1
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Liu J, Wang M, Tao Z, He L, Guo C, Liu B, Zhang Z. Photo-assisted Zn-air battery-driven self-powered aptasensor based on the 2D/2D Schottky heterojunction of cadmium-doped molybdenum disulfide and Ti 3C 2T x nanosheets for the sensitive detection of penicillin G. Anal Chim Acta 2023; 1270:341396. [PMID: 37311607 DOI: 10.1016/j.aca.2023.341396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 06/15/2023]
Abstract
A novel photocatalyzed Zn-air battery-driven (ZAB)-based aptasensor has been manufactured using the two dimensional (2D)/2D Schottky heterojunction as photocathode and Zn plate as photoanode. It was then employed to sensitively and selectively detect penicillin G (PG) in the complex environment. The 2D/2D Schottky heterojunction was established by the in situ growth of cadmium-doped molybdenum disulfide nanosheets (Cd-MoS2 NSs) around Ti3C2Tx NSs (denoted as Cd-MoS2@Ti3C2Tx) by using phosphomolybdic acid (PMo12) as precursor, thioacetamide as sulfur source, and Cd(NO3)2 as a doping agent through the hydrothermal method. The gained Cd-MoS2@Ti3C2Tx heterojunction possessed contact interface, hierarchical structure, and plenty of sulfur and oxygen vacancies, thus showing the enhanced separation ability of photocarriers and electron transfer. Due to the enhanced UV-vis light adsorption ability, high photoelectric conversion efficiency, and exposed catalytic active sites, the constructed photocatalyzed ZAB displayed a boosted output voltage of 1.43 V under UV-vis light irradiation. The developed ZAB-driven self-powered aptasensor demonstrated an ultralow detection limit of 0.06 fg mL-1 within a PG concentration ranged from 1.0 fg mL-1 to 0.1 ng mL-1, as deduced from the power density-current curves, along with high specificity, good stability and promising reproducibility, as well as excellent regeneration ability and wide applicability. The present work provided an alternative analysis method for the sensitive analysis of antibiotics based on the portable photocatalyzed ZAB-driven self-powered aptasensor.
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Affiliation(s)
- Jiameng Liu
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, 2001 Century Avenue, Jiaozuo, 454000, PR China
| | - Mengfei Wang
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, PR China
| | - Zheng Tao
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, PR China
| | - Linghao He
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, PR China
| | - Chuanpan Guo
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, PR China
| | - Baozhong Liu
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, 2001 Century Avenue, Jiaozuo, 454000, PR China.
| | - Zhihong Zhang
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, PR China.
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2
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Wilson J, Cui J, Nakao T, Kwok H, Zhang Y, Kayrouz CM, Pham TM, Roodhouse H, Ju KS. Discovery of Antimicrobial Phosphonopeptide Natural Products from Bacillus velezensis by Genome Mining. Appl Environ Microbiol 2023; 89:e0033823. [PMID: 37377428 PMCID: PMC10304907 DOI: 10.1128/aem.00338-23] [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: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 06/29/2023] Open
Abstract
Phosphonate natural products are renowned for inhibitory activities which underly their development as antibiotics and pesticides. Although most phosphonate natural products have been isolated from Streptomyces, bioinformatic surveys suggest that many other bacterial genera are replete with similar biosynthetic potential. While mining actinobacterial genomes, we encountered a contaminated Mycobacteroides data set which included a biosynthetic gene cluster predicted to produce novel phosphonate compounds. Sequence deconvolution revealed that the contig containing this cluster, as well as many others, belonged to a contaminating Bacillus and is broadly conserved among multiple species, including the epiphyte Bacillus velezensis. Isolation and structure elucidation revealed a new di- and tripeptide composed of l-alanine and a C-terminal l-phosphonoalanine which we name phosphonoalamides E and F. These compounds exhibit broad-spectrum antibacterial activity, including strong inhibition against the agricultural pests responsible for vegetable soft rot (Erwinia rhapontici), onion rot (Pantoea ananatis), and American foulbrood (Paenibacillus larvae). This work expands our knowledge of phosphonate metabolism and underscores the importance of including underexplored microbial taxa in natural product discovery. IMPORTANCE Phosphonate natural products produced by bacteria have been a rich source of clinical antibiotics and commercial pesticides. Here, we describe the discovery of two new phosphonopeptides produced by B. velezensis with antibacterial activity against human and plant pathogens, including those responsible for widespread soft rot in crops and American foulbrood. Our results provide new insight on the natural chemical diversity of phosphonates and suggest that these compounds could be developed as effective antibiotics for use in medicine or agriculture.
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Affiliation(s)
- Jake Wilson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio, USA
| | - Jerry Cui
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Toshiki Nakao
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Happy Kwok
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Yeying Zhang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Chase M. Kayrouz
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Tiffany M. Pham
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Hannah Roodhouse
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
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3
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Ayon NJ. High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery. Metabolites 2023; 13:625. [PMID: 37233666 PMCID: PMC10220967 DOI: 10.3390/metabo13050625] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.
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Affiliation(s)
- Navid J Ayon
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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4
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Barekatain Y, Khadka S, Harris K, Delacerda J, Yan VC, Chen KC, Pham CD, Uddin MN, Avritcher R, Eisenberg EJ, Kalluri R, Millward SW, Muller FL. Quantification of Phosphonate Drugs by 1H– 31P HSQC Shows That Rats Are Better Models of Primate Drug Exposure than Mice. Anal Chem 2022; 94:10045-10053. [DOI: 10.1021/acs.analchem.2c00553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yasaman Barekatain
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, Texas 77054, United States
| | - Sunada Khadka
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, Texas 77054, United States
| | - Kristen Harris
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Jorge Delacerda
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Victoria C. Yan
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, Texas 77054, United States
| | - Ko-Chien Chen
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, Texas 77054, United States
| | - Cong-Dat Pham
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Md. Nasir Uddin
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Rony Avritcher
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | | | - Raghu Kalluri
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Steven W. Millward
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Florian L. Muller
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
- SPOROS Bioventures, Houston, Texas 77054, United States
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5
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Zhang Y, Chen L, Wilson JA, Cui J, Roodhouse H, Kayrouz C, Pham TM, Ju KS. Valinophos Reveals a New Route in Microbial Phosphonate Biosynthesis That Is Broadly Conserved in Nature. J Am Chem Soc 2022; 144:9938-9948. [PMID: 35617676 DOI: 10.1021/jacs.2c02854] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Phosphonate natural products are potent inhibitors of cellular metabolism with an established record of commercialization in medicine and biotechnology. Although genome mining has emerged as an accelerated method for the discovery of new phosphonates, a robust framework of their metabolism is needed to identify the pathways most likely to yield compounds with desired activities. Here we expand our understanding of these natural products by reporting the complete biosynthetic pathway for valinophos, a phosphonopeptide natural product containing the unusual (R)-2,3-dihydroxypropylphosphonate (DHPPA) scaffold. The pathway was defined by several enzymatic transformations and intermediates previously unknown to phosphonate natural products. A dedicated dehydrogenase served as a new phosphoenolpyruvate mutase coupling enzyme. Notably, its reduction of phosphonopyruvate to phosphonolactate defined a new early branchpoint in phosphonate biosynthesis. Functionally interconnected kinase and reductase enzymes catalyzed reactions reminiscent of glycolysis and arginine biosynthesis to produce a transient, but essential, phosphonolactaldehyde intermediate. We demonstrate esterification of l-valine onto DHPPA as a new biochemical activity for ATP-Grasp ligase enzymes. Unexpectedly, a second amino acid ligase then adjoined additional amino acids at the valinyl moiety to produce a suite of DHPPA-dipeptides. The genes for DHPPA biosynthesis were discovered among genomes of bacteria from wide-ranging habitats, suggesting a wealth of unknown compounds that may originate from this core pathway. Our findings establish new biosynthetic principles for natural products and provide definition to unexplored avenues for bioactive phosphonate genome mining.
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Affiliation(s)
- Yeying Zhang
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Li Chen
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jake A Wilson
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States.,Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jerry Cui
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hannah Roodhouse
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chase Kayrouz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Tiffany M Pham
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States.,Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States.,Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, United States
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6
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Zhang Y, Pham TM, Kayrouz C, Ju KS. Biosynthesis of Argolaphos Illuminates the Unusual Biochemical Origins of Aminomethylphosphonate and N ε-Hydroxyarginine Containing Natural Products. J Am Chem Soc 2022; 144:9634-9644. [PMID: 35616638 DOI: 10.1021/jacs.2c00627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Phosphonate natural products have a history of successful application in medicine and biotechnology due to their ability to inhibit essential cellular pathways. This has inspired efforts to discover phosphonate natural products by prioritizing microbial strains whose genomes encode uncharacterized biosynthetic gene clusters (BGCs). Thus, success in genome mining is dependent on establishing the fundamental principles underlying the biosynthesis of inhibitory chemical moieties to facilitate accurate prediction of BGCs and the bioactivities of their products. Here, we report the complete biosynthetic pathway for the argolaphos phosphonopeptides. We uncovered the biochemical origins of aminomethylphosphonate (AMPn) and Nε-hydroxyarginine, two noncanonical amino acids integral to the antimicrobial function of argolaphos. Critical to this pathway were dehydrogenase and transaminase enzymes dedicated to the conversion of hydroxymethylphosphonate to AMPn. The interconnected activities of both enzymes provided a solution to overcome unfavorable energetics, empower cofactor regeneration, and mediate intermediate toxicity during these transformations. Sequential ligation of l-arginine and l-valine was afforded by two GCN5-related N-acetyltransferases in a tRNA-dependent manner. AglA was revealed to be an unusual heme-dependent monooxygenase that hydroxylated the Nε position of AMPn-Arg. As the first biochemically characterized member of the YqcI/YcgG protein family, AglA enlightens the potential functions of this elusive group, which remains biochemically distinct from the well-established P450 monooxygenases. The widespread distribution of AMPn and YqcI/YcgG genes among actinobacterial genomes suggests their involvement in diverse metabolic pathways and cellular functions. Our findings illuminate new paradigms in natural product biosynthesis and realize a significant trove of AmPn and Nε-hydroxyarginine natural products that await discovery.
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Affiliation(s)
- Yeying Zhang
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Tiffany M Pham
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chase Kayrouz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States.,Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States.,Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, United States
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7
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Abstract
Organophosphorus compounds play a vital role as nucleic acids, nucleotide coenzymes, metabolic intermediates and are involved in many biochemical processes. They are part of DNA, RNA, ATP and a number of important biological elements of living organisms. Synthetic compounds of this class have found practical application as agrochemicals, pharmaceuticals, bioregulators, and othrs. In recent years, a large number of phosphorus compounds containing P-O, P-N, P-C bonds have been isolated from natural sources. Many of them have shown interesting biological properties and have become the objects of intensive scientific research. Most of these compounds contain asymmetric centers, the absolute configurations of which have a significant effect on the biological properties of the products of their transformations. This area of research on natural phosphorus compounds is still little-studied, that prompted us to analyze and discuss it in our review. Moreover natural organophosphorus compounds represent interesting models for the development of new biologically active compounds, and a number of promising drugs and agrochemicals have already been obtained on their basis. The review also discusses the history of the development of ideas about the role of organophosphorus compounds and stereochemistry in the origin of life on Earth, starting from the prebiotic period, that allows us in a new way to consider this most important problem of fundamental science.
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8
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Shiraishi T, Kuzuyama T. Biosynthetic pathways and enzymes involved in the production of phosphonic acid natural products. Biosci Biotechnol Biochem 2021; 85:42-52. [PMID: 33577658 DOI: 10.1093/bbb/zbaa052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/04/2020] [Indexed: 02/07/2023]
Abstract
Phosphonates are organophosphorus compounds possessing a characteristic C-P bond in which phosphorus is directly bonded to carbon. As phosphonates mimic the phosphates and carboxylates of biological molecules to potentially inhibit metabolic enzymes, they could be lead compounds for the development of a variety of drugs. Fosfomycin (FM) is a representative phosphonate natural product that is widely used as an antibacterial drug. Here, we review the biosynthesis of FM, which includes a recent breakthrough to find a missing link in the biosynthetic pathway that had been a mystery for a quarter-century. In addition, we describe the genome mining of phosphonate natural products using the biosynthetic gene encoding an enzyme that catalyzes C-P bond formation. We also introduce the chemoenzymatic synthesis of phosphonate derivatives. These studies expand the repertoires of phosphonates and the related biosynthetic machinery. This review mainly covers the years 2012-2020.
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Affiliation(s)
- Taro Shiraishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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9
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Advances in antibiotic drug discovery: reducing the barriers for antibiotic development. Future Med Chem 2020; 12:2067-2087. [PMID: 33124460 DOI: 10.4155/fmc-2020-0247] [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] [Indexed: 12/26/2022] Open
Abstract
Antibiotic drug discovery has been an essential field of research since the early 1900s, but the threat from infectious bacteria has only increased over the decades because of the emergence of widespread multidrug resistance. In this review, we discuss the recent advances in natural product, computational and medicinal chemistry that have reinvigorated the field of antibiotic drug discovery while giving perspective on how easily, both in cost and in expertise, these methods can be implemented by other researchers with the goal of increasing the number of scientists contributing to this public health crisis.
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10
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Kayrouz CM, Zhang Y, Pham TM, Ju KS. Genome Mining Reveals the Phosphonoalamide Natural Products and a New Route in Phosphonic Acid Biosynthesis. ACS Chem Biol 2020; 15:1921-1929. [PMID: 32484327 DOI: 10.1021/acschembio.0c00256] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phosphonic acid natural products have potent inhibitory activities that have led to their application as antibiotics. Recent studies uncovered large collections of gene clusters encoding for unknown phosphonic acids across microbial genomes. However, our limited understanding of their metabolism presents a significant challenge toward accurately informing the discovery of new bioactive compounds directly from sequence information alone. Here, we use genome mining to identify a family of gene clusters encoding a conserved branch point unknown to bacterial phosphonic acid biosynthesis. The products of this gene cluster family are the phosphonoalamides, four new phosphonopeptides with l-phosphonoalanine as the common headgroup. Phosphonoalanine and phosphonoalamide A are antibacterials, with strongest inhibition observed against strains of Bacillus and Escherichia coli. Heterologous expression identified the gene required for transamination of phosphonopyruvate to phosphonoalanine, a new route for bacterial phosphonic acids encoded within genomes of diverse microbes. These results expand our knowledge of phosphonic acid diversity and pathways for their biosynthesis.
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Affiliation(s)
- Chase M. Kayrouz
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yeying Zhang
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Tiffany M. Pham
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, United States
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11
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Chu L, Huang J, Muhammad M, Deng Z, Gao J. Genome mining as a biotechnological tool for the discovery of novel marine natural products. Crit Rev Biotechnol 2020; 40:571-589. [PMID: 32308042 DOI: 10.1080/07388551.2020.1751056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Compared to terrestrial environments, the oceans harbor a variety of environments, creating higher biodiversity, which gives marine natural products a high occurrence of significant biology and novel chemistry. However, traditional bioassay-guided isolation and purification strategies are severely limiting the discovery of additional novel natural products from the ocean. With an increasing number of marine microorganisms being sequenced, genome mining is gradually becoming a powerful tool to retrieve novel marine natural products. In this review, we have summarized genome mining approaches used to analyze key enzymes of biosynthetic pathways and predict the chemical structure of new gene clusters by introducing successful stories that used genome mining strategy to identify new marine-derived compounds. Furthermore, we also put forward challenges for genome mining techniques and their proposed solutions. The detailed analysis of the genome mining strategy will help researchers to understand this novel technique and its application. With the development of a genome sequence, genome mining strategies will be applied more widely, which will drive rapid development in the field of marine natural product development.
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Affiliation(s)
- Leixia Chu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinping Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mustafa Muhammad
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangtao Gao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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12
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Zhou C, Luo X, Chen N, Zhang L, Gao J. C-P Natural Products as Next-Generation Herbicides: Chemistry and Biology of Glufosinate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:3344-3353. [PMID: 32125843 DOI: 10.1021/acs.jafc.0c00052] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In modern agriculture and weed management practices, herbicides have been widely used to control weeds effectively and represent more than 50% of commercial pesticides applied in the world. Herbicides with unique mechanisms of actions (MOA) have historically been discovered and commercialized every two or three years from the 1950s to the 1980s. However, this trend lowered dramatically as no herbicide with a novel MOA has been marketed for more than 30 years. The fast-growing resistance to commercial herbicides has reignited the agricultural chemical industry interest in new structural scaffolds targeting novel sites in plants. Carbon-phosphorus bonds (C-P) containing natural products (NPs) have played an essential role in herbicide discovery as the chemical diversity, and the promising bioactivity of natural C-P phytotoxins can provide exciting opportunities for the discovery of both natural and semisynthetic herbicides with novel targets. Among commercial herbicides, glyphosate (Roundup), a famous C-P containing herbicide, is by far the most universally used herbicide worldwide. Furthermore, glufosinate is one of the most widely used natural herbicides in the world. Therefore, C-P NPs are a treasure for discovering new herbicides with novel mechanisms of actions (MOAs). Here, we present an overview of the chemistry and biology of glufosinate including isolation and characterization, mode of action, herbicidal use, biosynthesis, and chemical synthesis since its discovery in order to not only help scientists reassess the role of this famous herbicide in the field of agrichemical chemistry but also build a new stage for discovering novel C-P herbicides with new MOAs.
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Affiliation(s)
- Chengzeng Zhou
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoxia Luo
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Science, Tarim University, Alar 843300, China
| | - Nengyi Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lili Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production & Construction Corps, College of Life Science, Tarim University, Alar 843300, China
| | - Jiangtao Gao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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13
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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14
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de la Torre AF, Ali A, Concepcion O, Montero-Alejo AL, Muñiz FM, Jiménez CA, Belmar J, Velázquez-Libera JL, Hernández-Rodríguez EW, Caballero J. A study of the cis–trans isomerization preference of N-alkylated peptides containing phosphorus in the side chain and backbone. NEW J CHEM 2019. [DOI: 10.1039/c9nj02234a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The current work provides a study on the cis–trans isomerization behaviour of N-alkylated peptides decorated with phosphonate ester groups.
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Affiliation(s)
- Alexander F. de la Torre
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción
- Chile
| | - Akbar Ali
- Department of Chemistry
- University of Sargodha
- Pakistan
| | - Odette Concepcion
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción
- Chile
| | | | - Francisco M. Muñiz
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción
- Chile
| | - Claudio A. Jiménez
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción
- Chile
| | - Julio Belmar
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción
- Chile
| | | | | | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM)
- Universidad de Talca
- Talca
- Chile
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15
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Gao SS, Naowarojna N, Cheng R, Liu X, Liu P. Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses. Nat Prod Rep 2018; 35:792-837. [PMID: 29932179 PMCID: PMC6093783 DOI: 10.1039/c7np00067g] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to 2018 α-Ketoglutarate (αKG, also known as 2-oxoglutarate)-dependent mononuclear non-haem iron (αKG-NHFe) enzymes catalyze a wide range of biochemical reactions, including hydroxylation, ring fragmentation, C-C bond cleavage, epimerization, desaturation, endoperoxidation and heterocycle formation. These enzymes utilize iron(ii) as the metallo-cofactor and αKG as the co-substrate. Herein, we summarize several novel αKG-NHFe enzymes involved in natural product biosyntheses discovered in recent years, including halogenation reactions, amino acid modifications and tailoring reactions in the biosynthesis of terpenes, lipids, fatty acids and phosphonates. We also conducted a survey of the currently available structures of αKG-NHFe enzymes, in which αKG binds to the metallo-centre bidentately through either a proximal- or distal-type binding mode. Future structure-function and structure-reactivity relationship investigations will provide crucial information regarding how activities in this large class of enzymes have been fine-tuned in nature.
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Affiliation(s)
- Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Xueting Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
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16
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Abstract
Covering: 2006 to 2017Actinomycetes have been, for decades, one of the most important sources for the discovery of new antibiotics with an important number of drugs and analogs successfully introduced in the market and still used today in clinical practice. The intensive antibacterial discovery effort that generated the large number of highly potent broad-spectrum antibiotics, has seen a dramatic decline in the large pharma industry in the last two decades resulting in a lack of new classes of antibiotics with novel mechanisms of action reaching the clinic. Whereas the decline in the number of new chemical scaffolds and the rediscovery problem of old known molecules has become a hurdle for industrial natural products discovery programs, new actinomycetes compounds and leads have continued to be discovered and developed to the preclinical stages. Actinomycetes are still one of the most important sources of chemical diversity and a reservoir to mine for novel structures that is requiring the integration of diverse disciplines. These can range from novel strategies to isolate species previously not cultivated, innovative whole cell screening approaches and on-site analytical detection and dereplication tools for novel compounds, to in silico biosynthetic predictions from whole gene sequences and novel engineered heterologous expression, that have inspired the isolation of new NPs and shown their potential application in the discovery of novel antibiotics. This review will address the discovery of antibiotics from actinomycetes from two different perspectives including: (1) an update of the most important antibiotics that have only reached the clinical development in the recent years despite their early discovery, and (2) an overview of the most recent classes of antibiotics described from 2006 to 2017 in the framework of the different strategies employed to untap novel compounds previously overlooked with traditional approaches.
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Affiliation(s)
- Olga Genilloud
- Fundación MEDINA, Avda Conocimiento 34, 18016 Granada, Spain.
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17
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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18
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Chin JP, McGrath JW, Quinn JP. Microbial transformations in phosphonate biosynthesis and catabolism, and their importance in nutrient cycling. Curr Opin Chem Biol 2016; 31:50-7. [DOI: 10.1016/j.cbpa.2016.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/24/2022]
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19
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Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes. Proc Natl Acad Sci U S A 2015; 112:12175-80. [PMID: 26324907 DOI: 10.1073/pnas.1500873112] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although natural products have been a particularly rich source of human medicines, activity-based screening results in a very high rate of rediscovery of known molecules. Based on the large number of natural product biosynthetic genes in microbial genomes, many have proposed "genome mining" as an alternative approach for discovery efforts; however, this idea has yet to be performed experimentally on a large scale. Here, we demonstrate the feasibility of large-scale, high-throughput genome mining by screening a collection of over 10,000 actinomycetes for the genetic potential to make phosphonic acids, a class of natural products with diverse and useful bioactivities. Genome sequencing identified a diverse collection of phosphonate biosynthetic gene clusters within 278 strains. These clusters were classified into 64 distinct groups, of which 55 are likely to direct the synthesis of unknown compounds. Characterization of strains within five of these groups resulted in the discovery of a new archetypical pathway for phosphonate biosynthesis, the first (to our knowledge) dedicated pathway for H-phosphinates, and 11 previously undescribed phosphonic acid natural products. Among these compounds are argolaphos, a broad-spectrum antibacterial phosphonopeptide composed of aminomethylphosphonate in peptide linkage to a rare amino acid N(5)-hydroxyarginine; valinophos, an N-acetyl l-Val ester of 2,3-dihydroxypropylphosphonate; and phosphonocystoximate, an unusual thiohydroximate-containing molecule representing a new chemotype of sulfur-containing phosphonate natural products. Analysis of the genome sequences from the remaining strains suggests that the majority of the phosphonate biosynthetic repertoire of Actinobacteria has been captured at the gene level. This dereplicated strain collection now provides a reservoir of numerous, as yet undiscovered, phosphonate natural products.
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20
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Johnson AR, Carlson EE. Collision-Induced Dissociation Mass Spectrometry: A Powerful Tool for Natural Product Structure Elucidation. Anal Chem 2015; 87:10668-78. [PMID: 26132379 DOI: 10.1021/acs.analchem.5b01543] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mass spectrometry is a powerful tool in natural product structure elucidation, but our ability to directly correlate fragmentation spectra to these structures lags far behind similar efforts in peptide sequencing and proteomics. Often, manual data interpretation is required and our knowledge of the expected fragmentation patterns for many scaffolds is limited, further complicating analysis. Here, we summarize advances in natural product structure elucidation based upon the application of collision induced dissociation fragmentation mechanisms.
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Affiliation(s)
- Andrew R Johnson
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Erin E Carlson
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.,Department of Molecular and Cellular Biochemistry, Indiana University , 212 South Hawthorne Drive, Bloomington, Indiana 47405, United States
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21
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Fei X, Holmes T, Diddle J, Hintz L, Delaney D, Stock A, Renner D, McDevitt M, Berkowitz DB, Soukup JK. Phosphatase-inert glucosamine 6-phosphate mimics serve as actuators of the glmS riboswitch. ACS Chem Biol 2014; 9:2875-82. [PMID: 25254431 PMCID: PMC4273988 DOI: 10.1021/cb500458f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
The glmS riboswitch is unique among gene-regulating
riboswitches and catalytic RNAs. This is because its own metabolite,
glucosamine-6-phosphate (GlcN6P), binds to the riboswitch and catalytically
participates in the RNA self-cleavage reaction, thereby providing
a novel negative feedback mechanism. Given that a number of pathogens
harbor the glmS riboswitch, artificial actuators
of this potential RNA target are of great interest. Structural/kinetic
studies point to the 2-amino and 6-phosphate ester functionalities
in GlcN6P as being crucial for this actuation. As a first step toward
developing artificial actuators, we have synthesized a series of nine
GlcN6P analogs bearing phosphatase-inert surrogates in place of the
natural phosphate ester. Self-cleavage assays with the Bacillus cereusglmS riboswitch
give a broad SAR. Two analogs display significant activity, namely,
the 6-deoxy-6-phosphonomethyl analog (5) and the 6-O-malonyl ether (13). Kinetic profiles show
a 22-fold and a 27-fold higher catalytic efficiency, respectively,
for these analogs vs glucosamine (GlcN). Given their nonhydrolyzable
phosphate surrogate functionalities, these analogs are arguably the
most robust artificial glmS riboswitch actuators
yet reported. Interestingly, the malonyl ether (13, extra
O atom) is much more effective than the simple malonate (17), and the “sterically true” phosphonate (5) is far superior to the chain-truncated (7) or chain-extended
(11) analogs, suggesting that positioning via Mg coordination
is important for activity. Docking results are consistent with this
view. Indeed, the viability of the phosphonate and 6-O-malonyl ether
mimics of GlcN6P points to a potential new strategy for artificial
actuation of the glmS riboswitch in a biological
setting, wherein phosphatase-resistance is paramount.
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Affiliation(s)
- Xiang Fei
- Department
of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Thomas Holmes
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Julianna Diddle
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Lauren Hintz
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Dan Delaney
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Alex Stock
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Danielle Renner
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Molly McDevitt
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - David B. Berkowitz
- Department
of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Juliane K. Soukup
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
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22
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Charlop-Powers Z, Milshteyn A, Brady SF. Metagenomic small molecule discovery methods. Curr Opin Microbiol 2014; 19:70-75. [PMID: 25000402 DOI: 10.1016/j.mib.2014.05.021] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/10/2014] [Accepted: 05/28/2014] [Indexed: 12/18/2022]
Abstract
Metagenomic approaches to natural product discovery provide the means to harvest bioactive small molecules synthesized by environmental bacteria without the requirement of first culturing these organisms. Advances in sequencing technologies and general metagenomic methods are beginning to provide the tools necessary to unlock the unexplored biosynthetic potential encoded by the genomes of uncultured environmental bacteria. Here, we highlight recent advances in sequence-based and functional-based metagenomic approaches that promise to facilitate antibiotic discovery from diverse environmental microbiomes.
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Affiliation(s)
- Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States.
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23
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Jarmusch AK, Cooks RG. Emerging capabilities of mass spectrometry for natural products. Nat Prod Rep 2014; 31:730-8. [PMID: 24700087 DOI: 10.1039/c3np70121b] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering up to the end of 2013 A brief history of mass spectrometry in natural products research serves to identify themes which have driven progress in this area of application and in mass spectrometry itself. This account covers six decades of ionization methods, starting with traditional electron ionization and progressing through today's ambient ionization methods. Corresponding developments in mass analyzers are indicated, ranging from sector magnetic fields, through hybrid quadrupole mass filters to miniature ion traps. Current capabilities of mass spectrometry in natural products studies include direct in situ analysis, mass spectrometry imaging, and the study of biosynthetic pathways using metabolomic information. The survey concludes with a discussion of new experiments and capabilities including ion soft landing, preparative mass spectrometry, and accelerated ionic reactions in confined volumes.
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Affiliation(s)
- Alan K Jarmusch
- Purdue University, Department of Chemistry, 560 Oval Drive, West Lafayette, IN, USA.
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24
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Cioni JP, Doroghazi J, Ju KS, Yu X, Evans BS, Lee J, Metcalf WW. Cyanohydrin phosphonate natural product from Streptomyces regensis. JOURNAL OF NATURAL PRODUCTS 2014; 77:243-249. [PMID: 24437999 PMCID: PMC3993929 DOI: 10.1021/np400722m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 06/03/2023]
Abstract
Streptomyces regensis strain WC-3744 was identified as a potential phosphonic acid producer in a large-scale screen of microorganisms for the presence of the pepM gene, which encodes the key phosphonate biosynthetic enzyme phosphoenolpyruvate phosphonomutase. (31)P NMR revealed the presence of several unidentified phosphonates in spent medium after growth of S. regensis. These compounds were purified and structurally characterized via extensive 1D and 2D NMR spectroscopic and mass spectrometric analyses. Three new phosphonic acid metabolites, whose structures were confirmed by comparison to chemically synthesized standards, were observed: (2-acetamidoethyl)phosphonic acid (1), (2-acetamido-1-hydroxyethyl)phosphonic (3), and a novel cyanohydrin-containing phosphonate, (cyano(hydroxy)methyl)phosphonic acid (4). The gene cluster responsible for synthesis of these molecules was also identified from the draft genome sequence of S. regensis, laying the groundwork for future investigations into the metabolic pathway leading to this unusual natural product.
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Affiliation(s)
- Joel P. Cioni
- Department of Microbiology and The Institute for Genomic Biology, University of Illinois, Urbana−Champaign, Illinois 61801, United States
| | - James
R. Doroghazi
- Department of Microbiology and The Institute for Genomic Biology, University of Illinois, Urbana−Champaign, Illinois 61801, United States
| | - Kou-San Ju
- Department of Microbiology and The Institute for Genomic Biology, University of Illinois, Urbana−Champaign, Illinois 61801, United States
| | - Xiaomin Yu
- Department of Microbiology and The Institute for Genomic Biology, University of Illinois, Urbana−Champaign, Illinois 61801, United States
| | - Bradley S. Evans
- Department of Microbiology and The Institute for Genomic Biology, University of Illinois, Urbana−Champaign, Illinois 61801, United States
| | - Jaeheon Lee
- Department of Microbiology and The Institute for Genomic Biology, University of Illinois, Urbana−Champaign, Illinois 61801, United States
| | - William W. Metcalf
- Department of Microbiology and The Institute for Genomic Biology, University of Illinois, Urbana−Champaign, Illinois 61801, United States
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25
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Purification and characterization of phosphonoglycans from Glycomyces sp. strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338. J Bacteriol 2014; 196:1768-79. [PMID: 24584498 DOI: 10.1128/jb.00036-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two related actinomycetes, Glycomyces sp. strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338, were identified as potential phosphonic acid producers by screening for the gene encoding phosphoenolpyruvate (PEP) mutase, which is required for the biosynthesis of most phosphonates. Using a variety of analytical techniques, both strains were subsequently shown to produce phosphonate-containing exopolysaccharides (EPS), also known as phosphonoglycans. The phosphonoglycans were purified by sequential organic solvent extractions, methanol precipitation, and ultrafiltration. The EPS from the Glycomyces strain has a mass of 40 to 50 kDa and is composed of galactose, xylose, and five distinct partially O-methylated galactose residues. Per-deutero-methylation analysis indicated that galactosyl residues in the polysaccharide backbone are 3,4-linked Gal, 2,4-linked 3-MeGal, 2,3-linked Gal, 3,6-linked 2-MeGal, and 4,6-linked 2,3-diMeGal. The EPS from the Stackebrandtia strain is comprised of glucose, galactose, xylose, and four partially O-methylated galactose residues. Isotopic labeling indicated that the O-methyl groups in the Stackebrandtia phosphonoglycan arise from S-adenosylmethionine. The phosphonate moiety in both phosphonoglycans was shown to be 2-hydroxyethylphosphonate (2-HEP) by (31)P nuclear magnetic resonance (NMR) and mass spectrometry following strong acid hydrolysis of the purified molecules. Partial acid hydrolysis of the purified EPS from Glycomyces yielded 2-HEP in ester linkage to the O-5 or O-6 position of a hexose and a 2-HEP mono(2,3-dihydroxypropyl)ester. Partial acid hydrolysis of Stackebrandtia EPS also revealed the presence of 2-HEP mono(2,3-dihydroxypropyl)ester. Examination of the genome sequences of the two strains revealed similar pepM-containing gene clusters that are likely to be required for phosphonoglycan synthesis.
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26
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Ju KS, Doroghazi JR, Metcalf WW. Genomics-enabled discovery of phosphonate natural products and their biosynthetic pathways. J Ind Microbiol Biotechnol 2014; 41:345-56. [PMID: 24271089 PMCID: PMC3946943 DOI: 10.1007/s10295-013-1375-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 10/22/2013] [Indexed: 01/01/2023]
Abstract
Phosphonate natural products have proven to be a rich source of useful pharmaceutical, agricultural, and biotechnology products, whereas study of their biosynthetic pathways has revealed numerous intriguing enzymes that catalyze unprecedented biochemistry. Here we review the history of phosphonate natural product discovery, highlighting technological advances that have played a key role in the recent advances in their discovery. Central to these developments has been the application of genomics, which allowed discovery and development of a global phosphonate metabolic framework to guide research efforts. This framework suggests that the future of phosphonate natural products remains bright, with many new compounds and pathways yet to be discovered.
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Affiliation(s)
- Kou-San Ju
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
| | - James R. Doroghazi
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
| | - William W. Metcalf
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
- Department of Microbiology, University of Illinois, Urbana-Champaign, IL 61801
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