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Jensen RO, Schulz F, Roux S, Klingeman DM, Mitchell WP, Udwary D, Moraïs S, Reynoso V, Winkler J, Nagaraju S, De Tissera S, Shapiro N, Ivanova N, Reddy TBK, Mizrahi I, Utturkar SM, Bayer EA, Woyke T, Mouncey NJ, Jewett MC, Simpson SD, Köpke M, Jones DT, Brown SD. Phylogenomics and genetic analysis of solvent-producing Clostridium species. Sci Data 2024; 11:432. [PMID: 38693191 PMCID: PMC11063209 DOI: 10.1038/s41597-024-03210-6] [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: 10/15/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024] Open
Abstract
The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.
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Affiliation(s)
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | | | | | | | | | - Nicole Shapiro
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Sagar M Utturkar
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Edward A Bayer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | | | - David T Jones
- Department of Microbiology, University of Otago, Dunedin, New Zealand.
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Zhong J, Sui WW, Bai XY, Qiu ZL, Li XG, Zhu JZ. Characterization and biocontrol mechanism of Streptomyces olivoreticuli as a potential biocontrol agent against Rhizoctonia solani. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 197:105681. [PMID: 38072538 DOI: 10.1016/j.pestbp.2023.105681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 12/18/2023]
Abstract
Rhizoctonia solani is a widespread and devastating plant pathogenic fungus that infects many important crops. This pathogen causes tobacco target spot, a disease that is widespread in many tobacco-growing countries and is destructive to tobacco. To identify antagonistic microorganisms with biocontrol potential against this disease, we isolated Streptomyces strains from forest inter-root soil and screened a promising biocontrol strain, ZZ-21. Based on in vitro antagonism assays, ZZ-21 showed a significant inhibitory effect on R. solani and various other phytopathogens. ZZ-21 was identified as Streptomyces olivoreticuli by its phenotypic, genetic, physiological and biochemical properties. Complete genome sequencing revealed that ZZ-21 harbored numerous antimicrobial biosynthesis gene clusters. ZZ-21 significantly reduced the lesion length in detached inoculated leaf assays and reduced the disease index under greenhouse and field conditions. Based on an in vitro antagonistic assay of ZZ-21 culture, the strain exhibited an antifungal activity against R. solani in a dose-dependent manner. The culture filtrate could impair membrane integrity, possibly through membrane lipid peroxidation. ZZ-21 could secrete multiple extracellular enzymes and siderophores. According to a series of antifungal assays, the extracellular metabolites of ZZ-21 contained antimicrobial bioactive compounds composed of proteins/peptides extracted using ammonium sulfate precipitation, which were stable under stress caused by high temperature and protease K. The EC50 value for ammonium sulfate precipitation was determined to be 21.11 μg/mL in this study. Moreover, the proteins/peptides also exhibited biocontrol ability and were observed to alter the plasma membrane integrity of R. solani which were evaluated by biocontrol efficacy assays on detached tobacco leaves and PI staining. Overall, strain ZZ-21 shows the potential to be developed into a biopesticide against tobacco target spot disease.
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Affiliation(s)
- Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China
| | - Wen Wen Sui
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China
| | - Xin Yi Bai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China
| | - Ze Lan Qiu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China
| | - Xiao Gang Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China.
| | - Jun Zi Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China.
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Li Y, Wang J, Li L, Song W, Li M, Hua X, Wang Y, Yuan J, Xue Z. Natural products of pentacyclic triterpenoids: from discovery to heterologous biosynthesis. Nat Prod Rep 2023; 40:1303-1353. [PMID: 36454108 DOI: 10.1039/d2np00063f] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Covering: up to 2022Pentacyclic triterpenoids are important natural bioactive substances that are widely present in plants and fungi. They have significant medicinal efficacy, play an important role in reducing blood glucose and protecting the liver, and have anti-inflammatory, anti-oxidation, anti-fatigue, anti-viral, and anti-cancer activities. Pentacyclic triterpenoids are derived from the isoprenoid biosynthetic pathway, which generates common precursors of triterpenes and steroids, followed by cyclization with oxidosqualene cyclases (OSCs) and decoration via cytochrome P450 monooxygenases (CYP450s) and glycosyltransferases (GTs). Many biosynthetic pathways of triterpenoid saponins have been elucidated by studying their metabolic regulation network through the use of multiomics and identifying their functional genes. Unfortunately, natural resources of pentacyclic triterpenoids are limited due to their low content in plant tissues and the long growth cycle of plants. Based on the understanding of their biosynthetic pathway and transcriptional regulation, plant bioreactors and microbial cell factories are emerging as alternative means for the synthesis of desired triterpenoid saponins. The rapid development of synthetic biology, metabolic engineering, and fermentation technology has broadened channels for the accumulation of pentacyclic triterpenoid saponins. In this review, we summarize the classification, distribution, structural characteristics, and bioactivity of pentacyclic triterpenoids. We further discuss the biosynthetic pathways of pentacyclic triterpenoids and involved transcriptional regulation. Moreover, the recent progress and characteristics of heterologous biosynthesis in plants and microbial cell factories are discussed comparatively. Finally, we propose potential strategies to improve the accumulation of triterpenoid saponins, thereby providing a guide for their future biomanufacturing.
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Affiliation(s)
- Yanlin Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, PR China
| | - Linyong Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Wenhui Song
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Min Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Xin Hua
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Yu Wang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, 361102, Fujian, PR China.
| | - Zheyong Xue
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
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Consolidated Bioprocessing: Synthetic Biology Routes to Fuels and Fine Chemicals. Microorganisms 2021; 9:microorganisms9051079. [PMID: 34069865 PMCID: PMC8157379 DOI: 10.3390/microorganisms9051079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/27/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022] Open
Abstract
The long road from emerging biotechnologies to commercial “green” biosynthetic routes for chemical production relies in part on efficient microbial use of sustainable and renewable waste biomass feedstocks. One solution is to apply the consolidated bioprocessing approach, whereby microorganisms convert lignocellulose waste into advanced fuels and other chemicals. As lignocellulose is a highly complex network of polymers, enzymatic degradation or “saccharification” requires a range of cellulolytic enzymes acting synergistically to release the abundant sugars contained within. Complications arise from the need for extracellular localisation of cellulolytic enzymes, whether they be free or cell-associated. This review highlights the current progress in the consolidated bioprocessing approach, whereby microbial chassis are engineered to grow on lignocellulose as sole carbon sources whilst generating commercially useful chemicals. Future perspectives in the emerging biofoundry approach with bacterial hosts are discussed, where solutions to existing bottlenecks could potentially be overcome though the application of high throughput and iterative Design-Build-Test-Learn methodologies. These rapid automated pathway building infrastructures could be adapted for addressing the challenges of increasing cellulolytic capabilities of microorganisms to commercially viable levels.
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Candicidin Isomer Production Is Essential for Biocontrol of Cucumber Rhizoctonia Rot by Streptomyces albidoflavus W68. Appl Environ Microbiol 2021; 87:AEM.03078-20. [PMID: 33608297 DOI: 10.1128/aem.03078-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/13/2021] [Indexed: 01/10/2023] Open
Abstract
Diseases caused by soilborne fungal pathogens result in significant crop yield losses and quality reduction. Streptomyces albidoflavus strain W68 is effective in controlling several soilborne fungal diseases. To identify antifungal substances critical for biocontrol activity of W68, the genome of W68 was sequenced and a linear chromosome of 6.80 Mb was assembled. A total of 21 secondary metabolite biosynthesis gene clusters (BGCs), accounting for 12.27% of the genome, were identified. Core gene deletion mutants for each of all 8 BGCs for nonribosomal peptide synthetases and polyketide synthases were created. Among them, only the mutant lacking ctg1-5755 (the gene was renamed as fscD W68) in BGC 19, which shares 100% sequence similarity with the BGC for candicidin synthesis, showed obvious reduction in antifungal activity. A pot experiment revealed that biocontrol effects of the ΔfscD W68 mutant in Rhizoctonia rot of cucumber were also significantly compromised relative to W68. Liquid chromatography-mass spectrometry (LC-MS) analysis revealed that W68 but not the ΔfscD W68 mutant can produce candicidin isomers, indicating that the production of candicidin isomers is key for antifungal activity and biocontrol activity of S. albidoflavus W68.IMPORTANCE This study reports that candicidin-like secondary metabolites produced by microbial cells in natural soil environments can effectively control soilborne fungal diseases, revealing a novel mechanism of microbial biocontrol agents. We demonstrated that the main antifungal activity and biocontrol activity of Streptomyces albidoflavus strain W68 are attributable to the production of candicidin isomers, suggesting that gene clusters for candicidin-like compound biosynthesis might be used as molecular markers to screen and breed microbial strains for biocontrol agent development.
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Samad N, Sodunke TE, Abubakar AR, Jahan I, Sharma P, Islam S, Dutta S, Haque M. The Implications of Zinc Therapy in Combating the COVID-19 Global Pandemic. J Inflamm Res 2021; 14:527-550. [PMID: 33679136 PMCID: PMC7930604 DOI: 10.2147/jir.s295377] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/27/2021] [Indexed: 12/15/2022] Open
Abstract
The global pandemic from COVID-19 infection has generated significant public health concerns, both health-wise and economically. There is no specific pharmacological antiviral therapeutic option to date available for COVID-19 management. Also, there is an urgent need to discover effective medicines, prevention, and control methods because of the harsh death toll from this novel coronavirus infection. Acute respiratory tract infections, significantly lower respiratory tract infections, and pneumonia are the primary cause of millions of deaths worldwide. The role of micronutrients, including trace elements, boosted the human immune system and was well established. Several vitamins such as vitamin A, B6, B12, C, D, E, and folate; microelement including zinc, iron, selenium, magnesium, and copper; omega-3 fatty acids as eicosapentaenoic acid and docosahexaenoic acid plays essential physiological roles in promoting the immune system. Furthermore, zinc is an indispensable microelement essential for a thorough enzymatic physiological process. It also helps regulate gene-transcription such as DNA replication, RNA transcription, cell division, and cell activation in the human biological system. Subsequently, zinc, together with natural scavenger cells and neutrophils, are also involved in developing cells responsible for regulating nonspecific immunity. The modern food habit often promotes zinc deficiency; as such, quite a few COVID-19 patients presented to hospitals were frequently diagnosed as zinc deficient. Earlier studies documented that zinc deficiency predisposes patients to a viral infection such as herpes simplex, common cold, hepatitis C, severe acute respiratory syndrome coronavirus (SARS-CoV-1), the human immunodeficiency virus (HIV) because of reducing antiviral immunity. This manuscript aimed to discuss the various roles played by zinc in the management of COVID-19 infection.
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Affiliation(s)
- Nandeeta Samad
- Department of Public Health, North South University, Dhaka, 1229, Bangladesh
| | | | - Abdullahi Rabiu Abubakar
- Department of Pharmacology and Therapeutics, Faculty of Pharmaceutical Sciences, Bayero University, Kano, 700233, Nigeria
| | - Iffat Jahan
- Department of Physiology, Eastern Medical College, Cumilla, Bangladesh
| | - Paras Sharma
- Department of Pharmacognosy, BVM College of Pharmacy, Gwalior, India
| | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh
| | - Siddhartha Dutta
- Department of Pharmacology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Malaysia
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Hilgers F, Habash SS, Loeschcke A, Ackermann YS, Neumann S, Heck A, Klaus O, Hage-Hülsmann J, Grundler FMW, Jaeger KE, Schleker ASS, Drepper T. Heterologous Production of β-Caryophyllene and Evaluation of Its Activity against Plant Pathogenic Fungi. Microorganisms 2021; 9:microorganisms9010168. [PMID: 33466643 PMCID: PMC7828715 DOI: 10.3390/microorganisms9010168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/08/2021] [Accepted: 01/10/2021] [Indexed: 11/16/2022] Open
Abstract
Terpenoids constitute one of the largest and most diverse groups within the class of secondary metabolites, comprising over 80,000 compounds. They not only exhibit important functions in plant physiology but also have commercial potential in the biotechnological, pharmaceutical, and agricultural sectors due to their promising properties, including various bioactivities against pathogens, inflammations, and cancer. In this work, we therefore aimed to implement the plant sesquiterpenoid pathway leading to β-caryophyllene in the heterologous host Rhodobacter capsulatus and achieved a maximum production of 139 ± 31 mg L-1 culture. As this sesquiterpene offers various beneficial anti-phytopathogenic activities, we evaluated the bioactivity of β-caryophyllene and its oxygenated derivative β-caryophyllene oxide against different phytopathogenic fungi. Here, both compounds significantly inhibited the growth of Sclerotinia sclerotiorum and Fusarium oxysporum by up to 40%, while growth of Alternaria brassicicola was only slightly affected, and Phoma lingam and Rhizoctonia solani were unaffected. At the same time, the compounds showed a promising low inhibitory profile for a variety of plant growth-promoting bacteria at suitable compound concentrations. Our observations thus give a first indication that β-caryophyllene and β-caryophyllene oxide are promising natural agents, which might be applicable for the management of certain plant pathogenic fungi in agricultural crop production.
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Affiliation(s)
- Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (F.H.); (A.L.); (Y.S.A.); (O.K.); (J.H.-H.); (K.-E.J.)
| | - Samer S. Habash
- INRES—Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany; (S.S.H.); (S.N.); (F.M.W.G.)
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (F.H.); (A.L.); (Y.S.A.); (O.K.); (J.H.-H.); (K.-E.J.)
| | - Yannic Sebastian Ackermann
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (F.H.); (A.L.); (Y.S.A.); (O.K.); (J.H.-H.); (K.-E.J.)
| | - Stefan Neumann
- INRES—Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany; (S.S.H.); (S.N.); (F.M.W.G.)
| | - Achim Heck
- Institute of Bio- and Geosciences (IBG-1: Biotechnology) Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany;
| | - Oliver Klaus
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (F.H.); (A.L.); (Y.S.A.); (O.K.); (J.H.-H.); (K.-E.J.)
| | - Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (F.H.); (A.L.); (Y.S.A.); (O.K.); (J.H.-H.); (K.-E.J.)
| | - Florian M. W. Grundler
- INRES—Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany; (S.S.H.); (S.N.); (F.M.W.G.)
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (F.H.); (A.L.); (Y.S.A.); (O.K.); (J.H.-H.); (K.-E.J.)
- Institute of Bio- and Geosciences (IBG-1: Biotechnology) Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany;
| | - A. Sylvia S. Schleker
- INRES—Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany; (S.S.H.); (S.N.); (F.M.W.G.)
- Correspondence: (A.S.S.S.); (T.D.)
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (F.H.); (A.L.); (Y.S.A.); (O.K.); (J.H.-H.); (K.-E.J.)
- Correspondence: (A.S.S.S.); (T.D.)
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Park D, Swayambhu G, Lyga T, Pfeifer BA. Complex natural product production methods and options. Synth Syst Biotechnol 2021; 6:1-11. [PMID: 33474503 PMCID: PMC7803631 DOI: 10.1016/j.synbio.2020.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/19/2020] [Accepted: 12/21/2020] [Indexed: 12/29/2022] Open
Abstract
Natural products have had a major impact upon quality of life, with antibiotics as a classic example of having a transformative impact upon human health. In this contribution, we will highlight both historic and emerging methods of natural product bio-manufacturing. Traditional methods of natural product production relied upon native cellular host systems. In this context, pragmatic and effective methodologies were established to enable widespread access to natural products. In reviewing such strategies, we will also highlight the development of heterologous natural product biosynthesis, which relies instead on a surrogate host system theoretically capable of advanced production potential. In comparing native and heterologous systems, we will comment on the base organisms used for natural product biosynthesis and how the properties of such cellular hosts dictate scaled engineering practices to facilitate compound distribution. In concluding the article, we will examine novel efforts in production practices that entirely eliminate the constraints of cellular production hosts. That is, cell free production efforts will be introduced and reviewed for the purpose of complex natural product biosynthesis. Included in this final analysis will be research efforts made on our part to test the cell free biosynthesis of the complex polyketide antibiotic natural product erythromycin.
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Affiliation(s)
- Dongwon Park
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Girish Swayambhu
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Thomas Lyga
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
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Heterologous biosynthesis as a platform for producing new generation natural products. Curr Opin Biotechnol 2020; 66:123-130. [DOI: 10.1016/j.copbio.2020.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
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Raghavan AR, Yadav VG. Harnessing emerging paradigms in chemical engineering to accelerate the development of pharmaceutical products. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Adhithi R. Raghavan
- Department of Chemical and Biological Engineering & School of Biomedical Engineering The University of British Columbia Vancouver British Columbia Canada
| | - Vikramaditya G. Yadav
- Department of Chemical and Biological Engineering & School of Biomedical Engineering The University of British Columbia Vancouver British Columbia Canada
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11
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An improved gene synthesis method with asymmetric directions of oligonucleotides designed using a simulation program. Biotechniques 2020; 69:211-219. [PMID: 32551895 DOI: 10.2144/btn-2020-0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Artificial gene synthesis based on oligonucleotide augmentation is known as overlap extension PCR which generates a variety of intermediate synthetic products. The orientation and concentration of oligomers can be adjusted to reduce the synthesis of intermediates and optimize the full-length process of DNA synthesis, using a simulation program for serial oligomer extension. The efficiency of the serial oligomer extension process is predicted to be greatest when oligomers are in a 'forward-reverse-reverse-reverse' direction. Oligomers with such designed directions demonstrated generation of the desired product in the shortest time (number of cycles) by repeated annealing and elongation. This method, named Asymmetric Extension supported by a Simulator for Oligonucleotide Extension (AESOE), has shown efficiency and effectiveness with potentials for future improvements and optimal usage in DNA synthesis.
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Hydroxychloroquine and Covid-19: A Cellular and Molecular Biology Based Update. Indian J Clin Biochem 2020; 35:274-284. [PMID: 32641874 PMCID: PMC7286553 DOI: 10.1007/s12291-020-00900-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022]
Abstract
As the time for finding a definitive and safe cure as a vaccine for novel Corona Virus Disease 2019 (Covid-19) is still far, there is need to study in depth about the other potential drugs, which can save millions of lives due to Covid-19 pandemic. Right at the center of the debate is the use of drug "Hydroxychloroquine" as a prophylaxis as well as a treatment strategy against Covid-19 in conjunction with azithromycin. In this review, we will study the cellular and molecular aspects of hydroxychloroquine, which had driven its use in Covid-19 patients, as well as its chemistry and pharmacokinetics along with clinical trials going on worldwide using hydroxychloroquine against Covid-19.
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Mechanisms of action of hydroxychloroquine and chloroquine: implications for rheumatology. Nat Rev Rheumatol 2020; 16:155-166. [PMID: 32034323 DOI: 10.1038/s41584-020-0372-x] [Citation(s) in RCA: 776] [Impact Index Per Article: 194.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2020] [Indexed: 12/15/2022]
Abstract
Despite widespread clinical use of antimalarial drugs such as hydroxychloroquine and chloroquine in the treatment of rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and other inflammatory rheumatic diseases, insights into the mechanism of action of these drugs are still emerging. Hydroxychloroquine and chloroquine are weak bases and have a characteristic 'deep' volume of distribution and a half-life of around 50 days. These drugs interfere with lysosomal activity and autophagy, interact with membrane stability and alter signalling pathways and transcriptional activity, which can result in inhibition of cytokine production and modulation of certain co-stimulatory molecules. These modes of action, together with the drug's chemical properties, might explain the clinical efficacy and well-known adverse effects (such as retinopathy) of these drugs. The unknown dose-response relationships of these drugs and the lack of definitions of the minimum dose needed for clinical efficacy and what doses are toxic pose challenges to clinical practice. Further challenges include patient non-adherence and possible context-dependent variations in blood drug levels. Available mechanistic data give insights into the immunomodulatory potency of hydroxychloroquine and provide the rationale to search for more potent and/or selective inhibitors.
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Trump BD, Siharulidze G, Cummings CL. Synthetic Biology and Risk Regulation: The Case of Singapore. RISK, SYSTEMS AND DECISIONS 2020. [DOI: 10.1007/978-3-030-27264-7_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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15
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Zhao C, Zhang Y, Li Y. Production of fuels and chemicals from renewable resources using engineered Escherichia coli. Biotechnol Adv 2019; 37:107402. [DOI: 10.1016/j.biotechadv.2019.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 05/23/2019] [Accepted: 06/02/2019] [Indexed: 02/06/2023]
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16
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Troost K, Loeschcke A, Hilgers F, Özgür AY, Weber TM, Santiago-Schübel B, Svensson V, Hage-Hülsmann J, Habash SS, Grundler FMW, Schleker ASS, Jaeger KE, Drepper T. Engineered Rhodobacter capsulatus as a Phototrophic Platform Organism for the Synthesis of Plant Sesquiterpenoids. Front Microbiol 2019; 10:1998. [PMID: 31555236 PMCID: PMC6742980 DOI: 10.3389/fmicb.2019.01998] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/15/2019] [Indexed: 12/11/2022] Open
Abstract
Sesquiterpenoids are a large class of natural compounds offering manifold properties valuable for food, cosmetics, agriculture, and pharma industry. Production in microorganisms is a sustainable approach to provide sesquiterpenoids for research and industrial use independent of their natural sources. This requires the functional transfer of the respective biocatalytic pathways in an adequate host microorganism offering a sufficient supply of precursors that is ideally adjusted to the individual demand of the recombinant biosynthesis route. The phototrophic purple bacterium Rhodobacter capsulatus offers unique physiological properties that are favorable for biosynthesis of hydrophobic terpenes. Under phototrophic conditions, it develops a large intracytoplasmic membrane suitable for hosting membrane-bound enzymes and metabolites of respective biosynthetic pathways. In addition, Rhodobacter harbors an intrinsic carotenoid biosynthesis that can be engineered toward the production of foreign terpenes. Here, we evaluate R. capsulatus as host for the production of plant sesquiterpenoids under phototrophic conditions using patchoulol and valencene as a proof of concept. The heterologous expression of patchoulol synthase PcPS from Pogostemon cablin as well as the valencene synthases CsVS from Citrus sinensis and CnVS from Callitropsis nootkatensis led to the production of the respective sesquiterpenoids in R. capsulatus. To analyze, if gradually adjustable formation of the key precursor farnesylpyrophosphate (FPP) is beneficial for sesquiterpene synthesis under phototrophic conditions, the intrinsic 1-deoxy-D-xylulose 5-phosphate (DXP) pathway genes as well as the heterologous mevalonate pathway genes were modularly expressed in various combinations. To this end, different plasmids and chromosomally integrated expression tools were developed harboring the strong and tightly controlled Pnif promoter for heterologous gene expression. Notably, comparative studies identified a distinct combination of precursor biosynthetic genes as best-performing setup for each of the tested sesquiterpene synthases. In summary, we could demonstrate that R. capsulatus is a promising alternative platform organism that is suited for sustainable sesquiterpenoid formation under phototrophic cultivation conditions. A modular engineering of R. capsulatus strains via tailored co-expression of FPP biosynthetic genes further allowed adaptation of sesquiterpene precursor formation to its catalytic conversion by different plant terpene synthases.
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Affiliation(s)
- Katrin Troost
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Armagan Yakup Özgür
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Tim Moritz Weber
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Beatrix Santiago-Schübel
- Central Institute for Engineering, Electronics and Analytics ZEA-3, Analytics, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Vera Svensson
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Samer S Habash
- INRES-Molecular Phytomedicine, Rhenish Friedrich-Wilhelm University of Bonn, Bonn, Germany
| | - Florian M W Grundler
- INRES-Molecular Phytomedicine, Rhenish Friedrich-Wilhelm University of Bonn, Bonn, Germany
| | - A Sylvia S Schleker
- INRES-Molecular Phytomedicine, Rhenish Friedrich-Wilhelm University of Bonn, Bonn, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
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17
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Li X, Li X, Li Y, Yu C, Xue W, Hu J, Li B, Wang P, Zhu F. What Makes Species Productive of Anti-Cancer Drugs? Clues from Drugs’ Species Origin, Druglikeness, Target and Pathway. Anticancer Agents Med Chem 2019; 19:194-203. [DOI: 10.2174/1871520618666181029132017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/22/2017] [Accepted: 03/21/2018] [Indexed: 12/18/2022]
Abstract
Background:Despite the substantial contribution of natural products to the FDA drug approval list, the discovery of anti-cancer drugs from the huge amount of species on the planet remains looking for a needle in a haystack. Objective: Drug-productive clusters in the phylogenetic tree are thus proposed to narrow the searching scope by focusing on much smaller amount of species within each cluster, which enable prioritized and rational bioprospecting for novel drug-like scaffolds. However, the way anti-cancer nature-derived drugs distribute in phylogenetic tree has not been reported, and it is oversimplified to just focus anti-cancer drug discovery on the drug-productive clusters, since the number of species in each cluster remains too large to be managed.Objective:Drug-productive clusters in the phylogenetic tree are thus proposed to narrow the searching scope by focusing on much smaller amount of species within each cluster, which enable prioritized and rational bioprospecting for novel drug-like scaffolds. However, the way anti-cancer nature-derived drugs distribute in phylogenetic tree has not been reported, and it is oversimplified to just focus anti-cancer drug discovery on the drug-productive clusters, since the number of species in each cluster remains too large to be managed.Methods:In this study, 260 anti-cancer drugs approved in the past 70 years were comprehensively analyzed by hierarchical clustering of phylogenetic distribution.Results:207 out of these 260 drugs were derived from or inspired by the natural products isolated from 58 species. Phylogenetic distribution of those drugs further revealed that nature-derived anti-cancer drugs originated mostly from drug-productive families that tend to be clustered rather than scattered on the phylogenetic tree. Moreover, based on their productivity, drug-producing species were categorized into productive (CPS), newly emerging (CNS) and lessproductive (CLS). Statistical significances in druglikeness between drugs from CPS and CLS were observed, and drugs from CNS were found to share similar drug-like properties to those from CPS.Conclusion:This finding indicated a great raise in drug approval standard, which suggested us to focus bioprospecting on the species yielding multiple drugs and keeping productive for long period of time.
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Affiliation(s)
- Xiaofeng Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Xiaoxu Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yinghong Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Chunyan Yu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jie Hu
- School of International Studies, Zhejiang University, Hangzhou 310058, China
| | - Bo Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Panpan Wang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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18
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Wang P, Wei W, Ye W, Li X, Zhao W, Yang C, Li C, Yan X, Zhou Z. Synthesizing ginsenoside Rh2 in Saccharomyces cerevisiae cell factory at high-efficiency. Cell Discov 2019; 5:5. [PMID: 30652026 PMCID: PMC6331602 DOI: 10.1038/s41421-018-0075-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/19/2018] [Accepted: 11/02/2018] [Indexed: 12/13/2022] Open
Abstract
Synthetic biology approach has been frequently applied to produce plant rare bioactive compounds in microbial cell factories by fermentation. However, to reach an ideal manufactural efficiency, it is necessary to optimize the microbial cell factories systemically by boosting sufficient carbon flux to the precursor synthesis and tuning the expression level and efficiency of key bioparts related to the synthetic pathway. We previously developed a yeast cell factory to produce ginsenoside Rh2 from glucose. However, the ginsenoside Rh2 yield was too low for commercialization due to the low supply of the ginsenoside aglycone protopanaxadiol (PPD) and poor performance of the key UDP-glycosyltransferase (UGT) (biopart UGTPg45) in the final step of the biosynthetic pathway. In the present study, we constructed a PPD-producing chassis via modular engineering of the mevalonic acid pathway and optimization of P450 expression levels. The new yeast chassis could produce 529.0 mg/L of PPD in shake flasks and 11.02 g/L in 10 L fed-batch fermentation. Based on this high PPD-producing chassis, we established a series of cell factories to produce ginsenoside Rh2, which we optimized by improving the C3–OH glycosylation efficiency. We increased the copy number of UGTPg45, and engineered its promoter to increase expression levels. In addition, we screened for more efficient and compatible UGT bioparts from other plant species and mutants originating from the direct evolution of UGTPg45. Combining all engineered strategies, we built a yeast cell factory with the greatest ginsenoside Rh2 production reported to date, 179.3 mg/L in shake flasks and 2.25 g/L in 10 L fed-batch fermentation. The results set up a successful example for improving yeast cell factories to produce plant rare natural products, especially the glycosylated ones.
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Affiliation(s)
- Pingping Wang
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
| | - Wei Wei
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
| | - Wei Ye
- 2University of Chinese Academy of Sciences, Beijing, 100049 China.,Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai, 200031 China
| | - Xiaodong Li
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China.,2University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenfang Zhao
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
| | - Chengshuai Yang
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China.,2University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chaojing Li
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China.,2University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xing Yan
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
| | - Zhihua Zhou
- 1CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032 China
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19
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Currin A, Dunstan MS, Johannissen LO, Hollywood KA, Vinaixa M, Jervis AJ, Swainston N, Rattray NJW, Gardiner JM, Kell DB, Takano E, Toogood HS, Scrutton NS. Engineering the "Missing Link" in Biosynthetic (-)-Menthol Production: Bacterial Isopulegone Isomerase. ACS Catal 2018; 8:2012-2020. [PMID: 29750129 PMCID: PMC5937688 DOI: 10.1021/acscatal.7b04115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/15/2018] [Indexed: 12/28/2022]
Abstract
![]()
The
realization of a synthetic biology approach to microbial (1R,2S,5R)-(−)-menthol (1) production relies on the identification
of a gene encoding an isopulegone isomerase (IPGI), the only enzyme
in the Mentha piperita biosynthetic
pathway as yet unidentified. We demonstrate that Δ5-3-ketosteroid
isomerase (KSI) from Pseudomonas putida can act as an IPGI, producing (R)-(+)-pulegone
((R)-2) from (+)-cis-isopulegone (3). Using a robotics-driven semirational
design strategy, we identified a key KSI variant encoding four active
site mutations, which confer a 4.3-fold increase in activity over
the wild-type enzyme. This was assisted by the generation of crystal
structures of four KSI variants, combined with molecular modeling
of 3 binding to identify key active site residue targets.
The KSI variant was demonstrated to function efficiently within cascade
biocatalytic reactions with downstream Mentha enzymes pulegone reductase and (−)-menthone:(−)-menthol
reductase to generate 1 from 3. This study
introduces the use of a recombinant IPGI, engineered to function efficiently
within a biosynthetic pathway for the production of 1 in microorganisms.
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20
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Metsä-Ketelä M. Evolution inspired engineering of antibiotic biosynthesis enzymes. Org Biomol Chem 2017; 15:4036-4041. [DOI: 10.1039/c7ob00189d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chimeragenesis is an effective tool to probe the structure/function relationships of proteins without high-throughput screening systems. Here the proof-of-principle is presented with three pairs of proteins.
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21
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Leitão AL, Costa MC, Enguita FJ. Applications of genome editing by programmable nucleases to the metabolic engineering of secondary metabolites. J Biotechnol 2016; 241:50-60. [PMID: 27845165 DOI: 10.1016/j.jbiotec.2016.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 11/06/2016] [Accepted: 11/10/2016] [Indexed: 12/17/2022]
Abstract
Genome engineering is a branch of modern biotechnology composed of a cohort of protocols designed to construct and modify a genotype with the main objective of giving rise to a desired phenotype. Conceptually, genome engineering is based on the so called genome editing technologies, a group of genetic techniques that allow either to delete or to insert genetic information in a particular genomic locus. Ten years ago, genome editing tools were limited to virus-driven integration and homologous DNA recombination. However, nowadays the uprising of programmable nucleases is rapidly changing this paradigm. There are two main families of modern tools for genome editing depending on the molecule that controls the specificity of the system and drives the editor machinery to its place of action. Enzymes such as Zn-finger and TALEN nucleases are protein-driven genome editors; while CRISPR system is a nucleic acid-guided editing system. Genome editing techniques are still not widely applied for the design of new compounds with pharmacological activity, but they are starting to be considered as promising tools for rational genome manipulation in biotechnology applications. In this review we will discuss the potential applications of programmable nucleases for the metabolic engineering of secondary metabolites with biological activity.
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Affiliation(s)
- Ana Lúcia Leitão
- Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, Campus de Caparica, 2829-516 Caparica, Portugal; MEtRICs, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, Campus de Caparica, 2829-516 Caparica, Portugal.
| | - Marina C Costa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.
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22
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Li J, Meng H, Wang Y. Synbiological systems for complex natural products biosynthesis. Synth Syst Biotechnol 2016; 1:221-229. [PMID: 29062947 PMCID: PMC5625725 DOI: 10.1016/j.synbio.2016.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 08/24/2016] [Accepted: 08/24/2016] [Indexed: 10/25/2022] Open
Abstract
Natural products (NPs) continue to play a pivotal role in drug discovery programs. The rapid development of synthetic biology has conferred the strategies of NPs production. Synthetic biology is a new engineering discipline that aims to produce desirable products by rationally programming the biological parts and manipulating the pathways. However, there is still a challenge for integrating a heterologous pathway in chassis cells for overproduction purpose due to the limited characterized parts, modules incompatibility, and cell tolerance towards product. Enormous endeavors have been taken for mentioned issues. Herein, in this review, the progresses in naturally discovering novel biological parts and rational design of synthetic biological parts are reviewed, combining with the advanced assembly technologies, pathway engineering, and pathway optimization in global network guidance. The future perspectives are also presented.
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Affiliation(s)
- Jianhua Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hailin Meng
- Bioengineering Research Center, Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Guangzhou 511458, China
| | - Yong Wang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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23
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An J, Minie M, Sasaki T, Woodward JJ, Elkon KB. Antimalarial Drugs as Immune Modulators: New Mechanisms for Old Drugs. Annu Rev Med 2016; 68:317-330. [PMID: 27813878 DOI: 10.1146/annurev-med-043015-123453] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The best known of the naturally occurring antimalarial compounds are quinine, extracted from cinchona bark, and artemisinin (qinghao), extracted from Artemisia annua in China. These and other derivatives are now chemically synthesized and remain the mainstay of therapy to treat malaria. The beneficial effects of several of the antimalarial drugs (AMDs) on clinical features of autoimmune disorders were discovered by chance during World War II. In this review, we discuss the chemistry of AMDs and their mechanisms of action, emphasizing how they may impact multiple pathways of innate immunity. These pathways include Toll-like receptors and the recently described cGAS-STING pathway. Finally, we discuss the current and future impact of AMDs on systemic lupus erythematosus, rheumatoid arthritis, and devastating monogenic disorders (interferonopathies) characterized by expression of type I interferon in the brain.
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Affiliation(s)
- Jie An
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington 98195; email
| | | | | | | | - Keith B Elkon
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington 98195; email .,Department of Immunology, University of Washington, Seattle, Washington 98195; , , ,
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24
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Biosynthesis of therapeutic natural products using synthetic biology. Adv Drug Deliv Rev 2016; 105:96-106. [PMID: 27094795 DOI: 10.1016/j.addr.2016.04.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/24/2016] [Accepted: 04/10/2016] [Indexed: 02/08/2023]
Abstract
Natural products are a group of bioactive structurally diverse chemicals produced by microorganisms and plants. These molecules and their derivatives have contributed to over a third of the therapeutic drugs produced in the last century. However, over the last few decades traditional drug discovery pipelines from natural products have become far less productive and far more expensive. One recent development with promise to combat this trend is the application of synthetic biology to therapeutic natural product biosynthesis. Synthetic biology is a young discipline with roots in systems biology, genetic engineering, and metabolic engineering. In this review, we discuss the use of synthetic biology to engineer improved yields of existing therapeutic natural products. We further describe the use of synthetic biology to combine and express natural product biosynthetic genes in unprecedented ways, and how this holds promise for opening up completely new avenues for drug discovery and production.
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25
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Wong VKW, Law BYK, Yao XJ, Chen X, Xu SW, Liu L, Leung ELH. Advanced research technology for discovery of new effective compounds from Chinese herbal medicine and their molecular targets. Pharmacol Res 2016; 111:546-555. [DOI: 10.1016/j.phrs.2016.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/19/2016] [Accepted: 07/19/2016] [Indexed: 02/07/2023]
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26
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Toogood HS, Tait S, Jervis A, Ní Cheallaigh A, Humphreys L, Takano E, Gardiner JM, Scrutton NS. Natural Product Biosynthesis in Escherichia coli: Mentha Monoterpenoids. Methods Enzymol 2016; 575:247-70. [PMID: 27417932 DOI: 10.1016/bs.mie.2016.02.020] [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: 03/07/2024]
Abstract
The era of synthetic biology heralds in a new, more "green" approach to fine chemical and pharmaceutical drug production. It takes the knowledge of natural metabolic pathways and builds new routes to chemicals, enables nonnatural chemical production, and/or allows the rapid production of chemicals in alternative, highly performing organisms. This route is particularly useful in the production of monoterpenoids in microorganisms, which are naturally sourced from plant essential oils. Successful pathways are constructed by taking into consideration factors such as gene selection, regulatory elements, host selection and optimization, and metabolic considerations of the host organism. Seamless pathway construction techniques enable a "plug-and-play" switching of genes and regulatory parts to optimize the metabolic functioning in vivo. Ultimately, synthetic biology approaches to microbial monoterpenoid production may revolutionize "natural" compound formation.
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Affiliation(s)
- H S Toogood
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - S Tait
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - A Jervis
- Manchester Institute of Biotechnology, SYNBIOCHEM, University of Manchester, Manchester, United Kingdom
| | - A Ní Cheallaigh
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - L Humphreys
- GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - E Takano
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - J M Gardiner
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - N S Scrutton
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
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Abstract
Synthetic biology (SB) is an emerging discipline, which is slowly reorienting the field of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell-cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity.
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Affiliation(s)
| | - Pablo Carbonell
- Faculty of Life Sciences, SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Department of Experimental and Health Sciences (DCEXS), Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Grocholski T, Dinis P, Niiranen L, Niemi J, Metsä-Ketelä M. Divergent evolution of an atypical S-adenosyl-l-methionine-dependent monooxygenase involved in anthracycline biosynthesis. Proc Natl Acad Sci U S A 2015; 112:9866-71. [PMID: 26216966 PMCID: PMC4538628 DOI: 10.1073/pnas.1501765112] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial secondary metabolic pathways are responsible for the biosynthesis of thousands of bioactive natural products. Many enzymes residing in these pathways have evolved to catalyze unusual chemical transformations, which is facilitated by an evolutionary pressure promoting chemical diversity. Such divergent enzyme evolution has been observed in S-adenosyl-L-methionine (SAM)-dependent methyltransferases involved in the biosynthesis of anthracycline anticancer antibiotics; whereas DnrK from the daunorubicin pathway is a canonical 4-O-methyltransferase, the closely related RdmB (52% sequence identity) from the rhodomycin pathways is an atypical 10-hydroxylase that requires SAM, a thiol reducing agent, and molecular oxygen for activity. Here, we have used extensive chimeragenesis to gain insight into the functional differentiation of RdmB and show that insertion of a single serine residue to DnrK is sufficient for introduction of the monooxygenation activity. The crystal structure of DnrK-Ser in complex with aclacinomycin T and S-adenosyl-L-homocysteine refined to 1.9-Å resolution revealed that the inserted serine S297 resides in an α-helical segment adjacent to the substrate, but in a manner where the side chain points away from the active site. Further experimental work indicated that the shift in activity is mediated by rotation of a preceding phenylalanine F296 toward the active site, which blocks a channel to the surface of the protein that is present in native DnrK. The channel is also closed in RdmB and may be important for monooxygenation in a solvent-free environment. Finally, we postulate that the hydroxylation ability of RdmB originates from a previously undetected 10-decarboxylation activity of DnrK.
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Affiliation(s)
- Thadée Grocholski
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Pedro Dinis
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Laila Niiranen
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Jarmo Niemi
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
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Effective Antibiofilm Polyketides against Staphylococcus aureus from the Pyranonaphthoquinone Biosynthetic Pathways of Streptomyces Species. Antimicrob Agents Chemother 2015. [PMID: 26195520 DOI: 10.1128/aac.00991-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces bacteria are renowned for their ability to produce bioactive secondary metabolites. Recently, synthetic biology has enabled the production of intermediates and shunt products, which may have altered biological activities compared to the end products of the pathways. Here, we have evaluated the potential of recently isolated alnumycins and other closely related pyranonaphthoquinone (PNQ) polyketides against Staphylococcus aureus biofilms. The antimicrobial potency of the compounds against planktonic cells and biofilms was determined by redox dye-based viability staining, and the antibiofilm efficacy of the compounds was confirmed by viable counting. A novel antistaphylococcal polyketide, alnumycin D, was identified. Unexpectedly, the C-ribosylated pathway shunt product alnumycin D was more active against planktonic and biofilm cells than the pathway end product alnumycin A, where a ribose unit has been converted into a dioxane moiety. The evaluation of the antibiofilm potential of other alnumycins revealed that the presence of the ribose moiety in pyranose form is essential for high activity against preformed biofilms. Furthermore, the antibiofilm potential of other closely related PNQ polyketides was examined. Based on their previously reported activity against planktonic S. aureus cells, granaticin B, kalafungin, and medermycin were also selected for testing, and among them, granaticin B was found to be the most potent against preformed biofilms. The most active antibiofilm PNQs, alnumycin D and granaticin B, share several structural features that may be important for their antibiofilm activity. They are uncharged, glycosylated, and also contain a similar oxygenation pattern of the lateral naphthoquinone ring. These findings highlight the potential of antibiotic biosynthetic pathways as a source of effective antibiofilm compounds.
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Patel S, Ahmed S, Eswari JS. Therapeutic cyclic lipopeptides mining from microbes: latest strides and hurdles. World J Microbiol Biotechnol 2015; 31:1177-93. [PMID: 26041368 DOI: 10.1007/s11274-015-1880-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 05/31/2015] [Indexed: 12/23/2022]
Abstract
Infectious diseases impose serious public health burdens and often have devastating consequences. The cyclic lipopeptides elaborated by bacteria Bacillus, Paenibacillus, Pseudomonas, Streptomyces, Serratia, Propionibacterium and fungus Fusarium are very crucial in restraining the pathogens. Composed of a peptide and a fatty acyl moiety these amphiphilic metabolites exhibit broad spectrum antimicrobial effects. Among the plethora of cyclic lipopeptides, only selective few have emerged as robust antibiotics. For their functional vigor, polymyxin, daptomycin, surfactin, iturin, fengysin, paenibacterin and pseudofactin have been integrated in mainstream healthcare. Daptomycin has been a significant part of antimicrobial arsenal since the past decade. As the magnitude of drug resistance rises in unprecedented manner, the urgency of prospecting novel cyclic lipopeptides is being perceived. Intense research has revealed the implication of these bioactive compounds stretching beyond antibacterial and antifungal. Anticancer, immunomodulatory, prosthetic parts disinfection and vaccine adjuvancy are some of the validated prospects. This review discusses the emerging applications, mechanisms governing the biological actions, role of genomics in refining structure and function, semi-synthetic analog discovery, novel strain isolation, setbacks etc. Though its beyond the scope of the current topic, for holistic purpose, the role of lipopeptides in bioremediation and crop biotechnology has been briefly outlined. This updated critique is expected to galvanize innovations and diversify therapeutic recruitment of microbial lipopeptides.
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, CA, 92182, USA,
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31
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Miura K, Satoh M, Kinouchi M, Yamamoto K, Hasegawa Y, Kakugawa Y, Kawai M, Uchimi K, Aizawa H, Ohnuma S, Kajiwara T, Sakurai H, Fujiya T. The use of natural products in colorectal cancer drug discovery. Expert Opin Drug Discov 2015; 10:411-26. [DOI: 10.1517/17460441.2015.1018174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Koh Miura
- 1Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan ;
| | - Masayuki Satoh
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Makoto Kinouchi
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Kuniharu Yamamoto
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Yasuhiro Hasegawa
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Yoichiro Kakugawa
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Masaaki Kawai
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Kiyoshi Uchimi
- 3Miyagi Cancer Center, Department of Gastroenterology, 47-1 Nodayama, Natori 981-1293, Japan
| | - Hiroki Aizawa
- 3Miyagi Cancer Center, Department of Gastroenterology, 47-1 Nodayama, Natori 981-1293, Japan
| | - Shinobu Ohnuma
- 4Tohoku University Graduate School of Medicine, Department of Surgery, 1-1 Seiryo-machi, Sendai 980-8574, Japan
| | - Taiki Kajiwara
- 4Tohoku University Graduate School of Medicine, Department of Surgery, 1-1 Seiryo-machi, Sendai 980-8574, Japan
| | - Hiroto Sakurai
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Tsuneaki Fujiya
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
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32
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Yuan L, Grotewold E. Metabolic engineering to enhance the value of plants as green factories. Metab Eng 2014; 27:83-91. [PMID: 25461830 DOI: 10.1016/j.ymben.2014.11.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 11/08/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022]
Abstract
The promise of plants to serve as the green factories of the future is ever increasing. Plants have been used traditionally for construction, energy, food and feed. Bioactive compounds primarily derived from specialized plant metabolism continue to serve as important scaffold molecules for pharmaceutical drug production. Yet, the past few years have witnessed a growing interest on plants as the ultimate harvesters of carbon and energy from the sun, providing carbohydrate and lipid biofuels that would contribute to balancing atmospheric carbon. How can the metabolic output from plants be increased even further, and what are the bottlenecks? Here, we present what we perceive to be the main opportunities and challenges associated with increasing the efficiency of plants as chemical factories. We offer some perspectives on when it makes sense to use plants as production systems because the amount of biomass needed makes any other system unfeasible. However, there are other instances in which plants serve as great sources of biological catalysts, yet are not necessarily the best-suited systems for production. We also present emerging opportunities for manipulating plant genomes to make plant synthetic biology a reality.
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Affiliation(s)
- Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, United States
| | - Erich Grotewold
- Center for Applied Plant Sciences (CAPS), Department of Molecular Genetics and Department of Horticulture and Crop Science, The Ohio State University, 012 Rightmire Hall, 1060 Carmack Rd, Columbus, OH 43210, United States.
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Wu J, Du G, Zhou J, Chen J. Systems metabolic engineering of microorganisms to achieve large-scale production of flavonoid scaffolds. J Biotechnol 2014; 188:72-80. [DOI: 10.1016/j.jbiotec.2014.08.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/07/2014] [Accepted: 08/18/2014] [Indexed: 11/25/2022]
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Li Y, Pfeifer BA. Heterologous production of plant-derived isoprenoid products in microbes and the application of metabolic engineering and synthetic biology. CURRENT OPINION IN PLANT BIOLOGY 2014; 19:8-13. [PMID: 24631884 DOI: 10.1016/j.pbi.2014.02.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
The value associated with plant-derived products has spurred efforts to engineer new production routes. One such option is heterologous biosynthesis which requires reconstitution of a biosynthetic pathway in a host that provides both innate and developed cellular advantages relative to the native producer. This review will summarize success to date in heterologously producing plant-derived isoprenoid products when using hosts such as E. coli and yeast. The article will also address the significant challenges that face such efforts, the approaches that have been used to overcome obstacles, and the tools of metabolic engineering and synthetic biology being applied both in the course of establishing heterologous biosynthesis and optimizing final production metrics.
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Affiliation(s)
- Yi Li
- Department of Chemical and Biological Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, United States
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, The State University of New York at Buffalo, Buffalo, NY 14260, United States.
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35
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Fesenko E, Edwards R. Plant synthetic biology: a new platform for industrial biotechnology. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1927-37. [PMID: 24638901 DOI: 10.1093/jxb/eru070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Thirty years after the production of the first generation of genetically modified plants we are now set to move into a new era of recombinant crop technology through the application of synthetic biology to engineer new and complex input and output traits. The use of synthetic biology technologies will represent more than incremental additions of transgenes, but rather the directed design of completely new metabolic pathways, physiological traits, and developmental control strategies. The need to enhance our ability to improve crops through new engineering capability is now increasingly pressing as we turn to plants not just for food, but as a source of renewable feedstocks for industry. These accelerating and diversifying demands for new output traits coincide with a need to reduce inputs and improve agricultural sustainability. Faced with such challenges, existing technologies will need to be supplemented with new and far-more-directed approaches to turn valuable resources more efficiently into usable agricultural products. While these objectives are challenging enough, the use of synthetic biology in crop improvement will face public acceptance issues as a legacy of genetically modified technologies in many countries. Here we review some of the potential benefits of adopting synthetic biology approaches in improving plant input and output traits for their use as industrial chemical feedstocks, as linked to the rapidly developing biorefining industry. Several promising technologies and biotechnological targets are identified along with some of the key regulatory and societal challenges in the safe and acceptable introduction of such technology.
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Affiliation(s)
- Elena Fesenko
- Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, UK
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36
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Expression, purification and activity assay of a patchoulol synthase cDNA variant fused to thioredoxin in Escherichia coli. Protein Expr Purif 2014; 97:61-71. [DOI: 10.1016/j.pep.2014.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/10/2014] [Accepted: 02/13/2014] [Indexed: 01/26/2023]
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37
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Elena C, Ravasi P, Castelli ME, Peirú S, Menzella HG. Expression of codon optimized genes in microbial systems: current industrial applications and perspectives. Front Microbiol 2014; 5:21. [PMID: 24550894 PMCID: PMC3912506 DOI: 10.3389/fmicb.2014.00021] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/14/2014] [Indexed: 11/24/2022] Open
Abstract
The efficient production of functional proteins in heterologous hosts is one of the major bases of modern biotechnology. Unfortunately, many genes are difficult to express outside their original context. Due to their apparent “silent” nature, synonymous codon substitutions have long been thought to be trivial. In recent years, this dogma has been refuted by evidence that codon replacement can have a significant impact on gene expression levels and protein folding. In the past decade, considerable advances in the speed and cost of gene synthesis have facilitated the complete redesign of entire gene sequences, dramatically improving the likelihood of high protein expression. This technology significantly impacts the economic feasibility of microbial-based biotechnological processes by, for example, increasing the volumetric productivities of recombinant proteins or facilitating the redesign of novel biosynthetic routes for the production of metabolites. This review discusses the current applications of this technology, particularly those regarding the production of small molecules and industrially relevant recombinant enzymes. Suggestions for future research and potential uses are provided as well.
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Affiliation(s)
- Claudia Elena
- Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet Rosario, Argentina
| | - Pablo Ravasi
- Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet Rosario, Argentina
| | - María E Castelli
- Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet Rosario, Argentina
| | - Salvador Peirú
- Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet Rosario, Argentina
| | - Hugo G Menzella
- Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet Rosario, Argentina
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38
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Vizcaino MI, Guo X, Crawford JM. Merging chemical ecology with bacterial genome mining for secondary metabolite discovery. J Ind Microbiol Biotechnol 2014; 41:285-99. [PMID: 24127069 PMCID: PMC3946945 DOI: 10.1007/s10295-013-1356-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/23/2013] [Indexed: 12/24/2022]
Abstract
The integration of chemical ecology and bacterial genome mining can enhance the discovery of structurally diverse natural products in functional contexts. By examining bacterial secondary metabolism in the framework of its ecological niche, insights into the upregulation of orphan biosynthetic pathways and the enhancement of the enzyme substrate supply can be obtained, leading to the discovery of new secondary metabolic pathways that would otherwise be silent or undetected under typical laboratory cultivation conditions. Access to these new natural products (i.e., the chemotypes) facilitates experimental genotype-to-phenotype linkages. Here, we describe certain functional natural products produced by Xenorhabdus and Photorhabdus bacteria with experimentally linked biosynthetic gene clusters as illustrative examples of the synergy between chemical ecology and bacterial genome mining in connecting genotypes to phenotypes through chemotype characterization. These Gammaproteobacteria share a mutualistic relationship with nematodes and a pathogenic relationship with insects and, in select cases, humans. The natural products encoded by these bacteria distinguish their interactions with their animal hosts and other microorganisms in their multipartite symbiotic lifestyles. Though both genera have similar lifestyles, their genetic, chemical, and physiological attributes are distinct. Both undergo phenotypic variation and produce a profuse number of bioactive secondary metabolites. We provide further detail in the context of regulation, production, processing, and function for these genetically encoded small molecules with respect to their roles in mutualism and pathogenicity. These collective insights more widely promote the discovery of atypical orphan biosynthetic pathways encoding novel small molecules in symbiotic systems, which could open up new avenues for investigating and exploiting microbial chemical signaling in host-bacteria interactions.
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Affiliation(s)
- Maria I. Vizcaino
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Xun Guo
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, 06510, USA
- Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
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39
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Chen X, Zhou L, Tian K, Kumar A, Singh S, Prior BA, Wang Z. Metabolic engineering of Escherichia coli: A sustainable industrial platform for bio-based chemical production. Biotechnol Adv 2013; 31:1200-23. [DOI: 10.1016/j.biotechadv.2013.02.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/04/2013] [Accepted: 02/25/2013] [Indexed: 12/20/2022]
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40
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Breitling R, Ceniceros A, Jankevics A, Takano E. Metabolomics for secondary metabolite research. Metabolites 2013; 3:1076-83. [PMID: 24958266 PMCID: PMC3937839 DOI: 10.3390/metabo3041076] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 10/25/2013] [Accepted: 11/01/2013] [Indexed: 01/26/2023] Open
Abstract
Metabolomics, the global characterization of metabolite profiles, is becoming an increasingly powerful tool for research on secondary metabolite discovery and production. In this review we discuss examples of recent technological advances and biological applications of metabolomics in the search for chemical novelty and the engineered production of bioactive secondary metabolites.
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Affiliation(s)
- Rainer Breitling
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Ana Ceniceros
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborg 7, Groningen 9747 AG, The Netherlands.
| | - Andris Jankevics
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Eriko Takano
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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41
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Putignani L, Massa O, Alisi A. Engineered Escherichia coli as new source of flavonoids and terpenoids. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.01.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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42
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Jain P, Krishnan NM, Panda B. Augmenting transcriptome assembly by combining de novo and genome-guided tools. PeerJ 2013; 1:e133. [PMID: 24024083 PMCID: PMC3746961 DOI: 10.7717/peerj.133] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/29/2013] [Indexed: 01/02/2023] Open
Abstract
Researchers interested in studying and constructing transcriptomes, especially for non-model species, face the conundrum of choosing from a number of available de novo and genome-guided assemblers. None of the popular assembly tools in use today achieve requisite sensitivity, specificity or recovery of full-length transcripts on their own. Here, we present a comprehensive comparative study of the performance of various assemblers. Additionally, we present an approach to combinatorially augment transciptome assembly by using both de novo and genome-guided tools. In our study, we obtained the best recovery and most full-length transcripts with Trinity and TopHat1-Cufflinks, respectively. The sensitivity of the assembly and isoform recovery was superior, without compromising much on the specificity, when transcripts from Trinity were augmented with those from TopHat1-Cufflinks.
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Affiliation(s)
- Prachi Jain
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Neeraja M Krishnan
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Binay Panda
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.,Strand Life Sciences, Hebbal, Bangalore, India
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43
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Lin Y, Sun X, Yuan Q, Yan Y. Combinatorial biosynthesis of plant-specific coumarins in bacteria. Metab Eng 2013; 18:69-77. [DOI: 10.1016/j.ymben.2013.04.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/10/2013] [Accepted: 04/17/2013] [Indexed: 01/17/2023]
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44
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Philp JC, Ritchie RJ, Allan JE. Synthetic biology, the bioeconomy, and a societal quandary. Trends Biotechnol 2013; 31:269-72. [DOI: 10.1016/j.tibtech.2013.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 10/27/2022]
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45
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Microfabricated devices in microbial bioenergy sciences. Trends Biotechnol 2013; 31:225-32. [DOI: 10.1016/j.tibtech.2012.12.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/01/2012] [Accepted: 12/11/2012] [Indexed: 01/18/2023]
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46
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Lucas X, Senger C, Erxleben A, Grüning BA, Döring K, Mosch J, Flemming S, Günther S. StreptomeDB: a resource for natural compounds isolated from Streptomyces species. Nucleic Acids Res 2013; 41:D1130-6. [PMID: 23193280 PMCID: PMC3531085 DOI: 10.1093/nar/gks1253] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/10/2012] [Accepted: 11/04/2012] [Indexed: 11/12/2022] Open
Abstract
Bacteria from the genus Streptomyces are very important for the production of natural bioactive compounds such as antibiotic, antitumour or immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria. An enormous quantity of crucial data related to this genus has been generated and published, but so far no freely available and comprehensive database exists. Here, we present StreptomeDB (http://www.pharmaceutical-bioinformatics.de/streptomedb/). To the best of our knowledge, this is the largest database of natural products isolated from Streptomyces. It contains >2400 unique and diverse compounds from >1900 different Streptomyces strains and substrains. In addition to names and molecular structures of the compounds, information about source organisms, references, biological role, activities and synthesis routes (e.g. polyketide synthase derived and non-ribosomal peptides derived) is included. Data can be accessed through queries on compound names, chemical structures or organisms. Extraction from the literature was performed through automatic text mining of thousands of articles from PubMed, followed by manual curation. All annotated compound structures can be downloaded from the website and applied for in silico screenings for identifying new active molecules with undiscovered properties.
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Affiliation(s)
| | | | | | | | | | | | | | - Stefan Günther
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, D-79104 Freiburg, Germany
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47
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Porcar M, Peretó J. Are we doing synthetic biology? SYSTEMS AND SYNTHETIC BIOLOGY 2012; 6:79-83. [PMID: 24294342 DOI: 10.1007/s11693-012-9101-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/27/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
Abstract
Synthetic Biology is a singular, revolutionary scenario with a vast range of practical applications but, is SB research really based on engineering principles? Is it contributing to the artificial synthesis of life or using approaches "sophisticated" enough to fall outside the scope of biotechnology or metabolic engineering? We have reviewed the state of the art on synthetic biology and we conclude that most research projects actually describe an extension of metabolic engineering. We draw this conclusion because the complexity of living organisms, their tight dependence on evolution and our limited knowledge of the interactions between the molecules they are made of, actually make life difficult to engineer. We therefore propose the term synthetic biology should be used more sparingly.
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Affiliation(s)
- Manuel Porcar
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartat, Postal 22085, 46071 Valencia, Spain ; Fundació General de la Universitat de València, Valencia, Spain ; Departament de Genètica, Universitat de València, Valencia, Spain
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NdgR, a common transcriptional activator for methionine and leucine biosynthesis in Streptomyces coelicolor. J Bacteriol 2012; 194:6837-46. [PMID: 23065973 DOI: 10.1128/jb.00695-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We show here that NdgR, a known transcriptional activator of isopropylmalate dehydratase in actinomycetes, may have other targets in the cell. An in-frame deletion mutant of ndgR showed unexpectedly poor growth in defined minimal medium even in the presence of leucine. To our surprise, it was supplementation of cysteine and methionine that corrected the growth. Based on this, we propose that NdgR induces cysteine-methionine biosynthesis. Direct involvement of NdgR in the very last steps of methionine synthesis with methionine synthase (metH) and 5,10-methylenetetrahydrofolate reductase (metF) was examined. From a pulldown assay, it was seen that NdgR was enriched from crude cell lysates with a strong affinity to metH and metF upstream sequences. Direct physical interaction of NdgR with these targets was further examined with a gel mobility shift assay. ndgR, leuC, metH, and metF were inducible in M145 cells upon nutrient downshift from rich to minimal medium but were not induced in the ndgR knockout mutant. Taking these observations together, NdgR-dependent metH-metF expression would account for the abnormal growth phenotype of the ndgR mutant although there may be additional NdgR-dependent genes in the Cys-Met metabolic pathways. As the first transcriptional factor reported for regulating Cys-Met metabolism in Streptomyces, NdgR links two disparate amino acid families, branched-chain amino acids (BCAAs) and sulfur amino acids, at the transcriptional level. Considering that Cys-Met metabolism is connected to mycothiol and one-carbon metabolism, NdgR may have broad physiological impacts.
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Yuzawa S, Kim W, Katz L, Keasling JD. Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli. Curr Opin Biotechnol 2012; 23:727-35. [DOI: 10.1016/j.copbio.2011.12.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 12/19/2011] [Accepted: 12/21/2011] [Indexed: 11/15/2022]
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Engineering plant metabolism into microbes: from systems biology to synthetic biology. Curr Opin Biotechnol 2012; 24:291-9. [PMID: 22985679 DOI: 10.1016/j.copbio.2012.08.010] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 08/21/2012] [Accepted: 08/27/2012] [Indexed: 12/11/2022]
Abstract
Plant metabolism represents an enormous repository of compounds that are of pharmaceutical and biotechnological importance. Engineering plant metabolism into microbes will provide sustainable solutions to produce pharmaceutical and fuel molecules that could one day replace substantial portions of the current fossil-fuel based economy. Metabolic engineering entails targeted manipulation of biosynthetic pathways to maximize yields of desired products. Recent advances in Systems Biology and the emergence of Synthetic Biology have accelerated our ability to design, construct and optimize cell factories for metabolic engineering applications. Progress in predicting and modeling genome-scale metabolic networks, versatile gene assembly platforms and delicate synthetic pathway optimization strategies has provided us exciting opportunities to exploit the full potential of cell metabolism. In this review, we will discuss how systems and synthetic biology tools can be integrated to create tailor-made cell factories for efficient production of natural products and fuel molecules in microorganisms.
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