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Shende VV, Bauman KD, Moore BS. The shikimate pathway: gateway to metabolic diversity. Nat Prod Rep 2024; 41:604-648. [PMID: 38170905 PMCID: PMC11043010 DOI: 10.1039/d3np00037k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.
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Affiliation(s)
- Vikram V Shende
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Katherine D Bauman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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2
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Skala LE, Philmus B, Mahmud T. Modifications of Protein-Bound Substrates by Trans-Acting Enzymes in Natural Products Biosynthesis. Chembiochem 2024; 25:e202400056. [PMID: 38386898 PMCID: PMC11021167 DOI: 10.1002/cbic.202400056] [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: 01/21/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/24/2024]
Abstract
Enzymatic modifications of small molecules are a common phenomenon in natural product biosynthesis, leading to the production of diverse bioactive compounds. In polyketide biosynthesis, modifications commonly take place after the completion of the polyketide backbone assembly by the polyketide synthases and the mature products are released from the acyl-carrier protein (ACP). However, exceptions to this rule appear to be widespread, as on-line hydroxylation, methyl transfer, and cyclization during polyketide assembly process are common, particularly in trans-AT PKS systems. Many of these modifications are catalyzed by specific domains within the modular PKS systems. However, several of the on-line modifications are catalyzed by stand-alone proteins. Those include the on-line Baeyer-Villiger oxidation, α-hydroxylation, halogenation, epoxidation, and methyl esterification during polyketide assembly, dehydrogenation of ACP-bound short fatty acids by acyl-CoA dehydrogenase-like enzymes, and glycosylation of ACP-bound intermediates by discrete glycosyltransferase enzymes. This review article highlights some of these trans-acting proteins that catalyze enzymatic modifications of ACP-bound small molecules in natural product biosynthesis.
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Affiliation(s)
- Leigh E Skala
- Department of Pharmaceutical Sciences, Oregon State University, 203 Pharmacy Building, Corvallis, Oregon, 97331, U.S.A
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, 203 Pharmacy Building, Corvallis, Oregon, 97331, U.S.A
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, 203 Pharmacy Building, Corvallis, Oregon, 97331, U.S.A
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3
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Blicharska N, Ben Ahmed Z, Jackson S, Rotondo D, Seidel V. In silico studies on the anti-acne potential of Garcinia mangostana xanthones and benzophenones. Z NATURFORSCH C 2024; 79:47-60. [PMID: 38549398 DOI: 10.1515/znc-2023-0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/09/2024] [Indexed: 05/01/2024]
Abstract
Garcinia mangostana fruits are used traditionally for inflammatory skin conditions, including acne. In this study, an in silico approach was employed to predict the interactions of G. mangostana xanthones and benzophenones with three proteins involved in the pathogenicity of acne, namely the human JNK1, Cutibacterium acnes KAS III and exo-β-1,4-mannosidase. Molecular docking analysis was performed using Autodock Vina. The highest docking scores and size-independent ligand efficiency values towards JNK1, C. acnes KAS III and exo-β-1,4-mannosidase were obtained for garcinoxanthone T, gentisein/2,4,6,3',5'-pentahydroxybenzophenone and mangostanaxanthone VI, respectively. To the best of our knowledge, this is the first report of the potential of xanthones and benzophenones to interact with C. acnes KAS III. Molecular dynamics simulations using GROMACS indicated that the JNK1-garcinoxanthone T complex had the highest stability of all ligand-protein complexes, with a high number of hydrogen bonds predicted to form between this ligand and its target. Petra/Osiris/Molinspiration (POM) analysis was also conducted to determine pharmacophore sites and predict the molecular properties of ligands influencing ADMET. All ligands, except for mangostanaxanthone VI, showed good membrane permeability. Garcinoxanthone T, gentisein and 2,4,6,3',5'-pentahydroxybenzophenone were identified as the most promising compounds to explore further, including in experimental studies, for their anti-acne potential.
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Affiliation(s)
- Natalia Blicharska
- Strathclyde Institute of Pharmacy & Biomedical Sciences, 3527 University of Strathclyde , Glasgow, UK
| | - Ziyad Ben Ahmed
- Laboratory of Fundamental Science, University Amar Telidji, Laghouat, Algeria
- Department of Analytical Chemistry, Applied Chemometrics and Molecular Modelling, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Simon Jackson
- Botanical Research Department, Davines S.p.A. Via Don Angelo Calzolari 55/A, Parma 43126, Italy
| | - Dino Rotondo
- Strathclyde Institute of Pharmacy & Biomedical Sciences, 3527 University of Strathclyde , Glasgow, UK
| | - Veronique Seidel
- Strathclyde Institute of Pharmacy & Biomedical Sciences, 3527 University of Strathclyde , Glasgow, UK
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4
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Yñigez-Gutierrez AE, Wurm JE, Froese JT, Rosenthal NE, Bachmann BO. Characterization of Dichloroisoeverninic Acid Biosynthesis and Chemoenzymatic Synthesis of New Orthosomycins. ACS Chem Biol 2024; 19:526-535. [PMID: 38289021 DOI: 10.1021/acschembio.3c00693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The orthosomycins are highly modified oligosaccharide natural products with a broad spectrum and potent antimicrobial activities. These include everninomicins and avilamycins, which inhibit protein translation by binding a unique site on the bacterial ribosome. Notably, ribosomal bound structures reveal a network of interactions between the 50S subunit and dichloroisoeverninic acid (DCIE), the aromatic A1-ring conserved across orthosomycins, but the relationship of these interactions to their antimicrobial activity remains undetermined. Genetic functional analysis of three genes putatively associated with DCIE biosynthesis in the everninomicin producer Micromonospora carbonacea delineates the native biosynthetic pathway and provides previously unreported advanced biosynthetic intermediates. Subsequent in vitro biochemical analyses demonstrate the complete DCIE biosynthetic pathway and provide access to novel everninomicin analogs. In addition to the orsellinate synthase EvdD3 and a flavin-dependent halogenase EvdD2, our results identified a key acyltransferase, EvdD1, responsible for transferring orsellinate from the acyl carrier protein domain of EvdD3 to a heptasaccharide orthosomycin biosynthetic intermediate. We have also shown that EvdD1 is able to transfer unnatural aryl groups via their N-acyl cysteamine thioesters to the everninomicin scaffold and used this as a biocatalyst to generate a panel of unnatural aryl analogs. The impact of diverse aryl functional group substitution on both ribosome inhibition and antibacterial activities demonstrates the importance of the DCIE moiety in the pharmacology of orthosomycins, notably revealing an uncoupling between ribosomal engagement and antibiotic activity. Control of A1-ring functionality in this class of molecules provides a potential handle to explore and address pharmacological roles of the DCIE ring in this potent and unique class of antibiotics.
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Affiliation(s)
| | - Jennifer E Wurm
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jordan T Froese
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nicholas E Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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Chang H, Ji R, Zhu Z, Wang Y, Yan S, He D, Jia Q, Huang P, Cheng T, Wang R, Zhou Y. Target identification, and optimization of dioxygenated amide derivatives as potent antibacterial agents with FabH inhibitory activity. Eur J Med Chem 2024; 265:116064. [PMID: 38159483 DOI: 10.1016/j.ejmech.2023.116064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
The enzyme FabH plays a critical role in the initial step of fatty acid biosynthesis, which is vital for the survival of bacteria. As a result, FabH has emerged as an appealing target for the development of novel antibacterial agents. In this study, employing the chemical proteomics method, we validated the previously identified skeleton amide derivatives bearing dioxygenated rings, potentially formed through metabolic processes. Building upon the proteomics findings, we then synthesized and evaluated 32 compounds containing N-heterocyclic amides for their antimicrobial activity for future optimizing the deoxygenated amides. Several compounds demonstrated potent antimicrobial properties with low toxicity, particularly compound 25, which exhibited remarkable potential as an agent with an MIC range of 1.25-3.13 μg/mL against the tested bacterial strains and an IC50 of 2.0 μM against E. coli-derived FabH. Furthermore, we evaluated nine analogues with relatively low MIC values through cytotoxicity and hemolytic activity assessments, Lipinski's rule-of-five criteria, and in silico ADMET predictions to ascertain their druggability potential. Notably, a detailed docking simulation was performed to investigate the binding interactions of compound 25 within the binding pocket of E. coli FabH, which encouragingly revealed strong binding interactions. Based on our findings, compound 25 emerges as the optimal candidate for in vivo therapy aimed at treating infected skin defects. Remarkably, the application of compound 25 demonstrated a significant reduction in the duration of wound infection and notably accelerated the healing process of infected wounds, achieving an impressive 94 % healing rate by day 10.
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Affiliation(s)
- Haoyun Chang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Ruiying Ji
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Zhiyu Zhu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Yapin Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Shaopeng Yan
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Dan He
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Qike Jia
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Peng Huang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
| | - Tao Cheng
- Pharmaron (Ningbo) Technology Development Co. Ltd., Ningbo, 315336, China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China.
| | - Yang Zhou
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China.
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Xiang L, Shi J, Zhu A, Xu ZF, Liu SH, Wang YS, Guo ZK, Jiao RH, Tan RX, Ge HM. Total Biosynthesis of Mutaxanthene Unveils a Flavoprotein Monooxygenase Catalyzing Xanthene Ring Formation. Angew Chem Int Ed Engl 2023; 62:e202218660. [PMID: 36727486 DOI: 10.1002/anie.202218660] [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: 12/17/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/03/2023]
Abstract
Flavoprotein monooxygenases (FPMOs) play important roles in generating structural complexity and diversity in natural products biosynthesized by type II polyketide synthases (PKSs). In this study, we used genome mining to discover novel mutaxanthene analogues and investigated the biosynthesis of these aromatic polyketides and their unusual xanthene framework. We determined the complete biosynthetic pathway of mutaxathene through in vivo gene deletion and in vitro biochemical experiments. We show that a multifunctional FPMO, MtxO4, catalyzes ring rearrangement and generates the required xanthene ring through a multistep transformation. In addition, we successfully obtained all necessary enzymes for in vitro reconstitution and completed the total biosynthesis of mutaxanthene in a stepwise manner. Our results revealed the formation of a rare xanthene ring in type II polyketide biosynthesis, and demonstrate the potential of using total biosynthesis for the discovery of natural products synthesized by type II PKSs.
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Affiliation(s)
- Lang Xiang
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jing Shi
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ao Zhu
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zi Fei Xu
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shuang He Liu
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yi Shuang Wang
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhi Kai Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Rui Hua Jiao
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Ph armaceutical Biotechnology, Institute of Functional Biomolecules, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing, 210023, China
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7
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Mund NK, Čellárová E. Recent advances in the identification of biosynthetic genes and gene clusters of the polyketide-derived pathways for anthraquinone biosynthesis and biotechnological applications. Biotechnol Adv 2023; 63:108104. [PMID: 36716800 DOI: 10.1016/j.biotechadv.2023.108104] [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: 11/14/2022] [Revised: 12/27/2022] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
Natural anthraquinones are represented by a large group of compounds. Some of them are widespread across the kingdoms, especially in bacteria, fungi and plants, while the others are restricted to certain groups of organisms. Despite the significant pharmacological potential of several anthraquinones (hypericin, skyrin and emodin), their biosynthetic pathways and candidate genes coding for key enzymes have not been experimentally validated. Understanding the genetic and epigenetic regulation of the anthraquinone biosynthetic gene clusters in fungal endophytes would help not only understand their pathways in plants, which ensure their commercial availability, but also favor them as promising systems for prospective biotechnological production.
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Affiliation(s)
- Nitesh Kumar Mund
- Pavol Jozef Šafárik University in Košice, Faculty of Science, Institute of Biology and Ecology, Department of Genetics, Mánesova 23, 041 54 Košice, Slovakia
| | - Eva Čellárová
- Pavol Jozef Šafárik University in Košice, Faculty of Science, Institute of Biology and Ecology, Department of Genetics, Mánesova 23, 041 54 Košice, Slovakia.
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8
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Liu Y, Tang Y, Ren S, Chen L. Antibacterial Components and Modes of the Methanol-Phase Extract from Commelina communis Linn. PLANTS (BASEL, SWITZERLAND) 2023; 12:890. [PMID: 36840240 PMCID: PMC9966474 DOI: 10.3390/plants12040890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Infectious diseases caused by pathogenic bacteria severely threaten human health. Traditional Chinese herbs are potential sources of new or alternative medicine. In this study, we analyzed for the first time antibacterial substances in the methanol-phase extract from a traditional Chinese herb-Commelina communis Linn-which showed an inhibition rate of 58.33% against 24 species of common pathogenic bacteria. The extract was further purified using preparative high-performance liquid chromatography (Prep-HPLC), which generated four single fragments (Fragments 1 to 4). The results revealed that Fragment 1 significantly increased bacterial cell surface hydrophobicity and membrane permeability and decreased membrane fluidity, showing disruptive effects on cell integrity of Gram-positive and Gram-negative bacteria, such as Bacillus cereus, Enterococcus faecalis, Staphylococcus aureus, and Salmonella enterica subsp., compared to the control groups (p < 0.05). In sum, 65 compounds with known functions in Fragment 1 were identified using liquid chromatography and mass spectrometry (LC-MS), of which quercetin-3-o-glucuronide was predominant (19.35%). Comparative transcriptomic analysis revealed multiple altered metabolic pathways mediated by Fragment 1, such as inhibited ABC transporters, ribosome, citrate cycle and oxidative phosphorylation, and upregulated nitrogen metabolism and purine metabolism, thereby resulting in the repressed bacterial growth and even death (p < 0.05). Overall, the results of this study demonstrate that Fragment 1 from C. communis Linn is a promising candidate against common pathogenic bacteria.
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Affiliation(s)
- Yue Liu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Shanghai 201306, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yingping Tang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Shanghai 201306, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Shunlin Ren
- Department of Internal Medicine, Virginia Commonwealth University/McGuire VA Medical Centre, Richmond, VA 23298, USA
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Shanghai 201306, China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
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9
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Lin Z, Qu X. Emerging diversity in polyketide synthase. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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10
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Wan Razali WA, Evans CA, Pandhal J. Comparative Proteomics Reveals Evidence of Enhanced EPA Trafficking in a Mutant Strain of Nannochloropsis oculata. Front Bioeng Biotechnol 2022; 10:838445. [PMID: 35646838 PMCID: PMC9134194 DOI: 10.3389/fbioe.2022.838445] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/29/2022] [Indexed: 01/23/2023] Open
Abstract
The marine microalga Nannochloropsis oculata is a bioproducer of eicosapentaenoic acid (EPA), a fatty acid. EPA is incorporated into monogalactosyldiacylglycerol within N. oculata thylakoid membranes, and there is a biotechnological need to remodel EPA synthesis to maximize production and simplify downstream processing. In this study, random mutagenesis and chemical inhibitor-based selection method were devised to increase EPA production and accessibility for improved extraction. Ethyl methanesulfonate was used as the mutagen with selective pressure achieved by using two enzyme inhibitors of lipid metabolism: cerulenin and galvestine-1. Fatty acid methyl ester analysis of a selected fast-growing mutant strain had a higher percentage of EPA (37.5% of total fatty acids) than the wild-type strain (22.2% total fatty acids), with the highest EPA quantity recorded at 68.5 mg/g dry cell weight, while wild-type cells had 48.6 mg/g dry cell weight. Label-free quantitative proteomics for differential protein expression analysis revealed that the wild-type and mutant strains might have alternative channeling pathways for EPA synthesis. The mutant strain showed potentially improved photosynthetic efficiency, thus synthesizing a higher quantity of membrane lipids and EPA. The EPA synthesis pathways could also have deviated in the mutant, where fatty acid desaturase type 2 (13.7-fold upregulated) and lipid droplet surface protein (LDSP) (34.8-fold upregulated) were expressed significantly higher than in the wild-type strain. This study increases the understanding of EPA trafficking in N. oculata, leading to further strategies that can be implemented to enhance EPA synthesis in marine microalgae.
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Affiliation(s)
- Wan Aizuddin Wan Razali
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom.,Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Caroline A Evans
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
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11
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Biosynthesis of cyanobacterin, a paradigm for furanolide core structure assembly. Nat Chem Biol 2022; 18:652-658. [PMID: 35618928 DOI: 10.1038/s41589-022-01013-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 03/11/2022] [Indexed: 11/08/2022]
Abstract
The γ-butyrolactone motif is found in many natural signaling molecules and other specialized metabolites. A prominent example is the potent aquatic phytotoxin cyanobacterin, which has a highly functionalized γ-butyrolactone core structure. The enzymatic machinery that assembles cyanobacterin and structurally related natural products (herein termed furanolides) has remained elusive for decades. Here, we elucidate the biosynthetic process of furanolide assembly. The cyanobacterin biosynthetic gene cluster was identified by targeted bioinformatic screening and validated by heterologous expression in Escherichia coli. Full functional evaluation of the recombinant key enzymes in vivo and in vitro, individually and in concert, provided in-depth mechanistic insights into a streamlined C-C bond-forming cascade that involves installation of compatible reactivity at seemingly unreactive Cα positions of amino acid precursors. Our work extends the biosynthetic and biocatalytic toolbox for γ-butyrolactone formation, provides a general paradigm for furanolide biosynthesis and sets the stage for their targeted discovery, biosynthetic engineering and enzymatic synthesis.
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12
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Improving Antimicrobial Activity and Physico-Chemical Properties by Isosteric Replacement of 2-Aminothiazole with 2-Aminooxazole. Pharmaceuticals (Basel) 2022; 15:ph15050580. [PMID: 35631406 PMCID: PMC9143880 DOI: 10.3390/ph15050580] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/28/2022] [Accepted: 05/03/2022] [Indexed: 02/01/2023] Open
Abstract
Antimicrobial drug resistance is currently one of the most critical health issues. Pathogens resistant to last-resort antibiotics are increasing, and very few effective antibacterial agents have been introduced in recent years. The promising drug candidates are often discontinued in the primary stages of the drug discovery pipeline due to their unspecific reactivity (PAINS), toxicity, insufficient stability, or low water solubility. In this work, we investigated a series of substituted N-oxazolyl- and N-thiazolylcarboxamides of various pyridinecarboxylic acids. Final compounds were tested against several microbial species. In general, oxazole-containing compounds showed high activity against mycobacteria, especially Mycobacterium tuberculosis (best MICH37Ra = 3.13 µg/mL), including the multidrug-resistant strains. Promising activities against various bacterial and fungal strains were also observed. None of the compounds was significantly cytotoxic against the HepG2 cell line. Experimental measurement of lipophilicity parameter log k’w and water solubility (log S) confirmed significantly (typically two orders in logarithmic scale) increased hydrophilicity/water solubility of oxazole derivatives in comparison with their thiazole isosteres. Mycobacterial β-ketoacyl-acyl carrier protein synthase III (FabH) was suggested as a probable target by molecular docking and molecular dynamics simulations.
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Yan X, Zhang J, Tan H, Liu Z, Jiang K, Tian W, Zheng M, Lin Z, Deng Z, Qu X. A Pair of Atypical KAS III Homologues with Initiation and Elongation Functions Program the Polyketide Biosynthesis in Asukamycin. Angew Chem Int Ed Engl 2022; 61:e202200879. [DOI: 10.1002/anie.202200879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Xiaoli Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Jun Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Hongqun Tan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Zhihao Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Kai Jiang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Wenya Tian
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
| | - Zhi Lin
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education School of Pharmaceutical Sciences Wuhan University 1 Luojiashan Rd. Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology Shanghai Jiao Tong University 800 Dongchuan Rd. Shanghai 200240 China
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14
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Castro-Falcón G, Creamer KE, Chase AB, Kim MC, Sweeney D, Glukhov E, Fenical W, Jensen PR. Structure and Candidate Biosynthetic Gene Cluster of a Manumycin-Type Metabolite from Salinispora pacifica. JOURNAL OF NATURAL PRODUCTS 2022; 85:980-986. [PMID: 35263117 PMCID: PMC9209988 DOI: 10.1021/acs.jnatprod.1c01117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A new manumycin-type natural product named pacificamide (1) and its candidate biosynthetic gene cluster (pac) were discovered from the marine actinobacterium Salinispora pacifica CNT-855. The structure of the compound was determined using NMR, electronic circular dichroism, and bioinformatic predictions. The pac gene cluster is unique to S. pacifica and found in only two of the 119 Salinispora genomes analyzed across nine species. Comparative analyses of biosynthetic gene clusters encoding the production of related manumycin-type compounds revealed genetic differences in accordance with the unique pacificamide structure. Further queries of manumycin-type gene clusters from public databases revealed their limited distribution across the phylum Actinobacteria and orphan diversity that suggests additional products remain to be discovered in this compound class. Production of the known metabolite triacsin D is also reported for the first time from the genus Salinispora. This study adds two classes of compounds to the natural product collective isolated from the genus Salinispora, which has proven to be a useful model for natural product research.
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Affiliation(s)
- Gabriel Castro-Falcón
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Kaitlin E Creamer
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Alexander B Chase
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Douglas Sweeney
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
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15
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Yan X, Zhang J, Tan H, Liu Z, Jiang K, Tian W, Zheng M, Lin Z, Deng Z, Qu X. A Pair of Atypical KAS III Homologues with Initiation and Elongation Functions Program the Polyketide Biosynthesis in Asukamycin. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiaoli Yan
- Wuhan University School of pharmaceutical Sciences CHINA
| | - Jun Zhang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Hongqun Tan
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Zhihao Liu
- Wuhan University School of pharmaceutical Sciences CHINA
| | - Kai Jiang
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Wenya Tian
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Mengmeng Zheng
- Wuhan University School of Pharmaceutical Sciences CHINA
| | - Zhi Lin
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Zixin Deng
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology CHINA
| | - Xudong Qu
- Shanghai Jiao Tong University School of Life Sciences and Biotechnology 800 Dongchuan Rd. 200240 Shanghai CHINA
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16
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Li LY, Hu YL, Sun JL, Yu LB, Shi J, Wang ZR, Guo ZK, Zhang B, Guo WJ, Tan RX, Ge HM. Resistance and phylogeny guided discovery reveals structural novelty of tetracycline antibiotics. Chem Sci 2022; 13:12892-12898. [DOI: 10.1039/d2sc03965f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
Using resistance gene genome mining strategy and refinement with chain length factor, we obtained 25 distinct tetracycline biosynthetic gene clusters and a novel tetracycline. The biosynthesis of the highly modified tetracycline was investigated.
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Affiliation(s)
- Ling Yu Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yi Ling Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jia Lin Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Long Bo Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zi Ru Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhi Kai Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Bio-technology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Wen Jie Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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17
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Wu B, Ruan C, Shah AH, Li D, Li H, Ding J, Li J, Du W. Identification of miRNA-mRNA Regulatory Modules Involved in Lipid Metabolism and Seed Development in a Woody Oil Tree ( Camellia oleifera). Cells 2021; 11:cells11010071. [PMID: 35011633 PMCID: PMC8750442 DOI: 10.3390/cells11010071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 12/29/2022] Open
Abstract
Tea oil camellia (Camellia oleifera), an important woody oil tree, is a source of seed oil of high nutritional and medicinal value that is widely planted in southern China. However, there is no report on the identification of the miRNAs involved in lipid metabolism and seed development in the high- and low-oil cultivars of tea oil camellia. Thus, we explored the roles of miRNAs in the key periods of oil formation and accumulation in the seeds of tea oil camellia and identified miRNA–mRNA regulatory modules involved in lipid metabolism and seed development. Sixteen small RNA libraries for four development stages of seed oil biosynthesis in high- and low-oil cultivars were constructed. A total of 196 miRNAs, including 156 known miRNAs from 35 families, and 40 novel miRNAs were identified, and 55 significantly differentially expressed miRNAs were found, which included 34 upregulated miRNAs, and 21 downregulated miRNAs. An integrated analysis of the miRNA and mRNA transcriptome sequence data revealed that 10 miRNA–mRNA regulatory modules were related to lipid metabolism; for example, the regulatory modules of ath-miR858b–MYB82/MYB3/MYB44 repressed seed oil biosynthesis, and a regulation module of csi-miR166e-5p–S-ACP-DES6 was involved in the formation and accumulation of oleic acid. A total of 23 miRNA–mRNA regulatory modules were involved in the regulation of the seed size, such as the regulatory module of hpe-miR162a_L-2–ARF19, involved in early seed development. A total of 12 miRNA–mRNA regulatory modules regulating growth and development were identified, such as the regulatory modules of han-miR156a_L+1–SPL4/SBP2, promoting early seed development. The expression changes of six miRNAs and their target genes were validated using quantitative real-time PCR, and the targeting relationship of the cpa-miR393_R-1–AFB2 regulatory module was verified by luciferase assays. These data provide important theoretical values and a scientific basis for the genetic improvement of new cultivars of tea oil camellia in the future.
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Affiliation(s)
- Bo Wu
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
- Correspondence: ; Tel.: +86-411-87652536
| | - Asad Hussain Shah
- Department of Biotechnology, Faculty of Sciences, University of Kotli Azad Jammu and Kashmir, Azad Jammu and Kashmir, Kotli 11100, Pakistan;
| | - Denghui Li
- Guizhou Wulingshan Youcha Technology Innovation Research Institute Co., Ltd., Tongren 554300, China;
| | - He Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
| | - Jian Ding
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
| | - Jingbin Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
| | - Wei Du
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China; (B.W.); (H.L.); (J.D.); (J.L.); (W.D.)
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18
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Del Rio Flores A, Twigg FF, Du Y, Cai W, Aguirre DQ, Sato M, Dror MJ, Narayanamoorthy M, Geng J, Zill NA, Zhai R, Zhang W. Biosynthesis of triacsin featuring an N-hydroxytriazene pharmacophore. Nat Chem Biol 2021; 17:1305-1313. [PMID: 34725510 PMCID: PMC8605994 DOI: 10.1038/s41589-021-00895-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/09/2021] [Indexed: 01/08/2023]
Abstract
Triacsins are an intriguing class of specialized metabolites possessing a conserved N-hydroxytriazene moiety not found in any other known natural products. Triacsins are notable as potent acyl-CoA synthetase inhibitors in lipid metabolism, yet their biosynthesis has remained elusive. Through extensive mutagenesis and biochemical studies, we here report all enzymes required to construct and install the N-hydroxytriazene pharmacophore of triacsins. Two distinct ATP-dependent enzymes were revealed to catalyze the two consecutive N-N bond formation reactions, including a glycine-utilizing, hydrazine-forming enzyme (Tri28) and a nitrite-utilizing, N-nitrosating enzyme (Tri17). This study paves the way for future mechanistic interrogation and biocatalytic application of enzymes for N-N bond formation.
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Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Frederick F Twigg
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Yongle Du
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Daniel Q Aguirre
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Moriel J Dror
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | | | - Jiaxin Geng
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, United States
| | - Nicholas A Zill
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Rui Zhai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, United States.
- Chan Zuckerberg Biohub, San Francisco, CA, United States.
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19
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Smith MD, Tassoulas LJ, Biernath TA, Richman JE, Aukema KG, Wackett LP. p-Nitrophenyl esters provide new insights and applications for the thiolase enzyme OleA. Comput Struct Biotechnol J 2021; 19:3087-3096. [PMID: 34141132 PMCID: PMC8180931 DOI: 10.1016/j.csbj.2021.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/21/2022] Open
Abstract
The OleA enzyme is distinct amongst thiolase enzymes in binding two long (≥C8) acyl chains into structurally-opposed hydrophobic channels, denoted A and B, to carry out a non-decarboxylative Claisen condensation reaction and initiate the biosynthesis of membrane hydrocarbons and β-lactone natural products. OleA has now been identified in hundreds of diverse bacteria via bioinformatics and high-throughput screening using p-nitrophenyl alkanoate esters as surrogate substrates. In the present study, p-nitrophenyl esters were used to probe the reaction mechanism of OleA and shown to be incorporated into Claisen condensation products for the first time. p-Nitrophenyl alkanoate substrates alone were shown not to undergo Claisen condensation, but co-incubation of p-nitrophenyl esters and CoA thioesters produced mixed Claisen products. Mixed product reactions were shown to initiate via acyl group transfer from a p-nitrophenyl carrier to the enzyme active site cysteine, C143. Acyl chains esterified to p-nitrophenol were synthesized and shown to undergo Claisen condensation with an acyl-CoA substrate, showing potential to greatly expand the range of possible Claisen products. Using p-nitrophenyl 1-13C-decanoate, the Channel A bound thioester chain was shown to act as the Claisen nucleophile, representing the first direct evidence for the directionality of the Claisen reaction in any OleA enzyme. These results both provide new insights into OleA catalysis and open a path for making unnatural hydrocarbon and β-lactone natural products for biotechnological applications using cheap and easily synthesized p-nitrophenyl esters.
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Affiliation(s)
- Megan D. Smith
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
- Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, USA
| | - Lambros J. Tassoulas
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Troy A. Biernath
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
| | - Jack E. Richman
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Kelly G. Aukema
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
| | - Lawrence P. Wackett
- Biotechnology Institute, University of Minnesota, St Paul, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, MN, USA
- Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN, USA
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20
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Price NPJ, Jackson MA, Hartman TM, Brändén G, Ek M, Koch AA, Kennedy PD. Branched Chain Lipid Metabolism As a Determinant of the N-Acyl Variation of Streptomyces Natural Products. ACS Chem Biol 2021; 16:116-124. [PMID: 33411499 DOI: 10.1021/acschembio.0c00799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Branched-chain fatty acids (BCFA) are encountered in Gram-positive bacteria, but less so in other organisms. The bacterial BCFA in membranes are typically saturated, with both odd- and even-numbered carbon chain lengths, and with methyl branches at either the ω-1 (iso) or ω-2 (anteiso) positions. The acylation with BCFA also contributes to the structural diversity of microbial natural products and potentially modulates biological activity. For the tunicamycin (TUN) family of natural products, the toxicity toward eukaryotes is highly dependent upon N-acylation with trans-2,3-unsaturated BCFA. The loss of the 2,3-unsaturation gives modified TUN with reduced eukaryotic toxicity but crucially with retention of the synergistic enhancement of the β-lactam group of antibiotics. Here, we infer from genomics, mass spectrometry, and deuterium labeling that the trans-2,3-unsaturated TUN variants and the saturated cellular lipids found in TUN-producing Streptomyces are derived from the same pool of BCFA metabolites. Moreover, non-natural primers of BCFA metabolism are selectively incorporated into the cellular lipids of TUN-producing Streptomyces and concomitantly produce structurally novel neo-branched TUN N-acyl variants.
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Affiliation(s)
- Neil P. J. Price
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Michael A. Jackson
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Trina M. Hartman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Margareta Ek
- Structure, Biophysics & FBLG, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Aaron A. Koch
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
| | - Paul D. Kennedy
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
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21
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Dashti Y, Nakou IT, Mullins AJ, Webster G, Jian X, Mahenthiralingam E, Challis GL. Discovery and Biosynthesis of Bolagladins: Unusual Lipodepsipeptides from Burkholderia gladioli Clinical Isolates*. Angew Chem Int Ed Engl 2020; 59:21553-21561. [PMID: 32780452 PMCID: PMC7756342 DOI: 10.1002/anie.202009110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Indexed: 01/01/2023]
Abstract
Two Burkholderia gladioli strains isolated from the lungs of cystic fibrosis patients were found to produce unusual lipodepsipeptides containing a unique citrate-derived fatty acid and a rare dehydro-β-alanine residue. The gene cluster responsible for their biosynthesis was identified by bioinformatics and insertional mutagenesis. In-frame deletions and enzyme activity assays were used to investigate the functions of several proteins encoded by the biosynthetic gene cluster, which was found in the genomes of about 45 % of B. gladioli isolates, suggesting that its metabolic products play an important role in the growth and/or survival of the species. The Chrome Azurol S assay indicated that these metabolites bind ferric iron, which suppresses their production when added to the growth medium. Moreover, a gene encoding a TonB-dependent ferric-siderophore receptor is adjacent to the biosynthetic genes, suggesting that these metabolites may function as siderophores in B. gladioli.
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Affiliation(s)
- Yousef Dashti
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Current address: The Centre for Bacterial Cell BiologyBiosciences InstituteMedical SchoolNewcastle UniversityNewcastle upon TyneNE2 4AXUK
| | - Ioanna T. Nakou
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
| | - Alex J. Mullins
- Microbiomes, Microbes and Informatics GroupOrganisms and Environment DivisionSchool of BiosciencesCardiff UniversityCardiffCF103 ATUK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics GroupOrganisms and Environment DivisionSchool of BiosciencesCardiff UniversityCardiffCF103 ATUK
| | - Xinyun Jian
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics GroupOrganisms and Environment DivisionSchool of BiosciencesCardiff UniversityCardiffCF103 ATUK
| | - Gregory L. Challis
- Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
- Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
- Department of Biochemistry and Molecular Biology, ARC Centre of Excellence for Innovations in Peptide and Protein ScienceMonash UniversityClaytonVIC3800Australia
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22
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Dashti Y, Nakou IT, Mullins AJ, Webster G, Jian X, Mahenthiralingam E, Challis GL. Discovery and Biosynthesis of Bolagladins: Unusual Lipodepsipeptides from
Burkholderia gladioli
Clinical Isolates**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yousef Dashti
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Current address: The Centre for Bacterial Cell Biology Biosciences Institute Medical School Newcastle University Newcastle upon Tyne NE2 4AX UK
| | - Ioanna T. Nakou
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
| | - Alex J. Mullins
- Microbiomes, Microbes and Informatics Group Organisms and Environment Division School of Biosciences Cardiff University Cardiff CF103 AT UK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics Group Organisms and Environment Division School of Biosciences Cardiff University Cardiff CF103 AT UK
| | - Xinyun Jian
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Warwick Integrative Synthetic Biology Centre University of Warwick Coventry CV4 7AL UK
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group Organisms and Environment Division School of Biosciences Cardiff University Cardiff CF103 AT UK
| | - Gregory L. Challis
- Department of Chemistry University of Warwick Coventry CV4 7AL UK
- Warwick Integrative Synthetic Biology Centre University of Warwick Coventry CV4 7AL UK
- Department of Biochemistry and Molecular Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton VIC 3800 Australia
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23
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Robinson SL, Smith MD, Richman JE, Aukema KG, Wackett LP. Machine learning-based prediction of activity and substrate specificity for OleA enzymes in the thiolase superfamily. Synth Biol (Oxf) 2020. [DOI: 10.1093/synbio/ysaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Abstract
Enzymes in the thiolase superfamily catalyze carbon–carbon bond formation for the biosynthesis of polyhydroxyalkanoate storage molecules, membrane lipids and bioactive secondary metabolites. Natural and engineered thiolases have applications in synthetic biology for the production of high-value compounds, including personal care products and therapeutics. A fundamental understanding of thiolase substrate specificity is lacking, particularly within the OleA protein family. The ability to predict substrates from sequence would advance (meta)genome mining efforts to identify active thiolases for the production of desired metabolites. To gain a deeper understanding of substrate scope within the OleA family, we measured the activity of 73 diverse bacterial thiolases with a library of 15 p-nitrophenyl ester substrates to build a training set of 1095 unique enzyme–substrate pairs. We then used machine learning to predict thiolase substrate specificity from physicochemical and structural features. The area under the receiver operating characteristic curve was 0.89 for random forest classification of enzyme activity, and our regression model had a test set root mean square error of 0.22 (R2 = 0.75) to quantitatively predict enzyme activity levels. Substrate aromaticity, oxygen content and molecular connectivity were the strongest predictors of enzyme–substrate pairing. Key amino acid residues A173, I284, V287, T292 and I316 in the Xanthomonas campestris OleA crystal structure lining the substrate binding pockets were important for thiolase substrate specificity and are attractive targets for future protein engineering studies. The predictive framework described here is generalizable and demonstrates how machine learning can be used to quantitatively understand and predict enzyme substrate specificity.
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Affiliation(s)
- Serina L Robinson
- Graduate Program in Bioinformatics and Computational Biology, University of Minnesota, 111 S. Broadway, Suite 300, Rochester, MN 55904, USA
- Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, 689 23rd Ave SE, Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Megan D Smith
- Graduate Program in Microbiology, Immunology, and Cancer Biology, University of Minnesota, 689 23rd Ave SE, Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Jack E Richman
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Kelly G Aukema
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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24
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Kandasamy M, Amalraj AJJ, Perumal G, Ganesan B, Senadi GC, Lin WY. Continuous flow as a benign strategy for the synthesis of Thioesters via selective C-N bond cleavage. J Flow Chem 2020. [DOI: 10.1007/s41981-020-00090-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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25
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Sigrist R, Luhavaya H, McKinnie SMK, Ferreira da Silva A, Jurberg ID, Moore BS, Gonzaga de Oliveira L. Nonlinear Biosynthetic Assembly of Alpiniamide by a Hybrid cis/ trans-AT PKS-NRPS. ACS Chem Biol 2020; 15:1067-1077. [PMID: 32195572 DOI: 10.1021/acschembio.0c00081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alpiniamide A is a linear polyketide produced by Streptomyces endophytic bacteria. Despite its relatively simple chemical structure suggestive of a linear assembly line biosynthetic construction involving a hybrid polyketide synthase-nonribosomal peptide synthetase enzymatic protein machine, we report an unexpected nonlinear synthesis of this bacterial natural product. Using a combination of genomics, heterologous expression, mutagenesis, isotope-labeling, and chain terminator experiments, we propose that alpiniamide A is assembled in two halves and then ligated into the mature molecule. We show that each polyketide half is constructed using orthogonal biosynthetic strategies, employing either cis- or trans-acyl transferase mechanisms, thus prompting an alternative proposal for the operation of this PKS-NRPS.
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Affiliation(s)
- Renata Sigrist
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Shaun M. K. McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Amanda Ferreira da Silva
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Igor D. Jurberg
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Luciana Gonzaga de Oliveira
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
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Reconstitution of polythioamide antibiotic backbone formation reveals unusual thiotemplated assembly strategy. Proc Natl Acad Sci U S A 2020; 117:8850-8858. [PMID: 32265283 PMCID: PMC7183216 DOI: 10.1073/pnas.1918759117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nonribosomal peptides (NRPs) are a vast class of natural products and an important source of therapeutics. Typically, these secondary metabolites are assembled by NRP synthetases (NRPSs) that function on substrates covalently linked to the enzyme by a thioester, in a process known as thiotemplated biosynthesis. Although NRPS-independent assembly pathways are known, all are nonthiotemplated. Here we report an NRPS-independent yet thiotemplated pathway for NRP biosynthesis and demonstrate that members of the ATP-grasp and cysteine protease families form the β-peptide backbone of an antibiotic. Armed with this knowledge, we provide genomic evidence that this noncanonical assembly pathway is widespread in bacteria. Our results will inspire future genome mining efforts for the discovery of potential therapeutics that otherwise would be overlooked. Closthioamide (CTA) is a rare example of a thioamide-containing nonribosomal peptide and is one of only a handful of secondary metabolites described from obligately anaerobic bacteria. Although the biosynthetic gene cluster responsible for CTA production and the thioamide synthetase that catalyzes sulfur incorporation were recently discovered, the logic for peptide backbone assembly has remained a mystery. Here, through the use of in vitro biochemical assays, we demonstrate that the amide backbone of CTA is assembled in an unusual thiotemplated pathway involving the cooperation of a transacylating member of the papain-like cysteine protease family and an iteratively acting ATP-grasp protein. Using the ATP-grasp protein as a bioinformatic handle, we identified hundreds of such thiotemplated yet nonribosomal peptide synthetase (NRPS)-independent biosynthetic gene clusters across diverse bacterial phyla. The data presented herein not only clarify the pathway for the biosynthesis of CTA, but also provide a foundation for the discovery of additional secondary metabolites produced by noncanonical biosynthetic pathways.
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Xing C, Chen J, Zheng X, Chen L, Chen M, Wang L, Li X. Functional metagenomic exploration identifies novel prokaryotic copper resistance genes from the soil microbiome. Metallomics 2020; 12:387-395. [PMID: 31942889 DOI: 10.1039/c9mt00273a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Functional metagenomics is a premise-free approach for exploring metal resistance genes, enabling more profound effects on the development of bioremediation tools than pure culture based selection. Six soil metagenomic libraries were screened for copper (Cu) resistance genes in the current study through conventional functional genomics. Clones from the six metagenomic libraries were randomly selected from solid medium supplied with Cu, resulting in 411 Cu resistance clones. Thirty-five clones with the strongest Cu resistance were sequenced and 12 unique sequences harboring 25 putative open reading frames were obtained. It is inferred by bioinformatic analysis that putative genes carried by these recombinant plasmids probably function in the pathways of responding to Cu stress, including energy metabolism, integral components of membrane, ion transport/chelation, protein/amino acid metabolism, carbohydrate/fatty acid metabolism, signal transduction and DNA binding. The sequenced clones were re-transformed into Escherichia coli strain DH5α, and the host's biomass and the metal sorption under Cu stress were subsequently determined. The results showed that the biomass of eight of the clones was significantly increased, whereas four of them were significantly reduced. A negative correlation (R = 0.86) was found between the biomass and Cu sorption capacity. The 12 positive clones were further transferred into a Cu-sensitive E. coli strain (ΔCopA), among which nine restored the host's Cu resistance substantially. The Cu resistant genes explored in this study by functional metagenomics possess a potential capacity for developing novel bioremediation strategies, and the findings imply a vast diversity of microbial Cu resistance genetic factors in soil yet to be discovered.
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Affiliation(s)
- Chao Xing
- Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
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