1
|
Soares NR, Huguet-Tapia JC, Guan D, Clark CA, Yang KT, Kluchka OR, Thombal RS, Kartika R, Badger JH, Pettis GS. Comparative genomics of the niche-specific plant pathogen Streptomyces ipomoeae reveal novel genome content and organization. Appl Environ Microbiol 2023; 89:e0030823. [PMID: 38009923 PMCID: PMC10734452 DOI: 10.1128/aem.00308-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/28/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE While most plant-pathogenic Streptomyces species cause scab disease on a variety of plant hosts, Streptomyces ipomoeae is the sole causative agent of soil rot disease of sweet potato and closely related plant species. Here, genome sequencing of virulent and avirulent S. ipomoeae strains coupled with comparative genomic analyses has identified genome content and organization features unique to this streptomycete plant pathogen. The results here will enable future research into the mechanisms used by S. ipomoeae to cause disease and to persist in its niche environment.
Collapse
Affiliation(s)
- Natasha R. Soares
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | | | - Dongli Guan
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Christopher A. Clark
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Kuei-Ting Yang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Olivia R. Kluchka
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Raju S. Thombal
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Rendy Kartika
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Jonathan H. Badger
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gregg S. Pettis
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| |
Collapse
|
2
|
Adhikari A, Shakya S, Shrestha S, Aryal D, Timalsina KP, Dhakal D, Khatri Y, Parajuli N. Biocatalytic role of cytochrome P450s to produce antibiotics: A review. Biotechnol Bioeng 2023; 120:3465-3492. [PMID: 37691185 DOI: 10.1002/bit.28548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/15/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C-H, C-C, and C-N bonds, including heteroatom oxidation, oxidative C-C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.
Collapse
Affiliation(s)
- Anup Adhikari
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sajan Shakya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Shreesti Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Dipa Aryal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Kavi Prasad Timalsina
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida, USA
| | | | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| |
Collapse
|
3
|
Haq IU, Mukhtar Z, Anwar-Ul-Haq M, Liaqat S. Deciphering host-pathogen interaction during Streptomyces spp. infestation of potato. Arch Microbiol 2023; 205:222. [PMID: 37149838 DOI: 10.1007/s00203-023-03560-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
Potato crop, currently, is the staple food crop of about 1.3 billion global population. Potato is attaining even more admiration globally day by day owing to its public acceptability. However, potato sustainable production is distinctly challenged by multiple factors like diseases, pests and climate change etc. Among diseases, common scab is one of the prime threats to potato crop due to its soil-borne nature and versatility in phytotoxins' secretion. Common scab is caused multiple number of phytopathogenic streptomyces strains. Despite extensive research programs, researchers are still unable to identify a significant solution to this threat that is proliferating exceptional rate across the globe. To develop feasible remedies, adequate information regarding host-pathogen interaction should be available. This review possesses insights on existing pathogenic species, the evolution of novel pathogenic streptomyces spp. and phytotoxins produced by the pathogenic strains. Furthermore, which type of physiological, biochemical and genetic activities occur during pathogen's infestation of the host are also canvassed.
Collapse
Affiliation(s)
- Ihtisham Ul Haq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.
- Ayub Agricultural Research Institute, Faisalabad, Pakistan.
| | - Zahid Mukhtar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | | | - Sana Liaqat
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| |
Collapse
|
4
|
Yee DA, Niwa K, Perlatti B, Chen M, Li Y, Tang Y. Genome mining for unknown-unknown natural products. Nat Chem Biol 2023; 19:633-640. [PMID: 36702957 PMCID: PMC10159913 DOI: 10.1038/s41589-022-01246-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/20/2022] [Indexed: 01/27/2023]
Abstract
Genome mining of biosynthetic pathways with no identifiable core enzymes can lead to discovery of the so-called unknown (biosynthetic route)-unknown (molecular structure) natural products. Here we focused on a conserved fungal biosynthetic pathway that lacks a canonical core enzyme and used heterologous expression to identify the associated natural product, a highly modified cyclo-arginine-tyrosine dipeptide. Biochemical characterization of the pathway led to identification of a new arginine-containing cyclodipeptide synthase (RCDPS), which was previously annotated as a hypothetical protein and has no sequence homology to non-ribosomal peptide synthetase or bacterial cyclodipeptide synthase. RCDPS homologs are widely encoded in fungal genomes; other members of this family can synthesize diverse cyclo-arginine-Xaa dipeptides, and characterization of a cyclo-arginine-tryptophan RCDPS showed that the enzyme is aminoacyl-tRNA dependent. Further characterization of the biosynthetic pathway led to discovery of new compounds whose structures would not have been predicted without knowledge of RCDPS function.
Collapse
Affiliation(s)
- Danielle A Yee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
- Hexagon Bio, Menlo Park, CA, USA
| | - Kanji Niwa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bruno Perlatti
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Hexagon Bio, Menlo Park, CA, USA
| | - Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Yuqing Li
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
5
|
Yang L, Yang D, Wang Q, Li J, Li HL, Pan L. Functional expression and purification of DoxA, a key cytochrome P450 from Streptomyces peucetius ATCC 27952. PeerJ 2022; 10:e14373. [PMID: 36411834 PMCID: PMC9675340 DOI: 10.7717/peerj.14373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
The antitumor drug doxorubicin is widely used in clinical practice. However, the low yield and high cost of this drug highlight the urgent need for cost-effective processes to rapidly manufacture antitumor drugs at scale. In the biosynthesis pathway, the multi-functional cytochrome P450 enzyme DoxA catalyzes the last three steps of hydroxylation. The final conversion of daunorubicin to doxorubicin is the rate-limiting step. In our work, the DoxA has been expressed with the ferredoxin reductase FDR2 and the ferredoxin FDX1 and purified to homogeneous. The reduced carbon monoxide difference spectroscopy, heme concentration, and enzymatic characteristic were characterized. These studies suggest an approach for engineering Streptomyces P450s with functional expression for mechanistic and structural studies.
Collapse
Affiliation(s)
- Liyan Yang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
| | - Dengfeng Yang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Qingyan Wang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
| | - Juan Li
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
| | - Hong-Liang Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, China
| | - Lixia Pan
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
| |
Collapse
|
6
|
Zhao P, Liu L, Cao J, Wang Z, Zhao Y, Zhong N. Transcriptome Analysis of Tryptophan-Induced Resistance against Potato Common Scab. Int J Mol Sci 2022; 23:ijms23158420. [PMID: 35955553 PMCID: PMC9369096 DOI: 10.3390/ijms23158420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Potato common scab (CS) is a worldwide soil-borne disease that severely reduces tuber quality and market value. We observed that foliar application of tryptophan (Trp) could induce resistance against CS. However, the mechanism of Trp as an inducer to trigger host immune responses is still unclear. To facilitate dissecting the molecular mechanisms, the transcriptome of foliar application of Trp and water (control, C) was compared under Streptomyces scabies (S) inoculation and uninoculation. Results showed that 4867 differentially expressed genes (DEGs) were identified under S. scabies uninoculation (C-vs-Trp) and 2069 DEGs were identified under S. scabies inoculation (S-vs-S+Trp). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that Trp induced resistance related to the metabolic process, response to stimulus, and biological regulation. As phytohormone metabolic pathways related to inducing resistance, the expression patterns of candidate genes involved in salicylic acid (SA) and jasmonic acid/ethylene (JA/ET) pathways were analyzed using qRT-PCR. Their expression patterns showed that the systemic acquired resistance (SAR) and induced systemic resistance (ISR) pathways could be co-induced by Trp under S. scabies uninoculation. However, the SAR pathway was induced by Trp under S. scabies inoculation. This study will provide insights into Trp-induced resistance mechanisms of potato for controlling CS, and extend the application methods of Trp as a plant resistance inducer in a way that is cheap, safe, and environmentally friendly.
Collapse
Affiliation(s)
- Pan Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (J.C.); (Z.W.); (Y.Z.)
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
- The Enterprise Key Laboratory of Advanced Technology for Potato Fertilizer and Pesticide, Hulunbuir 021000, China
- Correspondence: (P.Z.); (N.Z.)
| | - Lu Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (J.C.); (Z.W.); (Y.Z.)
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingjing Cao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (J.C.); (Z.W.); (Y.Z.)
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhiqin Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (J.C.); (Z.W.); (Y.Z.)
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonglong Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (J.C.); (Z.W.); (Y.Z.)
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
| | - Naiqin Zhong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (J.C.); (Z.W.); (Y.Z.)
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
- The Enterprise Key Laboratory of Advanced Technology for Potato Fertilizer and Pesticide, Hulunbuir 021000, China
- Correspondence: (P.Z.); (N.Z.)
| |
Collapse
|
7
|
Zhao X, Zong Y, Wei W, Lou C. Multiplexed Promoter Engineering for Improving Thaxtomin A Production in Heterologous Streptomyces Hosts. Life (Basel) 2022; 12:689. [PMID: 35629358 PMCID: PMC9146380 DOI: 10.3390/life12050689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022] Open
Abstract
Thaxtomin A is a potent bioherbicide in both organic and conventional agriculture; however, its low yield hinders its wide application. Here, we report the direct cloning and heterologous expression of the thaxtomin A gene cluster in three well-characterized Streptomyces hosts. Then, we present an efficient, markerless and multiplex large gene cluster editing method based on in vitro CRISPR/Cas9 digestion and yeast homologous recombination. With this method, we successfully engineered the thaxtomin A cluster by simultaneously replacing the native promoters of the txtED operon, txtABH operon and txtC gene with strong constitutive promoters, and the yield of thaxtomin A improved to 289.5 µg/mL in heterologous Streptomyces coelicolor M1154. To further optimize the biosynthetic pathway, we used constraint-based combinatorial design to build 27 refactored gene clusters by varying the promoter strength of every operon, and the highest titer of thaxtomin A production reached 504.6 μg/mL. Taken altogether, this work puts forward a multiplexed promoter engineering strategy to engineer secondary metabolism gene clusters for efficiently improving fermentation titers.
Collapse
Affiliation(s)
- Xuejin Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.Z.); (W.W.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yeqing Zong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.Z.); (W.W.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Weijia Wei
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (Y.Z.); (W.W.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Chunbo Lou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
- Center for Cell and Gene Circuit Design, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
8
|
Nigericin and Geldanamycin Are Phytotoxic Specialized Metabolites Produced by the Plant Pathogen
Streptomyces
sp. 11-1-2. Microbiol Spectr 2022; 10:e0231421. [PMID: 35225656 PMCID: PMC9045263 DOI: 10.1128/spectrum.02314-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plant pathogens use a variety of mechanisms, including the production of phytotoxic specialized metabolites, to establish an infection of host tissue. Although thaxtomin A is considered the key phytotoxin involved in the development of potato scab disease, there is increasing evidence that other phytotoxins can play a role in disease development in some instances.
Collapse
|
9
|
Liu L, Hao L, Liu N, Zhao Y, Zhong N, Zhao P. iTRAQ-Based Proteomics Analysis of Response to Solanum tuberosum Leaves Treated with the Plant Phytotoxin Thaxtomin A. Int J Mol Sci 2021; 22:ijms222112036. [PMID: 34769466 PMCID: PMC8585116 DOI: 10.3390/ijms222112036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
Thaxtomin A (TA) is a phytotoxin secreted by Streptomyces scabies that causes common scab in potatoes. However, the mechanism of potato proteomic changes in response to TA is barely known. In this study, the proteomic changes in potato leaves treated with TA were determined using the Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technique. A total of 693 proteins were considered as differentially expressed proteins (DEPs) following a comparison of leaves treated with TA and sterile water (as a control). Among the identified DEPs, 460 and 233 were upregulated and downregulated, respectively. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, many DEPs were found to be involved in defense and stress responses. Most DEPs were grouped in carbohydrate metabolism, amino acid metabolism, energy metabolism, and secondary metabolism including oxidation-reduction process, response to stress, plant-pathogen interaction, and plant hormone signal transduction. In this study, we analyzed the changes in proteins to elucidate the mechanism of potato response to TA, and we provided a molecular basis to further study the interaction between plant and TA. These results also offer the option for potato breeding through analysis of the resistant common scab.
Collapse
Affiliation(s)
- Lu Liu
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China;
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liaoyang Hao
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.H.); (Y.Z.)
| | - Ning Liu
- National Engineering Research Center for Vegetables (Beijing Vegetable Research Center), Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China;
| | - Yonglong Zhao
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.H.); (Y.Z.)
| | - Naiqin Zhong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
- The Enterprise Key Laboratory of Advanced Technology for Potato Fertilizer and Pesticide, Hulunbuir 021000, China
- Correspondence: (N.Z.); (P.Z.)
| | - Pan Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences, Beijing 100101, China
- The Enterprise Key Laboratory of Advanced Technology for Potato Fertilizer and Pesticide, Hulunbuir 021000, China
- Correspondence: (N.Z.); (P.Z.)
| |
Collapse
|
10
|
Li Z, Huang P, Wang M, Wang X, Wang L, Kong D, Niu G. Stepwise increase of thaxtomins production in Streptomyces albidoflavus J1074 through combinatorial metabolic engineering. Metab Eng 2021; 68:187-198. [PMID: 34673237 DOI: 10.1016/j.ymben.2021.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/23/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022]
Abstract
Herbicide-resistance in weeds has become a serious threat to agriculture across the world. Thus, there is an urgent need for the discovery and development of herbicides with new modes of action. Thaxtomin phytotoxins are a group of nitrated diketopiperazines produced by potato common scab-causing phytopathogen Streptomyces scabies and other actinobacterial pathogens. They are generally considered to function as inhibitors of cellulose synthesis in plants, and thus have great potential to be used as natural herbicides. Generation of an overproducing strain is crucial for the scale-up production of thaxtomins and their wide use in agriculture. In the present study, we employed a stepwise strategy by combining heterologous expression, repressor deletion, activator overexpression, and optimization of fermentation media for high-level production of thaxtomins. The maximum yield of 728 mg/L thaxtomins was achieved with engineered Streptomyces albidoflavus J1074 strains in shake-flask cultures, and it was approximately 36-fold higher than S. albidoflavus J1074 carrying the unmodified cluster. Moreover, the yield of thaxtomins could reach 1973 mg/L when the engineered strain was cultivated in a small-scale stirred-tank bioreactor. This is the highest titer reported to date, representing a significant leap forward for the scale-up production of thaxtomins. Our study presents a robust, easy-to-use system that will be broadly useful for improving titers of bioactive compounds in many Streptomyces species.
Collapse
Affiliation(s)
- Zhilei Li
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Pengju Huang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Meiyan Wang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xia Wang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Linqi Wang
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Dekun Kong
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing, 400715, China; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, 400715, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
11
|
Planckaert S, Deflandre B, de Vries AM, Ameye M, Martins JC, Audenaert K, Rigali S, Devreese B. Identification of Novel Rotihibin Analogues in Streptomyces scabies, Including Discovery of Its Biosynthetic Gene Cluster. Microbiol Spectr 2021; 9:e0057121. [PMID: 34346752 PMCID: PMC8552735 DOI: 10.1128/spectrum.00571-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 02/01/2023] Open
Abstract
Streptomyces scabies is a phytopathogen associated with common scab disease. This is mainly attributed to its ability to produce the phytotoxin thaxtomin A, the biosynthesis of which is triggered by cellobiose. During a survey of other metabolites released in the presence of cellobiose, we discovered additional compounds in the thaxtomin-containing extract from Streptomyces scabies. Structural analysis by mass spectrometry (MS) and nuclear magnetic resonance (NMR) revealed that these compounds are amino acid sequence variants of the TOR (target of rapamycin) kinase (TORK) pathway-inhibitory lipopeptide rotihibin A, and the main compounds were named rotihibins C and D. In contrast to thaxtomin, the production of rotihibins C and D was also elicited in the presence of glucose, indicating different regulation of their biosynthesis. Through a combination of shotgun and targeted proteomics, the putative rotihibin biosynthetic gene cluster rth was identified in the publicly available genome of S. scabies 87-22. This cluster spans 33 kbp and encodes 2 different nonribosomal peptide synthetases (NRPSs) and 12 additional enzymes. Homologous rth biosynthetic gene clusters were found in other publicly available and complete actinomycete genomes. Rotihibins C and D display herbicidal activity against Lemna minor and Arabidopsis thaliana at low concentrations, shown by monitoring the effects on growth and the maximal photochemistry efficiency of photosystem II. IMPORTANCE Rotihibins A and B are plant growth inhibitors acting on the TORK pathway. We report the isolation and characterization of new sequence analogues of rotihibin from Streptomyces scabies, a major cause of common scab in potato and other tuber and root vegetables. By combining proteomics data with genomic analysis, we found a cryptic biosynthetic gene cluster coding for enzyme machinery capable of rotihibin production. This work may lead to the biotechnological production of variants of this lipopeptide to investigate the exact mechanism by which it can target the plant TORK pathway in Arabidopsis thaliana. In addition, bioinformatics revealed the existence of other variants in plant-associated Streptomyces strains, both pathogenic and nonpathogenic species, raising new questions about the actual function of this lipopeptide. The discovery of a module in the nonribosomal peptide synthetase (NRPS) that incorporates the unusual citrulline residue may improve the prediction of peptides encoded by cryptic NRPS gene clusters.
Collapse
Affiliation(s)
- Sören Planckaert
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Benoit Deflandre
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | | | - Maarten Ameye
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - José C. Martins
- NMR and Structure Analysis Group, Ghent University, Ghent, Belgium
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Sébastien Rigali
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège, Belgium
| | - Bart Devreese
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
12
|
Martin CP, Chen M, Martinez MF, Ding Y, Caranto JD. The Ferric-Superoxo Intermediate of the TxtE Nitration Pathway Resists Reduction, Facilitating Its Reaction with Nitric Oxide. Biochemistry 2021; 60:2436-2446. [PMID: 34319079 DOI: 10.1021/acs.biochem.1c00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
TxtE is a cytochrome P450 (CYP) homologue that mediates the nitric oxide (NO)-dependent direct nitration of l-tryptophan (Trp) to form 4-nitro-l-tryptophan (4-NO2-Trp). A recent report showed evidence that TxtE activity requires NO to react with a ferric-superoxo intermediate. Given this minimal mechanism, it is not clear how TxtE avoids Trp hydroxylation, a mechanism that also traverses the ferric-superoxo intermediate. To provide insight into canonical CYP intermediates that TxtE can access, electron coupling efficiencies to form 4-NO2-Trp under single- or limited-turnover conditions were measured and compared to steady-state efficiencies. As previously reported, Trp nitration by TxtE is supported by the engineered self-sufficient variant, TB14, as well as by reduced putidaredoxin. Ferrous (FeII) TxtE exhibits excellent electron coupling (70%), which is 50-fold higher than that observed under turnover conditions. In addition, two- or four-electron reduced TB14 exhibits electron coupling (∼6%) that is 2-fold higher than that of one-electron reduced TB14 (3%). The combined results suggest (1) autoxidation is the sole TxtE uncoupling pathway and (2) the TxtE ferric-superoxo intermediate cannot be reduced by these electron transfer partners. The latter conclusion is further supported by ultraviolet-visible absorption spectral time courses showing neither spectral nor kinetic evidence for reduction of the ferric-superoxo intermediate. We conclude that resistance of the ferric-superoxo intermediate to reduction is a key feature of TxtE that increases the lifetime of the intermediate and enables its reaction with NO and efficient nitration activity.
Collapse
Affiliation(s)
- Christopher P Martin
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Room 255, Orlando, Florida 32816, United States
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, 1345 Center Drive, Room P6-27, Gainesville, Florida 32610, United States
| | - Maria F Martinez
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Room 255, Orlando, Florida 32816, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, 1345 Center Drive, Room P6-27, Gainesville, Florida 32610, United States
| | - Jonathan D Caranto
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Room 255, Orlando, Florida 32816, United States
| |
Collapse
|
13
|
Ashfield-Crook NR, Woodward Z, Soust M, Kurtböke Dİ. Bioactive Streptomycetes from Isolation to Applications: A Tasmanian Potato Farm Example. Methods Mol Biol 2021; 2232:219-249. [PMID: 33161551 DOI: 10.1007/978-1-0716-1040-4_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The genus Streptomyces constitutes approximately 50% of all soil actinomycetes, playing a significant role in the soil microbial community through vital functions including nutrient cycling, production of bioactive metabolites, disease-suppression and plant growth promotion. Streptomyces produce many bioactive compounds and are prime targets for industrial and biotechnological applications. In addition to their agrobiological roles, some Streptomyces spp. can, however, be phytopathogenic, examples include, common scab of potato that causes economic losses worldwide. Currently used chemical control measures can have detrimental effect to environmental and human health as a result alternative methods to chemical disease control are being investigated. One alternative is the use of streptomycete specific phages to remove this pathogenic bacterium before it can cause the disease on potatoes. However, due to co-existence of non-common scab-causing species belonging to the genus Streptomyces, phage treatment is likely to affect a wide range of non-target streptomycete species including the beneficial ones in the soil. Therefore, before such treatment starts the host range of the phages within the targeted family of bacteria should be determined. In a study conducted using soil samples from a Tasmanian potato farm, streptomycetes were isolated and tested against streptomycete-specific phages. Their antifungal activity was also determined using multiple assays against selected phytopathogens. The four strongest antifungal activity-displaying isolates were further tested for their persistent antifungal activity using wheat and Fusarium solani in a pot trial. A second pot trial was also conducted to evaluate whether the beneficial streptomycetes were affected by streptophage treatment and whether their removal via the phage battery would cause opportunistic fungal infections to plants in soil. The streptomycetes prevented the reduction in wheat shoot weight caused by F. solani indicating their disease suppressive effect. However, when phages were added into the pots, the growth of wheat was detrimentally impacted. This finding might suggest that the reduced presence of antifungal streptomycetes via phage-induced lysis might encourage opportunistic fungal infections in plants.
Collapse
Affiliation(s)
- Nina R Ashfield-Crook
- GeneCology Research Centre and the School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, Australia
| | | | - Martin Soust
- Terragen Biotech Pty. Ltd., Coolum Beach, QLD, Australia
| | - D İpek Kurtböke
- GeneCology Research Centre and the School of Science and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, Australia.
| |
Collapse
|
14
|
Li Y, Tahlan K, Bignell DR. Functional Cross-Talk of MbtH-Like Proteins During Thaxtomin Biosynthesis in the Potato Common Scab Pathogen Streptomyces scabiei. Front Microbiol 2020; 11:585456. [PMID: 33178168 PMCID: PMC7593251 DOI: 10.3389/fmicb.2020.585456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
Thaxtomin A is a potent phytotoxin that serves as the principle pathogenicity determinant of the common scab pathogen, Streptomyces scabiei, and is also a promising natural herbicide for agricultural applications. The biosynthesis of thaxtomin A involves the non-ribosomal peptide synthetases (NRPSs) TxtA and TxtB, and an MbtH-like protein (MLP), TxtH, which may function as a chaperone by promoting the proper folding of the two NRPS enzymes in S. scabiei. MLPs are required for the proper function of many NRPS enzymes in bacteria, and they are often capable of interacting with NRPSs from different biosynthetic pathways, though the mechanism by which this occurs is still poorly understood. To gain additional insights into MLP functional cross-talk, we conducted a broad survey of MLPs from diverse phylogenetic lineages to determine if they could functionally replace TxtH. The MLPs were assessed using a protein solubility assay to determine whether they could promote the soluble expression of the TxtA and TxtB adenylation domains. In addition, the MLPs were tested for their ability to restore thaxtomin production in a S. scabiei mutant that lacked TxtH and other endogenous MLPs. Our results showed that the MLPs investigated vary in their ability to exhibit functional cross-talk with TxtH, with two of the MLPs being unable to compensate for the loss of TxtH in the assays performed. The ability of an MLP to serve as a functional partner for the thaxtomin NRPS was not correlated with its overall amino acid similarity with TxtH, but instead with the presence of highly conserved residues. In silico structural analysis of TxtH in association with the TxtA and TxtB adenylation domains revealed that several such residues are situated at the predicted interaction interface, suggesting that they might be critical for promoting functional interactions between MLPs and the thaxtomin NRPS enzymes. Overall, our study provides additional insights into the mechanism of MLP cross-talk, and it enhances our understanding of the thaxtomin biosynthetic machinery. It is anticipated that our findings will have useful applications for both the control of common scab disease and the commercial production of thaxtomin A for agricultural use.
Collapse
|
15
|
Li Y, Yuan S, Yong X, zhao T, Liu J. Research progress on small peptides in Chinese Baijiu. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
|
16
|
Li M, Chen Z, Qian J, Wei F, Zhang G, Wang Y, Wei G, Hu Z, Dong L, Chen S. Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields. Chin Med 2020; 15:85. [PMID: 32793300 PMCID: PMC7418314 DOI: 10.1186/s13020-020-00364-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/03/2020] [Indexed: 11/21/2022] Open
Abstract
Background Panax notoginseng is a highly valuable medicinal plant. Reduced P. notoginseng yield is a common and serious problem that arises in a continuous cropping system. Variation in the composition and function of soil microbial community is considered the primary cause of yield reduction. Methods This study used shotgun metagenomic sequencing approaches to describe the taxonomic and functional features of P. notoginseng rhizosphere microbiome and screen microbial taxa and functional traits related to yields. Results At the family and genus level, a total of 43 families and 45 genera (relative abundance > 0.1%) were obtained, and the correlation with the yield of P. notoginseng was further analyzed. Nitrosomonadaceae, Xanthomonadaceae, Mycobacterium and Arthrobacter that were enriched in soils with higher yields were positively correlated with P. notoginseng yields, thereby suggesting that they might increase yields. Negative correlation coefficients indicated that Xanthobacteraceae, Caulobacteraceae, Oxalobacteraceae, Chitinophagaceae, Sphingomonas, Hyphomicrobium, Variovorax and Phenylobacterium might be detrimental to P. notoginseng growth. A total of 85 functional traits were significantly (P < 0.05) correlated with P. notoginseng yields. Functional traits, likely steroid biosynthesis and MAPK signaling pathway were positively correlated with P. notoginseng yields. In contrast, functional traits, such as bacterial secretion system, ABC transporters, metabolism of xenobiotics by cytochrome P450 and drug metabolism–cytochrome P450, were negatively associated with yields. Conclusions This study describes an overview of the rhizosphere microbiome of P. notoginseng with discrepant yields and identifies the taxa and functional traits related to yields. Our results provide valuable information to guide the isolation and culture of potentially beneficial microorganisms and to utilize the power of the microbiome to increase plant yields in a continuous cropping system.
Collapse
Affiliation(s)
- Mengzhi Li
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China.,Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan, 663000 China.,Wenshan Miaoxiang Notoginseng Technology, Co., Ltd, Wenshan, 663000 China
| | - Jun Qian
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China.,College of Pharmaceutical Science, Dali University, Dali, 671000 China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd, Wenshan, 663000 China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan, 663000 China
| | - Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Shilin Chen
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China.,Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China
| |
Collapse
|
17
|
Mnguni FC, Padayachee T, Chen W, Gront D, Yu JH, Nelson DR, Syed K. More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus, Cyanobacteria, and Mycobacterium. Int J Mol Sci 2020; 21:ijms21134814. [PMID: 32646068 PMCID: PMC7369989 DOI: 10.3390/ijms21134814] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/18/2022] Open
Abstract
Unraveling the role of cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins present in living and non-living entities, in secondary metabolite synthesis is gaining momentum. In this direction, in this study, we analyzed the genomes of 203 Streptomyces species for P450s and unraveled their association with secondary metabolism. Our analyses revealed the presence of 5460 P450s, grouped into 253 families and 698 subfamilies. The CYP107 family was found to be conserved and highly populated in Streptomyces and Bacillus species, indicating its key role in the synthesis of secondary metabolites. Streptomyces species had a higher number of P450s than Bacillus and cyanobacterial species. The average number of secondary metabolite biosynthetic gene clusters (BGCs) and the number of P450s located in BGCs were higher in Streptomyces species than in Bacillus, mycobacterial, and cyanobacterial species, corroborating the superior capacity of Streptomyces species for generating diverse secondary metabolites. Functional analysis via data mining confirmed that many Streptomyces P450s are involved in the biosynthesis of secondary metabolites. This study was the first of its kind to conduct a comparative analysis of P450s in such a large number (203) of Streptomyces species, revealing the P450s’ association with secondary metabolite synthesis in Streptomyces species. Future studies should include the selection of Streptomyces species with a higher number of P450s and BGCs and explore the biotechnological value of secondary metabolites they produce.
Collapse
Affiliation(s)
- Fanele Cabangile Mnguni
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI 53706, USA;
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Correspondence: (D.R.N.); (K.S.)
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
- Correspondence: (D.R.N.); (K.S.)
| |
Collapse
|
18
|
Prieto MC, Lapaz MI, Lucini EI, Pianzzola MJ, Grosso NR, Asensio CM. Thyme and suico essential oils: promising natural tools for potato common scab control. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:81-89. [PMID: 31539455 DOI: 10.1111/plb.13048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/13/2019] [Indexed: 06/10/2023]
Abstract
Potato common scab is a worldwide disease mainly caused by Streptomyces scabiei. It seriously affects potato crops by decreasing tuber quality. Essential oils (EO) are natural products with recognised antimicrobial properties. In this research, the antibacterial activities of thyme, oregano, suico and mint EO against S. scabiei were analysed. Infected tubers and soil samples were used for bacterial isolation; the obtained isolates were genetically identified. The chemical composition of the EO was determined by GC-MS. The broth microdilution method was used to analyse antibacterial properties of EO. Thirty-one bacterial isolates were obtained. The isolate chosen for antibacterial assays was morpho-physiologically and genetically identified as S. scabiei. Thyme EO was mainly composed of thymol and o-cymene; suico EO of dihydrotagetone, trans-tagetone and verbenone; oregano EO of trans-sabinene hydrate, thymol and ɣ-terpinene; and mint EO of menthone and menthol. All the EO tested were effective against S. scabiei, but thyme and suico EO were the most successful, with a minimum inhibitory concentration of 0.068 g·l-1 and 0.147 g·l-1 , respectively, and a minimum bactericidal concentration of 0.137 g·l-1 and 0.147 g·l-1 , respectively. Scanning electron microscopy showed similar damage caused by both thyme and suico EO to the bacterial envelope. Total phenolic content of EO was not related to their antibacterial activity. Thyme and suico EO are effective antibacterial agents against S. scabiei, impeding bacterial viability and disturbing the bacterial cell envelope. These EO are promising tools for control of potato common scab.
Collapse
Affiliation(s)
- M C Prieto
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - M I Lapaz
- Área de Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - E I Lucini
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
| | - M J Pianzzola
- Área de Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - N R Grosso
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
| | - C M Asensio
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
| |
Collapse
|
19
|
Li Y, Liu J, Adekunle D, Bown L, Tahlan K, Bignell DR. TxtH is a key component of the thaxtomin biosynthetic machinery in the potato common scab pathogen Streptomyces scabies. MOLECULAR PLANT PATHOLOGY 2019; 20:1379-1393. [PMID: 31282068 PMCID: PMC6792134 DOI: 10.1111/mpp.12843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Streptomyces scabies causes potato common scab disease, which reduces the quality and market value of affected tubers. The predominant pathogenicity determinant produced by S. scabies is the thaxtomin A phytotoxin, which is essential for common scab disease development. Production of thaxtomin A involves the nonribosomal peptide synthetases (NRPSs) TxtA and TxtB, both of which contain an adenylation (A-) domain for selecting and activating the appropriate amino acid during thaxtomin biosynthesis. The genome of S. scabies 87.22 contains three small MbtH-like protein (MLP)-coding genes, one of which (txtH) is present in the thaxtomin biosynthesis gene cluster. MLP family members are typically required for the proper folding of NRPS A-domains and/or stimulating their activities. This study investigated the importance of TxtH during thaxtomin biosynthesis in S. scabies. Biochemical studies showed that TxtH is required for promoting the soluble expression of both the TxtA and TxtB A-domains in Escherichia coli, and amino acid residues essential for this activity were identified. Deletion of txtH in S. scabies significantly reduced thaxtomin A production, and deletion of one of the two additional MLP homologues in S. scabies completely abolished production. Engineered expression of all three S. scabies MLPs could restore thaxtomin A production in a triple MLP-deficient strain, while engineered expression of MLPs from other Streptomyces spp. could not. Furthermore, the constructed MLP mutants were reduced in virulence compared to wild-type S. scabies. The results of our study confirm that TxtH plays a key role in thaxtomin A biosynthesis and plant pathogenicity in S. scabies.
Collapse
Affiliation(s)
- Yuting Li
- Department of BiologyMemorial University of Newfoundland232 Elizabeth AveSt. John'sNLA1B 3X9Canada
| | - Jingyu Liu
- Department of BiologyMemorial University of Newfoundland232 Elizabeth AveSt. John'sNLA1B 3X9Canada
| | - Damilola Adekunle
- Department of BiologyMemorial University of Newfoundland232 Elizabeth AveSt. John'sNLA1B 3X9Canada
| | - Luke Bown
- Department of BiologyMemorial University of Newfoundland232 Elizabeth AveSt. John'sNLA1B 3X9Canada
- Present address:
Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐Champaign1206 W Gregory DriveUrbana Il61801USA
| | - Kapil Tahlan
- Department of BiologyMemorial University of Newfoundland232 Elizabeth AveSt. John'sNLA1B 3X9Canada
| | - Dawn R.D. Bignell
- Department of BiologyMemorial University of Newfoundland232 Elizabeth AveSt. John'sNLA1B 3X9Canada
| |
Collapse
|
20
|
Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
Collapse
Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
| |
Collapse
|
21
|
Li Y, Liu J, Díaz-Cruz G, Cheng Z, Bignell DRD. Virulence mechanisms of plant-pathogenic Streptomyces species: an updated review. MICROBIOLOGY-SGM 2019; 165:1025-1040. [PMID: 31162023 DOI: 10.1099/mic.0.000818] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Gram-positive Actinobacteria from the genus Streptomyces are best known for their morphological complexity and for their ability to produce numerous bioactive specialized metabolites with useful applications in human and veterinary medicine and in agriculture. In contrast, the ability to infect living plant tissues and to cause diseases of root and tuber crops such as potato common scab (CS) is a rare attribute among members of this genus. Research on the virulence mechanisms of plant-pathogenic Streptomyces spp. has revealed the importance of the thaxtomin phytotoxins as key pathogenicity determinants produced by several species. In addition, other phytotoxic specialized metabolites may contribute to the development or severity of disease caused by Streptomyces spp., along with the production of phytohormones and secreted proteins. A thorough understanding of the molecular mechanisms of plant pathogenicity will enable the development of better management procedures for controlling CS and other plant diseases caused by the Streptomyces.
Collapse
Affiliation(s)
- Yuting Li
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Jingyu Liu
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Gustavo Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Zhenlong Cheng
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| |
Collapse
|
22
|
Jiang G, Zhang Y, Powell MM, Hylton SM, Hiller NW, Loria R, Ding Y. A Promiscuous Cytochrome P450 Hydroxylates Aliphatic and Aromatic C-H Bonds of Aromatic 2,5-Diketopiperazines. Chembiochem 2019; 20:1068-1077. [PMID: 30604585 PMCID: PMC8162728 DOI: 10.1002/cbic.201800736] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 11/06/2022]
Abstract
Cytochrome P450 enzymes generally functionalize inert C-H bonds, and thus, they are important biocatalysts for chemical synthesis. However, enzymes that catalyze both aliphatic and aromatic hydroxylation in the same biotransformation process have rarely been reported. A recent biochemical study demonstrated the P450 TxtC for the biosynthesis of herbicidal thaxtomins as the first example of this unique type of enzyme. Herein, the detailed characterization of substrate requirements and biocatalytic applications of TxtC are reported. The results reveal the importance of N-methylation of the thaxtomin diketopiperazine (DKP) core on enzyme reactions and demonstrate the tolerance of the enzyme to modifications on the indole and phenyl moieties of its substrates. Furthermore, hydroxylated, methylated, aromatic DKPs are synthesized through a biocatalytic route comprising TxtC and the promiscuous N-methyltransferase Amir_4628; thus providing a basis for the broad application of this unique P450.
Collapse
Affiliation(s)
- Guangde Jiang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Magan M Powell
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Sarah M Hylton
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Nicholas W Hiller
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Rosemary Loria
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| |
Collapse
|
23
|
Sarwar A, Latif Z, Zhang S, Hao J, Bechthold A. A Potential Biocontrol Agent Streptomyces violaceusniger AC12AB for Managing Potato Common Scab. Front Microbiol 2019; 10:202. [PMID: 30800116 PMCID: PMC6375851 DOI: 10.3389/fmicb.2019.00202] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Potato common scab (PCS) is an economically important disease worldwide. In this study we demonstrated the possible role of Streptomyces violaceusniger AC12AB in controlling PCS. Isolates of Streptomyces scabies were obtained from CS infected tubers collected from Maine United States, which were confirmed by morphological and molecular analysis including 16S rRNA sequencing and RFLP analysis of amplified 16S-23S ITS. Pathogenicity assays related genes including txtAB, nec1, and tomA were also identified in all S. scabies strains through PCR reaction. An antagonistic bacterial strain was isolated from soil in Punjab and identified as S. violaceusniger AC12AB based on 16S rRNA sequencing analysis. Methanolic extract of S. violaceusniger AC12AB contained azalomycin RS-22A which was confirmed by 1H and 13C-NMR, 1H/1H-COSY, HMBC and HMQC techniques. S. violaceusniger AC12AB exhibited plant growth promotion attributes including Indole-3-acetic acid production with 17 μgmL-1 titers, siderophores production, nitrogen fixation and phosphates solubilization potential. When tubers were inoculated with S. violaceusniger AC12AB, significant (P < 0.05) PCS disease reduction up to 90% was observed in greenhouse and field trials, respectively. Likewise, S. violaceusniger AC12AB significantly (P < 0.05) increased potato crop up to 26.8% in field trial. Therefore, plant growth promoting S. violaceusniger AC12AB could provide a dual benefit by decreasing PCS disease severity and increasing potato yield as an effective and inexpensive alternative strategy to manage this disease.
Collapse
Affiliation(s)
- Arslan Sarwar
- Department of Microbiology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Zakia Latif
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Songya Zhang
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jianjun Hao
- School of Food and Agriculture, The University of Maine, Orono, ME, United States
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| |
Collapse
|
24
|
Shi W, Li M, Wei G, Tian R, Li C, Wang B, Lin R, Shi C, Chi X, Zhou B, Gao Z. The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome. MICROBIOME 2019; 7:14. [PMID: 30709420 PMCID: PMC6359780 DOI: 10.1186/s40168-019-0629-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/17/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels. We aimed to determine the composition and putative function of the soil microbiome associated with potato CS. RESULTS The copy numbers of the scab phytotoxin biosynthetic gene txtAB and the bacterial 16S rRNA gene as well as the diversity and composition of each of the four soil-root system compartments were examined; GS was the only compartment that exhibited significant differences between the H and L groups. Compared to the H group, the L group exhibited a lower txtAB gene copy number, lower bacterial 16S copy number, higher diversity, higher co-occurrence network complexity, and higher community function similarity within the GS microbiome. The community composition and function of the GS samples were further revealed by shotgun metagenomic sequencing. Variovorax, Stenotrophomonas, and Agrobacterium were the most abundant genera that were significantly and positively correlated with the scab severity level, estimated absolute abundance (EAA) of pathogenic Streptomyces, and txtAB gene copy number. In contrast, Geobacillus, Curtobacterium, and unclassified Geodermatophilaceae were significantly negatively correlated with these three parameters. Compared to the function profiles in the L group, several genes involved in "ABC transporters," the "bacterial secretion system," "quorum sensing (QS)," "nitrogen metabolism," and some metabolism by cytochrome P450 were enriched in the H group. In contrast, some antibiotic biosynthesis pathways were enriched in the L group. Based on the differences in community composition and function, a simple model was proposed to explain the putative relationships between the soil microbiome and CS occurrence. CONCLUSIONS The GS microbiome was closely associated with CS severity in the soil-root system, and the occurrence of CS was accompanied by changes in community composition and function. The differential functions provide new clues to elucidate the mechanism underlying the interaction between CS occurrence and the soil microbiome, and varying community compositions provide novel insights into CS occurrence.
Collapse
Affiliation(s)
- Wencong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, 361005, China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Renmao Tian
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, USA
| | - Cuiping Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Bing Wang
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China
| | - Rongshan Lin
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China
| | - Chunyu Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiuli Chi
- Plant Protection Station, Jiaozhou Agricultural Bureau, Qingdao, 266300, China
| | - Bo Zhou
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China.
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China.
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, USA.
| |
Collapse
|
25
|
Abstract
Communication between and within communities of cells or independent organisms is a crucial prerequisite for species survival. In response to variations in the extracellular environment, the collective behavior of cell populations can be coordinated by regulating community-level gene expression. This mechanism is strongly conserved during evolution, being shared both by bacterial communities and central nervous system cells. Notably, cyclic dipeptides (CDPs) are molecules that are implicated in these quorum sensing behaviors in both settings. Bacteria coordinate their collective behavior by producing CDPs (quorum sensing inducers) that enhance the capacity of individual members of the community to detect these signals and thus amplify the community-level response. In this review, we highlight recent data indicating that strikingly similar molecular mechanisms control communications between glial and neuronal cells to maintain homeostasis in the central nervous system, with a specific focus on the role of the thyrotropin-releasing hormone—derived CDP cyclo(His-Pro) in the protection against neurotoxic insults.
Collapse
|
26
|
Alkhalaf LM, Barry SM, Rea D, Gallo A, Griffiths D, Lewandowski JR, Fulop V, Challis GL. Binding of Distinct Substrate Conformations Enables Hydroxylation of Remote Sites in Thaxtomin D by Cytochrome P450 TxtC. J Am Chem Soc 2018; 141:216-222. [DOI: 10.1021/jacs.8b08864] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lona M. Alkhalaf
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K
| | - Sarah M. Barry
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K
| | - Dean Rea
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Angelo Gallo
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K
| | - Daniel Griffiths
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K
| | | | - Vilmos Fulop
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Gregory L. Challis
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV4 7AL, U.K
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
27
|
Jiang G, Zuo R, Zhang Y, Powell MM, Zhang P, Hylton SM, Loria R, Ding Y. One-Pot Biocombinatorial Synthesis of Herbicidal Thaxtomins. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Guangde Jiang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Ran Zuo
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Magan M. Powell
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Peilan Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Sarah M. Hylton
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Rosemary Loria
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| |
Collapse
|
28
|
Nahar K, Goyer C, Zebarth BJ, Burton DL, Whitney S. Pathogenic Streptomyces spp. Abundance Affected by Potato Cultivars. PHYTOPATHOLOGY 2018; 108:1046-1055. [PMID: 29658842 DOI: 10.1094/phyto-03-18-0075-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Potato cultivars vary in their tolerance to common scab; however, how they affect common scab-causing Streptomyces spp. populations over time is poorly understood. This study investigated the effects of potato cultivar on pathogenic Streptomyces spp. abundance, measured using quantitative PCR, in three spatial locations in a common scab-infested field: (i) soil close to the plant (SCP); (ii) rhizosphere soil (RS); and (iii) geocaulosphere soil (GS). Two tolerant (Gold Rush, Hindenburg) and two susceptible cultivars (Green Mountain, Agria) were tested. The abundance of pathogenic Streptomyces spp. significantly increased in late August compared with other dates in RS of susceptible cultivars in both years. Abundance of pathogenic Streptomyces spp., when averaged over locations and time, was significantly greater in susceptible cultivars compared with tolerant cultivars in 2014. Principal coordinates analysis showed that SCP and RS soil properties (pH, organic carbon, and nitrogen concentrations) explained 68 and 76% of total variation in Streptomyces spp. abundance among cultivars in 2013, respectively, suggesting that cultivars influenced common scab pathogen growth conditions. The results suggested that the genetic background of potato cultivars influenced the abundance of pathogenic Streptomyces spp., with five to six times more abundant Streptomyces spp. in RS of susceptible cultivars compared with tolerant cultivars, which would result in substantially more inoculum left in the field after harvest.
Collapse
Affiliation(s)
- Kamrun Nahar
- First, second, third, and fifth authors: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB, Canada; and fourth author: Department of Environmental Sciences, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS, Canada
| | - Claudia Goyer
- First, second, third, and fifth authors: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB, Canada; and fourth author: Department of Environmental Sciences, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS, Canada
| | - Bernie J Zebarth
- First, second, third, and fifth authors: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB, Canada; and fourth author: Department of Environmental Sciences, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS, Canada
| | - David L Burton
- First, second, third, and fifth authors: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB, Canada; and fourth author: Department of Environmental Sciences, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS, Canada
| | - Sean Whitney
- First, second, third, and fifth authors: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB, Canada; and fourth author: Department of Environmental Sciences, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS, Canada
| |
Collapse
|
29
|
Zhang Y, Jiang G, Ding Y, Loria R. Genetic background affects pathogenicity island function and pathogen emergence in Streptomyces. MOLECULAR PLANT PATHOLOGY 2018; 19:1733-1741. [PMID: 29316196 PMCID: PMC6638181 DOI: 10.1111/mpp.12656] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/27/2017] [Accepted: 01/05/2018] [Indexed: 05/30/2023]
Abstract
With few exceptions, thaxtomin A (ThxA), a nitrated diketopiperazine, is the pathogenicity determinant for plant-pathogenic Streptomyces species. In Streptomyces scabiei (syn. S. scabies), the ThxA biosynthetic cluster is located within a 177-kb mobile pathogenicity island (PAI), called the toxicogenic region (TR). In S. turgidiscabies, the ThxA biosynthetic cluster is located within a 674-kb pathogenicity island (PAIst). The emergence of new plant pathogens occurs in this genus, but not frequently. This raises the question of whether the mobilization of these pathogenicity regions, through mating, is widespread and whether TR and PAIst can confer plant pathogenicity. We showed that ThxA biosynthetic clusters on TR and PAIst were transferred into strains from five non-pathogenic Streptomyces species through mating with S. scabiei and S. turgidiscabies. However, not all of the transconjugants produced ThxA and exhibited the virulence phenotype, indicating that the genetic background of the recipient strains affects the functionality of the ThxA biosynthetic cluster and therefore would be expected to affect the emergence of novel pathogenic Streptomyces species. Thxs have been patented as natural herbicides, but have yet to be commercialized. Our results also demonstrated the potential of the heterologous production of ThxA as a natural and biodegradable herbicide in non-pathogenic Streptomyces species.
Collapse
Affiliation(s)
- Yucheng Zhang
- Department of Plant PathologyUniversity of FloridaGainesvilleFL32611USA
| | - Guangde Jiang
- Department of Medicinal ChemistryUniversity of FloridaGainesvilleFL32610USA
| | - Yousong Ding
- Department of Medicinal ChemistryUniversity of FloridaGainesvilleFL32610USA
| | - Rosemary Loria
- Department of Plant PathologyUniversity of FloridaGainesvilleFL32611USA
| |
Collapse
|
30
|
Sarwar A, Latif Z, Zhang S, Zhu J, Zechel DL, Bechthold A. Biological Control of Potato Common Scab With Rare Isatropolone C Compound Produced by Plant Growth Promoting Streptomyces A1RT. Front Microbiol 2018; 9:1126. [PMID: 29899736 PMCID: PMC5989138 DOI: 10.3389/fmicb.2018.01126] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/14/2018] [Indexed: 12/01/2022] Open
Abstract
Potato is prone to many drastic diseases like potato common scab (CS). As no highly effective methods exist for managing CS, this study explored the possibility of using biological control. Ten bacterial strains were isolated from CS-infected potato tubers from four different locations of Punjab, Pakistan, and identified based on biochemical and molecular analysis. Analysis of 16s rDNA sequences amplified by PCR revealed the isolated bacterial strains to be Streptomyces scabies, S. turgidiscabies and S. stelliscabiei. Pathogenic islands were also confirmed among the isolates after identification of txtAB, nec1, and tomA genes with PCR amplification. One strain isolated from soil was antagonistic to the pathogenic Streptomyces spp., and determined to be Streptomyces A1RT on the basis of 16s rRNA sequencing. A methanolic extract of Streptomyces A1RT contained Isatropolone C, which was purified and structurally determined by 1H- and 13C-NMR, 1H/1H-COSY, HMQC, and HMBC techniques. Streptomyces A1RT also produced the plant growth hormone indole-3-acetic acid (IAA) with a titer of 26 μg ml-1 as confirmed by spectrophotometry and HPLC. In a greenhouse assay, disease severity index was established from 0 to 500. Average disease severity indexes were recorded as 63, 130.5, and 78 for Streptomyces scabies, S. turgidiscabies and S. stelliscabiei, respectively. When Streptomyces A1RT was applied in soil that contained one of these pathogenic isolates, the average disease severity indexes were significantly (P < 0.05) reduced to 11.1, 5.6 and 8.4, respectively. A significant increase in tuber weight and shoot development was also observed with the tubers treated with Streptomyces A1RT. The use of the plant growth-promoting Streptomyces A1RT against potato CS thus provides an alternative strategy to control the disease without affecting environmental, plants, animals and human health.
Collapse
Affiliation(s)
- Arslan Sarwar
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Zakia Latif
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Songya Zhang
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jing Zhu
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| | - David L Zechel
- Department of Chemistry, Queen's University, Kingston, ON, Canada
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| |
Collapse
|
31
|
Liang J, Cheng T, Huang Y, Liu J. Petroleum degradation by Pseudomonas sp. ZS1 is impeded in the presence of antagonist Alcaligenes sp. CT10. AMB Express 2018; 8:88. [PMID: 29808440 PMCID: PMC5972140 DOI: 10.1186/s13568-018-0620-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/23/2018] [Indexed: 12/03/2022] Open
Abstract
Enhanced bioremediation is a favorable approach for petroleum pollutant cleanup, which depends on the growth of oil-eating microorganisms. In this study, we show that, by using the modified T-RFLP (mT-RFLP) methodology, one of the four major microbial populations derived from oil sludge has failed to propagate in MS medium supplemented with 2% yeast extract (YE). rDNA sequence-based analysis indicated that the four populations were Donghicola sp. CT5, Bacillus sp. CT6, Alcaligenes sp. CT10, and Pseudomonas sp. ZS1. Four purified strains grow well individually in MS medium supplemented with 2% YE, suggesting that ZS1 growth is antagonized by other strains. Co-growth analysis using mT-RFLP methodology and plate inhibitory assay indicated that ZS1 exhibited antagonistic effect against CT5 and CT6. On the other hand, co-growth analysis and plate inhibition assay showed that CT10 antagonized against ZS1. To investigate the potential compounds responsible for the antagonism, supernatant of CT10 culture was subjected to GC-MS analysis. Analysis indicated that CT10 produced a number of antimicrobial compounds including cyclodipeptide c-(L-Pro-L-Phe), which was known to inhibit the growth of Pseudomonas sp. Growth test using the purified c-(L-Pro-L-Phe) from CT10 confirmed its inhibitory activity. We further showed that, using both gravimetric and GC analysis, CT10 antagonism against the oil-eating ZS1 led to the diminishing of crude oil degradation. Together, our results indicate that bioremediation can be affected by environmental antagonists.
Collapse
Affiliation(s)
- Jibei Liang
- Ocean College, Zhejiang University, Marine Science Building #379, Zhoushan Campus, 1 Zheda Road, Dinghai District, Zhoushan, 316000 ZJ China
| | - Tao Cheng
- Ocean College, Zhejiang University, Marine Science Building #379, Zhoushan Campus, 1 Zheda Road, Dinghai District, Zhoushan, 316000 ZJ China
| | - Yi Huang
- Ocean College, Zhejiang University, Marine Science Building #379, Zhoushan Campus, 1 Zheda Road, Dinghai District, Zhoushan, 316000 ZJ China
| | - Jianhua Liu
- Ocean College, Zhejiang University, Marine Science Building #379, Zhoushan Campus, 1 Zheda Road, Dinghai District, Zhoushan, 316000 ZJ China
- Ocean Research Center of Zhoushan, Zhejiang University, Zhoushan, 316021 ZJ China
| |
Collapse
|
32
|
High-Yield Production of Herbicidal Thaxtomins and Thaxtomin Analogs in a Nonpathogenic Streptomyces Strain. Appl Environ Microbiol 2018; 84:AEM.00164-18. [PMID: 29602787 DOI: 10.1128/aem.00164-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/27/2018] [Indexed: 12/13/2022] Open
Abstract
Thaxtomins are virulence factors of most plant-pathogenic Streptomyces strains. Due to their potent herbicidal activity, attractive environmental compatibility, and inherent biodegradability, thaxtomins are key active ingredients of bioherbicides approved by the U.S. Environmental Protection Agency. However, the low yield of thaxtomins in native Streptomyces producers limits their wide agricultural applications. Here, we describe the high-yield production of thaxtomins in a heterologous host. The thaxtomin gene cluster from S. scabiei 87.22 was cloned and expressed in S. albus J1074 after chromosomal integration. The production of thaxtomins and nitrotryptophan analogs was observed using liquid chromatography-mass spectrometry (LC-MS) analysis. When the engineered S. albus J1074 was cultured in the minimal medium Thx defined medium supplemented with 1% cellobiose (TDMc), the yield of the most abundant and herbicidal analog, thaxtomin A, was 10 times higher than that in S. scabiei 87.22, and optimization of the medium resulted in the highest yield of thaxtomin analogs at about 222 mg/liter. Further engineering of the thaxtomin biosynthetic gene cluster through gene deletion led to the production of multiple biosynthetic intermediates important to the chemical synthesis of new analogs. Additionally, the versatility of the thaxtomin biosynthetic system in S. albus J1074 was capitalized on to produce one unnatural fluorinated analog, 5-fluoro-thaxtomin A (5-F-thaxtomin A), whose structure was elucidated by a combination of MS and one-dimensional (1D) and 2D nuclear magnetic resonance (NMR) analyses. Natural and unnatural thaxtomins demonstrated potent herbicidal activity in radish seedling assays. These results indicated that S. albus J1074 has the potential to produce thaxtomins and analogs thereof with high yield, fostering their agricultural applications.IMPORTANCE Thaxtomins are agriculturally valuable herbicidal natural products, but the productivity of native producers is limiting. Heterologous expression of the thaxtomin gene cluster in S. albus J1074 resulted in the highest yield of thaxtomins ever reported, representing a significant leap forward in its wide agricultural use. Furthermore, current synthetic routes to thaxtomins and analogs are lengthy, and two thaxtomin biosynthetic intermediates produced at high yields in this work can provide precursors and building blocks to advanced synthetic routes. Importantly, the production of 5-F-thaxtomin A in engineered S. albus J1074 demonstrated a viable alternative to chemical methods in the synthesis of new thaxtomin analogs. Moreover, our work presents an attractive synthetic biology strategy to improve the supply of herbicidal thaxtomins, likely finding general applications in the discovery and production of many other bioactive natural products.
Collapse
|
33
|
Winn M, Francis D, Micklefield J. De novo Biosynthesis of “Non-Natural” Thaxtomin Phytotoxins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michael Winn
- School of Chemistry; Manchester Institute of Biotechnology; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Daniel Francis
- 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
| |
Collapse
|
34
|
Winn M, Francis D, Micklefield J. De novo Biosynthesis of "Non-Natural" Thaxtomin Phytotoxins. Angew Chem Int Ed Engl 2018; 57:6830-6833. [PMID: 29603527 PMCID: PMC6001691 DOI: 10.1002/anie.201801525] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 02/04/2023]
Abstract
Thaxtomins are diketopiperazine phytotoxins produced by Streptomyces scabies and other actinobacterial plant pathogens that inhibit cellulose biosynthesis in plants. Due to their potent bioactivity and novel mode of action there has been considerable interest in developing thaxtomins as herbicides for crop protection. To address the need for more stable derivatives, we have developed a new approach for structural diversification of thaxtomins. Genes encoding the thaxtomin NRPS from S. scabies, along with genes encoding a promiscuous tryptophan synthase (TrpS) from Salmonella typhimurium, were assembled in a heterologous host Streptomyces albus. Upon feeding indole derivatives to the engineered S. albus strain, tryptophan intermediates with alternative substituents are biosynthesized and incorporated by the NRPS to deliver a series of thaxtomins with different functionalities in place of the nitro group. The approach described herein, demonstrates how genes from different pathways and different bacterial origins can be combined in a heterologous host to create a de novo biosynthetic pathway to "non-natural" product target compounds.
Collapse
Affiliation(s)
- Michael Winn
- School of ChemistryManchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Daniel Francis
- School of ChemistryManchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Jason Micklefield
- School of ChemistryManchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| |
Collapse
|
35
|
Mishra AK, Choi J, Choi SJ, Baek KH. Cyclodipeptides: An Overview of Their Biosynthesis and Biological Activity. Molecules 2017; 22:molecules22101796. [PMID: 29065531 PMCID: PMC6151668 DOI: 10.3390/molecules22101796] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 01/06/2023] Open
Abstract
Cyclodipeptides (CDP) represent a diverse family of small, highly stable, cyclic peptides that are produced as secondary functional metabolites or side products of protein metabolism by bacteria, fungi, and animals. They are widespread in nature, and exhibit a broad variety of biological and pharmacological activities. CDP synthases (CDPSs) and non-ribosomal peptide synthetases (NRPSs) catalyze the biosynthesis of the CDP core structure, which is further modified by tailoring enzymes often associated with CDP biosynthetic gene clusters. In this review, we provide a comprehensive summary of CDP biosynthetic pathways and modifying enzymes. We also discuss the biological properties of some known CDPs and their possible applications in metabolic engineering.
Collapse
Affiliation(s)
- Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
| | - Jaehyuk Choi
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
| | - Seong-Jin Choi
- Department of Biotechnology, Daegu Catholic University, Gyeongsan 38430, Korea.
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
| |
Collapse
|
36
|
Coronafacoyl Phytotoxin Biosynthesis and Evolution in the Common Scab Pathogen Streptomyces scabiei. Appl Environ Microbiol 2017; 83:AEM.01169-17. [PMID: 28754703 DOI: 10.1128/aem.01169-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/19/2017] [Indexed: 01/08/2023] Open
Abstract
Coronafacoyl phytotoxins are an important family of plant toxins that are produced by several different phytopathogenic bacteria, including the gammaproteobacterium Pseudomonas syringae and the actinobacterium Streptomyces scabiei (formerly Streptomyces scabies). The phytotoxins consist of coronafacic acid (CFA) linked via an amide bond to different amino acids or amino acid derivatives. Previous work suggested that S. scabiei and P. syringae use distinct biosynthetic pathways for producing CFA, which is subsequently linked to its amino acid partner to form the complete phytotoxin. Here, we provide further evidence that the S. scabiei CFA biosynthetic pathway is novel by characterizing the role of CYP107AK1, a predicted cytochrome P450 that has no homologue in P. syringae Deletion of the CYP107AK1 gene abolished production of coronafacoyl-isoleucine (CFA-Ile), the primary coronafacoyl phytotoxin produced by S. scabiei Structural elucidation of accumulated biosynthetic intermediates in the ΔCYP107AK1 mutant indicated that CYP107AK1 is required for introducing the oxygen atom that ultimately forms the carbonyl group in the CFA backbone. The CYP107AK1 gene along with two additional genes involved in CFA-Ile biosynthesis in S. scabiei were found to be associated with putative CFA biosynthetic genes in other actinobacteria but not in other organisms. Analysis of the overall genetic content and organization of known and putative CFA biosynthetic gene clusters, together with phylogenetic analysis of the core biosynthetic genes, indicates that horizontal gene transfer has played an important role in the dissemination of the gene cluster and that rearrangement, insertion, and/or deletion events have likely contributed to the divergent biosynthetic evolution of coronafacoyl phytotoxins in bacteria.IMPORTANCE The ability of plants to defend themselves against invading pathogens relies on complex signaling pathways that are controlled by key phytohormones such as jasmonic acid (JA). Some phytopathogenic bacteria have evolved the ability to manipulate JA signaling in order to overcome host defenses by producing coronatine (COR), which functions as a potent JA mimic. COR and COR-like molecules, collectively referred to as coronafacoyl phytotoxins, are produced by several different plant-pathogenic bacteria, and this study provides supporting evidence that different biosynthetic pathways are utilized by different bacteria for production of these phytotoxins. In addition, our study provides a greater understanding of how coronafacoyl phytotoxin biosynthesis may have evolved in phylogenetically distinct bacteria, and we demonstrate that production of these compounds may be more widespread than previously recognized and that their role for the producing organism may not be limited to host-pathogen interactions.
Collapse
|
37
|
Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
Collapse
Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | | | | |
Collapse
|
38
|
Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
Collapse
Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| |
Collapse
|
39
|
Zhang Y, Bignell DRD, Zuo R, Fan Q, Huguet-Tapia JC, Ding Y, Loria R. Promiscuous Pathogenicity Islands and Phylogeny of Pathogenic Streptomyces spp. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:640-50. [PMID: 27502745 DOI: 10.1094/mpmi-04-16-0068-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Approximately 10 Streptomyces species cause disease on underground plant structures. The most economically important of these is potato scab, and the most studied of these pathogens is Streptomyces scabiei (syn. S. scabies). The main pathogenicity determinant of scab-causing Streptomyces species is a nitrated diketopiperazine, known as thaxtomin A (ThxA). In the pathogenic species Streptomyces turgidiscabies, ThxA biosynthetic genes reside on a mobile pathogenicity island (PAI). However, the mobilization of PAIs in other Streptomyces species remains uncharacterized. Here, we investigated the mobilization of the PAI of S. scabiei 87-22. Based on whole genome sequences, we inferred the evolutionary relationships of pathogenic Streptomyces species and discovered that Streptomyces sp. strain 96-12, a novel pathogenic species isolated from potatoes in Egypt, was phylogenetically grouped with nonpathogenic species rather than with known pathogenic species. We also found that Streptomyces sp. strain 96-12 contains a PAI that is almost identical to the PAI in S. scabiei 87-22, despite significant differences in their genome sequences. This suggested direct or indirect in vivo mobilization of the PAI between S. scabiei and nonpathogenic Streptomyces species. To test whether the S. scabiei 87-22 PAI could, indeed, be mobilized, S. scabiei 87-22 deletion mutants containing antibiotic resistance markers in the PAI were mated with Streptomyces diastatochromogenes, a nonpathogenic species. The PAI of S. scabiei was site-specifically inserted into the aviX1 gene of S. diastatochromogenes and conferred pathogenicity in radish seedling assays. Our results demonstrated that S. scabiei, the earliest described Streptomyces pathogen, could be the source of a PAI responsible for the emergence of novel pathogenic species.
Collapse
Affiliation(s)
- Yucheng Zhang
- 1 Department of Plant Pathology, University of Florida, Gainesville, Florida, U.S.A
| | - Dawn R D Bignell
- 2 Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Ran Zuo
- 3 Department of Medicinal Chemistry, University of Florida, Gainesville, Florida, U.S.A.; and
| | - Qiurong Fan
- 4 College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jose C Huguet-Tapia
- 1 Department of Plant Pathology, University of Florida, Gainesville, Florida, U.S.A
| | - Yousong Ding
- 3 Department of Medicinal Chemistry, University of Florida, Gainesville, Florida, U.S.A.; and
| | - Rosemary Loria
- 1 Department of Plant Pathology, University of Florida, Gainesville, Florida, U.S.A
| |
Collapse
|
40
|
McIntosh JA, Heel T, Buller AR, Chio L, Arnold FH. Structural Adaptability Facilitates Histidine Heme Ligation in a Cytochrome P450. J Am Chem Soc 2015; 137:13861-5. [PMID: 26299431 PMCID: PMC4635421 DOI: 10.1021/jacs.5b07107] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 11/29/2022]
Abstract
Almost all known members of the cytochrome P450 (CYP) superfamily conserve a key cysteine residue that coordinates the heme iron. Although mutation of this residue abolishes monooxygenase activity, recent work has shown that mutation to either serine or histidine unlocks non-natural carbene- and nitrene-transfer activities. Here we present the first crystal structure of a histidine-ligated P450. The T213A/C317H variant of the thermostable CYP119 from Sulfolobus acidocaldarius maintains heme iron coordination through the introduced ligand, an interaction that is accompanied by large changes in the overall protein structure. We also find that the axial cysteine C317 may be substituted with any other amino acid without abrogating folding and heme cofactor incorporation. Several of the axial mutants display unusual spectral features, suggesting that they have active sites with unique steric and electronic properties. These novel, highly stable enzyme active sites will be fruitful starting points for investigations of non-natural P450 catalysis and mechanisms.
Collapse
Affiliation(s)
- John A. McIntosh
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Thomas Heel
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Andrew R. Buller
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Linda Chio
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and
Chemical Engineering 210-41, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| |
Collapse
|
41
|
Arseneault T, Goyer C, Filion M. Pseudomonas fluorescens LBUM223 Increases Potato Yield and Reduces Common Scab Symptoms in the Field. PHYTOPATHOLOGY 2015; 105:1311-1317. [PMID: 25961336 DOI: 10.1094/phyto-12-14-0358-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Common scab of potato, caused by pathogenic Streptomyces spp., is an important disease not efficiently controlled by current methods. We previously demonstrated that Pseudomonas fluorescens LBUM223 reduces common scab development under controlled conditions through phenazine-1-carboxylic (PCA) production, leading to reduced thaxtomin A production by the pathogen, a key pathogenicity and virulence factor. Here, we aimed at determining if LBUM223 is able to increase potato yield and control common scab under field conditions, while characterizing the biocontrol mechanisms involved. We investigated if a reduction in pathogen soil populations, activation of induced systemic resistance in potato, and/or changes in txtA gene expression, involved in thaxtomin A biosynthesis in pathogenic Streptomyces spp. were involved in common scab control by LBUM223. Common scab symptoms were significantly reduced and total tuber weight increased by 46% using biweekly applications of LBUM223. LBUM223 did not reduce pathogen soil populations, nor was potato systemic defense-related gene expression significantly altered between treatments. However, a significant down-regulation of txtA expression occurred in the geocaulosphere. This is the first demonstration that a Pseudomonas strain can directly alter the transcriptional activity of a key pathogenesis gene in a plant pathogen under field conditions, contributing to disease control.
Collapse
Affiliation(s)
- Tanya Arseneault
- First and third authors: Université de Moncton, Department of Biology, Moncton, NB, Canada; and second author: Potato Research Center, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Claudia Goyer
- First and third authors: Université de Moncton, Department of Biology, Moncton, NB, Canada; and second author: Potato Research Center, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Martin Filion
- First and third authors: Université de Moncton, Department of Biology, Moncton, NB, Canada; and second author: Potato Research Center, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| |
Collapse
|
42
|
Johnston CW, Skinnider MA, Wyatt MA, Li X, Ranieri MRM, Yang L, Zechel DL, Ma B, Magarvey NA. An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products. Nat Commun 2015; 6:8421. [PMID: 26412281 PMCID: PMC4598715 DOI: 10.1038/ncomms9421] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 08/19/2015] [Indexed: 12/04/2022] Open
Abstract
Bacterial natural products are a diverse and valuable group of small molecules, and genome sequencing indicates that the vast majority remain undiscovered. The prediction of natural product structures from biosynthetic assembly lines can facilitate their discovery, but highly automated, accurate, and integrated systems are required to mine the broad spectrum of sequenced bacterial genomes. Here we present a genome-guided natural products discovery tool to automatically predict, combinatorialize and identify polyketides and nonribosomal peptides from biosynthetic assembly lines using LC–MS/MS data of crude extracts in a high-throughput manner. We detail the directed identification and isolation of six genetically predicted polyketides and nonribosomal peptides using our Genome-to-Natural Products platform. This highly automated, user-friendly programme provides a means of realizing the potential of genetically encoded natural products. Microbial natural products represent a large reservoir of potential pharmaceutical agents. Here, Johnston et al. describe a computer-automated programme for connecting genome sequences with identified and isolated natural products.
Collapse
Affiliation(s)
- Chad W Johnston
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Michael A Skinnider
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Morgan A Wyatt
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Xiang Li
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Michael R M Ranieri
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| | - Lian Yang
- The David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - David L Zechel
- Department of Chemistry; Queens University, Kingston, Ontario, Canada K7L 3N6
| | - Bin Ma
- The David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Nathan A Magarvey
- Department of Biochemistry &Biomedical Sciences, M. G. DeGroote Institute for Infectious Disease Research; McMaster University, Hamilton, Ontario, Canada L8N 3Z5.,Department of Chemistry &Chemical Biology, M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
| |
Collapse
|
43
|
Zhang C, Sheng C, Wang W, Hu H, Peng H, Zhang X. Identification of the Lomofungin Biosynthesis Gene Cluster and Associated Flavin-Dependent Monooxygenase Gene in Streptomyces lomondensis S015. PLoS One 2015; 10:e0136228. [PMID: 26305803 PMCID: PMC4549113 DOI: 10.1371/journal.pone.0136228] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023] Open
Abstract
Streptomyces lomondensis S015 synthesizes the broad-spectrum phenazine antibiotic lomofungin. Whole genome sequencing of this strain revealed a genomic locus consisting of 23 open reading frames that includes the core phenazine biosynthesis gene cluster lphzGFEDCB. lomo10, encoding a putative flavin-dependent monooxygenase, was also identified in this locus. Inactivation of lomo10 by in-frame partial deletion resulted in the biosynthesis of a new phenazine metabolite, 1-carbomethoxy-6-formyl-4,9-dihydroxy-phenazine, along with the absence of lomofungin. This result suggests that lomo10 is responsible for the hydroxylation of lomofungin at its C-7 position. This is the first description of a phenazine hydroxylation gene in Streptomyces, and the results of this study lay the foundation for further investigation of phenazine metabolite biosynthesis in Streptomyces.
Collapse
Affiliation(s)
- Chunxiao Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Chaolan Sheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- * E-mail:
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Huasong Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| |
Collapse
|
44
|
Giessen TW, Marahiel MA. Rational and combinatorial tailoring of bioactive cyclic dipeptides. Front Microbiol 2015; 6:785. [PMID: 26284060 PMCID: PMC4519757 DOI: 10.3389/fmicb.2015.00785] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/17/2015] [Indexed: 01/17/2023] Open
Abstract
Modified cyclic dipeptides represent a diverse family of microbial secondary metabolites. They display a broad variety of biological and pharmacological activities and have long been recognized as privileged structures with the ability to bind to a wide range of receptors. This is due to their conformationally constrained 2, 5-diketopiperazine (DKP) scaffold and the diverse set of DKP tailoring enzymes present in nature. After initial DKP assembly through different biosynthetic systems modifying enzymes are responsible for installing functional groups crucial for the biological activities of the resulting modified DKPs. They represent a vast and largely untapped enzyme repository very useful for synthetic biology approaches aiming at introducing structural variations into DKP scaffolds. In this review we focus on these DKP modification enzymes found in various microbial secondary metabolite gene clusters. We will give a brief overview of their distribution and highlight a select number of characterized DKP tailoring enzymes before turning to their application potential in combinatorial biosynthesis with the aim of producing molecules with improved or entirely new biological and medicinally relevant properties.
Collapse
Affiliation(s)
- Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston MA, USA ; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston MA, USA
| | - Mohamed A Marahiel
- Department of Chemistry, Philipps-University Marburg Marburg, Germany ; LOEWE Center for Synthetic Microbiology, Philipps-University Marburg Marburg, Germany
| |
Collapse
|
45
|
Giessen TW, Marahiel MA. The tRNA-dependent biosynthesis of modified cyclic dipeptides. Int J Mol Sci 2014; 15:14610-31. [PMID: 25196600 PMCID: PMC4159871 DOI: 10.3390/ijms150814610] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/01/2014] [Accepted: 08/18/2014] [Indexed: 01/28/2023] Open
Abstract
In recent years it has become apparent that aminoacyl-tRNAs are not only crucial components involved in protein biosynthesis, but are also used as substrates and amino acid donors in a variety of other important cellular processes, ranging from bacterial cell wall biosynthesis and lipid modification to protein turnover and secondary metabolite assembly. In this review, we focus on tRNA-dependent biosynthetic pathways that generate modified cyclic dipeptides (CDPs). The essential peptide bond-forming catalysts responsible for the initial generation of a CDP-scaffold are referred to as cyclodipeptide synthases (CDPSs) and use loaded tRNAs as their substrates. After initially discussing the phylogenetic distribution and organization of CDPS gene clusters, we will focus on structural and catalytic properties of CDPSs before turning to two recently characterized CDPS-dependent pathways that assemble modified CDPs. Finally, possible applications of CDPSs in the rational design of structural diversity using combinatorial biosynthesis will be discussed before concluding with a short outlook.
Collapse
Affiliation(s)
- Tobias W Giessen
- Department of Chemistry/Biochemistry and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Hans-Meerwein-Strasse-4, 35032 Marburg, Germany.
| | - Mohamed A Marahiel
- Department of Chemistry/Biochemistry and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Hans-Meerwein-Strasse-4, 35032 Marburg, Germany.
| |
Collapse
|
46
|
Structural insights into the mechanism for recognizing substrate of the cytochrome P450 enzyme TxtE. PLoS One 2013; 8:e81526. [PMID: 24282603 PMCID: PMC3840065 DOI: 10.1371/journal.pone.0081526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 10/14/2013] [Indexed: 11/19/2022] Open
Abstract
Thaxtomins, a family of phytotoxins produced by Streptomyces spp., can cause dramatic plant cell hypertrophy and seedling stunting. Thaxtomin A is the dominant form from Streptomyces scabies and has demonstrated herbicidal action. TxtE, a cytochrome P450 enzyme from Streptomyces scabies 87.22, catalyzes direct nitration of the indolyl moiety of L-tryptophan to L-4-nitrotryptophan using nitric oxide, dioxygen and NADPH. The crystal structure of TxtE was determined at 2.1 Å resolution and described in this work. A clearly defined substrate access channel is observed and can be classified as channel 2a, which is common in bacteria cytochrome P450 enzymes. A continuous hydrogen bond chain from the active site to the external solvent is observed. Compared with other cytochrome P450 enzymes, TxtE shows a unique proton transfer pathway which crosses the helix I distortion. Polar contacts of Arg59, Tyr89, Asn293, Thr296, and Glu394 with L-tryptophan are seen using molecular docking analysis, which are potentially important for substrate recognition and binding. After mutating Arg59, Asn293, Thr296 or Glu394 to leucine, the substrate binding ability of TxtE was lost or decreased significantly. Based on the docking and mutation results, a possible mechanism for substrate recognition and binding is proposed.
Collapse
|
47
|
Bignell D, Fyans J, Cheng Z. Phytotoxins produced by plant pathogenic Streptomyces
species. J Appl Microbiol 2013; 116:223-35. [DOI: 10.1111/jam.12369] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/11/2013] [Accepted: 10/12/2013] [Indexed: 01/18/2023]
Affiliation(s)
- D.R.D. Bignell
- Department of Biology; Memorial University of Newfoundland; St. John's NL Canada
| | - J.K. Fyans
- Department of Biology; Memorial University of Newfoundland; St. John's NL Canada
| | - Z. Cheng
- Department of Biology; Memorial University of Newfoundland; St. John's NL Canada
| |
Collapse
|
48
|
Arseneault T, Goyer C, Filion M. Phenazine production by Pseudomonas sp. LBUM223 contributes to the biological control of potato common scab. PHYTOPATHOLOGY 2013; 103:995-1000. [PMID: 23883153 DOI: 10.1094/phyto-01-13-0022-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Common scab of potato is mainly caused by Streptomyces scabies. Currently, no method can efficiently control this economically important disease. We have previously determined that Pseudomonas sp. LBUM223 exhibits antagonistic properties toward S. scabies under in vitro conditions. Inhibition was mainly attributed to phenazine-1-carboxylic acid (PCA) production because an isogenic mutant of LBUM223 (phzC-), not producing PCA, was incapable of significantly reducing S. scabies growth. In order to understand the impact of PCA production by LBUM223 in controlling common scab under soil conditions, pot experiments were performed to determine its effect on (i) reducing scab symptoms development, (ii) S. scabies population dynamics, and (iii) txtA expression in S. scabies, a key gene involved in thaxtomin A biosynthesis and required for pathogenesis. Symptoms were significantly reduced following inoculation with LBUM223 but not its mutant. Surprisingly, pathogen populations increased in the geocaulosphere in the presence of both wild-type and mutant strains of LBUM223; however, significant repression of txtA expression in S. scabies was only observed in the presence of PCA-producing LBUM223, not its mutant. These results suggest that, under soil conditions, PCA production by LBUM223 does not control common scab development by antibiosis but, instead, reduces S. scabies thaxtomin A production in the geocaulosphere, leading to reduced virulence.
Collapse
|
49
|
Gu B, He S, Yan X, Zhang L. Tentative biosynthetic pathways of some microbial diketopiperazines. Appl Microbiol Biotechnol 2013; 97:8439-53. [DOI: 10.1007/s00253-013-5175-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 01/20/2023]
|
50
|
Ba L, Li P, Zhang H, Duan Y, Lin Z. Engineering of a hybrid biotransformation system for cytochrome P450sca-2 in Escherichia coli. Biotechnol J 2013; 8:785-93. [PMID: 23744742 DOI: 10.1002/biot.201200097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/24/2013] [Accepted: 05/29/2013] [Indexed: 11/09/2022]
Abstract
P450sca-2 is an industrially important enzyme that stereoselectively converts mevastatin into pravastatin. However, little information or engineering efforts have been reported for this enzyme or its redox partner. In this study, we successfully reconstituted the P450sca-2 activity in Escherichia coli by co-expression with putidaredoxin reductase (Pdr) and putidaredoxin (Pdx) from the Pseudomonas putida cytochrome P450cam system. With an HPLC-based screening assay, random mutagenesis was applied to yield a mutant (R8-5C) with a pravastatin yield of the whole-cell biotransformation 4.1-fold that of the wild type. P450sca-2 wild-type and R8-5C were characterized in terms of mevastatin binding and hydroxylation, electron transfer, and circular dichroism spectroscopy. R8-5C showed an active P450 expression level that was 3.8-fold that of the wild type, with relatively smaller changes in the apparent k(cat)/K(M) with respect to the substrate mevastatin (1.3-fold) or Pdx (1.5-fold) compared with the wild type. Thus, the increase in the pravastatin yield of the whole-cell biotransformation primarily came from the improved active P450 expression, which has resulted largely from better heme incorporation, although none of the six mutations of R8-5C are located near the heme active site. These results will facilitate further engineering of this P450sca-2 system and provide useful clues for improving other hybrid P450 systems.
Collapse
Affiliation(s)
- Lina Ba
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes, Tsinghua University, Beijing, P.R. China
| | | | | | | | | |
Collapse
|