1
|
Ge H, Liu X, Lu D, Yang Z, Li H. Degradation of pyrene by Xanthobacteraceae bacterium strain S3 isolated from the rhizosphere sediment of Vallisneria natans: active conditions, metabolite identification, and proposed pathways. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:25659-25670. [PMID: 38483714 DOI: 10.1007/s11356-024-32724-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/27/2024] [Indexed: 04/19/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) were typical environmental contaminants that accumulated continuously in sediment. Microbial degradation is the main way of PAH degradation in the natural environment. Therefore, expanding the available pool of microbial resources and investigating the molecular degrading mechanisms of PAHs are critical to the efficient control of PAH-polluted sites. Here, a strain (identified as Xanthobacteraceae bacterium) with the ability to degrade pyrene was screened from the rhizosphere sediment of Vallisneria natans. Response surface analysis showed that the strain could degrade pyrene at pH 5-7, NaCl addition 0-1.5%, and temperature 25-40 °C, and the maximum pyrene degradation (~ 95.4%) was obtained under the optimum conditions (pH 7.0, temperature 28.5 °C, and NaCl-free addition) after 72 h. Also, it was observed that the effect of temperature on the degradation ratio was the most significant. Furthermore, eighteen metabolites were identified by mass spectrometry, among which (2Z)-2-hydroxy-3-(4-oxo-4H-phenalen-3-yl) prop-2-enoic acid, 7-(carboxymethyl)-8-formyl-1-naphthyl acetic acid, phthalic acid, naphthalene-1,2-diol, and phenol were the main metabolites. And the degradation pathway of pyrene was proposed, suggesting that pyrene undergoes initial ortho-cleavage under the catalysis of metapyrocatechase to form (2Z)-2-hydroxy-3-(4-oxo-4H-phenalen-3-yl) prop-2-enoic acid. Subsequently, this intermediate was progressively oxidized and degraded to phthalic acid or phenol, which could enter the tricarboxylic acid cycle. Furthermore, the pyrene biodegradation by the strain followed the first-order kinetic model and the degradation rate changed from fast to slow, with the rate remaining mostly slow in the later stages. The slow biodegradation rate was probably caused by a significant amount of phenol accumulation in the initial stage of degradation, which resulted in a decrease in bacterial activity or death.
Collapse
Affiliation(s)
- Huanying Ge
- Center for Environment and Water Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
- Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Changsha, 410083, People's Republic of China
| | - Xinghao Liu
- Center for Environment and Water Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
- Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Changsha, 410083, People's Republic of China
| | - Denglong Lu
- Center for Environment and Water Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
- Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Changsha, 410083, People's Republic of China
| | - Zhaoguang Yang
- Center for Environment and Water Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
- Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Changsha, 410083, People's Republic of China
| | - Haipu Li
- Center for Environment and Water Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China.
- Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Changsha, 410083, People's Republic of China.
| |
Collapse
|
2
|
Morales-Blancas GY, Reyna-Terán JD, Hernández-Eligio JA, Ortuño-Pineda C, Toribio-Jiménez J, Rodríguez-Barrera MÁ, Toledo-Hernández E, Rojas-Aparicio A, Romero-Ramírez Y. The catE gene of Bacillus licheniformis M2-7 is essential for growth in benzopyrene, and its expression is regulated by the Csr system. World J Microbiol Biotechnol 2023; 39:177. [PMID: 37115273 DOI: 10.1007/s11274-023-03630-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/25/2023] [Indexed: 04/29/2023]
Abstract
Benzopyrene is a high-molecular-weight polycyclic aromatic hydrocarbon that is highly recalcitrant and induces carcinogenic effects. CsrA is a conserved regulatory protein that controls the translation and stability of its target transcripts, having negative or positive effects depending on the target mRNAs. It is known that Bacillus licheniformis M2-7 has the ability to grow and survive in certain concentrations of hydrocarbons such as benzopyrene, prompted in part by CsrA, as is present in gasoline. However, there are a few studies that reveal the genes involved in that process. To identify the genes involved in the Bacillus licheniformis M2-7 degradation pathway, the plasmid pCAT-sp containing a mutation in the catE gene was constructed and used to transform B. licheniformis M2-7 and generate a CAT1 strain. We determined the capacity of the mutant B. licheniformis (CAT1) to grow in the presence of glucose or benzopyrene as a carbon source. We observed that the CAT1 strain presented increased growth in the presence of glucose but a statistically considerable decrease in the presence of benzopyrene compared with the wild-type parental strain. Additionally, we demonstrated that the Csr system positively regulates its expression since it was observed that the expression of the gene in the mutant strain LYA12 (M2-7 csrA:: Sp, SpR) was considerably lower than that in the wild-type strain. We were thus able to propose a putative regulation model for catE gene in B. licheniformis M2-7 strain by CsrA regulator in the presence of benzopyrene.
Collapse
Affiliation(s)
- Giselle Yamilet Morales-Blancas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Unidad Académica de Ciencias Químico- Biológicas, Universidad Autónoma de Guerrero, Avenida Lázaro Cárdenas sin número, Ciudad Universitaria, Chilpancingo, Guerrero, C. P. 39070, México
| | - José Daniel Reyna-Terán
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Unidad Académica de Ciencias Químico- Biológicas, Universidad Autónoma de Guerrero, Avenida Lázaro Cárdenas sin número, Ciudad Universitaria, Chilpancingo, Guerrero, C. P. 39070, México
| | - José Alberto Hernández-Eligio
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos, C. P. 62210, México
| | - Carlos Ortuño-Pineda
- Laboratorio de Ácidos Nucleicos y Proteínas, Universidad Autónoma de Guerrero, 16 México. Av. Lázaro Cárdenas. Ciudad Universitaria, Chilpancingo, Guerrero, C. P. 39070, México
| | - Jeiry Toribio-Jiménez
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Unidad Académica de Ciencias Químico- Biológicas, Universidad Autónoma de Guerrero, Avenida Lázaro Cárdenas sin número, Ciudad Universitaria, Chilpancingo, Guerrero, C. P. 39070, México
| | - Miguel Ángel Rodríguez-Barrera
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Unidad Académica de Ciencias Químico- Biológicas, Universidad Autónoma de Guerrero, Avenida Lázaro Cárdenas sin número, Ciudad Universitaria, Chilpancingo, Guerrero, C. P. 39070, México
| | - Erubiel Toledo-Hernández
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Unidad Académica de Ciencias Químico- Biológicas, Universidad Autónoma de Guerrero, Avenida Lázaro Cárdenas sin número, Ciudad Universitaria, Chilpancingo, Guerrero, C. P. 39070, México
| | - Augusto Rojas-Aparicio
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Unidad Académica de Ciencias Químico- Biológicas, Universidad Autónoma de Guerrero, Avenida Lázaro Cárdenas sin número, Ciudad Universitaria, Chilpancingo, Guerrero, C. P. 39070, México
| | - Yanet Romero-Ramírez
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Unidad Académica de Ciencias Químico- Biológicas, Universidad Autónoma de Guerrero, Avenida Lázaro Cárdenas sin número, Ciudad Universitaria, Chilpancingo, Guerrero, C. P. 39070, México.
| |
Collapse
|
3
|
Liang J, Roberts A, van Kranenburg R, Bolhuis A, Leak DJ. Relaxed control of sugar utilization in Parageobacillus thermoglucosidasius DSM 2542. Microbiol Res 2021; 256:126957. [PMID: 35032723 DOI: 10.1016/j.micres.2021.126957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/22/2021] [Accepted: 12/27/2021] [Indexed: 01/08/2023]
Abstract
Though carbon catabolite repression (CCR) has been intensively studied in some more characterised organisms, there is a lack of information of CCR in thermophiles. In this work, CCR in the thermophile, Parageobacillus thermoglucosidasius DSM 2542 has been studied during growth on pentose sugars in the presence of glucose. Physiological studies under fermentative conditions revealed a loosely controlled CCR when DSM 2542 was grown in minimal medium supplemented with a mixture of glucose and xylose. This atypical CCR pattern was also confirmed by studying xylose isomerase expression level by qRT-PCR. Fortuitously, the pheB gene, which encodes catechol 2, 3-dioxygenase was found to have a cre site highly similar to the consensus catabolite-responsive element (cre) at its 3' end and was used to confirm that expression of pheB from a plasmid was under stringent CCR control. Bioinformatic analysis suggested that the CCR regulation of xylose metabolism in P. thermoglucosidasius DSM 2542 might occur primarily via control of expression of pentose transporter operons. Relaxed control of sugar utilization might reflect a lower affinity of the CcpA-HPr (Ser46-P) or CcpA-Crh (Ser46-P) complexes to the cre(s) in these operons.
Collapse
Affiliation(s)
- Jinghui Liang
- Department of Biology and Biochemistry, University of Bath, UK.
| | - Adam Roberts
- Department of Biology and Biochemistry, University of Bath, UK
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, The Netherlands; Corbion, Arkelsedijk 46, 4206 AC, Gorinchem, The Netherlands
| | - Albert Bolhuis
- Department of Pharmacy and Pharmacology, University of Bath, UK
| | - David J Leak
- Department of Biology and Biochemistry, University of Bath, UK
| |
Collapse
|
4
|
Moraskie M, Roshid MHO, O'Connor G, Dikici E, Zingg JM, Deo S, Daunert S. Microbial whole-cell biosensors: Current applications, challenges, and future perspectives. Biosens Bioelectron 2021; 191:113359. [PMID: 34098470 PMCID: PMC8376793 DOI: 10.1016/j.bios.2021.113359] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/22/2022]
Abstract
Microbial Whole-Cell Biosensors (MWCBs) have seen rapid development with the arrival of 21st century biological and technological capabilities. They consist of microbial species which produce, or limit the production of, a reporter protein in the presence of a target analyte. The quantifiable signal from the reporter protein can be used to determine the bioavailable levels of the target analyte in a variety of sample types at a significantly lower cost than most widely used and well-established analytical instrumentation. Furthermore, the versatile and robust nature of MWCBs shows great potential for their use in otherwise unavailable settings and environments. While MWCBs have been developed for use in biomedical, environmental, and agricultural monitoring, they still face various challenges before they can transition from the laboratory into industrialized settings like their enzyme-based counterparts. In this comprehensive and critical review, we describe the underlying working principles of MWCBs, highlight developments for their use in a variety of fields, detail challenges and current efforts to address them, and discuss exciting implementations of MWCBs helping redefine what is thought to be possible with this expeditiously evolving technology.
Collapse
Affiliation(s)
- Michael Moraskie
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Md Harun Or Roshid
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA
| | - Gregory O'Connor
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Jean-Marc Zingg
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sapna Deo
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA; The Miami Clinical and Translational Science Institute, University of Miami, Miami, FL, 33146, USA; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33146, USA.
| |
Collapse
|
5
|
Shape-function of a novel metapyrocatechase, RW4-MPC: Metagenomics to SAXS data based insight into deciphering regulators of function. Int J Biol Macromol 2021; 188:1012-1024. [PMID: 34375665 DOI: 10.1016/j.ijbiomac.2021.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 11/23/2022]
Abstract
The oxygenases have attracted considerable attention in enzyme-mediated bioremediation of xenobiotic compounds due to their high specificity, cost-effectiveness, and targeted field applications. Here, we performed a functional metagenomics approach to cope with cultivability limitations to isolate a novel extradiol dioxygenase. Fosmid clone harboring dioxygenase gene was sequenced and analyzed by bioinformatics tools. One ring-cleaving dioxygenase RW4-MPC (metapyrocatechase) was purified and characterized to examine its degradation efficiency. The RW4-MPC was significantly active in the temperature and pH range of 5 to 40 °C, and 7-10, respectively, with an optimum temperature of 25 °C and pH 8. To gain insight into observed differential activity, Small-Angle X-ray Scattering (SAXS) data of the protein samples were analyzed, which brought forth that the RW4-MPC molecules form tight globular tetramers in solution. This native association was stable till 35 °C, and protein started to associate at higher temperatures, explaining heat-induced loss of function. Similarly, RW4-MPC aggregated or lost globular profile below pH 7 or at pH 10, respectively. The kinetic parameters showed the six folds high catalytic efficiency of RW4-MPC towards 2,3-dihydroxy biphenyl than catechol and its derivatives. RW4-MPC molecules showed remarkable retention of functionality in hypersaline conditions with more than 70% activity in a buffer having 3 M NaCl concentration. In concordance, SAXS data analysis showed retention of functional shape profile in hypersaline conditions. The halotolerant and oxygen insensitive nature of this enzyme makes it a potential candidate for bioremediation.
Collapse
|
6
|
Mukherjee M, Dey A. Electron Transfer Control of Reductase versus Monooxygenase: Catalytic C-H Bond Hydroxylation and Alkene Epoxidation by Molecular Oxygen. ACS CENTRAL SCIENCE 2019; 5:671-682. [PMID: 31041387 PMCID: PMC6487540 DOI: 10.1021/acscentsci.9b00046] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Indexed: 05/11/2023]
Abstract
Catalytic oxidation of organic substrates, using a green oxidant like O2, has been a long-term goal of the scientific community. In nature, these oxidations are performed by metalloenzymes that generate highly oxidizing species from O2, which, in turn, can oxidize very stable organic substrates, e.g., mono-/dioxygenases. The same oxidants are produced during O2 reduction/respiration in the mitochondria but are reduced by electron transfer, i.e., reductases. Iron porphyrin mimics of the active site of cytochrome P450 (Cyt P450) are created atop a self-assembled monolayer covered electrode. The rate of electron transfer from the electrode to the iron porphyrin site is attenuated to derive monooxygenase reactivity from these constructs that otherwise show O2 reductase activity. Catalytic hydroxylation of strong C-H bonds to alcohol and epoxidation of alkenes, using molecular O2 (with 18O2 incorporation), is demonstrated with turnover numbers >104. Uniquely, one of the two iron porphyrin catalysts used shows preferential oxidation of 2° C-H bonds of cycloalkanes to alcohols over 3° C-H bonds without overoxidation to ketones. Mechanistic investigations with labeled substrates indicate that a compound I (FeIV=O bound to a porphyrin cation radical) analogue, formed during O2 reduction, is the primary oxidant. The selectivity is determined by the shape of the distal pocket of the catalyst, which, in turn, is determined by the substituents on the periphery of the porphyrin macrocycle.
Collapse
Affiliation(s)
| | - Abhishek Dey
- Address:
Department of Inorganic
Chemistry, Indian Association for the Cultivation of Science, 2A&2B
Raja SC Mullick Road, Jadavpur, Kolkata, West Bengal, India 700032.
E-mail:
| |
Collapse
|
7
|
|
8
|
Sokolova A, Huang SL, Duff A, Gilbert EP, Li WH. Correlation of thermostability and conformational changes of catechol 2, 3-dioxygenases from two disparate micro-organisms. Biophys Chem 2013; 180-181:145-52. [PMID: 23994541 DOI: 10.1016/j.bpc.2013.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/21/2013] [Accepted: 07/22/2013] [Indexed: 11/26/2022]
Abstract
We have investigated the structure of recombinant catechol 2, 3-dioxygenase (C23O) purified from two species in which the enzyme has evolved to function at different temperature. The two species are mesophilic bacterium Pseudomonas putida strain mt-2 and thermophilic archaea Sulfolobus acidocaldariusDSM639. Using the primary sequence analysis, we show that both C23Os have only 30% identity and 48% similarity but contain conserved amino acid residues forming an active site area around the iron ion. The corresponding differences in homology, but structural similarity in active area residues, appear to provide completely different responses to heating the two enzymes. We confirm this by small angle X-ray scattering and demonstrate that the overall structure of C23O from P. putida is slightly different from its crystalline form whereas the solution scattering of C23O from S. acidocaldarius at temperatures between 4 and 85°C ideally fits the calculated scattering from the single crystal structure. The thermostability of C23O from S. acidocaldarius correlates well with conformation in solution during thermal treatment. The similarity of the two enzymes in primary and tertiary structure may be taken as a confirmation that two enzymes have evolved from a common ancestor.
Collapse
Affiliation(s)
- Anna Sokolova
- Bragg Institute, ANSTO, Locked Bag 2001, Kirrawee DC, NSW, 2232 Australia.
| | | | | | | | | |
Collapse
|
9
|
Wojcieszyńska D, Hupert-Kocurek K, Guzik U. Factors affecting activity of catechol 2,3-dioxygenase from 2-chlorophenol-degradingStenotrophomonas maltophiliastrain KB2. BIOCATAL BIOTRANSFOR 2013. [DOI: 10.3109/10242422.2013.796456] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|