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Yang Z, Chan KW, Abu Bakar MZ, Deng X. Unveiling Drimenol: A Phytochemical with Multifaceted Bioactivities. PLANTS (BASEL, SWITZERLAND) 2024; 13:2492. [PMID: 39273976 PMCID: PMC11397239 DOI: 10.3390/plants13172492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 09/02/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024]
Abstract
Drimenol, a phytochemical with a distinct odor is found in edible aromatic plants, such as Polygonum minus (known as kesum in Malaysia) and Drimys winteri. Recently, drimenol has received increasing attention owing to its diverse biological activities. This review offers the first extensive overview of drimenol, covering its sources, bioactivities, and derivatives. Notably, drimenol possesses a wide spectrum of biological activities, including antifungal, antibacterial, anti-insect, antiparasitic, cytotoxic, anticancer, and antioxidant effects. Moreover, some mechanisms of its activities, such as its antifungal effects against human mycoses and anticancer activities, have been investigated. However, there are still several crucial issues in the research on drimenol, such as the lack of experimental understanding of its pharmacokinetics, bioavailability, and toxicity. By synthesizing current research findings, this review aims to present a holistic understanding of drimenol, paving the way for future studies and its potential utilization in diverse fields.
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Affiliation(s)
- Zhongming Yang
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Kim Wei Chan
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Md Zuki Abu Bakar
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Veterinary Preclinical Science, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Xi Deng
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
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2
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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024; 41:1113-1151. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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Wang P, Huang X, Jiang C, Yang R, Wu J, Liu Y, Feng S, Wang T. Antibacterial properties of natural products from marine fungi reported between 2012 and 2023: a review. Arch Pharm Res 2024; 47:505-537. [PMID: 38850495 DOI: 10.1007/s12272-024-01500-6] [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: 09/01/2023] [Accepted: 05/04/2024] [Indexed: 06/10/2024]
Abstract
The oceans are rich in diverse microorganisms, animals, and plants. This vast biological complexity is a major source of unique secondary metabolites. In particular, marine fungi are a promising source of compounds with unique structures and potent antibacterial properties. Over the last decade, substantial progress has been made to identify these valuable antibacterial agents. This review summarizes the chemical structures and antibacterial activities of 223 compounds identified between 2012 and 2023. These compounds, effective against various bacteria including drug-resistant strains such as methicillin-resistant Staphylococcus aureus, exhibit strong potential as antibacterial therapeutics. The review also highlights the relevant challenges in transitioning from drug discovery to product commercialization. Emerging technologies such as metagenomics and synthetic biology are proposed as viable solutions. This paper sets the stage for further research on antibacterial compounds derived from marine fungi and advocates a multidisciplinary approach to combat drug-resistant bacteria.
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Affiliation(s)
- Ping Wang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Xiaomei Huang
- Department of Marine Biology, Xiamen Ocean Vocational College, Xiamen, 361100, Fujian, China
| | - Chenyuan Jiang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Rushuang Yang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Jialing Wu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yinghui Liu
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Shuangshuang Feng
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Tingting Wang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China.
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4
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Riedling O, Walker AS, Rokas A. Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning. Microbiol Spectr 2024; 12:e0340023. [PMID: 38193680 PMCID: PMC10846162 DOI: 10.1128/spectrum.03400-23] [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: 09/18/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Abstract
Fungal secondary metabolites (SMs) contribute to the diversity of fungal ecological communities, niches, and lifestyles. Many fungal SMs have one or more medically and industrially important activities (e.g., antifungal, antibacterial, and antitumor). The genes necessary for fungal SM biosynthesis are typically located right next to each other in the genome and are known as biosynthetic gene clusters (BGCs). However, whether fungal SM bioactivity can be predicted from specific attributes of genes in BGCs remains an open question. We adapted machine learning models that predicted SM bioactivity from bacterial BGC data with accuracies as high as 80% to fungal BGC data. We trained our models to predict the antibacterial, antifungal, and cytotoxic/antitumor bioactivity of fungal SMs on two data sets: (i) fungal BGCs (data set comprised of 314 BGCs) and (ii) fungal (314 BGCs) and bacterial BGCs (1,003 BGCs). We found that models trained on fungal BGCs had balanced accuracies between 51% and 68%, whereas training on bacterial and fungal BGCs had balanced accuracies between 56% and 68%. The low prediction accuracy of fungal SM bioactivities likely stems from the small size of the data set; this lack of data, coupled with our finding that including bacterial BGC data in the training data did not substantially change accuracies currently limits the application of machine learning approaches to fungal SM studies. With >15,000 characterized fungal SMs, millions of putative BGCs in fungal genomes, and increased demand for novel drugs, efforts that systematically link fungal SM bioactivity to BGCs are urgently needed.IMPORTANCEFungi are key sources of natural products and iconic drugs, including penicillin and statins. DNA sequencing has revealed that there are likely millions of biosynthetic pathways in fungal genomes, but the chemical structures and bioactivities of >99% of natural products produced by these pathways remain unknown. We used artificial intelligence to predict the bioactivities of diverse fungal biosynthetic pathways. We found that the accuracies of our predictions were generally low, between 51% and 68%, likely because the natural products and bioactivities of only very few fungal pathways are known. With >15,000 characterized fungal natural products, millions of putative biosynthetic pathways present in fungal genomes, and increased demand for novel drugs, our study suggests that there is an urgent need for efforts that systematically identify fungal biosynthetic pathways, their natural products, and their bioactivities.
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Affiliation(s)
- Olivia Riedling
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Allison S. Walker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
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5
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Riedling O, Walker AS, Rokas A. Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557468. [PMID: 37745539 PMCID: PMC10515863 DOI: 10.1101/2023.09.12.557468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Fungal secondary metabolites (SMs) play a significant role in the diversity of ecological communities, niches, and lifestyles in the fungal kingdom. Many fungal SMs have medically and industrially important properties including antifungal, antibacterial, and antitumor activity, and a single metabolite can display multiple types of bioactivities. The genes necessary for fungal SM biosynthesis are typically found in a single genomic region forming biosynthetic gene clusters (BGCs). However, whether fungal SM bioactivity can be predicted from specific attributes of genes in BGCs remains an open question. We adapted previously used machine learning models for predicting SM bioactivity from bacterial BGC data to fungal BGC data. We trained our models to predict antibacterial, antifungal, and cytotoxic/antitumor bioactivity on two datasets: 1) fungal BGCs (dataset comprised of 314 BGCs), and 2) fungal (314 BGCs) and bacterial BGCs (1,003 BGCs); the second dataset was our control since a previous study using just the bacterial BGC data yielded prediction accuracies as high as 80%. We found that the models trained only on fungal BGCs had balanced accuracies between 51-68%, whereas training on bacterial and fungal BGCs yielded balanced accuracies between 61-74%. The lower accuracy of the predictions from fungal data likely stems from the small number of BGCs and SMs with known bioactivity; this lack of data currently limits the application of machine learning approaches in studying fungal secondary metabolism. However, our data also suggest that machine learning approaches trained on bacterial and fungal data can predict SM bioactivity with good accuracy. With more than 15,000 characterized fungal SMs, millions of putative BGCs present in fungal genomes, and increased demand for novel drugs, efforts that systematically link fungal SM bioactivity to BGCs are urgently needed.
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Affiliation(s)
- Olivia Riedling
- Department of Biological Science, Vanderbilt University, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Allison S Walker
- Department of Biological Science, Vanderbilt University, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Antonis Rokas
- Department of Biological Science, Vanderbilt University, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
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6
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Peng J, Guo F, Liu S, Fang H, Xu Z, Wang T. Recent Advances and Future Prospects of Mycosporine-like Amino Acids. Molecules 2023; 28:5588. [PMID: 37513460 PMCID: PMC10384724 DOI: 10.3390/molecules28145588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Mycosporine-like amino acids (MAAs) are a class of water-soluble active substances produced by various aquatic organisms. However, due to the limitations of low accumulation of MAAs in organisms, the cumbersome extraction process, difficult identification, and high cost, MAAs have not yet been widely used in human life. Recently, there has been an emergence of heterologous synthesis for MAAs, making increasing yield the key to the quantification and application of MAAs. This review summarizes the latest research progress of MAAs, including: (1) introducing the biodistribution of MAAs and the content differences among different species to provide a reference for the selection of research subjects; (2) elaborating the species and molecular information of MAAs; (3) dissecting the synthesis mechanism and sorting out the synthesis pathways of various MAAs; (4) summarizing the methods of extraction and identification, summarizing the advantages and disadvantages, and providing a reference for the optimization of extraction protocols; (5) examining the heterologous synthesis method; and (6) summarizing the physiological functions of MAAs. This paper comprehensively updates the latest research status of MAAs and the various problems that need to be addressed, especially emphasizing the potential advantages of heterologous synthesis in the future production of MAAs.
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Affiliation(s)
- Jiahui Peng
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Fangyu Guo
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Sishi Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Haiyan Fang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Zhenshang Xu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
| | - Ting Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
- School of Bioengineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, China
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7
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Gasparek M, Steel H, Papachristodoulou A. Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. Biotechnol Adv 2023; 64:108117. [PMID: 36813010 DOI: 10.1016/j.biotechadv.2023.108117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.
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Affiliation(s)
- Miroslav Gasparek
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
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Devkar HU, Thakur NL, Kaur P. Marine-derived antimicrobial molecules from the sponges and their associated bacteria. Can J Microbiol 2023; 69:1-16. [PMID: 36288610 DOI: 10.1139/cjm-2022-0147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Antimicrobial resistance (AMR) is one of the leading global health issues that demand urgent attention. Very soon the world will have to bear the consequences of increased drug resistance if new anti-infectives are not pumped into the clinical pipeline in a short period. This presses on the need for novel chemical entities, and the marine environment is one such hotspot to look for. The Ocean harbours a variety of organisms, of which from this aspect, "Sponges (Phylum Porifera)" are of particular interest. To tackle the stresses faced due to their sessile and filter-feeding lifestyle, sponges produce various bioactive compounds, which can be tapped for human use. The sponges harbour several microorganisms of different types and in most cases; the microbial symbionts are the actual producers of the bioactive compounds. This review describes the alarming need for the development of new antimicrobials and how marine sponges can contribute to this. Selected antimicrobial compounds from the marine sponges and their associated bacteria have been described. Additionally, measures to tackle the supply problem have been covered, which is the primary obstacle in marine natural product drug discovery.
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Affiliation(s)
- Heena U Devkar
- CSIR- National Institute of Oceanography, Dona Paula 403004, Goa, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Narsinh L Thakur
- CSIR- National Institute of Oceanography, Dona Paula 403004, Goa, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Parvinder Kaur
- Foundation for Neglected Disease Research, Bangalore 561203, Karnataka, India
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Taton A, Rohrer S, Diaz B, Reher R, Caraballo Rodriguez AM, Pierce ML, Dorrestein PC, Gerwick L, Gerwick WH, Golden JW. Heterologous Expression in Anabaena of the Columbamide Pathway from the Cyanobacterium Moorena bouillonii and Production of New Analogs. ACS Chem Biol 2022; 17:1910-1923. [DOI: 10.1021/acschembio.2c00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arnaud Taton
- School of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Sebastian Rohrer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
| | - Brienna Diaz
- School of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Raphael Reher
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle (Saale) 06114, Germany
- Institute of Pharmaceutical Biology and Biotechnology, Philipps University of Marburg, Marburg 35037, Germany
| | | | - Marsha L. Pierce
- Department of Pharmacology, Midwestern University, Downers Grove, Illinois 60515, United States
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States
| | - James W. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
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Matsuda S, Tsunematsu Y, Matsushita T, Ogata Y, Hachiya S, Kishimoto S, Miyoshi N, Watanabe K. Toward Engineered Biosynthesis of Drugs in Human Cells. Chembiochem 2021; 23:e202100645. [PMID: 34889017 DOI: 10.1002/cbic.202100645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Indexed: 11/06/2022]
Abstract
Biosynthetic genes are not only responsible for the formation of bioactive substances but also suited for other applications including gene therapy. To test the feasibility of human cells producing antibiotics in situ when provided with a heterologous biosynthetic gene, we focused on cytochrome P450, the class of enzymes important in conferring bioactivity to natural product precursors. We selected Fma-P450 that plays a central role in the fumagillin antimicrobial biosynthesis in Aspergillus fumigatus to examine fungal metabolite production by HeLa cells that express fma-P450 heterologously. Here we show that HeLa cells harboring fma-P450 can biosynthesize 5-hydroxyl-β-trans-bergamoten and cytotoxic 5-epi-demethoxyfumagillol when supplemented with the nontoxic precursor β-trans-bergamotene. While the production level was insufficient to effect cell death, we demonstrate that programming human cells to autogenerate antibiotics by introducing a heterologous biosynthetic gene is feasible.
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Affiliation(s)
- Shinya Matsuda
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Yuta Tsunematsu
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Takuma Matsushita
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Yuji Ogata
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Shihomi Hachiya
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Shinji Kishimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Noriyuki Miyoshi
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan
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11
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Ren CY, Liu Y, Wei WP, Dai J, Ye BC. Reconstruction of Secondary Metabolic Pathway to Synthesize Novel Metabolite in Saccharopolyspora erythraea. Front Bioeng Biotechnol 2021; 9:628569. [PMID: 34277577 PMCID: PMC8283810 DOI: 10.3389/fbioe.2021.628569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/16/2021] [Indexed: 12/31/2022] Open
Abstract
Natural polyketides play important roles in clinical treatment, agriculture, and animal husbandry. Compared to natural hosts, heterologous chassis (especially Actinomycetes) have many advantages in production of polyketide compounds. As a widely studied model Actinomycete, Saccharopolyspora erythraea is an excellent host to produce valuable heterologous polyketide compounds. However, many host factors affect the expression efficiency of heterologous genes, and it is necessary to modify the host to adapt heterologous production. In this study, the CRISPR-Cas9 system was used to knock out the erythromycin biosynthesis gene cluster of Ab (erythromycin high producing stain). A fragment of 49491 bp in genome (from SACE_0715 to SACE_0733) was deleted, generating the recombinant strain AbΔery in which erythromycin synthesis was blocked and synthetic substrates methylmalonyl-CoA and propionyl-CoA accumulated enormously. Based on AbΔery as heterologous host, three genes, AsCHS, RgTAL, and Sc4CL, driven by strong promoters Pj23119, PermE, and PkasO, respectively, were introduced to produce novel polyketide by L-tyrosine and methylmalonyl-CoA. The product (E)-4-hydroxy-6-(4-hydroxystyryl)-3,5-dimethyl-2H-pyrone was identified in fermentation by LC-MS. High performance liquid chromatography analysis showed that knocking out ery BGC resulted in an increase of methylmalonyl-CoA by 142% and propionyl-CoA by 57.9% in AbΔery compared to WT, and the yield of heterologous product in AbΔery:AsCHS-RgTAL-Sc4CL was higher than WT:AsCHS-RgTAL-Sc4CL. In summary, this study showed that AbΔery could potentially serve as a precious heterologous host to boost the synthesis of other valuable polyketone compounds using methylmalonyl-CoA and propionyl-CoA in the future.
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Affiliation(s)
- Chong-Yang Ren
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Yong Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Wen-Ping Wei
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Junbiao Dai
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics and Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bang-Ce Ye
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China.,Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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12
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The Nonribosomal Peptide Valinomycin: From Discovery to Bioactivity and Biosynthesis. Microorganisms 2021; 9:microorganisms9040780. [PMID: 33917912 PMCID: PMC8068249 DOI: 10.3390/microorganisms9040780] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 12/17/2022] Open
Abstract
Valinomycin is a nonribosomal peptide that was discovered from Streptomyces in 1955. Over the past more than six decades, it has received continuous attention due to its special chemical structure and broad biological activities. Although many research papers have been published on valinomycin, there has not yet been a comprehensive review that summarizes the diverse studies ranging from structural characterization, biogenesis, and bioactivity to the identification of biosynthetic gene clusters and heterologous biosynthesis. In this review, we aim to provide an overview of valinomycin to address this gap, covering from 1955 to 2020. First, we introduce the chemical structure of valinomycin together with its chemical properties. Then, we summarize the broad spectrum of bioactivities of valinomycin. Finally, we describe the valinomycin biosynthetic gene cluster and reconstituted biosynthesis of valinomycin. With that, we discuss possible opportunities for the future research and development of valinomycin.
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13
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Gao EB, Kyere-Yeboah K, Wu J, Qiu H. Photoautotrophic production of p-Coumaric acid using genetically engineered Synechocystis sp. Pasteur Culture Collection 6803. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102180] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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14
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Atanasov AG, Zotchev SB, Dirsch VM, Supuran CT. Natural products in drug discovery: advances and opportunities. Nat Rev Drug Discov 2021; 20:200-216. [PMID: 33510482 PMCID: PMC7841765 DOI: 10.1038/s41573-020-00114-z] [Citation(s) in RCA: 1879] [Impact Index Per Article: 626.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 02/07/2023]
Abstract
Natural products and their structural analogues have historically made a major contribution to pharmacotherapy, especially for cancer and infectious diseases. Nevertheless, natural products also present challenges for drug discovery, such as technical barriers to screening, isolation, characterization and optimization, which contributed to a decline in their pursuit by the pharmaceutical industry from the 1990s onwards. In recent years, several technological and scientific developments - including improved analytical tools, genome mining and engineering strategies, and microbial culturing advances - are addressing such challenges and opening up new opportunities. Consequently, interest in natural products as drug leads is being revitalized, particularly for tackling antimicrobial resistance. Here, we summarize recent technological developments that are enabling natural product-based drug discovery, highlight selected applications and discuss key opportunities.
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Affiliation(s)
- Atanas G Atanasov
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzebiec, Poland.
- Department of Pharmacognosy, University of Vienna, Vienna, Austria.
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria.
| | - Sergey B Zotchev
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Verena M Dirsch
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Claudiu T Supuran
- Università degli Studi di Firenze, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche, Florence, Italy.
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15
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Swayambhu G, Bruno M, Gulick AM, Pfeifer BA. Siderophore natural products as pharmaceutical agents. Curr Opin Biotechnol 2021; 69:242-251. [PMID: 33640597 DOI: 10.1016/j.copbio.2021.01.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/09/2021] [Accepted: 01/25/2021] [Indexed: 11/27/2022]
Abstract
Siderophore natural products are characterized by an ability to tightly chelate metals. The origins of such compounds are often pathogenic microbes utilizing siderophores as virulence factors during host infection. The mechanism for siderophore formation typically involves the activity of nonribosomal peptide synthetases producing compounds across functional group classifications that include catecholate, phenolate, hydroxamate, and mixed categories. Though siderophore production has been a hallmark of pathogenicity, the evolutionarily-optimized binding abilities of siderophores suggest the possibility of re-directing the compounds towards alternative beneficial applications. In this mini-review, we will first describe siderophore formation origins before discussing alternative applications as pharmaceutical products. In so doing, we will cover examples and applications that include reducing metal overload, targeted antibiotic delivery, cancer treatment, vaccine development, and diagnostics. Included in this analysis will be a discussion on the native production hosts of siderophores and prospects for improvement in compound access through the adoption of heterologous biosynthesis.
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Affiliation(s)
- Girish Swayambhu
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Michael Bruno
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Andrew M Gulick
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, United States.
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16
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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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17
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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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18
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Qi R, Swayambhu G, Bruno M, Zhang G, Pfeifer BA. Consolidated plasmid Design for Stabilized Heterologous Production of the complex natural product Siderophore Yersiniabactin. Biotechnol Prog 2020; 37:e3103. [PMID: 33190425 DOI: 10.1002/btpr.3103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 10/24/2020] [Accepted: 11/11/2020] [Indexed: 11/09/2022]
Abstract
Yersiniabactin (Ybt) is a hybrid polyketide-nonribosomal complex natural product also known as a siderophore for its iron chelation properties. The native producer of Ybt, Yersinia pestis, is a priority pathogen responsible for the plague in which the siderophore properties of Ybt are used to sequester iron and other metal species upon host infection. Alternatively, the high metal binding properties of Ybt enable a plethora of potentially valuable applications benefiting from metal remediation and/or recovery. For these applications, a surrogate production source is highly preferred relative to the pathogenic native host. In this work, we present a modification to the heterologous Escherichia coli production system established for Ybt biosynthesis. In particular, the multiple plasmids originally used to express the genetic pathway required for Ybt biosynthesis were consolidated to a single, copy-amplifiable plasmid. In so doing, plasmid stability was improved from ~30% to ≥80% while production values maintained at 20-30% of the original system, which resulted in titers of 0.5-3 mg/L from shake flask vessels.
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Affiliation(s)
- Ruiquan Qi
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, New York, USA
| | - Girish Swayambhu
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, New York, USA
| | - Michael Bruno
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, New York, USA
| | - Guojian Zhang
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, New York, USA.,Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, New York, USA.,Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, People's Republic of China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China
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19
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Kumar G, Shankar R. 2-Isoxazolines: A Synthetic and Medicinal Overview. ChemMedChem 2020; 16:430-447. [PMID: 33029886 DOI: 10.1002/cmdc.202000575] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/26/2020] [Indexed: 02/03/2023]
Abstract
Isoxazolines are nitrogen- and oxygen-containing five-membered heterocyclic scaffolds with extensive biological activities. This framework can be readily obtained in good to excellent yields through 1,3-dipolar cycloaddition between nitrones with alkynes or allenes, aryl/alkyl halides, alkynes, and oxaziridines under mild conditions. This scaffold has been an emerging area of interest for many researchers given their wide range of bioactivities. Herein we review synthetic strategies toward isoxazolines and the role these efforts have had in enhancing the biological activity of natural products and synthetic compounds such as antitubercular agents, COX-1 inhibitors, COX-2 inhibitors (e. g., valdecoxib), nicotinic receptor modulators, and MIF inhibitors. With a focus on efforts from 2010 onward, this review provides in-depth coverage of the design and biological evaluation of isoxazoline systems and their impact on various pathologies.
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Affiliation(s)
- Gulshan Kumar
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Jammu Campus, Jammu, 180001, India.,Bio-organic Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu Campus, Jammu, 180001, India
| | - Ravi Shankar
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Jammu Campus, Jammu, 180001, India.,Bio-organic Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu Campus, Jammu, 180001, India
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20
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Liu R, Yu D, Deng Z, Liu T. Harnessing in vitro platforms for natural product research: in vitro driven rational engineering and mining (iDREAM). Curr Opin Biotechnol 2020; 69:1-9. [PMID: 33027693 DOI: 10.1016/j.copbio.2020.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 01/15/2023]
Abstract
Well-known issues amid in vivo research of natural product discovery and overproduction, such as unculturable or unmanipulable microorganisms, labor-intensive experimental cycles, and hidden rate-limiting steps, have hampered relevant investigations. To overcome these long-standing challenges, many researchers are turning toward in vitro platforms, which bypass the complicated cellular machinery and simplify the study of natural products. Here, we summarize the in vitro driven rational engineering and mining (iDREAM) strategy, which harnesses the flexibility and controllability of in vitro systems to rationally overproduce commodity chemicals and efficiently mine novel compounds. The iDREAM strategy promises to make further significant contributions toward both fundamental advances and industrial practices.
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Affiliation(s)
- Ran Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, PR China
| | - Dingchen Yu
- College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, PR China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, PR China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, PR China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, PR China.
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21
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Gonzalez-Garcia RA, Nielsen LK, Marcellin E. Heterologous Production of 6-Deoxyerythronolide B in Escherichia coli through the Wood Werkman Cycle. Metabolites 2020; 10:metabo10060228. [PMID: 32492827 PMCID: PMC7344785 DOI: 10.3390/metabo10060228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 11/29/2022] Open
Abstract
Polyketides are a remarkable class of natural products with diverse functional and structural diversity. The class includes many medicinally important molecules with antiviral, antimicrobial, antifungal and anticancer properties. Native bacterial, fungal and plant hosts are often difficult to cultivate and coax into producing the desired product. As a result, Escherichia coli has been used for the heterologous production of polyketides, with the production of 6-deoxyerythronolide B (6-dEB) being the first example. Current strategies for production in E. coli require feeding of exogenous propionate as a source for the precursors propionyl-CoA and S-methylmalonyl-CoA. Here, we show that heterologous polyketide production is possible from glucose as the sole carbon source. The heterologous expression of eight genes from the Wood-Werkman cycle found in Propionibacteria, in combination with expression of the 6-dEB synthases DEBS1, DEBS2 and DEBS3 resulted in 6-dEB formation from glucose as the sole carbon source. Our results show that the Wood-Werkman cycle provides the required propionyl-CoA and the extender unit S-methylmalonyl-CoA to produce up to 0.81 mg/L of 6-dEB in a chemically defined media.
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Affiliation(s)
- R. Axayacatl Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane QLD 4072, Australia; (R.A.G.-G.); (L.K.N.)
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane QLD 4072, Australia; (R.A.G.-G.); (L.K.N.)
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
- Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane QLD 4072, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane QLD 4072, Australia; (R.A.G.-G.); (L.K.N.)
- Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane QLD 4072, Australia
- Correspondence: ; Tel.: +61-7-334-64298; Fax: +61-7-3346-3973
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22
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Liu X, Hua K, Liu D, Wu ZL, Wang Y, Zhang H, Deng Z, Pfeifer BA, Jiang M. Heterologous Biosynthesis of Type II Polyketide Products Using E. coli. ACS Chem Biol 2020; 15:1177-1183. [PMID: 31825590 DOI: 10.1021/acschembio.9b00827] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The heterologous biosynthesis of complex natural products has enabled access to polyketide, nonribosomal peptide, isoprenoid, and other compounds with wide-spanning societal value. Though several surrogate host systems exist, Escherichia coli is often a preferred choice due to its rapid growth kinetics and extensive molecular biology protocols. However, a persistent challenge to the utilization of E. coli has been the successful in vivo reconstitution of type II polyketide synthase (PKS) systems. In particular, gene expression of the ketosynthase (KS) components of the minimal PKS has consistently yielded insoluble protein products. In the following report, two type II PKS systems were functionally reconstituted in E. coli. The approach to do so relied upon the utilization of the native transcriptional coupling between the dimeric KS subunits, leading to soluble recombinant protein products and successful polyketide biosynthesis. Resulting strains produced 10 mg/L TW95c and 25 mg/L dehydrorabelomycin. Hence, the strategy offers a new option in the biosynthetic engineering efforts for the heterologous production of type II polyketide products using E. coli.
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Affiliation(s)
- Xiangyang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, People’s Republic of China
| | - Kangmin Hua
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, People’s Republic of China
| | - Dongxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, People’s Republic of China
| | - Zhen-Long Wu
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Ying Wang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Haoran Zhang
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, People’s Republic of China
| | - Blaine A. Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14214, United States
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, People’s Republic of China
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23
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Swayambhu G, Moscatello N, Atilla-Gokcumen GE, Pfeifer BA. Flux Balance Analysis for Media Optimization and Genetic Targets to Improve Heterologous Siderophore Production. iScience 2020; 23:101016. [PMID: 32279062 PMCID: PMC7152677 DOI: 10.1016/j.isci.2020.101016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/15/2019] [Accepted: 03/23/2020] [Indexed: 01/02/2023] Open
Abstract
Siderophores are small molecule metal chelators secreted in sparse quantities by their native microbial hosts but can be engineered for enhanced production from heterologous hosts like Escherichia coli. These molecules have been proved to be capable of binding heavy metals of commercial and/or environmental interest. In this work, we incorporated, as needed, the appropriate pathways required to produce several siderophores (anguibactin, vibriobactin, bacillibactin, pyoverdine, and enterobactin) into the base E. coli K-12 MG1655 metabolic network model to computationally predict, via flux balance analysis methodologies, gene knockout targets, gene over-expression targets, and media modifications capable of improving siderophore reaction flux. E. coli metabolism proved supportive for the underlying production mechanisms of various siderophores. Within such a framework, the gene deletion and over-expression targets identified, coupled with complementary insights from medium optimization predictions, portend experimental implementation to both enable and improve heterologous siderophore production. Successful production of siderophores would then spur novel metal-binding applications.
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Affiliation(s)
- Girish Swayambhu
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Nicholas Moscatello
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - G Ekin Atilla-Gokcumen
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA.
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24
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Markina NM, Kotlobay AA, Tsarkova AS. Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts. Acta Naturae 2020; 12:28-39. [PMID: 32742725 PMCID: PMC7385092 DOI: 10.32607/actanaturae.10966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022] Open
Abstract
Heterologous pathways are linked series of biochemical reactions occurring in a host organism after the introduction of foreign genes. Incorporation of metabolic pathways into host organisms is a major strategy used to increase the production of valuable secondary metabolites. Unfortunately, simple introduction of the pathway genes into the heterologous host in most cases does not result in successful heterologous expression. Extensive modification of heterologous genes and the corresponding enzymes on many different levels is required to achieve high target metabolite production rates. This review summarizes the essential techniques used to create heterologous biochemical pathways, with a focus on the key challenges arising in the process and the major strategies for overcoming them.
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Affiliation(s)
- N. M. Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Planta LLC, Moscow, 121205 Russia
| | - A. A. Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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25
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Zhuang L, Huang S, Liu WQ, Karim AS, Jewett MC, Li J. Total in vitro biosynthesis of the nonribosomal macrolactone peptide valinomycin. Metab Eng 2020; 60:37-44. [PMID: 32224263 DOI: 10.1016/j.ymben.2020.03.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/20/2020] [Accepted: 03/22/2020] [Indexed: 11/16/2022]
Abstract
Natural products are important because of their significant pharmaceutical properties such as antiviral, antimicrobial, and anticancer activity. Recent breakthroughs in DNA sequencing reveal that a great number of cryptic natural product biosynthetic gene clusters are encoded in microbial genomes, for example, those of Streptomyces species. However, it is still challenging to access compounds from these clusters because many source organisms are uncultivable or the genes are silent during laboratory cultivation. To address this challenge, we develop an efficient cell-free platform for the rapid, in vitro total biosynthesis of the nonribosomal peptide valinomycin as a model. We achieve this goal in two ways. First, we used a cell-free protein synthesis (CFPS) system to express the entire valinomycin biosynthetic gene cluster (>19 kb) in a single-pot reaction, giving rise to approximately 37 μg/L of valinomycin after optimization. Second, we coupled CFPS with cell-free metabolic engineering system by mixing two enzyme-enriched cell lysates to perform a two-stage biosynthesis. This strategy improved valinomycin production ~5000-fold to nearly 30 mg/L. We expect that cell-free biosynthetic systems will provide a new avenue to express, discover, and characterize natural product gene clusters of interest in vitro.
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Affiliation(s)
- Lei Zhuang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shuhui Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, United States.
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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26
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Andrographolide: Chemical modification and its effect on biological activities. Bioorg Chem 2020; 95:103511. [DOI: 10.1016/j.bioorg.2019.103511] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/28/2019] [Accepted: 12/16/2019] [Indexed: 01/31/2023]
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27
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Vassaux A, Meunier L, Vandenbol M, Baurain D, Fickers P, Jacques P, Leclère V. Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnol Adv 2019; 37:107449. [PMID: 31518630 DOI: 10.1016/j.biotechadv.2019.107449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.
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Affiliation(s)
- Antoine Vassaux
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France
| | - Loïc Meunier
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Micheline Vandenbol
- TERRA Teaching and Research Centre, Microbiologie et Génomique, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France.
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Liang X, Luo D, Luesch H. Advances in exploring the therapeutic potential of marine natural products. Pharmacol Res 2019; 147:104373. [PMID: 31351913 PMCID: PMC6839689 DOI: 10.1016/j.phrs.2019.104373] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/26/2022]
Abstract
Marine natural products represent novel and diverse chemotypes that serve as templates for the discovery and development of therapeutic agents with distinct mechanisms of action. These genetically encoded compounds produced by an evolutionary optimized biosynthetic machinery are usually quite complex and can be difficult to recreate in the laboratory. The isolation from the source organism results in limited amount of material; however, the development of advanced NMR technologies and dereplication strategies has enabled the structure elucidation on small scale. In order to rigorously explore the therapeutic potential of marine natural products and advance them further, the biological characterization has to keep pace with the chemical characterization. The limited marine natural product supply has been a serious challenge for thorough investigation of the biological targets. Several marine drugs have reached the markets or are in clinical trials, where those challenges have been overcome, including through the development of scalable syntheses. However, the identification of mechanisms of action of marine natural products early in the discovery process is potentially game changing, since effectively linking marine natural products to potential therapeutic applications in turn triggers motivation to tackle challenging syntheses and solve the supply problem. An increasing number of sensitive technologies and methods have been developed in recent years, some of which have been successfully applied to marine natural products, increasing the value of these compounds with respect to their biomedical utility. In this review, we discuss advances in overcoming the bottlenecks in marine natural product research, emphasizing on the development and advances of diverse target identification technologies applicable for marine natural product research.
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Affiliation(s)
- Xiao Liang
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States
| | - Danmeng Luo
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States.
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29
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Marine Biosurfactants: Biosynthesis, Structural Diversity and Biotechnological Applications. Mar Drugs 2019; 17:md17070408. [PMID: 31323998 PMCID: PMC6669457 DOI: 10.3390/md17070408] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/16/2022] Open
Abstract
Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.
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30
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Yu L, Wu F, Chen G. Next‐Generation Industrial Biotechnology‐Transforming the Current Industrial Biotechnology into Competitive Processes. Biotechnol J 2019; 14:e1800437. [DOI: 10.1002/biot.201800437] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/01/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Lin‐Ping Yu
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
| | - Fu‐Qing Wu
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
| | - Guo‐Qiang Chen
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Manchester Institute of Biotechnology, Centre for Synthetic BiologyThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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31
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019. [DOI: 10.1039/c8np00091c [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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32
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Liu WQ, Zhang L, Chen M, Li J. Cell-free protein synthesis: Recent advances in bacterial extract sources and expanded applications. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.10.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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33
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Huo L, Hug JJ, Fu C, Bian X, Zhang Y, Müller R. Heterologous expression of bacterial natural product biosynthetic pathways. Nat Prod Rep 2019; 36:1412-1436. [DOI: 10.1039/c8np00091c] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The review highlights the 2013–2018 literature on the heterologous expression of bacterial natural product biosynthetic pathways and emphasises new techniques, heterologous hosts, and novel chemistry.
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Affiliation(s)
- Liujie Huo
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Joachim J. Hug
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Chengzhang Fu
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
| | - Xiaoying Bian
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Youming Zhang
- Helmholtz International Laboratory
- State Key Laboratory of Microbial Technology
- Shandong University
- Qingdao 266237
- P. R. China
| | - Rolf Müller
- Helmholtz International Laboratory
- Department of Microbial Natural Products (MINS)
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
- Helmholtz Centre for Infection Research (HZI)
- 66123 Saarbrücken
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34
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Zhang R, Li C, Wang J, Yang Y, Yan Y. Microbial production of small medicinal molecules and biologics: From nature to synthetic pathways. Biotechnol Adv 2018; 36:2219-2231. [DOI: 10.1016/j.biotechadv.2018.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/02/2018] [Accepted: 10/15/2018] [Indexed: 01/07/2023]
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35
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Advances in heterologous biosynthesis of plant and fungal natural products by modular co-culture engineering. Biotechnol Lett 2018; 41:27-34. [DOI: 10.1007/s10529-018-2619-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/27/2018] [Indexed: 12/18/2022]
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36
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Tu HF, Zhang X, Zheng C, Zhu M, You SL. Enantioselective dearomative prenylation of indole derivatives. Nat Catal 2018. [DOI: 10.1038/s41929-018-0111-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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37
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Cobalamin-Dependent C-Methyltransferases From Marine Microbes: Accessibility via Rhizobia Expression. Methods Enzymol 2018. [PMID: 29779655 DOI: 10.1016/bs.mie.2018.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cobalamin-dependent radical S-adenosylmethionine (rSAM) methyltransferases catalyze chemically challenging methylation reactions on diverse natural products at unactivated carbon centers. In vivo reconstitution and biosynthetic studies of natural product gene clusters encoding these enzymes are often severely limited by ineffective heterologous expression hosts, including the otherwise versatile Escherichia coli. In this chapter, we describe the use of rhizobia bacteria as effective expression hosts for cobalamin-dependent rSAM C-methyltransferases. We chose the natural product pathway encoding the heavily modified cytotoxic peptides, the polytheonamides, as our model pathway due to the presence of two methyltransferases responsible for a total of 17 C-methylations. Detailed protocols are given for vector construction, transformation, and heterologous expression in Rhizobium leguminosarum bv. viciae 3841. Additional methods pertaining to analytical separation and mass spectrometric analysis of modified peptides are also entailed. As genomics continues to uncover new enzymes and pathways from unknown and uncultivated microbes, use of metabolically distinct heterologous expression hosts like rhizobia will be a necessary tool to unravel the catalytic and metabolic diversity of marine microbial life.
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38
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He Y, Wang B, Chen W, Cox RJ, He J, Chen F. Recent advances in reconstructing microbial secondary metabolites biosynthesis in Aspergillus spp. Biotechnol Adv 2018; 36:739-783. [DOI: 10.1016/j.biotechadv.2018.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/28/2022]
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39
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Cell-free synthetic biology for in vitro biosynthesis of pharmaceutical natural products. Synth Syst Biotechnol 2018; 3:83-89. [PMID: 29900420 PMCID: PMC5995452 DOI: 10.1016/j.synbio.2018.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/29/2018] [Accepted: 02/08/2018] [Indexed: 01/26/2023] Open
Abstract
Natural products with significant biological activities continuously act as rich sources for drug discovery and development. To harness the potential of these valuable compounds, robust methods need to be developed for their rapid and sustainable production. Cell-free biosynthesis of pharmaceutical natural products by in vitro reconstruction of the entire biosynthetic pathways represents one such solution. In this review, we focus on in vitro biosynthesis of two important classes of natural products, polyketides (PKs) and nonribosomal peptides (NRPs). First, we summarize purified enzyme-based systems for the biosynthesis of PKs, NRPs, and PK/NRP hybrids. Then, we introduce the cell-free protein synthesis (CFPS)-based technology for natural product production. With that, we discuss challenges and opportunities of cell-free synthetic biology for in vitro biosynthesis of natural products.
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40
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Yang G, Cozad MA, Holland DA, Zhang Y, Luesch H, Ding Y. Photosynthetic Production of Sunscreen Shinorine Using an Engineered Cyanobacterium. ACS Synth Biol 2018; 7:664-671. [PMID: 29304277 DOI: 10.1021/acssynbio.7b00397] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycosporine-like amino acids (MAAs) are secondary metabolites of a variety of marine organisms including cyanobacteria and macroalgae. These compounds have strong ultraviolet (UV) absorption maxima between 310 and 362 nm and are biological sunscreens for counteracting the damaging effects of UV radiation in nature. The common MAA shinorine has been used as one key active ingredient of environmentally friendly sunscreen creams. Commercially used shinorine is isolated from one red algae that is generally harvested from the wild. Here, we describe the use of Synechocystis sp. PCC6803 as a host for the heterologous production of shinorine. We mined a shinorine gene cluster from the filamentous cyanobacterium Fischerella sp. PCC9339. When expressing the cluster in Synechocystis sp. PCC6803, we observed the production of shinorine using LC-MS analysis, but its productivity was three times lower than the native producer. Integrated transcriptional and metabolic profiling identified rate-limiting steps in the heterologous production of shinorine. The use of multiple promoters led to a 10-fold increase of its yield to 2.37 ± 0.21 mg/g dry biomass weight, comparable to commercially used shinorine producer. The UV protection of shinorine was further confirmed using the engineered Synechocystis sp. PCC6803. This work was the first time to demonstrate the photosynthetic overproduction of MAA. The results suggest that Synechocystis sp. PCC6803 can have broad applications as the synthetic biology chassis to produce other cyanobacterial natural products, expediting the translation of genomes into chemicals.
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Affiliation(s)
- Guang Yang
- Department of Medicinal Chemistry
and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Monica A. Cozad
- Department of Medicinal Chemistry
and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Destin A. Holland
- Department of Medicinal Chemistry
and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Yi Zhang
- Department of Medicinal Chemistry
and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry
and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Yousong Ding
- Department of Medicinal Chemistry
and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
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41
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He J, Melançon CE. Genetic Incorporation of Unnatural Amino Acids into Proteins of Interest in Streptomyces venezuelae ATCC 15439. Methods Mol Biol 2018; 1728:155-168. [PMID: 29404997 DOI: 10.1007/978-1-4939-7574-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Site-specific, genetic incorporation of unnatural amino acids (UAAs) into proteins in living cells using engineered orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs is a powerful tool for studying and manipulating protein structure and function. To date, UAA incorporation systems have been developed for several bacterial and eukaryotic model hosts. Due to the importance of Streptomyces as prolific producers of bioactive natural products and as model hosts for natural product biosynthesis and bioengineering studies, we have developed systems for the incorporation of the UAAs p-iodo-L-phenylalanine (pIPhe) and p-azido-L-phenylalanine (pAzPhe) into green fluorescent protein (GFP) in Streptomyces venezuelae ATCC 15439. Here, we describe the procedure for using this system to site-specifically incorporate pIPhe or pAzPhe into proteins of interest in S. venezuelae. The modular design of plasmids harboring UAA incorporation systems enables use of other aaRS or aaRS/tRNA pairs for the incorporation of other UAAs; and the vector backbone used allows the system to be transferred to diverse Streptomyces species via both protoplast transformation and conjugation.
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Affiliation(s)
- Jingxuan He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA
| | - Charles E Melançon
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA.
- Department of Biology, Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, USA.
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42
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Hu L, Liu Y, Wang Y, Wang Z, Huang J, Xue Y, Liu J, Liu Z, Chen Y, Zhang Y. Discovery of acylphloroglucinol-based meroterpenoid enantiomers as KSHV inhibitors from Hypericum japonicum. RSC Adv 2018; 8:24101-24109. [PMID: 35539193 PMCID: PMC9081833 DOI: 10.1039/c8ra04073g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 06/26/2018] [Indexed: 11/28/2022] Open
Abstract
Kaposi's sarcoma associated herpesvirus (KSHV) has gained considerable attention as a type of carcinogenic pathogen. Recent research suggests that KSHV has participated in the pathogenesis of Kaposi's sarcoma-related malignant neoplastic diseases. Viral lytic infection might be pivotal for the etiopathogenesis of KSHV-induced diseases; however, most clinical KSHV lytic replication inhibitors like ganciclovir, nelfinavir, or cidofovir do not restrain virus replication effectively enough to achieve clinical efficacy. In our continued pharmaceutical studies on Chinese herbal medicines, new acylphloroglucinol-based meroterpenoid enantiomers have been discovered from Hypericum japonicum. Most of these metabolites have potential inhibitory activities that target KSHV lytic replication. Amongst these analogues, compounds 1a and 1b possess an unreported ring system cyclopenta[b]chromene. Compounds 1a with 4a exhibit stronger inhibitory activities towards the lytic replication of KSHV in Vero cells. In addition, 1a and 4a have IC50 values of 8.30 and 4.90 μM and selectivity indexes of 23.49 and 25.70, respectively. Qualitative and quantitative SAR and molecular docking studies for acylphloroglucinol-based meroterpenoids with regard to anti-KSHV activity were conducted. An explanation for the variation in the activity and selectivity indexes was proposed in accordance with the predicted binding pose found with molecular docking to a putative target, thymidylate synthase (kTS). Compounds 1a and 4a have potential for further development and optimization of their anti-KSHV activities which could lead to new candidate drugs. New enantiomers (1a/1b–4a/4b) were discovered from Hypericum japonicum. 1a/1b possessed a novel ring system cyclopenta[b]chromene. 1a and 4a exhibited promising anti-KSHV activities. QSAR studies for enantiomers on anti-KSHV activity were conducted.![]()
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43
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Fang L, Guell M, Church GM, Pfeifer BA. Heterologous erythromycin production across strain and plasmid construction. Biotechnol Prog 2017; 34:271-276. [PMID: 28960932 DOI: 10.1002/btpr.2567] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/25/2017] [Indexed: 02/04/2023]
Abstract
The establishment of erythromycin production within the heterologous host E. coli marked an accomplishment in genetic transfer capacity. Namely, over 20 genes and 50 kb of DNA was introduced to E. coli for successful heterologous biosynthetic reconstitution. However, the prospect for production levels that approach those of the native host requires the application of engineering tools associated with E. coli. In this report, metabolic and genomic engineering were implemented to improve the E. coli cellular background and the plasmid platform supporting heterologous erythromycin formation. Results include improved plasmid stability and metabolic support for biosynthetic product formation. Specifically, the new plasmid design for erythromycin formation allowed for ≥89% stability relative to current standards (20% stability). In addition, the new strain (termed LF01) designed to improve carbon flow to the erythromycin biosynthetic pathway provided a 400% improvement in titer level. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:271-276, 2018.
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Affiliation(s)
- Lei Fang
- Dept. of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY
| | - Marc Guell
- Dept. of Genetics and Biological and Biomedical Sciences Program, Harvard Medical School, Boston, Massachusetts and Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA
| | - George M Church
- Dept. of Genetics and Biological and Biomedical Sciences Program, Harvard Medical School, Boston, Massachusetts and Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA
| | - Blaine A Pfeifer
- Dept. of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY
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44
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Liu T, Mazmouz R, Ongley SE, Chau R, Pickford R, Woodhouse JN, Neilan BA. Directing the Heterologous Production of Specific Cyanobacterial Toxin Variants. ACS Chem Biol 2017; 12:2021-2029. [PMID: 28570054 DOI: 10.1021/acschembio.7b00181] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microcystins are globally the most commonly occurring freshwater cyanotoxins, causing acute poisoning and chronically inducing hepatocellular carcinoma. However, the detection and toxicological study of microcystins is hampered by the limited availability and high cost of pure toxin standards. Biosynthesis of microcystin variants in a fast-growing heterologous host offers a promising method of achieving reliable and economically viable alternative to isolating toxin from slow-growing cyanobacterial cultures. Here, we report the heterologous expression of recombinant microcystin synthetases in Escherichia coli to produce [d-Asp3]microcystin-LR and microcystin-LR. We assembled a 55 kb hybrid polyketide synthase/nonribosomal peptide synthetase gene cluster from Microcystis aeruginosa PCC 7806 using Red/ET recombineering and replaced the native promoters with an inducible PtetO promoter to yield microcystin titers superior to M. aeruginosa. The expression platform described herein can be tailored to heterologously produce a wide variety of microcystin variants, and potentially other cyanobacterial natural products of commercial relevance.
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Affiliation(s)
- Tianzhe Liu
- School
of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales 2052, Sydney, Australia
| | - Rabia Mazmouz
- School
of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales 2052, Sydney, Australia
- School
of Environmental and Life Sciences, The University of Newcastle, New
South Wales 2308, Callaghan, Australia
| | - Sarah E. Ongley
- School
of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales 2052, Sydney, Australia
- School
of Environmental and Life Sciences, The University of Newcastle, New
South Wales 2308, Callaghan, Australia
| | - Rocky Chau
- School
of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales 2052, Sydney, Australia
| | - Russell Pickford
- Bioanalytical
Mass Spectrometry Facility, The University of New South Wales, New
South Wales 2052, Sydney, Australia
| | - Jason N. Woodhouse
- School
of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales 2052, Sydney, Australia
- Leibniz
Institute of Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, 12587, Berlin, Germany
| | - Brett A. Neilan
- School
of Biotechnology and Biomolecular Sciences, The University of New South Wales, New South Wales 2052, Sydney, Australia
- School
of Environmental and Life Sciences, The University of Newcastle, New
South Wales 2308, Callaghan, Australia
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45
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Moscatello N, Qi R, Ahmadi MK, Pfeifer BA. Increased production of yersiniabactin and an anthranilate analog through media optimization. Biotechnol Prog 2017; 33:1193-1200. [DOI: 10.1002/btpr.2496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/21/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Nicholas Moscatello
- Dept. of Chemical and Biological Engineering; University at Buffalo, The State University of New York; Buffalo 14260 NY
| | - Ruiquan Qi
- Dept. of Chemical and Biological Engineering; University at Buffalo, The State University of New York; Buffalo 14260 NY
| | - Mahmoud Kamal Ahmadi
- Dept. of Chemical and Biological Engineering; University at Buffalo, The State University of New York; Buffalo 14260 NY
| | - Blaine A. Pfeifer
- Dept. of Chemical and Biological Engineering; University at Buffalo, The State University of New York; Buffalo 14260 NY
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Covington BC, McLean JA, Bachmann BO. Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites. Nat Prod Rep 2017; 34:6-24. [PMID: 27604382 PMCID: PMC5214543 DOI: 10.1039/c6np00048g] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
| | - John A McLean
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA. and Center for Innovative Technology, Vanderbilt University, 5401 Stevenson Center, Nashville, TN 37235, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
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47
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Recent progress in therapeutic natural product biosynthesis using Escherichia coli. Curr Opin Biotechnol 2016; 42:7-12. [DOI: 10.1016/j.copbio.2016.02.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 01/29/2023]
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Affiliation(s)
- Silke C. Wenzel
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
| | - Rolf Müller
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
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49
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Ahmadi MK, Fang L, Moscatello N, Pfeifer BA. E. coli metabolic engineering for gram scale production of a plant-based anti-inflammatory agent. Metab Eng 2016; 38:382-388. [DOI: 10.1016/j.ymben.2016.10.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/13/2016] [Accepted: 10/03/2016] [Indexed: 02/08/2023]
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50
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Ahmadi MK, Pfeifer BA. Improved heterologous production of the nonribosomal peptide‐polyketide siderophore yersiniabactin through metabolic engineering and induction optimization. Biotechnol Prog 2016; 32:1412-1417. [DOI: 10.1002/btpr.2369] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/13/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Mahmoud Kamal Ahmadi
- Dept. of Chemical and Biological EngineeringUniversity at Buffalo, The State University of New YorkBuffalo NY
| | - Blaine A. Pfeifer
- Dept. of Chemical and Biological EngineeringUniversity at Buffalo, The State University of New YorkBuffalo NY
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