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Scholten N, Hartmann M, Abts S, Abts L, Reinartz E, Altavilla A, Müller TJJ, Zeier J. In-depth analysis of isochorismate synthase-derived metabolism in plant immunity: Identification of meta-substituted benzoates and salicyloyl-malate. J Biol Chem 2024; 300:107667. [PMID: 39128721 PMCID: PMC11416591 DOI: 10.1016/j.jbc.2024.107667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 07/24/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024] Open
Abstract
Isochorismate-derived metabolism enables biosynthesis of the plant defense hormone salicylic acid (SA) and its derivatives. In Arabidopsis thaliana, the stress-induced accumulation of SA depends on ISOCHORISMATE SYNTHASE1 (ICS1) and also requires the presumed isochorismate transporter ENHANCED DISEASE SUSCEPTIBILITY5 (EDS5) and the GH3 enzyme avrPphB SUSCEPTIBLE3 (PBS3). By comparative metabolite and structural analyses, we identified several hitherto unreported ICS1- and EDS5-dependent, biotic stress-inducible Arabidopsis metabolites. These involve meta-substituted SA derivatives (5-formyl-SA, 5-carboxy-SA, 5-carboxymethyl-SA), their benzoic acid (BA) analogs (3-formyl-BA, 3-carboxy-BA, 3-carboxymethyl-BA), and besides the previously detected salicyloyl-aspartate (SA-Asp), the ester conjugate salicyloyl-malate (SA-Mal). SA functions as a biosynthetic precursor for SA-Mal and SA-Asp, but not for the meta-substituted SA- and BA-derivatives, which accumulate to moderate levels at later stages of bacterial infection. Interestingly, Arabidopsis leaves possess oxidizing activity to effectively convert meta-formyl- into meta-carboxy-SA/BAs. In contrast to SA, exogenously applied meta-substituted SA/BA-derivatives and SA-Mal exert a moderate impact on plant immunity and defence-related gene expression. While the isochorismate-derived metabolites are negatively regulated by the SA receptor NON-EXPRESSOR OF PR GENES1, SA conjugates (SA-Mal, SA-Asp, SA-glucose conjugates) and meta-substituted SA/BA-derivatives are oppositely affected by PBS3. Notably, our data indicate a PBS3-independent path to isochorismate-derived SA at later stages of bacterial infection, which does not considerably impact immune-related characteristics. Moreover, our results argue against a previously proposed role of EDS5 in the biosynthesis of the immune signal N-hydroxypipecolic acid and associated transport processes. We propose a significantly extended biochemical scheme of plant isochorismate metabolism that involves an alternative generation mode for benzoate- and salicylate-derivatives.
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Affiliation(s)
- Nicola Scholten
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Michael Hartmann
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Sarah Abts
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Laura Abts
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Elke Reinartz
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Angelo Altavilla
- Department of Chemistry, Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Thomas J J Müller
- Department of Chemistry, Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Jürgen Zeier
- Department of Biology, Institute for Molecular Ecophysiology of Plants, Heinrich Heine University, Düsseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany.
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Kaari M, Manikkam R, Baskaran A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:448-467. [PMID: 35394575 DOI: 10.1007/s10126-022-10118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.
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Affiliation(s)
- Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India.
| | - Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
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Chen M, Pang B, Ding W, Zhao Q, Tang Z, Liu W. Investigation of 2,2'-Bipyridine Biosynthesis Reveals a Common Two-Component System for Aldehydes Production by Carboxylate Reduction. Org Lett 2022; 24:897-902. [PMID: 35044177 DOI: 10.1021/acs.orglett.1c04239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we report a two-component enzymatic system that efficiently catalyzes the reduction of a carboxylate to an aldehyde in the biosynthesis of 2,2'-bipyridine antibiotics caerulomycins. The associated paradigm involves the activation of carboxylate by ATP-dependent adenylation protein CaeF, followed by its reduction catalyzed by CaeB2, a new class of NADPH-dependent aldehyde dehydrogenase (ALDH) that directly reduces AMP-conjugated carboxylate, which is distinct from the known aldehyde-producing enzymes that reduce ACP- or CoA-conjugated carboxylates.
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Affiliation(s)
- Ming Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Bo Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wenping Ding
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qunfei Zhao
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.,Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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4
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Plaszkó T, Szűcs Z, Cziáky Z, Ács-Szabó L, Csoma H, Géczi L, Vasas G, Gonda S. Correlations Between the Metabolome and the Endophytic Fungal Metagenome Suggests Importance of Various Metabolite Classes in Community Assembly in Horseradish ( Armoracia rusticana, Brassicaceae) Roots. FRONTIERS IN PLANT SCIENCE 2022; 13:921008. [PMID: 35783967 PMCID: PMC9247618 DOI: 10.3389/fpls.2022.921008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/27/2022] [Indexed: 05/07/2023]
Abstract
The plant microbiome is an increasingly intensive research area, with significance in agriculture, general plant health, and production of bioactive natural products. Correlations between the fungal endophytic communities and plant chemistry can provide insight into these interactions, and suggest key contributors on both the chemical and fungal side. In this study, roots of various horseradish (Armoracia rusticana) accessions grown under the same conditions were sampled in two consecutive years and chemically characterized using a quality controlled, untargeted metabolomics approach by LC-ESI-MS/MS. Sinigrin, gluconasturtiin, glucoiberin, and glucobrassicin were also quantified. Thereafter, a subset of roots from eight accessions (n = 64) with considerable chemical variability was assessed for their endophytic fungal community, using an ITS2 amplicon-based metagenomic approach using a custom primer with high coverage on fungi, but no amplification of host internal transcribed spacer (ITS). A set of 335 chemical features, including putatively identified flavonoids, phospholipids, peptides, amino acid derivatives, indolic phytoalexins, a glucosinolate, and a glucosinolate downstream product was detected. Major taxa in horseradish roots belonged to Cantharellales, Glomerellales, Hypocreales, Pleosporales, Saccharomycetales, and Sordariales. Most abundant genera included typical endophytes such as Plectosphaerella, Thanatephorus, Podospora, Monosporascus, Exophiala, and Setophoma. A surprising dominance of single taxa was observed for many samples. In summary, 35.23% of reads of the plant endophytic fungal microbiome correlated with changes in the plant metabolome. While the concentration of flavonoid kaempferol glycosides positively correlated with the abundance of many fungal strains, many compounds showed negative correlations with fungi including indolic phytoalexins, a putative glucosinolate but not major glucosinolates and a glutathione isothiocyanate adduct. The latter is likely an in vivo glucosinolate decomposition product important in fungal arrest. Our results show the potency of the untargeted metabolomics approach in deciphering plant-microbe interactions and depicts a complex array of various metabolite classes in shaping the endophytic fungal community.
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Affiliation(s)
- Tamás Plaszkó
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Zsolt Szűcs
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Zoltán Cziáky
- Agricultural and Molecular Research and Service Institute, University of Nyíregyháza, Nyíregyháza, Hungary
| | - Lajos Ács-Szabó
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Hajnalka Csoma
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - László Géczi
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Gábor Vasas
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Sándor Gonda
- Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- *Correspondence: Sándor Gonda, ,
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Hubrich F, Müller M, Andexer JN. Chorismate- and isochorismate converting enzymes: versatile catalysts acting on an important metabolic node. Chem Commun (Camb) 2021; 57:2441-2463. [PMID: 33605953 DOI: 10.1039/d0cc08078k] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chorismate and isochorismate represent an important branching point connecting primary and secondary metabolism in bacteria, fungi, archaea and plants. Chorismate- and isochorismate-converting enzymes are potential targets for new bioactive compounds, as well as valuable biocatalysts for the in vivo and in vitro synthesis of fine chemicals. The diversity of the products of chorismate- and isochorismate-converting enzymes is reflected in the enzymatic three-dimensional structures and molecular mechanisms. Due to the high reactivity of chorismate and its derivatives, these enzymes have evolved to be accurately tailored to their respective reaction; at the same time, many of them exhibit a fascinating flexibility regarding side reactions and acceptance of alternative substrates. Here, we give an overview of the different (sub)families of chorismate- and isochorismate-converting enzymes, their molecular mechanisms, and three-dimensional structures. In addition, we highlight important results of mutagenetic approaches that generate a broader understanding of the influence of distinct active site residues for product formation and the conversion of one subfamily into another. Based on this, we discuss to what extent the recent advances in the field might influence the general mechanistic understanding of chorismate- and isochorismate-converting enzymes. Recent discoveries of new chorismate-derived products and pathways, as well as biocatalytic conversions of non-physiological substrates, highlight how this vast field is expected to continue developing in the future.
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Affiliation(s)
- Florian Hubrich
- ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
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Strategy for the Biosynthesis of Short Oligopeptides: Green and Sustainable Chemistry. Biomolecules 2019; 9:biom9110733. [PMID: 31766233 PMCID: PMC6920838 DOI: 10.3390/biom9110733] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023] Open
Abstract
Short oligopeptides are some of the most promising and functionally important amide bond-containing components, with widespread applications. Biosynthesis of these oligopeptides may potentially become the ultimate strategy because it has better cost efficiency and environmental-friendliness than conventional solid phase peptide synthesis and chemo-enzymatic synthesis. To successfully apply this strategy for the biosynthesis of structurally diverse amide bond-containing components, the identification and selection of specific biocatalysts is extremely important. Given that perspective, this review focuses on the current knowledge about the typical enzymes that might be potentially used for the synthesis of short oligopeptides. Moreover, novel enzymatic methods of producing desired peptides via metabolic engineering are highlighted. It is believed that this review will be helpful for technological innovation in the production of desired peptides.
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Pancrace C, Ishida K, Briand E, Pichi DG, Weiz AR, Guljamow A, Scalvenzi T, Sassoon N, Hertweck C, Dittmann E, Gugger M. Unique Biosynthetic Pathway in Bloom-Forming Cyanobacterial Genus Microcystis Jointly Assembles Cytotoxic Aeruginoguanidines and Microguanidines. ACS Chem Biol 2019; 14:67-75. [PMID: 30556994 DOI: 10.1021/acschembio.8b00918] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The cyanobacterial genus Microcystis is known to produce an elaborate array of structurally unique and biologically active natural products, including hazardous cyanotoxins. Cytotoxic aeruginoguanidines represent a yet unexplored family of peptides featuring a trisubstituted benzene unit and farnesylated arginine derivatives. In this study, we aimed at assigning these compounds to a biosynthetic gene cluster by utilizing biosynthetic attributes deduced from public genomes of Microcystis and the sporadic distribution of the metabolite in axenic strains of the Pasteur Culture Collection of Cyanobacteria. By integrating genome mining with untargeted metabolomics using liquid chromatography with mass spectrometry, we linked aeruginoguanidine (AGD) to a nonribosomal peptide synthetase gene cluster and coassigned a significantly smaller product to this pathway, microguanidine (MGD), previously only reported from two Microcystis blooms. Further, a new intermediate class of compounds named microguanidine amides was uncovered, thereby further enlarging this compound family. The comparison of structurally divergent AGDs and MGDs reveals an outstanding versatility of this biosynthetic pathway and provides insights into the assembly of the two compound subfamilies. Strikingly, aeruginoguanidines and microguanidines were found to be as widespread as the hepatotoxic microcystins, but the occurrence of both toxin families appeared to be mutually exclusive.
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Affiliation(s)
- Claire Pancrace
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
- UMR UPMC 113, CNRS 7618, IRD 242, INRA 1392, PARIS 7 113, UPEC, IEES Paris, 4 Place Jussieu, 75005 Paris, France
| | - Keishi Ishida
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Enora Briand
- Laboratoire Phycotoxines, Ifremer, rue de l’Ile d’Yeu, 44311 Nantes, France
| | - Douglas Gatte Pichi
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Annika R. Weiz
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Arthur Guljamow
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Thibault Scalvenzi
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Nathalie Sassoon
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Elke Dittmann
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Golm, Germany
| | - Muriel Gugger
- Collection des Cyanobactéries, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
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Abstract
Bacterial pathogens cause plant diseases that threaten the global food supply. To control diseases, it is important to understand how pathogenic bacteria evade plant defense and promote infection. We identify from the phytopathogen Pseudomonas syringae a small-molecule virulence factor—phevamine A. Both the chemical structure and mode of action of phevamine A are different from known bacterial phytotoxins. Phevamine A promotes bacterial growth by suppressing plant immune responses, including both early (the generation of reactive oxygen species) and late (the deposition of cell wall reinforcing callose in leaves and leaf cell death) markers. This work uncovers a widely distributed, small-molecule virulence factor and shows the power of a multidisciplinary approach to identify small molecules important for plant infection. Bacterial plant pathogens cause significant crop damage worldwide. They invade plant cells by producing a variety of virulence factors, including small-molecule toxins and phytohormone mimics. Virulence of the model pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) is regulated in part by the sigma factor HrpL. Our study of the HrpL regulon identified an uncharacterized, three-gene operon in Pto that is controlled by HrpL and related to the Erwinia hrp-associated systemic virulence (hsv) operon. Here, we demonstrate that the hsv operon contributes to the virulence of Pto on Arabidopsis thaliana and suppresses bacteria-induced immune responses. We show that the hsv-encoded enzymes in Pto synthesize a small molecule, phevamine A. This molecule consists of l-phenylalanine, l-valine, and a modified spermidine, and is different from known small molecules produced by phytopathogens. We show that phevamine A suppresses a potentiation effect of spermidine and l-arginine on the reactive oxygen species burst generated upon recognition of bacterial flagellin. The hsv operon is found in the genomes of divergent bacterial genera, including ∼37% of P. syringae genomes, suggesting that phevamine A is a widely distributed virulence factor in phytopathogens. Our work identifies a small-molecule virulence factor and reveals a mechanism by which bacterial pathogens overcome plant defense. This work highlights the power of omics approaches in identifying important small molecules in bacteria–host interactions.
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Ogasawara Y, Dairi T. Biosynthesis of Oligopeptides Using ATP-Grasp Enzymes. Chemistry 2017; 23:10714-10724. [PMID: 28488371 DOI: 10.1002/chem.201700674] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/08/2022]
Abstract
Peptides are biologically occurring oligomers of amino acids linked by amide bonds and are indispensable for all living organisms. Many bioactive peptides are used as antibiotics, antivirus agents, insecticides, pheromones, and food preservatives. Nature employs several different strategies to form amide bonds. ATP-grasp enzymes that catalyze amide bond formation (ATP-dependent carboxylate-amine ligases) utilize a strategy of activating carboxylic acid as an acylphosphate intermediate to form amide bonds and are involved in many different biological processes in both primary and secondary metabolisms. The recent discovery of several new ATP-dependent carboxylate-amine ligases has expanded the diversity of this group of enzymes and showed their usefulness for generating oligopeptides. In this review, an overview of findings on amide bond formation catalyzed by ATP-grasp enzymes in the past decade is presented.
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Affiliation(s)
- Yasushi Ogasawara
- Division of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
| | - Tohru Dairi
- Division of Applied Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido, 060-8628, Japan
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Abstract
Amides are widespread in biologically active compounds with a broad range of applications in biotechnology, agriculture and medicine. Therefore, as alternative to chemical synthesis the biocatalytic amide synthesis is a very interesting field of research. As usual, Nature can serve as guide in the quest for novel biocatalysts. Several mechanisms for carboxylate activation involving mainly acyl-adenylate, acyl-phosphate or acyl-enzyme intermediates have been discovered, but also completely different pathways to amides are found. In addition to ribosomes, selected enzymes of almost all main enzyme classes are able to synthesize amides. In this review we give an overview about amide synthesis in Nature, as well as biotechnological applications of these enzymes. Moreover, several examples of biocatalytic amide synthesis are given.
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Ross AC, Gulland LES, Dorrestein PC, Moore BS. Targeted capture and heterologous expression of the Pseudoalteromonas alterochromide gene cluster in Escherichia coli represents a promising natural product exploratory platform. ACS Synth Biol 2015; 4:414-20. [PMID: 25140825 PMCID: PMC4410906 DOI: 10.1021/sb500280q] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Marine
pseudoalteromonads represent a very promising source of
biologically important natural product molecules. To access and exploit
the full chemical capacity of these cosmopolitan Gram-(−) bacteria,
we sought to apply universal synthetic biology tools to capture, refactor,
and express biosynthetic gene clusters for the production of complex
organic compounds in reliable host organisms. Here, we report a platform
for the capture of proteobacterial gene clusters using a transformation-associated
recombination (TAR) strategy coupled with direct pathway manipulation
and expression in Escherichia coli. The ∼34
kb pathway for production of alterochromide lipopeptides by Pseudoalteromonas piscicida JCM 20779 was captured and heterologously
expressed in E. coli utilizing native and E. coli-based T7 promoter sequences. Our approach enabled
both facile production of the alterochromides and in vivo interrogation of gene function associated with alterochromide’s
unusual brominated lipid side chain. This platform represents a simple
but effective strategy for the discovery and biosynthetic characterization
of natural products from marine proteobacteria.
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Affiliation(s)
| | | | - Pieter C. Dorrestein
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, United States
| | - Bradley S. Moore
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, United States
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Whalen KE, Poulson-Ellestad KL, Deering RW, Rowley DC, Mincer TJ. Enhancement of antibiotic activity against multidrug-resistant bacteria by the efflux pump inhibitor 3,4-dibromopyrrole-2,5-dione isolated from a Pseudoalteromonas sp. JOURNAL OF NATURAL PRODUCTS 2015; 78:402-412. [PMID: 25646964 DOI: 10.1021/np500775e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Members of the resistance nodulation cell division (RND) of efflux pumps play essential roles in multidrug resistance (MDR) in Gram-negative bacteria. Here, we describe the search for new small molecules from marine microbial extracts to block efflux and thus restore antibiotic susceptibility in MDR bacterial strains. We report the isolation of 3,4-dibromopyrrole-2,5-dione (1), an inhibitor of RND transporters, from Enterobacteriaceae and Pseudomonas aeruginosa, from the marine bacterium Pseudoalteromonas piscicida. 3,4-Dibromopyrrole-2,5-dione decreased the minimum inhibitory concentrations (MICs) of two fluoroquinolones, an aminoglycoside, a macrolide, a beta-lactam, tetracycline, and chloramphenicol between 2- and 16-fold in strains overexpressing three archetype RND transporters (AcrAB-TolC, MexAB-OprM, and MexXY-OprM). 3,4-Dibromopyrrole-2,5-dione also increased the intracellular accumulation of Hoechst 33342 in wild-type but not in transporter-deficient strains and prevented H33342 efflux (IC50 = 0.79 μg/mL or 3 μM), a hallmark of efflux pump inhibitor (EPI) functionality. A metabolomic survey of 36 Pseudoalteromonas isolates mapped the presence of primarily brominated metabolites only within the P. piscicida phylogenetic clade, where a majority of antibiotic activity was also observed, suggesting a link between halogenation and enhanced secondary metabolite biosynthetic potential. In sum, 3,4-dibromopyrrole-2,5-dione is a potent EPI and deserves further attention as an adjuvant to enhance the effectiveness of existing antibiotics.
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Affiliation(s)
| | | | - Robert W Deering
- ‡College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - David C Rowley
- ‡College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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Goswami A, Van Lanen SG. Enzymatic strategies and biocatalysts for amide bond formation: tricks of the trade outside of the ribosome. MOLECULAR BIOSYSTEMS 2015; 11:338-53. [PMID: 25418915 PMCID: PMC4304603 DOI: 10.1039/c4mb00627e] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Amide bond-containing (ABC) biomolecules are some of the most intriguing and functionally significant natural products with unmatched utility in medicine, agriculture and biotechnology. The enzymatic formation of an amide bond is therefore a particularly interesting platform for engineering the synthesis of structurally diverse natural and unnatural ABC molecules for applications in drug discovery and molecular design. As such, efforts to unravel the mechanisms involved in carboxylate activation and substrate selection has led to the characterization of a number of structurally and functionally distinct protein families involved in amide bond synthesis. Unlike ribosomal synthesis and thio-templated synthesis using nonribosomal peptide synthetases, which couple the hydrolysis of phosphoanhydride bond(s) of ATP and proceed via an acyl-adenylate intermediate, here we discuss two mechanistically alternative strategies: ATP-dependent enzymes that generate acylphosphate intermediates and ATP-independent transacylation strategies. Several examples highlighting the function and synthetic utility of these amide bond-forming strategies are provided.
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Affiliation(s)
- Anwesha Goswami
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone, Lexington, KY 40536, USA.
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Petushkov VN, Dubinnyi MA, Tsarkova AS, Rodionova NS, Baranov MS, Kublitski VS, Shimomura O, Yampolsky IV. A novel type of luciferin from the Siberian luminous earthworm Fridericia heliota: structure elucidation by spectral studies and total synthesis. Angew Chem Int Ed Engl 2014; 53:5566-8. [PMID: 24737705 DOI: 10.1002/anie.201400529] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 02/18/2014] [Indexed: 11/05/2022]
Abstract
The structure elucidation and synthesis of the luciferin from the recently discovered luminous earthworm Fridericia heliota is reported. This luciferin is a key component of a novel ATP-dependent bioluminescence system. UV, fluorescence, NMR, and HRMS spectroscopy studies were performed on 0.005 mg of the isolated substance and revealed four isomeric structures that conform to spectral data. These isomers were chemically synthesized and one of them was found to produce light when reacted with a protein extract from F. heliota. The novel luciferin was found to have an unusual extensively modified peptidic nature, thus implying an unprecedented mechanism of action.
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Affiliation(s)
- Valentin N Petushkov
- Laboratory of Bioluminescent Biotechnologies, Institute of Fundamental Biology and Biotechnology, Siberian Federal University pr. Svobodnyi, 79, Krasnoyarsk 660041 (Russia); Laboratory of Photobiology, Institute of Biophysics, Siberian Branch of the Russian Academy of Sciences, Akademgorodok, Krasnoyarsk 660036 (Russia)
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Petushkov VN, Dubinnyi MA, Tsarkova AS, Rodionova NS, Baranov MS, Kublitski VS, Shimomura O, Yampolsky IV. A Novel Type of Luciferin from the Siberian Luminous EarthwormFridericia heliota: Structure Elucidation by Spectral Studies and Total Synthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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16
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Desriac F, Jégou C, Balnois E, Brillet B, Le Chevalier P, Fleury Y. Antimicrobial peptides from marine proteobacteria. Mar Drugs 2013; 11:3632-60. [PMID: 24084784 PMCID: PMC3826127 DOI: 10.3390/md11103632] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 07/30/2013] [Accepted: 08/05/2013] [Indexed: 01/03/2023] Open
Abstract
After years of inadequate use and the emergence of multidrug resistant (MDR) strains, the efficiency of "classical" antibiotics has decreased significantly. New drugs to fight MDR strains are urgently needed. Bacteria hold much promise as a source of unusual bioactive metabolites. However, the potential of marine bacteria, except for Actinomycetes and Cyanobacteria, has been largely underexplored. In the past two decades, the structures of several antimicrobial compounds have been elucidated in marine Proteobacteria. Of these compounds, polyketides (PKs), synthesised by condensation of malonyl-coenzyme A and/or acetyl-coenzyme A, and non-ribosomal peptides (NRPs), obtained through the linkage of (unusual) amino acids, have recently generated particular interest. NRPs are good examples of naturally modified peptides. Here, we review and compile the data on the antimicrobial peptides isolated from marine Proteobacteria, especially NRPs.
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Affiliation(s)
- Florie Desriac
- University of Brest, LUBEM EA 3882, SFR 148, Quimper 29000, France.
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Bacterial diversity associated with the tunic of the model chordate Ciona intestinalis. ISME JOURNAL 2013; 8:309-20. [PMID: 24048225 DOI: 10.1038/ismej.2013.156] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/07/2013] [Accepted: 07/29/2013] [Indexed: 01/09/2023]
Abstract
The sea squirt Ciona intestinalis is a well-studied model organism in developmental biology, yet little is known about its associated bacterial community. In this study, a combination of 454 pyrosequencing of 16S ribosomal RNA genes, catalyzed reporter deposition-fluorescence in situ hybridization and bacterial culture were used to characterize the bacteria living inside and on the exterior coating, or tunic, of C. intestinalis adults. The 454 sequencing data set demonstrated that the tunic bacterial community structure is different from that of the surrounding seawater. The observed tunic bacterial consortium contained a shared community of <10 abundant bacterial phylotypes across three individuals. Culture experiments yielded four bacterial strains that were also dominant groups in the 454 sequencing data set, including novel representatives of the classes Alphaproteobacteria and Flavobacteria. The relatively simple bacterial community and availability of dominant community members in culture make C. intestinalis a promising system in which to investigate functional interactions between host-associated microbiota and the development of host innate immunity.
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Kersten RD, Lane AL, Nett M, Richter TKS, Duggan BM, Dorrestein PC, Moore BS. Bioactivity-guided genome mining reveals the lomaiviticin biosynthetic gene cluster in Salinispora tropica. Chembiochem 2013; 14:955-62. [PMID: 23649992 DOI: 10.1002/cbic.201300147] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 12/27/2022]
Abstract
The use of genome sequences has become routine in guiding the discovery and identification of microbial natural products and their biosynthetic pathways. In silico prediction of molecular features, such as metabolic building blocks, physico-chemical properties or biological functions, from orphan gene clusters has opened up the characterization of many new chemo- and genotypes in genome mining approaches. Here, we guided our genome mining of two predicted enediyne pathways in Salinispora tropica CNB-440 by a DNA interference bioassay to isolate DNA-targeting enediyne polyketides. An organic extract of S. tropica showed DNA-interference activity that surprisingly was not abolished in genetic mutants of the targeted enediyne pathways, ST_pks1 and spo. Instead we showed that the product of the orphan type II polyketide synthase pathway, ST_pks2, is solely responsible for the DNA-interfering activity of the parent strain. Subsequent comparative metabolic profiling revealed the lomaiviticins, glycosylated diazofluorene polyketides, as the ST_pks2 products. This study marks the first report of the 59 open reading frame lomaiviticin gene cluster (lom) and supports the biochemical logic of their dimeric construction through a pathway related to the kinamycin monomer.
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Affiliation(s)
- Roland D Kersten
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204, USA
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Agarwal V, Pierce E, McIntosh J, Schmidt E, Nair S. Structures of Cyanobactin Maturation Enzymes Define a Family of Transamidating Proteases. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.chembiol.2012.09.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Wang J, Xiong Z, Meng H, Wang Y, Wang Y. Synthetic biology triggers new era of antibiotics development. Subcell Biochem 2012; 64:95-114. [PMID: 23080247 DOI: 10.1007/978-94-007-5055-5_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As a discipline to design and construct organisms with desired properties, synthetic biology has generated rapid progresses in the last decade. Combined synthetic biology with the traditional process, a new universal workflow for drug development has been becoming more and more attractive. The new methodology exhibits more efficient and inexpensive comparing to traditional methods in every aspect, such as new compounds discovery & screening, process design & drug manufacturing. This article reviews the application of synthetic biology in antibiotics development, including new drug discovery and screening, combinatorial biosynthesis to generate more analogues and heterologous expression of biosynthetic gene clusters with systematic engineering the recombinant microbial systems for large scale production.
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Affiliation(s)
- Jianfeng Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
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Abstract
Covering: 2010. Previous review: Nat. Prod. Rep., 2011, 28, 196. This review covers the literature published in 2010 for marine natural products, with 895 citations (590 for the period January to December 2010) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1003 for 2010), together with the relevant biological activities, source organisms and country of origin. Biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
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Du JZ, Long HY, Yuan YY, Song MM, Chen L, Bi H, Wang J. Micelle-to-vesicle morphological transition via light-induced rapid hydrophilic arm detachment from a star polymer. Chem Commun (Camb) 2011; 48:1257-9. [PMID: 22179503 DOI: 10.1039/c2cc16363b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Micelle-to-vesicle morphological transition has been achieved by light-induced rapid hydrophilic arm detachment from a star polymer. This provides a remote and clean method to control morphology transition of polymeric assemblies.
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Affiliation(s)
- Jin-Zhi Du
- CAS Key Laboratory of Soft Matter Chemistry and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China
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An ATP-grasp ligase involved in the last biosynthetic step of the iminomycosporine shinorine in Nostoc punctiforme ATCC 29133. J Bacteriol 2011; 193:5923-8. [PMID: 21890703 DOI: 10.1128/jb.05730-11] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the genetic basis for mycosporine sunscreen biosynthesis by the cyanobacterium Nostoc punctiforme ATCC 29133. Heterologous expression in Escherichia coli of three contiguous N. punctiforme genes (NpR5600, NpR5599, and NpR5598, here named mysA, mysB, and mysC, respectively) led to the production of mycosporine-glycine, an oxomycosporine. Additional expression of gene NpF5597 (mysD) led to the conversion of mycosporine-glycine into iminomycosporines (preferentially shinorine but also others like mycosporine-2-glycine and porphyra-334). This represents a new mode of enzymatic synthesis for iminomycosporines, one that differs in genetic origin, mechanism, and apparent substrate specificity from that known in Anabaena variabilis ATCC 29413. These results add to the emerging profile of the protein family of ATP-dependent ligases, to which the mysC product belongs, as important condensation enzymes in microbial secondary metabolism.
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Genome-based studies of marine microorganisms to maximize the diversity of natural products discovery for medical treatments. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2011; 2011:384572. [PMID: 21826184 PMCID: PMC3151524 DOI: 10.1155/2011/384572] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Revised: 04/15/2011] [Accepted: 06/03/2011] [Indexed: 01/22/2023]
Abstract
Marine microorganisms are rich source for natural products which play important roles in pharmaceutical industry. Over the past decade, genome-based studies of marine microorganisms have unveiled the tremendous diversity of the producers of natural products and also contributed to the efficiency of harness the strain diversity and chemical diversity, as well as the genetic diversity of marine microorganisms for the rapid discovery and generation of new natural products. In the meantime, genomic information retrieved from marine symbiotic microorganisms can also be employed for the discovery of new medical molecules from yet-unculturable microorganisms. In this paper, the recent progress in the genomic research of marine microorganisms is reviewed; new tools of genome mining as well as the advance in the activation of orphan pathways and metagenomic studies are summarized. Genome-based research of marine microorganisms will maximize the biodiscovery process and solve the problems of supply and sustainability of drug molecules for medical treatments.
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Winter JM, Behnken S, Hertweck C. Genomics-inspired discovery of natural products. Curr Opin Chem Biol 2010; 15:22-31. [PMID: 21111667 DOI: 10.1016/j.cbpa.2010.10.020] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 10/15/2010] [Indexed: 12/30/2022]
Abstract
The massive surge in genome sequencing projects has opened our eyes to the overlooked biosynthetic potential and metabolic diversity of microorganisms. While traditional approaches have been successful at identifying many useful therapeutic agents from these organisms, new tactics are needed in order to exploit their true biosynthetic potential. Several genomics-inspired strategies have been successful in unveiling new metabolites that were overlooked under standard fermentation and detection conditions. In addition, genome sequences have given us valuable insight for genetically engineering biosynthesis gene clusters that remain silent or are poorly expressed in the absence of a specific trigger. As more genome sequences are becoming available, we are noticing the emergence of underexplored or neglected organisms as alternative resources for new therapeutic agents.
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Affiliation(s)
- Jaclyn M Winter
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena D-07745, Germany
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Penesyan A, Kjelleberg S, Egan S. Development of novel drugs from marine surface associated microorganisms. Mar Drugs 2010; 8:438-59. [PMID: 20411108 PMCID: PMC2857370 DOI: 10.3390/md8030438] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 02/03/2010] [Accepted: 02/22/2010] [Indexed: 11/16/2022] Open
Abstract
While the oceans cover more than 70% of the Earth's surface, marine derived microbial natural products have been largely unexplored. The marine environment is a habitat for many unique microorganisms, which produce biologically active compounds ("bioactives") to adapt to particular environmental conditions. For example, marine surface associated microorganisms have proven to be a rich source for novel bioactives because of the necessity to evolve allelochemicals capable of protecting the producer from the fierce competition that exists between microorganisms on the surfaces of marine eukaryotes. Chemically driven interactions are also important for the establishment of cross-relationships between microbes and their eukaryotic hosts, in which organisms producing antimicrobial compounds ("antimicrobials"), may protect the host surface against over colonisation in return for a nutrient rich environment. As is the case for bioactive discovery in general, progress in the detection and characterization of marine microbial bioactives has been limited by a number of obstacles, such as unsuitable culture conditions, laborious purification processes, and a lack of de-replication. However many of these limitations are now being overcome due to improved microbial cultivation techniques, microbial (meta-) genomic analysis and novel sensitive analytical tools for structural elucidation. Here we discuss how these technical advances, together with a better understanding of microbial and chemical ecology, will inevitably translate into an increase in the discovery and development of novel drugs from marine microbial sources in the future.
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Affiliation(s)
- Anahit Penesyan
- School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio-Innovation, University of New South Wales, Sydney 2052, Australia; E-Mails:
(A.P.);
(S.K.)
| | - Staffan Kjelleberg
- School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio-Innovation, University of New South Wales, Sydney 2052, Australia; E-Mails:
(A.P.);
(S.K.)
| | - Suhelen Egan
- School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio-Innovation, University of New South Wales, Sydney 2052, Australia; E-Mails:
(A.P.);
(S.K.)
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