1
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Ding W, Tian D, Chen M, Xia Z, Tang X, Zhang S, Wei J, Li X, Yao X, Wu B, Tang J. Molecular Networking-Guided Isolation of Cyclopentapeptides from the Hydrothermal Vent Sediment Derived Fungus Aspergillus pseudoviridinutans TW58-5 and Their Anti-inflammatory Effects. JOURNAL OF NATURAL PRODUCTS 2023; 86:1919-1930. [PMID: 37368370 DOI: 10.1021/acs.jnatprod.3c00287] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Repetitive isolation of known compounds remains a major challenge in natural-product-based drug discovery. LC-MS/MS-based molecular networking has become a highly efficient strategy for the discovery of new natural products from complex mixtures. Herein, we report a molecular networking-guided isolation procedure, which resulted in the discovery of seven new cyclopentapeptides, namely, pseudoviridinutans A-F (1-7), from the marine-derived fungus Aspergillus pseudoviridinutans TW58-5. Compounds 1-7 feature a rare amino acid moiety, O,β-dimethyltyrosine, observed for the first time from a marine-derived fungus. The planar structures of 1-7 were elucidated by detailed analyses of IR, UV, HR ESI-Q-TOF MS, and 1D and 2D NMR spectroscopic data. Meanwhile, their absolute configurations were determined through a combination of Marfey's method and X-ray diffraction. Subsequent bioassay revealed the anti-inflammation potential of 1-7, especially 6, which inhibited the production of nitric oxide (NO), a vital inflammatory mediator, in LPS-induced murine macrophage RAW264.7 cells by regulating the expression level of NLRP3 and iNOS.
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Affiliation(s)
- Wenjuan Ding
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Danmei Tian
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Mei Chen
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Zixuan Xia
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Xiyang Tang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Sihao Zhang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Jihua Wei
- Ocean College, Zhejiang University, Zhoushan Campus, Zhoushan 316021, China
| | - Xunuo Li
- Ocean College, Zhejiang University, Zhoushan Campus, Zhoushan 316021, China
| | - Xinsheng Yao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Bin Wu
- Ocean College, Zhejiang University, Zhoushan Campus, Zhoushan 316021, China
| | - Jinshan Tang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy/Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drug Research/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
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2
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Wei X, Chan TK, Kong CTD, Matsuda Y. Biosynthetic Characterization, Heterologous Production, and Genomics-Guided Discovery of GABA-Containing Fungal Heptapeptides. JOURNAL OF NATURAL PRODUCTS 2023; 86:416-422. [PMID: 36715406 DOI: 10.1021/acs.jnatprod.2c01065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The biosynthetic gene cluster of γ-aminobutyric acid (GABA)-containing fungal cyclic heptapeptides unguisins A (1) and B (2) was identified in the fungus Aspergillus violaceofuscus CBS 115571. In vitro enzymatic reactions and gene deletion experiments revealed that the unguisin pathway involves the alanine racemase UngC to provide d-alanine, which is then accepted by the first adenylation domain of the nonribosomal peptide synthetase (NRPS) UngA. Intriguingly, the hydrolase UngD was found to transform unguisins into previously undescribed linear peptides. Subsequently, heterologous production of these peptides in Aspergillus oryzae was achieved, in which we established a methodology to readily introduce a large NRPS gene into the fungal host. Finally, genome mining revealed new unguisin congeners, each containing a (2R,3R)-β-methylphenylalanine residue.
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Affiliation(s)
- Xingxing Wei
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Tsz Ki Chan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Che Tung Derek Kong
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong 518057, China
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3
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Zhao Z, Gao P, Meng L, Wu Q, Yuan Y. A Convenient Iodine‐Promoted Synthesis of α‐Ketothioesters. ChemistrySelect 2022. [DOI: 10.1002/slct.202202939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zhengzheng Zhao
- College of Chemistry and Chemical Engineering Yangzhou University 88 Daxue South Road Yangzhou City Jiangsu Province China
| | - Pan Gao
- College of Chemistry and Chemical Engineering Yangzhou University 88 Daxue South Road Yangzhou City Jiangsu Province China
| | - Lei Meng
- College of Chemistry and Chemical Engineering Yangzhou University 88 Daxue South Road Yangzhou City Jiangsu Province China
| | - Qingyi Wu
- College of Chemistry and Chemical Engineering Yangzhou University 88 Daxue South Road Yangzhou City Jiangsu Province China
| | - Yu Yuan
- College of Chemistry and Chemical Engineering Yangzhou University 88 Daxue South Road Yangzhou City Jiangsu Province China
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4
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Müller M, Germer P, Andexer JN. Biocatalytic One-Carbon Transfer – A Review. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/s-0040-1719884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
AbstractThis review provides an overview of different C1 building blocks as substrates of enzymes, or part of their cofactors, and the resulting functionalized products. There is an emphasis on the broad range of possibilities of biocatalytic one-carbon extensions with C1 sources of different oxidation states. The identification of uncommon biosynthetic strategies, many of which might serve as templates for synthetic or biotechnological applications, towards one-carbon extensions is supported by recent genomic and metabolomic progress and hence we refer principally to literature spanning from 2014 to 2020.1 Introduction2 Methane, Methanol, and Methylamine3 Glycine4 Nitromethane5 SAM and SAM Ylide6 Other C1 Building Blocks7 Formaldehyde and Glyoxylate as Formaldehyde Equivalents8 Cyanide9 Formic Acid10 Formyl-CoA and Oxalyl-CoA11 Carbon Monoxide12 Carbon Dioxide13 Conclusions
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5
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Koper K, Han SW, Pastor DC, Yoshikuni Y, Maeda HA. Evolutionary Origin and Functional Diversification of Aminotransferases. J Biol Chem 2022; 298:102122. [PMID: 35697072 PMCID: PMC9309667 DOI: 10.1016/j.jbc.2022.102122] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Aminotransferases (ATs) are pyridoxal 5′-phosphate–dependent enzymes that catalyze the transamination reactions between amino acid donor and keto acid acceptor substrates. Modern AT enzymes constitute ∼2% of all classified enzymatic activities, play central roles in nitrogen metabolism, and generate multitude of primary and secondary metabolites. ATs likely diverged into four distinct AT classes before the appearance of the last universal common ancestor and further expanded to a large and diverse enzyme family. Although the AT family underwent an extensive functional specialization, many AT enzymes retained considerable substrate promiscuity and multifunctionality because of their inherent mechanistic, structural, and functional constraints. This review summarizes the evolutionary history, diverse metabolic roles, reaction mechanisms, and structure–function relationships of the AT family enzymes, with a special emphasis on their substrate promiscuity and multifunctionality. Comprehensive characterization of AT substrate specificity is still needed to reveal their true metabolic functions in interconnecting various branches of the nitrogen metabolic network in different organisms.
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Affiliation(s)
- Kaan Koper
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sang-Woo Han
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Yasuo Yoshikuni
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Global Center for Food, Land, and Water Resources, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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6
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Chen MH, Li YS, Hsu NS, Lin KH, Wang YL, Wang ZC, Chang CF, Lin JP, Chang CY, Li TL. Structural and Mechanistic Bases for StnK3 and Its Mutant-Mediated Lewis-Acid-Dependent Epimerization and Retro-Aldol Reactions. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mei-Hua Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Shan Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Zhe-Chong Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jin-Ping Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei 115, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan
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7
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Barry CP, Gillane R, Talbo GH, Plan M, Palfreyman R, Haber-Stuk AK, Power J, Nielsen LK, Marcellin E. Multi-omic characterisation of Streptomyces hygroscopicus NRRL 30439: detailed assessment of its secondary metabolic potential. Mol Omics 2022; 18:226-236. [PMID: 34989730 DOI: 10.1039/d1mo00150g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of multidrug-resistant pathogenic bacteria creates a demand for novel antibiotics with distinct mechanisms of action. Advances in next-generation genome sequencing promised a paradigm shift in the quest to find new bioactive secondary metabolites. Genome mining has proven successful for predicting putative biosynthetic elements in secondary metabolite superproducers such as Streptomycetes. However, genome mining approaches do not inform whether biosynthetic gene clusters are dormant or active under given culture conditions. Here we show that using a multi-omics approach in combination with antiSMASH, it is possible to assess the secondary metabolic potential of a Streptomyces strain capable of producing mannopeptimycin, an important cyclic peptide effective against Gram-positive infections. The genome of Streptomyces hygroscopicus NRRL 30439 was first sequenced using PacBio RSII to obtain a closed genome. A chemically defined medium was then used to elicit a nutrient stress response in S. hygroscopicus NRRL 30439. Detailed extracellular metabolomics and intracellular proteomics were used to profile and segregate primary and secondary metabolism. Our results demonstrate that the combination of genomics, proteomics and metabolomics enables rapid evaluation of a strain's performance in bioreactors for industrial production of secondary metabolites.
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Affiliation(s)
- Craig P Barry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Rosemary Gillane
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Gert H Talbo
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Manual Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | - Robin Palfreyman
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
| | | | - John Power
- Zoetis, 333 Portage Street, Kalamazoo, MI 49007, USA
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia. .,The Queensland Node of Metabolomics Australia, AIBN, The University of Queensland, 4072 St. Lucia, Australia
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8
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Li F, Yang LC, Zhang J, Chen JS, Renata H. Stereoselective Synthesis of β-Branched Aromatic α-Amino Acids by Biocatalytic Dynamic Kinetic Resolution*. Angew Chem Int Ed Engl 2021; 60:17680-17685. [PMID: 34056805 DOI: 10.1002/anie.202105656] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 01/18/2023]
Abstract
β-Branched noncanonical amino acids are valuable molecules in modern drug development efforts. However, they are still challenging to prepare due to the need to set multiple stereocenters in a stereoselective fashion, and contemporary methods for the synthesis of such compounds often rely on the use of rare-transition-metal catalysts with designer ligands. Herein, we report a highly diastereo- and enantioselective biocatalytic transamination method to prepare a broad range of aromatic β-branched α-amino acids. Mechanistic studies show that the transformation proceeds through dynamic kinetic resolution that is unique to the optimal enzyme. To highlight its utility and practicality, the biocatalytic reaction was applied to the synthesis of several sp3 -rich cyclic fragments and the first total synthesis of jomthonic acid A.
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Affiliation(s)
- Fuzhuo Li
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Li-Cheng Yang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Jingyang Zhang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Jason S Chen
- Automated Synthesis Facility, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
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9
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Li F, Yang L, Zhang J, Chen JS, Renata H. Stereoselective Synthesis of β‐Branched Aromatic α‐Amino Acids by Biocatalytic Dynamic Kinetic Resolution**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fuzhuo Li
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Li‐Cheng Yang
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Jingyang Zhang
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Jason S. Chen
- Automated Synthesis Facility The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Hans Renata
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
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10
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Naskar S, Mal K, Maity R, Das I. Recent Advances in the Synthesis and Applications of α‐Ketothioesters. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202001191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Sandip Naskar
- Organic and Medicinal Chemistry Division CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700 032 India
| | - Kanchan Mal
- Organic and Medicinal Chemistry Division CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700 032 India
| | - Rajib Maity
- Organic and Medicinal Chemistry Division CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700 032 India
| | - Indrajit Das
- Organic and Medicinal Chemistry Division CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700 032 India
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11
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Awakawa T, Barra L, Abe I. Biosynthesis of sulfonamide and sulfamate antibiotics in actinomycete. J Ind Microbiol Biotechnol 2021; 48:6123731. [PMID: 33928358 PMCID: PMC9113183 DOI: 10.1093/jimb/kuab001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/21/2020] [Indexed: 02/04/2023]
Abstract
Abstract
Sulfonamides and sulfamates are a group of organosulfur compounds that contain the signature sulfamoyl structural motif. These compounds were initially only known as synthetic antibacterial drugs but were later also discovered as natural products. Eight highly potent examples have been isolated from actinomycetes to date, illustrating the large biosynthetic repertoire of this bacterial genus. For the biosynthesis of these compounds, several distinct and unique biosynthetic machineries have been discovered, capable to generate the unique S–N bond. For the creation of novel, second generation natural products by biosynthetic engineering efforts, a detailed understanding of the underlying enzyme machinery toward potent structural motifs is crucial. In this review, we aim to summarize the current state of knowledge on sulfonamide and sulfamate biosynthesis. A detailed discussion for the secondary sulfamate ascamycin, the tertiary sulfonamide sulfadixiamycin A, and the secondary sulfonamide SB-203208 is provided and their bioactivities and mode of actions are discussed.
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Affiliation(s)
| | | | - Ikuro Abe
- Correspondence should be addressed to: Lena Barra at
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12
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Liao C, Seebeck FP. Asymmetric β‐Methylation of
l
‐ and
d
‐α‐Amino Acids by a Self‐Contained Enzyme Cascade. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916025] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Cangsong Liao
- Department for ChemistryUniversity of Basel Mattenstrasse 24a, BPR 1002 4056 Basel Switzerland
| | - Florian P. Seebeck
- Department for ChemistryUniversity of Basel Mattenstrasse 24a, BPR 1002 4056 Basel Switzerland
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13
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Liao C, Seebeck FP. Asymmetric β‐Methylation of
l
‐ and
d
‐α‐Amino Acids by a Self‐Contained Enzyme Cascade. Angew Chem Int Ed Engl 2020; 59:7184-7187. [DOI: 10.1002/anie.201916025] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Cangsong Liao
- Department for Chemistry University of Basel Mattenstrasse 24a, BPR 1002 4056 Basel Switzerland
| | - Florian P. Seebeck
- Department for Chemistry University of Basel Mattenstrasse 24a, BPR 1002 4056 Basel Switzerland
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14
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Ren SX, Zhang B, Lin Y, Ma DS, Li H. Mechanistic evaluation of anti-arthritic activity of β-methylphenylalanine in experimental rats. Biomed Pharmacother 2019; 113:108730. [PMID: 30861411 DOI: 10.1016/j.biopha.2019.108730] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 01/21/2023] Open
Abstract
Arthritis is a common chronic joint disorder, with general symptoms including stiffness and joint pain. β-methylphenylalanine is a well-known non-proteogenic unnatural amino acid. This study analyzes the anti-arthritic activity of β-methylphenylalanine in experimental rats. The experimental groups were as follows: group I, sham; group II, control; group III, 100 mg/kg of β-methylphenylalanine; and group IV, 200 mg/kg of β-methylphenylalanine. Lipid peroxidation, glutathione peroxidase (Gpx), reduced glutathione (GSH), superoxide dismutase (SOD), catalase, prostaglandin E2 (PGE2), matrix metalloproteinase-3 (MMP-3), ceruloplasmin, zinc, copper, mRNA, and protein expression of inducible nitric oxide synthase (iNOS) and nuclear factor-kappa B (NF-κB) were determined. Supplementation with β-methylphenylalanine significantly reduced lipid peroxidation, copper, PGE2 and MMP-3 levels, whereas GSH, Gpx, catalase, SOD and zinc levels were increased. Supplementation with β-methylphenylalanine significantly reduced NF-κB mRNA expression by 26% and 47.8% in groups III and IV, respectively (P < 0.045), while iNOS mRNA expression was reduced by 14.3 and 47.6% in groups III and IV, respectively. NF-κB and iNOS protein expression increased by 160% and 120% respectively, in the control rats compared to the sham rats. However, supplementation with β-methylphenylalanine significantly reduced NF-κB protein expression by 27% and 50% in groups III and IV, respectively, while iNOS protein expression was reduced by 22.7% and 45.4% in groups III and IV, respectively. Taken together, our data show that supplementation of β-methylphenylalanine was effective against arthritis in a rat model.
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Affiliation(s)
- Shi-Xiang Ren
- Department of Orthopedics, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, 100020, China
| | - Bo Zhang
- Department of Orthopedics, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, 100020, China
| | - Yuan Lin
- Department of Orthopedics, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, 100020, China
| | - De-Si Ma
- Department of Orthopedics, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, 100020, China
| | - Huan Li
- Department of Orthopedics, The First People's Hospital of Changzhou, Jiangsu Province (The Third Affiliated Hospital of Soochow University), Changzhou City, Jiangsu Province, 213003 China.
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15
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Hu Z, Awakawa T, Ma Z, Abe I. Aminoacyl sulfonamide assembly in SB-203208 biosynthesis. Nat Commun 2019; 10:184. [PMID: 30643149 PMCID: PMC6331615 DOI: 10.1038/s41467-018-08093-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
Sulfonamide is present in many important drugs, due to its unique chemical and biological properties. In contrast, naturally occurring sulfonamides are rare, and their biosynthetic knowledge are scarce. Here we identify the biosynthetic gene cluster of sulfonamide antibiotics, altemicidin, SB-203207, and SB-203208, from Streptomyces sp. NCIMB40513. The heterologous gene expression and biochemical analyses reveal unique aminoacyl transfer reactions, including the tRNA synthetase-like enzyme SbzA-catalyzed L-isoleucine transfer and the GNAT enzyme SbzC-catalyzed β-methylphenylalanine transfer. Furthermore, we elucidate the biogenesis of 2-sulfamoylacetic acid from L-cysteine, by the collaboration of the cupin dioxygenase SbzM and the aldehyde dehydrogenase SbzJ. Remarkably, SbzM catalyzes the two-step oxidation and decarboxylation of L-cysteine, and the subsequent intramolecular amino group rearrangement leads to N-S bond formation. This detailed analysis of the aminoacyl sulfonamide antibiotics biosynthetic machineries paves the way toward investigations of sulfonamide biosynthesis and its engineering.
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Affiliation(s)
- Zhijuan Hu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Zhongjun Ma
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
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16
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Kamenik Z, Gazak R, Kadlcik S, Steiningerova L, Rynd V, Janata J. C-C bond cleavage in biosynthesis of 4-alkyl-L-proline precursors of lincomycin and anthramycin cannot precede C-methylation. Nat Commun 2018; 9:3167. [PMID: 30093642 PMCID: PMC6085390 DOI: 10.1038/s41467-018-05455-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 07/10/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- Zdenek Kamenik
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic
| | - Radek Gazak
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic
| | - Stanislav Kadlcik
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic
| | - Lucie Steiningerova
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic
| | - Vit Rynd
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic
| | - Jiri Janata
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 142 20, Praha 4, Czech Republic.
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17
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García-Salcedo R, Álvarez-Álvarez R, Olano C, Cañedo L, Braña AF, Méndez C, de la Calle F, Salas JA. Characterization of the Jomthonic Acids Biosynthesis Pathway and Isolation of Novel Analogues in Streptomyces caniferus GUA-06-05-006A. Mar Drugs 2018; 16:md16080259. [PMID: 30065171 PMCID: PMC6117699 DOI: 10.3390/md16080259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/26/2018] [Accepted: 07/28/2018] [Indexed: 12/20/2022] Open
Abstract
Jomthonic acids (JAs) are a group of natural products (NPs) with adipogenic activity. Structurally, JAs are formed by a modified β-methylphenylalanine residue, whose biosynthesis involves a methyltransferase that in Streptomyces hygroscopicus has been identified as MppJ. Up to date, three JA members (A–C) and a few other natural products containing β-methylphenylalanine have been discovered from soil-derived microorganisms. Herein, we report the identification of a gene (jomM) coding for a putative methyltransferase highly identical to MppJ in the chromosome of the marine actinobacteria Streptomyces caniferus GUA-06-05-006A. In its 5’ region, jomM clusters with two polyketide synthases (PKS) (jomP1, jomP2), a nonribosomal peptide synthetase (NRPS) (jomN) and a thioesterase gene (jomT), possibly conforming a single transcriptional unit. Insertion of a strong constitutive promoter upstream of jomP1 led to the detection of JA A, along with at least two novel JA family members (D and E). Independent inactivation of jomP1, jomN and jomM abolished production of JA A, JA D and JA E, indicating the involvement of these genes in JA biosynthesis. Heterologous expression of the JA biosynthesis cluster in Streptomyces coelicolor M1152 and in Streptomyces albus J1074 led to the production of JA A, B, C and F. We propose a pathway for JAs biosynthesis based on the findings here described.
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Affiliation(s)
- Raúl García-Salcedo
- Department of Functional Biology and University Institute of Oncology of Principado de Asturias (U.I.O.P.A), University of Oviedo, 33006 Oviedo (Asturias), Spain.
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
- Drug Discovery Area, PharmaMar S.A. Avda. de los Reyes 1, 28770 Colmenar Viejo (Madrid), Spain.
| | - Rubén Álvarez-Álvarez
- Department of Functional Biology and University Institute of Oncology of Principado de Asturias (U.I.O.P.A), University of Oviedo, 33006 Oviedo (Asturias), Spain.
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
| | - Carlos Olano
- Department of Functional Biology and University Institute of Oncology of Principado de Asturias (U.I.O.P.A), University of Oviedo, 33006 Oviedo (Asturias), Spain.
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
| | - Librada Cañedo
- Drug Discovery Area, PharmaMar S.A. Avda. de los Reyes 1, 28770 Colmenar Viejo (Madrid), Spain.
| | - Alfredo F Braña
- Department of Functional Biology and University Institute of Oncology of Principado de Asturias (U.I.O.P.A), University of Oviedo, 33006 Oviedo (Asturias), Spain.
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
| | - Carmen Méndez
- Department of Functional Biology and University Institute of Oncology of Principado de Asturias (U.I.O.P.A), University of Oviedo, 33006 Oviedo (Asturias), Spain.
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
| | - Fernando de la Calle
- Drug Discovery Area, PharmaMar S.A. Avda. de los Reyes 1, 28770 Colmenar Viejo (Madrid), Spain.
| | - José A Salas
- Institute for Health Research of Principado de Asturias (IHRPA), 33006 Oviedo (Asturias), Spain.
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18
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Janata J, Kamenik Z, Gazak R, Kadlcik S, Najmanova L. Biosynthesis and incorporation of an alkylproline-derivative (APD) precursor into complex natural products. Nat Prod Rep 2018. [DOI: 10.1039/c7np00047b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review covers the biosynthetic and evolutionary aspects of lincosamide antibiotics, antitumour pyrrolobenzodiazepines (PBDs) and the quorum-sensing molecule hormaomycin.
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Affiliation(s)
- J. Janata
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - Z. Kamenik
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - R. Gazak
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - S. Kadlcik
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - L. Najmanova
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
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19
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Bennett MR, Shepherd SA, Cronin VA, Micklefield J. Recent advances in methyltransferase biocatalysis. Curr Opin Chem Biol 2017; 37:97-106. [DOI: 10.1016/j.cbpa.2017.01.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 11/29/2022]
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20
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Francis D, Winn M, Latham J, Greaney MF, Micklefield J. An Engineered Tryptophan Synthase Opens New Enzymatic Pathways to β-Methyltryptophan and Derivatives. Chembiochem 2017; 18:382-386. [PMID: 28005309 DOI: 10.1002/cbic.201600471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 01/23/2023]
Abstract
β-Methyltryptophans (β-mTrp) are precursors in the biosynthesis of bioactive natural products and are used in the synthesis of peptidomimetic-based therapeutics. Currently β-mTrp is produced by inefficient multistep synthetic methods. Here we demonstrate how an engineered variant of tryptophan synthase from Salmonella (StTrpS) can catalyse the efficient condensation of l-threonine and various indoles to generate β-mTrp and derivatives in a single step. Although l-serine is the natural substrate for TrpS, targeted mutagenesis of the StTrpS active site provided a variant (βL166V) that can better accommodate l-Thr as a substrate. The condensation of l-Thr and indole proceeds with retention of configuration at both α- and β-positions to give (2S,3S)-β-mTrp. The integration of StTrpS (βL166V) with l-amino acid oxidase, halogenase enzymes and palladium chemocatalysts provides access to further d-configured and regioselectively halogenated or arylated β-mTrp derivatives.
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Affiliation(s)
- Daniel Francis
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Michael Winn
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jonathan Latham
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Michael F Greaney
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jason Micklefield
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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21
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Characterization of a putative NsrR homologue in Streptomyces venezuelae reveals a new member of the Rrf2 superfamily. Sci Rep 2016; 6:31597. [PMID: 27605472 PMCID: PMC5015018 DOI: 10.1038/srep31597] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/25/2016] [Indexed: 01/06/2023] Open
Abstract
Members of the Rrf2 superfamily of transcription factors are widespread in bacteria but their functions are largely unexplored. The few that have been characterized in detail sense nitric oxide (NsrR), iron limitation (RirA), cysteine availability (CymR) and the iron sulfur (Fe-S) cluster status of the cell (IscR). In this study we combined ChIP- and dRNA-seq with in vitro biochemistry to characterize a putative NsrR homologue in Streptomyces venezuelae. ChIP-seq analysis revealed that rather than regulating the nitrosative stress response like Streptomyces coelicolor NsrR, Sven6563 binds to a conserved motif at a different, much larger set of genes with a diverse range of functions, including a number of regulators, genes required for glutamine synthesis, NADH/NAD(P)H metabolism, as well as general DNA/RNA and amino acid/protein turn over. Our biochemical experiments further show that Sven6563 has a [2Fe-2S] cluster and that the switch between oxidized and reduced cluster controls its DNA binding activity in vitro. To our knowledge, both the sensing domain and the putative target genes are novel for an Rrf2 protein, suggesting Sven6563 represents a new member of the Rrf2 superfamily. Given the redox sensitivity of its Fe-S cluster we have tentatively named the protein RsrR for Redox sensitive response Regulator.
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22
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Jiraskova P, Gazak R, Kamenik Z, Steiningerova L, Najmanova L, Kadlcik S, Novotna J, Kuzma M, Janata J. New Concept of the Biosynthesis of 4-Alkyl-L-Proline Precursors of Lincomycin, Hormaomycin, and Pyrrolobenzodiazepines: Could a γ-Glutamyltransferase Cleave the C-C Bond? Front Microbiol 2016; 7:276. [PMID: 27014201 PMCID: PMC4780272 DOI: 10.3389/fmicb.2016.00276] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/19/2016] [Indexed: 11/18/2022] Open
Abstract
Structurally different and functionally diverse natural compounds – antitumour agents pyrrolo[1,4]benzodiazepines, bacterial hormone hormaomycin, and lincosamide antibiotic lincomycin – share a common building unit, 4-alkyl-L-proline derivative (APD). APDs arise from L-tyrosine through a special biosynthetic pathway. Its generally accepted scheme, however, did not comply with current state of knowledge. Based on gene inactivation experiments and in vitro functional tests with recombinant enzymes, we designed a new APD biosynthetic scheme for the model of lincomycin biosynthesis. In the new scheme at least one characteristic in each of five final biosynthetic steps has been changed: the order of reactions, assignment of enzymes and/or reaction mechanisms. First, we demonstrate that LmbW methylates a different substrate than previously assumed. Second, we propose a unique reaction mechanism for the next step, in which a putative γ-glutamyltransferase LmbA indirectly cleaves off the oxalyl residue by transient attachment of glutamate to LmbW product. This unprecedented mechanism would represent the first example of the C–C bond cleavage catalyzed by a γ-glutamyltransferase, i.e., an enzyme that appears unsuitable for such activity. Finally, the inactivation experiments show that LmbX is an isomerase indicating that it transforms its substrate into a compound suitable for reduction by LmbY, thereby facilitating its subsequent complete conversion to APD 4-propyl-L-proline. Elucidation of the APD biosynthesis has long time resisted mainly due to the apparent absence of relevant C–C bond cleaving enzymatic activity. Our proposal aims to unblock this situation not only for lincomycin biosynthesis, but generally for all above mentioned groups of bioactive natural products with biotechnological potential.
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Affiliation(s)
- Petra Jiraskova
- Institute of Microbiology - Academy of Sciences of the Czech Republic Prague, Czech Republic
| | - Radek Gazak
- Institute of Microbiology - Academy of Sciences of the Czech Republic Prague, Czech Republic
| | - Zdenek Kamenik
- Institute of Microbiology - Academy of Sciences of the Czech Republic Prague, Czech Republic
| | - Lucie Steiningerova
- Institute of Microbiology - Academy of Sciences of the Czech Republic Prague, Czech Republic
| | - Lucie Najmanova
- Institute of Microbiology - Academy of Sciences of the Czech Republic Prague, Czech Republic
| | - Stanislav Kadlcik
- Institute of Microbiology - Academy of Sciences of the Czech Republic Prague, Czech Republic
| | - Jitka Novotna
- Institute of Microbiology - Academy of Sciences of the Czech Republic Prague, Czech Republic
| | - Marek Kuzma
- Institute of Microbiology - Academy of Sciences of the Czech Republic Prague, Czech Republic
| | - Jiri Janata
- Institute of Microbiology - Academy of Sciences of the Czech Republic Prague, Czech Republic
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23
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Fuse S, Koinuma H, Kimbara A, Izumikawa M, Mifune Y, He H, Shin-ya K, Takahashi T, Doi T. Total Synthesis and Stereochemistry Revision of Mannopeptimycin Aglycone. J Am Chem Soc 2014; 136:12011-7. [DOI: 10.1021/ja505105t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shinichiro Fuse
- Department
of Applied Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
| | - Hirotsugu Koinuma
- Department
of Applied Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
| | - Atsushi Kimbara
- Department
of Applied Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo 135-0064, Japan
| | - Yuto Mifune
- Department
of Applied Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8552, Japan
| | - Haiyin He
- Natural
Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan
| | | | - Takayuki Doi
- Graduate
School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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24
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Feng J, Wu J, Gao J, Xia Z, Deng Z, He X. Biosynthesis of the β-methylarginine residue of peptidyl nucleoside arginomycin in Streptomyces arginensis NRRL 15941. Appl Environ Microbiol 2014; 80:5021-7. [PMID: 24907335 PMCID: PMC4135772 DOI: 10.1128/aem.01172-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/03/2014] [Indexed: 11/20/2022] Open
Abstract
The peptidyl nucleoside arginomycin is active against Gram-positive bacteria and fungi but displays much lower toxicity to mice than its analog blasticidin S. It features a rare amino acid, β-methylarginine, which is attached to the deoxyhexose moiety via a 4'-aminoacyl bond. We here report cloning of the complete biosynthetic gene cluster for arginomycin from Streptomyces arginensis NRRL 15941. Among the 14 putative essential open reading frames, argM, encoding an aspartate aminotransferase (AAT), and adjacent argN, encoding an S-adenosyl methionine (SAM)-dependent methyltransferase, are coupled to catalyze arginine and yield β-methylarginine in Escherichia coli. Purified ArgM can transfer the α-amino group of l-arginine to α-ketoglutaric acid to give glutamate and thereby converts l-arginine to 5-guanidino-2-oxopentanoic acid, which is methylated at the C-3 position by ArgN to form 5-guanidino-3-methyl-2-oxopentanoic acid. Iteratively, ArgM specifically catalyzes transamination from the donor l-aspartate to the resulting 5-guanidino-3-methyl-2-oxopentanoic acid, generating β-methylarginine. The complete and concise biosynthetic pathway for the rare and bioactive amino acid revealed by this study may pave the way for the production of β-methylarginine either by enzymatic conversion or by engineered living cells.
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Affiliation(s)
- Jun Feng
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Health, and WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, China
| | - Jun Wu
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Gao
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhigui Xia
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Health, and WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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25
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Lyu SY, Liu YC, Chang CY, Huang CJ, Chiu YH, Huang CM, Hsu NS, Lin KH, Wu CJ, Tsai MD, Li TL. Multiple complexes of long aliphatic N-acyltransferases lead to synthesis of 2,6-diacylated/2-acyl-substituted glycopeptide antibiotics, effectively killing vancomycin-resistant enterococcus. J Am Chem Soc 2014; 136:10989-95. [PMID: 25095906 DOI: 10.1021/ja504125v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Teicoplanin A2-2 (Tei)/A40926 is the last-line antibiotic to treat multidrug-resistant Gram-positive bacterial infections, e.g., methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococcus (VRE). This class of antibiotics is powered by the N-acyltransferase (NAT) Orf11*/Dbv8 through N-acylation on glucosamine at the central residue of Tei/A40926 pseudoaglycone. The NAT enzyme possesses enormous value in untapped applications; its advanced development is hampered largely due to a lack of structural information. In this report, we present eight high-resolution X-ray crystallographic unary, binary, and ternary complexes in order to decipher the molecular basis for NAT's functionality. The enzyme undergoes a multistage conformational change upon binding of acyl-CoA, thus allowing the uploading of Tei pseudoaglycone to enable the acyl-transfer reaction to take place in the occlusion between the N- and C-halves of the protein. The acyl moiety of acyl-CoA can be bulky or lengthy, allowing a large extent of diversity in new derivatives that can be formed upon its transfer. Vancomycin/synthetic acyl-N-acetyl cysteamine was not expected to be able to serve as a surrogate for an acyl acceptor/donor, respectively. Most strikingly, NAT can catalyze formation of 2-N,6-O-diacylated or C6→C2 acyl-substituted Tei analogues through an unusual 1,4-migration mechanism under stoichiometric/solvational reaction control, wherein selected representatives showed excellent biological activities, effectively counteracting major types (VanABC) of VRE.
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Affiliation(s)
- Syue-Yi Lyu
- Genomics Research Center, Academia Sinica , Taipei 115, Taiwan
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26
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Zou XW, Liu YC, Hsu NS, Huang CJ, Lyu SY, Chan HC, Chang CY, Yeh HW, Lin KH, Wu CJ, Tsai MD, Li TL. Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase. ACTA ACUST UNITED AC 2014; 70:1549-60. [PMID: 24914966 DOI: 10.1107/s1399004714005239] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/06/2014] [Indexed: 12/16/2022]
Abstract
In biological systems, methylation is most commonly performed by methyltransferases (MTs) using the electrophilic methyl source S-adenosyl-L-methionine (SAM) via the S(N)2 mechanism. (2S,3S)-β-Methylphenylalanine, a nonproteinogenic amino acid, is a building unit of the glycopeptide antibiotic mannopeptimycin. The gene product of mppJ from the mannopeptimycin-biosynthetic gene cluster is the MT that methylates the benzylic C atom of phenylpyruvate (Ppy) to give βMePpy. Although the benzylic C atom of Ppy is acidic, how its nucleophilicity is further enhanced to become an acceptor for C-methylation has not conclusively been determined. Here, a structural approach is used to address the mechanism of MppJ and to engineer it for new functions. The purified MppJ displays a turquoise colour, implying the presence of a metal ion. The crystal structures reveal MppJ to be the first ferric ion SAM-dependent MT. An additional four structures of binary and ternary complexes illustrate the molecular mechanism for the metal ion-dependent methyltransfer reaction. Overall, MppJ has a nonhaem iron centre that bind, orients and activates the α-ketoacid substrate and has developed a sandwiched bi-water device to avoid the formation of the unwanted reactive oxo-iron(IV) species during the C-methylation reaction. This discovery further prompted the conversion of the MT into a structurally/functionally unrelated new enzyme. Through stepwise mutagenesis and manipulation of coordination chemistry, MppJ was engineered to perform both Lewis acid-assisted hydration and/or O-methyltransfer reactions to give stereospecific new compounds. This process was validated by six crystal structures. The results reported in this study will facilitate the development and design of new biocatalysts for difficult-to-synthesize biochemicals.
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Affiliation(s)
- Xiao-Wei Zou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chen Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | | | - Syue-Yi Lyu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsiu-Chien Chan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Yuan Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsien-Wei Yeh
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Ming-Daw Tsai
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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27
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Wang KC, Lyu SY, Liu YC, Chang CY, Wu CJ, Li TL. Insights into the binding specificity and catalytic mechanism of N-acetylhexosamine 1-phosphate kinases through multiple reaction complexes. ACTA ACUST UNITED AC 2014; 70:1401-10. [PMID: 24816108 DOI: 10.1107/s1399004714004209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 02/23/2014] [Indexed: 11/10/2022]
Abstract
Utilization of N-acetylhexosamine in bifidobacteria requires the specific lacto-N-biose/galacto-N-biose pathway, a pathway differing from the Leloir pathway while establishing symbiosis between humans and bifidobacteria. The gene lnpB in the pathway encodes a novel hexosamine kinase NahK, which catalyzes the formation of N-acetylhexosamine 1-phosphate (GlcNAc-1P/GalNAc-1P). In this report, seven three-dimensional structures of NahK in complex with GlcNAc, GalNAc, GlcNAc-1P, GlcNAc/AMPPNP and GlcNAc-1P/ADP from both Bifidobacterium longum (JCM1217) and B. infantis (ATCC15697) were solved at resolutions of 1.5-2.2 Å. NahK is a monomer in solution, and its polypeptide folds in a crescent-like architecture subdivided into two domains by a deep cleft. The NahK structures presented here represent the first multiple reaction complexes of the enzyme. This structural information reveals the molecular basis for the recognition of the given substrates and products, GlcNAc/GalNAc, GlcNAc-1P/GalNAc-1P, ATP/ADP and Mg(2+), and provides insights into the catalytic mechanism, enabling NahK and mutants thereof to form a choice of biocatalysts for enzymatic and chemoenzymatic synthesis of carbohydrates.
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Affiliation(s)
- Kuei-Chen Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Syue-Yi Lyu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chen Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Yuan Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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28
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Zou Y, Fang Q, Yin H, Liang Z, Kong D, Bai L, Deng Z, Lin S. Stereospecific biosynthesis of β-methyltryptophan from (L)-tryptophan features a stereochemical switch. Angew Chem Int Ed Engl 2013; 52:12951-5. [PMID: 24166888 DOI: 10.1002/anie.201306255] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/04/2013] [Indexed: 11/10/2022]
Abstract
Make the switch: The three-enzyme cassette MarG/H/I is responsible for stereospecific biosynthesis of β-methyltryptophan from L-tryptophan (1). MarG/I convert 1 into (2S,3R)-β-methyltryptophan, while MarG/I combined with MarH convert 1 into (2S,3S)-β-methyltryptophan. MarH serves as a stereochemical switch by catalyzing the stereoinversion of the β-stereocenter.
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Affiliation(s)
- Yi Zou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240 (P.R. China)
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Zou Y, Fang Q, Yin H, Liang Z, Kong D, Bai L, Deng Z, Lin S. Stereospecific Biosynthesis of β-Methyltryptophan fromL-Tryptophan Features a Stereochemical Switch. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306255] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Najmanová L, Kutejová E, Kadlec J, Polan M, Olšovská J, Benada O, Novotná J, Kameník Z, Halada P, Bauer J, Janata J. Characterization ofN-Demethyllincosamide Methyltransferases LmbJ and CcbJ. Chembiochem 2013; 14:2259-62. [DOI: 10.1002/cbic.201300389] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Indexed: 11/11/2022]
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31
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Xu F, Kong D, He X, Zhang Z, Han M, Xie X, Wang P, Cheng H, Tao M, Zhang L, Deng Z, Lin S. Characterization of streptonigrin biosynthesis reveals a cryptic carboxyl methylation and an unusual oxidative cleavage of a N-C bond. J Am Chem Soc 2013; 135:1739-48. [PMID: 23301954 DOI: 10.1021/ja3069243] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Streptonigrin (STN, 1) is a highly functionalized aminoquinone alkaloid with broad and potent antitumor activity. Here, we reported the biosynthetic gene cluster of STN identified by genome scanning of a STN producer Streptomyces flocculus CGMCC4.1223. This cluster consists of 48 genes determined by a series of gene inactivations. On the basis of the structures of intermediates and shunt products accumulated from five specific gene inactivation mutants and feeding experiments, the biosynthetic pathway was proposed, and the sequence of tailoring steps was preliminarily determined. In this pathway, a cryptic methylation of lavendamycin was genetically and biochemically characterized to be catalyzed by a leucine carboxyl methyltransferase StnF2. A [2Fe-2S](2+) cluster-containing aromatic ring dioxygenase StnB1/B2 system was biochemically characterized to catalyze a regiospecific cleavage of the N-C8' bond of the indole ring of the methyl ester of lavendamycin. This work provides opportunities to illuminate the enzymology of novel reactions involved in this pathway and to create, using genetic and chemo-enzymatic methods, new streptonigrinoid analogues as potential therapeutic agents.
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Affiliation(s)
- Fei Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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Struck AW, Thompson ML, Wong LS, Micklefield J. S-Adenosyl-Methionine-Dependent Methyltransferases: Highly Versatile Enzymes in Biocatalysis, Biosynthesis and Other Biotechnological Applications. Chembiochem 2012. [DOI: 10.1002/cbic.201200556] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Xie Y, Wang B, Liu J, Zhou J, Ma J, Huang H, Ju J. Identification of the Biosynthetic Gene Cluster and Regulatory Cascade for the Synergistic Antibacterial Antibiotics Griseoviridin and Viridogrisein inStreptomyces griseoviridis. Chembiochem 2012; 13:2745-57. [DOI: 10.1002/cbic.201200584] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Indexed: 11/06/2022]
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34
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Resch V, Schrittwieser JH, Siirola E, Kroutil W. Novel carbon-carbon bond formations for biocatalysis. Curr Opin Biotechnol 2011; 22:793-9. [PMID: 21354781 PMCID: PMC3271363 DOI: 10.1016/j.copbio.2011.02.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 02/01/2011] [Indexed: 11/25/2022]
Abstract
Carbon–carbon bond formation is the key transformation in organic synthesis to set up the carbon backbone of organic molecules. However, only a limited number of enzymatic C–C bond forming reactions have been applied in biocatalytic organic synthesis. Recently, further name reactions have been accomplished for the first time employing enzymes on a preparative scale, for instance the Stetter and Pictet–Spengler reaction or oxidative C–C bond formation. Furthermore, novel enzymatic C–C bond forming reactions have been identified like benzylation of aromatics, intermolecular Diels-Alder or reductive coupling of carbon monoxide.
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Affiliation(s)
- Verena Resch
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Chan HC, Huang YT, Lyu SY, Huang CJ, Li YS, Liu YC, Chou CC, Tsai MD, Li TL. Regioselective deacetylation based on teicoplanin-complexed Orf2* crystal structures. MOLECULAR BIOSYSTEMS 2011; 7:1224-31. [PMID: 21267472 DOI: 10.1039/c0mb00320d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lipoglycopeptide antibiotics are more effective than vancomycin against MRSA as they carry an extra aliphatic acyl side chain on glucosamine (Glm) at residue 4 (r4). The biosynthesis of the r4 N-acyl Glc moiety at teicoplanin (Tei) or A40926 has been elucidated, in which the primary amine nucleophile of Glm is freed from the r4 GlcNac pseudo-Tei precursor by Orf2* for the subsequent acylation reaction to occur. In this report, two Orf2* structures in complex with β-D-octyl glucoside or Tei were solved. Of the complexed structures, the substrate binding site and a previously unknown hydrophobic cavity were revealed, wherein r4 GlcNac acts as the key signature for molecular recognition and the cavity allows substrates carrying longer acyl side chains in addition to the acetyl group. On the basis of the complexed structures, a triple-mutation mutant S98A/V121A/F193Y is able to regioselectively deacetylate r6 GlcNac pseudo-Tei instead of that at r4. Thereby, novel analogs can be made at the r6 sugar moiety.
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