1
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Wang X, Guo N, Zhang Y, Wang G, Shi K. Cross-protection and cross-feeding between Enterobacter and Comamonas promoting their coexistence and cadmium tolerance in Oryza sativa L. Microbiol Res 2024; 286:127806. [PMID: 38924817 DOI: 10.1016/j.micres.2024.127806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/13/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Metabolic cross-feeding is a pervasive interaction between bacteria to acquire novel phenotypes. However, our current understanding of the survival mechanism for cross-feeding in cocultured bacterial biofilms under heavy-metal conditions remains limited. Herein, we found that Comamonas sp. A23 produces L-phenylalanine to activate the L-phenylalanine degradation pathway in Enterobacter sp. A11, enhancing biofilm formation and cadmium [Cd(II)] immobilization in A11. The genes responsible for L-phenylalanine-degradation (paaK) and cell attachment and aggregation (csgAD) are essential for biofilm formation and Cd(II) immobilization in A11 induced by L-phenylalanine. The augmentation of A11 biofilms, in turn, protects A23 under Cd(II) and H2O2 stresses. The plant-based experiments demonstrate that the induction of two rice Cd(II) transporters, OsCOPT4 and OsBCP1, by A11 and A23 enhances rice resistance against Cd(II) and H2O2 stresses. Overall, our findings unveil the mutual dependence between bacteria and rice on L-phenylalanine cross-feeding for survival under abiotic stress.
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Affiliation(s)
- Xing Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Naijiang Guo
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yao Zhang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Gejiao Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Kaixiang Shi
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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2
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Xu L, Zhao Y, Li Y, Sun JQ. Genomic and transcriptomic analyses provide new insights into the allelochemical degradation preference of a novel Acinetobacter strain. ENVIRONMENTAL RESEARCH 2024; 246:118145. [PMID: 38191044 DOI: 10.1016/j.envres.2024.118145] [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: 11/22/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024]
Abstract
A novel n-alkane- and phenolic acid-degrading Acinetobacter strain (designated C16S1T) was isolated from rhizosphere soil. The strain was identified as a novel species named Acinetobacter suaedae sp. nov. using a polyphasic taxonomic approach. Strain C16S1T showed preferential degradation of three compounds: p-hydroxybenzoate (PHBA) > ferulic acid (FA) > n-hexadecane. In a medium containing two or three of these allelochemicals, coexisting n-hexadecane and PHBA accelerated each other's degradation and that of FA. FA typically hindered the degradation of n-hexadecane but accelerated PHBA degradation. The upregulated expression of n-hexadecane- and PHBA-degrading genes induced, by their related substrates, was mutually enhanced by coexisting PHBA or n-hexadecane; in contrast, expression of both gene types was reduced by FA. Coexisting PHBA or n-hexadecane enhanced the upregulation of FA-degrading genes induced by FA. The expressions of degrading genes affected by coexisting chemicals coincided with the observed degradation efficiencies. Iron shortage limited the degradation efficiency of all three compounds and changed the degradation preference of Acinetobacter. The present study demonstrated that the biodegradability of the chemicals, the effects of coexisting chemicals on the expression of degrading genes and the strain's growth, the shortage of essential elements, and the toxicity of the chemicals were the four major factors affecting the removal rates of the coexisting allelochemicals.
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Affiliation(s)
- Lian Xu
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China; Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yang Zhao
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Yue Li
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China.
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3
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Tsagogiannis E, Asimakoula S, Drainas AP, Marinakos O, Boti VI, Kosma IS, Koukkou AI. Elucidation of 4-Hydroxybenzoic Acid Catabolic Pathways in Pseudarthrobacter phenanthrenivorans Sphe3. Int J Mol Sci 2024; 25:843. [PMID: 38255919 PMCID: PMC10815724 DOI: 10.3390/ijms25020843] [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: 12/12/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
4-hydroxybenzoic acid (4-HBA) is an aromatic compound with high chemical stability, being extensively used in food, pharmaceutical and cosmetic industries and therefore widely distributed in various environments. Bioremediation constitutes the most sustainable approach for the removal of 4-hydroxybenzoate and its derivatives (parabens) from polluted environments. Pseudarthrobacter phenanthrenivorans Sphe3, a strain capable of degrading several aromatic compounds, is able to grow on 4-HBA as the sole carbon and energy source. Here, an attempt is made to clarify the catabolic pathways that are involved in the biodegradation of 4-hydroxybenzoate by Sphe3, applying a metabolomic and transcriptomic analysis of cells grown on 4-HBA. It seems that in Sphe3, 4-hydroxybenzoate is hydroxylated to form protocatechuate, which subsequently is either cleaved in ortho- and/or meta-positions or decarboxylated to form catechol. Protocatechuate and catechol are funneled into the TCA cycle following either the β-ketoadipate or protocatechuate meta-cleavage branches. Our results also suggest the involvement of the oxidative decarboxylation of the protocatechuate peripheral pathway to form hydroxyquinol. As a conclusion, P. phenanthrenivorans Sphe3 seems to be a rather versatile strain considering the 4-hydroxybenzoate biodegradation, as it has the advantage to carry it out effectively following different catabolic pathways concurrently.
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Affiliation(s)
- Epameinondas Tsagogiannis
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (S.A.); (A.P.D.); (O.M.)
| | - Stamatia Asimakoula
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (S.A.); (A.P.D.); (O.M.)
| | - Alexandros P. Drainas
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (S.A.); (A.P.D.); (O.M.)
| | - Orfeas Marinakos
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (S.A.); (A.P.D.); (O.M.)
| | - Vasiliki I. Boti
- Unit of Environmental, Organic and Biochemical High-Resolution Analysis-Orbitrap-LC-MS, University of Ioannina, 451110 Ioannina, Greece;
| | - Ioanna S. Kosma
- Laboratory of Food Chemistry, Sector of Industrial Chemistry and Food Chemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece;
| | - Anna-Irini Koukkou
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (E.T.); (S.A.); (A.P.D.); (O.M.)
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4
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Li YX, Lin W, Han YH, Wang YQ, Wang T, Zhang H, Zhang Y, Wang SS. Biodegradation of p-hydroxybenzoic acid in Herbaspirillum aquaticum KLS-1 isolated from tailing soil: Characterization and molecular mechanism. JOURNAL OF HAZARDOUS MATERIALS 2023; 456:131669. [PMID: 37236108 DOI: 10.1016/j.jhazmat.2023.131669] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/09/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
The wide distribution of p-hydroxybenzoic acid (PHBA) in the environments has attracted great concerns due to its potential risks to organisms. Bioremediation is considered a green way to remove PHBA from environment. Here, a new PHBA-degrading bacterium Herbaspirillum aquaticum KLS-1was isolated and its PHBA degradation mechanisms were fully evaluated. Results showed that strain KLS-1 could utilize PHBA as the sole carbon source and completely degrade 500 mg/L PHBA within 18 h. The optimal conditions for bacterial growth and PHBA degradation were pH values of 6.0-8.0, temperatures of 30 °C-35 °C, shaking speed of 180 rpm, Mg2+ concentration of 2.0 mM and Fe2+ concentration of 1.0 mM. Draft genome sequencing and functional gene annotations identified three operons (i.e., pobRA, pcaRHGBD and pcaRIJ) and several free genes possibly participating in PHBA degradation. The key genes pobA, ubiA, fadA, ligK and ubiG involved in the regulation of protocatechuate and ubiquinone (UQ) metabolisms were successfully amplified in strain KLS-1 at mRNA level. Our data suggested that PHBA could be degraded by strain KLS-1 via the protocatechuate ortho-/meta-cleavage pathway and UQ biosynthesis pathway. This study has provided a new PHBA-degrading bacterium for potential bioremediation of PHBA pollution.
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Affiliation(s)
- Yi-Xi Li
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Wei Lin
- College of Life Science, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Yong-He Han
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China.
| | - Yao-Qiang Wang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Tao Wang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Hong Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Yong Zhang
- College of Environmental and Resource Science, Fujian Normal University, Fuzhou 350117, Fujian, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350117, Fujian, China
| | - Shan-Shan Wang
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.
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5
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Deciphering the transcriptional regulation of the catabolism of lignin-derived aromatics in Rhodococcus opacus PD630. Commun Biol 2022; 5:1109. [PMID: 36261484 DOI: 10.1038/s42003-022-04069-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022] Open
Abstract
Rhodococcus opacus PD630 has considerable potential as a platform for valorizing lignin due to its innate "biological funneling" pathways. However, the transcriptional regulation of the aromatic catabolic pathways and the mechanisms controlling aromatic catabolic operons in response to different aromatic mixtures are still underexplored. Here, we identified and studied the transcription factors for aromatic degradation using GFP-based sensors and comprehensive deletion analyses. Our results demonstrate that the funneling pathways for phenol, guaiacol, 4-hydroxybenzoate, and vanillate are controlled by transcriptional activators. The two different branches of the β-ketoadipate pathway, however, are controlled by transcriptional repressors. Additionally, promoter activity assays revealed that the substrate hierarchy in R. opacus may be ascribed to the transcriptional cross-regulation of the individual aromatic funneling pathways. These results provide clues to clarify the molecule-level mechanisms underlying the complex regulation of aromatic catabolism, which facilitates the development of R. opacus as a promising chassis for valorizing lignin.
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Dhamale T, Saha BK, Papade SE, Singh S, Phale PS. A unique global metabolic trait of Pseudomonas bharatica CSV86 T: metabolism of aromatics over simple carbon sources and co-metabolism with organic acids. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35925665 DOI: 10.1099/mic.0.001206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hierarchical utilization of substrate by microbes (utilization of simple carbon sources prior to complex ones) poses a major limitation to the efficient remediation of aromatic pollutants. Aromatic compounds, being complex and reduced in nature, appear to be a deferred choice as the carbon source in the presence of a plethora of simple organic compounds in the environment. The soil bacterium Pseudomonas bharatica CSV86T displays a unique carbon source utilization hierarchy. It preferentially utilizes aromatics over glucose and co-metabolizes them with succinate or pyruvate (Basu et al., 2006, Applied and Environmental Microbiology, 72 : 22226-2230). In the present study, the substrate utilization hierarchy for strain CSV86T was tested for additional simple carbon sources such as glycerol, acetate, and tri-carboxylic acid (TCA) cycle intermediates like α-ketoglutarate and fumarate. When grown on a mixture of aromatics (benzoate or naphthalene) plus glycerol, the strain displayed a diauxic growth profile with significantly high activity of aromatic utilization enzymes (catechol 1,2- or 2,3-dioxygenase, respectively) in the first-log phase. This suggests utilization of aromatics in the first-log phase followed by glycerol in the second-log phase. On a mixture of an aromatic plus organic acid (acetate, α-ketoglutarate or fumarate), the strain displayed a monoauxic growth profile, indicating co-metabolism. Interestingly, the presence of glycerol, acetate, α-ketoglutarate or fumarate does not repress metabolism/utilization of the aromatic. Thus, the substrate utilization hierarchy of strain CSV86T is aromatics=organic acids>glucose/glycerol, which is unique as compared to other Pseudomonas species, where degradation of aromatics is repressed by glycerol, glucose, acetate or organic acids, including TCA cycle intermediates. This novel substrate utilization hierarchy appears to be a global metabolic phenomenon in strain CSV86T, thus implying it to be an ideal host for metabolic engineering as well as for its potential application in bioremediation.
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Affiliation(s)
- Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Braja Kishor Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Sandesh E Papade
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Srushti Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India.,Present address: Presently affiliated to TCR Therapeutics, Inc., 100 Binney Street, Cambridge, MA 02142, USA
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
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7
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Yan L, Yan N, Gao XY, Liu Y, Liu ZP. Degradation of amoxicillin by newly isolated Bosea sp. Ads-6. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154411. [PMID: 35288139 DOI: 10.1016/j.scitotenv.2022.154411] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/15/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Amoxicillin (AMX), one of the micro-amount hazardous pollutants, was frequently detected in environments, and of great risks to environments and human health. Microbial degradation is a promising method to eliminate pollutants. In this study, an efficient AMX-degrading strain, Ads-6, was isolated and characterized. Strain Ads-6, belonging to the genus Bosea, was also able to grow on AMX as the sole carbon and nitrogen source, with a removal of ~60% TOC. Ads-6 exhibited strong AMX-degrading ability at initial concentrations of 0.5-2 mM and pH 6-8. Addition of yeast extract could significantly enhance its degrading ability. Many degradation intermediates were identified by HPLC-MS, including new ones such as two phosphorylated products which were firstly defined in AMX degradation. A new AMX degradation pathway was proposed accordingly. Moreover, the results of comparative transcriptomes and proteomes revealed that β-lactamase, L, D-transpeptidase or its homologous enzymes were responsible for the initial degradation of AMX. Protocatechuate branch of the beta-ketoadipate pathway was confirmed as the downstream degradation pathway. These results in the study suggested that Ads-6 is great potential in biodegradation of antibiotics as well as in the bioremediation of contaminated environments.
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Affiliation(s)
- Lei Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Yan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xi-Yan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Yáñez L, Rodríguez Y, Scott F, Vergara-Fernández A, Muñoz R. Production of (R)-3-hydroxybutyric acid from methane by in vivo depolymerization of polyhydroxybutyrate in Methylocystis parvus OBBP. BIORESOURCE TECHNOLOGY 2022; 353:127141. [PMID: 35405209 DOI: 10.1016/j.biortech.2022.127141] [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: 03/09/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Methylocystis parvus OBBP accumulates polyhydroxybutyrate (PHB) using methane as the sole carbon and energy source. In this work, the feasibility of producing (R)-3-hydroxybutyric acid (R3HBA) via intracellularly accumulated PHB through depolymerization (in-vivo) was investigated. Results showed that a PHB to R3HBA conversion of 77.2 ± 0.9% (R3HBA titer of 0.153 ± 0.002 g L-1) can be attained in a mineral medium containing 1 g L-1 KNO3 at 30 °C with shaking at 200 rpm and a constant pH of 11 for 72 h. Nitrogen deprivation and neutral or acidic pHs strongly reduced the excreted R3HBA concentration. Reduced oxygen availability negatively affected the R3HBA yield, which decreased to 73.6 ± 4.9% (titer of 0.139 ± 0.01 g L-1) under microaerobic conditions. Likewise, the presence of increasing concentrations of R3HBA in the medium before the onset of PHB depolymerization reduced the initial R3HBA release rate and R3HBA yield.
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Affiliation(s)
- Luz Yáñez
- Institute of Sustainable Processes, Universidad de Valladolid, Doctor Mergelina s/n, 47011, Spain; Green Technology Research Group, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Los Andes, 7550000, Chile.
| | - Yadira Rodríguez
- Institute of Sustainable Processes, Universidad de Valladolid, Doctor Mergelina s/n, 47011, Spain.
| | - Felipe Scott
- Green Technology Research Group, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Los Andes, 7550000, Chile.
| | - Alberto Vergara-Fernández
- Green Technology Research Group, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Los Andes, 7550000, Chile.
| | - Raúl Muñoz
- Institute of Sustainable Processes, Universidad de Valladolid, Doctor Mergelina s/n, 47011, Spain.
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Meng L, Sun C, Gao L, Saleem M, Li B, Wang C. Hydroxybenzoate hydroxylase genes underlying protocatechuic acid production in Valsa mali are required for full pathogenicity in apple trees. MOLECULAR PLANT PATHOLOGY 2021; 22:1370-1382. [PMID: 34390112 PMCID: PMC8518569 DOI: 10.1111/mpp.13119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/01/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Valsa mali is the causative agent of apple tree valsa canker, which causes significant losses in apple production. It produces various toxic compounds that kill plant cells, facilitating infection. Among these, protocatechuic acid exhibits the highest phytotoxic activity. However, those genes involved in toxin production have not been studied. In this study we identified four hydroxybenzoate hydroxylase genes (VmHbh1, VmHbh2, VmHbh3, and VmHbh4) from the transcriptome of V. mali. The VmHbh protein had high enzymatic activities of hydroxybenzoate hydroxylase, which could convert 4-hydroxybenzoate to protocatechuic acid. These four VmHbh genes all had highly elevated transcript levels during the V. mali infection process, especially VmHbh1 and VmHbh4, with 26.0- and 53.4-fold increases, respectively. Mutants of the four genes were generated to study whether VmHbhs are required for V. mali pathogenicity. Of the four genes, the VmHbh1 and VmHbh4 deletion mutants considerably attenuated V. mali virulence in apple leaves and in twigs, coupled with much reduced toxin levels. The VmHbh2 and VmHbh3 deletion mutants promoted the transcript levels of the other VmHbhs, suggesting functional redundancies of VmHbhs in V. mali virulence. The results provide insights into the functions of VmHbhs in the production of protocatechuic acid by V. mali during its infection of apple trees.
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Affiliation(s)
- Lulu Meng
- College of Plant Health and MedicineKey Laboratory of Integrated Crop Pest Management of Shandong ProvinceShandong Province Key Laboratory of Applied MycologyQingdao Agricultural UniversityQingdaoChina
| | - Cuicui Sun
- College of Plant Health and MedicineKey Laboratory of Integrated Crop Pest Management of Shandong ProvinceShandong Province Key Laboratory of Applied MycologyQingdao Agricultural UniversityQingdaoChina
| | - Liyong Gao
- College of Plant Health and MedicineKey Laboratory of Integrated Crop Pest Management of Shandong ProvinceShandong Province Key Laboratory of Applied MycologyQingdao Agricultural UniversityQingdaoChina
| | - Muhammad Saleem
- Department of Biological SciencesAlabama State UniversityMontgomeryAlabamaUSA
| | - Baohua Li
- College of Plant Health and MedicineKey Laboratory of Integrated Crop Pest Management of Shandong ProvinceShandong Province Key Laboratory of Applied MycologyQingdao Agricultural UniversityQingdaoChina
| | - Caixia Wang
- College of Plant Health and MedicineKey Laboratory of Integrated Crop Pest Management of Shandong ProvinceShandong Province Key Laboratory of Applied MycologyQingdao Agricultural UniversityQingdaoChina
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10
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Donoso RA, Ruiz D, Gárate-Castro C, Villegas P, González-Pastor JE, de Lorenzo V, González B, Pérez-Pantoja D. Identification of a self-sufficient cytochrome P450 monooxygenase from Cupriavidus pinatubonensis JMP134 involved in 2-hydroxyphenylacetic acid catabolism, via homogentisate pathway. Microb Biotechnol 2021; 14:1944-1960. [PMID: 34156761 PMCID: PMC8449657 DOI: 10.1111/1751-7915.13865] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/28/2022] Open
Abstract
The self-sufficient cytochrome P450 RhF and its homologues belonging to the CYP116B subfamily have attracted considerable attention due to the potential for biotechnological applications based in their ability to catalyse an array of challenging oxidative reactions without requiring additional protein partners. In this work, we showed for the first time that a CYP116B self-sufficient cytochrome P450 encoded by the ohpA gene harboured by Cupriavidus pinatubonensis JMP134, a β-proteobacterium model for biodegradative pathways, catalyses the conversion of 2-hydroxyphenylacetic acid (2-HPA) into homogentisate. Mutational analysis and HPLC metabolite detection in strain JMP134 showed that 2-HPA is degraded through the well-known homogentisate pathway requiring a 2-HPA 5-hydroxylase activity provided by OhpA, which was additionally supported by heterologous expression and enzyme assays. The ohpA gene belongs to an operon including also ohpT, coding for a substrate-binding subunit of a putative transporter, whose expression is driven by an inducible promoter responsive to 2-HPA in presence of a predicted OhpR transcriptional regulator. OhpA homologues can be found in several genera belonging to Actinobacteria and α-, β- and γ-proteobacteria lineages indicating a widespread distribution of 2-HPA catabolism via homogentisate route. These results provide first time evidence for the natural function of members of the CYP116B self-sufficient oxygenases and represent a significant input to support novel kinetic and structural studies to develop cytochrome P450-based biocatalytic processes.
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Affiliation(s)
- Raúl A Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile.,Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniela Ruiz
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.,Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Carla Gárate-Castro
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile.,Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Pamela Villegas
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - José Eduardo González-Pastor
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Bernardo González
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.,Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
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Chen B, Li RF, Zhou L, Qiu JH, Song K, Tang JL, He YW. The phytopathogen Xanthomonas campestris utilizes the divergently transcribed pobA/pobR locus for 4-hydroxybenzoic acid recognition and degradation to promote virulence. Mol Microbiol 2020; 114:870-886. [PMID: 32757400 DOI: 10.1111/mmi.14585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/29/2020] [Indexed: 01/26/2023]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot in crucifers. Our previous findings revealed that Xcc can degrade 4-hydroxybenzoic acid (4-HBA) via the β-ketoadipate pathway. This present study expands on this knowledge in several ways. First, we show that infective Xcc cells induce in situ biosynthesis of 4-HBA in host plants, and Xcc can efficiently degrade 4-HBA via the pobA/pobR locus, which encodes a 4-hydroxybenzoate hydroxylase and an AraC-family transcription factor respectively. Next, the transcription of pobA is specifically induced by 4-HBA and is positively regulated by PobR, which is constitutively expressed in Xcc. 4-HBA directly binds to PobR dimers, resulting in activation of pobA expression. Point mutation and subsequent isothermal titration calorimetry and size exclusion chromatography analysis identified nine key conserved residues required for 4-HBA binding and/or dimerization of PobR. Furthermore, overlapping promoters harboring fully overlapping -35 elements were identified between the divergently transcribed pobA and pobR. The 4-HBA/PobR dimer complex specifically binds to a 25-bp site, which encompasses the -35 elements shared by the overlapping promoters. Finally, GUS histochemical staining and subsequent quantitative assay showed that both pobA and pobR genes are transcribed during Xcc infection of Chinese radish, and the strain ΔpobR exhibited compromised virulence in Chinese radish. These findings suggest that the ability of Xcc to survive the 4-HBA stress might be important for its successful colonization of host plants.
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Affiliation(s)
- Bo Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui-Fang Li
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Lian Zhou
- Zhiyuan Innovation Research Centre, Student Innovation Institute, Zhiyuan College, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Hui Qiu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Song
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Sanz D, García JL, Díaz E. Expanding the current knowledge and biotechnological applications of the oxygen-independent ortho-phthalate degradation pathway. Environ Microbiol 2020; 22:3478-3493. [PMID: 32510798 DOI: 10.1111/1462-2920.15119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/31/2020] [Accepted: 06/03/2020] [Indexed: 11/29/2022]
Abstract
ortho-Phthalate derives from industrially produced phthalate esters, which are massively used as plasticizers and constitute major emerging environmental pollutants. The pht pathway for the anaerobic bacterial biodegradation of o-phthalate involves its activation to phthaloyl-CoA followed by decarboxylation to benzoyl-CoA. Here, we have explored further the pht peripheral pathway in denitrifying bacteria and shown that it requires also an active transport system for o-phthalate uptake that belongs to the poorly characterized class of TAXI-TRAP transporters. The construction of a fully functional pht cassette combining both catabolic and transport genes allowed to expand the o-phthalate degradation ecological trait to heterologous hosts. Unexpectedly, the pht cassette also allowed the aerobic conversion of o-phthalate to benzoyl-CoA when coupled to a functional box central pathway. Hence, the pht pathway may constitute an evolutionary acquisition for o-phthalate degradation by bacteria that thrive either in anoxic environments or in environments that face oxygen limitations and that rely on benzoyl-CoA, rather than on catecholic central intermediates, for the aerobic catabolism of aromatic compounds. Finally, the recombinant pht cassette was used both to screen for functional aerobic box pathways in bacteria and to engineer recombinant biocatalysts for o-phthalate bioconversion into sustainable bioplastics, e.g., polyhydroxybutyrate, in plastic recycling industrial processes.
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Affiliation(s)
- David Sanz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - José L García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - Eduardo Díaz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
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Lu Z, Sun W, Li C, Ao X, Yang C, Li S. Bioremoval of non-steroidal anti-inflammatory drugs by Pseudoxanthomonas sp. DIN-3 isolated from biological activated carbon process. WATER RESEARCH 2019; 161:459-472. [PMID: 31229727 DOI: 10.1016/j.watres.2019.05.065] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/04/2019] [Accepted: 05/20/2019] [Indexed: 05/12/2023]
Abstract
The presence of non-steroidal anti-inflammatory drugs (NSAIDs) in the environment is an emerging concern owing to their potential threat on aquatic ecosystems and living organisms. To investigate the bioremoval potential of a biological activated carbon (BAC) filter for the removal of NSAIDs, removal of diclofenac (DCF), ibuprofen (IBU), and naproxen (NAP) by biofilms on a bench-scaled BAC column operated for 400 days was studied. The results showed that the BAC column effectively removed the three NSAIDs (>90%). One bacterial strain isolated from the BAC, Pseudoxanthomonas sp. DIN-3, was able to simultaneously remove DCF, IBU, and NAP, which were supplied as the sole carbon source. In 14 days, 23%, 41%, and 39% of DCF, IBU, and NAP (50 μg L-1) were bioremoved, respectively, and strain DIN-3 eliminated IBU more rapidly than the other two NSAIDs. If only a single drug was added as the sole carbon source, ignoring the other drugs, the removal ability was overestimated by 5.0-27.0%. More efficient bioremoval was achieved, concomitantly with bacterial growth, via a co-metabolism with acetate, glucose, or methanol. Their intermediates were identified by UPLC-QQQ-MS, and their respective degradation pathways were also proposed. Moreover, based on the complete genome sequence of strain DIN-3, 49 related genes encoding the main enzymes involved in DCF, IBU, and NAP biodegradation were identified, including hemE, lpd, yihx, ligC, pobA, and ligA. These results suggested that Pseudoxanthomonas sp. DIN-3 is a potential degrader of DCF, IBU, and NAP, and to the best of our knowledge, this is the first report that demonstrates the bioremoval of DCF, IBU, and NAP simultaneously by an individual bacterial strain isolated from the environment. However, the bioremoval potential should be evaluated when assessing the applicability of the strain in the environment because of the combined effects of various pharmaceutical contaminants. The obtained results provide a foundation for the use of Pseudoxanthomonas sp. DIN-3 in the bioremoval of polycyclic NSAID-contaminated environments.
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Affiliation(s)
- Zedong Lu
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Wenjun Sun
- School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Chen Li
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xiuwei Ao
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Chao Yang
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Simiao Li
- School of Environment, Tsinghua University, Beijing, 100084, China
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Lazar JT, Shuvalova L, Rosas-Lemus M, Kiryukhina O, Satchell KJF, Minasov G. Structural comparison of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida with PobA from other Pseudomonas spp. and other monooxygenases. Acta Crystallogr F Struct Biol Commun 2019; 75:507-514. [PMID: 31282871 PMCID: PMC6613441 DOI: 10.1107/s2053230x19008653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/17/2019] [Indexed: 11/10/2022] Open
Abstract
The crystal structure is reported of p-hydroxybenzoate hydroxylase (PobA) from Pseudomonas putida, a possible drug target to combat tetracycline resistance, in complex with flavin adenine dinucleotide (FAD). The structure was refined at 2.2 Å resolution with four polypeptide chains in the asymmetric unit. Based on the results of pairwise structure alignments, PobA from P. putida is structurally very similar to PobA from P. fluorescens and from P. aeruginosa. Key residues in the FAD-binding and substrate-binding sites of PobA are highly conserved spatially across the proteins from all three species. Additionally, the structure was compared with two enzymes from the broader class of oxygenases: 2-hydroxybiphenyl 3-monooxygenase (HbpA) from P. nitroreducens and 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) from Mesorhizobium japonicum. Despite having only 14% similarity in their primary sequences, pairwise structure alignments of PobA from P. putida with HbpA from P. nitroreducens and MHPCO from M. japonicum revealed local similarities between these structures. Key secondary-structure elements important for catalysis, such as the βαβ fold, β-sheet wall and α12 helix, are conserved across this expanded class of oxygenases.
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Affiliation(s)
- John T. Lazar
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60201, USA
| | - Ludmilla Shuvalova
- Department of Microbiology–Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Monica Rosas-Lemus
- Department of Microbiology–Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Olga Kiryukhina
- Department of Microbiology–Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Karla J. F. Satchell
- Department of Microbiology–Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - George Minasov
- Department of Microbiology–Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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Fan X, Nie L, Shi K, Wang Q, Xia X, Wang G. Simultaneous 3-/4-Hydroxybenzoates Biodegradation and Arsenite Oxidation by Hydrogenophaga sp. H7. Front Microbiol 2019; 10:1346. [PMID: 31275273 PMCID: PMC6592069 DOI: 10.3389/fmicb.2019.01346] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 05/31/2019] [Indexed: 12/31/2022] Open
Abstract
Aromatic compounds and arsenic (As) often coexist in the environment. As(III)-oxidizing bacteria can oxidize the more toxic As(III) into the less toxic As(V), and As(V) is easily removed. Microorganisms with the ability to degrade aromatic compounds and oxidize arsenite [As(III)] may have strong potential to remediate co-contaminated water. In this study, a Gram-negative bacterium Hydrogenophaga sp. H7 was shown to simultaneously degrade 3-hydroxybenzoate (3-HBA) or 4-HBA (3-/4-HBA) and oxidize arsenite [As(III)] to arsenate [As(V)] during culture. Notably, the addition of As(III) enhanced the degradation rates of 3-/4-HBA, while the addition of 3-/4-HBA resulted in a slight delay in As(III) oxidation. Use of a 1% bacterial culture in combination with FeCl3 could completely degrade 250 mg/L 3-HBA or 4-HBA and remove 400 μM As(III) from simulated lake water within 28 h. Genomic analysis revealed the presence of As(III) oxidation/resistance genes and two putative 3-/4-HBA degradation pathways (the protocatechuate 4,5-dioxygenase degradation pathway and the catechol 2,3-dioxygenase degradation pathway). Comparative proteomics suggested that strain H7 degraded 4-HBA via the protocatechuate 4,5-dioxygenase degradation pathway in the absence of As(III); however, 4-HBA could be degraded via the catechol 2,3-dioxygenase degradation pathway in the presence of As(III). In the presence of As(III), more NADH was produced by the catechol 2,3-dioxygenase degradation pathway and/or by As(III) oxidation, which explained the enhancement of bacterial 4-HBA degradation in the presence of As(III). In addition, the key gene dmpB, which encodes catechol 2,3-dioxygenase in the catechol 2,3-dioxygenase degradation pathway, was knocked out, which resulted in the disappearance of As(III)-enhanced bacterial 4-HBA degradation from the dmpB mutant strain, which further confirmed that As(III) enhancement of 4-HBA degradation was due to the utilization of the catechol 2,3-dioxygenase pathway. These discoveries indicate that Hydrogenophaga sp. H7 has promise for the application to the removal of aromatic compounds and As co-contamination and reveal the relationship between As oxidation and aromatic compound degradation.
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Affiliation(s)
- Xia Fan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Nie
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kaixiang Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qian Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xian Xia
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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A functional 4-hydroxybenzoate degradation pathway in the phytopathogen Xanthomonas campestris is required for full pathogenicity. Sci Rep 2015; 5:18456. [PMID: 26672484 PMCID: PMC4682078 DOI: 10.1038/srep18456] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/17/2015] [Indexed: 11/23/2022] Open
Abstract
Plants contain significant levels of natural phenolic compounds essential for reproduction and growth, as well as defense mechanisms against pathogens. Xanthomonas campestris pv. campestris (Xcc) is the causal agent of crucifers black rot. Here we showed that genes required for the synthesis, utilization, transportation, and degradation of 4-hydroxybenzoate (4-HBA) are present in Xcc. Xcc rapidly degrades 4-HBA, but has no effect on 2-hydroxybenzoate and 3-hydroxybenzoate when grown in XOLN medium. The genes for 4-HBA degradation are organized in a superoperonic cluster. Bioinformatics, biochemical, and genetic data showed that 4-HBA is hydroxylated by 4-HBA 3-hydroxylase (PobA), which is encoded by Xcc0356, to yield PCA. The resulting PCA is further metabolized via the PCA branches of the β-ketoadipate pathway, including Xcc0364, Xcc0365, and PcaFHGBDCR. Xcc0364 and Xcc0365 encode a new form of β-ketoadipate succinyl-coenzyme A transferase that is required for 4-HBA degradation. pobA expression was induced by 4-HBA via the transcriptional activator, PobR. Radish and cabbage hydrolysates contain 2-HBA, 3-HBA, 4-HBA, and other phenolic compounds. Addition of radish and cabbage hydrolysates to Xcc culture significantly induced the expression of pobA via PobR. The 4-HBA degradation pathway is required for full pathogenicity of Xcc in radish.
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Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134. Appl Environ Microbiol 2015; 81:3914-24. [PMID: 25795675 DOI: 10.1128/aem.04207-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/17/2015] [Indexed: 12/23/2022] Open
Abstract
Cupriavidus pinatubonensis JMP134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. Previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. We carried out a systematic study on the substrate preference of C. pinatubonensis JMP134 growing on representative aromatic compounds channeled through different catabolic pathways described in aerobic bacteria. Growth tests of nearly the entire set of binary combinations and in mixtures composed of 5 or 6 aromatic components showed that benzoate and phenol were always the preferred and deferred growth substrates, respectively. This pattern was supported by kinetic analyses that showed shorter times to initiate consumption of benzoate in aromatic compound mixtures. Gene expression analysis by real-time reverse transcription-PCR (RT-PCR) showed that, in all mixtures, the repression by benzoate over other catabolic pathways was exerted mainly at the transcriptional level. Additionally, inhibition of benzoate catabolism suggests that its multiple repressive actions are not mediated by a sole mechanism, as suggested by dissimilar requirements of benzoate degradation for effective repression in different aromatic compound mixtures. The hegemonic preference for benzoate over multiple aromatic carbon sources is not explained on the basis of growth rate and/or biomass yield on each single substrate or by obvious chemical or metabolic properties of these aromatic compounds.
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Lahme S, Trautwein K, Strijkstra A, Dörries M, Wöhlbrand L, Rabus R. Benzoate mediates the simultaneous repression of anaerobic 4-methylbenzoate and succinate utilization in Magnetospirillum sp. strain pMbN1. BMC Microbiol 2014; 14:269. [PMID: 25344702 PMCID: PMC4268860 DOI: 10.1186/s12866-014-0269-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/15/2014] [Indexed: 11/13/2022] Open
Abstract
Background At high concentrations of organic substrates, microbial utilization of preferred substrates (i.e., supporting fast growth) often results in diauxic growth with hierarchical substrate depletion. Unlike the carbon catabolite repression-mediated discriminative utilization of carbohydrates, the substrate preferences of non-carbohydrate-utilizing bacteria for environmentally relevant compound classes (e.g., aliphatic or aromatic acids) are rarely investigated. The denitrifying alphaproteobacterium Magnetospirillum sp. strain pMbN1 anaerobically degrades a wide variety of aliphatic and aromatic compounds and is unique for anaerobic degradation of 4-methylbenzoate. The latter proceeds via a distinct reaction sequence analogous to the central anaerobic benzoyl-CoA pathway to intermediates of central metabolism. Considering the presence of these two different anaerobic “aromatic ring degrading” pathways, substrate preferences of Magnetospirillum sp. strain pMbN1 were investigated. Anaerobic growth and substrate consumption were monitored in binary and ternary mixtures of 4-methylbenzoate, benzoate and succinate, in conjuction with time-resolved abundance profiling of selected transcripts and/or proteins related to substrate uptake and catabolism. Results Diauxic growth with benzoate preference was observed for binary and ternary substrate mixtures containing 4-methylbenzoate and succinate (despite adaptation of Magnetospirillum sp. strain pMbN1 to one of the latter two substrates). On the contrary, 4-methylbenzoate and succinate were utilized simultaneously from a binary mixture, as well as after benzoate depletion from the ternary mixture. Apparently, simultaneous repression of 4-methylbenzoate and succinate utilization from the ternary substrate mixture resulted from (i) inhibition of 4-methylbenzoate uptake, and (ii) combined inhibition of succinate uptake (via the two transporters DctPQM and DctA) and succinate conversion to acetyl-CoA (via pyruvate dehydrogenase). The benzoate-mediated repression of C4-dicarboxylate utilization in Magnetospirillum sp. strain pMbN1 differs from that recently described for “Aromatoleum aromaticum” EbN1 (involving only DctPQM). Conclusions The preferential or simultaneous utilization of benzoate and other aromatic acids from mixtures with aliphatic acids may represent a more common nutritional behavior among (anaerobic) degradation specialist than previously thought. Preference of Magnetospirillum sp. strain pMbN1 for benzoate from mixtures with 4-methylbenzoate, and thus temporal separation of the benzoyl-CoA (first) and 4-methylbenzoyl-CoA (second) pathway, may reflect a catabolic tuning towards metabolic efficiency and the markedly broader range of aromatic substrates feeding into the central anaerobic benzoyl-CoA pathway. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0269-4) contains supplementary material, which is available to authorized users.
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Díaz E, Jiménez JI, Nogales J. Aerobic degradation of aromatic compounds. Curr Opin Biotechnol 2013; 24:431-42. [DOI: 10.1016/j.copbio.2012.10.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/04/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022]
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Simultaneous catabolism of plant-derived aromatic compounds results in enhanced growth for members of the Roseobacter lineage. Appl Environ Microbiol 2013; 79:3716-23. [PMID: 23563956 DOI: 10.1128/aem.00405-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plant-derived aromatic compounds are important components of the dissolved organic carbon pool in coastal salt marshes, and their mineralization by resident bacteria contributes to carbon cycling in these systems. Members of the roseobacter lineage of marine bacteria are abundant in coastal salt marshes, and several characterized strains, including Sagittula stellata E-37, utilize aromatic compounds as primary growth substrates. The genome sequence of S. stellata contains multiple, potentially competing, aerobic ring-cleaving pathways. Preferential hierarchies in substrate utilization and complex transcriptional regulation have been demonstrated to be the norm in many soil bacteria that also contain multiple ring-cleaving pathways. The purpose of this study was to ascertain whether substrate preference exists in S. stellata when the organism is provided a mixture of aromatic compounds that proceed through different ring-cleaving pathways. We focused on the protocatechuate (pca) and the aerobic benzoyl coenzyme A (box) pathways and the substrates known to proceed through them, p-hydroxybenzoate (POB) and benzoate, respectively. When these two substrates were provided at nonlimiting carbon concentrations, temporal patterns of cell density, gene transcript abundance, enzyme activity, and substrate concentrations indicated that S. stellata simultaneously catabolized both substrates. Furthermore, enhanced growth rates were observed when S. stellata was provided both compounds simultaneously compared to the rates of cells grown singly with an equimolar concentration of either substrate alone. This simultaneous-catabolism phenotype was also demonstrated in another lineage member, Ruegeria pomeroyi DSS-3. These findings challenge the paradigm of sequential aromatic catabolism reported for soil bacteria and contribute to the growing body of physiological evidence demonstrating the metabolic versatility of roseobacters.
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