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Liu J, Zeng Q, Lei H, Xin K, Xu A, Wei R, Li D, Zhou J, Dong W, Jiang M. Biodegradation of polyester polyurethane by Cladosporium sp. P7: Evaluating its degradation capacity and metabolic pathways. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130776. [PMID: 36706489 DOI: 10.1016/j.jhazmat.2023.130776] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms capable of decomposing polyurethane (PU) and other plastics have the potential to be used in bio-recycling processes. In this study, 20 PU-degrading strains were isolated, including 11 bacteria and 9 fungi, using a synthesized poly(1,4-butylene adipate)-based PU (PBA-PU) as the screening substrate. Three PU substrates with increasing structure complexities were used for a thorough evaluation of microbial degradation capacity: Impranil® DLN-SD, PBA-PU film and PU foam waste. After 4 days, the best fungal PBA-PU degrader, Cladosporium sp. P7, could degrade 94.5% of Impranil® DLN-SD. After 28 days of cultivation, 32.42% and 43.91% of solid PBA-PU film was converted into soluble small molecules when used as the sole carbon source or in a medium with other co-carbon sources, respectively. Accordingly, the weight loss of PU foam waste after 15 days was 15.3% for the sole carbon condition and 83.83% for the co-carbon conditions. Furthermore, PBA-PU was used for metabolic pathway analysis because of its known composition and chemical structure. Six metabolites were identified during the degradation process of PBA-PU, including adipic acid (AA), 1,4-butanediol (BDO), and 4,4'-methylenedianiline (MDA), which can also be used as the sole carbon source to grow the fungal strain P7, resulting in the discovery of two MDA metabolites during the cultivation processes. Based on the presence of these eight metabolites, we hypothesized that PBA-PU is first depolymerized by the fungal strain P7 via ester and urethane bond hydrolysis, followed by intracellular metabolism and mineralization of the three monomers to CO2 and H2O.
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Affiliation(s)
- Jiawei Liu
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Qingyi Zeng
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Huirui Lei
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Kaiyuan Xin
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Anming Xu
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Ren Wei
- Junior Research Group Plastic Biodegradation, Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Ding Li
- Institute of Veterinary Immunology & Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China
| | - Jie Zhou
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Weiliang Dong
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211800, PR China.
| | - Min Jiang
- Key Laboratory for Waste Plastics Biocatalytic Degradation and Recycling, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211800, PR China
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2
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Suman J, Strejcek M, Zubrova A, Capek J, Wald J, Michalikova K, Hradilova M, Sredlova K, Semerad J, Cajthaml T, Uhlik O. Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone. Front Microbiol 2021; 12:644708. [PMID: 34721309 PMCID: PMC8552027 DOI: 10.3389/fmicb.2021.644708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, the diversity of bphA genes was assessed in a 13C-enriched metagenome upon stable isotope probing (SIP) of microbial populations in legacy PCB-contaminated soil with 13C-biphenyl (BP). In total, 13 bphA sequence variants (SVs) were identified in the final amplicon dataset. Of these, one SV comprised 59% of all sequences, and when it was translated into a protein sequence, it exhibited 87, 77.4, and 76.7% identity to its homologs from Pseudomonas furukawaii KF707, Cupriavidus sp. WS, and Pseudomonas alcaliphila B-367, respectively. This same BphA sequence also contained unusual amino acid residues, Alanine, Valine, and Serine in region III, which had been reported to be crucial for the substrate specificity of the corresponding biphenyl dioxygenase (BPDO), and was accordingly designated BphA_AVS. The DNA locus of 18 kbp containing the BphA_AVS-coding sequence retrieved from the metagenome was comprised of 16 ORFs and was most likely borne by Paraburkholderia sp. The BPDO corresponding to bphAE_AVS was cloned and heterologously expressed in E. coli, and its substrate specificity toward PCBs and a spectrum of flavonoids was assessed. Although depleting a rather narrow spectrum of PCB congeners, the efficient transformation of flavone and flavanone was demonstrated through dihydroxylation of the B-ring of the molecules. The homology-based functional assignment of the putative proteins encoded by the rest of ORFs in the AVS region suggests their potential involvement in the transformation of aromatic compounds, such as flavonoids. In conclusion, this study contributes to the body of information on the involvement of soil-borne BPDOs in the metabolism of flavonoid compounds, and our paper provides a more advanced context for understanding the interactions between plants, microbes and anthropogenic compounds in the soil.
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Affiliation(s)
- Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Andrea Zubrova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Jan Capek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Jiri Wald
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Klara Michalikova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Miluse Hradilova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Kamila Sredlova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Jaroslav Semerad
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia.,Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czechia
| | - Tomas Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia.,Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czechia
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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3
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Zubrova A, Michalikova K, Semerad J, Strejcek M, Cajthaml T, Suman J, Uhlik O. Biphenyl 2,3-Dioxygenase in Pseudomonas alcaliphila JAB1 Is Both Induced by Phenolics and Monoterpenes and Involved in Their Transformation. Front Microbiol 2021; 12:657311. [PMID: 33995321 PMCID: PMC8119895 DOI: 10.3389/fmicb.2021.657311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/29/2021] [Indexed: 01/09/2023] Open
Abstract
The involvement of bacterial aromatic ring-hydroxylating dioxygenases (ARHDs) in the degradation of aromatic pollutants, such as polychlorinated biphenyls (PCBs), has been well studied. However, there is considerable speculation as to the origin of this ability. One hypothesis is centered on a connection between the ability to degrade aromatic pollutants and the necessity of soil bacteria to cope with and/or utilize secondary plant metabolites (SPMs). To investigate this connection, we researched the involvement of biphenyl 2,3-dioxygenase (BPDO), an ARHD essential for the degradation of PCBs, in the metabolism of SPMs in the soil bacterium Pseudomonas alcaliphila JAB1, a versatile degrader of PCBs. We demonstrated the ability of the strain JAB1 to transform a variety of SPMs, namely the flavonoids apigenin, flavone, flavanone, naringenin, fisetin, quercetin, morin, and catechin, caffeic acid, trans-cinnamic acid, and the monoterpenes (S)-limonene and (R)-carvone. Of those, the transformation of flavone, flavanone, and (S)-limonene was conditioned by the activity of JAB1-borne BPDO and thus was researched in more detail, and we found evidence for the limonene monooxygenase activity of the BPDO. Furthermore, the bphA gene in the strain JAB1 was demonstrated to be induced by a wide range of SPMs, with monoterpenes being the strongest inducers of the SPMs tested. Thus, our findings contribute to the growing body of evidence that ARHDs not only play a role in the catabolism of aromatic pollutants, but also of natural plant-derived aromatics, and this study supports the hypothesis that ARHDs participate in ecological processes mediated by SPMs.
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Affiliation(s)
- Andrea Zubrova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Klara Michalikova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Jaroslav Semerad
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Tomas Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia.,Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czechia
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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4
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Ren L, Jia Y, Zhang R, Lin Z, Zhen Z, Hu H, Yan Y. Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1. Front Microbiol 2018; 9:2438. [PMID: 30364317 PMCID: PMC6193132 DOI: 10.3389/fmicb.2018.02438] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/24/2018] [Indexed: 01/11/2023] Open
Abstract
The genus Arthrobacter is ubiquitously distributed in different natural environments. Many xenobiotic-degrading Arthrobacter strains have been isolated and described; however, few have been systematically characterized with regard to multiple interrelated metabolic pathways and the genes that encode them. In this study, the biodegradability of seven aromatic compounds by Arthrobacter sp. YC-RL1 was investigated. Strain YC-RL1 could efficiently degrade p-xylene (PX), naphthalene, phenanthrene, biphenyl, p-nitrophenol (PNP), and bisphenol A (BPA) under both separated and mixed conditions. Based on the detected metabolic intermediates, metabolic pathways of naphthalene, biphenyl, PNP, and BPA were proposed, which indicated that strain YC-RL1 harbors systematic metabolic pathways toward aromatic compounds. Further, genomic analysis uncovered part of genes involved in the proposed pathways. Both intradiol and extradiol ring-cleavage dioxygenase genes were identified in the genome of strain YC-RL1. Meanwhile, gene clusters predicted to encode the degradation of biphenyl (bph), para-substituted phenols (npd) and protocatechuate (pca) were identified, and bphA1A2BCD was proposed to be a novel biphenyl-degrading gene cluster. The complete metabolic pathway of biphenyl was deduced via intermediates and functional gene analysis (bph and pca gene clusters). One of the these genes encoding ring-cleavage dioxygenase in bph gene cluster, a predicted 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) gene, was cloned and its activity was confirmed by heterologous expression. This work systematically illuminated the metabolic versatility of aromatic compounds in strain YC-RL1 via the combination of metabolites identification, genomics analysis and laboratory experiments. These results suggested that strain YC-RL1 might be a promising candidate for the bioremediation of aromatic compounds pollution sites.
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Affiliation(s)
- Lei Ren
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Jia
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Zhang
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, China
| | - Zhong Lin
- Agricultural College, Guangdong Ocean University, Zhanjiang, China.,Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang, China
| | - Zhen Zhen
- Agricultural College, Guangdong Ocean University, Zhanjiang, China
| | - Hanqiao Hu
- Agricultural College, Guangdong Ocean University, Zhanjiang, China
| | - Yanchun Yan
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
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5
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Ohsumi M, Ito A, Nishiwaki N. Substrate switchable Suzuki–Miyaura coupling for benzyl ester vs. benzyl halide. RSC Adv 2018; 8:35056-35061. [PMID: 35547057 PMCID: PMC9087645 DOI: 10.1039/c8ra07841f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/08/2018] [Indexed: 11/21/2022] Open
Abstract
Two reaction conditions were developed to accomplish the substrate switchable (benzyl esters vs. benzyl halides) Suzuki–Miyaura coupling.
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Affiliation(s)
- Masato Ohsumi
- Kochi National College of Technology
- Nankoku
- Japan
- School of Environmental Science and Engineering
- Kochi University of Technology
| | - Akitaka Ito
- School of Environmental Science and Engineering
- Kochi University of Technology
- Kami
- Japan
- Research Center for Material Science and Engineering
| | - Nagatoshi Nishiwaki
- School of Environmental Science and Engineering
- Kochi University of Technology
- Kami
- Japan
- Research Center for Material Science and Engineering
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6
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Ohsumi M, Nishiwaki N. Selective Synthesis of (Benzyl)biphenyls by Successive Suzuki-Miyaura Coupling of Phenylboronic Acids with 4-Bromobenzyl Acetate under Air Atmosphere. ACS OMEGA 2017; 2:7767-7771. [PMID: 31457333 PMCID: PMC6645156 DOI: 10.1021/acsomega.7b01450] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/26/2017] [Indexed: 05/24/2023]
Abstract
An efficient Pd-catalyzed cross-coupling reaction of phenylboronic acids and benzyl carbonates was developed, producing diarylmethanes. Benzyl acetates could also be used as coupling partners instead of benzyl carbonates, affording diarylmethanes in comparable yields. This reaction can be conducted under air atmosphere without any care for moisture and oxygen. The ester function showed an intermediate reactivity between chloro and bromo groups. This property facilitated the selective synthesis of diverse (benzyl)biphenyls by successive Suzuki-Miyaura coupling reactions using bromo- and chloro-substituted benzyl esters with two types of boronic acids.
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Affiliation(s)
- Masato Ohsumi
- Kochi
National College of Technology, Nankoku, Kochi 783-8508, Japan
| | - Nagatoshi Nishiwaki
- School
of Environmental Science and Engineering and Research Center for Material Science
and Engineering, Kochi University of Technology, Tosayamada, Kami, Kochi 782-8502, Japan
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7
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Ferraro DJ, Okerlund A, Brown E, Ramaswamy S. One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase. IUCRJ 2017; 4:648-656. [PMID: 28989720 PMCID: PMC5619856 DOI: 10.1107/s2052252517008223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/02/2017] [Indexed: 06/07/2023]
Abstract
Rieske nonheme iron oxygenases (ROs) are a well studied class of enzymes. Naphthalene 1,2-dioxygenase (NDO) is used as a model to study ROs. Previous work has shown how side-on binding of oxygen to the mononuclear iron provides this enzyme with the ability to catalyze stereospecific and regiospecific cis-dihydroxylation reactions. It has been well documented that ROs catalyze a variety of other reactions, including mono-oxygenation, desaturation, O- and N-dealkylation, sulfoxidation etc. NDO itself catalyzes a variety of these reactions. Structures of NDO in complex with a number of different substrates show that the orientation of the substrate in the active site controls not only the regiospecificity and stereospecificity, but also the type of reaction catalyzed. It is proposed that the mononuclear iron-activated dioxygen attacks the atoms of the substrate that are most proximal to it. The promiscuity of delivering two products (apparently by two different reactions) from the same substrate can be explained by the possible binding of the substrate in slightly different orientations aided by the observed flexibility of residues in the binding pocket.
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Affiliation(s)
- Daniel J. Ferraro
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Adam Okerlund
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Eric Brown
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - S. Ramaswamy
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- TAS, Institute for Stem Cell Biology and Regenerative Medicine, GKVK POST, Bangalore 560 065, India
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8
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Structural Basis of the Enhanced Pollutant-Degrading Capabilities of an Engineered Biphenyl Dioxygenase. J Bacteriol 2016; 198:1499-512. [PMID: 26953337 DOI: 10.1128/jb.00952-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/25/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Biphenyl dioxygenase, the first enzyme of the biphenyl catabolic pathway, is a major determinant of which polychlorinated biphenyl (PCB) congeners are metabolized by a given bacterial strain. Ongoing efforts aim to engineer BphAE, the oxygenase component of the enzyme, to efficiently transform a wider range of congeners. BphAEII9, a variant of BphAELB400 in which a seven-residue segment, (335)TFNNIRI(341), has been replaced by the corresponding segment of BphAEB356, (333)GINTIRT(339), transforms a broader range of PCB congeners than does either BphAELB400 or BphAEB356, including 2,6-dichlorobiphenyl, 3,3'-dichlorobiphenyl, 4,4'-dichlorobiphenyl, and 2,3,4'-trichlorobiphenyl. To understand the structural basis of the enhanced activity of BphAEII9, we have determined the three-dimensional structure of this variant in substrate-free and biphenyl-bound forms. Structural comparison with BphAELB400 reveals a flexible active-site mouth and a relaxed substrate binding pocket in BphAEII9 that allow it to bind different congeners and which could be responsible for the enzyme's altered specificity. Biochemical experiments revealed that BphAEII9 transformed 2,3,4'-trichlorobiphenyl and 2,2',5,5'-tetrachlorobiphenyl more efficiently than did BphAELB400 and BphAEB356 BphAEII9 also transformed the insecticide dichlorodiphenyltrichloroethane (DDT) more efficiently than did either parental enzyme (apparent kcat/Km of 2.2 ± 0.5 mM(-1) s(-1), versus 0.9 ± 0.5 mM(-1) s(-1) for BphAEB356). Studies of docking of the enzymes with these three substrates provide insight into the structural basis of the different substrate selectivities and regiospecificities of the enzymes. IMPORTANCE Biphenyl dioxygenase is the first enzyme of the biphenyl degradation pathway that is involved in the degradation of polychlorinated biphenyls. Attempts have been made to identify the residues that influence the enzyme activity for the range of substrates among various species. In this study, we have done a structural study of one variant of this enzyme that was produced by family shuffling of genes from two different species. Comparison of the structure of this variant with those of the parent enzymes provided an important insight into the molecular basis for the broader substrate preference of this enzyme. The structural and functional details gained in this study can be utilized to further engineer desired enzymatic activity, producing more potent enzymes.
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Strejcek M, Wang Q, Ridl J, Uhlik O. Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences. Front Microbiol 2015; 6:1267. [PMID: 26635739 PMCID: PMC4656815 DOI: 10.3389/fmicb.2015.01267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/30/2015] [Indexed: 01/19/2023] Open
Abstract
Functional gene ecological analyses using amplicon sequencing can be challenging as translated sequences are often burdened with shifted reading frames. The aim of this work was to evaluate several bioinformatics tools designed to correct errors which arise during sequencing in an effort to reduce the number of frameshifts (FS). Genes encoding for alpha subunits of biphenyl (bphA) and benzoate (benA) dioxygenases were used as model sequences. FrameBot, a FS correction tool, was able to reduce the number of detected FS to zero. However, up to 44% of sequences were discarded by FrameBot as non-specific targets. Therefore, we proposed a de novo mode of FrameBot for FS correction, which works on a similar basis as common chimera identifying platforms and is not dependent on reference sequences. By nature of FrameBot de novo design, it is crucial to provide it with data as error free as possible. We tested the ability of several publicly available correction tools to decrease the number of errors in the data sets. The combination of maximum expected error filtering and single linkage pre-clustering proved to be the most efficient read processing approach. Applying FrameBot de novo on the processed data enabled analysis of BphA sequences with minimal losses of potentially functional sequences not homologous to those previously known. This experiment also demonstrated the extensive diversity of dioxygenases in soil. A script which performs FrameBot de novo is presented in the supplementary material to the study or available at https://github.com/strejcem/FBdenovo. The tool was also implemented into FunGene Pipeline available at http://fungene.cme.msu.edu/FunGenePipeline/.
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Affiliation(s)
- Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague Prague, Czech Republic
| | - Qiong Wang
- Center for Microbial Ecology, Michigan State University East Lansing, MI, USA
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague Prague, Czech Republic
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Overwin H, Standfuß-Gabisch C, González M, Méndez V, Seeger M, Reichelt J, Wray V, Hofer B. Permissivity of the biphenyl-specific aerobic bacterial metabolic pathway towards analogues with various steric requirements. Microbiology (Reading) 2015; 161:1844-1856. [DOI: 10.1099/mic.0.000138] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Heike Overwin
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Myriam González
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Valentina Méndez
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Joachim Reichelt
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Victor Wray
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Bernd Hofer
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Division of Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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11
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Pham TTM, Pino Rodriguez NJ, Hijri M, Sylvestre M. Optimizing Polychlorinated Biphenyl Degradation by Flavonoid-Induced Cells of the Rhizobacterium Rhodococcus erythropolis U23A. PLoS One 2015; 10:e0126033. [PMID: 25970559 PMCID: PMC4430277 DOI: 10.1371/journal.pone.0126033] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/27/2015] [Indexed: 01/11/2023] Open
Abstract
There is evidence that many plant secondary metabolites may act as signal molecules to trigger the bacterial ability to metabolize polychlorinated biphenyls (PCBs) during the rhizoremediation process. However, the bases for the PCB rhizoremediation process are still largely unknown. The rhizobacterium Rhodococcus erythropolis U23A is unable to use flavanone as a growth substrate. However, on the basis of an assay that monitors the amount of 4-chlorobenzoate produced from 4-chlorobiphenyl by cells grown co-metabolically on flavanone plus sodium acetate, this flavonoid was previously found to be a potential inducer of the U23A biphenyl catabolic pathway. In this work, and using the same assay, we identified ten other flavonoids that did not support growth, but that acted as inducers of the U23A biphenyl pathway, and we confirmed flavonoid induction of the biphenyl catabolic pathway using quantitative real-time polymerase chain reaction (RT-qPCR) on the bphA gene. We also examined the effect of the growth co-substrate on flavonoid induction. Sodium acetate was replaced by glucose, mannose, sucrose, or mannitol, which are sugars found in plant root exudates. The data showed that the level of induction of strain U23A biphenyl-degrading enzymes was significantly influenced by the nature and concentration of the flavonoid in the growth medium, as well as by the substrate used for growth. Sucrose allowed for an optimal induction response for most flavonoids. Some flavonoids, such as flavone and isoflavone, were better inducers of the biphenyl catabolic enzymes than biphenyl itself. We also found that all flavonoids tested in this work were metabolized by strain U23A during co-metabolic growth, but that the metabolite profiles, as well as the level of efficiency of degradation, differed for each flavonoid. To obtain insight into how flavonoids interact with strain U23A to promote polychlorinated biphenyl (PCB) degradation, we determined the concentration of flavanone at which optimal PCB-degrading performance of strain U23A was achieved. We showed that it corresponded to the concentration required to fully induce the biphenyl catabolic pathway of the strain. Together, our data demonstrate that optimal PCB degradation during the rhizoremediation process will require the adjustment of several parameters, including the presence of the appropriate flavonoids at the proper concentrations and the presence of proper growth substrates that positively influence the ability of flavonoids to induce the pathway.
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Affiliation(s)
- Thi Thanh My Pham
- Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, Laval, Québec, Canada
| | | | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Michel Sylvestre
- Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, Laval, Québec, Canada
- * E-mail:
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Metabolism of Doubly para-Substituted Hydroxychlorobiphenyls by Bacterial Biphenyl Dioxygenases. Appl Environ Microbiol 2015; 81:4860-72. [PMID: 25956777 DOI: 10.1128/aem.00786-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/06/2015] [Indexed: 11/20/2022] Open
Abstract
In this work, we examined the profile of metabolites produced from the doubly para-substituted biphenyl analogs 4,4'-dihydroxybiphenyl, 4-hydroxy-4'-chlorobiphenyl, 3-hydroxy-4,4'-dichlorobiphenyl, and 3,3'-dihydroxy-4,4'-chlorobiphenyl by biphenyl-induced Pandoraea pnomenusa B356 and by its biphenyl dioxygenase (BPDO). 4-Hydroxy-4'-chlorobiphenyl was hydroxylated principally through a 2,3-dioxygenation of the hydroxylated ring to generate 2,3-dihydro-2,3,4-trihydroxy-4'-chlorobiphenyl and 3,4-dihydroxy-4'-chlorobiphenyl after the removal of water. The former was further oxidized by the biphenyl dioxygenase to produce ultimately 3,4,5-trihydroxy-4'-chlorobiphenyl, a dead-end metabolite. 3-Hydroxy-4,4'-dichlorobiphenyl was oxygenated on both rings. Hydroxylation of the nonhydroxylated ring generated 2,3,3'-trihydroxy-4'-chlorobiphenyl with concomitant dechlorination, and 2,3,3'-trihydroxy-4'-chlorobiphenyl was ultimately metabolized to 2-hydroxy-4-chlorobenzoate, but hydroxylation of the hydroxylated ring generated dead-end metabolites. 3,3'-Dihydroxy-4,4'-dichlorobiphenyl was principally metabolized through a 2,3-dioxygenation to generate 2,3-dihydro-2,3,3'-trihydroxy-4,4'-dichlorobiphenyl, which was ultimately converted to 3-hydroxy-4-chlorobenzoate. Similar metabolites were produced when the biphenyl dioxygenase of Burkholderia xenovorans LB400 was used to catalyze the reactions, except that for the three substrates used, the BPDO of LB400 was less efficient than that of B356, and unlike that of B356, it was unable to further oxidize the initial reaction products. Together the data show that BPDO oxidation of doubly para-substituted hydroxychlorobiphenyls may generate nonnegligible amounts of dead-end metabolites. Therefore, biphenyl dioxygenase could produce metabolites other than those expected, corresponding to dihydrodihydroxy metabolites from initial doubly para-substituted substrates. This finding shows that a clear picture of the fate of polychlorinated biphenyls in contaminated sites will require more insights into the bacterial metabolism of hydroxychlorobiphenyls and the chemistry of the dihydrodihydroxylated metabolites derived from them.
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