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Chen IH, Cheng T, Wang YL, Huang SJ, Hsiao YH, Lai YT, Toh SI, Chu J, Rudolf JD, Chang CY. Characterization and Structural Determination of CmnG-A, the Adenylation Domain That Activates the Nonproteinogenic Amino Acid Capreomycidine in Capreomycin Biosynthesis. Chembiochem 2022; 23:e202200563. [PMID: 36278314 DOI: 10.1002/cbic.202200563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/23/2022] [Indexed: 01/25/2023]
Abstract
Capreomycidine (Cap) is a nonproteinogenic amino acid and building block of nonribosomal peptide (NRP) natural products. We report the formation and activation of Cap in capreomycin biosynthesis. CmnC and CmnD catalyzed hydroxylation and cyclization, respectively, of l-Arg to form l-Cap. l-Cap is then adenylated by CmnG-A before being incorporated into the nonribosomal peptide. The co-crystal structures of CmnG-A with l-Cap and adenosine nucleotides provide insights into the specificity and engineering opportunities of this unique adenylation domain.
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Affiliation(s)
- I-Hsuan Chen
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC.,Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Ting Cheng
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan ROC
| | - Szu-Jo Huang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Yu-Hsuan Hsiao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Yi-Ting Lai
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Shu-Ing Toh
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - John Chu
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan, ROC
| | - Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611-7011, USA
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC.,Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan ROC.,Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan ROC
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2
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Production of a broad spectrum streptothricin like antibiotic from halotolerant Streptomyces fimbriatus isolate G1 associated with marine sediments. Folia Microbiol (Praha) 2021; 66:639-649. [PMID: 33950512 DOI: 10.1007/s12223-021-00870-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/03/2021] [Indexed: 10/21/2022]
Abstract
Streptomyces have been reported as a remarkable source for bioactive secondary metabolites with complex structural and functional diversity. In this study, 35 isolates of genus Streptomyces were purified from rhizospheric and marine soils collected from previously unexplored habitats and screened for antimicrobial activities. One of these isolates, G1, when tested in vitro, was found highly active against wide range of microbes including Gram-positive, Gram-negative bacteria, and different fungal pathogens. It was identified as mesophilic, alkaliphilic, and moderately halotolerant as it showed optimum growth at temperature 30 °C, pH 8.0 in casein-starch-peptone-yeast extract-malt extract medium supplemented with 5% NaCl. Sequence analysis of the 16S rRNA gene indicated 100% identity of this isolate to Streptomyces fimbriatus. Moreover, maximum antimicrobial activity was achieved in starch nitrate medium supplemented with 1% glycerol as carbon and 0.03% soy meal as nitrogen source. The antimicrobial compounds produced by this isolate were extracted in methanol. Bioassay-guided fractionation through thin layer chromatography of methanolic extract resulted in the separation of a most active fraction with an Rf value of 0.46. This active fraction was characterized by FTIR and LCMS analysis and found similar to streptothricin D like antibiotic with m/z 758.42.
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3
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Engineering Heterologous Hosts for the Enhanced Production of Non-ribosomal Peptides. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0080-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Activation of paulomycin production by exogenous γ-butyrolactone signaling molecules in Streptomyces albidoflavus J1074. Appl Microbiol Biotechnol 2020; 104:1695-1705. [PMID: 31900559 DOI: 10.1007/s00253-019-10329-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
Abstract
The interspecies communication roles of γ-butyrolactones (GBLs) have been described for a long time but are still poorly understood. Herein, we analyzed more than 1000 Streptomyces strains and noticed a big quantitative gap between the strains with GBL biosynthetic genes and the strains with GBL receptor genes, which implies the wide-spread of GBLs as interspecies signals in Streptomyces and their great potential in the activation of silent natural product gene clusters. Streptomyces albidoflavus J1074, which has one GBL receptor gene but no GBL biosynthetic gene, was chosen as a target to study the possible interspecies communication roles of GBLs. At first, the GBL biosynthetic genes from Streptomyces coelicolor M145 were expressed in S. albidoflavus J1074, which enabled the S. albidoflavus strains to synthesize Streptomyces coelicolor butanolides (SCBs) and activated the production of paulomycins. Further studies showed that this activation process requires the participation of the GBL receptor gene XNR_4681. The results suggest that the expression of exogenous GBL biosynthetic genes can modulate the metabolisms of GBL non-producing strains, and this regulation role might be meaningful for silent gene cluster activation in Streptomyces. At final, we synthesized racemic-SCB2 and tried to simplify the activation process by adding SCB2 directly to S. albidoflavus J1074, which unfortunately failed to induce paulomycin production.
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Timmermans ML, Ross AC. Unearthing Hidden Chemical Potential from Discarded Actinobacterial Libraries. Trends Biotechnol 2019; 38:7-9. [PMID: 31785780 DOI: 10.1016/j.tibtech.2019.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022]
Abstract
The redundancy of natural product biosynthesis in microbes poses a practical challenge for discovering new antimicrobial compounds from bacteria. The recent application of clustered regularly interspaced short palindromic repeats (CRISPR) technology by Culp et al. to inactivate the production of abundant antibiotics generates a metabolic clean slate for the detection and/or isolation of new and less plentiful antibiotics activated in mutant strains.
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Affiliation(s)
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ONT, Canada.
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6
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Structural basis of the nonribosomal codes for nonproteinogenic amino acid selective adenylation enzymes in the biosynthesis of natural products. ACTA ACUST UNITED AC 2019; 46:515-536. [DOI: 10.1007/s10295-018-2084-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/25/2018] [Indexed: 01/09/2023]
Abstract
Abstract
Nonproteinogenic amino acids are the unique building blocks of nonribosomal peptides (NRPs) and hybrid nonribosomal peptide–polyketides (NRP–PKs) and contribute to their diversity of chemical structures and biological activities. In the biosynthesis of NRPs and NRP–PKs, adenylation enzymes select and activate an amino acid substrate as an aminoacyl adenylate, which reacts with the thiol of the holo form of the carrier protein to afford an aminoacyl thioester as the electrophile for the condensation reaction. Therefore, the substrate specificity of adenylation enzymes is a key determinant of the structure of NRPs and NRP–PKs. Here, we focus on nonproteinogenic amino acid selective adenylation enzymes, because understanding their unique selection mechanisms will lead to accurate functional predictions and protein engineering toward the rational biosynthesis of designed molecules containing amino acids. Based on recent progress in the structural analysis of adenylation enzymes, we discuss the nonribosomal codes of nonproteinogenic amino acid selective adenylation enzymes.
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Du YL, Ryan KS. Pyridoxal phosphate-dependent reactions in the biosynthesis of natural products. Nat Prod Rep 2019; 36:430-457. [DOI: 10.1039/c8np00049b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review reactions catalyzed by pyridoxal phosphate-dependent enzymes, highlighting enzymes reported in the recent natural product biosynthetic literature.
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Affiliation(s)
- Yi-Ling Du
- Institute of Pharmaceutical Biotechnology
- Zhejiang University School of Medicine
- Hangzhou
- China
| | - Katherine S. Ryan
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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Identification of the streptothricin and tunicamycin biosynthetic gene clusters by genome mining in Streptomyces sp. strain fd1-xmd. Appl Microbiol Biotechnol 2018; 102:2621-2633. [DOI: 10.1007/s00253-018-8748-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 10/18/2022]
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9
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Webb HE, Angulo FJ, Granier SA, Scott HM, Loneragan GH. Illustrative examples of probable transfer of resistance determinants from food animals to humans: Streptothricins, glycopeptides, and colistin. F1000Res 2017; 6:1805. [PMID: 29188021 PMCID: PMC5686510 DOI: 10.12688/f1000research.12777.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2017] [Indexed: 12/24/2022] Open
Abstract
Use, overuse, and misuse of antimicrobials contributes to selection and dissemination of bacterial resistance determinants that may be transferred to humans and constitute a global public health concern. Because of the continued emergence and expansion of antimicrobial resistance, combined with the lack of novel antimicrobial agents, efforts are underway to preserve the efficacy of current available life-saving antimicrobials in humans. As a result, uses of medically important antimicrobials in food animal production have generated debate and led to calls to reduce both antimicrobial use and the need for use. This manuscript, commissioned by the World Health Organization (WHO) to help inform the development of the WHO guidelines on the use of medically important antimicrobials in food animals, includes three illustrations of antimicrobial use in food animal production that has contributed to the selection-and subsequent transfer-of resistance determinants from food animals to humans. Herein, antimicrobial use and the epidemiology of bacterial resistance are described for streptothricins, glycopeptides, and colistin. Taken together, these historical and current narratives reinforce the need for actions that will preserve the efficacy of antimicrobials.
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Affiliation(s)
- Hattie E. Webb
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Frederick J. Angulo
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Sophie A. Granier
- Laboratory for Food Safety, Anses, Université Paris-Est, Maisons-Alfort, F-94701, France
| | - H. Morgan Scott
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Guy H. Loneragan
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, 79409, USA
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Meng X, Wang W, Xie Z, Li P, Li Y, Guo Z, Lu Y, Yang J, Guan K, Lu Z, Tan H, Chen Y. Neomycin biosynthesis is regulated positively by AfsA-g and NeoR in Streptomyces fradiae CGMCC 4.7387. SCIENCE CHINA-LIFE SCIENCES 2017; 60:980-991. [DOI: 10.1007/s11427-017-9120-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 05/12/2017] [Indexed: 10/19/2022]
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Nah HJ, Pyeon HR, Kang SH, Choi SS, Kim ES. Cloning and Heterologous Expression of a Large-sized Natural Product Biosynthetic Gene Cluster in Streptomyces Species. Front Microbiol 2017; 8:394. [PMID: 28360891 PMCID: PMC5350119 DOI: 10.3389/fmicb.2017.00394] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 02/24/2017] [Indexed: 12/14/2022] Open
Abstract
Actinomycetes family including Streptomyces species have been a major source for the discovery of novel natural products (NPs) in the last several decades thanks to their structural novelty, diversity and complexity. Moreover, recent genome mining approach has provided an attractive tool to screen potentially valuable NP biosynthetic gene clusters (BGCs) present in the actinomycetes genomes. Since many of these NP BGCs are silent or cryptic in the original actinomycetes, various techniques have been employed to activate these NP BGCs. Heterologous expression of BGCs has become a useful strategy to produce, reactivate, improve, and modify the pathways of NPs present at minute quantities in the original actinomycetes isolates. However, cloning and efficient overexpression of an entire NP BGC, often as large as over 100 kb, remain challenging due to the ineffectiveness of current genetic systems in manipulating large NP BGCs. This mini review describes examples of actinomycetes NP production through BGC heterologous expression systems as well as recent strategies specialized for the large-sized NP BGCs in Streptomyces heterologous hosts.
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Affiliation(s)
- Hee-Ju Nah
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Hye-Rim Pyeon
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Seung-Hoon Kang
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Si-Sun Choi
- Department of Biological Engineering, Inha University Incheon, South Korea
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University Incheon, South Korea
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12
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Draft Genome Sequence of the Streptothricin-Producing Strain
Streptomyces
sp. fd2-tb. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01277-15. [PMID: 26514767 PMCID: PMC4626613 DOI: 10.1128/genomea.01277-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Streptomyces sp. fd2-tb can produce streptothricin class antibiotics with broad antimicrobial spectra. To better understand the mechanism of streptothricin biosynthesis and to assess the capacity of this strain in secondary metabolism, we report the draft genome sequence of Streptomyces sp. strain fd2-tb.
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Guo Z, Li J, Qin H, Wang M, Lv X, Li X, Chen Y. Biosynthesis of the CarbamoylatedD-Gulosamine Moiety of Streptothricins: Involvement of a Guanidino-N-glycosyltransferase and anN-Acetyl-D-gulosamine Deacetylase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Guo Z, Li J, Qin H, Wang M, Lv X, Li X, Chen Y. Biosynthesis of the CarbamoylatedD-Gulosamine Moiety of Streptothricins: Involvement of a Guanidino-N-glycosyltransferase and anN-Acetyl-D-gulosamine Deacetylase. Angew Chem Int Ed Engl 2015; 54:5175-8. [DOI: 10.1002/anie.201412190] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 11/06/2022]
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15
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An efficient blue-white screening based gene inactivation system for Streptomyces. Appl Microbiol Biotechnol 2015; 99:1923-33. [DOI: 10.1007/s00253-014-6369-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 01/27/2023]
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16
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Xie F, Dai S, Shen J, Ren B, Huang P, Wang Q, Liu X, Zhang B, Dai H, Zhang L. A new salicylate synthase AmS is identified for siderophores biosynthesis in Amycolatopsis methanolica 239(T). Appl Microbiol Biotechnol 2015; 99:5895-905. [PMID: 25586582 DOI: 10.1007/s00253-014-6370-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/17/2014] [Accepted: 12/26/2014] [Indexed: 12/14/2022]
Abstract
Siderophores are important for the growth of bacteria or the applications in treatment of iron overload-associated diseases due to the iron-chelating property. Salicylate synthase played a key role in the biosynthesis of some NRPS-derived siderophores by the providing of an iron coordination moiety as the initial building block. A new salicylate synthase, namely AmS, was identified in the biosynthesis pathway of siderophore amychelin in Amycolatopsis methanolica 239(T), since it shunt chorismate, an integrant precursor, from primary to secondary metabolite flow. The amino acid sequence alignment and phylogenetic analysis showed that AmS grouped into a new cluster. In vitro assays of AmS revealed its wide temperature tolerance ranged from 0 to 40 °C and narrow pH tolerant ranged from 7.0 to 9.0. AmS was resistant to organic solvents and non-ionic detergents. Moreover, AmS converted chorismate to salicylate with K m of 129.05 μM, k cat of 2.20 min(-1) at optimal conditions, indicating its low substrate specificity and comparable velocity to reported counterparts (Irp9 and MbtI). These properties of AmS may improve the iron-seizing ability of A. methanolica to compete with its neighbors growing in natural environments. Most importantly, serine and cysteine residues were found to be important for the catalytic activity of AmS. This study presented AmS as a new cluster of salicylate synthase and the reaction mechanism and potential applications of salicylate synthase were highlighted as well.
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Affiliation(s)
- Feng Xie
- School of Life Sciences, University of Science and Technology of China, No. 443 HuangShan Road, Hefei, 230061, China
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Chang CY, Lyu SY, Liu YC, Hsu NS, Wu CC, Tang CF, Lin KH, Ho JY, Wu CJ, Tsai MD, Li TL. Biosynthesis of Streptolidine Involved Two Unexpected Intermediates Produced by a Dihydroxylase and a Cyclase through Unusual Mechanisms. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307989] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Chang CY, Lyu SY, Liu YC, Hsu NS, Wu CC, Tang CF, Lin KH, Ho JY, Wu CJ, Tsai MD, Li TL. Biosynthesis of streptolidine involved two unexpected intermediates produced by a dihydroxylase and a cyclase through unusual mechanisms. Angew Chem Int Ed Engl 2014; 53:1943-8. [PMID: 24505011 DOI: 10.1002/anie.201307989] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/30/2013] [Indexed: 11/11/2022]
Abstract
Streptothricin-F (STT-F), one of the early-discovered antibiotics, consists of three components, a β-lysine homopolymer, an aminosugar D-gulosamine, and an unusual bicyclic streptolidine. The biosynthesis of streptolidine is a long-lasting but unresolved puzzle. Herein, a combination of genetic/biochemical/structural approaches was used to unravel this problem. The STT gene cluster was first sequenced from a Streptomyces variant BCRC 12163, wherein two gene products OrfP and OrfR were characterized in vitro to be a dihydroxylase and a cyclase, respectively. Thirteen high-resolution crystal structures for both enzymes in different reaction intermediate states were snapshotted to help elucidate their catalytic mechanisms. OrfP catalyzes an Fe(II) -dependent double hydroxylation reaction converting L-Arg into (3R,4R)-(OH)2 -L-Arg via (3S)-OH-L-Arg, while OrfR catalyzes an unusual PLP-dependent elimination/addition reaction cyclizing (3R,4R)-(OH)2 -L-Arg to the six-membered (4R)-OH-capreomycidine. The biosynthetic mystery finally comes to light as the latter product was incorporation into STT-F by a feeding experiment.
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Affiliation(s)
- Chin-Yuan Chang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115 (Taiwan)
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Kudo F, Miyanaga A, Eguchi T. Biosynthesis of natural products containing β-amino acids. Nat Prod Rep 2014; 31:1056-73. [DOI: 10.1039/c4np00007b] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
β-Amino acids are unique components involved in a wide variety of natural products such as anticancer agents taxol, bleomycin, cytotoxic microcystin, enediyne compound C-1027 chromophore, nucleoside antibiotic blasticidin S, and macrolactam antibiotic vicenistatin. The biosynthesis and incorporation mechanisms are reviewed.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551, Japan
| | - Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science
- Tokyo Institute of Technology
- Tokyo 152-8551, Japan
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