1
|
Salvatti BA, Chagas MA, Fernandes PO, Ladeira YFX, Bozzi AS, Valadares VS, Valente AP, de Miranda AS, Rocha WR, Maltarollo VG, Moraes AH. Understanding the Enzyme ( S)-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones. J Chem Inf Model 2024; 64:4462-4474. [PMID: 38776464 DOI: 10.1021/acs.jcim.3c01773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The (S)-norcoclaurine synthase from Thalictrum flavum (TfNCS) stereoselectively catalyzes the Pictet-Spengler reaction between dopamine and 4-hydroxyphenylacetaldehyde to give (S)-norcoclaurine. TfNCS can catalyze the Pictet-Spengler reaction with various aldehydes and ketones, leading to diverse tetrahydroisoquinolines. This substrate promiscuity positions TfNCS as a highly promising enzyme for synthesizing fine chemicals. Understanding carbonyl-containing substrates' structural and electronic signatures that influence TfNCS activity can help expand its applications in the synthesis of different compounds and aid in protein optimization strategies. In this study, we investigated the influence of the molecular properties of aldehydes and ketones on their reactivity in the TfNCS-catalyzed Pictet-Spengler reaction. Initially, we compiled a library of reactive and unreactive compounds from previous publications. We also performed enzymatic assays using nuclear magnetic resonance to identify some reactive and unreactive carbonyl compounds, which were then included in the library. Subsequently, we employed QSAR and DFT calculations to establish correlations between substrate-candidate structures and reactivity. Our findings highlight correlations of structural and stereoelectronic features, including the electrophilicity of the carbonyl group, to the reactivity of aldehydes and ketones toward the TfNCS-catalyzed Pictet-Spengler reaction. Interestingly, experimental data of seven compounds out of fifty-three did not correlate with the electrophilicity of the carbonyl group. For these seven compounds, we identified unfavorable interactions between them and the TfNCS. Our results demonstrate the applications of in silico techniques in understanding enzyme promiscuity and specificity, with a particular emphasis on machine learning methodologies, DFT electronic structure calculations, and molecular dynamic (MD) simulations.
Collapse
Affiliation(s)
- Brunno A Salvatti
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Marcelo A Chagas
- Departamento de Ciências Exatas, Universidade do Estado de Minas Gerais, João Monlevade, Minas Gerais 35930-314, Brazil
| | - Phillipe O Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Yan F X Ladeira
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Aline S Bozzi
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Veronica S Valadares
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Ana Paula Valente
- Centro Nacional de Ressonância Magnética Nuclear, Instituto de Bioquímica Médica Leopoldo de Meis, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
| | - Amanda S de Miranda
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Willian R Rocha
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vinicius G Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| |
Collapse
|
2
|
Kim D, Na Y, Chang H, Boo J, Kang S, Jin C, Kang S, Lee SY, Lee B. Domain swapping of the C-terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis. Protein Sci 2023; 32:e4644. [PMID: 37070717 PMCID: PMC10182728 DOI: 10.1002/pro.4644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/22/2023] [Accepted: 04/16/2023] [Indexed: 04/19/2023]
Abstract
Polyketide metabolism-associated proteins in Mycobacterium tuberculosis play an essential role in the survival of the bacterium, which makes them potential drug targets for the treatment of tuberculosis (TB). The novel ribonuclease protein Rv1546 is predicted to be a member of the steroidogenic acute regulatory protein-related lipid-transfer (START) domain superfamily, which comprises bacterial polyketide aromatase/cyclases (ARO/CYCs). Here, we determined the crystal structure of Rv1546 in a V-shaped dimer. The Rv1546 monomer consists of four α-helices and seven antiparallel β-strands. Interestingly, in the dimeric state, Rv1546 forms a helix-grip fold, which is present in START domain proteins, via three-dimensional domain swapping. Structural analysis revealed that the conformational change of the C-terminal α-helix of Rv1546 might contribute to the unique dimer structure. Site-directed mutagenesis followed by in vitro ribonuclease activity assays was performed to identify catalytic sites of the protein. This experiment suggested that surface residues R63, K84, K88, and R113 are important in the ribonuclease function of Rv1546. In summary, this study presents the structural and functional characterization of Rv1546 and supplies new perspectives for exploiting Rv1546 as a novel drug target for TB treatment.
Collapse
Affiliation(s)
- Do‐Hee Kim
- Jeju Research Institute of Pharmaceutical SciencesCollege of Pharmacy, Jeju National UniversityJejuKorea
- Interdisciplinary Graduate Program in Advanced Convergence Technology and ScienceJeju National UniversityJejuKorea
| | - Youngseo Na
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National UniversitySeoulKorea
| | - Heesun Chang
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National UniversitySeoulKorea
| | - Jun‐Hyuk Boo
- Jeju Research Institute of Pharmaceutical SciencesCollege of Pharmacy, Jeju National UniversityJejuKorea
| | - Sung‐Min Kang
- College of Pharmacy, Duksung Women's UniversitySeoulKorea
| | - Chenglong Jin
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National UniversitySeoulKorea
| | - Su‐Jin Kang
- College of Pharmacy, Dongduk Women's UniversitySeoulKorea
| | - Su Yeon Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National UniversitySeoulKorea
| | - Bong‐Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National UniversitySeoulKorea
| |
Collapse
|
3
|
Huang C, Cui H, Ren H, Zhao H. Investigation of the Biosynthetic Mechanism of Bipentaromycin Featuring an Unprecedented Cyclic Head-to-Tail Dimeric Scaffold. JACS AU 2023; 3:195-203. [PMID: 36711095 PMCID: PMC9875255 DOI: 10.1021/jacsau.2c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Bipentaromycins are heterodimeric aromatic polyketides featuring two distinctive 5/6/6/6/5 pentacyclic ring systems and exhibit antibacterial activities. However, their overall biosynthetic mechanism, particularly the mechanism for early-stage modifications, such as hydrogenation and methylation, and late-stage dimerization, remains unknown. Herein, by integrating heterologous expression, isotope labeling, gene knockout and complementation, and computational modeling, we determined the biosynthetic origin of the skeleton, identified the enzymes involved in stereo-/regioselective hydrogenation and methylation, and provided new mechanistic insights into the dimerization. This work not only deciphers the biosynthetic mechanism of bipentaromycins but also provides new strategies for creating biologically active dimeric pharmacophores for drug discovery and development.
Collapse
Affiliation(s)
- Chunshuai Huang
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Haiyang Cui
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hengqian Ren
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Biochemistry, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
4
|
Yi D, Niroula D, Gutekunst WR, Loper JE, Yan Q, Agarwal V. A Nonfunctional Halogenase Masquerades as an Aromatizing Dehydratase in Biosynthesis of Pyrrolic Polyketides by Type I Polyketide Synthases. ACS Chem Biol 2022; 17:1351-1356. [PMID: 35675261 DOI: 10.1021/acschembio.2c00288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial modular type I polyketide synthases (PKSs) typically furnish nonaromatic lactone and lactam natural products. Here, by the complete in vitro enzymatic production of the polyketide antibiotic pyoluteorin, we describe the biosynthetic mechanism for the construction of an aromatic resorcylic ring by a type I PKS. We find that the pyoluteorin type I PKS does not produce an aromatic product, rather furnishing an alicyclic dihydrophloroglucinol that is later enzymatically dehydrated and aromatized. The aromatizing dehydratase is encoded in the pyoluteorin biosynthetic gene cluster (BGC), and its presence is conserved in other BGCs encoding production of pyrrolic polyketides. Sequence similarity and mutational analysis demonstrates that the overall structure and position of the active site for the aromatizing dehydratase is shared with flavin-dependent halogenases albeit with a loss in ability to perform redox catalysis. We demonstrate that the post-PKS dehydrative aromatization is critical for the antibiotic activity of pyoluteorin.
Collapse
Affiliation(s)
- Dongqi Yi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dhirendra Niroula
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Will R Gutekunst
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, United States.,USDA-Agricultural Research Service, Corvallis, Oregon 97330, United States
| | - Qing Yan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717, United States.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
5
|
Gao Y, Zhao Y, Zhou J, Yang M, Lin L, Wang W, Tao M, Deng Z, Jiang M. Unexpected Role of a Short‐Chain Dehydrogenase/Reductase Family Protein in Type II Polyketide Biosynthesis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yaojie Gao
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200030 P. R. China
| | - Yuchun Zhao
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200030 P. R. China
| | - Jie Zhou
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200030 P. R. China
| | - Maohua Yang
- Ministry of Education Key Laboratory of Computational Physical Sciences Department of Chemistry Institutes of Biomedical Sciences Fudan University Shanghai 200438 China
| | - Lin Lin
- Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders Ministry of Education Shanghai Jiao Tong University Shanghai 200240 China
| | - Wenning Wang
- Ministry of Education Key Laboratory of Computational Physical Sciences Department of Chemistry Institutes of Biomedical Sciences Fudan University Shanghai 200438 China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200030 P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200030 P. R. China
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200030 P. R. China
| |
Collapse
|
6
|
Differences at Species Level and in Repertoires of Secondary Metabolite Biosynthetic Gene Clusters among Streptomyces coelicolor A3(2) and Type Strains of S. coelicolor and Its Taxonomic Neighbors. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Streptomyces coelicolor A3(2) is used worldwide for genetic studies, and its complete genome sequence was published in 2002. However, as the whole genome of the type strain of S. coelicolor has not been analyzed, the relationship between S. coelicolor A3(2) and the type strain is not yet well known. To clarify differences in their biosynthetic potential, as well as their taxonomic positions, we sequenced whole genomes of S. coelicolor NBRC 12854T and type strains of its closely related species—such as Streptomyces daghestanicus, Streptomyces hydrogenans, and Streptomyces violascens—via PacBio. Biosynthetic gene clusters for polyketides and non-ribosomal peptides were surveyed by antiSMASH, followed by bioinformatic analyses. Type strains of Streptomyces albidoflavus, S. coelicolor, S. daghestanicus, S. hydrogenans, and S. violascens shared the same 16S rDNA sequence, but S. coelicolor A3(2) did not. S. coelicolor A3(2) and S. coelicolor NBRC 12854T can be classified as Streptomycesanthocyanicus and S. albidoflavus, respectively. In contrast, S. daghestanicus, S. hydrogenans, and S. violascens are independent species, despite their identical 16S rDNA sequences. S. coelicolor A3(2), S. coelicolor NBRC 12854T, S. daghestanicus NBRC 12762T, S. hydrogenans NBRC 13475T, and S. violascens NBRC 12920T each harbor specific polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters in their genomes, whereas PKS and NRPS gene clusters are well conserved between S. coelicolor A3(2) and S. anthocyanicus JCM 5058T, and between S. coelicolor NBRC 12854T and S. albidoflavus DSM 40455T, belonging to the same species. These results support our hypothesis that the repertoires of PKS and NRPS gene clusters are different between different species.
Collapse
|
7
|
Gao Y, Zhao Y, Zhou J, Yang M, Lin L, Wang W, Tao M, Deng Z, Jiang M. Unexpected Role of a Short-Chain Dehydrogenase/Reductase Family Protein in Type II Polyketide Biosynthesis. Angew Chem Int Ed Engl 2021; 61:e202110445. [PMID: 34927786 DOI: 10.1002/anie.202110445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Indexed: 11/05/2022]
Abstract
We investigated the biosynthetic pathway of type II polyketide murayaquinone. The murayaquinone biosynthetic cluster contains genes for three putative short-chain dehydrogenase/reductase family enzymes including MrqF and MrqH with known functions and MrqM with unclear function. We report the functional characterization of MrqM for its role in murayaquinone biosynthesis. Our gene deletion experiment and structural elucidation of the accumulated intermediates revealed that MrqM is related with the second polyketide ring cyclization, because the inactivation of mrqM resulted in the accumulation of an off-pathway intermediate SEK43 and disrupted the second and third ring cyclization. Site-directed mutagenesis studies showed that two conserved residues in MrqM and homologous proteins Y151 and K155 are essential for its activity. The previously proposed second/third ring cyclase, MrqD, might instead play another important role in the chain releasing step of the murayaquinone biosynthesis.
Collapse
Affiliation(s)
- Yaojie Gao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Yuchun Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jie Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Maohua Yang
- Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Lin Lin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenning Wang
- Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| |
Collapse
|
8
|
Alvarado SK, Miller MD, Bhardwaj M, Thorson JS, Van Lanen SG, Phillips GN. Structural characterization of DynU16, a START/Bet v1-like protein involved in dynemicin biosynthesis. Acta Crystallogr F Struct Biol Commun 2021; 77:328-333. [PMID: 34605436 PMCID: PMC8488855 DOI: 10.1107/s2053230x21008943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/27/2021] [Indexed: 11/10/2022] Open
Abstract
The 1.5 Å resolution crystal structure of DynU16, a protein identified in the dynemicin-biosynthetic gene cluster, is reported. The structure adopts a di-domain helix-grip fold with a uniquely positioned open cavity connecting the domains. The elongated dimensions of the cavity appear to be compatible with the geometry of a linear polyene, suggesting the involvement of DynU16 in the upstream steps of dynemicin biosynthesis.
Collapse
Affiliation(s)
- Sarah K. Alvarado
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Mitchell D. Miller
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Minakshi Bhardwaj
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
| | - George N. Phillips
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
| |
Collapse
|
9
|
Valadares VS, Martins LC, Roman EA, Valente AP, Cino EA, Moraes AH. Conformational dynamics of Tetracenomycin aromatase/cyclase regulate polyketide binding and enzyme aggregation propensity. Biochim Biophys Acta Gen Subj 2021; 1865:129949. [PMID: 34139289 DOI: 10.1016/j.bbagen.2021.129949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND The N-terminal domain of Tetracenomycin aromatase/cyclase (TcmN), an enzyme derived from Streptomyces glaucescens, is involved in polyketide cyclization, aromatization, and folding. Polyketides are a diverse class of secondary metabolites produced by certain groups of bacteria, fungi, and plants with various pharmaceutical applications. Examples include antibiotics, such as tetracycline, and anticancer drugs, such as doxorubicin. Because TcmN is a promising enzyme for in vitro production of polyketides, it is important to identify conditions that enhance its thermal resistance and optimize its function. METHODS TcmN unfolding, stability, and dynamics were evaluated by fluorescence spectroscopy, circular dichroism, nuclear magnetic resonance 15N relaxation experiments, and microsecond molecular dynamics (MD) simulations. RESULTS TcmN thermal resistance was enhanced at low protein and high salt concentrations, was pH-dependent, and denaturation was irreversible. Conformational dynamics on the μs-ms timescale were detected for residues in the substrate-binding cavity, and two predominant conformers representing opened and closed cavity states were observed in the MD simulations. CONCLUSION Based on the results, a mechanism was proposed in which the thermodynamics and kinetics of the TcmN conformational equilibrium modulate enzyme function by favoring ligand binding and avoiding aggregation. GENERAL SIGNIFICANCE Understanding the principles underlying TcmN stability and dynamics may help in designing mutants with optimal properties for biotechnological applications.
Collapse
Affiliation(s)
- Veronica S Valadares
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luan C Martins
- Graduate Program in Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ernesto A Roman
- Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ana Paula Valente
- National Center of Nuclear Magnetic Resonance, Leopoldo de Meis Institute of Medical Biochemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elio A Cino
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Adolfo H Moraes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Department of NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| |
Collapse
|
10
|
Kobayashi M, Kuzuyama T. Recent Advances in the Biosynthesis of Carbazoles Produced by Actinomycetes. Biomolecules 2020; 10:biom10081147. [PMID: 32764478 PMCID: PMC7466098 DOI: 10.3390/biom10081147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/01/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022] Open
Abstract
Structurally diverse carbazole alkaloids are valuable due to their pharmaceutical properties and have been isolated from nature. Experimental knowledge on carbazole biosynthesis is limited. The latest development of in silico analysis of the biosynthetic gene clusters for bacterial carbazoles has allowed studies on the biosynthesis of a carbazole skeleton, which was established by sequential enzyme-coupling reactions associated with an unprecedented carbazole synthase, a thiamine-dependent enzyme, and a ketosynthase-like enzyme. This review describes the carbazole biosynthetic mechanism, which includes a key step in enzymatic formation of a tricyclic carbazole skeleton, followed by modifications such as prenylation and hydroxylation in the skeleton.
Collapse
Affiliation(s)
- Masaya Kobayashi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan;
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Correspondence: ; Fax: +81-3-5841-3080
| |
Collapse
|
11
|
Kobayashi M, Tomita T, Shin‐ya K, Nishiyama M, Kuzuyama T. An Unprecedented Cyclization Mechanism in the Biosynthesis of Carbazole Alkaloids in
Streptomyces. Angew Chem Int Ed Engl 2019; 58:13349-13353. [DOI: 10.1002/anie.201906864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/20/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Masaya Kobayashi
- Biotechnology Research CentreThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Takeo Tomita
- Biotechnology Research CentreThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM)The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Kazuo Shin‐ya
- Biotechnology Research CentreThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- National Institute of Advanced Industrial Science and Technology 2-4-7 Aomi, Koto-ku Tokyo 135-0064 Japan
| | - Makoto Nishiyama
- Biotechnology Research CentreThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM)The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Tomohisa Kuzuyama
- Collaborative Research Institute for Innovative Microbiology (CRIIM)The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Graduate School of Agricultural and Life SciencesThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| |
Collapse
|
12
|
Kobayashi M, Tomita T, Shin‐ya K, Nishiyama M, Kuzuyama T. An Unprecedented Cyclization Mechanism in the Biosynthesis of Carbazole Alkaloids in
Streptomyces. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Masaya Kobayashi
- Biotechnology Research CentreThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Takeo Tomita
- Biotechnology Research CentreThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM)The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Kazuo Shin‐ya
- Biotechnology Research CentreThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- National Institute of Advanced Industrial Science and Technology 2-4-7 Aomi, Koto-ku Tokyo 135-0064 Japan
| | - Makoto Nishiyama
- Biotechnology Research CentreThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology (CRIIM)The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| | - Tomohisa Kuzuyama
- Collaborative Research Institute for Innovative Microbiology (CRIIM)The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Graduate School of Agricultural and Life SciencesThe University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
| |
Collapse
|
13
|
Cai C, Nie Y, Gong Y, Li S, Ramelot TA, Kennedy MA, Yue X, Zhu J, Liu M, Yang Y. Solution NMR structure of CGL2373, a polyketide cyclase-like protein from Corynebacterium glutamicum. Proteins 2019; 88:237-241. [PMID: 31294849 DOI: 10.1002/prot.25771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/17/2019] [Accepted: 07/06/2019] [Indexed: 11/11/2022]
Abstract
Protein CGL2373 from Corynebacterium glutamicum was previously proposed to be a member of the polyketide_cyc2 family, based on amino-acid sequence and secondary structure features derived from NMR chemical shift assignments. We report here the solution NMR structure of CGL2373, which contains three α-helices and one antiparallel β-sheet and adopts a helix-grip fold. This structure shows moderate similarities to the representative polyketide cyclases, TcmN, WhiE, and ZhuI. Nevertheless, unlike the structures of these homologs, CGL2373 structure looks like a half-open shell with a much larger pocket, and key residues in the representative polyketide cyclases for binding substrate and catalyzing aromatic ring formation are replaced with different residues in CGL2373. Also, the gene cluster where the CGL2373-encoding gene is located in C. glutamicum contains additional genes encoding nucleoside diphosphate kinase, folylpolyglutamate synthase, and valine-tRNA ligase, different from the typical gene cluster encoding polyketide cyclase in Streptomyces. Thus, although CGL2373 is structurally a polyketide cyclase-like protein, the function of CGL2373 may differ from the known polyketide cyclases and needs to be further investigated. The solution structure of CGL2373 lays a foundation for in silico ligand screening and binding site identifying in future functional study.
Collapse
Affiliation(s)
- Cong Cai
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Yao Nie
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yixuan Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, The Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, The Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio
| | - Xiali Yue
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
14
|
Hou XF, Song YJ, Zhang M, Lan W, Meng S, Wang C, Pan HX, Cao C, Tang GL. Enzymology of Anthraquinone-γ-Pyrone Ring Formation in Complex Aromatic Polyketide Biosynthesis. Angew Chem Int Ed Engl 2018; 57:13475-13479. [DOI: 10.1002/anie.201806729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Xian-Feng Hou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Yu-Jiao Song
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Mei Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Song Meng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Hai-Xue Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Gong-Li Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| |
Collapse
|
15
|
Hou XF, Song YJ, Zhang M, Lan W, Meng S, Wang C, Pan HX, Cao C, Tang GL. Enzymology of Anthraquinone-γ-Pyrone Ring Formation in Complex Aromatic Polyketide Biosynthesis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xian-Feng Hou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Yu-Jiao Song
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Mei Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Song Meng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Hai-Xue Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Gong-Li Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| |
Collapse
|
16
|
Tsai SC(S. The Structural Enzymology of Iterative Aromatic Polyketide Synthases: A Critical Comparison with Fatty Acid Synthases. Annu Rev Biochem 2018; 87:503-531. [DOI: 10.1146/annurev-biochem-063011-164509] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs. The potential application of FAS and aromatic PKS structures for bioengineering future drugs and biofuels is highlighted.
Collapse
Affiliation(s)
- Shiou-Chuan (Sheryl) Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
| |
Collapse
|
17
|
Zheng S, Zhou Y, Fleming J, Zhou Y, Zhang M, Li S, Li H, Sun B, Liu W, Bi L. Structural and genetic analysis of START superfamily protein MSMEG_0129 from Mycobacterium smegmatis. FEBS Lett 2018. [PMID: 29512898 DOI: 10.1002/1873-3468.13024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mycobacterium tuberculosis is a notorious pathogen that continues to threaten human health. Rv0164, an antigen of both T- and B cells conserved across mycobacteria, and MSMEG_0129, its close homolog in Mycobacterium smegmatis, are predicted members of the START domain superfamily, but their molecular function is unknown. Here, gene knockout studies demonstrate MSMEG_0129 is essential for bacterial growth, suggesting Rv0164 may be a potential drug target. The MSMEG_0129 crystal structure determined at 1.95 Å reveals a fold similar to that in polyketide aromatase/cyclases ZhuI and TcmN from Streptomyces sp. Structural comparisons and docking simulations, however, infer that MSMEG_0129 and Rv0164 are unlikely to catalyze polyketide aromatization/cyclization, but probably play an irreplaceable role during mycobacterial growth, for example, in lipid transfer during cell envelope synthesis.
Collapse
Affiliation(s)
- Shuping Zheng
- School of Stomatology and Medicine, Foshan University, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhou
- School of Stomatology and Medicine, Foshan University, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Joy Fleming
- School of Stomatology and Medicine, Foshan University, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yafeng Zhou
- School of Stomatology and Medicine, Foshan University, China
| | - Mengting Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | | | - Wei Liu
- Institute of Immunology, The Third Military Medical University, Chongqing, China
| | - Lijun Bi
- School of Stomatology and Medicine, Foshan University, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan, China
| |
Collapse
|
18
|
Liang C, Hu R, Ramelot TA, Kennedy MA, Li X, Yang Y, Zhu J, Liu M. Chemical shift assignments of polyketide cyclase_like protein CGL2373 from Corynebacterium glutamicum. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:289-292. [PMID: 28825188 DOI: 10.1007/s12104-017-9765-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/10/2017] [Indexed: 06/07/2023]
Abstract
Protein CGL2373 from Corynebacterium glutamicum, which is 155 amino acids long and 17.7 kDa, is a member of the polyketide_cyc2 family. As a potential polyketide cyclase, it may play an important role in the biosynthesis of aromatic polyketides that are the source of many bioactive molecules. Here we report the complete 1H, 13C and 15N chemical shift assignments of CGL2373, which lays a foundation for further structural and functional research.
Collapse
Affiliation(s)
- Chunjie Liang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, and the Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, USA
| | - Xuegang Li
- College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| |
Collapse
|
19
|
Yin GP, Wu YR, Yang MH, Li TX, Wang XB, Zhou MM, Lei JL, Kong LY. Citrifurans A-D, Four Dimeric Aromatic Polyketides with New Carbon Skeletons from the Fungus Aspergillus sp. Org Lett 2017; 19:4058-4061. [PMID: 28726414 DOI: 10.1021/acs.orglett.7b01823] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Citrifurans A-D (1-4), metabolized by an Aspergillus sp., are unusual dimers of azaphilone and furanone derivatives. Michael addition was thought to be the pivotal procedure in their biosynthesis, and different addition sites generated two new different carbon skeletons. Their structures were elucidated on the basis of spectroscopic methods, single-crystal X-ray diffraction, chemical conversion, and electronic circular dichroism analyses. Compounds 1-3 showed moderate inhibitory activities against LPS-induced NO production in RAW 264.7 macrophages with IC50 values of 18.3, 22.6, and 25.3 μM, respectively.
Collapse
Affiliation(s)
- Guo-Ping Yin
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Ya-Rong Wu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Ming-Hua Yang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Tian-Xiao Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Xiao-Bing Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Miao-Miao Zhou
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Jian-Li Lei
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Ling-Yi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University , 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| |
Collapse
|
20
|
Zheng S, Zhou Y, Fleming J, Zhou Y, Liu W, Bi L. The putative polyketide cyclase MSMEG_0129 from Mycobacterium smegmatis: purification, crystallization and X-ray crystallographic analysis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2017; 73:437-442. [PMID: 28695854 DOI: 10.1107/s2053230x17008937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022]
Abstract
Mycobacterium tuberculosis Rv0164 has previously been identified as a human T-cell antigen that induces significant production of IFN-γ in human peripheral blood mononuclear cells. M. smegmatis MSMEG_0129 shares 59% sequence identity with Rv0164. Based on sequence alignment, both proteins are predicted to be members of the cyclase/dehydrase family, which is part of a large group of enzymes referred to as type II polyketide synthases (PKSs). In biosynthetic pathways mediated by type II PKSs, cyclases catalyze the conversion of linear poly-β-ketones to cyclized intermediates. To date, no mycobacterial type II PKSs have been reported. Here, the goal is to determine whether these proteins adopt similar folds to reported cyclase structures, and to this end MSMEG_0129 was cloned, expressed, purified and crystallized. An X-ray diffraction data set was collected to 1.95 Å resolution from a crystal belonging to space group P62, with unit-cell parameters a = 109.76, b = 109.76, c = 56.5 Å, α = 90, β = 90, γ = 120°. Further crystallographic analysis should establish a basis for investigating the structure and function of this putative mycobacterial type II PKS enzyme.
Collapse
Affiliation(s)
- Shuping Zheng
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Ying Zhou
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Joy Fleming
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Yafeng Zhou
- School of Stomatology and Medicine, Foshan University, Foshan, Guangdong 528000, People's Republic of China
| | - Wei Liu
- Institute of Immunology, The Third Military Medical University, Chongqing 400038, People's Republic of China
| | - Lijun Bi
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| |
Collapse
|
21
|
Patel S. Disruption of aromatase homeostasis as the cause of a multiplicity of ailments: A comprehensive review. J Steroid Biochem Mol Biol 2017; 168:19-25. [PMID: 28109841 DOI: 10.1016/j.jsbmb.2017.01.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/20/2016] [Accepted: 01/15/2017] [Indexed: 01/15/2023]
Abstract
Human health is beset with a legion of ailments, which is exacerbated by lifestyle errors. Out of the numerous enzymes in human body, aromatase, a cytochrome P450 enzyme is particularly very critical. Occurring at the crossroads of multiple signalling pathways, its homeostasis is vital for optimal health. Unfortunately, medications, hormone therapy, chemical additives in food, and endocrine-disrupting personal care products are oscillating the aromatase concentration beyond the permissible level. As this enzyme converts androgens (C19) into estrogens (C18), its agitation has different outcomes in different genders and age groups. Some common pathologies associated with aromatase disruption include breast cancer, prostate cancer, polycystic ovary syndrome (PCOS), endometriosis, osteoporosis, ovarian cancer, gastric cancer, pituitary cancer, Alzheimer's disease, schizophrenia, male hypogonadism, and transgender issues. Several drugs, cosmetics and pesticides act as the activators and suppressors of this enzyme. This carefully-compiled critical review is expected to increase public awareness regarding the threats resultant of the perturbations of this enzyme and to motivate researchers for further investigation of this field.
Collapse
Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, CA 92182, USA.
| |
Collapse
|
22
|
Abstract
Polyketide biosynthesis engages a series of well-timed biosynthetic operations to generate elaborate natural products from simple building blocks. Mimicry of these processes has offered practical means for total synthesis and provided a foundation for reaction discovery. We now report an unusual intramolecular trans-amidation reaction discovered while preparing stabilized probes for the study of actinorhodin biosynthesis. This rapid cyclization event offers insight into the natural cyclization process inherent to the biosynthesis of type II polyketide antibiotics.
Collapse
|
23
|
Structural and functional analysis of two di-domain aromatase/cyclases from type II polyketide synthases. Proc Natl Acad Sci U S A 2015; 112:E6844-51. [PMID: 26631750 DOI: 10.1073/pnas.1512976112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Aromatic polyketides make up a large class of natural products with diverse bioactivity. During biosynthesis, linear poly-β-ketone intermediates are regiospecifically cyclized, yielding molecules with defined cyclization patterns that are crucial for polyketide bioactivity. The aromatase/cyclases (ARO/CYCs) are responsible for regiospecific cyclization of bacterial polyketides. The two most common cyclization patterns are C7-C12 and C9-C14 cyclizations. We have previously characterized three monodomain ARO/CYCs: ZhuI, TcmN, and WhiE. The last remaining uncharacterized class of ARO/CYCs is the di-domain ARO/CYCs, which catalyze C7-C12 cyclization and/or aromatization. Di-domain ARO/CYCs can further be separated into two subclasses: "nonreducing" ARO/CYCs, which act on nonreduced poly-β-ketones, and "reducing" ARO/CYCs, which act on cyclized C9 reduced poly-β-ketones. For years, the functional role of each domain in cyclization and aromatization for di-domain ARO/CYCs has remained a mystery. Here we present what is to our knowledge the first structural and functional analysis, along with an in-depth comparison, of the nonreducing (StfQ) and reducing (BexL) di-domain ARO/CYCs. This work completes the structural and functional characterization of mono- and di-domain ARO/CYCs in bacterial type II polyketide synthases and lays the groundwork for engineered biosynthesis of new bioactive polyketides.
Collapse
|
24
|
Yagüe P, Rodríguez-García A, López-García MT, Rioseras B, Martín JF, Sánchez J, Manteca A. Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures. PLoS One 2014; 9:e86296. [PMID: 24466012 PMCID: PMC3897704 DOI: 10.1371/journal.pone.0086296] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/12/2013] [Indexed: 11/18/2022] Open
Abstract
Streptomyces species produce many clinically relevant secondary metabolites and exhibit a complex development that includes hyphal differentiation and sporulation in solid cultures. Industrial fermentations are usually performed in liquid cultures, conditions in which Streptomyces strains generally do not sporulate, and it was traditionally assumed that no differentiation took place. The aim of this work was to compare the transcriptomes of S. coelicolor growing in liquid and solid cultures, deepening the knowledge of Streptomyces differentiation. Microarrays demonstrated that gene expression in liquid and solid cultures were comparable and data indicated that physiological differentiation was similar for both conditions. Eighty-six percent of all transcripts showed similar abundances in liquid and solid cultures, such as those involved in the biosynthesis of actinorhodin (actVA, actII-4) and undecylprodigiosin (redF); activation of secondary metabolism (absR1, ndsA); genes regulating hydrophobic cover formation (aerial mycelium) (bldB, bldC, bldM, bldN, sapA, chpC, chpD, chpE, chpH, ramA, ramC, ramS); and even some genes regulating early stages of sporulation (wblA, whiG, whiH, whiJ). The two most important differences between transcriptomes from liquid and solid cultures were: first, genes related to secondary metabolite biosynthesis (CDA, CPK, coelichelin, desferrioxamine clusters) were highly up-regulated in liquid but not in solid cultures; and second, genes involved in the final stages of hydrophobic cover/spore maturation (chpF, rdlA, whiE, sfr) were up-regulated in solid but not in liquid cultures. New information was also provided for several non-characterized genes differentially expressed in liquid and solid cultures which might be regulating, at least in part, the metabolic and developmental differences observed between liquid and solid cultures.
Collapse
Affiliation(s)
- Paula Yagüe
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
| | | | - María Teresa López-García
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
| | - Beatriz Rioseras
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
| | - Juan Francisco Martín
- Instituto de Biotecnología de León, INBIOTEC, Parque Científico de León, León, Spain
| | - Jesús Sánchez
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
| | - Angel Manteca
- Área de Microbiología, Departamento de Biología Funcional and IUOPA, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- * E-mail:
| |
Collapse
|
25
|
A thermoacidophile-specific protein family, DUF3211, functions as a fatty acid carrier with novel binding mode. J Bacteriol 2013; 195:4005-12. [PMID: 23836863 DOI: 10.1128/jb.00432-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
STK_08120 is a member of the thermoacidophile-specific DUF3211 protein family from Sulfolobus tokodaii strain 7. Its molecular function remains obscure, and sequence similarities for obtaining functional remarks are not available. In this study, the crystal structure of STK_08120 was determined at 1.79-Å resolution to predict its probable function using structure similarity searches. The structure adopts an α/β structure of a helix-grip fold, which is found in the START domain proteins with cavities for hydrophobic substrates or ligands. The detailed structural features implied that fatty acids are the primary ligand candidates for STK_08120, and binding assays revealed that the protein bound long-chain saturated fatty acids (>C14) and their trans-unsaturated types with an affinity equal to that for major fatty acid binding proteins in mammals and plants. Moreover, the structure of an STK_08120-myristic acid complex revealed a unique binding mode among fatty acid binding proteins. These results suggest that the thermoacidophile-specific protein family DUF3211 functions as a fatty acid carrier with a novel binding mode.
Collapse
|
26
|
Xu Y, Zhou T, Zhou Z, Su S, Roberts SA, Montfort WR, Zeng J, Chen M, Zhang W, Lin M, Zhan J, Molnár I. Rational reprogramming of fungal polyketide first-ring cyclization. Proc Natl Acad Sci U S A 2013; 110:5398-403. [PMID: 23509261 PMCID: PMC3619332 DOI: 10.1073/pnas.1301201110] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Resorcylic acid lactones and dihydroxyphenylacetic acid lactones represent important pharmacophores with heat shock response and immune system modulatory activities. The biosynthesis of these fungal polyketides involves a pair of collaborating iterative polyketide synthases (iPKSs): a highly reducing iPKS with product that is further elaborated by a nonreducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Biosynthesis of unreduced polyketides requires the sequestration and programmed cyclization of highly reactive poly-β-ketoacyl intermediates to channel these uncommitted, pluripotent substrates to defined subsets of the polyketide structural space. Catalyzed by product template (PT) domains of the fungal nrPKSs and discrete aromatase/cyclase enzymes in bacteria, regiospecific first-ring aldol cyclizations result in characteristically different polyketide folding modes. However, a few fungal polyketides, including the dihydroxyphenylacetic acid lactone dehydrocurvularin, derive from a folding event that is analogous to the bacterial folding mode. The structural basis of such a drastic difference in the way a PT domain acts has not been investigated until now. We report here that the fungal vs. bacterial folding mode difference is portable on creating hybrid enzymes, and we structurally characterize the resulting unnatural products. Using structure-guided active site engineering, we unravel structural contributions to regiospecific aldol condensations and show that reshaping the cyclization chamber of a PT domain by only three selected point mutations is sufficient to reprogram the dehydrocurvularin nrPKS to produce polyketides with a fungal fold. Such rational control of first-ring cyclizations will facilitate efforts to the engineered biosynthesis of novel chemical diversity from natural unreduced polyketides.
Collapse
Affiliation(s)
- Yuquan Xu
- Natural Products Center, School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85706
| | - Tong Zhou
- Department of Biological Engineering, Utah State University, Logan, UT 84322
| | - Zhengfu Zhou
- Natural Products Center, School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85706
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China; and
| | - Shiyou Su
- Natural Products Center, School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85706
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China; and
| | | | - William R. Montfort
- Department of Chemistry and Biochemistry and
- Bio5 Institute, University of Arizona, Tucson, AZ 85721
| | - Jia Zeng
- Department of Biological Engineering, Utah State University, Logan, UT 84322
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China; and
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China; and
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China; and
| | - Jixun Zhan
- Department of Biological Engineering, Utah State University, Logan, UT 84322
| | - István Molnár
- Natural Products Center, School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85706
- Bio5 Institute, University of Arizona, Tucson, AZ 85721
| |
Collapse
|