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Bueno D, Schäfer MKE, Wang S, Schmeisser MJ, Methner A. NECAB family of neuronal calcium-binding proteins in health and disease. Neural Regen Res 2025; 20:1236-1243. [PMID: 38934399 DOI: 10.4103/nrr.nrr-d-24-00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The N-terminal EF-hand calcium-binding proteins 1-3 (NECAB1-3) constitute a family of predominantly neuronal proteins characterized by the presence of at least one EF-hand calcium-binding domain and a functionally less well characterized C-terminal antibiotic biosynthesis monooxygenase domain. All three family members were initially discovered due to their interactions with other proteins. NECAB1 associates with synaptotagmin-1, a critical neuronal protein involved in membrane trafficking and synaptic vesicle exocytosis. NECAB2 interacts with predominantly striatal G-protein-coupled receptors, while NECAB3 partners with amyloid-β A4 precursor protein-binding family A members 2 and 3, key regulators of amyloid-β production. This demonstrates the capacity of the family for interactions with various classes of proteins. NECAB proteins exhibit distinct subcellular localizations: NECAB1 is found in the nucleus and cytosol, NECAB2 resides in endosomes and the plasma membrane, and NECAB3 is present in the endoplasmic reticulum and Golgi apparatus. The antibiotic biosynthesis monooxygenase domain, an evolutionarily ancient component, is akin to atypical heme oxygenases in prokaryotes but is not well-characterized in vertebrates. Prokaryotic antibiotic biosynthesis monooxygenase domains typically form dimers, suggesting that calcium-mediated conformational changes in NECAB proteins may induce antibiotic biosynthesis monooxygenase domain dimerization, potentially activating some enzymatic properties. However, the substrate for this enzymatic activity remains uncertain. Alternatively, calcium-mediated conformational changes might influence protein interactions or the subcellular localization of NECAB proteins by controlling the availability of protein-protein interaction domains situated between the EF hands and the antibiotic biosynthesis monooxygenase domain. This review summarizes what is known about genomic organization, tissue expression, intracellular localization, interaction partners, and the physiological and pathophysiological role of the NECAB family.
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Affiliation(s)
- Diones Bueno
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Michael K E Schäfer
- Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Sudena Wang
- Department of Anesthesiology, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Michael J Schmeisser
- Institute of Anatomy, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Axel Methner
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
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2
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Gao J, Li L, Shen S, Ai G, Wang B, Guo F, Yang T, Han H, Xu Z, Pan G, Fan K. Cofactor-independent C-C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis. Beilstein J Org Chem 2024; 20:1198-1206. [PMID: 38887580 PMCID: PMC11181247 DOI: 10.3762/bjoc.20.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 05/07/2024] [Indexed: 06/20/2024] Open
Abstract
Biosynthesis of atypical angucyclines involves unique oxidative B-ring cleavage and rearrangement reactions, which are catalyzed by AlpJ-family oxygenases, including AlpJ, JadG, and GilOII. Prior investigations established the essential requirement for FADH2/FMNH2 as cofactors when utilizing the quinone intermediate dehydrorabelomycin as a substrate. In this study, we unveil a previously unrecognized facet of these enzymes as cofactor-independent oxygenases when employing the hydroquinone intermediate CR1 as a substrate. The enzymes autonomously drive oxidative ring cleavage and rearrangement reactions of CR1, yielding products identical to those observed in cofactor-dependent reactions of AlpJ-family oxygenases. Furthermore, the AlpJ- and JadG-catalyzed reactions of CR1 could be quenched by superoxide dismutase, supporting a catalytic mechanism wherein the substrate CR1 reductively activates molecular oxygen, generating a substrate radical and the superoxide anion O2 •-. Our findings illuminate a substrate-controlled catalytic mechanism of AlpJ-family oxygenases, expanding the realm of cofactor-independent oxygenases. Notably, AlpJ-family oxygenases stand as a pioneering example of enzymes capable of catalyzing oxidative reactions in either an FADH2/FMNH2-dependent or cofactor-independent manner.
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Affiliation(s)
- Jinmin Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Beijing 101408, China
| | - Liyuan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
| | - Shijie Shen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Beijing 101408, China
| | - Guomin Ai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
| | - Bin Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Beijing 101408, China
| | - Fang Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
| | - Tongjian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Beijing 101408, China
| | - Hui Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Road, Beijing 101408, China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China
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3
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Kudo K, Nishimura T, Izumikawa M, Kozone I, Hashimoto J, Fujie M, Suenaga H, Ikeda H, Satoh N, Shin-Ya K. Capability of a large bacterial artificial chromosome clone harboring multiple biosynthetic gene clusters for the production of diverse compounds. J Antibiot (Tokyo) 2024; 77:288-298. [PMID: 38438499 DOI: 10.1038/s41429-024-00711-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/06/2024]
Abstract
The biosynthetic gene clusters (BGCs) for the macrocyclic lactone-based polyketide compounds are extremely large-sized because the polyketide synthases that generate the polyketide chains of the basic backbone are of very high molecular weight. In developing a heterologous expression system for the large BGCs amenable to the production of such natural products, we selected concanamycin as an appropriate target. We obtained a bacterial artificial chromosome (BAC) clone with a 211-kb insert harboring the entire BGC responsible for the biosynthesis of concanamycin. Heterologous expression of this clone in a host strain, Streptomyces avermitilis SUKA32, permitted the production of concanamycin, as well as that of two additional aromatic polyketides. Structural elucidation identified these additional products as ent-gephyromycin and a novel compound that was designated JBIR-157. We describe herein sequencing and expression studies performed on these BGCs, demonstrating the utility of large BAC clones for the heterologous expression of cryptic or near-silent loci.
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Affiliation(s)
- Kei Kudo
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Takehiro Nishimura
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Hikaru Suenaga
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Nori Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Kazuo Shin-Ya
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
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4
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Gui C, Kalkreuter E, Liu YC, Li G, Steele AD, Yang D, Chang C, Shen B. Cofactorless oxygenases guide anthraquinone-fused enediyne biosynthesis. Nat Chem Biol 2024; 20:243-250. [PMID: 37945897 DOI: 10.1038/s41589-023-01476-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
The anthraquinone-fused enediynes (AFEs) combine an anthraquinone moiety and a ten-membered enediyne core capable of generating a cytotoxic diradical species. AFE cyclization is triggered by opening the F-ring epoxide, which is also the site of the most structural diversity. Previous studies of tiancimycin A, a heavily modified AFE, have revealed a cryptic aldehyde blocking installation of the epoxide, and no unassigned oxidases could be predicted within the tnm biosynthetic gene cluster. Here we identify two consecutively acting cofactorless oxygenases derived from methyltransferase and α/β-hydrolase protein folds, TnmJ and TnmK2, respectively, that are responsible for F-ring tailoring in tiancimycin biosynthesis by comparative genomics. Further biochemical and structural characterizations reveal that the electron-rich AFE anthraquinone moiety assists in catalyzing deformylation, epoxidation and oxidative ring cleavage without exogenous cofactors. These enzymes therefore fill important knowledge gaps for the biosynthesis of this class of molecules and the underappreciated family of cofactorless oxygenases.
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Affiliation(s)
- Chun Gui
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Edward Kalkreuter
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Yu-Chen Liu
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Gengnan Li
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Andrew D Steele
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Dong Yang
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Changsoo Chang
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Ben Shen
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA.
- Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA.
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA.
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5
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Elsayed SS, van der Heul HU, Xiao X, Nuutila A, Baars LR, Wu C, Metsä-Ketelä M, van Wezel GP. Unravelling key enzymatic steps in C-ring cleavage during angucycline biosynthesis. Commun Chem 2023; 6:281. [PMID: 38110491 PMCID: PMC10728087 DOI: 10.1038/s42004-023-01059-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/08/2023] [Indexed: 12/20/2023] Open
Abstract
Angucyclines are type II polyketide natural products, often characterized by unusual structural rearrangements through B- or C-ring cleavage of their tetracyclic backbone. While the enzymes involved in B-ring cleavage have been extensively studied, little is known of the enzymes leading to C-ring cleavage. Here, we unravel the function of the oxygenases involved in the biosynthesis of lugdunomycin, a highly rearranged C-ring cleaved angucycline derivative. Targeted deletion of the oxygenase genes, in combination with molecular networking and structural elucidation, showed that LugOI is essential for C12 oxidation and maintaining a keto group at C6 that is reduced by LugOII, resulting in a key intermediate towards C-ring cleavage. An epoxide group is then inserted by LugOIII, and stabilized by the novel enzyme LugOV for the subsequent cleavage. Thus, for the first time we describe the oxidative enzymatic steps that form the basis for a wide range of rearranged angucycline natural products.
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Affiliation(s)
- Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands.
| | - Helga U van der Heul
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands
| | - Xiansha Xiao
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Aleksi Nuutila
- Department of Life Technologies, University of Turku, Tykistökatu 6, FIN-20014, Turku, Finland
| | - Laura R Baars
- Department of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237, Qingdao, P.R. China
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, Tykistökatu 6, FIN-20014, Turku, Finland
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands.
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708PB, Wageningen, The Netherlands.
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6
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Santos RGD, Hurtado R, Rodrigues DLN, Lima A, Dos Anjos WF, Rifici C, Attili AR, Tiwari S, Jaiswal AK, Spier SJ, Mazzullo G, Morais-Rodrigues F, Gomide ACP, de Jesus LCL, Aburjaile FF, Brenig B, Cuteri V, Castro TLDP, Seyffert N, Santos A, Góes-Neto A, de Jesus Sousa T, Azevedo V. Comparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation. Res Microbiol 2023; 174:103998. [PMID: 36375718 DOI: 10.1016/j.resmic.2022.103998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Dietzia strains are widely distributed in the environment, presenting an opportunistic role, and some species have undetermined taxonomic characteristics. Here, we propose the existence of errors in the classification of species in this genus using comparative genomics. We performed ANI, dDDH, pangenome and genomic plasticity analyses better to elucidate the phylogenomic relationships between Dietzia strains. For this, we used 55 genomes of Dietzia downloaded from public databases that were combined with a newly sequenced. Sequence analysis of a phylogenetic tree based on genome similarity comparisons and dDDH, ANI analyses supported grouping different Dietzia species into four distinct groups. The pangenome analysis corroborated the classification of these groups, supporting the idea that some species of Dietzia could be reassigned in a possible classification into three distinct species, each containing less variability than that found within the global pangenome of all strains. Additionally, analysis of genomic plasticity based on groups containing Dietzia strains found differences in the presence and absence of symbiotic Islands and pathogenic islands related to their isolation site. We propose that the comparison of pangenome subsets together with phylogenomic approaches can be used as an alternative for the classification and differentiation of new species of the genus Dietzia.
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Affiliation(s)
- Roselane Gonçalves Dos Santos
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Raquel Hurtado
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Diego Lucas Neres Rodrigues
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alessandra Lima
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Claudia Rifici
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario dell'Annunziata, 98168 Messina (ME), Italy.
| | - Anna Rita Attili
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica (MC), Italy.
| | - Sandeep Tiwari
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil; Postgraduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Arun Kumar Jaiswal
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sharon J Spier
- Department of Veterinary Medicine and Epidemiology, University of California, Davis, CA, USA.
| | - Giuseppe Mazzullo
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario dell'Annunziata, 98168 Messina (ME), Italy.
| | - Francielly Morais-Rodrigues
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Anne Cybelle Pinto Gomide
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luís Cláudio Lima de Jesus
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flavia Figueira Aburjaile
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany.
| | - Vincenzo Cuteri
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica (MC), Italy.
| | - Thiago Luiz de Paula Castro
- Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil; Postgraduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil; Department of Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil.
| | - Núbia Seyffert
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil.
| | - Anderson Santos
- Department of Computer Science, Federal University of Uberlandia, Uberlandia, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais Brazil.
| | - Thiago de Jesus Sousa
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Vasco Azevedo
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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7
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Zhang QY, Li X, Luo J, Li X, Song J, Wei D. Cofactor-Free Dioxygenases-Catalyzed Reaction Pathway via Proton-Coupled Electron Transfer. J Phys Chem B 2023; 127:95-103. [PMID: 36525303 DOI: 10.1021/acs.jpcb.2c03161] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding the general mechanism of the metal-free and cofactor-free oxidases and oxygenases catalyzed activation of triplet O2 is one of the most challenging questions in the field of enzymatic catalysis. Herein, we have performed Quantum Mechanics/Molecular Mechanics (QM/MM) multiscale simulations to reveal the detailed mechanism of the HOD catalyzed (i.e., 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase from Arthrobacter nitroguajacolicus Rü61a) decomposition of N-heteroaromatic compounds. The complete catalytic mechanism includes four steps: (1) proton transfer from 1-H-3-hydroxy-4-oxoquinaldine (QND) substrate to His251 residue coupled with an electron transfer from QND to triplet O2 (i.e., PCET), (2) formation of C-O bond via an open-shell singlet diradical recombination pathway, (3) ring-closure to form a bicyclic ring, and (4) dissociation of CO. The dissociation of CO is determined as the rate-limiting step, and its calculated energy barrier of 14.9 kcal/mol is consistent with the 15.5 kcal/mol barrier derived from experimental kinetic data. The mechanistic profile is not only valuable for understanding the fundamental pathway of cofactor-free oxidases and oxygenases-catalyzed reactions involving the triplet O2 activation but also discloses a new pathway that undergoes the processes of PCET and open-shell singlet transition state.
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Affiliation(s)
- Qiao-Yu Zhang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
| | - Xing Li
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong510280, China
| | - Jing Luo
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
| | - Xue Li
- Key Laboratory for Special Functional Materials of Ministry of Education, School of Materials and Engineering, Henan University, Kaifeng475001, China
| | - Jinshuai Song
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
| | - Donghui Wei
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou, Henan450001, China
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8
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Genomic and Functional Variation of the Chlorophyll d-Producing Cyanobacterium Acaryochloris marina. Microorganisms 2022; 10:microorganisms10030569. [PMID: 35336144 PMCID: PMC8949462 DOI: 10.3390/microorganisms10030569] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 02/01/2023] Open
Abstract
The Chlorophyll d-producing cyanobacterium Acaryochloris marina is widely distributed in marine environments enriched in far-red light, but our understanding of its genomic and functional diversity is limited. Here, we take an integrative approach to investigate A. marina diversity for 37 strains, which includes twelve newly isolated strains from previously unsampled locations in Europe and the Pacific Northwest of North America. A genome-wide phylogeny revealed both that closely related A. marina have migrated within geographic regions and that distantly related A. marina lineages can co-occur. The distribution of traits mapped onto the phylogeny provided evidence of a dynamic evolutionary history of gene gain and loss during A. marina diversification. Ancestral genes that were differentially retained or lost by strains include plasmid-encoded sodium-transporting ATPase and bidirectional NiFe-hydrogenase genes that may be involved in salt tolerance and redox balance under fermentative conditions, respectively. The acquisition of genes by horizontal transfer has also played an important role in the evolution of new functions, such as nitrogen fixation. Together, our results resolve examples in which genome content and ecotypic variation for nutrient metabolism and environmental tolerance have diversified during the evolutionary history of this unusual photosynthetic bacterium.
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9
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Schneider T, Tan Y, Li H, Fisher JS, Zhang D. Photoglobin, a distinct family of non-heme binding globins, defines a potential photosensor in prokaryotic signal transduction systems. Comput Struct Biotechnol J 2022; 20:261-273. [PMID: 35024098 PMCID: PMC8717448 DOI: 10.1016/j.csbj.2021.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Globins constitute an ancient superfamily of proteins, exhibiting enormous structural and functional diversity, as demonstrated by many heme-binding families and two non-heme binding families that were discovered in bacterial stressosome component RsbR and in light-harvesting phycobiliproteins (phycocyanin) in cyanobacteria and red algae. By comprehensively exploring the globin repertoire using sensitive computational analyses of sequences, structures, and genomes, we present the identification of the third family of non-heme binding globins—the photoglobin. By conducting profile-based comparisons, clustering analyses, and structural modeling, we demonstrate that photoglobin is related to, but distinct from, the phycocyanin family. Photoglobin preserves a potential ligand-binding pocket, whose residue configuration closely resembles that of phycocyanin, indicating that photoglobin potentially binds to a comparable linear tetrapyrrole. By exploring the contextual information provided by the photoglobin’s domain architectures and gene-neighborhoods, we found that photoglobin is frequently associated with the B12-binding light sensor domain and many domains typical of prokaryotic signal transduction systems. Structural modeling using AlphaFold2 demonstrated that photoglobin and B12-binding domains form a structurally conserved hub among different domain architecture contexts. Based on these strong associations, we predict that the coupled photoglobin and B12-binding domains act as a light-sensing regulatory bundle, with each domain sensing different wavelengths of light resulting in switch-like regulation of downstream signaling effectors. Thus, based on the above lines of evidence, we present a distinct non-heme binding globin family and propose that it may define a new type of light sensor, by means of a linear tetrapyrrole, in complex prokaryotic signal transduction systems.
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Affiliation(s)
- Theresa Schneider
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Yongjun Tan
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Huan Li
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Jonathan S Fisher
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States
| | - Dapeng Zhang
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63105, United States.,Program of Bioinformatics and Computational Biology, College of Arts & Sciences, Saint Louis University, MO 63103, United States
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10
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Li X, Li X, Zhang QY, Lv P, Jia Y, Wei D. Cofactor-free ActVA-Orf6 monooxygenase catalysis via proton-coupled electron transfer: A QM/MM study. Org Biomol Chem 2022; 20:5525-5534. [DOI: 10.1039/d2ob00848c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Uncovering the comprehensive catalytic mechanism for the activation of triplet O2 through metal-free and cofactor-free oxidases and oxygenases remains one of the most challenging questions in the area of enzymatic...
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11
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Liu J, Zhao Y, Fu ZQ, Liu F. Monooxygenase LaPhzX is Involved in Self-Resistance Mechanisms during the Biosynthesis of N-Oxide Phenazine Myxin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13524-13532. [PMID: 34735148 DOI: 10.1021/acs.jafc.1c05206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Self-resistance genes are deployed by many microbial producers of bioactive natural products to avoid self-toxicity. Myxin, a di-N-oxide phenazine produced by Lysobacter antibioticus OH13, is toxic to many microorganisms and tumor cells. Here, we uncovered a self-defense strategy featuring the antibiotic biosynthesis monooxygenase (ABM) family protein LaPhzX for myxin degradation. The gene LaPhzX is located in the myxin biosynthetic gene cluster (LaPhz), and its deletion resulted in bacterial mutants that are more sensitive to myxin. In addition, the LaPhzX mutants showed increased myxin accumulation and reduction of its derivative, compound 4, compared to the wild-type strain. Meanwhile, in vitro biochemical assays demonstrated that LaPhzX significantly degraded myxin in the presence of nicotinamide adenine dinucleotide phosphate (NADPH), nicotinamide adenine dinucleotide (NADH), flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD). In addition, heterologous expression of LaPhzX in Xanthomonas oryzae pv. oryzae and Escherichia coli increased their resistance to myxin. Overall, our work illustrates a monooxygenase-mediated self-resistance mechanism for phenazine antibiotic biosynthesis.
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Affiliation(s)
- Jiayu Liu
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, China
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety─State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Yangyang Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety─State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Fengquan Liu
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, China
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety─State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
- College of Plant Protection/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou 570228, China
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Alali A, Zhang L, Li J, Zuo C, Wassouf D, Yan X, Schwarzer P, Günther S, Einsle O, Bechthold A. Biosynthesis of the Tricyclic Aromatic Type II Polyketide Rishirilide: New Potential Third Ring Oxygenation after Three Cyclization Steps. Mol Biotechnol 2021; 63:502-514. [PMID: 33763824 PMCID: PMC8093152 DOI: 10.1007/s12033-021-00314-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/05/2021] [Indexed: 11/30/2022]
Abstract
Rishirilides are a group of PKS II secondary metabolites produced by Streptomyces bottropensis Gö C4/4. Biosynthetic studies in the past have elucidated early and late steps of rishirilide biosynthesis. This work is aiming to solve the remaining steps in the rishirilide biosynthesis. Inactivation of the cyclase gene rslC3 in Streptomyces bottropensis resulted in an interruption of rishirilide production. Instead, accumulation of the tricyclic aromatic galvaquinones was observed. Similar results were observed after deletion of rslO4. Closer inspection into RslO4 crystal structure in addition to site-directed mutagenesis and molecular dynamic simulations revealed that RslO4 might be responsible for quinone formation on the third ring. The RslO1 three-dimensional structure shows a high similarity to FMN-dependent luciferase-like monooxygenases such as the epoxy-forming MsnO8 which acts with the flavin reductase MsnO3 in mensacarcin biosynthesis in the same strain. The high sequence similarity between RslO2 and MsnO3 suggests that RslO2 provides RslO1 with reduced FMN to form an epoxide that serves as substrate for RslO5.
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Affiliation(s)
- Ahmad Alali
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Lin Zhang
- Institute of Biochemistry, Albert-Ludwigs-Universität, Albertstr 21, 79104, Freiburg, Germany
| | - Jianyu Li
- Institute of Pharmaceutical Bioinformatics, Albert-Ludwigs-Universität, Hermann-Herder-Str 9, 79104, Freiburg, Germany
| | - Chijian Zuo
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Dimah Wassouf
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Xiaohui Yan
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Philipp Schwarzer
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmaceutical Bioinformatics, Albert-Ludwigs-Universität, Hermann-Herder-Str 9, 79104, Freiburg, Germany
| | - Oliver Einsle
- Institute of Biochemistry, Albert-Ludwigs-Universität, Albertstr 21, 79104, Freiburg, Germany
| | - Andreas Bechthold
- Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany.
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13
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Ben Ayed A, Saint-Genis G, Vallon L, Linde D, Turbé-Doan A, Haon M, Daou M, Bertrand E, Faulds CB, Sciara G, Adamo M, Marmeisse R, Comtet-Marre S, Peyret P, Abrouk D, Ruiz-Dueñas FJ, Marchand C, Hugoni M, Luis P, Mechichi T, Record E. Exploring the Diversity of Fungal DyPs in Mangrove Soils to Produce and Characterize Novel Biocatalysts. J Fungi (Basel) 2021; 7:jof7050321. [PMID: 33919051 PMCID: PMC8143184 DOI: 10.3390/jof7050321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 01/21/2023] Open
Abstract
The functional diversity of the New Caledonian mangrove sediments was examined, observing the distribution of fungal dye-decolorizing peroxidases (DyPs), together with the complete biochemical characterization of the main DyP. Using a functional metabarcoding approach, the diversity of expressed genes encoding fungal DyPs was investigated in surface and deeper sediments, collected beneath either Avicennia marina or Rhizophora stylosa trees, during either the wet or the dry seasons. The highest DyP diversity was observed in surface sediments beneath the R. stylosa area during the wet season, and one particular operational functional unit (OFU1) was detected as the most abundant DyP isoform. This OFU was found in all sediment samples, representing 51–100% of the total DyP-encoding sequences in 70% of the samples. The complete cDNA sequence corresponding to this abundant DyP (OFU 1) was retrieved by gene capture, cloned, and heterologously expressed in Pichia pastoris. The recombinant enzyme, called DyP1, was purified and characterized, leading to the description of its physical–chemical properties, its ability to oxidize diverse phenolic substrates, and its potential to decolorize textile dyes; DyP1 was more active at low pH, though moderately stable over a wide pH range. The enzyme was very stable at temperatures up to 50 °C, retaining 60% activity after 180 min incubation. Its ability to decolorize industrial dyes was also tested on Reactive Blue 19, Acid Black, Disperse Blue 79, and Reactive Black 5. The effect of hydrogen peroxide and sea salt on DyP1 activity was studied and compared to what is reported for previously characterized enzymes from terrestrial and marine-derived fungi.
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Affiliation(s)
- Amal Ben Ayed
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Laboratoire de Biochimie et de Génie, Enzymatique des Lipases, Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, 3038 Sfax, Tunisia;
| | - Geoffroy Saint-Genis
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Laurent Vallon
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, 28040 Madrid, Spain; (D.L.); (F.J.R.-D.)
| | - Annick Turbé-Doan
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Mireille Haon
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Marianne Daou
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Department of Chemistry, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Emmanuel Bertrand
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Craig B. Faulds
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Giuliano Sciara
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Martino Adamo
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, 10125 Torino, Italy
| | - Roland Marmeisse
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, 10125 Torino, Italy
| | - Sophie Comtet-Marre
- Université Clermont Auvergne, INRAE, MEDiS, 63000 Clermont-Ferrand, France; (S.C.-M.); (P.P.)
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000 Clermont-Ferrand, France; (S.C.-M.); (P.P.)
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Francisco J. Ruiz-Dueñas
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, 28040 Madrid, Spain; (D.L.); (F.J.R.-D.)
| | - Cyril Marchand
- IMPMC, Institut de Recherche Pour le Développement (IRD), UPMC, CNRS, MNHN, 98851 Noumea, France;
- ISEA, EA, Université de la Nouvelle-Calédonie (UNC), 3325, BP R4, 98851 Noumea, France
| | - Mylène Hugoni
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Patricia Luis
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Tahar Mechichi
- Laboratoire de Biochimie et de Génie, Enzymatique des Lipases, Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, 3038 Sfax, Tunisia;
| | - Eric Record
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Correspondence:
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14
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Thakuri B, O'Rourke BD, Graves AB, Liptak MD. A Dynamic Substrate is Required for MhuD-Catalyzed Degradation of Heme to Mycobilin. Biochemistry 2021; 60:918-928. [PMID: 33729746 PMCID: PMC8628293 DOI: 10.1021/acs.biochem.0c00892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The noncanonical heme oxygenase MhuD from Mycobacterium tuberculosis binds a heme substrate that adopts a dynamic equilibrium between planar and out-of-plane ruffled conformations. MhuD degrades this substrate to an unusual mycobilin product via successive monooxygenation and dioxygenation reactions. This article establishes a causal relationship between heme substrate dynamics and MhuD-catalyzed heme degradation, resulting in a refined enzymatic mechanism. UV/vis absorption (Abs) and electrospray ionization mass spectrometry (ESI-MS) data demonstrated that a second-sphere substitution favoring the population of the ruffled heme conformation changed the rate-limiting step of the reaction, resulting in a measurable buildup of the monooxygenated meso-hydroxyheme intermediate. In addition, UV/vis Abs and ESI-MS data for a second-sphere variant that favored the planar substrate conformation showed that this change altered the enzymatic mechanism resulting in an α-biliverdin product. Single-turnover kinetic analyses for three MhuD variants revealed that the rate of heme monooxygenation depends upon the population of the ruffled substrate conformation. These kinetic analyses also revealed that the rate of meso-hydroxyheme dioxygenation by MhuD depends upon the population of the planar substrate conformation. Thus, the ruffled heme conformation supports rapid heme monooxygenation by MhuD, but further oxygenation to the mycobilin product is inhibited. In contrast, the planar substrate conformation exhibits altered heme monooxygenation regiospecificity followed by rapid oxygenation of meso-hydroxyheme. Altogether, these data yielded a refined enzymatic mechanism for MhuD where access to both substrate conformations is needed for rapid incorporation of three oxygen atoms into heme yielding mycobilin.
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Affiliation(s)
- Biswash Thakuri
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Bruce D O'Rourke
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Amanda B Graves
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Matthew D Liptak
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
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15
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Matroodi S, Siitonen V, Baral B, Yamada K, Akhgari A, Metsä-Ketelä M. Genotyping-Guided Discovery of Persiamycin A From Sponge-Associated Halophilic Streptomonospora sp. PA3. Front Microbiol 2020; 11:1237. [PMID: 32582127 PMCID: PMC7296137 DOI: 10.3389/fmicb.2020.01237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
Microbial natural products have been a cornerstone of the pharmaceutical industry, but the supply of novel bioactive secondary metabolites has diminished due to extensive exploration of the most easily accessible sources, namely terrestrial Streptomyces species. The Persian Gulf is a unique habitat for marine sponges, which contain diverse communities of microorganisms including marine Actinobacteria. These exotic ecosystems may cradle rare actinomycetes with high potential to produce novel secondary metabolites. In this study, we harvested 12 different species of sponges from two locations in the Persian Gulf and isolated 45 symbiotic actinomycetes to assess their biodiversity and sponge-microbe relationships. The isolates were classified into Nocardiopsis (24 isolates), Streptomyces (17 isolates) and rare genera (4 isolates) by 16S rRNA sequencing. Antibiotic activity tests revealed that culture extracts from half of the isolates displayed growth inhibitory effects against seven pathogenic bacteria. Next, we identified five strains with the genetic potential to produce aromatic polyketides by genotyping ketosynthase genes responsible for synthesis of carbon scaffolds. The combined data led us to focus on Streptomonospora sp. PA3, since the genus has rarely been examined for its capacity to produce secondary metabolites. Analysis of culture extracts led to the discovery of a new bioactive aromatic polyketide denoted persiamycin A and 1-hydroxy-4-methoxy-2-naphthoic acid. The genome harbored seven gene clusters involved in secondary metabolism, including a tetracenomycin-type polyketide synthase pathway likely involved in persiamycin formation. The work demonstrates the use of multivariate data and underexplored ecological niches to guide the drug discovery process for antibiotics and anticancer agents.
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Affiliation(s)
- Soheila Matroodi
- Laboratory of Biotechnology, Department of Marine Biology, Faculty of Marine Science and Oceanography, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Vilja Siitonen
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Bikash Baral
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Keith Yamada
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Amir Akhgari
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
| | - Mikko Metsä-Ketelä
- Laboratory of Antibiotic Biosynthesis Engineering, Department of Biochemistry, University of Turku, Turku, Finland
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16
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Wang J, Zhang R, Chen X, Sun X, Yan Y, Shen X, Yuan Q. Biosynthesis of aromatic polyketides in microorganisms using type II polyketide synthases. Microb Cell Fact 2020; 19:110. [PMID: 32448179 PMCID: PMC7247197 DOI: 10.1186/s12934-020-01367-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Aromatic polyketides have attractive biological activities and pharmacological properties. Different from other polyketides, aromatic polyketides are characterized by their polycyclic aromatic structure. The biosynthesis of aromatic polyketides is usually accomplished by the type II polyketide synthases (PKSs), which produce highly diverse polyketide chains by sequential condensation of the starter units with extender units, followed by reduction, cyclization, aromatization and tailoring reactions. Recently, significant progress has been made in characterization and engineering of type II PKSs to produce novel products and improve product titers. In this review, we briefly summarize the architectural organizations and genetic contributions of PKS genes to provide insight into the biosynthetic process. We then review the most recent progress in engineered biosynthesis of aromatic polyketides, with emphasis on generating novel molecular structures. We also discuss the current challenges and future perspectives in the rational engineering of type II PKSs for large scale production of aromatic polyketides.
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Affiliation(s)
- Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Ruihua Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA, 30602, USA
| | - Xin Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA, 30602, USA
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15 Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
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17
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Early Steps in the Biosynthetic Pathway of Rishirilide B. Molecules 2020; 25:molecules25081955. [PMID: 32340131 PMCID: PMC7221717 DOI: 10.3390/molecules25081955] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
The biological active compound rishirilide B is produced by Streptomyces bottropensis. The cosmid cos4 contains the complete rishirilide B biosynthesis gene cluster. Its heterologous expression in the host Streptomyces albus J1074 led to the production of rishirilide B as a major compound and to small amounts of rishirilide A, rishirilide D and lupinacidin A. In order to gain more insights into the biosynthesis, gene inactivation experiments and gene expression experiments were carried out. This study lays the focus on the functional elucidation of the genes involved in the early biosynthetic pathway. A total of eight genes were deleted and six gene cassettes were generated. Rishirilide production was not strongly affected by mutations in rslO2, rslO6 and rslH. The deletion of rslK4 and rslO3 led to the formation of polyketides with novel structures. These results indicated that RslK4 and RslO3 are involved in the generation or selection of the starter unit for rishirilide biosynthesis. In the rslO10 mutant strain, two novel compounds were detected, which were also produced by a strain containing solely the genes rslK1, rslK2, rslK3, rslK4, and rslA. rslO1 and rslO4 mutants predominately produce galvaquinones. Therefore, the ketoreductase RslO10 is involved in an early step of rishirilide biosynthesis and the oxygenases RslO1 and RslO4 are most probably acting on an anthracene moiety. This study led to the functional elucidation of several genes of the rishirilide pathway, including rslK4, which is involved in selecting the unusual starter unit for polyketide synthesis.
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18
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Qin Z, Devine R, Hutchings MI, Wilkinson B. A role for antibiotic biosynthesis monooxygenase domain proteins in fidelity control during aromatic polyketide biosynthesis. Nat Commun 2019; 10:3611. [PMID: 31399587 PMCID: PMC6689052 DOI: 10.1038/s41467-019-11538-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/19/2019] [Indexed: 11/09/2022] Open
Abstract
The formicamycin biosynthetic gene cluster encodes two groups of type 2 polyketide antibiotics: the formicamycins and their biosynthetic precursors the fasamycins, both of which have activity against methicillin-resistant Staphylococcus aureus. Here, we report the formicapyridines which are encoded by the same gene cluster and are structurally and biosynthetically related to the fasamycins and formicamycins but comprise a rare pyridine moiety. These compounds are trace-level metabolites formed by derailment of the major biosynthetic pathway. Inspired by evolutionary logic we show that rational mutation of a single gene in the biosynthetic gene cluster encoding an antibiotic biosynthesis monooxygenase (ABM) superfamily protein leads to a significant increase both in total formicapyridine production and their enrichment relative to the fasamycins/formicamycins. Our observations broaden the polyketide biosynthetic landscape and identify a non-catalytic role for ABM superfamily proteins in type II polyketide synthase assemblages for maintaining biosynthetic pathway fidelity.
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Affiliation(s)
- Zhiwei Qin
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rebecca Devine
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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19
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Enzyme-catalysed [6+4] cycloadditions in the biosynthesis of natural products. Nature 2019; 568:122-126. [PMID: 30867595 DOI: 10.1038/s41586-019-1021-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/07/2019] [Indexed: 01/01/2023]
Abstract
Pericyclic reactions are powerful transformations for the construction of carbon-carbon and carbon-heteroatom bonds in organic synthesis. Their role in biosynthesis is increasingly apparent, and mechanisms by which pericyclases can catalyse reactions are of major interest1. [4+2] cycloadditions (Diels-Alder reactions) have been widely used in organic synthesis2 for the formation of six-membered rings and are now well-established in biosynthesis3-6. [6+4] and other 'higher-order' cycloadditions were predicted7 in 1965, and are now increasingly common in the laboratory despite challenges arising from the generation of a highly strained ten-membered ring system8,9. However, although enzyme-catalysed [6+4] cycloadditions have been proposed10-12, they have not been proven to occur. Here we demonstrate a group of enzymes that catalyse a pericyclic [6+4] cycloaddition, which is a crucial step in the biosynthesis of streptoseomycin-type natural products. This type of pericyclase catalyses [6+4] and [4+2] cycloadditions through a single ambimodal transition state, which is consistent with previous proposals11,12. The [6+4] product is transformed to a less stable [4+2] adduct via a facile Cope rearrangement, and the [4+2] adduct is converted into the natural product enzymatically. Crystal structures of three pericyclases, computational simulations of potential energies and molecular dynamics, and site-directed mutagenesis establish the mechanism of this transformation. This work shows how enzymes are able to catalyse concerted pericyclic reactions involving ambimodal transition states.
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Machovina MM, Ellis ES, Carney TJ, Brushett FR, DuBois JL. How a cofactor-free protein environment lowers the barrier to O 2 reactivity. J Biol Chem 2019; 294:3661-3669. [PMID: 30602564 DOI: 10.1074/jbc.ra118.006144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/01/2019] [Indexed: 11/06/2022] Open
Abstract
Molecular oxygen (O2)-utilizing enzymes are among the most important in biology. The abundance of O2, its thermodynamic power, and the benign nature of its end products have raised interest in oxidases and oxygenases for biotechnological applications. Although most O2-dependent enzymes have an absolute requirement for an O2-activating cofactor, several classes of oxidases and oxygenases accelerate direct reactions between substrate and O2 using only the protein environment. Nogalamycin monooxygenase (NMO) from Streptomyces nogalater is a cofactor-independent enzyme that catalyzes rate-limiting electron transfer between its substrate and O2 Here, using enzyme-kinetic, cyclic voltammetry, and mutagenesis methods, we demonstrate that NMO initially activates the substrate, lowering its pKa by 1.0 unit (ΔG* = 1.4 kcal mol-1). We found that the one-electron reduction potential, measured for the deprotonated substrate both inside and outside the protein environment, increases by 85 mV inside NMO, corresponding to a ΔΔG 0' of 2.0 kcal mol-1 (0.087 eV) and that the activation barrier, ΔG ‡, is lowered by 4.8 kcal mol-1 (0.21 eV). Applying the Marcus model, we observed that this suggests a sizable decrease of 28 kcal mol-1 (1.4 eV) in the reorganization energy (λ), which constitutes the major portion of the protein environment's effect in lowering the reaction barrier. A similar role for the protein has been proposed in several cofactor-dependent systems and may reflect a broader trend in O2-utilizing proteins. In summary, NMO's protein environment facilitates direct electron transfer, and NMO accelerates rate-limiting electron transfer by strongly lowering the reorganization energy.
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Affiliation(s)
- Melodie M Machovina
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400 and
| | - Emerald S Ellis
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400 and
| | | | - Fikile R Brushett
- Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400 and
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Fan K, Zhang Q. The functional differentiation of the post-PKS tailoring oxygenases contributed to the chemical diversities of atypical angucyclines. Synth Syst Biotechnol 2018; 3:275-282. [PMID: 30533539 PMCID: PMC6260466 DOI: 10.1016/j.synbio.2018.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/05/2018] [Accepted: 11/06/2018] [Indexed: 12/31/2022] Open
Abstract
Angucyclines are one of the largest families of aromatic polyketides with various chemical structures and bioactivities. Decades of studies have made it easy for us to depict the picture of their early biosynthetic pathways. Two families of oxygenases, the FAD-dependent oxygenases and the ring opening oxygenases, contribute to the formation of some unique skeletons of atypical angucyclines. The FAD-dependent oxygenases involved in the biosynthetic gene clusters of typical angucyclines catalyze two hydroxylation reactions at C-12 and C-12b of prejadomycin, while their homolog JadH in jadomycin gene cluster catalyze the C-12 hydroxylation and 4a,12b-dehydration reactions of prejadomycin, which leads to the production of dehydrorabelomycin, a common intermediate during the biosynthesis of atypical angucyclines. Ring opening oxygenases of a unique family of oxygenases catalyze the oxidative C—C bond cleavage reaction of dehydrorabelomycin, followed by different rearrangement reactions, resulting in the formation of the various chemical skeletons of atypical angucyclines. These results suggested that the functional differentiation of these oxygenases could apparently enrich the sources of aromatic polyketides with greater structure diversities.
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Affiliation(s)
- Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Qian Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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22
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Cantú Reinhard FG, DuBois JL, de Visser SP. Catalytic Mechanism of Nogalamycin Monoxygenase: How Does Nature Synthesize Antibiotics without a Metal Cofactor? J Phys Chem B 2018; 122:10841-10854. [DOI: 10.1021/acs.jpcb.8b09648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fabián G. Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400, United States
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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23
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In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides. BMC Genomics 2018; 19:757. [PMID: 30340510 PMCID: PMC6194562 DOI: 10.1186/s12864-018-5151-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/08/2018] [Indexed: 11/23/2022] Open
Abstract
Background An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to external cues, the internal metabolic state of any bacterium plays a major role in determining its ability to reside and thrive in its current environment. Similar to external signaling molecules, cytoplasmic signals are also sensed by methyl-accepting chemotaxis proteins (MCPs) via diverse ligand binding domains. Myxobacteria are complex soil-dwelling social microbes that can perform a variety of physiologic and metabolic activities ranging from gliding motility, sporulation, biofilm formation, carotenoid and secondary metabolite biosynthesis, predation, and slime secretion. To live such complex lifestyles, they have evolved efficient signal transduction systems with numerous one- and two-component regulatory system along with a large array of chemosensory systems to perceive and integrate both external and internal cues. Results Here we report the in silico characterization of a putative energy taxis cluster, Cc-5, which is present in only one amongst 34 known and sequenced myxobacterial genomes, Corallococcus coralloides. In addition, we propose that this energy taxis cluster is involved in oxygen sensing, suggesting that C. coralloides can sense (either directly or indirectly) and then respond to changing concentrations of molecular oxygen. Conclusions This hypothesis is based on the presence of a unique MCP encoded in this gene cluster that contains two different oxygen-binding sensor domains, PAS and globin. In addition, the two monooxygenases encoded in this cluster may contribute to aerobic respiration via ubiquinone biosynthesis, which is part of the cytochrome bc1 complex. Finally, we suggest that this cluster was acquired from Actinobacteria, Gammaproteobacteria or Cyanobacteria. Overall, this in silico study has identified a potentially innovative and evolved mechanism of energy taxis in only one of the myxobacteria, C. coralloides. Electronic supplementary material The online version of this article (10.1186/s12864-018-5151-6) contains supplementary material, which is available to authorized users.
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24
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Sporer AJ, Beierschmitt C, Bendebury A, Zink KE, Price-Whelan A, Buzzeo MC, Sanchez LM, Dietrich LEP. Pseudomonas aeruginosa PumA acts on an endogenous phenazine to promote self-resistance. MICROBIOLOGY-SGM 2018; 164:790-800. [PMID: 29629858 DOI: 10.1099/mic.0.000657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The activities of critical metabolic and regulatory proteins can be altered by exposure to natural or synthetic redox-cycling compounds. Many bacteria, therefore, possess mechanisms to transport or transform these small molecules. The opportunistic pathogen Pseudomonas aeruginosa PA14 synthesizes phenazines, redox-active antibiotics that are toxic to other organisms but have beneficial effects for their producer. Phenazines activate the redox-sensing transcription factor SoxR and thereby induce the transcription of a small regulon, including the operon mexGHI-opmD, which encodes an efflux pump that transports phenazines, and PA14_35160 (pumA), which encodes a putative monooxygenase. Here, we provide evidence that PumA contributes to phenazine resistance and normal biofilm development, particularly during exposure to or production of strongly oxidizing N-methylated phenazines. We show that phenazine resistance depends on the presence of residues that are conserved in the active sites of other putative and characterized monooxygenases found in the antibiotic producer Streptomyces coelicolor. We also show that during biofilm growth, PumA is required for the conversion of phenazine methosulfate to unique phenazine metabolites. Finally, we compare ∆mexGHI-opmD and ∆pumA strains in assays for colony biofilm morphogenesis and SoxR activation, and find that these deletions have opposing phenotypic effects. Our results suggest that, while MexGHI-OpmD-mediated efflux has the effect of making the cellular phenazine pool more reducing, PumA acts on cellular phenazines to make the pool more oxidizing. We present a model in which these two SoxR targets function simultaneously to control the biological activity of the P. aeruginosa phenazine pool.
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Affiliation(s)
- Abigail J Sporer
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | | | - Katherine E Zink
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago, IL, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Marisa C Buzzeo
- Department of Chemistry, Barnard College, Columbia University, New York, NY, USA
| | - Laura M Sanchez
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago, IL, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, NY, USA
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25
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Tirion MM, ben-Avraham D. PDB-NMA of a protein homodimer reproduces distinct experimental motility asymmetry. Phys Biol 2018; 15:026004. [DOI: 10.1088/1478-3975/aaa277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Kosugi N, Araki T, Fujita J, Tanaka S, Fujiwara T. Growth phenotype analysis of heme synthetic enzymes in a halophilic archaeon, Haloferax volcanii. PLoS One 2017; 12:e0189913. [PMID: 29284023 PMCID: PMC5746218 DOI: 10.1371/journal.pone.0189913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 12/05/2017] [Indexed: 01/09/2023] Open
Abstract
Halophilic euryarchaea lack many of the genes necessary for the protoporphyrin-dependent heme biosynthesis pathway previously identified in animals and plants. Bioinformatic analysis suggested the presence of two heme biosynthetic processes, an Fe-coproporphyrinogen III (coproheme) decarboxylase (ChdC) pathway and an alternative heme biosynthesis (Ahb) pathway, in Haloferax volcanii. PitA is specific to the halophilic archaea and has a unique molecular structure in which the ChdC domain is joined to the antibiotics biosynthesis monooxygenase (ABM)-like domain by a histidine-rich linker sequence. The pitA gene deletion variant of H. volcanii showed a phenotype with a significant reduction of aerobic growth. Addition of a protoheme complemented the phenotype, supporting the assumption that PitA participates in the aerobic heme biosynthesis. Deletion of the ahbD gene caused a significant reduction of only anaerobic growth by denitrification or dimethylsulfoxide (DMSO) respiration, and the growth was also complemented by addition of a protoheme. The experimental results suggest that the two heme biosynthesis pathways are utilized selectively under aerobic and anaerobic conditions in H. volcanii. The molecular structure and physiological function of PitA are also discussed on the basis of the limited proteolysis and sequence analysis.
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Affiliation(s)
- Naoki Kosugi
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Takuma Araki
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Junpei Fujita
- Department of Biological Sciences, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Satoru Tanaka
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Taketomo Fujiwara
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
- * E-mail:
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27
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Motojima F, Nuylert A, Asano Y. The crystal structure and catalytic mechanism of hydroxynitrile lyase from passion fruit, Passiflora edulis. FEBS J 2017; 285:313-324. [PMID: 29155493 DOI: 10.1111/febs.14339] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/12/2017] [Accepted: 11/15/2017] [Indexed: 11/30/2022]
Abstract
Hydroxynitrile lyases (HNLs) are enzymes used in the synthesis of chiral cyanohydrins. The HNL from Passiflora edulis (PeHNL) is R-selective and is the smallest HNL known to date. The crystal structures of PeHNL and its C-terminal peptide depleted derivative were determined by molecular replacement method using the template structure of a heat stable protein, SP1, from Populus tremula at 2.8 and 1.8 Å resolution, respectively. PeHNL belongs to dimeric α+β barrel superfamily consisting of a central β-barrel in the middle of a dimer. The structure of PeHNL complexed with (R)-mandelonitrile ((R)-MAN) was also determined. The hydroxyl group of (R)-MAN forms hydrogen bonds with His8 and Tyr30 in the active site, whereas the nitrile group is oriented toward the carboxyl group of Glu54, unlike other HNLs, where it interacts with basic residues typically. The results of mutational analysis indicate that the catalytic dyad of His8-Asn101 is critical for the enzymatic reaction. The length of the hydrogen bond between His-Nδ1 and Asn101-Oδ1 is short in the PeHNL-(R)-MAN complex (~ 2.6 Å), which would increase the basicity of His8 to abstract a proton from the hydroxyl group of (R)-MAN. The cyanide ion released from the nitrile group abstracts a proton from the protonated His8 to generate a hydrogen cyanide. Thus, the His8 in the active site of PeHNL acts both as a general acid and a general base in the reaction. ENZYMES EC 4.1.2.10 DATABASE: Structural data are available in PDB database under the accession numbers 5XZQ, 5XZT, and 5Y02.
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Affiliation(s)
- Fumihiro Motojima
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Japan
| | - Aem Nuylert
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Japan
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28
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Miranda H, Immerzeel P, Gerber L, Hörnaeus K, Lind SB, Pattanaik B, Lindberg P, Mamedov F, Lindblad P. Sll1783, a monooxygenase associated with polysaccharide processing in the unicellular cyanobacterium Synechocystis PCC 6803. PHYSIOLOGIA PLANTARUM 2017; 161:182-195. [PMID: 28429526 DOI: 10.1111/ppl.12582] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/25/2017] [Accepted: 03/31/2017] [Indexed: 06/07/2023]
Abstract
Cyanobacteria play a pivotal role as the primary producer in many aquatic ecosystems. The knowledge on the interacting processes of cyanobacteria with its environment - abiotic and biotic factors - is still very limited. Many potential exocytoplasmic proteins in the model unicellular cyanobacterium Synechocystis PCC 6803 have unknown functions and their study is essential to improve our understanding of this photosynthetic organism and its potential for biotechnology use. Here we characterize a deletion mutant of Synechocystis PCC 6803, Δsll1783, a strain that showed a remarkably high light resistance which is related with its lower thylakoid membrane formation. Our results suggests Sll1783 to be involved in a mechanism of polysaccharide degradation and uptake and we hypothesize it might function as a sensor for cell density in cyanobacterial cultures.
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Affiliation(s)
- Hélder Miranda
- Department of Chemistry - Ångström Laboratory, Molecular Biomimetics and Science for Life Laboratory, Uppsala University, Uppsala, SE-75120, Sweden
| | - Peter Immerzeel
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Lorenz Gerber
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Katarina Hörnaeus
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Uppsala, SE-751 24, Sweden
| | - Sara Bergström Lind
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Uppsala, SE-751 24, Sweden
| | - Bagmi Pattanaik
- Department of Chemistry - Ångström Laboratory, Molecular Biomimetics and Science for Life Laboratory, Uppsala University, Uppsala, SE-75120, Sweden
| | - Pia Lindberg
- Department of Chemistry - Ångström Laboratory, Molecular Biomimetics and Science for Life Laboratory, Uppsala University, Uppsala, SE-75120, Sweden
| | - Fikret Mamedov
- Department of Chemistry - Ångström Laboratory, Molecular Biomimetics and Science for Life Laboratory, Uppsala University, Uppsala, SE-75120, Sweden
| | - Peter Lindblad
- Department of Chemistry - Ångström Laboratory, Molecular Biomimetics and Science for Life Laboratory, Uppsala University, Uppsala, SE-75120, Sweden
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29
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Jeong DW, Heo S, Ryu S, Blom J, Lee JH. Genomic insights into the virulence and salt tolerance of Staphylococcus equorum. Sci Rep 2017; 7:5383. [PMID: 28710456 PMCID: PMC5511256 DOI: 10.1038/s41598-017-05918-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/06/2017] [Indexed: 11/09/2022] Open
Abstract
To shed light on the genetic background behind the virulence and salt tolerance of Staphylococcus equorum, we performed comparative genome analysis of six S. equorum strains. Data on four previously published genome sequences were obtained from the NCBI database, while those on strain KM1031 displaying resistance to multiple antibiotics and strain C2014 causing haemolysis were determined in this study. Examination of the pan-genome of five of the six S. equorum strains showed that the conserved core genome retained the genes for general physiological processes and survival of the species. In this comparative genomic analysis, the factors that distinguish the strains from each other, including acquired genomic factors in mobile elements, were identified. Additionally, the high salt tolerance of strains enabling growth at a NaCl concentration of 25% (w/v) was attributed to the genes encoding potassium voltage-gated channels. Among the six strains, KS1039 does not possess any of the functional virulence determinants expressed in the other strains.
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Affiliation(s)
- Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women's University, Seoul, 02748, Republic of Korea
| | - Sojeong Heo
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, 16227, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, and Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jochen Blom
- Bioinformatics and System Biology, Justus-Liebig-University Giessen, 35392, Giessen, Germany
| | - Jong-Hoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, 16227, Republic of Korea.
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30
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Lojek LJ, Farrand AJ, Wisecaver JH, Blaby-Haas CE, Michel BW, Merchant SS, Rokas A, Skaar EP. Chlamydomonas reinhardtii LFO1 Is an IsdG Family Heme Oxygenase. mSphere 2017; 2:e00176-17. [PMID: 28815214 PMCID: PMC5557675 DOI: 10.1128/msphere.00176-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/27/2017] [Indexed: 01/13/2023] Open
Abstract
Heme is essential for respiration across all domains of life. However, heme accumulation can lead to toxicity if cells are unable to either degrade or export heme or its toxic by-products. Under aerobic conditions, heme degradation is performed by heme oxygenases, enzymes which utilize oxygen to cleave the tetrapyrrole ring of heme. The HO-1 family of heme oxygenases has been identified in both bacterial and eukaryotic cells, whereas the IsdG family has thus far been described only in bacteria. We identified a hypothetical protein in the eukaryotic green alga Chlamydomonas reinhardtii, which encodes a protein containing an antibiotic biosynthesis monooxygenase (ABM) domain consistent with those associated with IsdG family members. This protein, which we have named LFO1, degrades heme, contains similarities in predicted secondary structures to IsdG family members, and retains the functionally conserved catalytic residues found in all IsdG family heme oxygenases. These data establish LFO1 as an IsdG family member and extend our knowledge of the distribution of IsdG family members beyond bacteria. To gain further insight into the distribution of the IsdG family, we used the LFO1 sequence to identify 866 IsdG family members, including representatives from all domains of life. These results indicate that the distribution of IsdG family heme oxygenases is more expansive than previously appreciated, underscoring the broad relevance of this enzyme family. IMPORTANCE This work establishes a protein in the freshwater alga Chlamydomonas reinhardtii as an IsdG family heme oxygenase. This protein, LFO1, exhibits predicted secondary structure and catalytic residues conserved in IsdG family members, in addition to a chloroplast localization sequence. Additionally, the catabolite that results from the degradation of heme by LFO1 is distinct from that of other heme degradation products. Using LFO1 as a seed, we performed phylogenetic analysis, revealing that the IsdG family is conserved in all domains of life. Additionally, C. reinhardtii contains two previously identified HO-1 family heme oxygenases, making C. reinhardtii the first organism shown to contain two families of heme oxygenases. These data indicate that C. reinhardtii may have unique mechanisms for regulating iron homeostasis within the chloroplast.
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Affiliation(s)
- Lisa J. Lojek
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Graduate Program in Microbiology & Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Allison J. Farrand
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Crysten E. Blaby-Haas
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Brian W. Michel
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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31
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Pan G, Gao X, Fan K, Liu J, Meng B, Gao J, Wang B, Zhang C, Han H, Ai G, Chen Y, Wu D, Liu ZJ, Yang K. Structure and Function of a C-C Bond Cleaving Oxygenase in Atypical Angucycline Biosynthesis. ACS Chem Biol 2017; 12:142-152. [PMID: 28103689 DOI: 10.1021/acschembio.6b00621] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
C-C bond ring cleaving oxygenases represent a unique family of enzymes involved in the B ring cleavage reaction only observed in atypical angucycline biosynthesis. B ring cleavage is the key reaction leading to dramatic divergence in the final structures of atypical angucyclines. Here, we present the crystal structure of AlpJ, the first structure of this family of enzymes. AlpJ has been verified as the enzyme catalyzing C-C bond cleavage in kinamycin biosynthesis. The crystal structure of the AlpJ monomer resembles the dimeric structure of ferredoxin-like proteins. The N- and C-terminal halves of AlpJ are homologous, and both contain a putative hydrophobic substrate binding pocket in the "closed" and "open" conformations, respectively. Structural comparison of AlpJ with ActVA-Orf6 and protein-ligand docking analysis suggest that the residues including Asn60, Trp64, and Trp181 are possibly involved in substrate recognition. Site-directed mutagenesis results supported our hypothesis, as mutation of these residues led to nearly a complete loss of the activity of AlpJ. Structural analysis also revealed that AlpJ possesses an intramolecular domain-domain interface, where the residues His50 and Tyr178 form a hydrogen bond that probably stabilizes the three-dimensional structure of AlpJ. Site-directed mutagenesis showed that the two residues, His50 and Tyr178, were vital for the activity of AlpJ. Our findings shed light on the structure and catalytic mechanism of the AlpJ family of oxygenases, which presumably involves two active sites that might function in a cooperative manner.
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Affiliation(s)
- Guohui Pan
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xiaoqin Gao
- National
Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Keqiang Fan
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Junlin Liu
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, People’s Republic of China
| | - Bing Meng
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, People’s Republic of China
| | - Jinmin Gao
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Bin Wang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Chaobo Zhang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Hui Han
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Guomin Ai
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Yihua Chen
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Dong Wu
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, People’s Republic of China
| | - Zhi-Jie Liu
- National
Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Institute
of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, China
| | - Keqian Yang
- State
Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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New insight into cofactor-free oxygenation from combined experimental and computational approaches. Curr Opin Struct Biol 2016; 41:109-118. [DOI: 10.1016/j.sbi.2016.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 06/22/2016] [Indexed: 01/07/2023]
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Yoneda A, Wittmann BJ, King JD, Blankenship RE, Dantas G. Transcriptomic analysis illuminates genes involved in chlorophyll synthesis after nitrogen starvation in Acaryochloris sp. CCMEE 5410. PHOTOSYNTHESIS RESEARCH 2016; 129:171-182. [PMID: 27276888 DOI: 10.1007/s11120-016-0279-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/19/2016] [Indexed: 06/06/2023]
Abstract
Acaryochloris species are a genus of cyanobacteria that utilize chlorophyll (chl) d as their primary chlorophyll molecule during oxygenic photosynthesis. Chl d allows Acaryochloris to harvest red-shifted light, which gives them the ability to live in filtered light environments that are depleted in visible light. Although genomes of multiple Acaryochloris species have been sequenced, their analysis has not revealed how chl d is synthesized. Here, we demonstrate that Acaryochloris sp. CCMEE 5410 cells undergo chlorosis by nitrogen depletion and exhibit robust regeneration of chl d by nitrogen repletion. We performed a time course RNA-Seq experiment to quantify global transcriptomic changes during chlorophyll recovery. We observed upregulation of numerous known chl biosynthesis genes and also identified an oxygenase gene with a similar transcriptional profile as these chl biosynthesis genes, suggesting its possible involvement in chl d biosynthesis. Moreover, our data suggest that multiple prochlorophyte chlorophyll-binding homologs are important during chlorophyll recovery, and light-independent chl synthesis genes are more dominant than the light-dependent gene at the transcription level. Transcriptomic characterization of this organism provides crucial clues toward mechanistic elucidation of chl d biosynthesis.
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Affiliation(s)
- Aki Yoneda
- Department of Pathology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Bruce J Wittmann
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
- Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St. Louis, MO, USA
| | - Jeremy D King
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
- Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St. Louis, MO, USA
| | - Robert E Blankenship
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.
- Photosynthetic Antenna Research Center (PARC), Washington University in St. Louis, St. Louis, MO, USA.
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.
| | - Gautam Dantas
- Department of Pathology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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Machovina MM, Usselman RJ, DuBois JL. Monooxygenase Substrates Mimic Flavin to Catalyze Cofactorless Oxygenations. J Biol Chem 2016; 291:17816-28. [PMID: 27307041 DOI: 10.1074/jbc.m116.730051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 01/16/2023] Open
Abstract
Members of the antibiotic biosynthesis monooxygenase family catalyze O2-dependent oxidations and oxygenations in the absence of any metallo- or organic cofactor. How these enzymes surmount the kinetic barrier to reactions between singlet substrates and triplet O2 is unclear, but the reactions have been proposed to occur via a flavin-like mechanism, where the substrate acts in lieu of a flavin cofactor. To test this model, we monitored the uncatalyzed and enzymatic reactions of dithranol, a substrate for the nogalamycin monooxygenase (NMO) from Streptomyces nogalater As with flavin, dithranol oxidation was faster at a higher pH, although the reaction did not appear to be base-catalyzed. Rather, conserved asparagines contributed to suppression of the substrate pKa The same residues were critical for enzymatic catalysis that, consistent with the flavoenzyme model, occurred via an O2-dependent slow step. Evidence for a superoxide/substrate radical pair intermediate came from detection of enzyme-bound superoxide during turnover. Small molecule and enzymatic superoxide traps suppressed formation of the oxygenation product under uncatalyzed conditions, whereas only the small molecule trap had an effect in the presence of NMO. This suggested that NMO both accelerated the formation and directed the recombination of a superoxide/dithranyl radical pair. These catalytic strategies are in some ways flavin-like and stand in contrast to the mechanisms of urate oxidase and (1H)-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase, both cofactor-independent enzymes that surmount the barriers to direct substrate/O2 reactivity via markedly different means.
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Affiliation(s)
- Melodie M Machovina
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400
| | - Robert J Usselman
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715-3400
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Molecular Genetic Characterization of an Anthrabenzoxocinones Gene Cluster in Streptomyces Sp. FJS31-2 for the Biosynthesis of BE-24566B and Zunyimycin Ale. Molecules 2016; 21:molecules21060711. [PMID: 27248985 PMCID: PMC6273070 DOI: 10.3390/molecules21060711] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/08/2016] [Accepted: 05/18/2016] [Indexed: 12/05/2022] Open
Abstract
Genome mining is an effective tool used to discover novel natural products from actinomycetes. Genome sequence analysis of Streptomyces sp. FJS31-2 revealed the presence of one putative type II polyketide gene cluster (ABX), which may correspond to type II polyketide products including BE-24566B and its chloro-derivatives. The addition of natural humus acid successfully activated the biosynthsis of the abx gene cluster. BE-24566B and its chloro-derivatives, named zunyimycin A, were also detected. The targeted deletion of the polyketide skeleton synthesis genes such as abxp, abxk, and abxs was performed in the wild strain to identify the gene cluster for BE-24566B biosynthesis.
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Acharya G, Kaur G, Subramanian S. Evolutionary relationships between heme-binding ferredoxin α + β barrels. BMC Bioinformatics 2016; 17:168. [PMID: 27089923 PMCID: PMC4835899 DOI: 10.1186/s12859-016-1033-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/12/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. The barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. Several members of this superfamily bind heme in order to carry out their functions. RESULTS We analyze the heme-binding sites in these proteins as well as their barrel topologies. Our comparative structural analysis of these heme-binding barrels reveals two distinct modes of packing of the ferredoxin-like domains to constitute the α + β barrel, which is typified by the Type-1/IsdG-like and Type-2/OxdA-like proteins, respectively. We examine the heme-binding pockets and explore the versatility of the α + β barrels ability to accommodate heme or heme-related moieties, such as siroheme, in at least three different sites, namely, the mode seen in IsdG/OxdA, Cld/DyP/EfeB/HemQ and siroheme decarboxylase barrels. CONCLUSIONS Our study offers insights into the plausible evolutionary relationships between the two distinct barrel packing topologies and relate the observed heme-binding sites to these topologies.
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Affiliation(s)
- Giriraj Acharya
- CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, India
| | - Gurmeet Kaur
- CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh, India
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37
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Yang X, Matsui T, Kodama T, Mori T, Zhou X, Taura F, Noguchi H, Abe I, Morita H. Structural basis for olivetolic acid formation by a polyketide cyclase from Cannabis sativa. FEBS J 2016; 283:1088-106. [PMID: 26783002 DOI: 10.1111/febs.13654] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/06/2016] [Accepted: 01/12/2016] [Indexed: 11/27/2022]
Abstract
UNLABELLED In polyketide biosynthesis, ring formation is one of the key diversification steps. Olivetolic acid cyclase (OAC) from Cannabis sativa, involved in cannabinoid biosynthesis, is the only known plant polyketide cyclase. In addition, it is the only functionally characterized plant α+β barrel (DABB) protein that catalyzes the C2-C7 aldol cyclization of the linear pentyl tetra-β-ketide CoA as the substrate, to generate olivetolic acid (OA). Herein, we solved the OAC apo and OAC-OA complex binary crystal structures at 1.32 and 1.70 Å resolutions, respectively. The crystal structures revealed that the enzyme indeed belongs to the DABB superfamily, as previously proposed, and possesses a unique active-site cavity containing the pentyl-binding hydrophobic pocket and the polyketide binding site, which have never been observed among the functionally and structurally characterized bacterial polyketide cyclases. Furthermore, site-directed mutagenesis studies indicated that Tyr72 and His78 function as acid/base catalysts at the catalytic center. Structural and/or functional studies of OAC suggested that the enzyme lacks thioesterase and aromatase activities. These observations demonstrated that OAC employs unique catalytic machinery utilizing acid/base catalytic chemistry for the formation of the precursor of OA. The structural and functional insights obtained in this work thus provide the foundation for analyses of the plant polyketide cyclases that will be discovered in the future. DATA DEPOSITION Structural data reported in this paper are available in the Protein Data Bank under the accession numbers 5B08 for the OAC apo, 5B09 for the OAC-OA binary complex and 5B0A, 5B0B, 5B0C, 5B0D, 5B0E, 5B0F and 5B0G for the OAC His5Q, Ile7F, Tyr27F, Tyr27W, Val59M, Tyr72F and His78S mutant enzymes, respectively.
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Affiliation(s)
- Xinmei Yang
- Institute of Natural Medicine, University of Toyama, Japan
| | - Takashi Matsui
- Institute of Natural Medicine, University of Toyama, Japan
| | - Takeshi Kodama
- Institute of Natural Medicine, University of Toyama, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Japan
| | - Xiaoxi Zhou
- Institute of Natural Medicine, University of Toyama, Japan
| | - Futoshi Taura
- Graduate School of Medicine and Pharmaceutical Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, University of Toyama, Japan
| | - Hiroshi Noguchi
- School of Pharmaceutical Sciences, University of Shizuoka, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Japan
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Yang X, Matsui T, Mori T, Taura F, Noguchi H, Abe I, Morita H. Expression, purification and crystallization of a plant polyketide cyclase from Cannabis sativa. Acta Crystallogr F Struct Biol Commun 2015; 71:1470-4. [PMID: 26625288 PMCID: PMC4666474 DOI: 10.1107/s2053230x15020385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/28/2015] [Indexed: 11/10/2022] Open
Abstract
Plant polyketides are a structurally diverse family of natural products. In the biosynthesis of plant polyketides, the construction of the carbocyclic scaffold is a key step in diversifying the polyketide structure. Olivetolic acid cyclase (OAC) from Cannabis sativa L. is the only known plant polyketide cyclase that catalyzes the C2-C7 intramolecular aldol cyclization of linear pentyl tetra-β-ketide-CoA to generate olivetolic acid in the biosynthesis of cannabinoids. The enzyme is also thought to belong to the dimeric α+β barrel (DABB) protein family. However, because of a lack of functional analysis of other plant DABB proteins and low sequence identity with the functionally distinct bacterial DABB proteins, the catalytic mechanism of OAC has remained unclear. To clarify the intimate catalytic mechanism of OAC, the enzyme was overexpressed in Escherichia coli and crystallized using the vapour-diffusion method. The crystals diffracted X-rays to 1.40 Å resolution and belonged to space group P3121 or P3221, with unit-cell parameters a = b = 47.3, c = 176.0 Å. Further crystallographic analysis will provide valuable insights into the structure-function relationship and catalytic mechanism of OAC.
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Affiliation(s)
- Xinmei Yang
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, Japan
| | - Takashi Matsui
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Futoshi Taura
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, Japan
| | - Hiroshi Noguchi
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Morita
- Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, Japan
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Skinnider MA, Dejong CA, Rees PN, Johnston CW, Li H, Webster ALH, Wyatt MA, Magarvey NA. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM). Nucleic Acids Res 2015; 43:9645-62. [PMID: 26442528 PMCID: PMC4787774 DOI: 10.1093/nar/gkv1012] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 09/24/2015] [Indexed: 12/05/2022] Open
Abstract
Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/.
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Affiliation(s)
- Michael A Skinnider
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Chris A Dejong
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Philip N Rees
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Chad W Johnston
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Haoxin Li
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Andrew L H Webster
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Morgan A Wyatt
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Nathan A Magarvey
- Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, L8S 4K1, Canada
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40
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Liu S, Guo H, Zhang T, Han L, Yao P, Zhang Y, Rong N, Yu Y, Lan W, Wang C, Ding J, Wang R, Liu W, Cao C. Structure-based Mechanistic Insights into Terminal Amide Synthase in Nosiheptide-Represented Thiopeptides Biosynthesis. Sci Rep 2015; 5:12744. [PMID: 26244829 PMCID: PMC4525488 DOI: 10.1038/srep12744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/08/2015] [Indexed: 01/07/2023] Open
Abstract
Nosiheptide is a parent compound of thiopeptide family that exhibit potent activities against various bacterial pathogens. Its C-terminal amide formation is catalyzed by NosA, which is an unusual strategy for maturating certain thiopeptides by processing their precursor peptides featuring a serine extension. We here report the crystal structure of truncated NosA1-111 variant, revealing three key elements, including basic lysine 49 (K49), acidic glutamic acid 101 (E101) and flexible C-terminal loop NosA112-151, are crucial to the catalytic terminal amide formation in nosiheptide biosynthesis. The side-chain of residue K49 and the C-terminal loop fasten the substrate through hydrogen bonds and hydrophobic interactions. The side-chain of residue E101 enhances nucleophilic attack of H2O to the methyl imine intermediate, leading to Cα-N bond cleavage and nosiheptide maturation. The sequence alignment of NosA and its homologs NocA, PbtH, TpdK and BerI, and the enzymatic assay suggest that the mechanistic studies on NosA present an intriguing paradigm about how NosA family members function during thiopeptide biosynthesis.
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Affiliation(s)
- Shanshan Liu
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Heng Guo
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Tianlong Zhang
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Li Han
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Pengfei Yao
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yan Zhang
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Naiyan Rong
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yi Yu
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Wenxian Lan
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Chunxi Wang
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jianping Ding
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Renxiao Wang
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Wen Liu
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China,
| | - Chunyang Cao
- State Key Laboratory of Bio-Organic and Natural Product Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China,
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41
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Celis AI, DuBois JL. Substrate, product, and cofactor: The extraordinarily flexible relationship between the CDE superfamily and heme. Arch Biochem Biophys 2015; 574:3-17. [PMID: 25778630 PMCID: PMC4414885 DOI: 10.1016/j.abb.2015.03.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 12/21/2022]
Abstract
PFam Clan 0032, also known as the CDE superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. Of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. Focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature's most important small molecules.
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Affiliation(s)
- Arianna I Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States.
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Maier S, Heitzler T, Asmus K, Brötz E, Hardter U, Hesselbach K, Paululat T, Bechthold A. Functional characterization of different ORFs including luciferase-like monooxygenase genes from the mensacarcin gene cluster. Chembiochem 2015; 16:1175-82. [PMID: 25907804 DOI: 10.1002/cbic.201500048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Indexed: 11/06/2022]
Abstract
The biologically active compound mensacarcin is produced by Streptomyces bottropensis. The cosmid cos2 contains a large part of the mensacarcin biosynthesis gene cluster. Heterologous expression of this cosmid in Streptomyces albus J1074 led to the production of the intermediate didesmethylmensacarcin (DDMM). In order to gain more insights into the biosynthesis, gene inactivation experiments were carried out by λ-Red/ET-mediated recombination, and the deletion mutants were introduced into the host S. albus. In total, 23 genes were inactivated. Analysis of the metabolic profiles of the mutant strains showed the complete collapse of DDMM biosynthesis, but upon overexpression of the SARP regulatory gene msnR1 in each mutant new intermediates were detected. The compounds were isolated, and their structures were elucidated. Based on the results the specific functions of several enzymes were determined, and a pathway for mensacarcin biosynthesis is proposed.
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Affiliation(s)
- Sarah Maier
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
| | - Tanja Heitzler
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
| | - Katharina Asmus
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
| | - Elke Brötz
- Organic Chemsitry II, Universität Siegen, Adolf-Reichwein-Strasse 2, 57068 Siegen (Germany).,Present address: Helmholtz Institut für Pharmazeutische Forschung Saarland, Postfach 151150, 66041 Saarbrücken (Germany)
| | - Uwe Hardter
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
| | - Katharina Hesselbach
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany)
| | - Thomas Paululat
- Organic Chemsitry II, Universität Siegen, Adolf-Reichwein-Strasse 2, 57068 Siegen (Germany)
| | - Andreas Bechthold
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg (Germany).
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43
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Sheldon JR, Heinrichs DE. Recent developments in understanding the iron acquisition strategies of gram positive pathogens. FEMS Microbiol Rev 2015; 39:592-630. [DOI: 10.1093/femsre/fuv009] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 12/26/2022] Open
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Ogasawara Y, Yackley BJ, Greenberg JA, Rogelj S, Melançon CE. Expanding our understanding of sequence-function relationships of type II polyketide biosynthetic gene clusters: bioinformatics-guided identification of Frankiamicin A from Frankia sp. EAN1pec. PLoS One 2015; 10:e0121505. [PMID: 25837682 PMCID: PMC4383371 DOI: 10.1371/journal.pone.0121505] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/31/2015] [Indexed: 01/04/2023] Open
Abstract
A large and rapidly increasing number of unstudied “orphan” natural product biosynthetic gene clusters are being uncovered in sequenced microbial genomes. An important goal of modern natural products research is to be able to accurately predict natural product structures and biosynthetic pathways from these gene cluster sequences. This requires both development of bioinformatic methods for global analysis of these gene clusters and experimental characterization of select products produced by gene clusters with divergent sequence characteristics. Here, we conduct global bioinformatic analysis of all available type II polyketide gene cluster sequences and identify a conserved set of gene clusters with unique ketosynthase α/β sequence characteristics in the genomes of Frankia species, a group of Actinobacteria with underexploited natural product biosynthetic potential. Through LC-MS profiling of extracts from several Frankia species grown under various conditions, we identified Frankia sp. EAN1pec as producing a compound with spectral characteristics consistent with the type II polyketide produced by this gene cluster. We isolated the compound, a pentangular polyketide which we named frankiamicin A, and elucidated its structure by NMR and labeled precursor feeding. We also propose biosynthetic and regulatory pathways for frankiamicin A based on comparative genomic analysis and literature precedent, and conduct bioactivity assays of the compound. Our findings provide new information linking this set of Frankia gene clusters with the compound they produce, and our approach has implications for accurate functional prediction of the many other type II polyketide clusters present in bacterial genomes.
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Affiliation(s)
- Yasushi Ogasawara
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Benjamin J. Yackley
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Jacob A. Greenberg
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Snezna Rogelj
- Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, New Mexico, United States of America
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, New Mexico, United States of America
| | - Charles E. Melançon
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, United States of America
- * E-mail:
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Naseer N, Shapiro JA, Chander M. RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor. PLoS One 2014; 9:e106181. [PMID: 25162599 PMCID: PMC4146615 DOI: 10.1371/journal.pone.0106181] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/31/2014] [Indexed: 11/26/2022] Open
Abstract
The redox-regulated transcription factor SoxR is conserved in diverse bacteria, but emerging studies suggest that this protein plays distinct physiological roles in different bacteria. SoxR regulates a global oxidative stress response (involving >100 genes) against exogenous redox-cycling drugs in Escherichia coli and related enterics. In the antibiotic producers Streptomyces coelicolor and Pseudomonas aeruginosa, however, SoxR regulates a smaller number of genes that encode membrane transporters and proteins with homology to antibiotic-tailoring enzymes. In both S. coelicolor and P. aeruginosa, SoxR-regulated genes are expressed in stationary phase during the production of endogenously-produced redox-active antibiotics. These observations suggest that SoxR evolved to sense endogenous secondary metabolites and activate machinery to process and transport them in antibiotic-producing bacteria. Previous bioinformatics analysis that searched the genome for SoxR-binding sites in putative promoters defined a five-gene SoxR regulon in S. coelicolor including an ABC transporter, two oxidoreductases, a monooxygenase and an epimerase/dehydratase. Since this in silico screen may have missed potential SoxR-targets, we conducted a whole genome transcriptome comparison of wild type S. coelicolor and a soxR-deficient mutant in stationary phase using RNA-Seq. Our analysis revealed a sixth SoxR-regulated gene in S. coelicolor that encodes a putative quinone oxidoreductase. Knowledge of the full complement of genes regulated by SoxR will facilitate studies to elucidate the function of this regulatory molecule in antibiotic producers.
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Affiliation(s)
- Nawar Naseer
- Department of Biology, Bryn Mawr College, Bryn Mawr, Pennsylvania, United States of America
| | - Joshua A Shapiro
- Department of Biology, Bryn Mawr College, Bryn Mawr, Pennsylvania, United States of America
| | - Monica Chander
- Department of Biology, Bryn Mawr College, Bryn Mawr, Pennsylvania, United States of America
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Thierbach S, Bui N, Zapp J, Chhabra SR, Kappl R, Fetzner S. Substrate-assisted O2 activation in a cofactor-independent dioxygenase. ACTA ACUST UNITED AC 2014; 21:217-25. [PMID: 24388758 DOI: 10.1016/j.chembiol.2013.11.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/22/2013] [Accepted: 11/27/2013] [Indexed: 11/29/2022]
Abstract
In contrast to the majority of O2-activating enzymes, which depend on an organic cofactor or a metal ion for catalysis, a particular group of structurally unrelated oxygenases is functional without any cofactor. In this study, we characterized the mechanism of O2 activation in the reaction pathway of a cofactor-independent dioxygenase with an α/β-hydrolase fold, which catalyzes the oxygenolytic cleavage of 2-alkyl-3-hydroxy-4(1H)-quinolones. Chemical analysis and electron paramagnetic resonance spectroscopic data revealed that O2 activation in the enzyme's active site is substrate-assisted, relying on single electron transfer from the bound substrate anion to O2 to form a radical pair, which recombines to a C2-peroxide intermediate. Thus, an oxygenase can function without a cofactor, if the organic substrate itself, after activation to a (carb)anion by an active-site base, is intrinsically reactive toward molecular oxygen.
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Affiliation(s)
- Sven Thierbach
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany
| | - Nguyen Bui
- Department of Biophysics, School of Medicine, Saarland University, Clinical Center, Building 76, 66421 Homburg, Germany
| | - Josef Zapp
- Pharmaceutical Biology, Saarland University, Campus, Building C2, 66123 Saarbrücken, Germany
| | - Siri Ram Chhabra
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Reinhard Kappl
- Department of Biophysics, School of Medicine, Saarland University, Clinical Center, Building 76, 66421 Homburg, Germany
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany.
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Hayes RP, Lewis KM, Xun L, Kang C. Catalytic mechanism of 5-chlorohydroxyhydroquinone dehydrochlorinase from the YCII superfamily of largely unknown function. J Biol Chem 2013; 288:28447-56. [PMID: 23955343 DOI: 10.1074/jbc.m113.499368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TftG, 5-chloro-2-hydroxyhydroquinone (5-CHQ) dehydrochlorinase, is involved in the biodegradation of 2,4,5-trichlorophenoxyacetate by Burkholderia phenoliruptrix AC1100. It belongs to the YCII superfamily, a group of proteins with largely unknown function. In this work, we utilized structural and functional studies, including the apo-form and 2,5-dihydroxybenzoquinone binary complex crystal structures, computational analysis, and site-directed mutagenesis, to determine the dehydrochlorination mechanism. The His-Asp dyad, which initiates catalysis, is strongly conserved in YCII-like proteins. In addition, other catalytically important residues such as Pro-76, which orients the His-Asp catalytic dyad; Arg-17 and Ser-56, which form an oxyanion hole; and Asp-9, which stabilizes the oxyanion hole, are among the most highly conserved residues across the YCII superfamily members. The comprehensive characterization of TftG helps not only for identifying effective mechanisms for chloroaromatic dechlorination but also for understanding the functions of YCII superfamily members, which we propose to be lyases.
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Affiliation(s)
- Artur Gora
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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Metsä-Ketelä M, Oja T, Taguchi T, Okamoto S, Ichinose K. Biosynthesis of pyranonaphthoquinone polyketides reveals diverse strategies for enzymatic carbon–carbon bond formation. Curr Opin Chem Biol 2013; 17:562-70. [DOI: 10.1016/j.cbpa.2013.06.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/30/2013] [Accepted: 06/25/2013] [Indexed: 11/26/2022]
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50
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Paananen P, Patrikainen P, Kallio P, Mäntsälä P, Niemi J, Niiranen L, Metsä-Ketelä M. Structural and Functional Analysis of Angucycline C-6 Ketoreductase LanV Involved in Landomycin Biosynthesis. Biochemistry 2013; 52:5304-14. [DOI: 10.1021/bi400712q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Pasi Paananen
- Department
of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Pekka Patrikainen
- Department
of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Pauli Kallio
- Department
of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Pekka Mäntsälä
- Department
of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Jarmo Niemi
- Department
of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Laila Niiranen
- Department
of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Mikko Metsä-Ketelä
- Department
of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
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