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Elisée E, Ducrot L, Méheust R, Bastard K, Fossey-Jouenne A, Grogan G, Pelletier E, Petit JL, Stam M, de Berardinis V, Zaparucha A, Vallenet D, Vergne-Vaxelaire C. A refined picture of the native amine dehydrogenase family revealed by extensive biodiversity screening. Nat Commun 2024; 15:4933. [PMID: 38858403 PMCID: PMC11164908 DOI: 10.1038/s41467-024-49009-2] [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: 09/21/2023] [Accepted: 05/20/2024] [Indexed: 06/12/2024] Open
Abstract
Native amine dehydrogenases offer sustainable access to chiral amines, so the search for scaffolds capable of converting more diverse carbonyl compounds is required to reach the full potential of this alternative to conventional synthetic reductive aminations. Here we report a multidisciplinary strategy combining bioinformatics, chemoinformatics and biocatalysis to extensively screen billions of sequences in silico and to efficiently find native amine dehydrogenases features using computational approaches. In this way, we achieve a comprehensive overview of the initial native amine dehydrogenase family, extending it from 2,011 to 17,959 sequences, and identify native amine dehydrogenases with non-reported substrate spectra, including hindered carbonyls and ethyl ketones, and accepting methylamine and cyclopropylamine as amine donor. We also present preliminary model-based structural information to inform the design of potential (R)-selective amine dehydrogenases, as native amine dehydrogenases are mostly (S)-selective. This integrated strategy paves the way for expanding the resource of other enzyme families and in highlighting enzymes with original features.
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Affiliation(s)
- Eddy Elisée
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Laurine Ducrot
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Raphaël Méheust
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Bastard
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Aurélie Fossey-Jouenne
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Mark Stam
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Véronique de Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - David Vallenet
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
| | - Carine Vergne-Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
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Liu H, Yang H, Yin X, Wang S, Fang S, Zhang H. A novel pbd gene cluster responsible for pyrrole and pyridine ring cleavage in Rhodococcus ruber A5. JOURNAL OF HAZARDOUS MATERIALS 2024; 464:132992. [PMID: 37976859 DOI: 10.1016/j.jhazmat.2023.132992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/23/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Pyridine and pyrrole, which are regarded as recalcitrant chemicals, are released into the environment as a result of industrial manufacturing processes, posing serious hazards to both the environment and human health. However, the pyrrole degradation mechanism and the pyridine-degrading gene in Rhodococcus are unknown. Herein, a highly efficient pyridine and pyrrole degradation strain Rhodococcus ruber A5 was isolated. Strain A5 completely degraded 1000 mg/L pyridine in a mineral salt medium within 24 h. The pyridine degradation of strain A5 was optimized using the BoxBehnken design. The optimum degradation conditions were found to be pH 7.15, temperature 28.06 ℃, and inoculation amount 1290.94 mg/L. The pbd gene clusters involved in pyridine degradation were discovered via proteomic analysis. The initial ring cleavage of pyridine and pyrrole in strain A5 was carried out by the two-component flavin-dependent monooxygenase PbdA/PbdE. The degradation pathways of pyridine and pyrrole were proposed by the identification of metabolites and comparisons of homologous genes. Additionally, homologous pbd gene clusters were found to exist in different bacterial genomes. Our study revealed the ring cleavage mechanisms of pyrrole and pyridine, and strain A5 was identified as a promising resource for pyridine bioremediation.
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Affiliation(s)
- Hongming Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Hao Yang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Xiaye Yin
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Siwen Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, PR China; Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, Anhui, PR China
| | - Shangping Fang
- School of Anesthesiology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Hao Zhang
- Key Laboratory of Metallurgical Emission Reduction and Comprehensive Utilization of Resources, Ministry of Education (Anhui University of Technology), Ma'anshan 243002, Anhui, China.
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Vinacour M, Moiana M, Forné I, Jung K, Bertea M, Calero Valdayo PM, Nikel PI, Imhof A, Palumbo MC, Fernández Do Porto D, Ruiz JA. Genetic dissection of the degradation pathways for the mycotoxin fusaric acid in Burkholderia ambifaria T16. Appl Environ Microbiol 2023; 89:e0063023. [PMID: 38054732 PMCID: PMC10734416 DOI: 10.1128/aem.00630-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/25/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Fusaric acid (FA) is an important virulence factor produced by several Fusarium species. These fungi are responsible for wilt and rot diseases in a diverse range of crops. FA is toxic for animals, humans and soil-borne microorganisms. This mycotoxin reduces the survival and competition abilities of bacterial species able to antagonize Fusarium spp., due to its negative effects on viability and the production of antibiotics effective against these fungi. FA biodegradation is not a common characteristic among bacteria, and the determinants of FA catabolism have not been identified so far in any microorganism. In this study, we identified genes, enzymes, and metabolic pathways involved in the degradation of FA in the soil bacterium Burkholderia ambifaria T16. Our results provide insights into the catabolism of a pyridine-derivative involved in plant pathogenesis by a rhizosphere bacterium.
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Affiliation(s)
- Matias Vinacour
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauro Moiana
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Faculty Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Micaela Bertea
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Patricia M. Calero Valdayo
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pablo I. Nikel
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Miranda C. Palumbo
- Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario Fernández Do Porto
- Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jimena A. Ruiz
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Faculty Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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Xiang Y, Li S, Rene ER, Lun X, Zhang P, Ma W. Detoxification of fluoroglucocorticoid by Acinetobacter pittii C3 via a novel defluorination pathway with hydrolysis, oxidation and reduction: Performance, genomic characteristics, and mechanism. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131302. [PMID: 37031670 DOI: 10.1016/j.jhazmat.2023.131302] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/10/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Biological dehalogenation degradation was an important detoxification method for the ecotoxicity and teratogenic toxicity of fluorocorticosteroids (FGCs). The functional strain Acinetobacter pittii C3 can effectively biodegrade and defluorinate to 1 mg/L Triamcinolone acetonide (TA), a representative FGCs, with 86 % and 79 % removal proportion in 168 h with the biodegradation and detoxification kinetic constant of 0.031/h and 0.016/h. The dehalogenation and degradation ability of strain C3 was related to its dehalogenation genomic characteristics, which manifested in the functional gene expression of dehalogenation, degradation, and toxicity tolerance. Three detoxification mechanisms were positively correlated with defluorination pathways through hydrolysis, oxidation, and reduction, which were regulated by the expression of the haloacid dehalogenase (HAD) gene (mupP, yrfG, and gph), oxygenase gene (dmpA and catA), and reductase gene (nrdAB and TgnAB). Hydrolysis defluorination was the most critical way for TA detoxification metabolism, which could rapidly generate low-toxicity metabolites and reduce toxic bioaccumulation due to hydrolytic dehalogenase-induced defluorination. The mechanism of hydrolytic defluorination was that the active pocket of hydrolytic dehalogenase was matched well with the spatial structure of TA under the adjustment of the hydrogen bond, and thus induced molecular recognition to promote the catalytic hydrolytic degradation of various amino acid residues. This work provided an effective bioremediation method and mechanism for improving defluorination and detoxification performance.
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Affiliation(s)
- Yayun Xiang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Sinuo Li
- Beijing No. 80 High School, Beijing 100102, China
| | - Eldon R Rene
- IHE-Delft, Institute for Water Education, Department of Environmental Engineering and Water Technology, Westvest 7, 2611AX Delft, the Netherlands
| | - Xiaoxiu Lun
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Panyue Zhang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Weifang Ma
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
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Li Y, Xu Z, Chen L, Zhu M, Wang D, Jing M, Chen Y, Sun Z, Wang Y, He B, Yan W, Jiao R, Ye Y. New metabolites from Streptomyces pseudovenezuelae NA07424 and their potential activity of inducing resistance in plants against Phytophthora capsici. PEST MANAGEMENT SCIENCE 2023; 79:349-356. [PMID: 36153708 DOI: 10.1002/ps.7204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 09/19/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The lack of novel fungicide and appearance of resistance are the most emergent problems in the control of Phytophthora diseases. Plant immunity elicitors that induce systemic resistance in plants are regarded as the new strategy for plant disease control. Streptomyces can produce a variety of bioactive natural products, which are important resources for lead compounds of plant immunity elicitors. RESULTS A novel peptidendrocin C (1) together with the known analog peptidendrocin B (2) were isolated from Streptomyces pseudovenezuelae NA07424. Their structures were confirmed by spectroscopic data and Marfey's reaction. In bioactive assays, compound 1 played an important role in inducing systemic resistance of Nicotiana benthamiana against Phytophthora capsici growth, with a 90.5% inhibition ratio at 400 μg/mL, while compound 2 showed moderate activity, inhibiting P. capsici growth by a 50.8% decrease at 400 μg/mL. Simultaneously, two compounds promoted enhanced expression of the PR1 gene and callose accumulation in N. benthamiana and Arabidopsis thaliana. In this paper, we also provide the first insights into their biosynthesis by confirming their biosynthesis gene cluster and related functional genes. CONCLUSION Our findings show that 1 and 2 have the potential to be used as lead compounds for development of new plant immunity elicitors to control Phytophthora diseases. The study of the biosynthesis pathway lays the groundwork for further application of the bioactive natural products. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Yu Li
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
| | - Zifei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing, China
| | - Liyifan Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
| | - Mengyue Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dacheng Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
| | - Maofeng Jing
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yiliang Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
| | - Ziqian Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yiming Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
| | - Bo He
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
| | - Wei Yan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
| | - Ruihua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yonghao Ye
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, P. R. China
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Ducrot L, Bennett M, André-Leroux G, Elisée E, Marynberg S, Fossey-Jouenne A, Zaparucha A, Grogan G, Vergne-Vaxelaire C. Expanding the Substrate Scope of Native Amine Dehydrogenases through In Silico Structural Exploration and Targeted Protein Engineering. ChemCatChem 2022. [DOI: 10.1002/cctc.202200880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Laurine Ducrot
- Commissariat a l'energie atomique et aux energies alternatives Institut de biologie Francois Jacob Genoscope 2 rue Gaston Cremieux 91000 EVRY FRANCE
| | | | - Gwenaëlle André-Leroux
- Paris-Saclay University: Universite Paris-Saclay MaIAGE: Mathematiques et Informatique Appliquees du Genome a l'Environnement FRANCE
| | - Eddy Elisée
- Commissariat a l'energie atomique et aux energies alternatives Institut de biologie Francois Jacob Genoscope 2 rue Gaston Cremieux 91000 EVRY FRANCE
| | - Sacha Marynberg
- Commissariat a l'energie atomique et aux energies alternatives Institut de biologie Francois Jacob Genoscope FRANCE
| | - Aurélie Fossey-Jouenne
- Commissariat a l'energie atomique et aux energies alternatives Institut de biologie Francois Jacob Genoscope FRANCE
| | - Anne Zaparucha
- Commissariat a l'energie atomique et aux energies alternatives Institut de biologie Francois Jacob Genoscope FRANCE
| | | | - Carine Vergne-Vaxelaire
- Commissariat a l'energie atomique et aux energies alternatives Institut de biologie Francois Jacob Genoscope 2 rue Gaston Cremieux 91000 EVRY FRANCE
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Genome mining of Burkholderia ambifaria strain T16, a rhizobacterium able to produce antimicrobial compounds and degrade the mycotoxin fusaric acid. World J Microbiol Biotechnol 2022; 38:114. [PMID: 35578144 DOI: 10.1007/s11274-022-03299-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
Burkholderia ambifaria T16 is a bacterium isolated from the rhizosphere of barley plants that showed a remarkable antifungal activity. This strain was also able to degrade fusaric acid (5-Butylpyridine-2-carboxylic acid) and detoxify this mycotoxin in inoculated barley seedlings. Genes and enzymes responsible for fusaric acid degradation have an important biotechnological potential in the control of fungal diseases caused by fusaric acid producers, or in the biodegradation/bio catalysis processes of pyridine derivatives. In this study, the complete genome of B. ambifaria T16 was sequenced and analyzed to identify genes involved in survival and competition in the rhizosphere, plant growth promotion, fungal growth inhibition, and degradation of aromatic compounds. The genomic analysis revealed the presence of several operons for the biosynthesis of antimicrobial compounds, such as pyrrolnitrin, ornibactin, occidiofungin and the membrane-associated AFC-BC11. These compounds were also detected in bacterial culture supernatants by mass spectrometry analysis. In addition, this strain has multiple genes contributing to its plant growth-promoting profile, including those for acetoin, 2,3-butanediol and indole-3-acetic acid production, siderophores biosynthesis, and solubilisation of organic and inorganic phosphate. A pan-genomic analysis demonstrated that the genome of strain T16 possesses large gene clusters that are absent in the genomes of B. ambifaria reference strains. According to predictions, most of these clusters would be involved in aromatic compounds degradation. One genomic region, encoding flavin-dependent monooxygenases of unknown function, is proposed as a candidate responsible for fusaric acid degradation.
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Baek JH, Kim KH, Lee Y, Jeong SE, Jin HM, Jia B, Jeon CO. Elucidating the biodegradation pathway and catabolic genes of benzophenone-3 in Rhodococcus sp. S2-17. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 299:118890. [PMID: 35085657 DOI: 10.1016/j.envpol.2022.118890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
A new bacterium, Rhodococcus sp. S2-17, which could completely degrade an emerging organic pollutant, benzophenone-3 (BP-3), was isolated from contaminated sediment through an enrichment procedure, and its BP-3 catabolic pathway and genes were identified through metabolic intermediate and transcriptomic analyses and biochemical and genetic studies. Metabolic intermediate analysis suggested that strain S2-17 may degrade BP-3 using a catabolic pathway progressing via the intermediates BP-1, 2,4,5-trihydroxy-benzophenone, 3-hydroxy-4-benzoyl-2,4-hexadienedioic acid, 4-benzoyl-3-oxoadipic acid, 3-oxoadipic acid, and benzoic acid. A putative BP-3 catabolic gene cluster including cytochrome P450, flavin-dependent oxidoreductase, hydroxyquinol 1,2-dioxygenase, maleylacetate reductase, and α/β hydrolase genes was identified through genomic and transcriptomic analyses. Genes encoding the cytochrome P450 complex that demethylates BP-3 to BP-1 were functionally verified through protein expression, and the functions of the other genes were also verified through knockout mutant construction and intermediate analysis. This study suggested that strain S2-17 might have acquired the ability to catabolize BP-3 by recruiting the cytochrome P450 complex and α/β hydrolase, which hydrolyzes 4-benzoyl-3-oxoadipic acid to benzoic acid and 3-oxoadipic acid, genes, providing insights into the recruitment of genes of for the catabolism of emerging organic pollutants.
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Affiliation(s)
- Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Yunhee Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea; Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea
| | - Hyun Mi Jin
- Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do, 37242, Republic of Korea
| | - Baolei Jia
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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da Silva MCS, da Luz JMR, Veloso TGR, Gomes WDS, Oliveira ECDS, Anastácio LM, Cunha Neto A, Moreli AP, Guarçoni RC, Kasuya MCM, Pereira LL. Processing techniques and microbial fermentation on microbial profile and chemical and sensory quality of the coffee beverage. Eur Food Res Technol 2022. [DOI: 10.1007/s00217-022-03980-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Overexpression of a Gene Encoding Trigonelline Synthase from Areca catechu L. Promotes Drought Resilience in Transgenic Arabidopsis. PLANTS 2022; 11:plants11040487. [PMID: 35214824 PMCID: PMC8877179 DOI: 10.3390/plants11040487] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 11/27/2022]
Abstract
Areca catechu L. is a commercially important palm tree widely cultured in tropical and subtropical areas. Its growth and production are severely hindered by the increasing threat of drought. In the present study, we investigated the physiological responses of areca seedlings to drought stress. The results showed that prolonged drought-induced yellowing on the overall area of most leaves significantly altered the chlorophyll fluorescence parameters, including maximum chemical efficiency (Fv/Fm), photochemical efficiency of PSII (Y(II)), photochemical chlorophyll fluorescence quenching (qP) and non-photochemical chlorophyll fluorescence quenching (NPQ). On the 10th day of drought treatment, the contents of proline in the areca leaves and roots increased, respectively, by 12.2 times and 8.4 times compared to normal watering. The trigonelline levels in the leaves rose from 695.35 µg/g to 1125.21 µg/g under 10 days of water shortage, while no significant changes were detected in the content of trigonelline in the roots. We determined the gene encoding areca trigonelline synthase (AcTS) by conducting a bioinformatic search of the areca genome database. Sequence analysis revealed that AcTS is highly homologous to the trigonelline synthases in Coffea arabica (CaTS 1 and CaTS 2) and all possess a conserved S-adenosyl- L-methionine binding motif. The overexpression of AcTS in Arabidopsis thaliana demonstrated that AcTS is responsible for the generation of trigonelline in transgenic Arabidopsis, which in turn improves the drought resilience of transgenic Arabidopsis. This finding enriches our understanding of the molecular regulatory mechanism of the response of areca to water shortage and provides a foundation for improving the drought tolerance of areca seedlings.
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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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Bessonnet T, Mariage A, Petit JL, Pellouin V, Debard A, Zaparucha A, Vergne-Vaxelaire C, de Berardinis V. Purification and Characterization of Nit phym , a Robust Thermostable Nitrilase From Paraburkholderia phymatum. Front Bioeng Biotechnol 2021; 9:686362. [PMID: 34277586 PMCID: PMC8280356 DOI: 10.3389/fbioe.2021.686362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Despite the success of some nitrilases in industrial applications, there is a constant demand to broaden the catalog of these hydrolases, especially robust ones with high operational stability. By using the criteria of thermoresistance to screen a collection of candidate enzymes heterologously expressed in Escherichia coli, the enzyme Nit phym from the mesophilic organism Paraburkholderia phymatum was selected and further characterized. Its quick and efficient purification by heat treatment is of major interest for large-scale applications. The purified nitrilase displayed a high thermostability with 90% of remaining activity after 2 days at 30°C and a half-life of 18 h at 60°C, together with a broad pH range of 5.5-8.5. Its high resistance to various miscible cosolvents and tolerance to high substrate loadings enabled the quantitative conversion of 65.5 g⋅L-1 of 3-phenylpropionitrile into 3-phenylpropionic acid at 50°C in 8 h at low enzyme loadings of 0.5 g⋅L-1, with an isolated yield of 90%. This study highlights that thermophilic organisms are not the only source of industrially relevant thermostable enzymes and extends the scope of efficient nitrilases for the hydrolysis of a wide range of nitriles, especially trans-cinnamonitrile, terephthalonitrile, cyanopyridines, and 3-phenylpropionitrile.
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Affiliation(s)
- Thomas Bessonnet
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Aline Mariage
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Virginie Pellouin
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Adrien Debard
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Carine Vergne-Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Véronique de Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
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13
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Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research. Nat Methods 2021; 18:733-746. [PMID: 33972782 DOI: 10.1038/s41592-021-01116-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/12/2021] [Indexed: 02/03/2023]
Abstract
Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites. Here we discuss current common strategies for UHPLC-HRMS-based metabolomics, with a focus on expanding metabolome coverage.
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Abstract
Phytoplankton transform inorganic carbon into thousands of biomolecules that represent an important pool of fixed carbon, nitrogen, and sulfur in the surface ocean. Metabolite production differs between phytoplankton, and the flux of these molecules through the microbial food web depends on compound-specific bioavailability to members of a wider microbial community. Yet relatively little is known about the diversity or concentration of metabolites within marine plankton. Here, we compare 313 polar metabolites in 21 cultured phytoplankton species and in natural planktonic communities across environmental gradients to show that bulk community metabolomes reflect the chemical composition of the phytoplankton community. We also show that groups of compounds have similar patterns across space and taxonomy, suggesting that the concentrations of these compounds in the environment are controlled by similar sources and sinks. We quantify several compounds in the surface ocean that represent substantial understudied pools of labile carbon. For example, the N-containing metabolite homarine was up to 3% of particulate carbon and is produced in high concentrations by cultured Synechococcus, and S-containing gonyol accumulated up to 2.5 nM in surface particles and likely originates from dinoflagellates or haptophytes. Our results show that phytoplankton composition directly shapes the carbon composition of the surface ocean. Our findings suggest that in order to access these pools of bioavailable carbon, the wider microbial community must be adapted to phytoplankton community composition. IMPORTANCE Microscopic phytoplankton transform 100 million tons of inorganic carbon into thousands of different organic compounds each day. The structure of each chemical is critical to its biological and ecosystem function, yet the diversity of biomolecules produced by marine microbial communities remained mainly unexplored, especially small polar molecules which are often considered the currency of the microbial loop. Here, we explore the abundance and diversity of small biomolecules in planktonic communities across ecological gradients in the North Pacific and within 21 cultured phytoplankton species. Our work demonstrates that phytoplankton diversity is an important determinant of the chemical composition of the highly bioavailable pool of organic carbon in the ocean, and we highlight understudied yet abundant compounds in both the environment and cultured organisms. These findings add to understanding of how the chemical makeup of phytoplankton shapes marine microbial communities where the ability to sense and use biomolecules depends on the chemical structure.
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The First Step of Biodegradation of 7-Hydroxycoumarin in Pseudomonas mandelii 7HK4 Depends on an Alcohol Dehydrogenase-Type Enzyme. Int J Mol Sci 2021; 22:ijms22041552. [PMID: 33557119 PMCID: PMC7913881 DOI: 10.3390/ijms22041552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 11/23/2022] Open
Abstract
Coumarins are well known secondary metabolites widely found in various plants. However, the degradation of these compounds in the environment has not been studied in detail, and, especially, the initial stages of the catabolic pathways of coumarins are not fully understood. A soil isolate Pseudomonas mandelii 7HK4 is able to degrade 7-hydroxycoumarin (umbelliferone) via the formation of 3-(2,4-dihydroxyphenyl)propionic acid, but the enzymes catalyzing the α-pyrone ring transformations have not been characterized. To elucidate an upper pathway of the catabolism of 7-hydroxycoumarin, 7-hydroxycoumarin-inducible genes hcdD, hcdE, hcdF, and hcdG were identified by RT-qPCR analysis. The DNA fragment encoding a putative alcohol dehydrogenase HcdE was cloned, and the recombinant protein catalyzed the NADPH-dependent reduction of 7-hydroxycoumarin both in vivo and in vitro. The reaction product was isolated and characterized as a 7-hydroxy-3,4-dihydrocoumarin based on HPLC-MS and NMR analyses. In addition, the HcdE was active towards 6,7-dihydroxycoumarin, 6-hydroxycoumarin, 6-methylcoumarin and coumarin. Thus, in contrast to the well-known fact that the ene-reductases usually participate in the reduction of the double bond, an alcohol dehydrogenase catalyzing such reaction has been identified, and, for P. mandelii 7HK4, 7-hydroxycoumarin degradation via a 7-hydroxy-3,4-dihydrocoumarin pathway has been proposed.
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Effect of solid-state fungal fermentation on the non-volatiles content and volatiles composition of Coffea canephora (Robusta) coffee beans. Food Chem 2020; 337:128023. [PMID: 32920275 DOI: 10.1016/j.foodchem.2020.128023] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 11/21/2022]
Abstract
In this study, the effects of fungal fermentation on green canephora coffee beans were evaluated by observing the changes to selected non-volatile parameters before roasting, and subsequently the volatile profile after roasting. Solid-state fermentation (SSF) by Aspergillus spp. and Mucor spp. on green canephora coffee beans was shown to modulate the contents of free sugars, free amino acids and polyphenolic compounds such as caffeoylquinic acids (CQAs). Significant strain-specific differences were observed in the contents of aroma compounds after roasting. A significant increase in pyrazines was observed in the Aspergillus oryzae-fermented samples, while higher levels of furans were detected in the Mucor plumbeus-fermented samples. The present work shows that fungal fermentation of green canephora coffee beans is a potentially promising method for the modulation and improvement of coffee flavour and aroma.
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Microbial Degradation of Pyridine: a Complete Pathway in Arthrobacter sp. Strain 68b Deciphered. Appl Environ Microbiol 2020; 86:AEM.00902-20. [PMID: 32471913 DOI: 10.1128/aem.00902-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/23/2020] [Indexed: 11/20/2022] Open
Abstract
Pyridine and its derivatives constitute the majority of heterocyclic aromatic compounds that occur largely as a result of human activities and contribute to environmental pollution. It is known that they can be degraded by various bacteria in the environment; however, the degradation of unsubstituted pyridine has not yet been completely resolved. In this study, we present data on the pyridine catabolic pathway in Arthrobacter sp. strain 68b at the level of genes, enzymes, and metabolites. The pyr gene cluster, responsible for the degradation of pyridine, was identified in a catabolic plasmid, p2MP. The pathway of pyridine metabolism consisted of four enzymatic steps and ended by the formation of succinic acid. The first step in the degradation of pyridine proceeds through a direct ring cleavage catalyzed by a two-component flavin-dependent monooxygenase system, encoded by pyrA (pyridine monooxygenase) and pyrE genes. The genes pyrB, pyrC, and pyrD were found to encode (Z)-N-(4-oxobut-1-enyl)formamide dehydrogenase, amidohydrolase, and succinate semialdehyde dehydrogenase, respectively. These enzymes participate in the subsequent steps of pyridine degradation. The metabolites of these enzymatic reactions were identified, and this allowed us to reconstruct the entire pyridine catabolism pathway in Arthrobacter sp. 68b.IMPORTANCE The biodegradation pathway of pyridine, a notorious toxicant, is relatively unexplored, as no genetic data related to this process have ever been presented. In this paper, we describe the plasmid-borne pyr gene cluster, which includes the complete set of genes responsible for the degradation of pyridine. A key enzyme, the monooxygenase PyrA, which is responsible for the first step of the catabolic pathway, performs an oxidative cleavage of the pyridine ring without typical activation steps such as reduction or hydroxylation of the heterocycle. This work provides new insights into the metabolism of N-heterocyclic compounds in nature.
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Xiang W, Wei X, Tang H, Li L, Huang R. Complete Genome Sequence and Biodegradation Characteristics of Benzoic Acid-Degrading Bacterium Pseudomonas sp. SCB32. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6146104. [PMID: 32714981 PMCID: PMC7354641 DOI: 10.1155/2020/6146104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/17/2020] [Indexed: 11/25/2022]
Abstract
Allelochemicals are metabolites produced by living organisms that have a detrimental effect on other species when released into the environment. These chemicals play critical roles in the problems associated with crop replanting. Benzoic acid is a representative allelochemical found in root exudates and rhizosphere soil of crops and inhibits crop growth. The bioremediation of allelochemicals by microorganisms is an efficient decontamination process. In this research, a bacterial strain capable of degrading benzoic acid as the sole carbon source was isolated. The genome of the strain was sequenced, and biodegradation characteristics and metabolic mechanisms were examined. Strain SCB32 was identified as Pseudomonas sp. based on 16S rRNA gene analysis coupled with physiological and biochemical analyses. The degradation rate of 800 mg L-1 benzoic acid by strain SCB32 was greater than 97.0% in 24 h. The complete genome of strain SCB32 was 6.3 Mbp with a GC content of 64.6% and 5960 coding genes. Potential benzoic acid degradation genes were found by comparison to the KEGG database. Some key intermediate metabolites of benzoic acid, such as catechol, were detected by gas chromatography-mass spectrometry. The biodegradation pathway of benzoic acid, the ortho pathway, is proposed for strain SCB32 based on combined data from genome annotation and mass spectrometry. Moreover, the benzoic acid degradation products from strain SCB32 were essentially nontoxic to lettuce seedlings, while seeds in the benzoic acid-treated group showed significant inhibition of germination. This indicates a possible application of strain SCB32 in the bioremediation of benzoic acid contamination in agricultural environments.
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Affiliation(s)
- Wei Xiang
- Department of Agronomy, Agricultural College of Guangxi University, Nanning 530004, China
| | - Xiaolan Wei
- Department of Agronomy, Agricultural College of Guangxi University, Nanning 530004, China
| | - Hui Tang
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin 541006, China
| | - Liangbo Li
- Department of Agronomy, Agricultural College of Guangxi University, Nanning 530004, China
| | - Rongshao Huang
- Department of Agronomy, Agricultural College of Guangxi University, Nanning 530004, China
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19
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Caparco AA, Pelletier E, Petit JL, Jouenne A, Bommarius BR, Berardinis V, Zaparucha A, Champion JA, Bommarius AS, Vergne‐Vaxelaire C. Metagenomic Mining for Amine Dehydrogenase Discovery. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000094] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Adam A. Caparco
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Jean Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Aurélie Jouenne
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Bettina R. Bommarius
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Véronique Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
| | - Julie A. Champion
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology Atlanta, GA USA
| | - Carine Vergne‐Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 91057 Evry France
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20
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Lelièvre CM, Balandras M, Petit J, Vergne‐Vaxelaire C, Zaparucha A. ATP Regeneration System in Chemoenzymatic Amide Bond Formation with Thermophilic CoA Ligase. ChemCatChem 2020. [DOI: 10.1002/cctc.201901870] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chloé M. Lelièvre
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 2 rue Gaston Crémieux 91057 Evry France
| | - Mélanie Balandras
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 2 rue Gaston Crémieux 91057 Evry France
| | - Jean‐Louis Petit
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 2 rue Gaston Crémieux 91057 Evry France
| | - Carine Vergne‐Vaxelaire
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 2 rue Gaston Crémieux 91057 Evry France
| | - Anne Zaparucha
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris-Saclay 2 rue Gaston Crémieux 91057 Evry France
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21
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Li K, Wang D, Gong L, Lyu Y, Guo H, Chen W, Jin C, Liu X, Fang C, Luo J. Comparative analysis of metabolome of rice seeds at three developmental stages using a recombinant inbred line population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:908-922. [PMID: 31355982 PMCID: PMC6899760 DOI: 10.1111/tpj.14482] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/13/2019] [Accepted: 07/23/2019] [Indexed: 05/23/2023]
Abstract
Plants are considered an important food and nutrition source for humans. Despite advances in plant seed metabolomics, knowledge about the genetic and molecular bases of rice seed metabolomes at different developmental stages is still limited. Here, using Zhenshan 97 (ZS97) and Minghui 63 (MH63), we performed a widely targeted metabolic profiling in seeds during grain filling, mature seeds and germinating seeds. The diversity between MH63 and ZS97 was characterized in terms of the content of metabolites and the metabolic shifting across developmental stages. Taking advantage of the ultra-high-density genetic map of a population of 210 recombinant inbred lines (RILs) derived from a cross between ZS97 and MH63, we identified 4681 putative metabolic quantitative trait loci (mQTLs) in seeds across the three stages. Further analysis of the mQTLs for the codetected metabolites across the three stages revealed that the genetic regulation of metabolite accumulation was closely related to developmental stage. Using in silico analyses, we characterized 35 candidate genes responsible for 30 structurally identified or annotated compounds, among which LOC_Os07g04970 and LOC_Os06g03990 were identified to be responsible for feruloylserotonin and l-asparagine content variation across populations, respectively. Metabolite-agronomic trait association and colocation between mQTLs and phenotypic quantitative trait loci (pQTLs) revealed the complexity of the metabolite-agronomic trait relationship and the corresponding genetic basis.
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Affiliation(s)
- Kang Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Dehong Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Liang Gong
- The Jackson Laboratory for Genomic MedicineFarmingtonCTUSA
| | - Yuanyuan Lyu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Hao Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Wei Chen
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Cheng Jin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Xianqing Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourceCollege of Tropical CropsHainan UniversityHaikou570288China
| | - Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourceCollege of Tropical CropsHainan UniversityHaikou570288China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant ResearchHuazhong Agricultural UniversityWuhan430070China
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourceCollege of Tropical CropsHainan UniversityHaikou570288China
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Padhi EMT, Maharaj N, Lin SY, Mishchuk DO, Chin E, Godfrey K, Foster E, Polek M, Leveau JHJ, Slupsky CM. Metabolome and Microbiome Signatures in the Roots of Citrus Affected by Huanglongbing. PHYTOPATHOLOGY 2019; 109:2022-2032. [PMID: 31433274 DOI: 10.1094/phyto-03-19-0103-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Huanglongbing (HLB) is a severe, incurable citrus disease caused by the bacterium 'Candidatus Liberibacter asiaticus' (CLas). Although citrus leaves serve as the site of initial infection, CLas is known to migrate to and colonize the root system; however, little is known about the impact of CLas infection on root metabolism and resident microbial communities. Scions of 'Lisbon' lemon and 'Washington Navel' orange grafted onto 'Carrizo' rootstock were grafted with either CLas-infected citrus budwood or uninfected budwood. Roots were obtained from trees 46 weeks after grafting and analyzed via 1H nuclear magnetic resonance spectroscopy to identify water-soluble root metabolites and high-throughput sequencing of 16S rRNA and ITS gene amplicons to determine the relative abundance of bacterial and fungal taxa in the root rhizosphere and endosphere. In both citrus varieties, 27 metabolites were identified, of which several were significantly different between CLas(+) and control plants. CLas infection also appeared to alter the microbial community structure near and inside the roots of citrus plants. Nonmetric multidimensional scaling (NMDS) and a principal coordinate analysis (PCoA) revealed distinct metabolite and microbial profiles, demonstrating that CLas impacts the root metabolome and microbiome in a manner that is variety-specific.
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Affiliation(s)
- Emily M T Padhi
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616
| | - Nilesh Maharaj
- Department of Plant Pathology, University of California at Davis, Davis, CA 95616
| | - Shin-Yi Lin
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616
| | - Darya O Mishchuk
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616
| | - Elizabeth Chin
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616
| | - Kris Godfrey
- Contained Research Facility, University of California at Davis, Davis, CA 95616
| | - Elizabeth Foster
- Contained Research Facility, University of California at Davis, Davis, CA 95616
| | - Marylou Polek
- U.S. Department of Agriculture-Agricultural Research Service National Germplasm Repository, Riverside, CA 92507
| | - Johan H J Leveau
- Department of Plant Pathology, University of California at Davis, Davis, CA 95616
| | - Carolyn M Slupsky
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616
- Department of Nutrition, University of California at Davis, Davis, CA 95616
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23
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Identification of evolutionary and kinetic drivers of NAD-dependent signaling. Proc Natl Acad Sci U S A 2019; 116:15957-15966. [PMID: 31341085 DOI: 10.1073/pnas.1902346116] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) provides an important link between metabolism and signal transduction and has emerged as central hub between bioenergetics and all major cellular events. NAD-dependent signaling (e.g., by sirtuins and poly-adenosine diphosphate [ADP] ribose polymerases [PARPs]) consumes considerable amounts of NAD. To maintain physiological functions, NAD consumption and biosynthesis need to be carefully balanced. Using extensive phylogenetic analyses, mathematical modeling of NAD metabolism, and experimental verification, we show that the diversification of NAD-dependent signaling in vertebrates depended on 3 critical evolutionary events: 1) the transition of NAD biosynthesis to exclusive usage of nicotinamide phosphoribosyltransferase (NamPT); 2) the occurrence of nicotinamide N-methyltransferase (NNMT), which diverts nicotinamide (Nam) from recycling into NAD, preventing Nam accumulation and inhibition of NAD-dependent signaling reactions; and 3) structural adaptation of NamPT, providing an unusually high affinity toward Nam, necessary to maintain NAD levels. Our results reveal an unexpected coevolution and kinetic interplay between NNMT and NamPT that enables extensive NAD signaling. This has implications for therapeutic strategies of NAD supplementation and the use of NNMT or NamPT inhibitors in disease treatment.
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Mandrone M, Antognoni F, Aloisi I, Potente G, Poli F, Cai G, Faleri C, Parrotta L, Del Duca S. Compatible and Incompatible Pollen-Styles Interaction in Pyrus communis L. Show Different Transglutaminase Features, Polyamine Pattern and Metabolomics Profiles. FRONTIERS IN PLANT SCIENCE 2019; 10:741. [PMID: 31249577 PMCID: PMC6584118 DOI: 10.3389/fpls.2019.00741] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/17/2019] [Indexed: 05/25/2023]
Abstract
Pollen-stigma interaction is a highly selective process, which leads to compatible or incompatible pollination, in the latter case, affecting quantitative and qualitative aspects of productivity in species of agronomic interest. While the genes and the corresponding protein partners involved in this highly specific pollen-stigma recognition have been studied, providing important insights into pollen-stigma recognition in self-incompatible (SI), many other factors involved in the SI response are not understood yet. This work concerns the study of transglutaminase (TGase), polyamines (PAs) pattern and metabolomic profiles following the pollination of Pyrus communis L. pistils with compatible and SI pollen in order to deepen their possible involvement in the reproduction of plants. Immunolocalization, abundance and activity of TGase as well as the content of free, soluble-conjugated and insoluble-bound PAs have been investigated. 1H NMR-profiling coupled with multivariate data treatment (PCA and PLS-DA) allowed to compare, for the first time, the metabolic patterns of not-pollinated and pollinated styles. Results clearly indicate that during the SI response TGase activity increases, resulting in the accumulation of PAs conjugated to hydroxycinnamic acids and other small molecules. Metabolomic analysis showed a remarkable differences between pollinated and not-pollinated styles, where, except for glucose, all the other metabolites where less concentrated. Moreover, styles pollinated with compatible pollen showed the highest amount of sucrose than SI pollinated ones, which, in turn, contained highest amount of all the other metabolites, including aromatic compounds, such as flavonoids and a cynnamoil derivative.
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Affiliation(s)
- Manuela Mandrone
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Fabiana Antognoni
- Department for Life Quality Studies, University of Bologna, Rimini, Italy
| | - Iris Aloisi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giulia Potente
- Department for Life Quality Studies, University of Bologna, Rimini, Italy
| | - Ferruccio Poli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Claudia Faleri
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Luigi Parrotta
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Stefano Del Duca
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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Characterization of l-Carnitine Metabolism in Sinorhizobium meliloti. J Bacteriol 2019; 201:JB.00772-18. [PMID: 30670548 DOI: 10.1128/jb.00772-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 11/20/2022] Open
Abstract
l-Carnitine is a trimethylammonium compound mostly known for its contribution to fatty acid transport into mitochondria. In bacteria, it is synthesized from γ-butyrobetaine (GBB) and can be used as a carbon source. l-Carnitine can be formed directly by GBB hydroxylation or synthesized via a biosynthetic route analogous to fatty acid degradation. However, this multistep pathway has not been experimentally characterized. In this work, we identified by gene context analysis a cluster of l-carnitine anabolic genes next to those involved in its catabolism and proceeded to the complete in vitro characterization of l-carnitine biosynthesis and degradation in Sinorhizobium meliloti The five enzymes catalyzing the seven steps that convert GBB to glycine betaine are described. Metabolomic analysis confirmed the multistage synthesis of l-carnitine in GBB-grown cells but also revealed that GBB is synthesized by S. meliloti To our knowledge, this is the first report of aerobic GBB synthesis in bacteria. The conservation of l-carnitine metabolism genes in different bacterial taxonomic classes underscores the role of l-carnitine as a ubiquitous nutrient.IMPORTANCE The experimental characterization of novel metabolic pathways is essential for realizing the value of genome sequences and improving our knowledge of the enzymatic capabilities of the bacterial world. However, 30% to 40% of genes of a typical genome remain unannotated or associated with a putative function. We used enzyme kinetics, liquid chromatography-mass spectroscopy (LC-MS)-based metabolomics, and mutant phenotyping for the characterization of the metabolism of l-carnitine in Sinorhizobium meliloti to provide an accurate annotation of the corresponding genes. The occurrence of conserved gene clusters for carnitine metabolism in soil, plant-associated, and marine bacteria underlines the environmental abundance of carnitine and suggests this molecule might make a significant contribution to ecosystem nitrogen and carbon cycling.
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Fang C, Luo J. Metabolic GWAS-based dissection of genetic bases underlying the diversity of plant metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:91-100. [PMID: 30231195 DOI: 10.1111/tpj.14097] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 05/21/2023]
Abstract
Plants have served as sources providing humans with metabolites for food and nutrition, biomaterials for living, and treatment for pain and disease. Plants produce a huge array of metabolites, with an immense diversity at both the population and individual levels. Dissection of the genetic bases for metabolic diversity has attracted increasing research attention. The concept of genome-wide association study (GWAS) was extended to studies on the diversity of plant metabolome that benefitted from the development of mass-spectrometry-based analytical systems and genome sequencing technologies. Metabolic genome-wide association study (mGWAS) is one of the most powerful tools for global identification of genetic determinants for diversity of plant metabolism. Recently, mGWAS has been performed for various species with continuous improvements, providing deeper insights into the genetic bases of metabolic diversity. In this review, we discuss fully the achievements to date and remaining challenges that are associated with both mGWAS and mGWAS-based multi-dimensional analysis. We begin with a summary of GWAS and its development based on statistical methods and populations. As variation in targeted traits is essential for GWAS, we review metabolic diversity and its rise at both the population and individual levels. Subsequently, the application of mGWAS for plants and its corresponding achievements are fully discussed. We address the current knowledge on mGWAS-based multi-dimensional analysis and emerging insights into the diversity of metabolism.
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Affiliation(s)
- Chuanying Fang
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 470228, China
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilisation of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 470228, China
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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Gupta N, O’Loughlin EJ, Sims GK. Microbial Degradation of Pyridine and Pyridine Derivatives. MICROORGANISMS FOR SUSTAINABILITY 2019. [DOI: 10.1007/978-981-13-7462-3_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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