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Duport C, Armengaud J, Schmitt C, Morin D, Lacapère JJ. Elucidating the pivotal role of TSPO in porphyrin-related cellular processes, in Bacillus cereus. Biochimie 2024:S0300-9084(24)00046-4. [PMID: 38423451 DOI: 10.1016/j.biochi.2024.02.008] [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: 01/11/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
A structural homolog of the mammalian TSPO has been identified in the human pathogen Bacillus cereus. BcTSPO, in its recombinant form, has previously been shown to bind and degrade porphyrins. In this study, we generated a ΔtspO mutant strain in B. cereus ATCC 14579 and assessed the impact of the absence of BcTSPO on cellular proteomics and physiological characteristics. The proteomic analysis revealed correlations between the lack of BcTSPO and the observed growth defects, increased oxygen consumption, ATP deficiency, heightened tryptophan catabolism, reduced motility, and impaired biofilm formation in the ΔtspO mutant strain. Our results also suggested that BcTSPO plays a crucial role in regulating intracellular levels of metabolites from the coproporphyrin-dependent branch of the heme biosynthetic pathway. This regulation potentially underlies alterations in the metabolic landscape, emphasizing the pivotal role of BcTSPO in B. cereus aerobic metabolism. Notably, our study unveils, for the first time, the involvement of TSPO in tryptophan metabolism. These findings underscore the multifaceted role of TSPO, not only in metabolic pathways but also potentially in the microorganism's virulence mechanisms.
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Affiliation(s)
| | - Jean Armengaud
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
| | - Caroline Schmitt
- Assistance Publique Hôpitaux de Paris (AP-HP), Centre Français des Porphyries, Hôpital Louis Mourier, 92700, Colombes, France; INSERM U1149, Center for Research on Inflammation (CRI), Université de Paris, 75018, Paris, France
| | - Didier Morin
- INSERM, U955, équipe 3, Faculté de Médecine, Université Paris Est, 94010, Creteil, France
| | - Jean-Jacques Lacapère
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS UMR 7203, Laboratoire des BioMolécules (LBM), 4 place Jussieu, F-75005, Paris, France
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2
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Liu J, Xi K, Zhang L, Han M, Wang Q, Liu X. Tryptophan metabolites and gut microbiota play an important role in pediatric migraine diagnosis. J Headache Pain 2024; 25:2. [PMID: 38177986 PMCID: PMC10768287 DOI: 10.1186/s10194-023-01708-9] [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: 10/08/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND The pathogenesis of pediatric migraine remains unclear and presents challenges in diagnosis. Recently, growing evidence has indicated that the gut microbiota can exert modulatory functions at the gut-brain axis by directly or indirectly regulating tryptophan metabolism. Consequently, we aimed to elucidate the potential association among gut microbiota, tryptophan metabolism, and pediatric migraine while also identifying diagnostic biomarkers for pediatric migraine. METHODS The gut microbiota composition of 33 migraine children and 42 healthy children, aged less than ten years, from the GMrepo database, was analyzed using the Shannon index, Simpson index, principal coordinates analysis, and Wilcoxon rank-sum test. Microbial diagnostic biomarkers were identified using linear discriminant analysis effect size, ridge regression, and random forest. Plasma concentrations of tryptophan metabolites investigated by enzyme-linked immunosorbent assay were compared between 51 migraine children and 120 healthy children, aged less than eighteen years, using t tests and analysis of variance. The receiver operating characteristic curve was performed to evaluate the diagnostic value of microbial and metabolite biomarkers in pediatric migraine. RESULTS Differences in the composition of gut microbiota, notably the genera that regulate tryptophan metabolism, were observed in pediatric migraine children. Further investigations revealed a significant decrease in plasma kynurenic acid levels (p < 0.001) among migraine children, along with a significant increase in serotonin (p < 0.05) and quinolinic acid (p < 0.001). Subsequently, we established the normal reference intervals for plasma concentrations of tryptophan metabolites in children. More importantly, the ratio of kynurenic acid to quinolinic acid (AUC: 0.871, sensitivity: 86.3%, specificity: 83.3%) exhibited excellent diagnostic efficacy for pediatric migraine. CONCLUSION Our study suggests that the gut microbiota may play an important role in the development of pediatric migraine by regulating tryptophan metabolism. We believe that microbial and metabolite biomarkers are sensitive diagnostic tests for pediatric migraine. TRIAL REGISTRATION The study was registered at ClinicalTrials.gov (NCT05969990).
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Affiliation(s)
- Junhui Liu
- Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012, Shandong Province, China
| | - Kaiyan Xi
- Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012, Shandong Province, China
| | - Linlin Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012, Shandong Province, China
| | - Mugu Han
- Shandong First Medical University Affiliated Provincial Hospital, Huaiyin Distinct, Jingwuweiliu Road, Jinan, 250021, Shandong Province, China
| | - Qingran Wang
- Qilu Hospital of Shandong University Dezhou Hospital, 1166 Dongfanghong West Road, Decheng District, Dezhou, 253000, Shandong Province, China
| | - Xinjie Liu
- Department of Pediatrics, Qilu Hospital of Shandong University, No.107 West Wenhua Road, Jinan, 250012, Shandong Province, China.
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3
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Donoso-Piñol P, Briceño G, Evaristo JAM, Nogueira FCS, Leiva B, Lamilla C, Schalchli H, Diez MC. Metabolic Profiling and Comparative Proteomic Insight in Respect of Amidases during Iprodione Biodegradation. Microorganisms 2023; 11:2367. [PMID: 37894025 PMCID: PMC10608976 DOI: 10.3390/microorganisms11102367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The fungicide iprodione (IPR) (3-(3,5-dichlorophenyl) N-isopropyl-2,4-dioxoimidazolidine-1-carboxamide) is a highly toxic compound. Although IPR has been restricted, it is still being applied in many places around the world, constituting an environmental risk. The biodegradation of IPR is an attractive option for reducing its residues. In this study, we isolated thirteen IPR-tolerant bacteria from a biopurification system designed to treat pesticides. A study of biodegradation using different strains was comparatively evaluated, and the best degradation rate of IPR was presented by Achromobacter sp. C1 with a half-life (T1/2) of 9 days. Based on a nano-LC-MS/MS analysis for the strains, proteins solely expressed in the IPR treatment were identified by highlighting the strain Achromobacter sp. C1, with 445 proteins primarily involved in the biosynthesis of secondary metabolites and microbial metabolism in diverse environments. Differentially expressed protein amidases were involved in six metabolic pathways. Interestingly, formamidase was inhibited while other cyclases, i.e., amidase and mandelamide hydrolase, were overexpressed, thereby minimizing the effect of IPR on the metabolism of strain C1. The dynamic changes in the protein profiles of bacteria that degrade IPR have been poorly studied; therefore, our results offer new insight into the metabolism of IPR-degrading microorganisms, with special attention paid to amidases.
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Affiliation(s)
- Pamela Donoso-Piñol
- Doctoral Program in Science of Natural Resources, University of La Frontera, Temuco 4780000, Chile; (P.D.-P.); (B.L.)
| | - Gabriela Briceño
- Department of Chemistry Science and Natural Resources, University of La Frontera, Temuco 4780000, Chile
- Biotechnological Research Centre Applied to the Environment (CIBAMA-BIOREN), University of La Frontera, Temuco 4780000, Chile; (C.L.); (H.S.)
| | - Joseph A. M. Evaristo
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 22775-000, Brazil; (J.A.M.E.); (F.C.S.N.)
| | - Fábio C. S. Nogueira
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 22775-000, Brazil; (J.A.M.E.); (F.C.S.N.)
| | - Barbara Leiva
- Doctoral Program in Science of Natural Resources, University of La Frontera, Temuco 4780000, Chile; (P.D.-P.); (B.L.)
- Biotechnological Research Centre Applied to the Environment (CIBAMA-BIOREN), University of La Frontera, Temuco 4780000, Chile; (C.L.); (H.S.)
| | - Claudio Lamilla
- Biotechnological Research Centre Applied to the Environment (CIBAMA-BIOREN), University of La Frontera, Temuco 4780000, Chile; (C.L.); (H.S.)
| | - Heidi Schalchli
- Biotechnological Research Centre Applied to the Environment (CIBAMA-BIOREN), University of La Frontera, Temuco 4780000, Chile; (C.L.); (H.S.)
| | - María Cristina Diez
- Biotechnological Research Centre Applied to the Environment (CIBAMA-BIOREN), University of La Frontera, Temuco 4780000, Chile; (C.L.); (H.S.)
- Department of Chemical Engineering, University of La Frontera, Temuco 4780000, Chile
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4
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Rassbach J, Hilsberg N, Haensch VG, Dörner S, Gressler J, Sonnabend R, Semm C, Voigt K, Hertweck C, Gressler M. Non-canonical two-step biosynthesis of anti-oomycete indole alkaloids in Kickxellales. Fungal Biol Biotechnol 2023; 10:19. [PMID: 37670394 PMCID: PMC10478498 DOI: 10.1186/s40694-023-00166-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/06/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Fungi are prolific producers of bioactive small molecules of pharmaceutical or agricultural interest. The secondary metabolism of higher fungi (Dikarya) has been well-investigated which led to > 39,000 described compounds. However, natural product researchers scarcely drew attention to early-diverging fungi (Mucoro- and Zoopagomycota) as they are considered to rarely produce secondary metabolites. Indeed, only 15 compounds have as yet been isolated from the entire phylum of the Zoopagomycota. RESULTS Here, we showcase eight species of the order Kickxellales (phylum Zoopagomycota) as potent producers of the indole-3-acetic acid (IAA)-derived compounds lindolins A and B. The compounds are produced both under laboratory conditions and in the natural soil habitat suggesting a specialized ecological function. Indeed, lindolin A is a selective agent against plant-pathogenic oomycetes such as Phytophthora sp. Lindolin biosynthesis was reconstituted in vitro and relies on the activity of two enzymes of dissimilar evolutionary origin: Whilst the IAA-CoA ligase LinA has evolved from fungal 4-coumaryl-CoA synthetases, the subsequently acting IAA-CoA:anthranilate N-indole-3-acetyltransferase LinB is a unique enzyme across all kingdoms of life. CONCLUSIONS This is the first report on bioactive secondary metabolites in the subphylum Kickxellomycotina and the first evidence for a non-clustered, two-step biosynthetic route of secondary metabolites in early-diverging fungi. Thus, the generally accepted "gene cluster hypothesis" for natural products needs to be reconsidered for early diverging fungi.
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Affiliation(s)
- Johannes Rassbach
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Nathalie Hilsberg
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Veit G Haensch
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Sebastian Dörner
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Julia Gressler
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Robin Sonnabend
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Caroline Semm
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
- Jena Microbial Resource Collection (JMRC), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Kerstin Voigt
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
- Jena Microbial Resource Collection (JMRC), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Markus Gressler
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany.
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany.
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Shaw C, Hess M, Weimer BC. Microbial-Derived Tryptophan Metabolites and Their Role in Neurological Disease: Anthranilic Acid and Anthranilic Acid Derivatives. Microorganisms 2023; 11:1825. [PMID: 37512997 PMCID: PMC10384668 DOI: 10.3390/microorganisms11071825] [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: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The gut microbiome provides the host access to otherwise indigestible nutrients, which are often further metabolized by the microbiome into bioactive components. The gut microbiome can also shift the balance of host-produced compounds, which may alter host health. One precursor to bioactive metabolites is the essential aromatic amino acid tryptophan. Tryptophan is mostly shunted into the kynurenine pathway but is also the primary metabolite for serotonin production and the bacterial indole pathway. Balance between tryptophan-derived bioactive metabolites is crucial for neurological homeostasis and metabolic imbalance can trigger or exacerbate neurological diseases. Alzheimer's, depression, and schizophrenia have been linked to diverging levels of tryptophan-derived anthranilic, kynurenic, and quinolinic acid. Anthranilic acid from collective microbiome metabolism plays a complex but important role in systemic host health. Although anthranilic acid and its metabolic products are of great importance for host-microbe interaction in neurological health, literature examining the mechanistic relationships between microbial production, host regulation, and neurological diseases is scarce and at times conflicting. This narrative review provides an overview of the current understanding of anthranilic acid's role in neurological health and disease, with particular focus on the contribution of the gut microbiome, the gut-brain axis, and the involvement of the three major tryptophan pathways.
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Affiliation(s)
- Claire Shaw
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, University of California Davis, Davis, CA 95616, USA
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USA
| | - Matthias Hess
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, University of California Davis, Davis, CA 95616, USA
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6
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Chiang YM, Lin TS, Wang CCC. Total Heterologous Biosynthesis of Fungal Natural Products in Aspergillus nidulans. JOURNAL OF NATURAL PRODUCTS 2022; 85:2484-2518. [PMID: 36173392 PMCID: PMC9621686 DOI: 10.1021/acs.jnatprod.2c00487] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fungal natural products comprise a wide range of bioactive compounds including important drugs and agrochemicals. Intriguingly, bioinformatic analyses of fungal genomes have revealed that fungi have the potential to produce significantly more natural products than what have been discovered so far. It has thus become widely accepted that most biosynthesis pathways of fungal natural products are silent or expressed at very low levels under laboratory cultivation conditions. To tap into this vast chemical reservoir, the reconstitution of entire biosynthetic pathways in genetically tractable fungal hosts (total heterologous biosynthesis) has become increasingly employed in recent years. This review summarizes total heterologous biosynthesis of fungal natural products accomplished before 2020 using Aspergillus nidulans as heterologous hosts. We review here Aspergillus transformation, A. nidulans hosts, shuttle vectors for episomal expression, and chromosomal integration expression. These tools, collectively, not only facilitate the discovery of cryptic natural products but can also be used to generate high-yield strains with clean metabolite backgrounds. In comparison with total synthesis, total heterologous biosynthesis offers a simplified strategy to construct complex molecules and holds potential for commercial application.
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Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Tzu-Shyang Lin
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, United States
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7
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Breisch J, Huber LS, Kraiczy P, Hubloher J, Averhoff B. The ß-ketoadipate pathway of Acinetobacter baumannii is involved in complement resistance and affects resistance against aromatic antibiotics. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:170-178. [PMID: 35023294 DOI: 10.1111/1758-2229.13042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Acinetobacter baumannii can thrive on a broad range of substrates such as sugars, alcohols, lipids, amino acids and aromatic compounds. The latter three are abundant in the human host and are potential candidates as carbon sources for the metabolic adaptation of A. baumannii to the human host. In this study we determined the biodegradative activities of A. baumannii AYE with monocyclic aromatic compounds. Deletion of genes encoding the key enzymes of the ß-ketoadipate pathway, the protocatechuate-3,4-dioxygenase (ΔpcaHG) and the catechol-1,2-dioxygenase (ΔcatA), led to a complete loss of growth on benzoate and p-hydroxybenzoate, suggesting that these substrates are metabolized via the two distinct branches (pca and cat) of this pathway. Furthermore, we investigated the potential role of these gene products in host adaptation by analyzing the capability of the mutants to resist complement-mediated killing. These studies revealed that the mutants exhibit a decreased complement resistance, but a dramatic increase in survival in normal human serum in the presence of p-hydroxybenzoate or protocatechuate. These results indicate that the ß-ketoadipate pathway plays a role in adaptation of A. baumannii to the human host. Moreover, the single and double mutants exhibited increased antibiotic resistances indicating a link between the two dioxygenases and antibiotic resistance.
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Affiliation(s)
- Jennifer Breisch
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Lisa Sophie Huber
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Peter Kraiczy
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Josephine Hubloher
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
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8
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Ma GL, Candra H, Pang LM, Xiong J, Ding Y, Tran HT, Low ZJ, Ye H, Liu M, Zheng J, Fang M, Cao B, Liang ZX. Biosynthesis of Tasikamides via Pathway Coupling and Diazonium-Mediated Hydrazone Formation. J Am Chem Soc 2022; 144:1622-1633. [DOI: 10.1021/jacs.1c10369] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Juan Xiong
- School of Pharmacy, Fudan University, Shanghai 201203, P. R. China
| | - Yichen Ding
- Temasek Life Sciences Laboratory Limited, Research Link, National University of Singapore, 117604 Singapore
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Hong Ye
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Min Liu
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Jie Zheng
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798 Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
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Oliver Huidobro M, Tica J, Wachter GKA, Isalan M. Synthetic spatial patterning in bacteria: advances based on novel diffusible signals. Microb Biotechnol 2021; 15:1685-1694. [PMID: 34843638 PMCID: PMC9151330 DOI: 10.1111/1751-7915.13979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/14/2021] [Accepted: 11/14/2021] [Indexed: 12/22/2022] Open
Abstract
Engineering multicellular patterning may help in the understanding of some fundamental laws of pattern formation and thus may contribute to the field of developmental biology. Furthermore, advanced spatial control over gene expression may revolutionize fields such as medicine, through organoid or tissue engineering. To date, foundational advances in spatial synthetic biology have often been made in prokaryotes, using artificial gene circuits. In this review, engineered patterns are classified into four levels of increasing complexity, ranging from spatial systems with no diffusible signals to systems with complex multi‐diffusor interactions. This classification highlights how the field was held back by a lack of diffusible components. Consequently, we provide a summary of both previously characterized and some new potential candidate small‐molecule signals that can regulate gene expression in Escherichia coli. These diffusive signals will help synthetic biologists to successfully engineer increasingly intricate, robust and tuneable spatial structures.
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Affiliation(s)
| | - Jure Tica
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Georg K A Wachter
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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10
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Mora-Ocampo IY, Pirovani CP, Luz EDMN, Rêgo APB, Silva EMA, Rhodes-Valbuena M, Corrêa RX. Ceratocystis cacaofunesta differentially modulates the proteome in xylem-enriched tissue of cocoa genotypes with contrasting resistance to Ceratocystis wilt. PLANTA 2021; 254:94. [PMID: 34642817 DOI: 10.1007/s00425-021-03747-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
Decreased accumulation of polyphenol oxidase, H2O2 accumulation, effective regulation of programmed cell death, and a protein predicted as allergenic can play key roles in cacao defense against Ceratocystis cacaofunesta. Ceratocystis wilt, caused by the fungus Ceratocystis cacaofunesta, has destroyed millions of Theobroma cacao trees in several countries of the Americas. Through proteomics, systems biology, and enzymatic analyses of infected stems, it was possible to infer mechanisms used by resistant (TSH1188) and susceptible (CCN51) cacao genotypes during infection. Protein extraction from xylem-enriched tissue of stems inoculated with the fungus and their controls 1 day after inoculation was carried out, followed by separation through two-dimensional gel electrophoresis and identification by mass spectrometry. Enzyme activity was determined at 1, 3, 7 and 15 days after inoculation. A total of 50 differentially accumulated distinct proteins were identified in the treatments of both genotypes and were classified into 10 different categories. An interaction network between homologous proteins from Arabidospsis thaliana was generated for each genotype, using the STRING database and Cytoscape software. Primary metabolism processes were apparently repressed in both genotypes. The resistance factors suggested for genotype TSH1188 were: H2O2 accumulation, effective regulation of programmed cell death, production of phytoalexins derived from tryptophan and furanocoumarins, and participation of a predicted allergenic protein with probable ribonuclease function inhibiting the germination and propagation of the fungus. In the susceptible genotype, it is possible that its recognition and signaling mechanism through proteins from the SEC14 family is easily overcome by the pathogen. Our results will help to better understand the interaction between cacao and one of its most aggressive pathogens, to create disease control strategies.
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Affiliation(s)
- Irma Y Mora-Ocampo
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Carlos P Pirovani
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Edna D M N Luz
- Comissão Executiva de Planejamento da Lavoura Cacaueira (CEPLAC), Centro de Pesquisas do Cacau (CEPEC), Itabuna, BA, 45600-919, Brazil
| | - Angra P B Rêgo
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Edson M A Silva
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Mateo Rhodes-Valbuena
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Ronan X Corrêa
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil.
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11
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Więdłocha M, Marcinowicz P, Janoska-Jaździk M, Szulc A. Gut microbiota, kynurenine pathway and mental disorders - Review. Prog Neuropsychopharmacol Biol Psychiatry 2021; 106:110145. [PMID: 33203568 DOI: 10.1016/j.pnpbp.2020.110145] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 02/08/2023]
Abstract
The intestine and the gut-associated limphoid tissue constitute the largest immunity organ of the human body. Among several possible tryptophan metabolism routes, the kynurenine pathway can be influenced by the gut microbiota. Disturbances of gut biodiversity may cause increased gut permeability and cause systemic inflammation, also related to central nervous system. Proinflammatory cytokines induce kynurenine pathway enzymes resulting in formation of neuroactive metabolites, which are being associated with several psychiatric disorders. The kynurenine pathway may also be influenced by certain bacteria species directly. The aim of this review is to highlight the current knowledge on the interaction of gut microbiota and the central nervous system with the kynurenine pathway taken into special account. Up to date study results on specific psychiatric disorders such as schizophrenia, bipolar disorder, Alzheimer's disease, autism spectrum disorders, depression and alcoholism are presented. Available evidence suggests that toxicity of kynurenine metabolites may be reduced by adjunction of probiotics which can affect proinflammatory cytokines. Due to their potential for modulation of the kynurenine pathway, gut microbiota pose an interesting target for future therapies.
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Affiliation(s)
- Magdalena Więdłocha
- Department of Psychiatry, Faculty of Health Sciences, Medical University of Warsaw, Poland.
| | - Piotr Marcinowicz
- Department of Psychiatry, Faculty of Health Sciences, Medical University of Warsaw, Poland
| | | | - Agata Szulc
- Department of Psychiatry, Faculty of Health Sciences, Medical University of Warsaw, Poland
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12
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Lopez-Echartea E, Suman J, Smrhova T, Ridl J, Pajer P, Strejcek M, Uhlik O. Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility. G3-GENES GENOMES GENETICS 2021; 11:6029021. [PMID: 33693598 PMCID: PMC8022969 DOI: 10.1093/g3journal/jkaa030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/30/2020] [Indexed: 11/30/2022]
Abstract
Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.
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Affiliation(s)
- Eglantina Lopez-Echartea
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Tereza Smrhova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 40 Prague, Czech Republic.,Division of Animal Evolutionary Biology, Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske nemocnice 1200, 169 02 Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
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13
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Bacterial Metabolites of Human Gut Microbiota Correlating with Depression. Int J Mol Sci 2020; 21:ijms21239234. [PMID: 33287416 PMCID: PMC7730936 DOI: 10.3390/ijms21239234] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023] Open
Abstract
Depression is a global threat to mental health that affects around 264 million people worldwide. Despite the considerable evolution in our understanding of the pathophysiology of depression, no reliable biomarkers that have contributed to objective diagnoses and clinical therapy currently exist. The discovery of the microbiota-gut-brain axis induced scientists to study the role of gut microbiota (GM) in the pathogenesis of depression. Over the last decade, many of studies were conducted in this field. The productions of metabolites and compounds with neuroactive and immunomodulatory properties among mechanisms such as the mediating effects of the GM on the brain, have been identified. This comprehensive review was focused on low molecular weight compounds implicated in depression as potential products of the GM. The other possible mechanisms of GM involvement in depression were presented, as well as changes in the composition of the microbiota of patients with depression. In conclusion, the therapeutic potential of functional foods and psychobiotics in relieving depression were considered. The described biomarkers associated with GM could potentially enhance the diagnostic criteria for depressive disorders in clinical practice and represent a potential future diagnostic tool based on metagenomic technologies for assessing the development of depressive disorders.
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14
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Nair V, Kim MC, Golen JA, Rheingold AL, Castro GA, Jensen PR, Fenical W. Verrucosamide, a Cytotoxic 1,4-Thiazepane-Containing Thiodepsipeptide from a Marine-Derived Actinomycete. Mar Drugs 2020; 18:md18110549. [PMID: 33167356 PMCID: PMC7694325 DOI: 10.3390/md18110549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/22/2022] Open
Abstract
A new cytotoxic thiodepsipeptide, verrucosamide (1), was isolated along with the known, related cyclic peptide thiocoraline, from the extract of a marine-derived actinomycete, a Verrucosispora sp., our strain CNX-026. The new peptide, which is composed of two rare seven-membered 1,4-thiazepane rings, was elucidated by a combination of spectral methods and the absolute configuration was determined by a single X-ray diffraction study. Verrucosamide (1) showed moderate cytotoxicity and selectivity in the NCI 60 cell line bioassay. The most susceptible cell lines were MDA-MB-468 breast carcinoma with an LD50 of 1.26 µM, and COLO 205 colon adenocarcinoma with an LD50 of 1.4 µM. Also isolated along with verrucosamide were three small 3-hydroxy(alkoxy)-quinaldic acid derivatives that appear to be products of the same biosynthetic pathway.
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Affiliation(s)
- Vimal Nair
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093-0204, USA; (V.N.); (M.C.K.); (G.A.C.); (P.R.J.)
| | - Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093-0204, USA; (V.N.); (M.C.K.); (G.A.C.); (P.R.J.)
| | - James A. Golen
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA; (J.A.G.); (A.L.R.)
| | - Arnold L. Rheingold
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA; (J.A.G.); (A.L.R.)
| | - Gabriel A. Castro
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093-0204, USA; (V.N.); (M.C.K.); (G.A.C.); (P.R.J.)
| | - Paul R. Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093-0204, USA; (V.N.); (M.C.K.); (G.A.C.); (P.R.J.)
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093-0204, USA; (V.N.); (M.C.K.); (G.A.C.); (P.R.J.)
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego, CA 92093, USA
- Moores Comprehensive Cancer Center, University of California, San Diego, CA 92093, USA
- Correspondence: ; Tel.: +1-858-534-2133
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15
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Brown J, Robusto B, Morel L. Intestinal Dysbiosis and Tryptophan Metabolism in Autoimmunity. Front Immunol 2020; 11:1741. [PMID: 32849620 PMCID: PMC7417361 DOI: 10.3389/fimmu.2020.01741] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 06/30/2020] [Indexed: 12/12/2022] Open
Abstract
The development of autoimmunity involves complex interactions between genetics and environmental triggers. The gut microbiota is an important environmental constituent that can heavily influence both local and systemic immune reactivity through distinct mechanisms. It is therefore a relevant environmental trigger or amplifier to consider in autoimmunity. This review will examine recent evidence for an association between intestinal dysbiosis and autoimmune diseases, and the mechanisms by which the gut microbiota may contribute to autoimmune activation. We will specifically focus on recent studies connecting tryptophan metabolism to autoimmune disease pathogenesis and discuss evidence for a microbial origin. This will be discussed in the context of our current understanding of how tryptophan metabolites regulate immune responses, and how it may, or may not, be applicable to autoimmunity.
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Affiliation(s)
- Josephine Brown
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Brian Robusto
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Laurence Morel
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, United States
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16
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The Desotamide Family of Antibiotics. Antibiotics (Basel) 2020; 9:antibiotics9080452. [PMID: 32727132 PMCID: PMC7459860 DOI: 10.3390/antibiotics9080452] [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: 06/19/2020] [Revised: 07/14/2020] [Accepted: 07/25/2020] [Indexed: 12/22/2022] Open
Abstract
Microbial natural products underpin the majority of antimicrobial compounds in clinical use and the discovery of new effective antibacterial treatments is urgently required to combat growing antimicrobial resistance. Non-ribosomal peptides are a major class of natural products to which many notable antibiotics belong. Recently, a new family of non-ribosomal peptide antibiotics were discovered-the desotamide family. The desotamide family consists of desotamide, wollamide, surugamide, ulleungmycin and noursamycin/curacomycin, which are cyclic peptides ranging in size between six and ten amino acids in length. Their biosynthesis has attracted significant attention because their highly functionalised scaffolds are cyclised by a recently identified standalone cyclase. Here, we provide a concise review of the desotamide family of antibiotics with an emphasis on their biosynthesis.
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17
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Li H, Gilchrist CLM, Phan CS, Lacey HJ, Vuong D, Moggach SA, Lacey E, Piggott AM, Chooi YH. Biosynthesis of a New Benzazepine Alkaloid Nanangelenin A from Aspergillus nanangensis Involves an Unusual l-Kynurenine-Incorporating NRPS Catalyzing Regioselective Lactamization. J Am Chem Soc 2020; 142:7145-7152. [PMID: 32182055 DOI: 10.1021/jacs.0c01605] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
1-Benzazepine is a pharmaceutically important scaffold but is rare among natural products. Nanangelenin A (1), containing an unprecedented 3,4-dihydro-1-benzazepine-2,5-dione-N-prenyl-N-acetoxy-anthranilamide scaffold, was isolated from a novel species of Australian fungus, Aspergillus nanangensis. Genomic and retrobiosynthetic analyses identified a putative nonribosomal peptide synthetase (NRPS) gene cluster (nan). The detailed biosynthetic pathway to 1 was established by heterologous pathway reconstitution in A. nidulans, which led to biosynthesis of intermediates nanagelenin B-F (2-5 and 7). We demonstrated that the NRPS NanA incorporates anthranilic acid (Ant) and l-kynurenine (l-Kyn), which is supplied by a dedicated indoleamine-2,3-dioxygenase NanC encoded in the gene cluster. Using heterologous in vivo assays and mutagenesis, we demonstrated that the C-terminal condensation (CT) and thiolation (T3) domains of NanA are responsible for the regioselective cyclization of the tethered Ant-l-Kyn dipeptide to form the unusual benzazepine scaffold in 1. We also showed that NanA-CT catalyzes the regioselective cyclization of a surrogate synthetic substrate, Ant-l-Kyn-N-acetylcysteamine, to give the benzazepine scaffold, while spontaneous cyclization of the dipeptide yielded the alternative kinetically favored benzodiazepine scaffold. The discovery of 1 and the characterization of NanA have expanded the chemical and functional diversities of fungal NRPSs.
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Affiliation(s)
| | | | | | - Heather J Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | | | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia.,Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew M Piggott
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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18
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Evrensel A, Ünsalver BÖ, Ceylan ME. Immune-Kynurenine Pathways and the Gut Microbiota-Brain Axis in Anxiety Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1191:155-167. [PMID: 32002928 DOI: 10.1007/978-981-32-9705-0_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Anxiety disorders are a complex set of illnesses in which genetic factors, particularly stress, play a role in the etiopathogenesis. In recent years, inflammation and intestinal microbiota have also been included in this complex network of relationships. The functions associated with tryptophan catabolism and serotonin biosynthesis have long been associated with anxiety disorders. Tryptophan catabolism progresses toward the path of the kynurenine in the presence of stress and inflammation. The catabolism of kynurenine is a pathway in which many enzymes play a role and a large number of catabolites with neuroactive properties occur. The body's serotonin biosynthesis is primarily performed by enterochromaffin cells located in the intestines. A change in the intestinal microbiota composition (dysbiosis) directly affects the serotonin biosynthesis. Stress, unhealthy nutrition, and the use of antibiotics cause dysbiosis. In the light of this new perspective, the role of dysbiosis-induced inflammation and kynurenine pathway catabolites activated sequentially come into prominence in the etiopathogenesis of anxiety disorders.
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Affiliation(s)
- Alper Evrensel
- Department of Psychiatry, Uskudar University, Umraniye, Istanbul, Turkey.
| | - Barış Önen Ünsalver
- Vocational School of Health Services, Department of Medical Documentation and Secretariat, Uskudar University, Istanbul, Turkey
| | - Mehmet Emin Ceylan
- Departments of Psychology and Philosophy, Uskudar University, Istanbul, Turkey
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19
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Rodríguez Estévez M, Gummerlich N, Myronovskyi M, Zapp J, Luzhetskyy A. Benzanthric Acid, a Novel Metabolite From Streptomyces albus Del14 Expressing the Nybomycin Gene Cluster. Front Chem 2020; 7:896. [PMID: 31998688 PMCID: PMC6965495 DOI: 10.3389/fchem.2019.00896] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/12/2019] [Indexed: 11/17/2022] Open
Abstract
Streptomycetes constitute a diverse bacterial group able to produce a wide variety of secondary metabolites with potential applications in the pharmacy industry. However, the genes responsible for the biosynthesis of these compounds are very frequently inactive or expressed at very low levels under standard laboratory cultivation conditions. Therefore, the activation or upregulation of secondary metabolite biosynthesis genes is a crucial step for the discovery of new bioactive natural products. We have recently reported the discovery of the biosynthetic genes for the antibiotic nybomycin (nyb genes) in Streptomyces albus subsp. chlorinus. The nyb genes were expressed in the heterologous host Streptomyces albus Del14, which produces not only nybomycin, but also a novel compound. In this study, we describe the isolation, purification, and structure elucidation of the new substance named benzanthric acid.
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Affiliation(s)
| | - Nils Gummerlich
- Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
| | - Josef Zapp
- Department of Pharmacy, Institute of Pharmaceutical Biology, University of Saarland, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany.,Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
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20
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Götze S, Stallforth P. Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads. Nat Prod Rep 2020; 37:29-54. [DOI: 10.1039/c9np00022d] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacteria of the genusPseudomonasdisplay a fascinating metabolic diversity. In this review, we focus our attention on the natural product class of nonribosomal lipopeptides, which help pseudomonads to colonize a wide range of ecological niches.
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Affiliation(s)
- Sebastian Götze
- Faculty 7: Natural and Environmental Sciences
- Institute for Environmental Sciences
- University Koblenz Landau
- 76829 Landau
- Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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21
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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22
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Kaur H, Bose C, Mande SS. Tryptophan Metabolism by Gut Microbiome and Gut-Brain-Axis: An in silico Analysis. Front Neurosci 2019; 13:1365. [PMID: 31920519 PMCID: PMC6930238 DOI: 10.3389/fnins.2019.01365] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/03/2019] [Indexed: 12/14/2022] Open
Abstract
The link between gut microbiome and brain is being slowly acknowledged due to the speculated role of resident gut microbial community in altering the functions of gut-brain axis (GBA). Recently, a number of microbial metabolites (referred to as neuro-active metabolites) produced through tryptophan metabolism have been suggested to influence the GBA. In view of this, the current study focuses on microbial tryptophan metabolism pathways which produce neuro-active metabolites. An in silico analysis was performed on bacterial genomes as well as publicly available gut microbiome data. The results provide a comprehensive catalog of the analyzed pathways across bacteria. The analysis indicates an enrichment of tryptophan metabolism pathways in five gut-associated phyla, namely, Actinobacteria, Firmicutes, Bacteroidetes, Proteobacteria, and Fusobacteria. Further, five genera, namely, Clostridium, Burkholderia, Streptomyces, Pseudomonas, and Bacillus have been predicted to be enriched in terms of number of the analyzed tryptophan metabolism pathways, suggesting a higher potential of these bacterial groups to metabolize tryptophan in gut. Analysis of available microbiome data corresponding to gut samples from patients of neurological diseases and healthy individuals suggests probable association of different sets of tryptophan metabolizing bacterial pathways with the etiology of different diseases. The insights obtained from the present study are expected to provide directions toward designing of microbiome based diagnostic and therapeutic approaches for neurological diseases/disorders.
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Affiliation(s)
| | | | - Sharmila S. Mande
- Life Sciences R&D, TCS Research, Tata Consultancy Services, Pune, India
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23
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Metagenomic analysis of relationships between the denitrification process and carbon metabolism in a bioaugmented full-scale tannery wastewater treatment plant. World J Microbiol Biotechnol 2019; 35:149. [PMID: 31549239 DOI: 10.1007/s11274-019-2716-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/21/2019] [Indexed: 01/08/2023]
Abstract
The goal of this study was to investigate the relationship between the denitrification process and carbon metabolism in a full-scale tannery wastewater treatment plant bioaugmented with the microbial consortium BM-S-1. The metagenomic analysis of the microbial community showed that Brachymonas denitrificans, a known denitrifier, was present at a high level in the treatment stages of buffering (B), primary aeration (PA), and sludge digestion (SD). The occurrences of the amino acid-degrading enzymes alpha ketoglutarate dehydrogenase (α-KGDH) and tryptophan synthase were highly correlated with the presence of denitrification genes, such as napA, narG, nosZ and norB. The occurrence of glutamate dehydrogenase (GDH) was also highly paralleled with the occurrence of denitrification genes such as napA, narG, and norZ. The denitrification genes (nosZ, narG, napA, norB and nrfA) and amino acid degradation enzymes (tryptophan synthase, α-KGDH and pyridoxal phosphate dependent enzymes) were observed at high levels in B. This indicates that degradation of amino acids and denitrification of nitrate may potentially occur in B. The high concentrations of the fatty acid degradation enzyme groups (enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and β-ketothiolase) were observed together with the denitrification genes, such as napA, narG and nosZ. Phospholipase/carboxylesterase, enoyl-CoA hydratase/isomerase, acyl-CoA dehydrogenase, phenylacetate degradation enzyme and 3-hydroxyacyl-CoA dehydrogenase 2 were also dominant in B. All these results clearly indicate that the denitrification pathways are potentially linked to the degradation pathways of amino acids and fatty acids whose degradation products go through the TCA cycle, generating the NADH that is used as electron donors for denitrification.
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Bright Green Biofluorescence in Sharks Derives from Bromo-Kynurenine Metabolism. iScience 2019; 19:1291-1336. [PMID: 31402257 PMCID: PMC6831821 DOI: 10.1016/j.isci.2019.07.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/26/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
Although in recent years there has been an increased awareness of the widespread nature of biofluorescence in the marine environment, the diversity of the molecules responsible for this luminescent phenotype has been mostly limited to green fluorescent proteins (GFPs), GFP-like proteins, and fluorescent fatty acid-binding proteins (FABPs). In the present study, we describe a previously undescribed group of brominated tryptophan-kynurenine small molecule metabolites responsible for the green biofluorescence in two species of sharks and provide their structural, antimicrobial, and spectral characterization. Multi-scale fluorescence microscopy studies guided the discovery of metabolites that were differentially produced in fluorescent versus non-fluorescent skin, as well as the species-specific structural details of their unusual light-guiding denticles. Overall, this study provides the detailed description of a family of small molecules responsible for marine biofluorescence and opens new questions related to their roles in central nervous system signaling, resilience to microbial infections, and photoprotection. We describe a new form of biofluorescence from the skin of catsharks Bromo-tryptophan-kynurenines are biofluorescent and show antimicrobial activities Specific dermal denticles in the chain catshark act as optical light-guides This study opens questions related to biological function of shark fluorescence
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25
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Luhavaya H, Sigrist R, Chekan JR, McKinnie SMK, Moore BS. Biosynthesis of l-4-Chlorokynurenine, an Antidepressant Prodrug and a Non-Proteinogenic Amino Acid Found in Lipopeptide Antibiotics. Angew Chem Int Ed Engl 2019; 58:8394-8399. [PMID: 30963655 DOI: 10.1002/anie.201901571] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/06/2019] [Indexed: 12/18/2022]
Abstract
l-4-Chlorokynurenine (l-4-Cl-Kyn) is a neuropharmaceutical drug candidate that is in development for the treatment of major depressive disorder. Recently, this amino acid was naturally found as a residue in the lipopeptide antibiotic taromycin. Herein, we report the unprecedented conversion of l-tryptophan into l-4-Cl-Kyn catalyzed by four enzymes in the taromycin biosynthetic pathway from the marine bacterium Saccharomonospora sp. CNQ-490. We used genetic, biochemical, structural, and analytical techniques to establish l-4-Cl-Kyn biosynthesis, which is initiated by the flavin-dependent tryptophan chlorinase Tar14 and its flavin reductase partner Tar15. This work revealed the first tryptophan 2,3-dioxygenase (Tar13) and kynurenine formamidase (Tar16) enzymes that are selective for chlorinated substrates. The substrate scope of Tar13, Tar14, and Tar16 was examined and revealed intriguing promiscuity, thereby opening doors for the targeted engineering of these enzymes as useful biocatalysts.
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Affiliation(s)
- Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Renata Sigrist
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.,Department of Organic Chemistry, University of Campinas UNICAMP, Cidade Universitária Zeferino Vaz s/n, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shaun M K McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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Luhavaya H, Sigrist R, Chekan JR, McKinnie SMK, Moore BS. Biosynthesis of
l
‐4‐Chlorokynurenine, an Antidepressant Prodrug and a Non‐Proteinogenic Amino Acid Found in Lipopeptide Antibiotics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hanna Luhavaya
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
| | - Renata Sigrist
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Department of Organic ChemistryUniversity of Campinas UNICAMPCidade Universitária Zeferino Vaz s/n P.O. Box 6154 13083-970 Campinas SP Brazil
| | - Jonathan R. Chekan
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
| | - Shaun M. K. McKinnie
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San Diego La Jolla CA 92093 USA
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27
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Bulzu PA, Andrei AŞ, Salcher MM, Mehrshad M, Inoue K, Kandori H, Beja O, Ghai R, Banciu HL. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat Microbiol 2019; 4:1129-1137. [DOI: 10.1038/s41564-019-0404-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/08/2019] [Indexed: 11/09/2022]
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Effects of Co-Inoculation of Indole-3-Acetic Acid-Producing and -Degrading Bacterial Endophytes on Plant Growth. HORTICULTURAE 2019. [DOI: 10.3390/horticulturae5010017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bacterial production of indole-3-acetic acid (IAA) and its effects on plant growth have been frequently studied but there have been few studies on the ecology of IAA-degrading bacteria. In this study, among eight endophytic bacterial strains previously isolated from the same sweet potato sample including two IAA producers, Klebsiella sp. Sal 1 and Enterobacter sp. Sal 3, all of the strains showed IAA-degrading ability to some extent. Herbaspirillum sp. Sal 6 had the highest activity for IAA and tryptophan. When the IAA producers and the degrader were co-cultured in tryptophan-amended N+MR liquid medium, the concentrations of IAA decreased. Inoculation with Klebsiella sp. Sal 1, the highest IAA producer among the test strains, increased fresh root weight of tomato and radish, but the effect decreased by co-inoculation with IAA-degrading Herbaspirillum sp. Sal 6. Since both strains colonized plant parts at high populations, it was likely that the IAA degrader decreased IAA levels in the plants by degrading IAA and/or its precursor tryptophan. When IAA-producing biofertilizers are used, interactions with IAA degraders in plants should be considered.
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Mihăşan M, Babii C, Aslebagh R, Channaveerappa D, Dupree EJ, Darie CC. Exploration of Nicotine Metabolism in Paenarthrobacter nicotinovorans pAO1 by Microbial Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:515-529. [DOI: 10.1007/978-3-030-15950-4_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Proteomics based analysis of the nicotine catabolism in Paenarthrobacter nicotinovorans pAO1. Sci Rep 2018; 8:16239. [PMID: 30390017 PMCID: PMC6214936 DOI: 10.1038/s41598-018-34687-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 10/24/2018] [Indexed: 12/22/2022] Open
Abstract
Paenarthrobacter nicotinovorans is a nicotine-degrading microorganism that shows a promising biotechnological potential for the production of compounds with industrial and pharmaceutical importance. Its ability to use nicotine was linked to the presence of the catabolic megaplasmid pAO1. Although extensive work has been performed on the molecular biology of nicotine degradation in this bacterium, only half of the genes putatively involved have been experimentally linked to nicotine. In the current approach, we used nanoLC-MS/MS to identify a total of 801 proteins grouped in 511 non-redundant protein clusters when P. nicotinovorans was grown on citrate, nicotine and nicotine and citrate as the only carbon sources. The differences in protein abundance showed that deamination is preferred when citrate is present. Several putative genes from the pAO1 megaplasmid have been shown to have a nicotine-dependent expression, including a hypothetical polyketide cyclase. We hypothesize that the enzyme would hydrolyze the N1-C6 bond from the pyridine ring with the formation of α-keto- glutaramate. Two chromosomally-encoded proteins, a malate dehydrogenase, and a D-3-phosphoglycerate dehydrogenase were shown to be strongly up-regulated when nicotine was the sole carbon source and could be related to the production the α-keto-glutarate. The data have been deposited to the ProteomeXchange with identifier PXD008756.
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Van Houdt R, Provoost A, Van Assche A, Leys N, Lievens B, Mijnendonckx K, Monsieurs P. Cupriavidus metallidurans Strains with Different Mobilomes and from Distinct Environments Have Comparable Phenomes. Genes (Basel) 2018; 9:genes9100507. [PMID: 30340417 PMCID: PMC6210171 DOI: 10.3390/genes9100507] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 12/16/2022] Open
Abstract
Cupriavidus metallidurans has been mostly studied because of its resistance to numerous heavy metals and is increasingly being recovered from other environments not typified by metal contamination. They host a large and diverse mobile gene pool, next to their native megaplasmids. Here, we used comparative genomics and global metabolic comparison to assess the impact of the mobilome on growth capabilities, nutrient utilization, and sensitivity to chemicals of type strain CH34 and three isolates (NA1, NA4 and H1130). The latter were isolated from water sources aboard the International Space Station (NA1 and NA4) and from an invasive human infection (H1130). The mobilome was expanded as prophages were predicted in NA4 and H1130, and a genomic island putatively involved in abietane diterpenoids metabolism was identified in H1130. An active CRISPR-Cas system was identified in strain NA4, providing immunity to a plasmid that integrated in CH34 and NA1. No correlation between the mobilome and isolation environment was found. In addition, our comparison indicated that the metal resistance determinants and properties are conserved among these strains and thus maintained in these environments. Furthermore, all strains were highly resistant to a wide variety of chemicals, much broader than metals. Only minor differences were observed in the phenomes (measured by phenotype microarrays), despite the large difference in mobilomes and the variable (shared by two or three strains) and strain-specific genomes.
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Affiliation(s)
- Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Ann Provoost
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Ado Van Assche
- Laboratory for Process Microbial Ecology and Bioinspirational Management, KU Leuven, B-2860 Sint-Katelijne-Waver, Belgium.
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management, KU Leuven, B-2860 Sint-Katelijne-Waver, Belgium.
| | - Kristel Mijnendonckx
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
| | - Pieter Monsieurs
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), B-2400 Mol, Belgium.
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32
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A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase. Sci Rep 2018; 8:13104. [PMID: 30166577 PMCID: PMC6117287 DOI: 10.1038/s41598-018-31259-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/15/2018] [Indexed: 11/18/2022] Open
Abstract
The catalytic mechanism of the cyclic amidohydrolase isatin hydrolase depends on a catalytically active manganese in the substrate-binding pocket. The Mn2+ ion is bound by a motif also present in other metal dependent hydrolases like the bacterial kynurenine formamidase. The crystal structures of the isatin hydrolases from Labrenzia aggregata and Ralstonia solanacearum combined with activity assays allow for the identification of key determinants specific for the reaction mechanism. Active site residues central to the hydrolytic mechanism include a novel catalytic triad Asp-His-His supported by structural comparison and hybrid quantum mechanics/classical mechanics simulations. A hydrolytic mechanism for a Mn2+ dependent amidohydrolases that disfavour Zn2+ as the primary catalytically active site metal proposed here is supported by these likely cases of convergent evolution. The work illustrates a fundamental difference in the substrate-binding mode between Mn2+ dependent isatin hydrolase like enzymes in comparison with the vast number of Zn2+ dependent enzymes.
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Zhang K, Yuan X, Zang J, Wang M, Zhao F, Li P, Cao H, Han J, Xing J, Dong J. The Kynurenine 3-Monooxygenase Encoding Gene, BcKMO, Is Involved in the Growth, Development, and Pathogenicity of Botrytis cinerea. Front Microbiol 2018; 9:1039. [PMID: 29867912 PMCID: PMC5968091 DOI: 10.3389/fmicb.2018.01039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/02/2018] [Indexed: 11/13/2022] Open
Abstract
A pathogenic mutant, BCG183, was obtained by screening the T-DNA insertion library of Botrytis cinerea. A novel pathogenicity-related gene BcKMO, which encodes kynurenine 3-monooxygenase (KMO), was isolated and identified via thermal asymmetric interlaced PCR, bioinformatics analyses, and KMO activity measurement. The mutant BCG183 grew slowly, did not produce conidia and sclerotia, had slender hyphae, and presented enhanced pathogenicity. The phenotype and pathogenicity of the BcKMO-complementing mutant (BCG183/BcKMO) were similar to those of the wild-type (WT) strain. The activities of polymethylgalacturonase, polygalacturonase, and toxins were significantly higher, whereas acid production was significantly decreased in the mutant BCG183, when compared with those in the WT and BCG183/BcKMO. Moreover, the sensitivity of mutant BCG183 to NaCl and KCl was remarkably increased, whereas that to fluconazole, Congo Red, menadione, H2O2, and SQ22536 and U0126 [cAMP-dependent protein kinase (cAMP) and mitogen-activated protein kinase (MAPK) signaling pathways inhibitors, respectively] were significantly decreased compared with the other strains. Furthermore, the key genes involved in the cAMP and MAPK signaling pathways, Pka1, Pka2, PkaR, Bcg2, Bcg3, bmp1, and bmp3, were significantly upregulated or downregulated in the mutant BCG183. BcKMO expression levels were also upregulated or downregulated in the RNAi mutants of the key genes involved in the cAMP and MAPK signaling pathways. These findings indicated that BcKMO positively regulates growth and development, but negatively regulates pathogenicity of B. cinerea. Furthermore, BcKMO was found to be involved in controlling cell wall degrading enzymes activity, toxins activity, acid production, and cell wall integrity, and participate in cAMP and MAPK signaling pathways of B. cinerea.
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Affiliation(s)
- Kang Zhang
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.,Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, China
| | - Xuemei Yuan
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.,Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, China
| | - Jinping Zang
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.,Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, China
| | - Min Wang
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.,Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, China
| | - Fuxin Zhao
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.,Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, China
| | - Peifen Li
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.,Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, China
| | - Hongzhe Cao
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.,Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, China
| | - Jianmin Han
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.,Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, China
| | - Jihong Xing
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.,Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, China
| | - Jingao Dong
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.,Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Agricultural University, Baoding, China
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Karimi E, Slaby BM, Soares AR, Blom J, Hentschel U, Costa R. Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges. FEMS Microbiol Ecol 2018; 94:4985835. [DOI: 10.1093/femsec/fiy074] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022] Open
Affiliation(s)
- Elham Karimi
- Centre of Marine Sciences (CCMAR), Faculty of Science and Technology (FCT), Algarve University, 8005-139 Faro, Portugal
| | - Beate M Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| | - André R Soares
- Institute of Geography and Earth Sciences, Aberystwyth University, SY23 3DB Aberystwyth, Wales, UK
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
- Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany
| | - Rodrigo Costa
- Centre of Marine Sciences (CCMAR), Faculty of Science and Technology (FCT), Algarve University, 8005-139 Faro, Portugal
- Institute for Bioengineering and Biosciences (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
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Anti-biofilm effects of anthranilate on a broad range of bacteria. Sci Rep 2017; 7:8604. [PMID: 28819217 PMCID: PMC5561115 DOI: 10.1038/s41598-017-06540-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/14/2017] [Indexed: 01/16/2023] Open
Abstract
Anthranilate, one of tryptophan degradation products has been reported to interfere with biofilm formation by Pseudomonas aeruginosa. Here, we investigated the effects of anthranilate on biofilm formation by various bacteria and the mechanisms responsible. Anthranilate commonly inhibited biofilm formation by P. aeruginosa, Vibrio vulnificus, Bacillus subtilis, Salmonella enterica serovar Typhimurium, and Staphylococcus aureus, and disrupted biofilms preformed by these bacteria. Because anthranilate reduced intracellular c-di-GMP and enhanced swimming and swarming motilities in P. aeruginosa, V. vulnificus, B. subtilis, and S. enterica, it is likely that anthranilate disrupts biofilms by inducing the dispersion of these bacteria. On the other hand, in S. aureus, a non-flagellate bacterium that has no c-di-GMP signaling, anthranilate probably inhibits biofilm formation by reducing slime production. These results suggest that anthranilate has multiple ways for biofilm inhibition. Furthermore, because of its good biofilm inhibitory effects and lack of cytotoxicity to human cells even at high concentration, anthranilate appears to be a promising agent for inhibiting biofilm formation by a broad range of bacteria.
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36
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Popovic A, Hai T, Tchigvintsev A, Hajighasemi M, Nocek B, Khusnutdinova AN, Brown G, Glinos J, Flick R, Skarina T, Chernikova TN, Yim V, Brüls T, Paslier DL, Yakimov MM, Joachimiak A, Ferrer M, Golyshina OV, Savchenko A, Golyshin PN, Yakunin AF. Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families. Sci Rep 2017; 7:44103. [PMID: 28272521 PMCID: PMC5341072 DOI: 10.1038/srep44103] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/01/2017] [Indexed: 11/29/2022] Open
Abstract
Metagenomics has made accessible an enormous reserve of global biochemical diversity. To tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. We have validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalytic residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.
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Affiliation(s)
- Ana Popovic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Tran Hai
- School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, UK
| | - Anatoly Tchigvintsev
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Mahbod Hajighasemi
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Julia Glinos
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | | | - Veronica Yim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Thomas Brüls
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction de la Recherche Fondamentale, Institut de Génomique, Université de d'Evry Val d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS), UMR8030, Génomique métabolique, Evry, France
| | - Denis Le Paslier
- Université de d'Evry Val d'Essonne (UEVE), Centre National de la Recherche, Scientifique (CNRS), UMR8030, Génomique métabolique, Commissariat à l'Energie, Atomique et aux Energies Alternatives (CEA), Direction de la Recherche, Fondamentale, Institut de Génomique, Evry, France
| | | | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | | | - Olga V Golyshina
- School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, UK
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, UK
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
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37
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Kynurenine pathway metabolism and the microbiota-gut-brain axis. Neuropharmacology 2017; 112:399-412. [DOI: 10.1016/j.neuropharm.2016.07.002] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/30/2016] [Accepted: 07/04/2016] [Indexed: 02/07/2023]
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38
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Rodrigues EP, Soares CDP, Galvão PG, Imada EL, Simões-Araújo JL, Rouws LFM, de Oliveira ALM, Vidal MS, Baldani JI. Identification of Genes Involved in Indole-3-Acetic Acid Biosynthesis by Gluconacetobacter diazotrophicus PAL5 Strain Using Transposon Mutagenesis. Front Microbiol 2016; 7:1572. [PMID: 27774087 PMCID: PMC5053998 DOI: 10.3389/fmicb.2016.01572] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/20/2016] [Indexed: 02/03/2023] Open
Abstract
Gluconacetobacter diazotrophicus is a beneficial nitrogen-fixing endophyte found in association with sugarcane plants and other important crops. Beneficial effects of G. diazotrophicus on sugarcane growth and productivity have been attributed to biological nitrogen fixation process and production of phytohormones especially indole-3-acetic acid (IAA); however, information about the biosynthesis and function of IAA in G. diazotrophicus is still scarce. Therefore, the aim of this work was to identify genes and pathways involved in IAA biosynthesis in this bacterium. In our study, the screening of two independent Tn5 mutant libraries of PAL5T strain using the Salkowski colorimetric assay revealed two mutants (Gdiaa34 and Gdiaa01), which exhibited 95% less indolic compounds than the parental strain when grown in LGIP medium supplemented with L-tryptophan. HPLC chromatograms of the wild-type strain revealed the presence of IAA and of the biosynthetic intermediates indole-3-pyruvic acid (IPyA) and indole-3-lactate (ILA). In contrast, the HPLC profiles of both mutants showed no IAA but only a large peak of non-metabolized tryptophan and low levels of IPyA and ILA were detected. Molecular characterization revealed that Gdiaa01 and Gdiaa34 mutants had unique Tn5 insertions at different sites within the GDI2456 open read frame, which is predicted to encode a L-amino acid oxidase (LAAO). GDI2456 (lao gene) forms a cluster with GDI2455 and GDI2454 ORFs, which are predicted to encode a cytochrome C and an RidA protein, respectively. RT-qPCR showed that transcript levels of lao. cccA, and ridA genes were reduced in the Gdiaa01 as compared to PAL5T. In addition, rice plants inoculated with Gdiaa01 showed significantly smaller root development (length, surface area, number of forks and tips) than those plants inoculated with PAL5T. In conclusion, our study demonstrated that G. diazotrophicus PAL5T produces IAA via the IPyA pathway in cultures supplemented with tryptophan and provides evidence for the involvement of an L-amino acid oxidase gene cluster in the biosynthesis of IAA. Furthermore, we showed that the mutant strains with reduction in IAA biosynthesis ability, in consequence of the lower transcription levels of genes of the lao cluster, had remarkable effects on development of rice roots.
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Affiliation(s)
- Elisete P Rodrigues
- Laboratório de Genética de Microrganismos, Departamento de Biologia, Universidade Estadual de Londrina Londrina, Brazil
| | | | | | - Eddie L Imada
- Laboratório de Genética de Microrganismos, Departamento de Biologia, Universidade Estadual de Londrina Londrina, Brazil
| | | | | | - André L M de Oliveira
- Laboratório de Bioquímica Molecular, Departamento de Bioquímica e Biotecnologia, Universidade Estadual de Londrina Londrina, Brazil
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Bortolotti P, Hennart B, Thieffry C, Jausions G, Faure E, Grandjean T, Thepaut M, Dessein R, Allorge D, Guery BP, Faure K, Kipnis E, Toussaint B, Le Gouellec A. Tryptophan catabolism in Pseudomonas aeruginosa and potential for inter-kingdom relationship. BMC Microbiol 2016; 16:137. [PMID: 27392067 PMCID: PMC4938989 DOI: 10.1186/s12866-016-0756-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/30/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa (Pa) is a Gram-negative bacteria frequently involved in healthcare-associated pneumonia with poor clinical outcome. To face the announced post-antibiotic era due to increasing resistance and lack of new antibiotics, new treatment strategies have to be developed. Immunomodulation of the host response involved in outcome could be an alternative therapeutic target in Pa-induced lung infection. Kynurenines are metabolites resulting from tryptophan catabolism and are known for their immunomodulatory properties. Pa catabolizes tryptophan through the kynurenine pathway. Interestingly, many host cells also possess the kynurenine pathway, whose metabolites are known to control immune system homeostasis. Thus, bacterial metabolites may interfere with the host's immune response. However, the kynurenine pathway in Pa, including functional enzymes, types and amounts of secreted metabolites remains poorly known. Using liquid chromatography coupled to mass spectrometry and different strains of Pa, we determined types and levels of metabolites produced by Pa ex vivo in growth medium, and the relevance of this production in vivo in a murine model of acute lung injury. RESULTS Ex vivo, Pa secretes clinically relevant kynurenine levels (μM to mM). Pa also secretes kynurenic acid and 3-OH-kynurenine, suggesting that the bacteria possess both a functional kynurenine aminotransferase and kynurenine monooxygenase. The bacterial kynurenine pathway is the major pathway leading to anthranilate production both ex vivo and in vivo. In the absence of the anthranilate pathway, the kynurenine pathway leads to kynurenic acid production. CONCLUSION Pa produces and secretes several metabolites of the kynurenine pathway. Here, we demonstrate the existence of new metabolic pathways leading to synthesis of bioactive molecules, kynurenic acid and 3-OH-kynurenine in Pa. The kynurenine pathway in Pa is critical to produce anthranilate, a crucial precursor of some Pa virulence factors. Metabolites (anthranilate, kynurenine, kynurenic acid) are produced at sustained levels both ex vivo and in vivo leading to a possible immunomodulatory interplay between bacteria and host. These data may imply that pulmonary infection with bacteria highly expressing the kynurenine pathway enzymes could influence the equilibrium of the host's tryptophan metabolic pathway, known to be involved in the immune response to infection. Further studies are needed to explore the effects of these metabolic changes on the pathophysiology of Pa infection.
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Affiliation(s)
- Perrine Bortolotti
- Université Lille CHU Lille, EA 7366 - Recherche translationnelle: relations hôte pathogènes, F-59000, Lille, France
| | - Benjamin Hennart
- Laboratoire de Toxicologie - Pôle de Biologie-Pathologie-Génétique - CHRU de Lille - France, EA4483 - IMPECS, Université Lille Nord de France, Lille, France
| | - Camille Thieffry
- Université Lille CHU Lille, EA 7366 - Recherche translationnelle: relations hôte pathogènes, F-59000, Lille, France
| | - Guillaume Jausions
- Université Lille CHU Lille, EA 7366 - Recherche translationnelle: relations hôte pathogènes, F-59000, Lille, France
| | - Emmanuel Faure
- Université Lille CHU Lille, EA 7366 - Recherche translationnelle: relations hôte pathogènes, F-59000, Lille, France
| | - Teddy Grandjean
- Translational host pathogen research group, Faculté de Médecine de Lille UDSL, Univ Lille Nord de France, Lille, France
| | - Marion Thepaut
- Translational host pathogen research group, Faculté de Médecine de Lille UDSL, Univ Lille Nord de France, Lille, France
| | - Rodrigue Dessein
- Translational host pathogen research group, Faculté de Médecine de Lille UDSL, Univ Lille Nord de France, Lille, France
| | - Delphine Allorge
- Laboratoire de Toxicologie - Pôle de Biologie-Pathologie-Génétique - CHRU de Lille - France, EA4483 - IMPECS, Université Lille Nord de France, Lille, France
| | - Benoit P Guery
- Faculté de Médecine de Lille UDSL, Univ Lille Nord de France, Lille, France
| | - Karine Faure
- Translational host pathogen research group, Faculté de Médecine de Lille UDSL, Univ Lille Nord de France, Lille, France
| | - Eric Kipnis
- Translational host pathogen research group, Faculté de Médecine de Lille UDSL, Univ Lille Nord de France, Lille, France
| | - Bertrand Toussaint
- Laboratoire TIMC-TheREx (UMR5525 CNRS-UGA) Université Grenoble Alpes, Faculté de médecine, La Tronche, France.,Unité médicale de Biochimie des enzymes et des protéines, CHUGA de Grenoble , CS10207, Grenoble, 38043, Rhone alpes, France
| | - Audrey Le Gouellec
- Laboratoire TIMC-TheREx (UMR5525 CNRS-UGA) Université Grenoble Alpes, Faculté de médecine, La Tronche, France. .,Unité médicale de Biochimie des enzymes et des protéines, CHUGA de Grenoble , CS10207, Grenoble, 38043, Rhone alpes, France.
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Tryptophan Biochemistry: Structural, Nutritional, Metabolic, and Medical Aspects in Humans. JOURNAL OF AMINO ACIDS 2016; 2016:8952520. [PMID: 26881063 PMCID: PMC4737446 DOI: 10.1155/2016/8952520] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/06/2015] [Indexed: 12/27/2022]
Abstract
L-Tryptophan is the unique protein amino acid (AA) bearing an indole ring: its biotransformation in living organisms contributes either to keeping this chemical group in cells and tissues or to breaking it, by generating in both cases a variety of bioactive molecules. Investigations on the biology of Trp highlight the pleiotropic effects of its small derivatives on homeostasis processes. In addition to protein turn-over, in humans the pathways of Trp indole derivatives cover the synthesis of the neurotransmitter/hormone serotonin (5-HT), the pineal gland melatonin (MLT), and the trace amine tryptamine. The breakdown of the Trp indole ring defines instead the "kynurenine shunt" which produces cell-response adapters as L-kynurenine, kynurenic and quinolinic acids, or the coenzyme nicotinamide adenine dinucleotide (NAD(+)). This review aims therefore at tracing a "map" of the main molecular effectors in human tryptophan (Trp) research, starting from the chemistry of this AA, dealing then with its biosphere distribution and nutritional value for humans, also focusing on some proteins responsible for its tissue-dependent uptake and biotransformation. We will thus underscore the role of Trp biochemistry in the pathogenesis of human complex diseases/syndromes primarily involving the gut, neuroimmunoendocrine/stress responses, and the CNS, supporting the use of -Omics approaches in this field.
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Liu J, Zhu X, Kim SJ, Zhang W. Antimycin-type depsipeptides: discovery, biosynthesis, chemical synthesis, and bioactivities. Nat Prod Rep 2016; 33:1146-65. [DOI: 10.1039/c6np00004e] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review discusses the isolation, structural variation, biosynthesis, chemical synthesis, and biological activities of antimycin-type depsipeptides.
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Affiliation(s)
- Joyce Liu
- Department of Bioengineering
- University of California
- Berkeley
- USA
| | - Xuejun Zhu
- Department of Chemical and Biomolecular Engineering
- University of California
- Berkeley
- USA
| | - Seong Jong Kim
- Department of Chemical and Biomolecular Engineering
- University of California
- Berkeley
- USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering
- University of California
- Berkeley
- USA
- Physical Biosciences Division
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42
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O'Neill S, Brault J, Stasia MJ, Knaus UG. Genetic disorders coupled to ROS deficiency. Redox Biol 2015; 6:135-156. [PMID: 26210446 PMCID: PMC4550764 DOI: 10.1016/j.redox.2015.07.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/15/2015] [Accepted: 07/16/2015] [Indexed: 12/24/2022] Open
Abstract
Maintaining the redox balance between generation and elimination of reactive oxygen species (ROS) is critical for health. Disturbances such as continuously elevated ROS levels will result in oxidative stress and development of disease, but likewise, insufficient ROS production will be detrimental to health. Reduced or even complete loss of ROS generation originates mainly from inactivating variants in genes encoding for NADPH oxidase complexes. In particular, deficiency in phagocyte Nox2 oxidase function due to genetic variants (CYBB, CYBA, NCF1, NCF2, NCF4) has been recognized as a direct cause of chronic granulomatous disease (CGD), an inherited immune disorder. More recently, additional diseases have been linked to functionally altered variants in genes encoding for other NADPH oxidases, such as for DUOX2/DUOXA2 in congenital hypothyroidism, or for the Nox2 complex, NOX1 and DUOX2 as risk factors for inflammatory bowel disease. A comprehensive overview of novel developments in terms of Nox/Duox-deficiency disorders is presented, combined with insights gained from structure-function studies that will aid in predicting functional defects of clinical variants.
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Affiliation(s)
- Sharon O'Neill
- Conway Institute, University College Dublin, Dublin, Ireland
| | - Julie Brault
- Université Grenoble Alpes, TIMC-IMAG Pôle Biologie, CHU de Grenoble, Grenoble, France; CGD Diagnosis and Research Centre, Pôle Biologie, CHU de Grenoble, Grenoble, France
| | - Marie-Jose Stasia
- Université Grenoble Alpes, TIMC-IMAG Pôle Biologie, CHU de Grenoble, Grenoble, France; CGD Diagnosis and Research Centre, Pôle Biologie, CHU de Grenoble, Grenoble, France
| | - Ulla G Knaus
- Conway Institute, University College Dublin, Dublin, Ireland.
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43
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Butt A, Halliday N, Williams P, Atkins HS, Bancroft GJ, Titball RW. Burkholderia pseudomallei kynB plays a role in AQ production, biofilm formation, bacterial swarming and persistence. Res Microbiol 2015; 167:159-67. [PMID: 26654915 DOI: 10.1016/j.resmic.2015.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 02/07/2023]
Abstract
Kynurenine formamidase (KynB) forms part of the kynurenine pathway which metabolises tryptophan to anthranilate. This metabolite can be used for downstream production of 2-alkyl-4-quinolone (AQ) signalling molecules that control virulence in Pseudomonas aeruginosa. Here we investigate the role of kynB in the production of AQs and virulence-associated phenotypes of Burkholderia pseudomallei K96243, the causative agent of melioidosis. Deletion of kynB resulted in reduced AQ production, increased biofilm formation, decreased swarming and increased tolerance to ciprofloxacin. Addition of exogenous anthranilic acid restored the biofilm phenotype, but not the persister phenotype. This study suggests the kynurenine pathway is a critical source of anthranilate and signalling molecules that may regulate B. pseudomallei virulence.
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Affiliation(s)
- Aaron Butt
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
| | - Nigel Halliday
- Centre for Biomolecular Sciences, School of Biosciences, University of Nottingham, Nottingham, UK.
| | - Paul Williams
- Centre for Biomolecular Sciences, School of Biosciences, University of Nottingham, Nottingham, UK.
| | - Helen S Atkins
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK.
| | - Gregory J Bancroft
- Department of Immunology and Infection, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Richard W Titball
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
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44
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Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TYS, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol 2015; 6:1118. [PMID: 26528266 PMCID: PMC4604316 DOI: 10.3389/fmicb.2015.01118] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/28/2015] [Indexed: 12/13/2022] Open
Abstract
The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.
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Affiliation(s)
- Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Alisha G Campbell
- Department of Natural Sciences, Northwest Missouri State University Maryville, MO, USA
| | - Sagar M Utturkar
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Se-Ran Jun
- Joint Institute for Computational Sciences, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Rebecca E Parales
- Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
| | - Watumesa A Tan
- Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
| | - Michael S Robeson
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Fish, Wildlife and Conservation Biology, Colorado State University Fort Collins, CO, USA
| | - Tse-Yuan S Lu
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - David W Ussery
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Department of Microbiology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
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45
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Fiore CL, Longnecker K, Kido Soule MC, Kujawinski EB. Release of ecologically relevant metabolites by the cyanobacterium Synechococcus elongates CCMP 1631. Environ Microbiol 2015; 17:3949-63. [PMID: 25970745 DOI: 10.1111/1462-2920.12899] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/04/2015] [Accepted: 05/04/2015] [Indexed: 01/08/2023]
Abstract
Photoautotrophic plankton in the surface ocean release organic compounds that fuel secondary production by heterotrophic bacteria. Here we show that an abundant marine cyanobacterium, Synechococcus elongatus, contributes a variety of nitrogen-rich and sulfur-containing compounds to dissolved organic matter. A combination of targeted and untargeted metabolomics and genomic tools was used to characterize the intracellular and extracellular metabolites of S. elongatus. Aromatic compounds, such as 4-hydroxybenzoic acid and phenylalanine, as well as nucleosides (e.g. thymidine, 5'-methylthioadenosine, xanthosine), the organosulfur compound 3-mercaptopropionate, and the plant auxin indole 3-acetic acid, were released by S. elongatus at multiple time points during its growth. Further, the amino acid kynurenine was found to accumulate in the media even though it was not present in the predicted metabolome of S. elongatus. This indicates that some metabolites, including those not predicted by an organism's genome, are likely excreted into the environment as waste; however, these molecules may have broader ecological relevance if they are labile to nearby microbes. The compounds described herein provide excellent targets for quantitative analysis in field settings to assess the source and lability of dissolved organic matter in situ.
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Affiliation(s)
- Cara L Fiore
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 360 Woods Hole Rd. MS#4, Woods Hole, MA, 02543, USA
| | - Krista Longnecker
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 360 Woods Hole Rd. MS#4, Woods Hole, MA, 02543, USA
| | - Melissa C Kido Soule
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 360 Woods Hole Rd. MS#4, Woods Hole, MA, 02543, USA
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 360 Woods Hole Rd. MS#4, Woods Hole, MA, 02543, USA
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46
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Indole: a signaling molecule or a mere metabolic byproduct that alters bacterial physiology at a high concentration? J Microbiol 2015; 53:421-8. [PMID: 26115989 DOI: 10.1007/s12275-015-5273-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/17/2015] [Accepted: 06/18/2015] [Indexed: 10/23/2022]
Abstract
Indole is an organic compound that is widespread in microbial communities inhabiting diverse habitats, like the soil environment and human intestines. Measurement of indole production is a traditional method for the identification of microbial species. Escherichia coli can produce millimolar concentrations of indole in the stationary growth phase under nutrient-rich conditions. Indole has received considerable attention because of its remarkable effects on various biological functions of the microbial communities, for example, biofilm formation, motility, virulence, plasmid stability, and antibiotic resistance. Indole may function as an intercellular signaling molecule, like a quorum-sensing signal. Nevertheless, a receptor system for indole and the function of this compound in coordinated behavior of a microbial population (which are requirements for a true signaling molecule) have not yet been confirmed. Recent findings suggest that a long-known quorum-sensing regulator, E. coli's SdiA, cannot recognize indole and that this compound may simply cause membrane disruption and energy reduction, which can lead to various changes in bacterial physiology including unstable folding of a quorum-sensing regulator. Indole appears to be responsible for acquisition of antibiotic resistance via the formation of persister cells and activation of an exporter. This review highlights and summarizes the current knowledge about indole as a multitrophic molecule among bacteria, together with recently identified new avenues of research.
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47
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Liu J, Zhu X, Seipke RF, Zhang W. Biosynthesis of antimycins with a reconstituted 3-formamidosalicylate pharmacophore in Escherichia coli. ACS Synth Biol 2015; 4:559-65. [PMID: 25275920 DOI: 10.1021/sb5003136] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Antimycins are a family of natural products generated from a hybrid nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) assembly line. Although they possess an array of useful biological activities, their structural complexity makes chemical synthesis challenging, and their biosynthesis has thus far been dependent on slow-growing source organisms. Here, we reconstituted the biosynthesis of antimycins in Escherichia coli, a versatile host that is robust and easy to manipulate genetically. Along with Streptomyces genetic studies, the heterologous expression of different combinations of ant genes enabled us to systematically confirm the functions of the modification enzymes, AntHIJKL and AntO, in the biosynthesis of the 3-formamidosalicylate pharmacophore of antimycins. Our E. coli-based antimycin production system can not only be used to engineer the increased production of these bioactive compounds, but it also paves the way for the facile generation of novel and diverse antimycin analogues through combinatorial biosynthesis.
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Affiliation(s)
| | | | - Ryan F. Seipke
- School
of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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48
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Li Q, Song Y, Qin X, Zhang X, Sun A, Ju J. Identification of the Biosynthetic Gene Cluster for the Anti-infective Desotamides and Production of a New Analogue in a Heterologous Host. JOURNAL OF NATURAL PRODUCTS 2015; 78:944-8. [PMID: 25747118 DOI: 10.1021/acs.jnatprod.5b00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The desotamides (DSAs) are potent antibacterial cyclohexapeptides produced by Streptomyces scopuliridis SCSIO ZJ46. We have identified the 39-kb dsa biosynthetic gene cluster by whole-genome scanning. Composed of 17 open reading frames, the cluster codes for four nonribosomal peptide synthetases and associated resistance, transport, regulatory, and precursor biosynthesis proteins. Heterologous expression of the dsa gene cluster in S. coelicolor M1152 afforded desotamides A and B and the new desotamide G. Cluster identification and its demonstrated amenability to heterologous expression provide the foundation for future mechanistic studies as well as the generation of new and potentially clinically significant DSA analogues.
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Affiliation(s)
- Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
| | - Yongxiang Song
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
| | - Xiangjing Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
| | - Xing Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
| | - Aijun Sun
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
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49
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Anthranilate deteriorates the structure of Pseudomonas aeruginosa biofilms and antagonizes the biofilm-enhancing indole effect. Appl Environ Microbiol 2015; 81:2328-38. [PMID: 25616795 DOI: 10.1128/aem.03551-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anthranilate and indole are alternative degradation products of tryptophan, depending on the bacterial species. While indole enhances the biofilm formation of Pseudomonas aeruginosa, we found that anthranilate, the tryptophan degradation product of P. aeruginosa, had an opposite effect on P. aeruginosa biofilm formation, in which anthranilate deteriorated the mushroom structure of biofilm. The anthranilate effect on biofilm formation was differentially exerted depending on the developmental stage and the presence of shear force. Anthranilate slightly accelerated the initial attachment of P. aeruginosa at the early stage of biofilm development and appeared to build more biofilm without shear force. But anthranilate weakened the biofilm structure in the late stage, deteriorating the mushroom structure of biofilms with shear force to make a flat biofilm. To investigate the interplay of anthranilate with indole in biofilm formation, biofilms were cotreated with anthranilate and indole, and the results showed that anthranilate antagonized the biofilm-enhancing effect of indole. Anthranilate was able to deteriorate the preformed biofilm. The effect of anthranilate and indole on biofilm formation was quorum sensing independent. AntR, a regulator of anthranilate-degrading metabolism was synergistically activated by cotreatment with anthranilate and indole, suggesting that indole might enhance biofilm formation by facilitating the degradation of anthranilate. Anthranilate slightly but significantly affected the cyclic diguaniylate (c-di-GMP) level and transcription of major extracellular polysaccharide (Psl, Pel, and alginate) operons. These results suggest that anthranilate may be a promising antibiofilm agent and antagonize the effect of indole on P. aeruginosa biofilm formation.
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50
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Structures of bacterial kynurenine formamidase reveal a crowded binuclear zinc catalytic site primed to generate a potent nucleophile. Biochem J 2014; 462:581-9. [PMID: 24942958 PMCID: PMC4243253 DOI: 10.1042/bj20140511] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Tryptophan is an important precursor for chemical entities that ultimately support the biosynthesis of key metabolites. The second stage of tryptophan catabolism is catalysed by kynurenine formamidase, an enzyme that is different between eukaryotes and prokaryotes. In the present study, we characterize the catalytic properties and present the crystal structures of three bacterial kynurenine formamidases. The structures reveal a new amidase protein fold, a highly organized and distinctive binuclear Zn2+ catalytic centre in a confined, hydrophobic and relatively rigid active site. The structure of a complex with 2-aminoacetophenone delineates aspects of molecular recognition extending to the observation that the substrate itself may be conformationally restricted to assist binding in the confined space of the active site and for subsequent processing. The cations occupy a crowded environment, and, unlike most Zn2+-dependent enzymes, there is little scope to increase co-ordination number during catalysis. We propose that the presence of a bridging water/hydroxide ligand in conjunction with the placement of an active site histidine supports a distinctive amidation mechanism. Catalytic properties and structures of three bacterial kynurenine formamidases are presented. The dimeric enzyme possesses an uncommon fold and crowded binuclear zinc active site. Fluorescence and structure of a complex inform on molecular recognition and a plausible mechanism is proposed.
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