. The diversity and complexity of polyketide and non-ribosomal peptide biosynthesis has required the development of unique bioinformatics tools to identify, annotate, and predict the structures of these natural products from their biosynthetic gene clusters. This review highlights and evaluates web-based bioinformatics tools currently available to the natural product community for genome mining to discover new polyketides and non-ribosomal peptides.
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Affiliation(s)
- Christopher N Boddy
- grid.28046.38 0000000121822255 Departments of Chemistry and Biology, Center for Advanced Research in Environmental Genomics University of Ottawa K1N 6N5 Ottawa ON Canada
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43
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Rebets Y, Brötz E, Tokovenko B, Luzhetskyy A. Actinomycetes biosynthetic potential: how to bridge in silico and in vivo? J Ind Microbiol Biotechnol 2013; 41:387-402. [PMID: 24127068 DOI: 10.1007/s10295-013-1352-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
Abstract
Actinomycetes genome sequencing and bioinformatic analyses revealed a large number of "cryptic" gene clusters coding for secondary metabolism. These gene clusters have the potential to increase the chemical diversity of natural products. Indeed, reexamination of well-characterized actinomycetes strains revealed a variety of hidden treasures. Growing information about this metabolic diversity has promoted further development of strategies to discover novel biologically active compounds produced by actinomycetes. This new task for actinomycetes genetics requires the development and use of new approaches and tools. Application of synthetic biology approaches led to the development of a set of strategies and tools to satisfy these new requirements. In this review, we discuss strategies and methods to discover small molecules produced by these fascinating bacteria and also discuss a variety of genetic instruments and regulatory elements used to activate secondary metabolism cryptic genes for the overproduction of these metabolites.
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Affiliation(s)
- Yuriy Rebets
- Helmholtz-Institute for Pharmaceutical Research Saarland, Campus, Building C2.3, Saarbrücken, 66123, Germany
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44
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Stevens DC, Hari TPA, Boddy CN. The role of transcription in heterologous expression of polyketides in bacterial hosts. Nat Prod Rep 2013; 30:1391-411. [DOI: 10.1039/c3np70060g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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