1
|
Bopp C, Bernet NM, Meyer F, Khan R, Robinson SL, Kohler HPE, Buller R, Hofstetter TB. Elucidating the Role of O 2 Uncoupling for the Adaptation of Bacterial Biodegradation Reactions Catalyzed by Rieske Oxygenases. ACS ENVIRONMENTAL AU 2024; 4:204-218. [PMID: 39035869 PMCID: PMC11258757 DOI: 10.1021/acsenvironau.4c00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 07/23/2024]
Abstract
Oxygenation of aromatic and aliphatic hydrocarbons by Rieske oxygenases is the initial step of various biodegradation pathways for environmental organic contaminants. Microorganisms carrying Rieske oxygenases are able to quickly adapt their substrate spectra to alternative carbon and energy sources that are structurally related to the original target substrate, yet the molecular events responsible for this rapid adaptation are not well understood. Here, we evaluated the hypothesis that reactive oxygen species (ROS) generated by unproductive activation of O2, the so-called O2 uncoupling, in the presence of the alternative substrate exert a selective pressure on the bacterium for increasing the oxygenation efficiency of Rieske oxygenases. To that end, we studied wild-type 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42 and five enzyme variants that have evolved from adaptive laboratory evolution experiments with 3- and 4-nitrotoluene as alternative growth substrates. The enzyme variants showed a substantially increased oxygenation efficiency toward the new target substrates concomitant with a reduction of ROS production, while mechanisms and kinetics of enzymatic O2 activation remained unchanged. Structural analyses and docking studies suggest that amino acid substitutions in enzyme variants occurred at residues lining both substrate and O2 transport tunnels, enabling tighter binding of the target substrates in the active site. Increased oxygenation efficiencies measured in vitro for the various enzyme (variant)-substrate combinations correlated linearly with in vivo changes in growth rates for evolved Acidovorax strains expressing the variants. Our data suggest that the selective pressure from oxidative stress toward more efficient oxygenation by Rieske oxygenases was most notable when O2 uncoupling exceeded 60%.
Collapse
Affiliation(s)
- Charlotte
E. Bopp
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Fabian Meyer
- Competence
Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Riyaz Khan
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Serina L. Robinson
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Rebecca Buller
- Competence
Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Thomas B. Hofstetter
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| |
Collapse
|
2
|
Runda ME, Miao H, de Kok NAW, Schmidt S. Developing hybrid systems to address oxygen uncoupling in multi-component Rieske oxygenases. J Biotechnol 2024; 389:22-29. [PMID: 38697360 DOI: 10.1016/j.jbiotec.2024.04.019] [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: 02/28/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
Rieske non-heme iron oxygenases (ROs) are redox enzymes essential for microbial biodegradation and natural product synthesis. These enzymes utilize molecular oxygen for oxygenation reactions, making them very useful biocatalysts due to their broad reaction scope and high selectivities. The mechanism of oxygen activation in ROs involves electron transfers between redox centers of associated protein components, forming an electron transfer chain (ETC). Although the ETC is essential for electron replenishment, it carries the risk of reactive oxygen species (ROS) formation due to electron loss during oxygen activation. Our previous study linked ROS formation to O2 uncoupling in the flavin-dependent reductase of the three-component cumene dioxygenase (CDO). In the present study, we extend this finding by investigating the effects of ROS formation on the multi-component CDO system in a cell-free environment. In particular, we focus on the effects of hydrogen peroxide (H2O2) formation in the presence of a NADH cofactor regeneration system on the catalytic efficiency of CDO in vitro. Based on this, we propose the implementation of hybrid systems with alternative (non-native) redox partners for CDO, which are highly advantageous in terms of reduced H2O2 formation and increased product formation. The hybrid system consisting of the RO-reductase from phthalate dioxygenase (PDR) and CDO proved to be the most promising for the oxyfunctionalization of indene, showing a 4-fold increase in product formation (20 mM) over 24 h (TTN of 1515) at a 3-fold increase in production rate.
Collapse
Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713AV, the Netherlands
| | - Hui Miao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713AV, the Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713AV, the Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen 9713AV, the Netherlands.
| |
Collapse
|
3
|
Beech JL, Maurya AK, Rodrigues da Silva R, Akpoto E, Asundi A, Fecko JA, Yennawar NH, Sarangi R, Tassone C, Weiss TM, DuBois JL. Understanding the stability of a plastic-degrading Rieske iron oxidoreductase system. Protein Sci 2024; 33:e4997. [PMID: 38723110 PMCID: PMC11081424 DOI: 10.1002/pro.4997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/01/2024] [Accepted: 04/06/2024] [Indexed: 05/13/2024]
Abstract
Rieske oxygenases (ROs) are a diverse metalloenzyme class with growing potential in bioconversion and synthetic applications. We postulated that ROs are nonetheless underutilized because they are unstable. Terephthalate dioxygenase (TPADO PDB ID 7Q05) is a structurally characterized heterohexameric α3β3 RO that, with its cognate reductase (TPARED), catalyzes the first intracellular step of bacterial polyethylene terephthalate plastic bioconversion. Here, we showed that the heterologously expressed TPADO/TPARED system exhibits only ~300 total turnovers at its optimal pH and temperature. We investigated the thermal stability of the system and the unfolding pathway of TPADO through a combination of biochemical and biophysical approaches. The system's activity is thermally limited by a melting temperature (Tm) of 39.9°C for the monomeric TPARED, while the independent Tm of TPADO is 50.8°C. Differential scanning calorimetry revealed a two-step thermal decomposition pathway for TPADO with Tm values of 47.6 and 58.0°C (ΔH = 210 and 509 kcal mol-1, respectively) for each step. Temperature-dependent small-angle x-ray scattering and dynamic light scattering both detected heat-induced dissociation of TPADO subunits at 53.8°C, followed by higher-temperature loss of tertiary structure that coincided with protein aggregation. The computed enthalpies of dissociation for the monomer interfaces were most congruent with a decomposition pathway initiated by β-β interface dissociation, a pattern predicted to be widespread in ROs. As a strategy for enhancing TPADO stability, we propose prioritizing the re-engineering of the β subunit interfaces, with subsequent targeted improvements of the subunits.
Collapse
Affiliation(s)
- Jessica Lusty Beech
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| | - Anjani K. Maurya
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | | | - Emmanuel Akpoto
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| | - Arun Asundi
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Julia Ann Fecko
- The Huck Institutes of the Life SciencesThe Pennsylvania State University, University ParkState CollegePennsylvaniaUSA
| | - Neela H. Yennawar
- The Huck Institutes of the Life SciencesThe Pennsylvania State University, University ParkState CollegePennsylvaniaUSA
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Christopher Tassone
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | - Jennifer L. DuBois
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMontanaUSA
| |
Collapse
|
4
|
Rodríguez-Castro L, Durán RE, Méndez V, Dorochesi F, Zühlke D, Riedel K, Seeger M. The long-chain flavodoxin FldX1 improves the biodegradation of 4-hydroxyphenylacetate and 3-hydroxyphenylacetate and counteracts the oxidative stress associated to aromatic catabolism in Paraburkholderia xenovorans. Biol Res 2024; 57:12. [PMID: 38561836 PMCID: PMC10983741 DOI: 10.1186/s40659-024-00491-4] [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: 11/08/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Bacterial aromatic degradation may cause oxidative stress. The long-chain flavodoxin FldX1 of Paraburkholderia xenovorans LB400 counteracts reactive oxygen species (ROS). The aim of this study was to evaluate the protective role of FldX1 in P. xenovorans LB400 during the degradation of 4-hydroxyphenylacetate (4-HPA) and 3-hydroxyphenylacetate (3-HPA). METHODS The functionality of FldX1 was evaluated in P. xenovorans p2-fldX1 that overexpresses FldX1. The effects of FldX1 on P. xenovorans were studied measuring growth on hydroxyphenylacetates, degradation of 4-HPA and 3-HPA, and ROS formation. The effects of hydroxyphenylacetates (HPAs) on the proteome (LC-MS/MS) and gene expression (qRT-PCR) were quantified. Bioaugmentation with strain p2-fldX1 of 4-HPA-polluted soil was assessed, measuring aromatic degradation (HPLC), 4-HPA-degrading bacteria, and plasmid stability. RESULTS The exposure of P. xenovorans to 4-HPA increased the formation of ROS compared to 3-HPA or glucose. P. xenovorans p2-fldX1 showed an increased growth on 4-HPA and 3-HPA compared to the control strain WT-p2. Strain p2-fldX1 degraded faster 4-HPA and 3-HPA than strain WT-p2. Both WT-p2 and p2-fldX1 cells grown on 4-HPA displayed more changes in the proteome than cells grown on 3-HPA in comparison to glucose-grown cells. Several enzymes involved in ROS detoxification, including AhpC2, AhpF, AhpD3, KatA, Bcp, CpoF1, Prx1 and Prx2, were upregulated by hydroxyphenylacetates. Downregulation of organic hydroperoxide resistance (Ohr) and DpsA proteins was observed. A downregulation of the genes encoding scavenging enzymes (katE and sodB), and gstA and trxB was observed in p2-fldX1 cells, suggesting that FldX1 prevents the antioxidant response. More than 20 membrane proteins, including porins and transporters, showed changes in expression during the growth of both strains on hydroxyphenylacetates. An increased 4-HPA degradation by recombinant strain p2-fldX1 in soil microcosms was observed. In soil, the strain overexpressing the flavodoxin FldX1 showed a lower plasmid loss, compared to WT-p2 strain, suggesting that FldX1 contributes to bacterial fitness. Overall, these results suggest that recombinant strain p2-fldX1 is an attractive bacterium for its application in bioremediation processes of aromatic compounds. CONCLUSIONS The long-chain flavodoxin FldX1 improved the capability of P. xenovorans to degrade 4-HPA in liquid culture and soil microcosms by protecting cells against the degradation-associated oxidative stress.
Collapse
Affiliation(s)
- Laura Rodríguez-Castro
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123, Valparaíso, Chile
| | - Roberto E Durán
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123, Valparaíso, Chile
- Millenium Nucleus Bioproducts, Genomics and Environmental Genomics (BioGEM), Avenida España 1680, 2390123, Valparaíso, Chile
| | - Valentina Méndez
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123, Valparaíso, Chile
- Millenium Nucleus Bioproducts, Genomics and Environmental Genomics (BioGEM), Avenida España 1680, 2390123, Valparaíso, Chile
| | - Flavia Dorochesi
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123, Valparaíso, Chile
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17489, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17489, Greifswald, Germany
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123, Valparaíso, Chile.
- Millenium Nucleus Bioproducts, Genomics and Environmental Genomics (BioGEM), Avenida España 1680, 2390123, Valparaíso, Chile.
| |
Collapse
|
5
|
Son Y, Jeong D, Kim K, Cho J. Mechanistic Insights into Nitrile Activation by Cobalt(III)-Hydroperoxo Intermediates: The Influence of Ligand Basicity. JACS AU 2023; 3:3204-3212. [PMID: 38034966 PMCID: PMC10685436 DOI: 10.1021/jacsau.3c00532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 12/02/2023]
Abstract
The versatile applications of nitrile have led to the widespread use of nitrile activation in the synthesis of pharmacologically and industrially valuable compounds. We reported the activation of nitriles using mononuclear cobalt(III)-hydroperoxo complexes, [CoIII(Me3-TPADP)(O2H)(RCN)]2+ [R = Me (2) and Ph (2Ph)], to form cobalt(III)-peroxyimidato complexes, [CoIII(Me3-TPADP)(R-C(=NH)O2)]2+ [R = Me (3) and Ph (3Ph)]. The independence of the rate on the nitrile concentration and the positive Hammett value of 3.2(2) indicated that the reactions occur via an intramolecular nucleophilic attack of the hydroperoxide ligand to the coordinated nitrile carbon atom. In contrast, the previously reported cobalt(III)-hydroperoxo complex, [CoIII(TBDAP)(O2H)(CH3CN)]2+ (2TBDAP), exhibited the deficiency of reactivity toward nitrile. The comparison of pKa values and redox potentials of 2 and 2TBDAP showed that Me3-TPADP had a stronger ligand field strength than that of TBDAP. The density functional theory calculations for 2 and 2TBDAP support that the strengthened ligand field in 2 is mainly due to the replacement of two tert-butyl amine donors in TBDAP with methyl groups in Me3-TPADP, resulting in the compression of the Co-Nax bond lengths. These results provide mechanistic evidence of nitrile activation by the cobalt(III)-hydroperoxo complex and indicate that the basicity dependent on the ligand framework contributes to the ability of nitrile activation.
Collapse
Affiliation(s)
- Yeongjin Son
- Department
of Chemistry, Ulsan National Institute of
Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department
of Emerging Materials Science, Daegu Gyeongbuk
Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Donghyun Jeong
- Department
of Chemistry, Ulsan National Institute of
Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyungmin Kim
- Department
of Chemistry, Ulsan National Institute of
Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department
of Emerging Materials Science, Daegu Gyeongbuk
Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Jaeheung Cho
- Department
of Chemistry, Ulsan National Institute of
Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Graduate
School of Carbon Neutrality, Ulsan National
Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| |
Collapse
|
6
|
Matturro B, Di Franca ML, Tonanzi B, Cruz Viggi C, Aulenta F, Di Leo M, Giandomenico S, Rossetti S. Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy). Microorganisms 2023; 11:2782. [PMID: 38004793 PMCID: PMC10673493 DOI: 10.3390/microorganisms11112782] [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: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.
Collapse
Affiliation(s)
- Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Maria Letizia Di Franca
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Barbara Tonanzi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
- National Biodiversity Future Center, 90133 Palermo, Italy
| | - Magda Di Leo
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Santina Giandomenico
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti, Italy (F.A.); (S.R.)
| |
Collapse
|
7
|
Ma Y, Wang J, Liu Y, Wang X, Zhang B, Zhang W, Chen T, Liu G, Xue L, Cui X. Nocardioides: "Specialists" for Hard-to-Degrade Pollutants in the Environment. Molecules 2023; 28:7433. [PMID: 37959852 PMCID: PMC10649934 DOI: 10.3390/molecules28217433] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Nocardioides, a genus belonging to Actinomycetes, can endure various low-nutrient conditions. It can degrade pollutants using multiple organic materials such as carbon and nitrogen sources. The characteristics and applications of Nocardioides are described in detail in this review, with emphasis on the degradation of several hard-to-degrade pollutants by using Nocardioides, including aromatic compounds, hydrocarbons, haloalkanes, nitrogen heterocycles, and polymeric polyesters. Nocardioides has unique advantages when it comes to hard-to-degrade pollutants. Compared to other strains, Nocardioides has a significantly higher degradation rate and requires less time to break down substances. This review can be a theoretical basis for developing Nocardioides as a microbial agent with significant commercial and application potential.
Collapse
Affiliation(s)
- Yecheng Ma
- College of Biotechnology and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Jinxiu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xinyue Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Lingui Xue
- College of Biotechnology and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Xiaowen Cui
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, China
| |
Collapse
|
8
|
Guo L, Ouyang X, Wang W, Huang Y, Qiu X, Xu P, Tang H. Characterization of a novel aromatic ring-hydroxylating oxygenase, NarA2B2, from thermophilic Hydrogenibacillus sp. strain N12. Appl Environ Microbiol 2023; 89:e0086523. [PMID: 37819076 PMCID: PMC10617421 DOI: 10.1128/aem.00865-23] [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: 05/24/2023] [Accepted: 08/11/2023] [Indexed: 10/13/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are harmful to human health due to their carcinogenic, teratogenic, and mutagenic effects. A thermophilic Hydrogenibacillus sp. strain N12 capable of degrading a variety of PAHs and derivatives was previously isolated. In this study, an aromatic ring-hydroxylating oxygenase, NarA2B2, was identified from strain N12, with substrate specificity including naphthalene, phenanthrene, dibenzothiophene, fluorene, acenaphthene, carbazole, biphenyl, and pyrene. NarA2B2 was proposed to add one or two atoms of molecular oxygen to the substrate and catalyze biphenyl at C-2, 2 or C-3, 4 positions with different characteristics than before. The key catalytic amino acids, H222, H227, and D379, were identified as playing a pivotal role in the formation of the 2-his-1-carboxylate facial triad. Furthermore, we conducted molecular docking and molecular dynamics simulations, notably, D219 enhanced the stability of the iron center by forming two stable hydrogen bonds with H222, while the mutation of F216, T223, and H302 modulated the catalytic activity by altering the pocket's size and shape. Compared to the wild-type (WT) enzyme, the degradation ratios of acenaphthene by F216A, T223A, and H302A had an improvement of 23.08%, 26.87%, and 29.52%, the degradation ratios of naphthalene by T223A and H302A had an improvement of 51.30% and 65.17%, while the degradation ratio of biphenyl by V236A had an improvement of 77.94%. The purified NarA2B2 was oxygen-sensitive when it was incubated with L-ascorbic acid in an anaerobic environment, and its catalytic activity was restored in vitro. These results contribute to a better understanding of the molecular mechanism responsible for PAHs' degradation in thermophilic microorganisms.IMPORTANCE(i) A novel aromatic ring-hydroxylating oxygenase named NarA2B2, capable of degrading multiple polycyclic aromatic hydrocarbons and derivatives, was identified from the thermophilic microorganism Hydrogenibacillus sp. N12. (ii) The degradation characteristics of NarA2B2 were characterized by adding one or two atoms of molecular oxygen to the substrate. Unlike the previous study, NarA2B2 catalyzed biphenyl at C-2, 2 or C-3, 4 positions. (iii) Catalytic sites of NarA2B2 were conserved, and key amino acids F216, D219, H222, T223, H227, V236, F243, Y300, H302, W316, F369, and D379 played pivotal roles in catalysis, as confirmed by protein structure prediction, molecular docking, molecular dynamics simulations, and point mutation.
Collapse
Affiliation(s)
- Lihua Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yiqun Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyu Qiu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
9
|
Ghafouri M, Pourjafar F, Ghobadi Nejad Z, Yaghmaei S. Biological treatment of triclosan using a novel strain of Enterobacter cloacae and introducing naphthalene dioxygenase as an effective enzyme. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:131833. [PMID: 37473572 DOI: 10.1016/j.jhazmat.2023.131833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/22/2023] [Accepted: 06/09/2023] [Indexed: 07/22/2023]
Abstract
In recent years, triclosan (TCS) has been widely used as an antibacterial agent in personal care products due to the spread of the Coronavirus. TSC is an emerging contaminant, and due to its stability and toxicity, it cannot be completely degraded through traditional wastewater treatment methods. In this study, a novel strain of Enterobacter cloacae was isolated and identified that can grow in high TCS concentrations. Also, we introduced naphthalene dioxygenase as an effective enzyme in TCS biodegradation, and its role during the removal process was investigated along with the laccase enzyme. The change of cell surface hydrophobicity during TCS removal revealed that a glycolipid biosurfactant called rhamnolipid was involved in TCS removal, leading to enhanced biodegradation of TCS. The independent variables, such as initial TCS concentration, pH, removal duration, and temperature, were optimized using the response surface method (RSM). As a result, the maximum TCS removal (97%) was detected at a pH value of 7 and a temperature of 32 °C after 9 days and 12 h of treatment. Gas chromatography-mass spectrometry (GC/MS) analysis showed five intermediate products and a newly proposed pathway for TCS degradation. Finally, the phytotoxicity experiment conducted on Cucumis sativus and Lens culinaris seeds demonstrated an increase in germination power and growth of stems and roots in comparison to untreated water. These results indicate that the final treated water was less toxic.
Collapse
Affiliation(s)
- Mahsa Ghafouri
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Fatemeh Pourjafar
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Zahra Ghobadi Nejad
- Biochemical & Bioenvironmental Research Center, Sharif University of Technology, Azadi Avenue, P.O Box 11155-1399, Tehran, Iran
| | - Soheila Yaghmaei
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran; Biochemical & Bioenvironmental Research Center, Sharif University of Technology, Azadi Avenue, P.O Box 11155-1399, Tehran, Iran.
| |
Collapse
|
10
|
Tian J, Boggs DG, Donnan PH, Barroso GT, Garcia AA, Dowling DP, Buss JA, Bridwell-Rabb J. The NADH recycling enzymes TsaC and TsaD regenerate reducing equivalents for Rieske oxygenase chemistry. J Biol Chem 2023; 299:105222. [PMID: 37673337 PMCID: PMC10579966 DOI: 10.1016/j.jbc.2023.105222] [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: 05/27/2023] [Revised: 08/22/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023] Open
Abstract
Many microorganisms use both biological and nonbiological molecules as sources of carbon and energy. This resourcefulness means that some microorganisms have mechanisms to assimilate pollutants found in the environment. One such organism is Comamonas testosteroni, which metabolizes 4-methylbenzenesulfonate and 4-methylbenzoate using the TsaMBCD pathway. TsaM is a Rieske oxygenase, which in concert with the reductase TsaB consumes a molar equivalent of NADH. Following this step, the annotated short-chain dehydrogenase/reductase and aldehyde dehydrogenase enzymes TsaC and TsaD each regenerate a molar equivalent of NADH. This co-occurrence ameliorates the need for stoichiometric addition of reducing equivalents and thus represents an attractive strategy for integration of Rieske oxygenase chemistry into biocatalytic applications. Therefore, in this work, to overcome the lack of information regarding NADH recycling enzymes that function in partnership with Rieske non-heme iron oxygenases (Rieske oxygenases), we solved the X-ray crystal structure of TsaC to a resolution of 2.18 Å. Using this structure, a series of substrate analog and protein variant combination reactions, and differential scanning fluorimetry experiments, we identified active site features involved in binding NAD+ and controlling substrate specificity. Further in vitro enzyme cascade experiments demonstrated the efficient TsaC- and TsaD-mediated regeneration of NADH to support Rieske oxygenase chemistry. Finally, through in-depth bioinformatic analyses, we illustrate the widespread co-occurrence of Rieske oxygenases with TsaC-like enzymes. This work thus demonstrates the utility of these NADH recycling enzymes and identifies a library of short-chain dehydrogenase/reductase enzyme prospects that can be used in Rieske oxygenase pathways for in situ regeneration of NADH.
Collapse
Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David G Boggs
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Gage T Barroso
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daniel P Dowling
- Department of Chemistry, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Joshua A Buss
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | | |
Collapse
|
11
|
Runda ME, de Kok NAW, Schmidt S. Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities. Chembiochem 2023; 24:e202300078. [PMID: 36964978 DOI: 10.1002/cbic.202300078] [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: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.
Collapse
Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| |
Collapse
|
12
|
Babicz JT, Rogers MS, DeWeese DE, Sutherlin KD, Banerjee R, Böttger LH, Yoda Y, Nagasawa N, Saito M, Kitao S, Kurokuzu M, Kobayashi Y, Tamasaku K, Seto M, Lipscomb JD, Solomon EI. Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage. J Am Chem Soc 2023; 145:15230-15250. [PMID: 37414058 PMCID: PMC10804917 DOI: 10.1021/jacs.3c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.
Collapse
Affiliation(s)
- Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Kyle D. Sutherlin
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Lars H. Böttger
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Nobumoto Nagasawa
- Japan Synchrotron Radiation Research Institute, Hyogo 679-5198, Japan
| | - Makina Saito
- Department of Physics, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shinji Kitao
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Masayuki Kurokuzu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Yasuhiro Kobayashi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - Kenji Tamasaku
- RIKEN SPring-8 Center, RIKEN, Sayo, Hyogo 679-5148, Japan
| | - Makoto Seto
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka 590-0494, Japan
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, 380 Roth Way, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| |
Collapse
|
13
|
Tian J, Garcia AA, Donnan PH, Bridwell-Rabb J. Leveraging a Structural Blueprint to Rationally Engineer the Rieske Oxygenase TsaM. Biochemistry 2023. [PMID: 37188334 DOI: 10.1021/acs.biochem.3c00150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Rieske nonheme iron oxygenases use two metallocenters, a Rieske-type [2Fe-2S] cluster and a mononuclear iron center, to catalyze oxidation reactions on a broad range of substrates. These enzymes are widely used by microorganisms to degrade environmental pollutants and to build complexity in a myriad of biosynthetic pathways that are industrially interesting. However, despite the value of this chemistry, there is a dearth of understanding regarding the structure-function relationships in this enzyme class, which limits our ability to rationally redesign, optimize, and ultimately exploit the chemistry of these enzymes. Therefore, in this work, by leveraging a combination of available structural information and state-of-the-art protein modeling tools, we show that three "hotspot" regions can be targeted to alter the site selectivity, substrate preference, and substrate scope of the Rieske oxygenase p-toluenesulfonate methyl monooxygenase (TsaM). Through mutation of six to 10 residues distributed between three protein regions, TsaM was engineered to behave as either vanillate monooxygenase (VanA) or dicamba monooxygenase (DdmC). This engineering feat means that TsaM was rationally engineered to catalyze an oxidation reaction at the meta and ortho positions of an aromatic substrate, rather than its favored native para position, and that TsaM was redesigned to perform chemistry on dicamba, a substrate that is not natively accepted by the enzyme. This work thus contributes to unlocking our understanding of structure-function relationships in the Rieske oxygenase enzyme class and expands foundational principles for future engineering of these metalloenzymes.
Collapse
Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
14
|
Hecko S, Schiefer A, Badenhorst CPS, Fink MJ, Mihovilovic MD, Bornscheuer UT, Rudroff F. Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity. Chem Rev 2023; 123:2832-2901. [PMID: 36853077 PMCID: PMC10037340 DOI: 10.1021/acs.chemrev.2c00304] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.
Collapse
Affiliation(s)
- Sebastian Hecko
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Astrid Schiefer
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Christoffel P S Badenhorst
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Michael J Fink
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| |
Collapse
|
15
|
Rhodococcus Strains from the Specialized Collection of Alkanotrophs for Biodegradation of Aromatic Compounds. Molecules 2023; 28:molecules28052393. [PMID: 36903638 PMCID: PMC10005059 DOI: 10.3390/molecules28052393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
The ability to degrade aromatic hydrocarbons, including (i) benzene, toluene, o-xylene, naphthalene, anthracene, phenanthrene, benzo[a]anthracene, and benzo[a]pyrene; (ii) polar substituted derivatives of benzene, including phenol and aniline; (iii) N-heterocyclic compounds, including pyridine; 2-, 3-, and 4-picolines; 2- and 6-lutidine; 2- and 4-hydroxypyridines; (iv) derivatives of aromatic acids, including coumarin, of 133 Rhodococcus strains from the Regional Specialized Collection of Alkanotrophic Microorganisms was demonstrated. The minimal inhibitory concentrations of these aromatic compounds for Rhodococcus varied in a wide range from 0.2 up to 50.0 mM. o-Xylene and polycyclic aromatic hydrocarbons (PAHs) were the less-toxic and preferred aromatic growth substrates. Rhodococcus bacteria introduced into the PAH-contaminated model soil resulted in a 43% removal of PAHs at an initial concentration 1 g/kg within 213 days, which was three times higher than that in the control soil. As a result of the analysis of biodegradation genes, metabolic pathways for aromatic hydrocarbons, phenol, and nitrogen-containing aromatic compounds in Rhodococcus, proceeding through the formation of catechol as a key metabolite with its following ortho-cleavage or via the hydrogenation of aromatic rings, were verified.
Collapse
|
16
|
Huynh TN, Stewart V. Purine catabolism by enterobacteria. Adv Microb Physiol 2023; 82:205-266. [PMID: 36948655 DOI: 10.1016/bs.ampbs.2023.01.001] [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] [Indexed: 02/13/2023]
Abstract
Purines are abundant among organic nitrogen sources and have high nitrogen content. Accordingly, microorganisms have evolved different pathways to catabolize purines and their metabolic products such as allantoin. Enterobacteria from the genera Escherichia, Klebsiella and Salmonella have three such pathways. First, the HPX pathway, found in the genus Klebsiella and very close relatives, catabolizes purines during aerobic growth, extracting all four nitrogen atoms in the process. This pathway includes several known or predicted enzymes not previously observed in other purine catabolic pathways. Second, the ALL pathway, found in strains from all three species, catabolizes allantoin during anaerobic growth in a branched pathway that also includes glyoxylate assimilation. This allantoin fermentation pathway originally was characterized in a gram-positive bacterium, and therefore is widespread. Third, the XDH pathway, found in strains from Escherichia and Klebsiella spp., at present is ill-defined but likely includes enzymes to catabolize purines during anaerobic growth. Critically, this pathway may include an enzyme system for anaerobic urate catabolism, a phenomenon not previously described. Documenting such a pathway would overturn the long-held assumption that urate catabolism requires oxygen. Overall, this broad capability for purine catabolism during either aerobic or anaerobic growth suggests that purines and their metabolites contribute to enterobacterial fitness in a variety of environments.
Collapse
Affiliation(s)
- TuAnh Ngoc Huynh
- Department of Food Science, University of Wisconsin, Madison, WI, United States
| | - Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, CA, United States.
| |
Collapse
|
17
|
Rogers MS, Gordon AM, Rappe TM, Goodpaster JD, Lipscomb JD. Contrasting Mechanisms of Aromatic and Aryl-Methyl Substituent Hydroxylation by the Rieske Monooxygenase Salicylate 5-Hydroxylase. Biochemistry 2023; 62:507-523. [PMID: 36583545 PMCID: PMC9854337 DOI: 10.1021/acs.biochem.2c00610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The hydroxylase component (S5HH) of salicylate-5-hydroxylase catalyzes C5 ring hydroxylation of salicylate but switches to methyl hydroxylation when a C5 methyl substituent is present. The use of 18O2 reveals that both aromatic and aryl-methyl hydroxylations result from monooxygenase chemistry. The functional unit of S5HH comprises a nonheme Fe(II) site located 12 Å across a subunit boundary from a one-electron reduced Rieske-type iron-sulfur cluster. Past studies determined that substrates bind near the Fe(II), followed by O2 binding to the iron to initiate catalysis. Stopped-flow-single-turnover reactions (STOs) demonstrated that the Rieske cluster transfers an electron to the iron site during catalysis. It is shown here that fluorine ring substituents decrease the rate constant for Rieske electron transfer, implying a prior reaction of an Fe(III)-superoxo intermediate with a substrate. We propose that the iron becomes fully oxidized in the resulting Fe(III)-peroxo-substrate-radical intermediate, allowing Rieske electron transfer to occur. STO using 5-CD3-salicylate-d8 occurs with an inverse kinetic isotope effect (KIE). In contrast, STO of a 1:1 mixture of unlabeled and 5-CD3-salicylate-d8 yields a normal product isotope effect. It is proposed that aromatic and aryl-methyl hydroxylation reactions both begin with the Fe(III)-superoxo reaction with a ring carbon, yielding the inverse KIE due to sp2 → sp3 carbon hybridization. After Rieske electron transfer, the resulting Fe(III)-peroxo-salicylate intermediate can continue to aromatic hydroxylation, whereas the equivalent aryl-methyl intermediate formation must be reversible to allow the substrate exchange necessary to yield a normal product isotope effect. The resulting Fe(III)-(hydro)peroxo intermediate may be reactive or evolve through a high-valent iron intermediate to complete the aryl-methyl hydroxylation.
Collapse
Affiliation(s)
- Melanie S. Rogers
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Adrian M. Gordon
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Todd M. Rappe
- Minnesota NMR Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
18
|
Vahalová P, Cifra M. Biological autoluminescence as a perturbance-free method for monitoring oxidation in biosystems. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 177:80-108. [PMID: 36336139 DOI: 10.1016/j.pbiomolbio.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Biological oxidation processes are in the core of life energetics, play an important role in cellular biophysics, physiological cell signaling or cellular pathophysiology. Understanding of biooxidation processes is also crucial for biotechnological applications. Therefore, a plethora of methods has been developed for monitoring oxidation so far, each with distinct advantages and disadvantages. We review here the available methods for monitoring oxidation and their basic characteristics and capabilities. Then we focus on a unique method - the only one that does not require input of additional external energy or chemicals - which employs detection of biological autoluminescence (BAL). We highlight the pros and cons of this method and provide an overview of how BAL can be used to report on various aspects of cellular oxidation processes starting from oxygen consumption to the generation of oxidation products such as carbonyls. This review highlights the application potential of this completely non-invasive and label-free biophotonic diagnostic method.
Collapse
Affiliation(s)
- Petra Vahalová
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague, 18200, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague, 18200, Czech Republic.
| |
Collapse
|
19
|
Hu WY, Li K, Weitz A, Wen A, Kim H, Murray JC, Cheng R, Chen B, Naowarojna N, Grinstaff MW, Elliott SJ, Chen JS, Liu P. Light-Driven Oxidative Demethylation Reaction Catalyzed by a Rieske-Type Non-heme Iron Enzyme Stc2. ACS Catal 2022; 12:14559-14570. [PMID: 37168530 PMCID: PMC10168674 DOI: 10.1021/acscatal.2c04232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rieske-type non-heme iron oxygenases/oxidases catalyze a wide range of transformations. Their applications in bioremediation or biocatalysis face two key barriers: the need of expensive NAD(P)H as a reductant and a proper reductase to mediate the electron transfer from NAD(P)H to the oxygenases. To bypass the need of both the reductase and NAD(P)H, using Rieske-type oxygenase (Stc2) catalyzed oxidative demethylation as the model system, we report Stc2 photocatalysis using eosin Y/sulfite as the photosensitizer/sacrificial reagent pair. In a flow-chemistry setting to separate the photo-reduction half-reaction and oxidation half-reaction, Stc2 photo-biocatalysis outperforms the Stc2-NAD(P)H-reductase (GbcB) system. In addition, in a few other selected Rieske enzymes (NdmA, CntA, and GbcA), and a flavin-dependent enzyme (iodotyrosine deiodinase, IYD), the eosin Y/sodium sulfite photo-reduction pair could also serve as the NAD(P)H-reductase surrogate to support catalysis, which implies the potential applicability of this photo-reduction system to other redox enzymes.
Collapse
Affiliation(s)
- Wei-Yao Hu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai200240, P. R. China
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Kelin Li
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Andrew Weitz
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Aiwen Wen
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Hyomin Kim
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Jessica C. Murray
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Baixiong Chen
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Nathchar Naowarojna
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Mark W. Grinstaff
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Sean J. Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| | - Jie-Sheng Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai200240, P. R. China
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts02215, United States
| |
Collapse
|
20
|
Aukema KG, Bygd MD, Tassoulas LJ, Richman JE, Wackett LP. Fluoro-recognition: New in vivo fluorescent assay for toluene dioxygenase probing induction by and metabolism of polyfluorinated compounds. Environ Microbiol 2022; 24:5202-5216. [PMID: 36054238 PMCID: PMC9828342 DOI: 10.1111/1462-2920.16187] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/30/2022] [Indexed: 01/12/2023]
Abstract
The present study examined the regulatory and metabolic response of the aromatic degrader Pseudomonas putida F1 and its tod operon, controlling toluene degradation, to fluorinated aromatic and aliphatic compounds. The tod operon is upregulated by inducer binding to the TodS sensing domain of a two-component regulator. The induced enzymes include toluene dioxygenase that initiates catabolic assimilation of benzenoid hydrocarbons. Toluene dioxygenase was shown to oxidize 6-fluoroindole to a meta-stable fluorescent product, 6-fluoroindoxyl. The fluorescent output allowed monitoring relative levels of tod operon induction in whole cells using microtiter well plates. Mono- and polyfluorinated aromatic compounds were shown to induce toluene dioxygenase, in some cases to a greater extent than compounds serving as growth substrates. Compounds that are oxidized by toluene dioxygenase and undergoing defluorination were shown to induce their own metabolism. 1,2,4-Trifluorobenzene caused significant induction and computational modelling indicated productive binding to the TodS sensor domain of the TodST regulator. Toluene dioxygenase also showed preferential binding of 1,2,4-trifluorobenzene such that defluorination was favoured. Fluorinated aliphatic compounds were shown to induce toluene dioxygenase. An aliphatic ether with seven fluorine atoms, 1,1,1,2-tetrafluoro-2-trifluoromethoxy-4-iodobutane (TTIB), was an excellent inducer of toluene dioxygenase activity and shown to undergo transformation in cultures of P. putida F1.
Collapse
Affiliation(s)
- Kelly G. Aukema
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Madison D. Bygd
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Lambros J. Tassoulas
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Jack E. Richman
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| | - Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and Biotechnology InstituteUniversity of Minnesota, Twin CitiesMinnesotaUSA
| |
Collapse
|
21
|
Bopp CE, Bernet NM, Kohler HPE, Hofstetter TB. Elucidating the Role of O 2 Uncoupling in the Oxidative Biodegradation of Organic Contaminants by Rieske Non-heme Iron Dioxygenases. ACS ENVIRONMENTAL AU 2022; 2:428-440. [PMID: 36164353 PMCID: PMC9502038 DOI: 10.1021/acsenvironau.2c00023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Oxygenations of aromatic
soil and water contaminants with molecular
O2 catalyzed by Rieske dioxygenases are frequent initial
steps of biodegradation in natural and engineered environments. Many
of these non-heme ferrous iron enzymes are known to be involved in
contaminant metabolism, but the understanding of enzyme–substrate
interactions that lead to successful biodegradation is still elusive.
Here, we studied the mechanisms of O2 activation and substrate
hydroxylation of two nitroarene dioxygenases to evaluate enzyme- and
substrate-specific factors that determine the efficiency of oxygenated
product formation. Experiments in enzyme assays of 2-nitrotoluene
dioxygenase (2NTDO) and nitrobenzene dioxygenase (NBDO) with methyl-,
fluoro-, chloro-, and hydroxy-substituted nitroaromatic substrates
reveal that typically 20–100% of the enzyme’s activity
involves unproductive paths of O2 activation with generation
of reactive oxygen species through so-called O2 uncoupling.
The 18O and 13C kinetic isotope effects of O2 activation and nitroaromatic substrate hydroxylation, respectively,
suggest that O2 uncoupling occurs after generation of FeIII-(hydro)peroxo species in the catalytic cycle. While 2NTDO
hydroxylates ortho-substituted nitroaromatic substrates
more efficiently, NBDO favors meta-substituted, presumably
due to distinct active site residues of the two enzymes. Our data
implies, however, that the O2 uncoupling and hydroxylation
activity cannot be assessed from simple structure–reactivity
relationships. By quantifying O2 uncoupling by Rieske dioxygenases,
our work provides a mechanistic link between contaminant biodegradation,
the generation of reactive oxygen species, and possible adaptation
strategies of microorganisms to the exposure of new contaminants.
Collapse
Affiliation(s)
- Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Nora M. Bernet
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| |
Collapse
|
22
|
Wackett LP. Strategies for the Biodegradation of Polyfluorinated Compounds. Microorganisms 2022; 10:microorganisms10081664. [PMID: 36014082 PMCID: PMC9415301 DOI: 10.3390/microorganisms10081664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 01/01/2023] Open
Abstract
Many cite the strength of C–F bonds for the poor microbial biodegradability of polyfluorinated organic compounds (PFCs). However, commercial PFCs almost invariably contain more functionality than fluorine. The additional functionality provides a weak entry point for reactions that activate C–F bonds and lead to their eventual cleavage. This metabolic activation strategy is common in microbial biodegradation pathways and is observed with aromatic hydrocarbons, chlorinated compounds, phosphonates and many other compounds. Initial metabolic activation precedes critical bond breakage and assimilation of nutrients. A similar strategy with commercial PFCs proceeds via initial attack at the non-fluorinated functionalities: sulfonates, carboxylates, chlorines, phenyl rings, or phosphonates. Metabolic transformation of these non-fluorinated groups can activate the C–F bonds, allowing more facile cleavage than a direct attack on the C–F bonds. Given that virtually all compounds denoted as “PFAS” are not perfluorinated and are not alkanes, it is posited here that considering their individual chemical classes is more useful for both chemical and microbiological considerations of their fate.
Collapse
Affiliation(s)
- Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
23
|
Li S, Shen W, Lian S, Wu Y, Qu Y, Deng Y. DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129230. [PMID: 35739750 DOI: 10.1016/j.jhazmat.2022.129230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Biodegradation of aromatic compounds is ubiquitous in the environment and important for controlling organic pollutants. Aromatic ring-hydroxylating dioxygenases (ARHDs) are responsible for the first and rate-limiting step of aerobic biodegradation of aromatic compounds. The ARHD α subunit is a good biomarker for studying functional microorganisms in the environment, however their diversity and corresponding primer coverage are unclear, both of which require a comprehensive sequence database for the ARHD α subunit. Here amino acid sequences of the ARHD α subunit were collected, and a total of 103 sequences were selected as seed sequences that were distributed in 72 bacterial genera with 34 gene names. Based on both homolog search and keyword confirmation against the GenBank, a sequence database of ARHD (DARHD) has been established and 6367 highly credible sequences were retrieved. DARHD contained 407 bacterial genera capable of degrading 38 aromatic substrates, and intricate relationships among the gene name, aromatic substrate and microbial taxa were observed. Thereafter, a total of 136 pairs of primers were collected and assessed. Results showed coverages of most published primers were low. Our research provides new insights for understanding the diversity of ARHD α subunit, and gives guidance on the design and application of primers in the future.
Collapse
Affiliation(s)
- Shuzhen Li
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Wenli Shen
- Institute for Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Shengyang Lian
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yueni Wu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute for Marine Science and Technology, Shandong University, Qingdao 266237, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
24
|
The α- and β-Subunit Boundary at the Stem of the Mushroom-Like α
3
β
3
-Type Oxygenase Component of Rieske Non-Heme Iron Oxygenases Is the Rieske-Type Ferredoxin-Binding Site. Appl Environ Microbiol 2022; 88:e0083522. [PMID: 35862661 PMCID: PMC9361823 DOI: 10.1128/aem.00835-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cumene dioxygenase (CumDO) is an initial enzyme in the cumene degradation pathway of Pseudomonas fluorescens IP01 and is a Rieske non-heme iron oxygenase (RO) that comprises two electron transfer components (reductase [CumDO-R] and Rieske-type ferredoxin [CumDO-F]) and one catalytic component (α3β3-type oxygenase [CumDO-O]). Catalysis is triggered by electrons that are transferred from NAD(P)H to CumDO-O by CumDO-R and CumDO-F. To investigate the binding mode between CumDO-F and CumDO-O and to identify the key CumDO-O amino acid residues for binding, we simulated docking between the CumDO-O crystal structure and predicted model of CumDO-F and identified two potential binding sites: one is at the side-wise site and the other is at the top-wise site in mushroom-like CumDO-O. Then, we performed alanine mutagenesis of 16 surface amino acid residues at two potential binding sites. The results of reduction efficiency analyses using the purified components indicated that CumDO-F bound at the side-wise site of CumDO-O, and K117 of the α-subunit and R65 of the β-subunit were critical for the interaction. Moreover, these two positively charged residues are well conserved in α3β3-type oxygenase components of ROs whose electron donors are Rieske-type ferredoxins. Given that these residues were not conserved if the electron donors were different types of ferredoxins or reductases, the side-wise site of the mushroom-like structure is thought to be the common binding site between Rieske-type ferredoxin and α3β3-type oxygenase components in ROs. IMPORTANCE We clarified the critical amino acid residues of the oxygenase component (Oxy) of Rieske non-heme iron oxygenase (RO) for binding with Rieske-type ferredoxin (Fd). Our results showed that Rieske-type Fd-binding site is commonly located at the stem (side-wise site) of the mushroom-like α3β3 quaternary structure in many ROs. The resultant binding site was totally different from those reported at the top-wise site of the doughnut-like α3-type Oxy, although α3-type Oxys correspond to the cap (α3 subunit part) of the mushroom-like α3β3-type Oxys. Critical amino acid residues detected in this study were not conserved if the electron donors of Oxys were different types of Fds or reductases. Altogether, we can suggest that unique binding modes between Oxys and electron donors have evolved, depending on the nature of the electron donors, despite Oxy molecules having shared α3β3 quaternary structures.
Collapse
|
25
|
Pati SG, Bopp CE, Kohler HPE, Hofstetter TB. Substrate-Specific Coupling of O 2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases. ACS Catal 2022; 12:6444-6456. [PMID: 35692249 PMCID: PMC9171724 DOI: 10.1021/acscatal.2c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/09/2022] [Indexed: 02/07/2023]
Abstract
![]()
Rieske dioxygenases
catalyze the initial steps in the hydroxylation
of aromatic compounds and are critical for the metabolism of xenobiotic
substances. Because substrates do not bind to the mononuclear non-heme
FeII center, elementary steps leading to O2 activation
and substrate hydroxylation are difficult to delineate, thus making
it challenging to rationalize divergent observations on enzyme mechanisms,
reactivity, and substrate specificity. Here, we show for nitrobenzene
dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes
to nitrite and substituted catechols, that unproductive O2 activation with the release of the unreacted substrate and reactive
oxygen species represents an important path in the catalytic cycle.
Through correlation of O2 uncoupling for a series of substituted
nitroaromatic compounds with 18O and 13C kinetic
isotope effects of dissolved O2 and aromatic substrates,
respectively, we show that O2 uncoupling occurs after the
rate-limiting formation of FeIII-(hydro)peroxo species
from which substrates are hydroxylated. Substituent effects on the
extent of O2 uncoupling suggest that the positioning of
the substrate in the active site rather than the susceptibility of
the substrate for attack by electrophilic oxygen species is responsible
for unproductive O2 uncoupling. The proposed catalytic
cycle provides a mechanistic basis for assessing the very different
efficiencies of substrate hydroxylation vs unproductive O2 activation and generation of reactive oxygen species in reactions
catalyzed by Rieske dioxygenases.
Collapse
Affiliation(s)
- Sarah G. Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| |
Collapse
|
26
|
Mohapatra B, Nain S, Sharma R, Phale PS. Functional genome mining and taxono-genomics reveal eco-physiological traits and species distinctiveness of aromatic-degrading Pseudomonas bharatica sp. nov. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:464-474. [PMID: 35388632 DOI: 10.1111/1758-2229.13066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Assistive eco-physiological traits are necessary for microbes to adapt and colonize at polluted niches, enabling efficient clean-up. To demarcate species distinctiveness and eco-physiological traits of aromatic compounds metabolizing Pseudomonas sp. CSV86T (earlier identified as Pseudomonas putida), an Indian isolate from a petrol station soil, comparative genome mining, taxono-genomic, and physiological analyses were performed. A 6.79 Mbp genome (62.72 G + C mol%) of CSV86T encodes 6798 CDS and 238 unique genes. Naphthalene metabolism and Co-Zn-Cd resistance gene clusters were part of distinct genomic islands. Abundance of transporters (aromatics, organic acids, amino acids, and metals) and mobile elements (integrases, transposases, conjugative proteins) differentiated CSV86T from its closest relatives. Enhanced siderophore production for Fe-uptake during aromatic metabolism, indole acetic acid production, and fusaric acid resistance wasvalidated by genomic attributes. Full-length 16S-rRNA phylogeny revealed Pseudomonas japonica WLT as a closest relative of CSV86T . However, lower genomic indices (<97% gyrB-rpoB-rpoD homology, <90% ANI, <50% DNA-DNA relatedness) and taxonomic differences (assimilation of organic acids, amino acids, fatty acids composition) substantially differentiated CSV86T from its closest relatives, indicating it to be a novel species as Pseudomonas bharatica. Preferential metabolism of aromatics with advantageous eco-physiological traits renders CSV86T an ideal candidate for bioremediation and host for metabolic engineering.
Collapse
Affiliation(s)
- Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, Maharashtra, India
| | - Sonam Nain
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Rakesh Sharma
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, Maharashtra, India
| |
Collapse
|
27
|
Alghuthaymi MA, Awad AM, Hassan HA. Isolation and Characterization a Novel Catabolic Gene Cluster Involved in Chlorobenzene Degradation in Haloalkaliphilic Alcanivorax sp. HA03. BIOLOGY 2022; 11:biology11050724. [PMID: 35625452 PMCID: PMC9138330 DOI: 10.3390/biology11050724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/16/2022]
Abstract
Chlorobenzene (CB) poses a serious risk to human health and the environment, and because of its low degradation rate by microorganisms, it persists in the environment. Some bacterial strains can use CB as growth substrates and their degradative pathways have evolved; very little is known about these pathways and the enzymes for CB degradation in high pH and salinity environments. Alcanivorax sp. HA03 was isolated from the extremely saline and alkaline site. HA03 has the capability to degrade benzene, toluene and chlorobenzene (CB). CB catabolic genes were isolated from HA03, which have a complete gene cluster comprising α and β subunits, ferredoxin and ferredoxin reductase (CBA1A2A3A4), as well as one gene-encoding enzyme for chlorocatechol 1,2-dioxygenase (CC12DOs). Based on the deduced amino acid sequence homology, the gene cluster was thought to be responsible for the upper and lower catabolic pathways of CB degradation. The CBA1A2A3A4 genes probably encoding a chlorobenzene dioxygenase was confirmed by expression during the growth on CB by RT-PCR. Heterologous expression revealed that CBA1A2A3A4 exhibited activity for CB transformation into 3-chlorocatechol, while CC12DOs catalyze 3-chlorocatechol, transforming it into 2-chloromucounate. SDS-PAGE analysis indicated that the sizes of CbA1 and (CC12DOs) gene products were 51.8, 27.5 kDa, respectively. Thus, Alcanivorax sp. HA03 constitutes the first bacterial strain described in the metabolic pathway of CB degradation under high pH and salinity conditions. This finding may have obvious potential for the bioremediation of CB in both highly saline and alkaline contaminated sites.
Collapse
Affiliation(s)
- Mousa A. Alghuthaymi
- Biology Department, Science and Humanities College, Shaqra University, Alquwayiyah 11726, Saudi Arabia;
| | - Ahmed M. Awad
- Department of Environmental Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt;
| | - Hamdy A. Hassan
- Biology Department, Science and Humanities College, Shaqra University, Alquwayiyah 11726, Saudi Arabia;
- Department of Environmental Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt;
- Correspondence:
| |
Collapse
|
28
|
Microwell Fluoride Screen for Chemical, Enzymatic, and Cellular Reactions Reveals Latent Microbial Defluorination Capacity for -CF 3 Groups. Appl Environ Microbiol 2022; 88:e0028822. [PMID: 35435713 DOI: 10.1128/aem.00288-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The capacity to defluorinate polyfluorinated organic compounds is a rare phenotype in microbes but is increasingly considered important for maintaining the environment. New discoveries will be greatly facilitated by the ability to screen many natural and engineered microbes in a combinatorial manner against large numbers of fluorinated compounds simultaneously. Here, we describe a low-volume, high-throughput screening method to determine defluorination capacity of microbes and their enzymes. The method is based on selective binding of fluoride to a lanthanum chelate complex that gives a purple-colored product. It was miniaturized to determine biodefluorination in 96-well microtiter plates by visual inspection or robotic handling and spectrophotometry. Chemicals commonly used in microbiological studies were examined to define usable buffers and reagents. Base-catalyzed, purified enzyme and whole-cell defluorination reactions were demonstrated with fluoroatrazine and showed correspondence between the microtiter assay and a fluoride electrode. For discovering new defluorination reactions and mechanisms, a chemical library of 63 fluorinated compounds was screened in vivo with Pseudomonas putida F1 in microtiter well plates. These data were also calibrated against a fluoride electrode. Our new method revealed 21 new compounds undergoing defluorination. A compound with four fluorine substituents, 4-fluorobenzotrifluoride, was shown to undergo defluorination to the greatest extent. The mechanism of its defluorination was studied to reveal a latent microbial propensity to defluorinate trifluoromethylphenyl groups, a moiety that is commonly incorporated into numerous pharmaceutical and agricultural chemicals. IMPORTANCE Thousands of organofluorine chemicals are known, and a number are considered to be persistent and toxic environmental pollutants. Environmental bioremediation methods are avidly being sought, but few bacteria biodegrade fluorinated chemicals. To find new organofluoride biodegradation, a rapid screening method was developed. The method is versatile, monitoring chemical, enzymatic, and whole-cell biodegradation. Biodegradation of organofluorine compounds invariably releases fluoride anions, which was sensitively detected. Our method uncovered 21 new microbial defluorination reactions. A general mechanism was delineated for the biodegradation of trifluoromethylphenyl groups that are increasingly being used in drugs and pesticides.
Collapse
|
29
|
Brennerova MV, Zavala-Meneses SG, Josefiova J, Branny P, Buriankova K, Vetrovsky T, Junca H. A global survey reveals a divergent extradiol dioxygenase clade as a widespread complementary contributor to the biodegradation of mono- and polycyclic aromatic hydrocarbons. ENVIRONMENTAL RESEARCH 2022; 204:111954. [PMID: 34474030 DOI: 10.1016/j.envres.2021.111954] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (EXDOs) with broad substrate specificity, the HrbC EXDOs. The new clade belongs to the XII cluster within family 2 of the vicinal oxygen chelate superfamily (EXDO-VC2), which is typically characterized by a preference for bicyclic substrates. Coding hrbC orthologs were isolated by activity-based screening of fosmid metagenomic libraries from large DNA fragments derived from heavily PAH-contaminated soils. They occurred as solitary genes within conserved sequences encoding enzymes for amino acid metabolism and were stably maintained in the chromosomes of the Betaproteobacteria lineages harboring them. Analysis of contaminated aquifers revealed coexpression of hrbC as a polycistronic mRNA component. The predicted open reading frames were verified by cloning and heterologous expression, confirming the expected molecular mass and meta-cleavage activity of the recombinant enzymes. Evolutionary analysis of the HrbC protein sequences grouped them into a discrete cluster of 1,2-dihydroxynaphthalene dioxygenases represented by a cultured PAH degrader, Rugosibacter aromaticivorans strain Ca6. The ecological importance and relevance of the new EXDO genes were confirmed by PCR-based mapping in different biogeographical localities contaminated with a variety of mono- and polycyclic aromatic compounds. The cosmopolitan distribution of hrbC in PAH-contaminated aquifers supports our hypothesis about its auxiliary role in the degradation of toxic catecholic intermediates, contributing to the composite EXDO catabolic capacity of the world's microbiomes.
Collapse
Affiliation(s)
- Maria V Brennerova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic.
| | - Sofía G Zavala-Meneses
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic; Charles University, Faculty of Science, Vinicna 5, 12844, Prague, Czech Republic
| | - Jirina Josefiova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Pavel Branny
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Karolina Buriankova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Tomas Vetrovsky
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div. Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, 250008, Chia, Colombia
| |
Collapse
|
30
|
Monga D, Kaur P, Singh B. Microbe mediated remediation of dyes, explosive waste and polyaromatic hydrocarbons, pesticides and pharmaceuticals. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100092. [PMID: 35005657 PMCID: PMC8717453 DOI: 10.1016/j.crmicr.2021.100092] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/16/2021] [Accepted: 12/08/2021] [Indexed: 01/30/2023] Open
Abstract
Environmental pollutants dyes, pesticides, pharmaceuticals, explosive waste and polyaromatic hydrocarbons. Environmental pollutants toxicity. Possible microbial biodegradation pathways of environmental pollutants.
Industrialization and human activities have led to serious effects on environment. With the progress taking place in the biodegradation field, it is important to summarize the latest advancement. In this review, we intend to provide insights on the recent progress on the biodegradation of environmental contaminants such as dyes, pesticides, pharmaceuticals, explosive waste and polyaromatic hydrocarbons by microorganisms. Along with the biodegradation of environmental contaminants, toxicity effects have also been discussed.
Collapse
|
31
|
Seoane GA, Daher GM. Readily accessible azido-alkyne-functionalized monomers for the synthesis of cyclodextrin analogues using click chemistry. Org Biomol Chem 2022; 20:1690-1698. [DOI: 10.1039/d1ob02496e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A set of linear and cyclic oligomers were synthesized starting from a suitable azido-alkyne monomer through click oligomerization. The synthesis of these monomers starting from bromobenzene features an enzymatic dihydroxylation...
Collapse
|
32
|
Hara T, Takatsuka Y, Nakata E, Morii T. Augmentation of an Engineered Bacterial Strain Potentially Improves the Cleanup of PCB Water Pollution. Microbiol Spectr 2021; 9:e0192621. [PMID: 34937186 PMCID: PMC8694117 DOI: 10.1128/spectrum.01926-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 12/04/2022] Open
Abstract
Polychlorinated biphenyls (PCBs) are recalcitrant organohalide pollutants, consisting of 209 congeners. PCB cleanup in natural landscapes is expected to be achieved by the metabolic activity of microorganisms, but aerobic PCB-degrading bacteria that inhabit sites polluted by PCBs cannot degrade all PCB congeners due to the specificity of their enzymes. In this study, we investigated the degradability of PCBs when a genetically modified PCB-degrading bacterium was compounded with wild-type PCB-degrading bacteria. We used two bacterial strains, Comamonas testosteroni YAZ2 isolated from a PCB-uncontaminated natural landscape and Escherichia coli BL21(DE3) transformed with a biphenyl dioxygenase (BphA) gene from a well-known PCB degrader, Burkholderia xenovorans LB400. The enzymatic specificities of BphA were 2,3-dioxygenation in the YAZ2 and 2,3- and 3,4-dioxygenations in the recombinant E. coli. For the PCB-degrading experiment, a dedicated bioreactor capable of generating oxygen microbubbles was prototyped and used. The combined cells of the recombinant and the wild-type strains with an appropriate composite ratio degraded 40 mg/L of Kaneclor KC-300 to 0.3 ± 0.1 mg/L within 24 h. All of the health-toxic coplanar PCB congeners in KC-300 were degraded. This study suggested that the augmentation of an engineered bacterial strain could improve the cleanup of PCB water pollution. It also revealed the importance of the ratio of the strains with different PCB-degrading profiles to efficient degradation and that the application of oxygen microbubbles could rapidly accelerate the cleanup. IMPORTANCE PCB cleanup technique in a natural environment relies on the use of enzymes from microorganisms, primarily biphenyl dioxygenase and dehalogenase. Herein, we focused on biphenyl dioxygenase and created a recombinant PCB-degrading E. coli strain. Despite the development of environments for the field use of transgenic microbial strains around the world, verification of the applicability of transgenic microbial strains for PCB cleanup in the field has not yet been reported. We tentatively verified the extent to which degradability could be obtained by an augmentation model of a transgenic strain, the enzyme expression of which is easily regulated in rivers and lakes with PCB pollution. Our experiments used a dedicated bioreactor to model the natural landscape and produced results superior to those of bioremediation or biostimulation methods. The application of micro-nano bubbles, which has recently been discussed, to the cleanup of environmental pollution was also found to be useful in this study.
Collapse
Affiliation(s)
- Tomijiro Hara
- Environmental Microbiology Research Section, Laboratory for Complex Energy Processes, Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Yumiko Takatsuka
- Environmental Microbiology Research Section, Laboratory for Complex Energy Processes, Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| |
Collapse
|
33
|
Ramdass AC, Rampersad SN. Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism. BMC Microbiol 2021; 21:287. [PMID: 34670489 PMCID: PMC8527658 DOI: 10.1186/s12866-021-02346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022] Open
Abstract
Background Janthinobacterium lividum is considered to be a psychrotrophic bacterial species. For the first time in the literature, J. lividum strains were isolated from Trinidad presenting with atypical features - hydrocarbonoclastic and able to survive in a tropical environment. Methods Identification of the Trinidad strains was carried out through 16S rRNA phylogenetic analysis. Gene-specific primers were designed to target the VioA which encodes violacein pigment and the EstA/B gene which encodes secreted extracellular lipase. Bioinformatics analyses were carried out on the nucleotide and amino acid sequences of VioA and EstA/B genes of the Trinidad Janthinobacterium strains to assess functionality and phylogenetic relatedness to other Janthinobacterium sequences specifically and more broadly, to other members of the Oxalobacteraceae family of betaproteobacteria. Results 16S rRNA confirmed the identity of the Trinidad strains as J. lividum and resolved three of the Trinidad strains at the intra-specific level. Typical motility patterns of this species were recorded. VioAp sequences were highly conserved, however, synonymous substitutions located outside of the critical sites for enzyme function were detected for the Trinidad strains. Comparisons with PDB 6g2p model from aa231 to aa406 further indicated no functional disruption of the VioA gene of the Trinidad strains. Phylogeny of the VioA protein sequences inferred placement of all J. lividum taxa into a highly supported species-specific clade (bs = 98%). EstA/Bp sequences were highly conserved, however, synonymous substitutions were detected that were unique to the Trinidad strains. Phylogenetic inference positioned the Trinidad consensus VioA and EstA protein sequences in a clearly distinct branch. Conclusions The findings showed that the primary sequence of VioAp and EstA/Bp were unique to the Trinidad strains and these molecular signatures were reflected in phylogenetic inference. Our results supported chemotaxis, possible elective inactivation of VioA gene expression and secreted lipase activity as survival mechanisms of the Trinidad strains in petrogenic conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02346-4.
Collapse
Affiliation(s)
- Amanda C Ramdass
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Sephra N Rampersad
- Biochemistry Research Lab (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago.
| |
Collapse
|
34
|
Abstract
The Pd-catalyzed carbon-carbon bond formation pioneered by Heck in 1969 has dominated medicinal chemistry development for the ensuing fifty years. As the demand for more complex three-dimensional active pharmaceuticals continues to increase, preparative enzyme-mediated assembly, by virtue of its exquisite selectivity and sustainable nature, is poised to provide a practical and affordable alternative for accessing such compounds. In this minireview, we summarize recent state-of-the-art developments in practical enzyme-mediated assembly of carbocycles. When appropriate, background information on the enzymatic transformation is provided and challenges and/or limitations are also highlighted.
Collapse
Affiliation(s)
- Weijin Wang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Douglass F Taber
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Hans Renata
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| |
Collapse
|
35
|
Xu A, Zhang X, Wu S, Xu N, Huang Y, Yan X, Zhou J, Cui Z, Dong W. Pollutant Degrading Enzyme: Catalytic Mechanisms and Their Expanded Applications. Molecules 2021; 26:4751. [PMID: 34443339 PMCID: PMC8401168 DOI: 10.3390/molecules26164751] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/03/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
The treatment of environmental pollution by microorganisms and their enzymes is an innovative and socially acceptable alternative to traditional remediation approaches. Microbial biodegradation is often characterized with high efficiency as this process is catalyzed via degrading enzymes. Various naturally isolated microorganisms were demonstrated to have considerable ability to mitigate many environmental pollutants without external intervention. However, only a small fraction of these strains are studied in detail to reveal the mechanisms at the enzyme level, which strictly limited the enhancement of the degradation efficiency. Accordingly, this review will comprehensively summarize the function of various degrading enzymes with an emphasis on catalytic mechanisms. We also inspect the expanded applications of these pollutant-degrading enzymes in industrial processes. An in-depth understanding of the catalytic mechanism of enzymes will be beneficial for exploring and exploiting more degrading enzyme resources and thus ameliorate concerns associated with the ineffective biodegradation of recalcitrant and xenobiotic contaminants with the help of gene-editing technology and synthetic biology.
Collapse
Affiliation(s)
- Anming Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Xiaoxiao Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Shilei Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Ning Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.H.); (X.Y.)
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.H.); (X.Y.)
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (Y.H.); (X.Y.)
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China; (A.X.); (X.Z.); (S.W.); (N.X.); (J.Z.)
| |
Collapse
|
36
|
Rosas-Díaz J, Escobar-Zepeda A, Adaya L, Rojas-Vargas J, Cuervo-Amaya DH, Sánchez-Reyes A, Pardo-López L. Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance. Front Microbiol 2021; 12:713702. [PMID: 34413843 PMCID: PMC8369764 DOI: 10.3389/fmicb.2021.713702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Paenarthrobacter sp. GOM3, which is a strain that represents a new species-specific context within the genus Paenarthrobacter, is clearly a branched member independent of any group described thus far. This strain was recovered from marine sediments in the Gulf of Mexico, and despite being isolated from a consortium capable of growing with phenanthrene as a sole carbon source, this strain could not grow successfully in the presence of this substrate alone. We hypothesized that the GOM3 strain could participate in the assimilation of intermediate metabolites for the degradation of aromatic compounds. To date, there are no experimental reports of Paenarthrobacter species that degrade polycyclic aromatic hydrocarbons (PAHs) or their intermediate metabolites. In this work, we report genomic and experimental evidence of metabolic benzoate, gentisate, and protocatechuate degradation by Paenarthrobacter sp. GOM3. Gentisate was the preferred substrate with the highest volumetric consumption rate, and genomic analysis revealed that this strain possesses multiple gene copies for the specific transport of gentisate. Furthermore, upon analyzing the GOM3 genome, we found five different dioxygenases involved in the activation of aromatic compounds, suggesting its potential for complete remediation of PAH-contaminated sites in combination with strains capable of assimilating the upper PAH degradation pathway. Additionally, this strain was characterized experimentally for its pathogenic potential and in silico for its antimicrobial resistance. An overview of the potential ecological role of this strain in the context of other members of this taxonomic clade is also reported.
Collapse
Affiliation(s)
- Jaime Rosas-Díaz
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Alejandra Escobar-Zepeda
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Libertad Adaya
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Jorge Rojas-Vargas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Diego Humberto Cuervo-Amaya
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| | - Ayixon Sánchez-Reyes
- Cátedras Conacyt – Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autoónoma de México, Cuernavaca, Mexico
| |
Collapse
|
37
|
Bacosa HP, Mabuhay-Omar JA, Balisco RAT, Omar DM, Inoue C. Biodegradation of binary mixtures of octane with benzene, toluene, ethylbenzene or xylene (BTEX): insights on the potential of Burkholderia, Pseudomonas and Cupriavidus isolates. World J Microbiol Biotechnol 2021; 37:122. [PMID: 34151386 DOI: 10.1007/s11274-021-03093-4] [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: 03/12/2021] [Accepted: 06/14/2021] [Indexed: 01/20/2023]
Abstract
The contamination of the environment by crude oil and its by-products, mainly composed of aliphatic and aromatic hydrocarbons, is a widespread problem. Biodegradation by bacteria is one of the processes responsible for the removal of these pollutants. This study was conducted to determine the abilities of Burkholderia sp. B5, Cupriavidus sp. B1, Pseudomonas sp. T1, and another Cupriavidus sp. X5 to degrade binary mixtures of octane (representing aliphatic hydrocarbons) with benzene, toluene, ethylbenzene, or xylene (BTEX as aromatic hydrocarbons) at a final concentration of 100 ppm under aerobic conditions. These strains were isolated from an enriched bacterial consortium (Yabase or Y consortium) that prefer to degrade aromatic hydrocarbon over aliphatic hydrocarbons. We found that B5 degraded all BTEX compounds more rapidly than octane. In contrast, B1, T1 and X5 utilized more of octane over BTX compounds. B5 also preferred to use benzene over octane with varying concentrations of up to 200 mg/l. B5 possesses alkane hydroxylase (alkB) and catechol 2,3-dioxygenase (C23D) genes, which are responsible for the degradation of alkanes and aromatic hydrocarbons, respectively. This study strongly supports our notion that Burkholderia played a key role in the preferential degradation of aromatic hydrocarbons over aliphatic hydrocarbons in the previously characterized Y consortium. The preferential degradation of more toxic aromatic hydrocarbons over aliphatics is crucial in risk-based bioremediation.
Collapse
Affiliation(s)
- Hernando P Bacosa
- Environmental Science Program, Department of Biological Sciences, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Tibanga, 9200, Iligan, Lanao del Norte, Philippines.,Graduate School of Environmental Studies, Tohoku University, 6-6-20 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Jhonamie A Mabuhay-Omar
- College of Fisheries and Aquatic Sciences, Western Philippines University-Puerto Princesa, Sta. Monica, 5300, Puerto Princesa, Palawan, Philippines.
| | - Rodulf Anthony T Balisco
- College of Fisheries and Aquatic Sciences, Western Philippines University-Puerto Princesa, Sta. Monica, 5300, Puerto Princesa, Palawan, Philippines
| | - Dawin M Omar
- College of Engineering, Architecture and Technology, Palawan State University, Tiniguiban, 5300, Puerto Princesa, Palawan, Philippines
| | - Chihiro Inoue
- Graduate School of Environmental Studies, Tohoku University, 6-6-20 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| |
Collapse
|
38
|
Gallo G, Puopolo R, Carbonaro M, Maresca E, Fiorentino G. Extremophiles, a Nifty Tool to Face Environmental Pollution: From Exploitation of Metabolism to Genome Engineering. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5228. [PMID: 34069056 PMCID: PMC8157027 DOI: 10.3390/ijerph18105228] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 12/13/2022]
Abstract
Extremophiles are microorganisms that populate habitats considered inhospitable from an anthropocentric point of view and are able to tolerate harsh conditions such as high temperatures, extreme pHs, high concentrations of salts, toxic organic substances, and/or heavy metals. These microorganisms have been broadly studied in the last 30 years and represent precious sources of biomolecules and bioprocesses for many biotechnological applications; in this context, scientific efforts have been focused on the employment of extremophilic microbes and their metabolic pathways to develop biomonitoring and bioremediation strategies to face environmental pollution, as well as to improve biorefineries for the conversion of biomasses into various chemical compounds. This review gives an overview on the peculiar metabolic features of certain extremophilic microorganisms, with a main focus on thermophiles, which make them attractive for biotechnological applications in the field of environmental remediation; moreover, it sheds light on updated genetic systems (also those based on the CRISPR-Cas tool), which expand the potentialities of these microorganisms to be genetically manipulated for various biotechnological purposes.
Collapse
Affiliation(s)
- Giovanni Gallo
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
- Consiglio Nazionale delle Ricerche CNR, Institute of Polymers, Composites and Biomaterials (IPCB), Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
| | - Rosanna Puopolo
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
| | - Miriam Carbonaro
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
| | - Emanuela Maresca
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
| | - Gabriella Fiorentino
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy; (G.G.); (R.P.); (M.C.); (E.M.)
- Consiglio Nazionale delle Ricerche CNR, Institute of Polymers, Composites and Biomaterials (IPCB), Via Campi Flegrei, 34, 80078 Pozzuoli, Italy
| |
Collapse
|
39
|
A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2. Appl Environ Microbiol 2021; 87:AEM.01589-20. [PMID: 33741620 DOI: 10.1128/aem.01589-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 03/09/2021] [Indexed: 11/20/2022] Open
Abstract
A novel gene cluster involved in the degradation of lignin-derived monoaromatics such as p-hydroxybenzoate, vanillate, and ferulate has been identified in the thermophilic nitrate reducer Thermus oshimai JL-2. Based on conserved domain analyses and metabolic pathway mapping, the cluster was classified into upper- and peripheral-pathway operons. The upper-pathway genes, responsible for the degradation of p-hydroxybenzoate and vanillate, are located on a 0.27-Mb plasmid, whereas the peripheral-pathway genes, responsible for the transformation of ferulate, are spread throughout the plasmid and the chromosome. In addition, a lower-pathway operon was also identified in the plasmid that corresponds to the meta-cleavage pathway of catechol. Spectrophotometric and gene induction data suggest that the upper and lower operons are induced by p-hydroxybenzoate, which the strain can degrade completely within 4 days of incubation, whereas the peripheral genes are expressed constitutively. The upper degradation pathway follows a less common route, proceeding via the decarboxylation of protocatechuate to form catechol, and involves a novel thermostable γ-carboxymuconolactone decarboxylase homolog, identified as protocatechuate decarboxylase based on gene deletion experiments. This gene cluster is conserved in only a few members of the Thermales and shows traces of vertical expansion of catabolic pathways in these organisms toward lignoaromatics.IMPORTANCE High-temperature steam treatment of lignocellulosic biomass during the extraction of cellulose and hemicellulose fractions leads to the release of a wide array of lignin-derived aromatics into the natural ecosystem, some of which can have detrimental effects on the environment. Not only will identifying organisms capable of using such aromatics aid in environmental cleanup, but thermostable enzymes, if characterized, can also be used for efficient lignin valorization. However, no thermophilic lignin degraders have been reported thus far. The present study reports T. oshimai JL-2 as a thermophilic bacterium with the potential to use lignin-derived aromatics. The identification of a novel thermostable protocatechuate decarboxylase gene in the strain further adds to its significance, as such an enzyme can be efficiently used in the biosynthesis of cis,cis-muconate, an important intermediate in the commercial production of plastics.
Collapse
|
40
|
Vega FE, Emche S, Shao J, Simpkins A, Summers RM, Mock MB, Ebert D, Infante F, Aoki S, Maul JE. Cultivation and Genome Sequencing of Bacteria Isolated From the Coffee Berry Borer ( Hypothenemus hampei), With Emphasis on the Role of Caffeine Degradation. Front Microbiol 2021; 12:644768. [PMID: 33889142 PMCID: PMC8055839 DOI: 10.3389/fmicb.2021.644768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
The coffee berry borer, the most economically important insect pest of coffee worldwide, is the only insect capable of feeding and reproducing solely on the coffee seed, a food source containing the purine alkaloid caffeine. Twenty-one bacterial species associated with coffee berry borers from Hawai’i, Mexico, or a laboratory colony in Maryland (Acinetobacter sp. S40, S54, S55, Bacillus aryabhattai, Delftia lacustris, Erwinia sp. S38, S43, S63, Klebsiella oxytoca, Ochrobactrum sp. S45, S46, Pantoea sp. S61, Pseudomonas aeruginosa, P. parafulva, and Pseudomonas sp. S30, S31, S32, S37, S44, S60, S75) were found to have at least one of five caffeine N-demethylation genes (ndmA, ndmB, ndmC, ndmD, ndmE), with Pseudomonas spp. S31, S32, S37, S60 and P. parafulva having the full complement of these genes. Some of the bacteria carrying the ndm genes were detected in eggs, suggesting possible vertical transmission, while presence of caffeine-degrading bacteria in frass, e.g., P. parafulva (ndmABCDE) and Bacillus aryabhattai (ndmA) could result in horizontal transmission to all insect life stages. Thirty-five bacterial species associated with the insect (Acinetobacter sp. S40, S54, S55, B. aryabhattai, B. cereus group, Bacillus sp. S29, S70, S71, S72, S73, D. lacustris, Erwinia sp. S38, S43, S59, S63, K. oxytoca, Kosakonia cowanii, Ochrobactrum sp. S45, S46, Paenibacillus sp. S28, Pantoea sp. S61, S62, P. aeruginosa, P. parafulva, Pseudomonas sp. S30, S31, S32, S37, S44, S60, S75, Stenotrophomonas sp. S39, S41, S48, S49) might contribute to caffeine breakdown using the C-8 oxidation pathway, based on presence of genes required for this pathway. It is possible that caffeine-degrading bacteria associated with the coffee berry borer originated as epiphytes and endophytes in the coffee plant microbiota.
Collapse
Affiliation(s)
- Fernando E Vega
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Sarah Emche
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Jonathan Shao
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Ann Simpkins
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Ryan M Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, United States
| | - Meredith B Mock
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL, United States
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | | | - Sayaka Aoki
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Jude E Maul
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| |
Collapse
|
41
|
Pérez-Pantoja D, Nikel PI, Chavarría M, de Lorenzo V. Transcriptional control of 2,4-dinitrotoluene degradation in Burkholderia sp. R34 bears a regulatory patch that eases pathway evolution. Environ Microbiol 2021; 23:2522-2531. [PMID: 33734558 DOI: 10.1111/1462-2920.15472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/27/2021] [Accepted: 03/16/2021] [Indexed: 11/26/2022]
Abstract
The dnt pathway of Burkholderia sp. R34 is in the midst of an evolutionary journey from its ancestral, natural substrate (naphthalene) towards a new xenobiotic one [2,4-dinitrotoluene (DNT)]. The gene cluster encoding the leading multicomponent ring dioxygenase (DntA) has activity on the old and the new substrate, but it is induced by neither. Instead, the transcriptional factor encoded by the adjacent gene (dntR) activates expression of the dnt cluster upon addition of salicylate, one degradation intermediate of the ancestral naphthalene route but not any longer a substrate/product of the evolved DntA enzyme. Fluorescence of cells bearing dntA-gfp fusions revealed that induction of the dnt genes by salicylate was enhanced upon exposure to bona fide DntA substrates, i.e., naphthalene or DNT. Such amplification was dependent on effective dioxygenation of these pathway-specific head compounds, which thereby fostered expression of the cognate catabolic operon. The phenomenon seems to happen not through direct binding to a cognate transcriptional factor but through the interplay of a non-specific regulator with a substrate-specific enzyme. This regulatory scenario may ease transition of complete catabolic operons (i.e. enzymes plus regulatory devices) from one substrate to another without loss of fitness during the evolutionary roadmap between two optimal specificities.
Collapse
Affiliation(s)
- Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, 8940577, Chile
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
| | - Max Chavarría
- Escuela de Química and CIPRONA, Universidad de Costa Rica, San José, 2060, Costa Rica
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| |
Collapse
|
42
|
Marsh WS, Heise BW, Krzmarzick MJ, Murdoch RW, Fathepure BZ. Isolation and characterization of a halophilic Modicisalibacter sp. strain Wilcox from produced water. Sci Rep 2021; 11:6943. [PMID: 33767228 PMCID: PMC7994583 DOI: 10.1038/s41598-021-86196-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
We report the isolation a halophilic bacterium that degrades both aromatic and aliphatic hydrocarbons as the sole sources of carbon at high salinity from produced water. Phylogenetic analysis of 16S rRNA-gene sequences shows the isolate is a close relative of Modicisalibacter tunisiensis isolated from an oil-field water in Tunisia. We designate our isolate as Modicisalibacter sp. strain Wilcox. Genome analysis of strain Wilcox revealed the presence of a repertoire of genes involved in the metabolism of aliphatic and aromatic hydrocarbons. Laboratory culture studies corroborated the predicted hydrocarbon degradation potential. The strain degraded benzene, toluene, ethylbenzene, and xylenes at salinities ranging from 0.016 to 4.0 M NaCl, with optimal degradation at 1 M NaCl. Also, the strain degraded phenol, benzoate, biphenyl and phenylacetate as the sole sources of carbon at 2.5 M NaCl. Among aliphatic compounds, the strain degraded n-decane and n-hexadecane as the sole sources of carbon at 2.5 M NaCl. Genome analysis also predicted the presence of many heavy metal resistance genes including genes for metal efflux pumps, transport proteins, and enzymatic detoxification. Overall, due to its ability to degrade many hydrocarbons and withstand high salt and heavy metals, strain Wilcox may prove useful for remediation of produced waters.
Collapse
Affiliation(s)
- William S Marsh
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Brenden W Heise
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Mark J Krzmarzick
- Civil and Environmental Engineering, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Robert W Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, 37996, USA
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | - Babu Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA.
| |
Collapse
|
43
|
Kahla O, Melliti Ben Garali S, Karray F, Ben Abdallah M, Kallel N, Mhiri N, Zaghden H, Barhoumi B, Pringault O, Quéméneur M, Tedetti M, Sayadi S, Sakka Hlaili A. Efficiency of benthic diatom-associated bacteria in the removal of benzo(a)pyrene and fluoranthene. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141399. [PMID: 32866829 DOI: 10.1016/j.scitotenv.2020.141399] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
We investigated the efficiency of a benthic diatom-associated bacteria in removing benzo(a)pyrene (BaP) and fluoranthene (Flt). The diatom, isolated from a PAH-contaminated sediment of the Bizerte Lagoon (Tunisia), was exposed in axenic and non-axenic cultures to PAHs over 7 days. The diversity of the associated bacteria, both attached (AB) and free-living bacteria (FB), was analyzed by the 16S rRNA amplicon sequencing. The diatom, which maintained continuous growth under PAH treatments, was able to accumulate BaP and Flt, with different efficiencies between axenic and non-axenic cultures. Biodegradation, which constituted the main process for PAH elimination, was enhanced in the presence of bacteria, indicating the co-metabolic synergy of microalgae and associated bacteria in removing BaP and Flt. Diatom and bacteria showed different capacities in the degradation of BaP and Flt. Nitzschia sp. harbored bacterial communities with a distinct composition between attached and free-living bacteria. The AB fraction exhibited higher diversity and abundance relative to FB, while the FB fraction contained genera with the known ability of PAH degradation, such as Marivita, Erythrobacter, and Alcaligenes. Moreover, strains of Staphylococcus and Micrococcus, isolated from the FB community, showed the capacity to grow in the presence of crude oil. These results suggest that a "benthic Nitzschia sp.-associated hydrocarbon-degrading bacteria" consortium can be applied in the bioremediation of PAH-contaminated sites.
Collapse
Affiliation(s)
- Oumayma Kahla
- Laboratoire of Phytoplanctonology, Faculty of Sciences of Bizerte, University of Carthage, Bizerte, Tunisia; University El Manar of Tunis, Faculty of Sciences of Tunis, Laboratory of Environmental Sciences, Biology and Physiology of Aquatic Organisms LR18ES41, Tunis, Tunisia
| | - Sondes Melliti Ben Garali
- Laboratoire of Phytoplanctonology, Faculty of Sciences of Bizerte, University of Carthage, Bizerte, Tunisia; University El Manar of Tunis, Faculty of Sciences of Tunis, Laboratory of Environmental Sciences, Biology and Physiology of Aquatic Organisms LR18ES41, Tunis, Tunisia
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018 Sfax, Tunisia
| | - Manel Ben Abdallah
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018 Sfax, Tunisia
| | - Najwa Kallel
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018 Sfax, Tunisia
| | - Najla Mhiri
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018 Sfax, Tunisia
| | - Hatem Zaghden
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018 Sfax, Tunisia
| | - Badreddine Barhoumi
- Laboratory of Hetero-Organic Compounds and Nanostructured Materials (LR18ES11), Department of Chemistry, Faculty of Sciences of Bizerte, University of Carthage, 7021 Zarzouna, Tunisia
| | - Olivier Pringault
- Aix Marseille Univ., University of Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Marianne Quéméneur
- Aix Marseille Univ., University of Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Marc Tedetti
- Aix Marseille Univ., University of Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Sami Sayadi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha 2713, Qatar
| | - Asma Sakka Hlaili
- Laboratoire of Phytoplanctonology, Faculty of Sciences of Bizerte, University of Carthage, Bizerte, Tunisia; University El Manar of Tunis, Faculty of Sciences of Tunis, Laboratory of Environmental Sciences, Biology and Physiology of Aquatic Organisms LR18ES41, Tunis, Tunisia.
| |
Collapse
|
44
|
Complete Genome Sequence of Sphingobium barthaii KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Soil Bacterium. Microbiol Resour Announc 2021; 10:10/1/e01250-20. [PMID: 33414343 PMCID: PMC8407719 DOI: 10.1128/mra.01250-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Sphingobium barthaii KK22T is a high-molecular-weight polycyclic aromatic hydrocarbon-degrading soil bacterium that has been investigated in biotransformation, microbial ecology, and DNA damage studies. The complete genome sequence of S. barthaii revealed four closed circular sequences, including two chromosomes, a megaplasmid, and a smaller plasmid, by hybrid assembly using short- and long-read sequencing technologies. Sphingobium barthaii KK22T is a high-molecular-weight polycyclic aromatic hydrocarbon-degrading soil bacterium that has been investigated in biotransformation, microbial ecology, and DNA damage studies. The complete genome sequence of S. barthaii revealed four closed circular sequences, including two chromosomes, a megaplasmid, and a smaller plasmid, by hybrid assembly using short- and long-read sequencing technologies.
Collapse
|
45
|
Holochová P, Mašlaňová I, Sedláček I, Švec P, Králová S, Kovařovic V, Busse HJ, Staňková E, Barták M, Pantůček R. Description of Massilia rubra sp. nov., Massilia aquatica sp. nov., Massilia mucilaginosa sp. nov., Massilia frigida sp. nov., and one Massilia genomospecies isolated from Antarctic streams, lakes and regoliths. Syst Appl Microbiol 2020; 43:126112. [PMID: 32847787 DOI: 10.1016/j.syapm.2020.126112] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 11/24/2022]
Abstract
Bacteria of the genus Massilia often colonize extreme ecosystems, however, a detailed study of the massilias from the Antarctic environment has not yet been performed. Here, sixty-four Gram-stain-negative, aerobic, motile rods isolated from different environmental samples on James Ross Island (Antarctica) were subjected to a polyphasic taxonomic study. The psychrophilic isolates exhibited slowly growing, moderately slimy colonies revealing bold pink-red pigmentation on R2A agar. The set of strains exhibited the highest 16S rRNA gene sequence similarities (99.5-99.9%) to Massilia violaceinigra B2T and Massilia atriviolacea SODT and formed several phylogenetic groups based on the analysis of gyrB and lepA genes. Phenotypic characteristics allowed four of them to be distinguished from each other and from their closest relatives. Compared to the nearest phylogenetic neighbours the set of six genome-sequenced representatives exhibited considerable phylogenetic distance at the whole-genome level. Bioinformatic analysis of the genomic sequences revealed a high number of putative genes involved in oxidative stress response, heavy-metal resistance, bacteriocin production, the presence of putative genes involved in nitrogen metabolism and auxin biosynthesis. The identification of putative genes encoding aromatic dioxygenases suggests the biotechnology potential of the strains. Based on these results four novel species and one genomospecies of the genus Massilia are described and named Massilia rubra sp. nov. (P3094T=CCM 8692T=LMG 31213T), Massilia aquatica sp. nov. (P3165T=CCM 8693T=LMG 31211T), Massilia mucilaginosa sp. nov. (P5902T=CCM 8733T=LMG 31210T), and Massilia frigida sp. nov. (P5534T=CCM 8695T=LMG 31212T).
Collapse
Affiliation(s)
- Pavla Holochová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Ivana Mašlaňová
- Department of Experimental Biology, Section of Genetics and Molecular Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Vojtěch Kovařovic
- Department of Experimental Biology, Section of Genetics and Molecular Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Miloš Barták
- Department of Experimental Biology, Section of Experimental Plant Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Roman Pantůček
- Department of Experimental Biology, Section of Genetics and Molecular Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic.
| |
Collapse
|
46
|
Cauduro GP, Leal AL, Lopes TF, Marmitt M, Valiati VH. Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us? Int J Microbiol 2020; 2020:8831331. [PMID: 32908529 PMCID: PMC7474390 DOI: 10.1155/2020/8831331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/04/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022] Open
Abstract
Petroleum is the major energy matrix in the world whose refining generates chemical byproducts that may damage the environment. Among such waste, polycyclic aromatic hydrocarbons (PAH) are considered persistent pollutants. Sixteen of these are considered priority for remediation, and among them is benzo(a)pyrene. Amid remediation techniques, bioremediation stands out. The genus Burkholderia is amongst the microorganisms known for being capable of degrading persistent compounds; its strains are used as models to study such ability. High-throughput sequencing allows researchers to reach a wider knowledge about biodegradation by bacteria. Using transcripts and mRNA analysis, the genomic regions involved in this aptitude can be detected. To unravel these processes, we used the model B. vietnamiensis strain G4 in two experimental groups: one was exposed to benzo(a)pyrene and the other one (control) was not. Six transcriptomes were generated from each group aiming to compare gene expression and infer which genes are involved in degradation pathways. One hundred fifty-six genes were differentially expressed in the benzo(a)pyrene exposed group, from which 33% are involved in catalytic activity. Among these, the most significant genomic regions were phenylacetic acid degradation protein paaN, involved in the degradation of organic compounds to obtain energy; oxidoreductase FAD-binding subunit, related to the regulation of electrons within groups of dioxygenase enzymes with potential to cleave benzene rings; and dehydrogenase, described as accountable for phenol degradation. These data provide the basis for understanding the bioremediation of benzo(a)pyrene and the possible applications of this strain in polluted environments.
Collapse
Affiliation(s)
| | - Ana Lusia Leal
- Companhia Riograndense de Saneamento, Biology Laboratory, Triunfo, RS, Brazil
| | - Tiago Falcón Lopes
- Centro de Terapia Gênica, Centro de Pesquisa Experimental, Hospital de Clínicas, Porto Alegre, RS, Brazil
| | - Marcela Marmitt
- Universidade do Vale do Rio dos Sinos, Biology Graduate Program, São Leopoldo, RS, Brazil
| | - Victor Hugo Valiati
- Universidade do Vale do Rio dos Sinos, Biology Graduate Program, São Leopoldo, RS, Brazil
| |
Collapse
|
47
|
Peidro-Guzmán H, Pérez-Llano Y, González-Abradelo D, Fernández-López MG, Dávila-Ramos S, Aranda E, Hernández DRO, García AO, Lira-Ruan V, Pliego OR, Santana MA, Schnabel D, Jiménez-Gómez I, Mouriño-Pérez RR, Aréchiga-Carvajal ET, Del Rayo Sánchez-Carbente M, Folch-Mallol JL, Sánchez-Reyes A, Vaidyanathan VK, Cabana H, Gunde-Cimerman N, Batista-García RA. Transcriptomic analysis of polyaromatic hydrocarbon degradation by the halophilic fungus Aspergillus sydowii at hypersaline conditions. Environ Microbiol 2020; 23:3435-3459. [PMID: 32666586 DOI: 10.1111/1462-2920.15166] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/11/2020] [Accepted: 07/12/2020] [Indexed: 01/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are among the most persistent xenobiotic compounds, with high toxicity effects. Mycoremediation with halophilic Aspergillus sydowii was used for their removal from a hypersaline medium (1 M NaCl). A. sydowii metabolized PAHs as sole carbon sources, resulting in the removal of up to 90% for both PAHs [benzo [a] pyrene (BaP) and phenanthrene (Phe)] after 10 days. Elimination of Phe and BaP was almost exclusively due to biotransformation and not adsorption by dead mycelium and did not correlate with the activity of lignin modifying enzymes (LME). Transcriptomes of A. sydowii grown on PAHs, or on glucose as control, both at hypersaline conditions, revealed 170 upregulated and 76 downregulated genes. Upregulated genes were related to starvation, cell wall remodelling, degradation and metabolism of xenobiotics, DNA/RNA metabolism, energy generation, signalling and general stress responses. Changes of LME expression levels were not detected, while the chloroperoxidase gene, possibly related to detoxification processes in fungi, was strongly upregulated. We propose that two parallel metabolic pathways (mitochondrial and cytosolic) are involved in degradation and detoxification of PAHs in A. sydowii resulting in intracellular oxidation of PAHs. To the best of our knowledge, this is the most comprehensive transcriptomic analysis on fungal degradation of PAHs.
Collapse
Affiliation(s)
- Heidy Peidro-Guzmán
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Yordanis Pérez-Llano
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Deborah González-Abradelo
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Maikel Gilberto Fernández-López
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Elisabet Aranda
- Instituto Universitario de Investigación del Agua, Universidad de Granada, Granada, Spain
| | | | - Angélica Ortega García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Verónica Lira-Ruan
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Oscar Ramírez Pliego
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - María Angélica Santana
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Denhi Schnabel
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Irina Jiménez-Gómez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Rosa R Mouriño-Pérez
- Centro de Investigación Cientifica y Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Elva T Aréchiga-Carvajal
- Facultad de Ciencias Biológicas, Unidad de Manipulación Genética, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | | | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Ayixon Sánchez-Reyes
- Cátedras Conacyt - Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Hubert Cabana
- Faculté de Genié, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Nina Gunde-Cimerman
- Departament of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| |
Collapse
|
48
|
Liguori L, Monticelli M, Allocca M, Cubellis MV, Hay Mele B. Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach. BMC Bioinformatics 2020; 21:348. [PMID: 32838733 PMCID: PMC7447578 DOI: 10.1186/s12859-020-03560-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students. RESULTS We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology to non-culturable microbes. We presuppose that a probe for the screening of metagenomic cosmid library is needed. The students start from the chemical structure of the substrate that should be acted on by the novel enzyme and end with the sequence of the probe. To attain their goal, they discover databases such as BRENDA and programs such as BLAST and Clustal Omega. Students' answers to a satisfaction questionnaire show that a multistep tutorial integrated into a research wet-lab project is preferable to conventional lectures illustrating bioinformatics tools. CONCLUSION Experimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.
Collapse
Affiliation(s)
- Ludovica Liguori
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
- Istituto di Chimica Biomolecolare -CNR, 80078, Pozzuoli, Italy
| | - Maria Monticelli
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy
| | - Mariateresa Allocca
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
- Istituto di Chimica Biomolecolare -CNR, 80078, Pozzuoli, Italy
| | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy.
- Biology and Evolution of Marine Organisms Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Bruno Hay Mele
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| |
Collapse
|
49
|
Weyrauch P, Heker I, Zaytsev AV, von Hagen CA, Arnold ME, Golding BT, Meckenstock RU. The 5,6,7,8-Tetrahydro-2-Naphthoyl-Coenzyme A Reductase Reaction in the Anaerobic Degradation of Naphthalene and Identification of Downstream Metabolites. Appl Environ Microbiol 2020; 86:e00996-20. [PMID: 32444470 PMCID: PMC7376553 DOI: 10.1128/aem.00996-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/15/2020] [Indexed: 11/20/2022] Open
Abstract
Anaerobic degradation of polycyclic aromatic hydrocarbons has been investigated mostly with naphthalene as a model compound. Naphthalene degradation by sulfate-reducing bacteria proceeds via carboxylation to 2-naphthoic acid, formation of a coenzyme A thioester, and subsequent reduction to 5,6,7,8-tetrahydro-2-naphthoyl-coenzyme A (THNCoA), which is further reduced to hexahydro-2-naphthoyl-CoA (HHNCoA) by tetrahydronaphthoyl-CoA reductase (THNCoA reductase), an enzyme similar to class I benzoyl-CoA reductases. When analyzing THNCoA reductase assays with crude cell extracts and NADH as electron donor via liquid chromatography-mass spectrometry (LC-MS), scanning for putative metabolites, we found that small amounts of the product of an HHNCoA hydratase were formed in the assays, but the downstream conversion by an NAD+-dependent β-hydroxyacyl-CoA dehydrogenase was prevented by the excess of NADH in those assays. Experiments with alternative electron donors indicated that 2-oxoglutarate can serve as an indirect electron donor for the THNCoA-reducing system via a 2-oxoglutarate:ferredoxin oxidoreductase. With 2-oxoglutarate as electron donor, THNCoA was completely converted and further metabolites resulting from subsequent β-oxidation-like reactions and hydrolytic ring cleavage were detected. These metabolites indicate a downstream pathway with water addition to HHNCoA and ring fission via a hydrolase acting on a β'-hydroxy-β-oxo-decahydro-2-naphthoyl-CoA intermediate. Formation of the downstream intermediate cis-2-carboxycyclohexylacetyl-CoA, which is the substrate for the previously described lower degradation pathway leading to the central metabolism, completes the anaerobic degradation pathway of naphthalene.IMPORTANCE Anaerobic degradation of polycyclic aromatic hydrocarbons is poorly investigated despite its significance in anoxic sediments. Using alternative electron donors for the 5,6,7,8-tetrahydro-2-naphthoyl-CoA reductase reaction, we observed intermediary metabolites of anaerobic naphthalene degradation via in vitro enzyme assays with cell extracts of anaerobic naphthalene degraders. The identified metabolites provide evidence that ring reduction terminates at the stage of hexahydro-2-naphthoyl-CoA and a sequence of β-oxidation-like degradation reactions starts with a hydratase acting on this intermediate. The final product of this reaction sequence was identified as cis-2-carboxycyclohexylacetyl-CoA, a compound for which a further downstream degradation pathway has recently been published (P. Weyrauch, A. V. Zaytsev, S. Stephan, L. Kocks, et al., Environ Microbiol 19:2819-2830, 2017, https://doi.org/10.1111/1462-2920.13806). Our study reveals the first ring-cleaving reaction in the anaerobic naphthalene degradation pathway. It closes the gap between the reduction of the first ring of 2-naphthoyl-CoA by 2-napthoyl-CoA reductase and the lower degradation pathway starting from cis-2-carboxycyclohexylacetyl-CoA, where the second ring cleavage takes place.
Collapse
Affiliation(s)
- Philip Weyrauch
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Isabelle Heker
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Andrey V Zaytsev
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Meike E Arnold
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Bernard T Golding
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | |
Collapse
|
50
|
Matturro B, Mascolo G, Rossetti S. Microbiome changes and oxidative capability of an anaerobic PCB dechlorinating enrichment culture after oxygen exposure. N Biotechnol 2020; 56:96-102. [DOI: 10.1016/j.nbt.2019.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 12/16/2022]
|