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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Back D, O’Donnell TJ, Axt KK, Gurr JR, Vanegas JM, Williams PG, Philmus B. Identification, Heterologous Expression, and Characterization of the Tolypodiol Biosynthetic Gene Cluster through an Integrated Approach. ACS Chem Biol 2023; 18:1797-1807. [PMID: 37487226 PMCID: PMC10529828 DOI: 10.1021/acschembio.3c00225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Cyanobacteria are tremendous producers of biologically active natural products, including the potent anti-inflammatory compound tolypodiol. However, linking biosynthetic gene clusters with compound production in cyanobacteria has lagged behind that in other bacterial genera. Tolypodiol is a meroterpenoid originally isolated from the cyanobacterium HT-58-2. Here we describe the identification of the tolypodiol biosynthetic gene cluster through heterologous expression in Anabaena and in vitro protein assays of a methyltransferase found in the tolypodiol biosynthetic gene cluster. We have also identified similar biosynthetic gene clusters in cyanobacterial and actinobacterial genomes, suggesting that meroterpenoids with structural similarity to the tolypodiols may be synthesized by other microbes. We also report the identification of two new analogs of tolypodiol that we have identified in both the original and heterologous producer. This work further illustrates the usefulness of Anabaena as a heterologous expression host for cyanobacterial compounds and how integrated approaches can help to link natural product compounds with their producing biosynthetic gene clusters.
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Affiliation(s)
- Daniel Back
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Timothy J. O’Donnell
- Department of Chemistry, University of Hawai’i at Mānoa, Honolulu, HI 96822, U.S.A
| | - Kyle K. Axt
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Joshua R. Gurr
- Department of Chemistry, University of Hawai’i at Mānoa, Honolulu, HI 96822, U.S.A
| | - Juan M. Vanegas
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Philip G. Williams
- Department of Chemistry, University of Hawai’i at Mānoa, Honolulu, HI 96822, U.S.A
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331, U.S.A
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3
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Jagels A, Adpressa DA, Kaweesa EN, McCauley M, Philmus B, Strother JA, Loesgen S. Metabolomics-Guided Discovery, Isolation, Structure Elucidation, and Bioactivity of Myropeptins C-E from Myrothecium inundatum. J Nat Prod 2023. [PMID: 37411007 DOI: 10.1021/acs.jnatprod.3c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The saprotrophic filamentous fungus Myrothecium inundatum represents a chemically underexplored ascomycete with a high number of putative biosynthetic gene clusters in its genome. Here, we present new linear lipopeptides from nongenetic gene activation experiments using nutrient and salt variations. Metabolomics studies revealed four myropeptins, and structural analyses by NMR, HRMS, Marfey's analysis, and ECD assessment for their helical properties established their absolute configuration. A myropeptin biosynthetic gene cluster in the genome was identified. The myropeptins exhibit general nonspecific toxicity against all cancer cell lines in the NCI-60 panel, larval zebrafish with EC50 concentrations of 5-30 μM, and pathogenic bacteria and fungi (MICs of 4-32 μg/mL against multidrug-resistant S. aureus and C. auris). In vitro hemolysis, cell viability, and ionophore assays indicate that the myropeptins target mitochondrial and cellular membranes, inducing cell depolarization and cell death. The toxic activity is modulated by the length of the lipid side chain, which provides valuable insight into their structure-activity relationships.
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Affiliation(s)
- Annika Jagels
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, United States
| | | | - Elizabeth N Kaweesa
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, United States
| | - Mark McCauley
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, United States
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - James A Strother
- Department of Biology, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, United States
| | - Sandra Loesgen
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, United States
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4
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Tanoeyadi S, Tsunoda T, Ito T, Philmus B, Mahmud T. Acarbose May Function as a Competitive Exclusion Agent for the Producing Bacteria. ACS Chem Biol 2023; 18:367-376. [PMID: 36648321 PMCID: PMC9957957 DOI: 10.1021/acschembio.2c00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Acarbose is a well-known microbial specialized metabolite used clinically to treat type 2 diabetes. This natural pseudo-oligosaccharide (PsOS) shows potent inhibitory activity toward various glycosyl hydrolases, including α-glucosidases and α-amylases. While acarbose and other PsOSs are produced by many different bacteria, their ecological or biological role in microbial communities is still an open question. Here, we show that several PsOS-producing actinobacteria, i.e., Actinoplanes sp. SE50/110 (acarbose producer), Streptomyces glaucescens GLA.O (acarbose producer), and Streptomyces dimorphogenes ATCC 31484 (trestatin producer), can grow in the presence of acarbose, while the growth of the non-PsOS-producing organism Streptomyces coelicolor M1152 was suppressed when starch is the main source of energy. Further investigations using recombinant α-amylases from S. coelicolor M1152 and the PsOS-producing actinobacteria revealed that the S. coelicolor α-amylase was inhibited by acarbose, whereas those from the PsOS-producing bacteria were not inhibited by acarbose. Bioinformatic and protein modeling studies suggested that a point mutation in the α-amylases of the PsOS-producing actinobacteria is responsible for the resistance of those enzymes toward acarbose. Converting the acarbose-resistant α-amylase AcbE to its A304H variant diminished its acarbose-resistance property. Taken together, the results suggest that acarbose is used by the producing bacteria as a competitive exclusion agent to suppress the growth of other microorganisms in their natural environment, while the producing organisms equip themselves with α-amylase variants that are resistant to acarbose.
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Affiliation(s)
- Samuel Tanoeyadi
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Takuya Ito
- Laboratory of Natural Medicines, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nisikiorikita, Tondabayashi 584-8540 (Japan)
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507 (USA)
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5
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Terlouw BR, Blin K, Navarro-Muñoz JC, Avalon NE, Chevrette MG, Egbert S, Lee S, Meijer D, Recchia MJ, Reitz Z, van Santen J, Selem-Mojica N, Tørring T, Zaroubi L, Alanjary M, Aleti G, Aguilar C, Al-Salihi SA, Augustijn H, Avelar-Rivas J, Avitia-Domínguez L, Barona-Gómez F, Bernaldo-Agüero J, Bielinski VA, Biermann F, Booth T, Carrion Bravo V, Castelo-Branco R, Chagas F, Cruz-Morales P, Du C, Duncan K, Gavriilidou A, Gayrard D, Gutiérrez-García K, Haslinger K, Helfrich EN, van der Hooft JJ, Jati A, Kalkreuter E, Kalyvas N, Kang K, Kautsar S, Kim W, Kunjapur A, Li YX, Lin GM, Loureiro C, Louwen JR, Louwen NL, Lund G, Parra J, Philmus B, Pourmohsenin B, Pronk LU, Rego A, Rex D, Robinson S, Rosas-Becerra L, Roxborough E, Schorn M, Scobie D, Singh K, Sokolova N, Tang X, Udwary D, Vigneshwari A, Vind K, Vromans SJM, Waschulin V, Williams S, Winter J, Witte T, Xie H, Yang D, Yu J, Zdouc M, Zhong Z, Collemare J, Linington R, Weber T, Medema M. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Res 2022; 51:D603-D610. [PMID: 36399496 PMCID: PMC9825592 DOI: 10.1093/nar/gkac1049] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/07/2022] [Accepted: 10/21/2022] [Indexed: 11/19/2022] Open
Abstract
With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.
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Affiliation(s)
| | | | - Jorge C Navarro-Muñoz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0212, USA
| | - Marc G Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Susan Egbert
- Department of Chemistry, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada
| | - Sanghoon Lee
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - David Meijer
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Michael J J Recchia
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Zachary L Reitz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Jeffrey A van Santen
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada,Unnatural Products, 2161 Delaware Ave. Suite A, Santa Cruz, CA 95060, USA
| | | | - Thomas Tørring
- Department of Biological and Chemical Engineering, Aarhus University, Denmark
| | - Liana Zaroubi
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Gajender Aleti
- Food and Animal Sciences, Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - César Aguilar
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands
| | - J Abraham Avelar-Rivas
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Luis A Avitia-Domínguez
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Francisco Barona-Gómez
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Jordan Bernaldo-Agüero
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Friederike Biermann
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Institute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Thomas J Booth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark,School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Victor J Carrion Bravo
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Raquel Castelo-Branco
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal,Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal
| | - Fernanda O Chagas
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Pablo Cruz-Morales
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Chao Du
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK
| | - Athina Gavriilidou
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Damien Gayrard
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Karina Gutiérrez-García
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Kristina Haslinger
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Eric J N Helfrich
- Institute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Afif P Jati
- Indonesian Society of Bioinformatics And Biodiversity, Indonesia
| | - Edward Kalkreuter
- Department of Chemistry, University of Florida Scripps Biomedical Research, 110 Scripps Way, Jupiter, FL 33458, USA
| | - Nikolaos Kalyvas
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, South Korea
| | - Satria Kautsar
- Department of Chemistry, University of Florida Scripps Biomedical Research, 110 Scripps Way, Jupiter, FL 33458, USA
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National Universtiy, Suncheon, South Korea
| | - Aditya M Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P.R. China
| | - Geng-Min Lin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catarina Loureiro
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Joris J R Louwen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Nico L L Louwen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - George Lund
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Jonathan Parra
- Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, 11501-2060, Costa Rica,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica,Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, USA
| | - Bita Pourmohsenin
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany,Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Lotte J U Pronk
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Portugal
| | | | - Serina Robinson
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - L Rodrigo Rosas-Becerra
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands,Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México
| | - Eve T Roxborough
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Darren J Scobie
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK
| | - Kumar Saurabh Singh
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Nika Sokolova
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | | | - Kristiina Vind
- Host-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands,NAICONS Srl, 20139 Milan, Italy
| | - Sophie P J M Vromans
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Valentin Waschulin
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK
| | - Sam E Williams
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Jaclyn M Winter
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Thomas E Witte
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Huali Xie
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands,Key laboratory of Detection for Biotoxins, Ministry of Agriculture and Rural Affairs and Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China
| | - Dong Yang
- Department of Chemistry and Natural Products Discovery Center, UF Scripps Biomedical Research, University of Florida, Jupiter, FL 33458, USA
| | - Jingwei Yu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Mitja Zdouc
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands
| | - Zheng Zhong
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Tilmann Weber
- Correspondence may also be addressed to Tilmann Weber. Tel: +45 24896132;
| | - Marnix H Medema
- To whom correspondence should be addressed. Tel: +31 317484706;
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6
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Back D, Shaffer BT, Loper JE, Philmus B. Untargeted Identification of Alkyne-Containing Natural Products Using Ruthenium-Catalyzed Azide Alkyne Cycloaddition Reactions Coupled to LC-MS/MS. J Nat Prod 2022; 85:105-114. [PMID: 35044192 PMCID: PMC8853637 DOI: 10.1021/acs.jnatprod.1c00798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Alkyne-containing natural products have been identified from plants, insects, algae, fungi, and bacteria. This class of natural products has been characterized as having a variety of biological activities. Polyynes are a subclass of acetylenic natural products that contain conjugated alkynes and are underrepresented in natural product databases due to the fact that they decompose during purification. Here we report a workflow that utilizes alkyne azide cycloaddition (AAC) reactions followed by LC-MS/MS analysis to identify acetylenic natural products. In this report, we demonstrate that alkyne azide cycloaddition reactions with p-bromobenzyl azide result in p-bromobenzyl-substituted triazole products that fragment to a common brominated tropylium ion. We were able to identify a synthetic alkyne spiked into the extract of Anabaena sp. PCC 7120 at a concentration of 10 μg/mL after optimization of MS/MS conditions. We then successfully identified the known natural product fischerellin A in the extract of Fischerella muscicola PCC 9339. Lastly, we identified the recently identified natural products protegenins A and C from Pseudomonas protegens Pf-5 through a combination of genome mining and RuAAC reactions. This is the first report of RuAAC reactions to detect acetylenic natural products. We also compare CuAAC and RuAAC reactions and find that CuAAC reactions produce fewer byproducts compared to RuAAC but is limited to terminal-alkyne-containing compounds. In contrast, RuAAC is capable of identification of both terminal and internal acetylenic natural products, but byproducts need to be eliminated from analysis by creation of an exclusion list. We believe that both CuAAC and RuAAC reactions coupled to LC-MS/MS represent a method for the untargeted identification of acetylenic natural products, but each method has strengths and weaknesses.
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Affiliation(s)
- Daniel Back
- Department of Pharmaceutical Sciences, 203 Pharmacy Bldg., Oregon State University, Corvallis, OR 97331
| | - Brenda T. Shaffer
- Agricultural Research Service, US Department of Agriculture, 3420 N.W. Orchard Avenue, Corvallis, OR 97330
| | - Joyce E. Loper
- Agricultural Research Service, US Department of Agriculture, 3420 N.W. Orchard Avenue, Corvallis, OR 97330
- College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, 203 Pharmacy Bldg., Oregon State University, Corvallis, OR 97331
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7
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Svoboda J, Cisneros B, Philmus B. Evaluation of inducible promoter-riboswitch constructs for heterologous protein expression in the cyanobacterial species Anabaena sp. PCC 7120. Synth Biol (Oxf) 2021; 6:ysab019. [PMID: 34712843 PMCID: PMC8546608 DOI: 10.1093/synbio/ysab019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 07/13/2021] [Accepted: 08/27/2021] [Indexed: 11/14/2022] Open
Abstract
Cyanobacteria are promising chassis for synthetic biology applications due to the fact that they are photosynthetic organisms capable of growing in simple, inexpensive media. Given their slower growth rate than other model organisms such as Escherichia coli and Saccharomyces cerevisiae, there are fewer synthetic biology tools and promoters available for use in model cyanobacteria. Here, we compared a small library of promoter–riboswitch constructs for synthetic biology applications in Anabaena sp. PCC 7120, a model filamentous cyanobacterium. These constructs were designed from six cyanobacterial promoters of various strengths, each paired with one of two theophylline-responsive riboswitches. The promoter–riboswitch pairs were cloned upstream of a chloramphenicol acetyltransferase (cat) gene, and CAT activity was quantified using an in vitro assay. Addition of theophylline to cultures increased the CAT activity in almost all cases, allowing inducible protein production with natively constitutive promoters. We found that riboswitch F tended to have a lower induced and uninduced production compared to riboswitch E for the weak and medium promoters, although the difference was larger for the uninduced production, in accord with previous research. The strong promoters yielded a higher baseline CAT activity than medium strength and weak promoters. In addition, we observed no appreciable difference between CAT activity measured from strong promoters cultured in uninduced and induced conditions. The results of this study add to the genetic toolbox for cyanobacteria and allow future natural product and synthetic biology researchers to choose a construct that fits their needs.
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Affiliation(s)
- Jessee Svoboda
- College of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR, USA
| | - Brenda Cisneros
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Benjamin Philmus
- College of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, OR, USA
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8
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Rodrigues RR, Gurung M, Li Z, García-Jaramillo M, Greer R, Gaulke C, Bauchinger F, You H, Pederson JW, Vasquez-Perez S, White KD, Frink B, Philmus B, Jump DB, Trinchieri G, Berry D, Sharpton TJ, Dzutsev A, Morgun A, Shulzhenko N. Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes. Nat Commun 2021; 12:101. [PMID: 33397942 PMCID: PMC7782853 DOI: 10.1038/s41467-020-20313-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
Western diet (WD) is one of the major culprits of metabolic disease including type 2 diabetes (T2D) with gut microbiota playing an important role in modulating effects of the diet. Herein, we use a data-driven approach (Transkingdom Network analysis) to model host-microbiome interactions under WD to infer which members of microbiota contribute to the altered host metabolism. Interrogation of this network pointed to taxa with potential beneficial or harmful effects on host's metabolism. We then validate the functional role of the predicted bacteria in regulating metabolism and show that they act via different host pathways. Our gene expression and electron microscopy studies show that two species from Lactobacillus genus act upon mitochondria in the liver leading to the improvement of lipid metabolism. Metabolomics analyses revealed that reduced glutathione may mediate these effects. Our study identifies potential probiotic strains for T2D and provides important insights into mechanisms of their action.
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Affiliation(s)
| | - Manoj Gurung
- Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Zhipeng Li
- Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | | | - Renee Greer
- Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | | | - Franziska Bauchinger
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Hyekyoung You
- Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Jacob W Pederson
- Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | | | - Kimberly D White
- Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Briana Frink
- Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Benjamin Philmus
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Donald B Jump
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Berry
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | | | - Amiran Dzutsev
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA.
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9
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Fraser VN, Philmus B, Megraw M. Metabolomics analysis reveals both plant variety and choice of hormone treatment modulate vinca alkaloid production in Catharanthus roseus. Plant Direct 2020; 4:e00267. [PMID: 33005857 PMCID: PMC7520646 DOI: 10.1002/pld3.267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 05/09/2023]
Abstract
The medicinal plant Catharanthus roseus produces numerous secondary metabolites of interest for the treatment of many diseases - most notably for the terpene indole alkaloid (TIA) vinblastine, which is used in the treatment of leukemia and Hodgkin's lymphoma. Historically, methyl jasmonate (MeJA) has been used to induce TIA production, but in the past, this has only been investigated in whole seedlings, cell culture, or hairy root culture. This study examines the effects of the phytohormones MeJA and ethylene on the induction of TIA biosynthesis and accumulation in the shoots and roots of 8-day-old seedlings of two varieties of C. roseus. Using LCMS and RT-qPCR, we demonstrate the importance of variety selection, as we observe markedly different induction patterns of important TIA precursor compounds. Additionally, both phytohormone choice and concentration have significant effects on TIA biosynthesis. Finally, our study suggests that several early-induction pathway steps as well as pathway-specific genes are likely to be transcriptionally regulated. Our findings highlight the need for a complete set of'omics resources in commonly used C. roseus varieties and the need for caution when extrapolating results from one cultivar to another.
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Affiliation(s)
- Valerie N. Fraser
- Molecular and Cellular Biology ProgramOregon State UniversityCorvallisORUSA
- Department of Botany and Plant PathologyOregon State UniversityCorvallisORUSA
| | - Benjamin Philmus
- Department of Pharmaceutical SciencesOregon State UniversityCorvallisORUSA
- Center for Genome Research and BiocomputingOregon State UniversityCorvallisORUSA
| | - Molly Megraw
- Department of Botany and Plant PathologyOregon State UniversityCorvallisORUSA
- Center for Genome Research and BiocomputingOregon State UniversityCorvallisORUSA
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10
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Videau P, Wells KN, Singh AJ, Eiting J, Proteau PJ, Philmus B. Expanding the Natural Products Heterologous Expression Repertoire in the Model Cyanobacterium Anabaena sp. Strain PCC 7120: Production of Pendolmycin and Teleocidin B-4. ACS Synth Biol 2020; 9:63-75. [PMID: 31846576 DOI: 10.1021/acssynbio.9b00334] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cyanobacteria are prolific producers of natural products, and genome mining has shown that many orphan biosynthetic gene clusters can be found in sequenced cyanobacterial genomes. New tools and methodologies are required to investigate these biosynthetic gene clusters, and here we present the use of Anabaena sp. strain PCC 7120 as a host for combinatorial biosynthesis of natural products using the indolactam natural products (lyngbyatoxin A, pendolmycin, and teleocidin B-4) as a test case. We were able to successfully produce all three compounds using codon optimized genes from Actinobacteria. We also introduce a new plasmid backbone based on the native Anabaena 7120 plasmid pCC7120ζ and show that production of teleocidin B-4 can be accomplished using a two-plasmid system, which can be introduced by coconjugation.
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Affiliation(s)
- Patrick Videau
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Kaitlyn N. Wells
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
- Undergraduate Honors College, Oregon State University, Corvallis, Oregon 97331, United States
| | - Arun J. Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Jessie Eiting
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Philip J. Proteau
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
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11
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Wells KN, Videau P, Nelson D, Eiting JE, Philmus B. The influence of sigma factors and ribosomal recognition elements on heterologous expression of cyanobacterial gene clusters in Escherichia coli. FEMS Microbiol Lett 2019; 365:5047307. [PMID: 29982530 DOI: 10.1093/femsle/fny164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/28/2018] [Indexed: 12/16/2022] Open
Abstract
Cyanobacterial natural products offer new possibilities for drugs and lead compounds but many factors can inhibit the production of sufficient yields for pharmaceutical processes. While Escherichia coli and Streptomyces sp. have been used as heterologous expression hosts to produce cyanobacterial natural products, they have not met with resounding success largely due to their inability to recognize cyanobacterial promoter regions. Recent work has shown that the filamentous freshwater cyanobacterium Anabaena sp. strain PCC 7120 recognizes various cyanobacterial promoter regions and can produce lyngbyatoxin A from the native promoter. Introduction of Anabaena sigma factors into E. coli might allow the native transcriptional machinery to recognize cyanobacterial promoters. Here, all 12 Anabaena sigma factors were expressed in E. coli and subsets were found to initiate transcription from several cyanobacterial promoters based on transcriptional fusions to the chloramphenicol acetyltransferase (CAT) reporter. Expression of individual Anabaena sigma factors in E. coli did not result in lyngbyatoxin A production from its native cyanobacterial gene cluster, possibly hindered by deficiencies in recognition of cyanobacterial ribosomal binding sites by native E. coli translational machinery. This represents an important step toward engineering E. coli into a general heterologous expression host for cyanobacterial biosynthetic gene cluster expression.
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Affiliation(s)
- Kaitlyn N Wells
- Undergraduate Honors College, 450 Learning Innovation Center, Oregon State University, Corvallis, OR 97331, USA
| | - Patrick Videau
- Department of Pharmaceutical Sciences, College of Pharmacy, 203 Pharmacy Bldg., Oregon State University, Corvallis, OR 97331, USA
| | - Dylan Nelson
- Department of Pharmaceutical Sciences, College of Pharmacy, 203 Pharmacy Bldg., Oregon State University, Corvallis, OR 97331, USA
| | - Jessie E Eiting
- Department of Pharmaceutical Sciences, College of Pharmacy, 203 Pharmacy Bldg., Oregon State University, Corvallis, OR 97331, USA
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, College of Pharmacy, 203 Pharmacy Bldg., Oregon State University, Corvallis, OR 97331, USA
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12
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Alanjary M, Kronmiller B, Adamek M, Blin K, Weber T, Huson D, Philmus B, Ziemert N. The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Res 2019; 45:W42-W48. [PMID: 28472505 PMCID: PMC5570205 DOI: 10.1093/nar/gkx360] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/20/2017] [Indexed: 11/12/2022] Open
Abstract
With the rise of multi-drug resistant pathogens and the decline in number of potential new antibiotics in development there is a fervent need to reinvigorate the natural products discovery pipeline. Most antibiotics are derived from secondary metabolites produced by microorganisms and plants. To avoid suicide, an antibiotic producer harbors resistance genes often found within the same biosynthetic gene cluster (BGC) responsible for manufacturing the antibiotic. Existing mining tools are excellent at detecting BGCs or resistant genes in general, but provide little help in prioritizing and identifying gene clusters for compounds active against specific and novel targets. Here we introduce the 'Antibiotic Resistant Target Seeker' (ARTS) available at https://arts.ziemertlab.com. ARTS allows for specific and efficient genome mining for antibiotics with interesting and novel targets. The aim of this web server is to automate the screening of large amounts of sequence data and to focus on the most promising strains that produce antibiotics with new modes of action. ARTS integrates target directed genome mining methods, antibiotic gene cluster predictions and 'essential gene screening' to provide an interactive page for rapid identification of known and putative targets in BGCs.
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Affiliation(s)
- Mohammad Alanjary
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Biotechnology, University of Tübingen, 72076 Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Brent Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, 97331 OR, USA
| | - Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Biotechnology, University of Tübingen, 72076 Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Daniel Huson
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, 97331 OR, USA
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Biotechnology, University of Tübingen, 72076 Tübingen, Germany.,German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
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13
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Nofiani R, Philmus B, Nindita Y, Mahmud T. 3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis. Medchemcomm 2019; 10:1517-1530. [PMID: 31673313 DOI: 10.1039/c9md00162j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 11/21/2022]
Abstract
The 3-ketoacyl-ACP synthase (KAS) III proteins are one of the most abundant enzymes in nature, as they are involved in the biosynthesis of fatty acids and natural products. KAS III enzymes catalyse a carbon-carbon bond formation reaction that involves the α-carbon of a thioester and the carbonyl carbon of another thioester. In addition to the typical KAS III enzymes involved in fatty acid and polyketide biosynthesis, there are proteins homologous to KAS III enzymes that catalyse reactions that are different from that of the traditional KAS III enzymes. Those include enzymes that are responsible for a head-to-head condensation reaction, the formation of acetoacetyl-CoA in mevalonate biosynthesis, tailoring processes via C-O bond formation or esterification, as well as amide formation. This review article highlights the diverse reactions catalysed by this class of enzymes and their role in natural product biosynthesis.
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Affiliation(s)
- Risa Nofiani
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA . .,Department of Chemistry , Universitas Tanjungpura , Pontianak , Indonesia
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Yosi Nindita
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
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14
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Gallegos DA, Saurí J, Cohen RD, Wan X, Videau P, Vallota-Eastman AO, Shaala LA, Youssef DTA, Williamson RT, Martin GE, Philmus B, Sikora AE, Ishmael JE, McPhail KL. Jizanpeptins, Cyanobacterial Protease Inhibitors from a Symploca sp. Cyanobacterium Collected in the Red Sea. J Nat Prod 2018; 81:1417-1425. [PMID: 29808677 PMCID: PMC7847313 DOI: 10.1021/acs.jnatprod.8b00117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Jizanpeptins A-E (1-5) are micropeptin depsipeptides isolated from a Red Sea specimen of a Symploca sp. cyanobacterium. The planar structures of the jizanpeptins were established using NMR spectroscopy and mass spectrometry and contain 3-amino-6-hydroxy-2-piperidone (Ahp) as one of eight residues in a typical micropeptin motif, as well as a side chain terminal glyceric acid sulfate moiety. The absolute configurations of the jizanpeptins were assigned using a combination of Marfey's methodology and chiral-phase HPLC analysis of hydrolysis products compared to commercial and synthesized standards. Jizanpeptins A-E showed specific inhibition of the serine protease trypsin (IC50 = 72 nM to 1 μM) compared to chymotrypsin (IC50 = 1.4 to >10 μM) in vitro and were not overtly cytotoxic to HeLa cervical or NCI-H460 lung cancer cell lines at micromolar concentrations.
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Affiliation(s)
- David A. Gallegos
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Josep Saurí
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Ryan D. Cohen
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc.,126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Xuemei Wan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Patrick Videau
- Department of Biology, College of Arts and Sciences, Dakota State University, Madison, SD 57042
| | - Alec O. Vallota-Eastman
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Lamiaa A. Shaala
- Suez Canal University Hospital, Suez Canal University, Ismailia 41522, Egypt
| | - Diaa T. A. Youssef
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - R. Thomas Williamson
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc.,126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Gary E. Martin
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc.,126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Jane E. Ishmael
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
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15
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Almabruk KH, Dinh LK, Philmus B. Self-Resistance of Natural Product Producers: Past, Present, and Future Focusing on Self-Resistant Protein Variants. ACS Chem Biol 2018; 13:1426-1437. [PMID: 29763292 DOI: 10.1021/acschembio.8b00173] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nature is a prolific producers of bioactive natural products with an array of biological activities and impact on human and animal health. But with great power comes great responsibility, and the organisms that produce a bioactive compound must be resistant to its biological effects to survive during production/accumulation. Microorganisms, particularly bacteria, have developed different strategies to prevent self-toxicity. Here, we review a few of the major mechanisms including the mechanism of resistance with a focus on self-resistant protein variants, target proteins that contain amino acid substitutions to reduce the binding of the bioactive natural product, and therefore its inhibitory effects are highlighted in depth. We also try to identify some future avenues of research and challenges that need to be addressed.
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Affiliation(s)
- Khaled H. Almabruk
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Linh K. Dinh
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
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16
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Videau P, Rivers OS, Tom SK, Oshiro RT, Ushijima B, Swenson VA, Philmus B, Gaylor MO, Cozy LM. The hetZ gene indirectly regulates heterocyst development at the level of pattern formation in Anabaena sp. strain PCC 7120. Mol Microbiol 2018; 109:91-104. [PMID: 29676808 DOI: 10.1111/mmi.13974] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2018] [Indexed: 01/08/2023]
Abstract
Multicellular development requires the careful orchestration of gene expression to correctly create and position specialized cells. In the filamentous cyanobacterium Anabaena sp. strain PCC 7120, nitrogen-fixing heterocysts are differentiated from vegetative cells in a reproducibly periodic and physiologically relevant pattern. While many genetic factors required for heterocyst development have been identified, the role of HetZ has remained unclear. Here, we present evidence to clarify the requirement of hetZ for heterocyst production and support a model where HetZ functions in the patterning stage of differentiation. We show that a clean, nonpolar deletion of hetZ fails to express the developmental genes hetR, patS, hetP and hetZ correctly and fails to produce heterocysts. Complementation and overexpression of hetZ in a hetP mutant revealed that hetZ was incapable of bypassing hetP, suggesting that it acts upstream of hetP. Complementation and overexpression of hetZ in a hetR mutant, however, demonstrated bypass of hetR, suggesting that it acts downstream of hetR and is capable of bypassing the need for hetR for differentiation irrespective of nitrogen status. Finally, protein-protein interactions were observed between HetZ and HetR, Alr2902 and HetZ itself. Collectively, this work suggests a regulatory role for HetZ in the patterning phase of cellular differentiation in Anabaena.
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Affiliation(s)
- Patrick Videau
- Department of Biology, College of Arts and Sciences, Dakota State University, Madison, SD, USA
| | - Orion S Rivers
- Department of Microbiology, University of Hawaii, Honolulu, HI, USA
| | - Sasa K Tom
- Department of Microbiology, University of Hawaii, Honolulu, HI, USA
| | - Reid T Oshiro
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Blake Ushijima
- Department of Microbiology, University of Hawaii, Honolulu, HI, USA
| | - Vaille A Swenson
- Department of Biology, College of Arts and Sciences, Dakota State University, Madison, SD, USA
- Department of Chemistry, College of Arts and Sciences, Dakota State University, Madison, SD, USA
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Michael O Gaylor
- Department of Chemistry, College of Arts and Sciences, Dakota State University, Madison, SD, USA
| | - Loralyn M Cozy
- Department of Biology, Illinois Wesleyan University, Bloomington, IL, USA
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17
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Fenwick MK, Almabruk KH, Ealick SE, Begley TP, Philmus B. Biochemical Characterization and Structural Basis of Reactivity and Regioselectivity Differences between Burkholderia thailandensis and Burkholderia glumae 1,6-Didesmethyltoxoflavin N-Methyltransferase. Biochemistry 2017; 56:3934-3944. [PMID: 28665591 DOI: 10.1021/acs.biochem.7b00476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Burkholderia glumae converts the guanine base of guanosine triphosphate into an azapteridine and methylates both the pyrimidine and triazine rings to make toxoflavin. Strains of Burkholderia thailandensis and Burkholderia pseudomallei have a gene cluster encoding seven putative biosynthetic enzymes that resembles the toxoflavin gene cluster. Four of the enzymes are similar in sequence to BgToxBCDE, which have been proposed to make 1,6-didesmethyltoxoflavin (1,6-DDMT). One of the remaining enzymes, BthII1283 in B. thailandensis E264, is a predicted S-adenosylmethionine (SAM)-dependent N-methyltransferase that shows a low level of sequence identity to BgToxA, which sequentially methylates N6 and N1 of 1,6-DDMT to form toxoflavin. Here we show that, unlike BgToxA, BthII1283 catalyzes a single methyl transfer to N1 of 1,6-DDMT in vitro. In addition, we investigated the differences in reactivity and regioselectivity by determining crystal structures of BthII1283 with bound S-adenosylhomocysteine (SAH) or 1,6-DDMT and SAH. BthII1283 contains a class I methyltransferase fold and three unique extensions used for 1,6-DDMT recognition. The active site structure suggests that 1,6-DDMT is bound in a reduced form. The plane of the azapteridine ring system is orthogonal to its orientation in BgToxA. In BthII1283, the modeled SAM methyl group is directed toward the p orbital of N1, whereas in BgToxA, it is first directed toward an sp2 orbital of N6 and then toward an sp2 orbital of N1 after planar rotation of the azapteridine ring system. Furthermore, in BthII1283, N1 is hydrogen bonded to a histidine residue whereas BgToxA does not supply an obvious basic residue for either N6 or N1 methylation.
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Affiliation(s)
- Michael K Fenwick
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Khaled H Almabruk
- College of Pharmacy, Oregon State University , Corvallis, Oregon 97331, United States
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - Benjamin Philmus
- College of Pharmacy, Oregon State University , Corvallis, Oregon 97331, United States
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18
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Yan Q, Philmus B, Chang JH, Loper JE. Novel mechanism of metabolic co-regulation coordinates the biosynthesis of secondary metabolites in Pseudomonas protegens. eLife 2017; 6. [PMID: 28262092 PMCID: PMC5395296 DOI: 10.7554/elife.22835] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/16/2017] [Indexed: 12/02/2022] Open
Abstract
Metabolic co-regulation between biosynthetic pathways for secondary metabolites is common in microbes and can play an important role in microbial interactions. Here, we describe a novel mechanism of metabolic co-regulation in which an intermediate in one pathway is converted into signals that activate a second pathway. Our study focused on the co-regulation of 2,4-diacetylphloroglucinol (DAPG) and pyoluteorin, two antimicrobial metabolites produced by the soil bacterium Pseudomonas protegens. We show that an intermediate in DAPG biosynthesis, phloroglucinol, is transformed by a halogenase encoded in the pyoluteorin gene cluster into mono- and di-chlorinated phloroglucinols. The chlorinated phloroglucinols function as intra- and inter-cellular signals that induce the expression of pyoluteorin biosynthetic genes, pyoluteorin production, and pyoluteorin-mediated inhibition of the plant-pathogenic bacterium Erwinia amylovora. This metabolic co-regulation provides a strategy for P. protegens to optimize the deployment of secondary metabolites with distinct roles in cooperative and competitive microbial interactions. DOI:http://dx.doi.org/10.7554/eLife.22835.001 Bacteria live almost everywhere on Earth and often compete with one another for limited resources, like space or nutrients. Certain bacteria produce molecules that are toxic to other microorganisms to give themselves a competitive advantage. These toxic molecules are more commonly referred as antibiotics, and are perhaps best known for their importance in medicine. Yet, antibiotics benefit the bacteria that produce them in other ways too. Some bacteria, for example, use antibiotics as chemical signals to communicate with one another and coordinate their activities. Some bacteria produce many antibiotics with different toxic and signaling activities. These bacteria often coordinate the production of different antibiotics such that the production of one antibiotic shuts down the production of another. This kind of coordination would allow the bacterium to focus its energy on producing only the antibiotic that gives it a competitive advantage at that time. Yet, in most cases, it was not known how the bacterial cell coordinates the production of two different antibiotics. Pseudomonas protegens is a species of bacteria that lives in soil, and produces many antibiotics that are toxic to other bacteria or fungi. The antibiotics are made via distinct pathways of chemical reactions that are catalyzed by different enzymes. However, the production of two antibiotics, called 2,4-diacetylphloroglucinol and pyoluteorin, is tightly coordinated in some strains of P. protegens. Now, Yan et al. have discovered how P. protegens coordinates the production of these two antibiotics. It turns out that the bacterium produces an enzyme that adds chlorine atoms onto one of the intermediate building blocks used to make 2,4-diacetylphloroglucinol. These “chlorinated derivatives” then activate the genes required to make the second antibiotic, pyoluteorin. The derivatives also signal to other P. protegens cells and trigger them to produce pyoluteorin too. Lastly, Yan et al. confirmed that pyoluteorin could inhibit the growth of another species of bacteria called Erwinia amylovora. These new findings highlight an important role played by chemicals that might have previously been considered as merely stepping stones in other biochemical reactions. An important challenge for the future will be to evaluate if other microbes use chemical intermediates in similar ways. Understanding the natural role of more antibiotics and their intermediates should help us to more wisely use existing antibiotics, and might eventually lead to new treatments for infections in humans and other animals. DOI:http://dx.doi.org/10.7554/eLife.22835.002
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Affiliation(s)
- Qing Yan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, United States
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, United States.,US Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, United States
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Abugrain ME, Brumsted CJ, Osborn AR, Philmus B, Mahmud T. A Highly Promiscuous ß-Ketoacyl-ACP Synthase (KAS) III-like Protein Is Involved in Pactamycin Biosynthesis. ACS Chem Biol 2017; 12:362-366. [PMID: 28060484 DOI: 10.1021/acschembio.6b01043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
β-Ketoacyl-acyl carrier protein (β-Ketoacyl-ACP) synthase (KAS) III catalyzes the first step in fatty acid biosynthesis, involving a Claisen condensation of the acetyl-CoA starter unit with the first extender unit, malonyl-ACP, to form acetoacetyl-ACP. KAS III-like proteins have also been reported to catalyze acyltransferase reactions using coenzyme A esters or discrete ACP-bound substrates. Here, we report the in vivo and in vitro characterizations of a KAS III-like protein (PtmR), which directly transfers a 6-methylsalicylyl moiety from an iterative type I polyketide synthase to an aminocyclopentitol unit in pactamycin biosynthesis. PtmR is highly promiscuous, recognizing a wide array of S-acyl-N-acetylcysteamines as substrates to produce a suite of pactamycin derivatives with diverse alkyl and aromatic features. The results suggest that KAS III-like proteins may be used as versatile tools for modifications of complex natural products.
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Affiliation(s)
- Mostafa E. Abugrain
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97333, United States
| | - Corey J. Brumsted
- Department
of Chemistry, Oregon State University, Corvallis, Oregon 97333, United States
| | - Andrew R. Osborn
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97333, United States
| | - Benjamin Philmus
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97333, United States
| | - Taifo Mahmud
- Department
of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97333, United States
- Department
of Chemistry, Oregon State University, Corvallis, Oregon 97333, United States
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20
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Videau P, Wells KN, Singh AJ, Gerwick WH, Philmus B. Assessment of Anabaena sp. Strain PCC 7120 as a Heterologous Expression Host for Cyanobacterial Natural Products: Production of Lyngbyatoxin A. ACS Synth Biol 2016; 5:978-88. [PMID: 27176641 DOI: 10.1021/acssynbio.6b00038] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are well-known producers of natural products of highly varied structure and biological properties. However, the long doubling times, difficulty in establishing genetic methods for marine cyanobacteria, and low compound titers have hindered research into the biosynthesis of their secondary metabolites. While a few attempts to heterologously express cyanobacterial natural products have occurred, the results have been of varied success. Here, we report the first steps in developing the model freshwater cyanobacterium Anabaena sp. strain PCC 7120 (Anabaena 7120) as a general heterologous expression host for cyanobacterial secondary metabolites. We show that Anabaena 7120 can heterologously synthesize lyngbyatoxin A in yields comparable to those of the native producer, Moorea producens, and detail the design and use of replicative plasmids for compound production. We also demonstrate that Anabaena 7120 recognizes promoters from various biosynthetic gene clusters from both free-living and obligate symbiotic marine cyanobacteria. Through simple genetic manipulations, the titer of lyngbyatoxin A can be improved up to 13-fold. The development of Anabaena 7120 as a general heterologous expression host enables investigation of interesting cyanobacterial biosynthetic reactions and genetic engineering of their biosynthetic pathways.
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Affiliation(s)
| | | | | | - William H. Gerwick
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography
and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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21
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Xu H, Chakrabarty Y, Philmus B, Mehta AP, Bhandari D, Hohmann HP, Begley TP. Identification of the First Riboflavin Catabolic Gene Cluster Isolated from Microbacterium maritypicum G10. J Biol Chem 2016; 291:23506-23515. [PMID: 27590337 DOI: 10.1074/jbc.m116.729871] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 11/06/2022] Open
Abstract
Riboflavin is a common cofactor, and its biosynthetic pathway is well characterized. However, its catabolic pathway, despite intriguing hints in a few distinct organisms, has never been established. This article describes the isolation of a Microbacterium maritypicum riboflavin catabolic strain, and the cloning of the riboflavin catabolic genes. RcaA, RcaB, RcaD, and RcaE were overexpressed and biochemically characterized as riboflavin kinase, riboflavin reductase, ribokinase, and riboflavin hydrolase, respectively. Based on these activities, a pathway for riboflavin catabolism is proposed.
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Affiliation(s)
- Hui Xu
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Yindrila Chakrabarty
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Benjamin Philmus
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Angad P Mehta
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Dhananjay Bhandari
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Hans-Peter Hohmann
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Tadhg P Begley
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843
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22
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Naurin S, Bennett J, Videau P, Philmus B, Soule T. The response regulator Npun_F1278 is essential for scytonemin biosynthesis in the cyanobacterium Nostoc punctiforme ATCC 29133. J Phycol 2016; 52:564-571. [PMID: 27020740 DOI: 10.1111/jpy.12414] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/15/2016] [Indexed: 06/05/2023]
Abstract
Following exposure to long-wavelength ultraviolet radiation (UVA), some cyanobacteria produce the indole-alkaloid sunscreen scytonemin. The genomic region associated with scytonemin biosynthesis in the cyanobacterium Nostoc punctiforme includes 18 cotranscribed genes. A two-component regulatory system (Npun_F1277/Npun_F1278) directly upstream from the biosynthetic genes was identified through comparative genomics and is likely involved in scytonemin regulation. In this study, the response regulator (RR), Npun_F1278, was evaluated for its ability to regulate scytonemin biosynthesis using a mutant strain of N. punctiforme deficient in this gene, hereafter strain Δ1278. Following UVA radiation, the typical stimulus to initiate scytonemin biosynthesis, Δ1278 was incapable of producing scytonemin. A phenotypic characterization of Δ1278 suggests that aside from the ability to produce scytonemin, the deletion of the Npun_F1278 gene does not affect the cellular morphology, cellular differentiation capability, or lipid-soluble pigment complement of Δ1278 compared to the wildtype. The mutant, however, had a slower specific growth rate under white light and produced ~2.5-fold more phycocyanin per cell under UVA than the wildtype. Since Δ1278 does not produce scytonemin, this study demonstrates that the RR gene, Npun_F1278, is essential for scytonemin biosynthesis in N. punctiforme. While most of the evaluated effects of this gene appear to be specific for scytonemin, this regulator may also influence the overall health of the cell and phycobiliprotein synthesis, directly or indirectly. This is the first study to identify a regulatory gene involved in the biosynthesis of the sunscreen scytonemin and posits a link between cell growth, pigment synthesis, and sunscreen production.
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Affiliation(s)
- Sejuti Naurin
- Department of Biology, Indiana University-Purdue University Fort Wayne, Fort Wayne, Indiana, 46805, USA
| | - Janine Bennett
- Department of Biology, Indiana University-Purdue University Fort Wayne, Fort Wayne, Indiana, 46805, USA
| | - Patrick Videau
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Tanya Soule
- Department of Biology, Indiana University-Purdue University Fort Wayne, Fort Wayne, Indiana, 46805, USA
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23
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Fenwick MK, Philmus B, Begley TP, Ealick SE. Burkholderia glumae ToxA Is a Dual-Specificity Methyltransferase That Catalyzes the Last Two Steps of Toxoflavin Biosynthesis. Biochemistry 2016; 55:2748-59. [PMID: 27070241 PMCID: PMC4870115 DOI: 10.1021/acs.biochem.6b00167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Toxoflavin is a major virulence factor of the rice pathogen Burkholderia glumae. The tox operon of B. glumae contains five putative toxoflavin biosynthetic genes toxABCDE. ToxA is a predicted S-adenosylmethionine-dependent methyltransferase, and toxA knockouts of B. glumae are less virulent in plant infection models. In this study, we show that ToxA performs two consecutive methylations to convert the putative azapteridine intermediate, 1,6-didemethyltoxoflavin, to toxoflavin. In addition, we report a series of crystal structures of ToxA complexes that reveals the molecular basis of the dual methyltransferase activity. The results suggest sequential methylations with initial methylation at N6 of 1,6-didemethyltoxoflavin followed by methylation at N1. The two azapteridine orientations that position N6 or N1 for methylation are coplanar with a 140° rotation between them. The structure of ToxA contains a class I methyltransferase fold having an N-terminal extension that either closes over the active site or is largely disordered. The ordered conformation places Tyr7 at a position of a structurally conserved tyrosine site of unknown function in various methyltransferases. Crystal structures of ToxA-Y7F consistently show a closed active site, whereas structures of ToxA-Y7A consistently show an open active site, suggesting that the hydroxyl group of Tyr7 plays a role in opening and closing the active site during the multistep reaction.
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Affiliation(s)
- Michael K Fenwick
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Benjamin Philmus
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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24
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Yan Q, Philmus B, Hesse C, Kohen M, Chang JH, Loper JE. The Rare Codon AGA Is Involved in Regulation of Pyoluteorin Biosynthesis in Pseudomonas protegens Pf-5. Front Microbiol 2016; 7:497. [PMID: 27148187 PMCID: PMC4836200 DOI: 10.3389/fmicb.2016.00497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/27/2016] [Indexed: 11/24/2022] Open
Abstract
The soil bacterium Pseudomonas protegens Pf-5 can colonize root and seed surfaces of many plants, protecting them from infection by plant pathogenic fungi and oomycetes. The capacity to suppress disease is attributed to Pf-5's production of a large spectrum of antibiotics, which is controlled by complex regulatory circuits operating at the transcriptional and post-transcriptional levels. In this study, we analyzed the genomic sequence of Pf-5 for codon usage patterns and observed that the six rarest codons in the genome are present in all seven known antibiotic biosynthesis gene clusters. In particular, there is an abundance of rare codons in pltR, which encodes a member of the LysR transcriptional regulator family that controls the expression of pyoluteorin biosynthetic genes. To test the hypothesis that rare codons in pltR influence pyoluteorin production, we generated a derivative of Pf-5 in which 23 types of rare codons in pltR were substituted with synonymous preferred codons. The resultant mutant produced pyoluteorin at levels 15 times higher than that of the wild-type Pf-5. Accordingly, the promoter activity of the pyoluteorin biosynthetic gene pltL was 20 times higher in the codon-modified stain than in the wild-type. pltR has six AGA codons, which is the rarest codon in the Pf-5 genome. Substitution of all six AGA codons with preferred Arg codons resulted in a variant of pltR that conferred increased pyoluteorin production and pltL promoter activity. Furthermore, overexpression of tRNAUCUArg, the cognate tRNA for the AGA codon, significantly increased pyoluteorin production by Pf-5. A bias in codon usage has been linked to the regulation of many phenotypes in eukaryotes and prokaryotes but, to our knowledge, this is the first example of the role of a rare codon in the regulation of antibiotic production by a Gram-negative bacterium.
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Affiliation(s)
- Qing Yan
- Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA
| | | | - Cedar Hesse
- Horticultural Crops Research Laboratory, US Department of Agriculture, Agricultural Research Service Corvallis, OR, USA
| | - Max Kohen
- Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA; Horticultural Crops Research Laboratory, US Department of Agriculture, Agricultural Research ServiceCorvallis, OR, USA
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25
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Philmus B, Shaffer BT, Kidarsa TA, Yan Q, Raaijmakers JM, Begley TP, Loper JE. Investigations into the Biosynthesis, Regulation, and Self-Resistance of Toxoflavin in Pseudomonas protegens Pf-5. Chembiochem 2015; 16:1782-90. [PMID: 26077901 DOI: 10.1002/cbic.201500247] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Indexed: 11/10/2022]
Abstract
Pseudomonas spp. are prolific producers of natural products from many structural classes. Here we show that the soil bacterium Pseudomonas protegens Pf-5 is capable of producing trace levels of the triazine natural product toxoflavin (1) under microaerobic conditions. We evaluated toxoflavin production by derivatives of Pf-5 with deletions in specific biosynthesis genes, which led us to propose a revised biosynthetic pathway for toxoflavin that shares the first two steps with riboflavin biosynthesis. We also report that toxM, which is not present in the well-characterized cluster of Burkholderia glumae, encodes a monooxygenase that degrades toxoflavin. The toxoflavin degradation product of ToxM is identical to that of TflA, the toxoflavin lyase from Paenibacillus polymyxa. Toxoflavin production by P. protegens causes inhibition of several plant-pathogenic bacteria, and introduction of toxM into the toxoflavin-sensitive strain Pseudomonas syringae DC3000 results in resistance to toxoflavin.
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Affiliation(s)
- Benjamin Philmus
- College of Pharmacy, Oregon State University, 203 Pharmacy Building, Corvallis, OR 97331 (USA).
| | - Brenda T Shaffer
- Agricultural Research Service, US Department of Agriculture, 3420 N.W. Orchard Avenue, Corvallis, OR 97330 (USA)
| | - Teresa A Kidarsa
- Agricultural Research Service, US Department of Agriculture, 3420 N.W. Orchard Avenue, Corvallis, OR 97330 (USA)
| | - Qing Yan
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331 (USA)
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB Wageningen (The Netherlands).,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden (The Netherlands)
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University, College Station, TX 77843 (USA)
| | - Joyce E Loper
- Agricultural Research Service, US Department of Agriculture, 3420 N.W. Orchard Avenue, Corvallis, OR 97330 (USA). .,Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331 (USA).
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26
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Philmus B, Decamps L, Berteau O, Begley TP. Biosynthetic versatility and coordinated action of 5'-deoxyadenosyl radicals in deazaflavin biosynthesis. J Am Chem Soc 2015; 137:5406-13. [PMID: 25781338 PMCID: PMC4416281 DOI: 10.1021/ja513287k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 12/30/2022]
Abstract
Coenzyme F420 is a redox cofactor found in methanogens and in various actinobacteria. Despite the major biological importance of this cofactor, the biosynthesis of its deazaflavin core (8-hydroxy-5-deazaflavin, F(o)) is still poorly understood. F(o) synthase, the enzyme involved, is an unusual multidomain radical SAM enzyme that uses two separate 5'-deoxyadenosyl radicals to catalyze F(o) formation. In this paper, we report a detailed mechanistic study on this complex enzyme that led us to identify (1) the hydrogen atoms abstracted from the substrate by the two radical SAM domains, (2) the second tyrosine-derived product, (3) the reaction product of the CofH-catalyzed reaction, (4) the demonstration that this product is a substrate for CofG, and (5) a stereochemical study that is consistent with the formation of a p-hydroxybenzyl radical at the CofH active site. These results enable us to propose a mechanism for F(o) synthase and uncover a new catalytic motif in radical SAM enzymology involving the use of two 5'-deoxyadenosyl radicals to mediate the formation of a complex heterocycle.
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Affiliation(s)
- Benjamin Philmus
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Laure Decamps
- ChemSyBio,
UMR 1319 Micalis, INRA, F-78350 Jouy-en-Josas, France
- ChemSyBio,
UMR Micalis, AgroParisTech, F-78350 Jouy-en-Josas, France
| | - Olivier Berteau
- ChemSyBio,
UMR 1319 Micalis, INRA, F-78350 Jouy-en-Josas, France
- ChemSyBio,
UMR Micalis, AgroParisTech, F-78350 Jouy-en-Josas, France
| | - Tadhg P. Begley
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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27
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Mehta AP, Abdelwahed SH, Mahanta N, Fedoseyenko D, Philmus B, Cooper LE, Liu Y, Jhulki I, Ealick SE, Begley TP. Radical S-adenosylmethionine (SAM) enzymes in cofactor biosynthesis: a treasure trove of complex organic radical rearrangement reactions. J Biol Chem 2014; 290:3980-6. [PMID: 25477515 DOI: 10.1074/jbc.r114.623793] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this minireview, we describe the radical S-adenosylmethionine enzymes involved in the biosynthesis of thiamin, menaquinone, molybdopterin, coenzyme F420, and heme. Our focus is on the remarkably complex organic rearrangements involved, many of which have no precedent in organic or biological chemistry.
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Affiliation(s)
- Angad P Mehta
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Sameh H Abdelwahed
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Nilkamal Mahanta
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Dmytro Fedoseyenko
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Benjamin Philmus
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Lisa E Cooper
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Yiquan Liu
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Isita Jhulki
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
| | - Steven E Ealick
- the Department of Chemistry, Cornell University, Ithaca, New York 14850
| | - Tadhg P Begley
- From the Department of Chemistry, Texas A&M University, College Station, Texas 77843 and
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Decamps L, Philmus B, Benjdia A, White R, Begley TP, Berteau O. Biosynthesis of F0, Precursor of the F420 Cofactor, Requires a Unique Two Radical-SAM Domain Enzyme and Tyrosine as Substrate. J Am Chem Soc 2012; 134:18173-6. [DOI: 10.1021/ja307762b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laure Decamps
- Institut National de la Recherche Agronomique, UMR 1319 Micalis, F-78350
Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, F-78350 Jouy-en-Josas,
France
| | - Benjamin Philmus
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Alhosna Benjdia
- Department
of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse
29, 69120 Heidelberg, Germany
| | - Robert White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United
States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Olivier Berteau
- Institut National de la Recherche Agronomique, UMR 1319 Micalis, F-78350
Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, F-78350 Jouy-en-Josas,
France
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29
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Lai RY, Huang S, Fenwick MK, Hazra A, Zhang Y, Rajashankar K, Philmus B, Kinsland C, Sanders JM, Ealick SE, Begley TP. Thiamin pyrimidine biosynthesis in Candida albicans : a remarkable reaction between histidine and pyridoxal phosphate. J Am Chem Soc 2012; 134:9157-9. [PMID: 22568620 DOI: 10.1021/ja302474a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In Saccharomyces cerevisiae , thiamin pyrimidine is formed from histidine and pyridoxal phosphate (PLP). The origin of all of the pyrimidine atoms has been previously determined using labeling studies and suggests that the pyrimidine is formed using remarkable chemistry that is without chemical or biochemical precedent. Here we report the overexpression of the closely related Candida albicans pyrimidine synthase (THI5p) and the reconstitution and preliminary characterization of the enzymatic activity. A structure of the C. albicans THI5p shows PLP bound at the active site via an imine with Lys62 and His66 in close proximity to the PLP. Our data suggest that His66 of the THI5 protein is the histidine source for pyrimidine formation and that the pyrimidine synthase is a single-turnover enzyme.
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Affiliation(s)
- Rung-Yi Lai
- Department of Chemistry, Texas A&M University, College Station, 77843, United States
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Philmus B, Abdelwahed S, Williams HJ, Fenwick MK, Ealick SE, Begley TP. Identification of the product of toxoflavin lyase: degradation via a Baeyer-Villiger oxidation. J Am Chem Soc 2012; 134:5326-30. [PMID: 22304755 PMCID: PMC3332044 DOI: 10.1021/ja211759n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Toxoflavin (an azapteridine) is degraded to a single product by toxoflavin lyase (TflA) in a reaction dependent on reductant, Mn(II), and oxygen. The isolated product was fully characterized by NMR and MS and was identified as a triazine in which the pyrimidine ring was oxidatively degraded. A mechanism for toxoflavin degradation based on the identification of the enzymatic product and the recently determined crystal structure of toxoflavin lyase is proposed.
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Affiliation(s)
- Benjamin Philmus
- Dept. of Chemistry, Texas A&M University, College Station, TX 77843
- Dept. of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Sameh Abdelwahed
- Dept. of Chemistry, Texas A&M University, College Station, TX 77843
- Dept. of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Howard J. Williams
- Dept. of Chemistry, Texas A&M University, College Station, TX 77843
- Dept. of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Michael K. Fenwick
- Dept. of Chemistry, Texas A&M University, College Station, TX 77843
- Dept. of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Steven E. Ealick
- Dept. of Chemistry, Texas A&M University, College Station, TX 77843
- Dept. of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
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Pribat A, Blaby IK, Lara-Núñez A, Jeanguenin L, Fouquet R, Frelin O, Gregory JF, Philmus B, Begley TP, de Crécy-Lagard V, Hanson AD. A 5-formyltetrahydrofolate cycloligase paralog from all domains of life: comparative genomic and experimental evidence for a cryptic role in thiamin metabolism. Funct Integr Genomics 2011; 11:467-78. [PMID: 21538139 PMCID: PMC6078417 DOI: 10.1007/s10142-011-0224-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/19/2011] [Accepted: 04/03/2011] [Indexed: 12/18/2022]
Abstract
A paralog (here termed COG0212) of the ATP-dependent folate salvage enzyme 5-formyltetrahydrofolate cycloligase (5-FCL) occurs in all domains of life and, although typically annotated as 5-FCL in pro- and eukaryotic genomes, is of unknown function. COG0212 is similar in overall structure to 5-FCL, particularly in the substrate binding region, and has distant similarity to other kinases. The Arabidopsis thaliana COG0212 protein was shown to be targeted to chloroplasts and to be required for embryo viability. Comparative genomic analysis revealed that a high proportion (19%) of archaeal and bacterial COG0212 genes are clustered on the chromosome with various genes implicated in thiamin metabolism or transport but showed no such association between COG0212 and folate metabolism. Consistent with the bioinformatic evidence for a role in thiamin metabolism, ablating COG0212 in the archaeon Haloferax volcanii caused accumulation of thiamin monophosphate. Biochemical and functional complementation tests of several known and hypothetical thiamin-related activities (involving thiamin, its breakdown products, and their phosphates) were, however, negative. Also consistent with the bioinformatic evidence, the COG0212 proteins from A. thaliana and prokaryote sources lacked 5-FCL activity in vitro and did not complement the growth defect or the characteristic 5-formyltetrahydrofolate accumulation of a 5-FCL-deficient (ΔygfA) Escherichia coli strain. We therefore propose (a) that COG0212 has an unrecognized yet sometimes crucial role in thiamin metabolism, most probably in salvage or detoxification, and (b) that is not a 5-FCL and should no longer be so annotated.
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Affiliation(s)
- Anne Pribat
- Horticultural Sciences Department, University of Florida, Gainesville, 32611, USA
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Abstract
High-resolution crystal structures are reported for apo, holo, and substrate-bound forms of a toxoflavin-degrading metalloenzyme (TflA). In addition, the degradation reaction is shown to be dependent on oxygen, Mn(II), and dithiothreitol in vitro. Despite its low sequence identity with proteins of known structure, TflA is structurally homologous to proteins of the vicinal oxygen chelate superfamily. Like other metalloenzymes in this superfamily, the TflA fold contains four modules that associate to form a metal binding site; however, the fold displays a rare rearrangement of the structural modules indicative of domain permutation. Moreover, unlike the 2-His-1-carboxylate facial triad commonly utilized by vicinal oxygen chelate dioxygenases and other dioxygen-activating non-heme Fe(II) enzymes, the metal center in TflA consists of a 1-His-2-carboxylate facial triad. The substrate-bound complex shows square-pyramidal geometry in which one position is occupied by O5 of toxoflavin. The open coordination site is predicted to be the dioxygen binding site. TflA appears to stabilize the reduced form of toxoflavin through second-sphere interactions. This anionic species is predicted to be the electron source responsible for reductive activation of oxygen to produce a peroxytoxoflavin intermediate.
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Affiliation(s)
- Michael K. Fenwick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Benjamin Philmus
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, TX 77843,To whom correspondence should be addressed at the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853. Telephone: (607) 255-7961. Fax: (607) 255-1227. ,
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853,To whom correspondence should be addressed at the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853. Telephone: (607) 255-7961. Fax: (607) 255-1227. ,
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Philmus B, Guerrette JP, Hemscheidt TK. Substrate specificity and scope of MvdD, a GRASP-like ligase from the microviridin biosynthetic gene cluster. ACS Chem Biol 2009; 4:429-34. [PMID: 19445532 DOI: 10.1021/cb900088r] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cyanobacterial protease inhibitor microviridin K is ribosomally biosynthesized as a prepeptide (MvdE) and subsequently modified posttranslationally by double lactonization followed by lactamization. Two proteins belonging to the GRASP superfamily of ligases catalyze these ring closures. We here show that one of these ligases (MvdD) forms the lactones in a specific order, the larger ring being formed first, and that the ring size requirement for both lactonizations is stringent. However, for the first cyclization MvdD accepts alanine substitution in all C-terminal positions of the microviridin prepeptide that are not directly involved in the cross-linking, whereas the second lactonization is dependent on the presence of specific residues in MvdE. This suggests that MvdD possesses some, albeit limited, substrate tolerance that might be useful for the modification of peptides and proteins not belonging to the microviridin group of metabolites.
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Affiliation(s)
- Benjamin Philmus
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822
| | - Joshua P. Guerrette
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822
| | - Thomas K. Hemscheidt
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822
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Okumura HS, Philmus B, Portmann C, Hemscheidt TK. Homotyrosine-containing cyanopeptolins 880 and 960 and anabaenopeptins 908 and 915 from Planktothrix agardhii CYA 126/8. J Nat Prod 2009; 72:172-6. [PMID: 19115837 PMCID: PMC2673918 DOI: 10.1021/np800557m] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Two homotyrosine-bearing cyanopeptolins are described from Planktothrix agardhii CYA 126/8. The compounds feature a common homotyrosine-containing cyclohexadepsipeptide and differ by sulfation of an exocyclically located 2-O-methyl-d-glyceric acid residue. In addition we describe two anabaenopeptins, which contain two homotyrosine residues, one of which is N-methylated. The anabaenopeptins have a common cyclopentapeptide portion and differ in the amino acid linked to it via an ureido bond, arginine and tyrosine, respectively.
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Affiliation(s)
- Hilary S. Okumura
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822
| | - Benjamin Philmus
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822
| | - Cyril Portmann
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822
| | - Thomas K. Hemscheidt
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822
- Natural Products & Cancer Biology Program, Cancer Research Center of Hawaii, 651 Ilalo Street, Honolulu, Hawaii 96813
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Christiansen G, Molitor C, Philmus B, Kurmayer R. Nontoxic strains of cyanobacteria are the result of major gene deletion events induced by a transposable element. Mol Biol Evol 2008; 25:1695-704. [PMID: 18502770 PMCID: PMC2464740 DOI: 10.1093/molbev/msn120] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2008] [Indexed: 01/05/2023] Open
Abstract
Blooms that are formed by cyanobacteria consist of toxic and nontoxic strains. The mechanisms that result in the occurrence of nontoxic strains are enigmatic. All the nontoxic strains of the filamentous cyanobacterium Planktothrix that were isolated from 9 European countries were found to have lost 90% of a large microcystin synthetase (mcy) gene cluster that encoded the synthesis of the toxic peptide microcystin (MC). Those strains still contain the flanking regions of the mcy gene cluster along with remnants of the transposable elements that are found in between. The majority of the strains still contain a gene coding for a distinct thioesterase type II (mcyT), which is putatively involved in MC synthesis. The insertional inactivation of mcyT in an MC-producing strain resulted in the reduction of MC synthesis by 94 +/- 2% (1 standard deviation). Nontoxic strains that occur in shallow lakes throughout Europe form a monophyletic lineage. A second lineage consists of strains that contain the mcy gene cluster but differ in their photosynthetic pigment composition, which is due to the occurrence of strains that contain phycocyanin or large amounts of phycoerythrin in addition to phycocyanin. Strains containing phycoerythrin typically occur in deep-stratified lakes. The rare occurrence of gene cluster deletion, paired with the evolutionary diversification of the lineages of strains that lost or still contain the mcy gene cluster, needs to be invoked in order to explain the absence or dominance of toxic cyanobacteria in various habitats.
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Affiliation(s)
- Guntram Christiansen
- Austrian Academy of Sciences, Institute for Limnology, Mondseestrasse 9, Mondsee, Austria
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