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Zotchev SB. Unlocking the potential of bacterial endophytes from medicinal plants for drug discovery. Microb Biotechnol 2024; 17:e14382. [PMID: 38345183 PMCID: PMC10884874 DOI: 10.1111/1751-7915.14382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/02/2023] [Accepted: 11/20/2023] [Indexed: 02/24/2024] Open
Abstract
Among the plant-associated microorganisms, the so-called endophytes continue to attract much attention because of their ability not only to protect host plants from biotic and abiotic stress factors, but also the potential to produce bioactive secondary metabolites. The latter property can elicit growth-promoting effects on plants, as well as boost the production of plant-specific secondary metabolites with valuable pharmacological properties. In addition, endophyte-derived secondary metabolites may be a rich source for the discovery of drugs to treat various diseases, including infections and cancer. However, the full potential of endophytes to produce bioactive secondary metabolites is often not revealed upon conventional cultivation in the laboratory. New advances in genomics and metabolic engineering offer exciting opportunities for the exploration and exploitation of endophytes' biosynthetic potential. This review focuses on bacterial endophytes of medicinal plants, some of their secondary metabolites and recent advances in deciphering their biosynthesis. The latter may assist in genetic engineering efforts aimed at the discovery of novel bioactive compounds with the potential to be developed into drugs.
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Affiliation(s)
- Sergey B. Zotchev
- Division of Pharmacognosy, Department of Pharmaceutical SciencesUniversity of ViennaViennaAustria
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2
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He HY, Niikura H, Du YL, Ryan KS. Synthetic and biosynthetic routes to nitrogen-nitrogen bonds. Chem Soc Rev 2022; 51:2991-3046. [PMID: 35311838 DOI: 10.1039/c7cs00458c] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nitrogen-nitrogen bond is a core feature of diverse functional groups like hydrazines, nitrosamines, diazos, and pyrazoles. Such functional groups are found in >300 known natural products. Such N-N bond-containing functional groups are also found in significant percentage of clinical drugs. Therefore, there is wide interest in synthetic and enzymatic methods to form nitrogen-nitrogen bonds. In this review, we summarize synthetic and biosynthetic approaches to diverse nitrogen-nitrogen-bond-containing functional groups, with a focus on biosynthetic pathways and enzymes.
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Affiliation(s)
- Hai-Yan He
- Department of Chemistry, University of British Columbia, Vancouver, Canada. .,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Haruka Niikura
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
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3
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Peng J, Lelis T, Chen R, Barphagha I, Osti S, Ham JH. tepR encoding a bacterial enhancer-binding protein orchestrates the virulence and interspecies competition of Burkholderia glumae through qsmR and a type VI secretion system. MOLECULAR PLANT PATHOLOGY 2020; 21:1042-1054. [PMID: 32608174 PMCID: PMC7368122 DOI: 10.1111/mpp.12947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/23/2020] [Accepted: 05/04/2020] [Indexed: 05/05/2023]
Abstract
The pathogenesis of the rice pathogenic bacterium Burkholderia glumae is under the tight regulation of the tofI/tofR quorum-sensing (QS) system. tepR, encoding a group I bacterial enhancer-binding protein, negatively regulates the production of toxoflavin, the phytotoxin acting as a major virulence factor in B. glumae. In this study, through a transcriptomic analysis, we identified the genes that were modulated by tepR and/or the tofI/tofR QS system. More than half of the differentially expressed genes, including the genes for the biosynthesis and transport of toxoflavin, were significantly more highly expressed in the ΔtepR mutant but less expressed in the ΔtofI-tofR (tofI/tofR QS-defective) mutant. In consonance with the transcriptome data, other virulence-related functions of B. glumae, extracellular protease activity and flagellum-dependent motility, were also negatively regulated by tepR, and this negative regulatory function of tepR was dependent on the IclR-type transcriptional regulator gene qsmR. Likewise, the ΔtepR mutant exhibited a higher level of heat tolerance in congruence with the higher transcription levels of heat shock protein genes in the mutant. Interestingly, tepR also exhibited its positive regulatory function on a previously uncharacterized type VI secretion system (denoted as BgT6SS-1). The survival of the both ΔtepR and ΔtssD (BgT6SS-1-defective) mutants was significantly compromised compared to the wild-type parent strain 336gr-1 in the presence of the natural rice-inhabiting bacterium, Pantoea sp. RSPAM1. Taken together, this study revealed pivotal regulatory roles of tepR in orchestrating multiple biological functions of B. glumae, including pathogenesis, heat tolerance, and bacterial interspecies competition.
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Affiliation(s)
- Jingyu Peng
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMI48824USA
| | - Tiago Lelis
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Tropical Research and Education CenterInstitute of Food and Agriculture SciencesUniversity of FloridaHomesteadFLUSA
| | - Ruoxi Chen
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
1501 Capitol AvenueSacramentoCA95814USA
| | - Inderjit Barphagha
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Surendra Osti
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
Department of Agricultural Economics and AgribusinessLouisiana State UniversityBaton RougeLA70803USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
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Hussain A, Shahbaz M, Tariq M, Ibrahim M, Hong X, Naeem F, Khalid Z, Raza HMZ, Bo Z, Bin L. Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin. Comput Biol Chem 2020; 86:107245. [PMID: 32172200 DOI: 10.1016/j.compbiolchem.2020.107245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 12/29/2022]
Abstract
Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from rice plant as the reference. Re-sequencing results revealed that the genome of strain AU6208 comprised 96 contigs corresponding to a 6.1 Mbp genome of the strain AU6208, with 5322 coding sequences and 68.2 % GC content; this is much larger compared to the genome previously sequenced by us and described by Seo et al (2015), which was reported to be 4.1 Mbp comprising >1200 contigs, 4361 coding sequences, and 67.31 % GC content. Moreover, this updated genome shares >80 % identity to the 7.2 Mbp genome of BGR1, which encodes 6491 coding sequences and has 68.3 % GC content. Further computational analysis revealed that the strain AU6208 encodes several bacteriocin biosynthesis genes, antibiotic, as well as virulent genes such as toxoflavin genes, which included 425 specialty genes and 12 toxoflavin genes. Upon further characterization, 12 toxoflavins (ToxA, B, C, D, E, F, G, H, I, J, TofI, and TofR) were found in AU6208 with 70-100 % sequence, family, and domain similarity with that of BGR1. Upon comparison with BGR1, the structural characterizations of selected toxoflavin genes (ToxB, ToxC, ToxG, H, and TofI) revealed variations in 2D and 3D structures such as differences in α-helix, β-sheets, loops, physiological properties of proteins, RMSD values, etc. These variations may play significant role in different mode of action in different hosts thereby indicating that in addition to their respective hosts, toxoflavins could also contribute to exploit other hosts across the kingdom. In addition to understanding the epidemiology of strain AU6208, this updated genomics data will also unfold the pathogenicity of bacteria in diversity of various hosts and anti-virulence.
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Affiliation(s)
- Annam Hussain
- State Key Laboratory of Rice Biology and Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China; Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Maham Shahbaz
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Maria Tariq
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Muhammad Ibrahim
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Xianxian Hong
- State Key Laboratory of Rice Biology and Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Faryal Naeem
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Zunera Khalid
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Hafiz Muhammad Zeeshan Raza
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Pakistan
| | - Zhu Bo
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| | - Li Bin
- State Key Laboratory of Rice Biology and Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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Moon K, Xu F, Zhang C, Seyedsayamdost MR. Bioactivity-HiTES Unveils Cryptic Antibiotics Encoded in Actinomycete Bacteria. ACS Chem Biol 2019; 14:767-774. [PMID: 30830740 DOI: 10.1021/acschembio.9b00049] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria harbor an immense reservoir of potentially new and therapeutic small molecules in the form of "silent" biosynthetic gene clusters (BGCs). These BGCs can be identified bioinformatically but are sparingly expressed under normal laboratory growth conditions, or not at all, and therefore do not produce significant levels of the corresponding small molecule product. Several methods have been developed for activating silent BGCs. A major limitation for nearly all methods is that they require genetic procedures and/or do not report on the bioactivity of the cryptic metabolite. We herein report "Bioactivty-HiTES", an approach that links the bioactivity of cryptic metabolites to their induction while at the same time obviating the need for genetic manipulations. Using this method, we detected induction of cryptic antibiotics in three actinomycete strains that were tested. Follow-up studies in one case allowed us to structurally elucidate two cryptic metabolites, elicited by the β-blocker atenolol in Streptomyces hiroshimensis, with selective growth-inhibitory activity against Gram-negative bacteria, notably Escherichia coli and Acinetobacter baumannii. Atenolol turned out to be a global elicitor of secondary metabolism, and characterization of additional cryptic metabolites led to the discovery of a novel naphthoquinone epoxide. Bioactivity-HiTES is a general, widely applicable procedure that will be useful in identifying cryptic bioactive metabolites in the future.
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Affiliation(s)
- Kyuho Moon
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Fei Xu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Chen Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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6
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Su C, Yan Y, Guo X, Luo J, Liu C, Zhang Z, Xiang WS, Huang SX. Characterization of the N-methyltransferases involved in the biosynthesis of toxoflavin, fervenulin and reumycin from Streptomyces hiroshimensis ATCC53615. Org Biomol Chem 2019; 17:477-481. [PMID: 30565634 DOI: 10.1039/c8ob02847h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Toxoflavin (1), fervenulin (2), and reumycin (3), known to be produced by plant pathogen Burkholderia glumae BGR1, are structurally related 7-azapteridine antibiotics. Previous biosynthetic studies revealed that N-methyltransferase ToxA from B. glumae BGR1 catalyzed the sequential methylation at N6 and N1 in pyrimido[5,4-e]-as-triazine-5,7(6H,8H)-dione (4) to generate 1. However, the N8 methylation of 4 in the biosynthesis of fervenulin remains unclear. To explore the N-methyltransferases required for the biosynthesis of 1 and 2, we identified and characterized the fervenulin and toxoflavin biosynthetic gene clusters in S. hiroshimensis ATCC53615. On the basis of the structures of intermediates accumulated from the four N-methyltransferase gene inactivation mutants and systematic enzymatic methylation reactions, the tailoring steps for the methylation order in the biosynthesis of 1 and 2 were proposed. The N-methylation order and routes for the biosynthesis of fervenulin and toxoflavin in S. hiroshimensis are more complex and represent an obvious departure from those in B. glumae BGR1.
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Affiliation(s)
- Can Su
- State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
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7
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Baldeweg F, Hoffmeister D, Nett M. A genomics perspective on natural product biosynthesis in plant pathogenic bacteria. Nat Prod Rep 2019; 36:307-325. [DOI: 10.1039/c8np00025e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This review summarizes findings from genomics-inspired natural product research in plant pathogenic bacteria and discusses emerging trends in this field.
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Affiliation(s)
- Florian Baldeweg
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute
- Friedrich-Schiller-University Jena
- 07745 Jena
- Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute
- Friedrich-Schiller-University Jena
- 07745 Jena
- Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering
- TU Dortmund University
- 44227 Dortmund
- Germany
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8
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Fenwick MK, Ealick SE. Towards the structural characterization of the human methyltransferome. Curr Opin Struct Biol 2018; 53:12-21. [DOI: 10.1016/j.sbi.2018.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/06/2018] [Indexed: 10/17/2022]
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9
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Fenwick MK, Almabruk KH, Ealick SE, Begley TP, Philmus B. Biochemical Characterization and Structural Basis of Reactivity and Regioselectivity Differences between Burkholderia thailandensis and Burkholderia glumae 1,6-Didesmethyltoxoflavin N-Methyltransferase. Biochemistry 2017; 56:3934-3944. [PMID: 28665591 DOI: 10.1021/acs.biochem.7b00476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Burkholderia glumae converts the guanine base of guanosine triphosphate into an azapteridine and methylates both the pyrimidine and triazine rings to make toxoflavin. Strains of Burkholderia thailandensis and Burkholderia pseudomallei have a gene cluster encoding seven putative biosynthetic enzymes that resembles the toxoflavin gene cluster. Four of the enzymes are similar in sequence to BgToxBCDE, which have been proposed to make 1,6-didesmethyltoxoflavin (1,6-DDMT). One of the remaining enzymes, BthII1283 in B. thailandensis E264, is a predicted S-adenosylmethionine (SAM)-dependent N-methyltransferase that shows a low level of sequence identity to BgToxA, which sequentially methylates N6 and N1 of 1,6-DDMT to form toxoflavin. Here we show that, unlike BgToxA, BthII1283 catalyzes a single methyl transfer to N1 of 1,6-DDMT in vitro. In addition, we investigated the differences in reactivity and regioselectivity by determining crystal structures of BthII1283 with bound S-adenosylhomocysteine (SAH) or 1,6-DDMT and SAH. BthII1283 contains a class I methyltransferase fold and three unique extensions used for 1,6-DDMT recognition. The active site structure suggests that 1,6-DDMT is bound in a reduced form. The plane of the azapteridine ring system is orthogonal to its orientation in BgToxA. In BthII1283, the modeled SAM methyl group is directed toward the p orbital of N1, whereas in BgToxA, it is first directed toward an sp2 orbital of N6 and then toward an sp2 orbital of N1 after planar rotation of the azapteridine ring system. Furthermore, in BthII1283, N1 is hydrogen bonded to a histidine residue whereas BgToxA does not supply an obvious basic residue for either N6 or N1 methylation.
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Affiliation(s)
- Michael K Fenwick
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Khaled H Almabruk
- College of Pharmacy, Oregon State University , Corvallis, Oregon 97331, United States
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - Benjamin Philmus
- College of Pharmacy, Oregon State University , Corvallis, Oregon 97331, United States
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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: 98] [Impact Index Per Article: 14.0] [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.
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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
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