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Susman M, Yan J, Makris C, Butler A. Discovery, isolation, and characterization of diazeniumdiolate siderophores. Methods Enzymol 2024; 702:189-214. [PMID: 39155111 DOI: 10.1016/bs.mie.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
The C-diazeniumdiolate (N-nitrosohydroxylamine) group in the amino acid graminine (Gra) is a newly discovered Fe(III) ligand in microbial siderophores. Graminine was first identified in the siderophore gramibactin, and since this discovery, other Gra-containing siderophores have been identified, including megapolibactins, plantaribactin, gladiobactin, trinickiabactin (gramibactin B), and tistrellabactins. The C-diazeniumdiolate is photoreactive in UV light which provides a convenient characterization tool for this type of siderophore. This report details the process of genomics-driven identification of bacteria producing Gra-containing siderophores based on selected biosynthetic enzymes, as well as bacterial culturing, isolation and characterization of the C-diazeniumdiolate siderophores containing Gra.
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Affiliation(s)
- Melanie Susman
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA, United States
| | - Jin Yan
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA, United States
| | - Christina Makris
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA, United States
| | - Alison Butler
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA, United States.
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2
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Fan C, Zhou F, Huang W, Xue Y, Xu C, Zhang R, Xian M, Feng X. Characterization of an efficient N-oxygenase from Saccharothrix sp. and its application in the synthesis of azomycin. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:194. [PMID: 38104149 PMCID: PMC10724926 DOI: 10.1186/s13068-023-02446-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND The nitro group constitutes a significant functional moiety within numerous valuable substances, such as nitroimidazoles, a class of antimicrobial drugs exhibiting broad spectrum activity. Conventional chemical methods for synthesizing nitro compounds suffer from harsh conditions, multiple steps, and environmental issues. Biocatalysis has emerged as a promising alternative to overcome these drawbacks, with certain enzymes capable of catalyzing nitro group formation gradually being discovered in nature. Nevertheless, the practical application is hindered by the restricted diversity and low catalytic activity exhibited by the reported nitrifying enzymes. RESULTS A novel N-oxygenase SaRohS harboring higher catalytic capability of transformation 2-aminoimidazole to azomycin was characterized from Saccharothrix sp. Phylogenetic tree analysis revealed that SaRohS belongs to the heme-oxygenase-like diiron oxygenase (HDOs) family. SaRohS exhibited optimal activity at pH 5.5 and 25 ℃, respectively. The enzyme maintained relatively stable activity within the pH range of 4.5 to 6.5 and the temperature range of 20 ℃ to 35 ℃. Following sequence alignment and structural analysis, several promising amino acid residues were meticulously chosen for catalytic performance evaluation. Site-directed mutations showed that threonine 75 was essential for the catalytic activity. The dual mutant enzyme G95A/K115T exhibited the highest catalytic efficiency, which was approximately 5.8-fold higher than that of the wild-type and 22.3-fold higher than that of the reported N-oxygenase KaRohS from Kitasatospora azatica. The underlying catalytic mechanism was investigated through molecular docking and molecular dynamics. Finally, whole-cell biocatalysis was performed and 2-aminoimidazole could be effectively converted into azomycin with a reaction conversion rate of 42% within 14 h. CONCLUSIONS An efficient N-oxygenase that catalyzes 2-aminoimidazole to azomycin was screened form Saccharothrix sp., its phylogenetics and enzymatic properties were analyzed. Through site-directed mutation, enhancements in catalytic competence were achieved, and the molecular basis underlying the enhanced enzymatic activity of the mutants was revealed via molecular docking and dynamic simulation. Furthermore, the application potential of this enzyme was assessed through whole cell biocatalysis, demonstrating it as a promising alternative method for azomycin production.
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Affiliation(s)
- Chuanle Fan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Fang Zhou
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Wei Huang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Yi Xue
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Chao Xu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Rubing Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
| | - Xinjun Feng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
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3
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Wang M, Ryan KS. Reductases Produce Nitric Oxide in an Alternative Pathway to Form the Diazeniumdiolate Group of l-Alanosine. J Am Chem Soc 2023. [PMID: 37478476 DOI: 10.1021/jacs.3c04447] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
l-Alanosine is a diazeniumdiolate (N-nitrosohydroxylamine) antibiotic that inhibits MTAP-deficient tumor cells by blocking de novo adenine biosynthesis. Previous work revealed the early steps in the biosynthesis of l-alanosine. In the present study, we used genome mining to discover two new l-alanosine-producing strains that lack the aspartate-nitrosuccinate pathway genes found in the original l-alanosine producer. Instead, nitrate is reduced with a unique set of nitrate-nitrite reductases. These enzymes are typically used as part of the nitrogen cycle for denitrification or assimilation, and our report here shows how enzymes from the nitrogen cycle can be repurposed for the biosynthesis of specialized metabolites. The widespread distribution of nitric-oxide-producing reductases also indicates a potential for the discovery of new nitric-oxide-derived natural products.
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Affiliation(s)
- Menghua Wang
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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4
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Acken KA, Li B. Pseudomonas virulence factor controls expression of virulence genes in Pseudomonas entomophila. PLoS One 2023; 18:e0284907. [PMID: 37200397 DOI: 10.1371/journal.pone.0284907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/11/2023] [Indexed: 05/20/2023] Open
Abstract
Quorum sensing is a communication strategy that bacteria use to collectively alter gene expression in response to cell density. Pathogens use quorum sensing systems to control activities vital to infection, such as the production of virulence factors and biofilm formation. The Pseudomonas virulence factor (pvf) gene cluster encodes a signaling system (Pvf) that is present in over 500 strains of proteobacteria, including strains that infect a variety of plant and human hosts. We have shown that Pvf regulates the production of secreted proteins and small molecules in the insect pathogen Pseudomonas entomophila L48. Here, we identified genes that are likely regulated by Pvf using the model strain P. entomophila L48 which does not contain other known quorum sensing systems. Pvf regulated genes were identified through comparing the transcriptomes of wildtype P. entomophila and a pvf deletion mutant (ΔpvfA-D). We found that deletion of pvfA-D affected the expression of approximately 300 genes involved in virulence, the type VI secretion system, siderophore transport, and branched chain amino acid biosynthesis. Additionally, we identified seven putative biosynthetic gene clusters with reduced expression in ΔpvfA-D. Our results indicate that Pvf controls multiple virulence mechanisms in P. entomophila L48. Characterizing genes regulated by Pvf will aid understanding of host-pathogen interactions and development of anti-virulence strategies against P. entomophila and other pvf-containing strains.
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Affiliation(s)
- Katie A Acken
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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5
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Ushimaru R, Abe I. Unusual Dioxygen-Dependent Reactions Catalyzed by Nonheme Iron Enzymes in Natural Product Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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6
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Matsuda K, Arima K, Akiyama S, Yamada Y, Abe Y, Suenaga H, Hashimoto J, Shin-Ya K, Nishiyama M, Wakimoto T. A Natural Dihydropyridazinone Scaffold Generated from a Unique Substrate for a Hydrazine-Forming Enzyme. J Am Chem Soc 2022; 144:12954-12960. [PMID: 35771530 DOI: 10.1021/jacs.2c05269] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Nitrogen-nitrogen bond-containing functional groups are rare, but they are found in a considerably wide class of natural products. Recent clarifications of the biosynthetic routes for such functional groups shed light onto overlooked biosynthetic genes distributed across the bacterial kingdom, highlighting the presence of yet-to-be identified natural products with peculiar functional groups. Here, the genome-mining approach targeting a unique hydrazine-forming gene led to the discovery of actinopyridazinones A (1) and B (2), the first natural products with dihydropyridazinone rings. The structure of actinopyridazinone A was unambiguously established by total synthesis. Biosynthetic studies unveiled the structural diversity of natural hydrazines derived from this family of N-N bond-forming enzymes.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
| | - Kuga Arima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoko Akiyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Yuito Yamada
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Yo Abe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Hikaru Suenaga
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), Tokyo 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Makoto Nishiyama
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
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7
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Morgan GL, Li K, Crawford DM, Aubé J, Li B. Enzymatic Synthesis of Diverse Heterocycles by a Noncanonical Nonribosomal Peptide Synthetase. ACS Chem Biol 2021; 16:2776-2786. [PMID: 34767712 PMCID: PMC8917869 DOI: 10.1021/acschembio.1c00623] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are typically multimodular enzymes that assemble amino acids or carboxylic acids into complex natural products. Here, we characterize a monomodular NRPS, PvfC, encoded by the Pseudomonas virulence factor (pvf) gene cluster that is essential for virulence and signaling in different bacterial species. PvfC exhibits a unique adenylation-thiolation-reductase (ATR) domain architecture that is understudied in bacteria. We show that the activity of PvfC is essential in the production of seven leucine-derived heterocyclic natural products, including two pyrazines, a pyrazinone, and a rare disubstituted imidazole, as well as three pyrazine N-oxides that require an additional N-oxygenation step. Mechanistic studies reveal that PvfC, without a canonical peptide-forming domain, makes a dipeptide aldehyde intermediate en route to both the pyrazinone and imidazole. Our work identifies a novel biosynthetic route for the production of pyrazinones, an emerging class of signaling molecules and virulence factors. Our discovery also showcases the ability of monomodular NRPSs to generate amino acid- and dipeptide-aldehydes that lead to diverse natural products. The diversity-prone biosynthesis by the pvf-encoded enzymes sets the stage for further understanding the functions of pvf in bacterial cell-to-cell signaling.
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Affiliation(s)
- Gina L Morgan
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kelin Li
- The Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Drake M Crawford
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey Aubé
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- The Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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8
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Petkevičius V, Vaitekūnas J, Gasparavičiūtė R, Tauraitė D, Meškys R. An efficient and regioselective biocatalytic synthesis of aromatic N-oxides by using a soluble di-iron monooxygenase PmlABCDEF produced in the Pseudomonas species. Microb Biotechnol 2021; 14:1771-1783. [PMID: 34115446 PMCID: PMC8313251 DOI: 10.1111/1751-7915.13849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/26/2021] [Accepted: 05/19/2021] [Indexed: 11/27/2022] Open
Abstract
Here, we present an improved whole-cell biocatalysis system for the synthesis of heteroaromatic N-oxides based on the production of a soluble di-iron monooxygenase PmlABCDEF in Pseudomonas sp. MIL9 and Pseudomonas putida KT2440. The presented biocatalysis system performs under environmentally benign conditions, features a straightforward and inexpensive procedure and possesses a high substrate conversion and product yield. The capacity of gram-scale production was reached in the simple shake-flask cultivation. The template substrates (pyridine, pyrazine, 2-aminopyrimidine) have been converted into pyridine-1-oxide, pyrazine-1-oxide and 2-aminopyrimidine-1-oxide in product titres of 18.0, 19.1 and 18.3 g l-1 , respectively. To our knowledge, this is the highest reported productivity of aromatic N-oxides using biocatalysis methods. Moreover, comparing to the chemical method of aromatic N-oxides synthesis based on meta-chloroperoxybenzoic acid, the developed approach is applicable for a regioselective oxidation that is an additional advantageous option in the preparation of the anticipated N-oxides.
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Affiliation(s)
- Vytautas Petkevičius
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySaulėtekio 7VilniusLT‐10257Lithuania
| | - Justas Vaitekūnas
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySaulėtekio 7VilniusLT‐10257Lithuania
| | - Renata Gasparavičiūtė
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySaulėtekio 7VilniusLT‐10257Lithuania
| | - Daiva Tauraitė
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySaulėtekio 7VilniusLT‐10257Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and BiotechnologyInstitute of BiochemistryLife Sciences CenterVilnius UniversitySaulėtekio 7VilniusLT‐10257Lithuania
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9
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He HY, Ryan KS. Glycine-derived nitronates bifurcate to O-methylation or denitrification in bacteria. Nat Chem 2021; 13:599-606. [PMID: 33782561 DOI: 10.1038/s41557-021-00656-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 02/08/2021] [Indexed: 02/01/2023]
Abstract
Natural products with rare functional groups are likely to be constructed by unique biosynthetic enzymes. One such rare functional group is the O-methyl nitronate, which can undergo [3 + 2] cycloaddition reactions with olefins in mild conditions. O-methyl nitronates are found in some natural products; however, how such O-methyl nitronates are assembled biosynthetically is unknown. Here we show that the assembly of the O-methyl nitronate in the natural product enteromycin carboxamide occurs via activation of glycine on a peptidyl carrier protein, followed by reaction with a diiron oxygenase to give a nitronate intermediate and then with a methyltransferase to give an O-methyl nitronate. Guided by the discovery of this pathway, we then identify related cryptic biosynthetic gene cassettes in other bacteria and show that these alternative gene cassettes can, instead, facilitate oxidative denitrification of glycine-derived nitronates. Altogether, our work reveals bifurcating pathways from a central glycine-derived nitronate intermediate in bacteria.
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Affiliation(s)
- Hai-Yan He
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.
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10
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Chen XB, Huang ST, Li J, Yang Q, Yang L, Yu F. Highly Regioselective and Chemoselective [3 + 3] Annulation of Enaminones with ortho-Fluoronitrobenzenenes: Divergent Synthesis of Aposafranones and Their N-Oxides. Org Lett 2021; 23:3032-3037. [PMID: 33792341 DOI: 10.1021/acs.orglett.1c00710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A base-promoted unprecedented strategy for the regioselective and chemoselective divergent synthesis of highly functionalized aposafranones and their N-oxides has been developed from the [3 + 3] annulation of enaminones with o-fluoronitrobenzenenes. This novel synthetic strategy offers an alternative method for the construction of aposafranones and their N-oxides are meaningful in the fields of both biology and organic synthesis. The established protocol explores the annulation scope of enaminones, and it expands the application of nitro-based cyclization.
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Affiliation(s)
- Xue-Bing Chen
- College of Science, Honghe University, Mengzi, 661199, Yunnan, China
| | - Shun-Tao Huang
- College of Science, Honghe University, Mengzi, 661199, Yunnan, China
| | - Jie Li
- College of Science, Honghe University, Mengzi, 661199, Yunnan, China
| | - Qi Yang
- College of Science, Honghe University, Mengzi, 661199, Yunnan, China
| | - Li Yang
- College of Science, Honghe University, Mengzi, 661199, Yunnan, China
| | - Fuchao Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, People's Republic of China
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11
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Chen L, Deng Z, Zhao C. Nitrogen-Nitrogen Bond Formation Reactions Involved in Natural Product Biosynthesis. ACS Chem Biol 2021; 16:559-570. [PMID: 33721494 DOI: 10.1021/acschembio.1c00052] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Construction of nitrogen-nitrogen bonds involves sophisticated biosynthetic mechanisms to overcome the difficulties inherent to the nucleophilic nitrogen atom of amine. Over the past decade, a multitude of reactions responsible for nitrogen-nitrogen bond formation in natural product biosynthesis have been uncovered. On the basis of the intrinsic properties of these reactions, this Review classifies these reactions into three categories: comproportionation, rearrangement, and radical recombination reactions. To expound the metallobiochemistry underlying nitrogen-nitrogen bond formation reactions, we discuss the enzymatic mechanisms in comparison to well characterized canonical heme-dependent enzymes, mononuclear nonheme iron-dependent enzymes, and nonheme di-iron enzymes. We also illuminate the intermediary properties of nitrogen oxide species NO2-, NO+, and N2O3 in nitrogen-nitrogen bond formation reactions with clues derived from inorganic nitrogen metabolism driven by anammox bacteria and nitrifying bacteria. These multidimentional discussions will provide further insights into the mechanistic proposals of nitrogen-nitrogen bond formation in natural product biosynthesis.
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Affiliation(s)
- Linyue Chen
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
| | - Changming Zhao
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Hubei 430072, People’s Republic of China
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12
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Kalia VC, Gong C, Patel SKS, Lee JK. Regulation of Plant Mineral Nutrition by Signal Molecules. Microorganisms 2021; 9:microorganisms9040774. [PMID: 33917219 PMCID: PMC8068062 DOI: 10.3390/microorganisms9040774] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/30/2021] [Accepted: 04/03/2021] [Indexed: 01/15/2023] Open
Abstract
Microbes operate their metabolic activities at a unicellular level. However, it has been revealed that a few metabolic activities only prove beneficial to microbes if operated at high cell densities. These cell density-dependent activities termed quorum sensing (QS) operate through specific chemical signals. In Gram-negative bacteria, the most widely reported QS signals are acylhomoserine lactones. In contrast, a novel QS-like system has been elucidated, regulating communication between microbes and plants through strigolactones. These systems regulate bioprocesses, which affect the health of plants, animals, and human beings. This mini-review presents recent developments in the QS and QS-like signal molecules in promoting plant health.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (V.C.K.); (S.K.S.P.)
| | - Chunjie Gong
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China;
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (V.C.K.); (S.K.S.P.)
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea; (V.C.K.); (S.K.S.P.)
- Correspondence:
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13
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Kretsch AM, Morgan GL, Acken KA, Barr SA, Li B. Pseudomonas Virulence Factor Pathway Synthesizes Autoinducers That Regulate the Secretome of a Pathogen. ACS Chem Biol 2021; 16:501-509. [PMID: 33595276 DOI: 10.1021/acschembio.0c00901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cell-to-cell communication via chemical signals is an essential mechanism that pathogenic bacteria use to coordinate group behaviors and promote virulence. The Pseudomonas virulence factor (pvf) gene cluster is distributed in more than 500 strains of proteobacteria including both plant and human pathogens. The pvf cluster has been implicated in the production of signaling molecules important for virulence; however, the regulatory impact of these signaling molecules on virulence had not been elucidated. Using the insect pathogen Pseudomonas entomophila L48 as a model, we demonstrated that pvf-encoded biosynthetic enzymes produce PVF autoinducers that regulate the expression of pvf genes and a gene encoding the toxin monalysin via quorum sensing. In addition, PVF autoinducers regulate the expression of nearly 200 secreted and membrane proteins, including toxins, motility proteins, and components of the type VI secretion system, which play key roles in bacterial virulence, colonization, and competition with other microbes. Deletion of pvf also altered the secondary metabolome. Six major compounds upregulated by PVF autoinducers were isolated and structurally characterized, including three insecticidal 3-indolyl oxazoles, the labradorins, and three antimicrobial pyrrolizidine alkaloids, the pyreudiones. The signaling properties of PVF autoinducers and their wide-ranging regulatory effects indicate multifaceted roles of PVF in controlling cell physiology and promoting virulence. The broad genome distribution of pvf suggests that PVF-mediated signaling is relevant to many bacteria of agricultural and biomedical significance.
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Shi J, Xu X, Liu PY, Hu YL, Zhang B, Jiao RH, Bashiri G, Tan RX, Ge HM. Discovery and biosynthesis of guanipiperazine from a NRPS-like pathway. Chem Sci 2021; 12:2925-2930. [PMID: 34164059 PMCID: PMC8179380 DOI: 10.1039/d0sc06135b] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are modular enzymes that use a thiotemplate mechanism to assemble the peptide backbones of structurally diverse and biologically active natural products in bacteria and fungi. Unlike these canonical multi-modular NRPSs, single-module NRPS-like enzymes, which lack the key condensation (C) domain, are rare in bacteria, and have been largely unexplored to date. Here, we report the discovery of a gene cluster (gup) encoding a NRPS-like megasynthetase through genome mining. Heterologous expression of the gup cluster led to the production of two unprecedented alkaloids, guanipiperazines A and B. The NRPS-like enzyme activates two l-tyrosine molecules, reduces them to the corresponding amino aldehydes, and forms an unstable imine product. The subsequent enzymatic reduction affords piperazine, which can be morphed by a P450 monooxygenase into a highly strained compound through C–O bond formation. Further intermolecular oxidative coupling forming the C–C or C–O bond is catalyzed by another P450 enzyme. This work reveals the huge potential of NRPS-like biosynthetic gene clusters in the discovery of novel natural products. Genome mining of a NRPS-like gene cluster led to the identification of two novel alkaloids with antimicrobial activity. This work reveals the huge potential of NRPS-like biosynthetic gene clusters in the discovery of novel natural products.![]()
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Affiliation(s)
- Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Xiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Pei Yi Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Yi Ling Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Ghader Bashiri
- Laboratory of Structural Biology, Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland Auckland 1010 New Zealand
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
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