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Lin Q, Yang Y, Zhang S, Sun F, Shen C, Su X. Enhanced biodegradation of polychlorinated biphenyls by co-cultivation of resuscitated strains with unique advantages. ENVIRONMENTAL RESEARCH 2024:119699. [PMID: 39074776 DOI: 10.1016/j.envres.2024.119699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/14/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024]
Abstract
The investigation into viable but non-culturable (VBNC) bacteria through the implementation of resuscitation promoting factors (Rpfs) has broadened the potential sources for isolating strains capable of degrading polychlorinated biphenyls (PCBs). Nonetheless, there has been limited research on the efficacy of resuscitated strains and the potential improvement of their performance through co-cultivation. In this work, the PCB degradation potential of resuscitated strains, specifically Pseudomonas sp. HR1 and Achromobacter sp. HR2, as well as their co-cultures, was investigated. Of particular importance was the comparative analysis between the optimal co-culture and individual strains regarding their ability to degrade PCB homologs and mineralize intermediate metabolites. The results suggested that the resuscitated strains HR1 and HR2 demonstrated robust growth and effective degradation of Aroclor 1242. The co-culture CO13, with an optimal HR1 to HR2 ratio of 1:3, exhibited a remarkable improvement in PCB degradation and intermediate metabolite mineralization compared to individual strains. Analysis of functional genes and degradation metabolites revealed that both the individual strains and co-culture CO13 degraded PCBs via the HOPDA-benzoate pathway, then mineralized through protocatechuate meta- and ortho-cleavage pathways, as well as the catechol ortho-cleavage pathway. This study represents the first documentation of the improved PCB degradation through the co-cultivation of resuscitated strains, which highlights the great promise of these resuscitated strains and their co-cultures as effective bio-inoculants for enhanced bioremediation.
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Affiliation(s)
- Qihua Lin
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Yingying Yang
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Shusheng Zhang
- The Management Center of Wuyanling National Natural Reserve in Zhejiang, Wenzhou 325500, China
| | - Faqian Sun
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China.
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2
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Mahmoodi A, Farinas ET. Applications of Bacillus subtilis Protein Display for Medicine, Catalysis, Environmental Remediation, and Protein Engineering. Microorganisms 2024; 12:97. [PMID: 38257924 PMCID: PMC10821481 DOI: 10.3390/microorganisms12010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Bacillus subtilis spores offer several advantages that make them attractive for protein display. For example, protein folding issues associated with unfolded polypeptide chains crossing membranes are circumvented. In addition, they can withstand physical and chemical extremes such as heat, desiccation, radiation, ultraviolet light, and oxidizing agents. As a result, the sequence of the displayed protein can be easily obtained even under harsh screening conditions. Next, immobilized proteins have many economic and technological advantages. They can be easily separated from the reaction and the protein stability is increased in harsh environments. In traditional immobilization methods, proteins are expressed and purified and then they are attached to a matrix. In contrast, immobilization occurs naturally during the sporulation process. They can be easily separated from the reaction and the protein stability is increased in harsh environments. Spores are also amenable to high-throughput screening for protein engineering and optimization. Furthermore, they can be used in a wide array of biotechnological and industrial applications such as vaccines, bioabsorbants to remove toxic chemicals, whole-cell catalysts, bioremediation, and biosensors. Lastly, spores are easily produced in large quantities, have a good safety record, and can be used as additives in foods and drugs.
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The unusual convergence of steroid catabolic pathways in Mycobacterium abscessus. Proc Natl Acad Sci U S A 2022; 119:e2207505119. [PMID: 36161908 DOI: 10.1073/pnas.2207505119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium abscessus, an opportunistic pathogen responsible for pulmonary infections, contains genes predicted to encode two steroid catabolic pathways: a cholesterol catabolic pathway similar to that of Mycobacterium tuberculosis and a 4-androstenedione (4-AD) catabolic pathway. Consistent with this prediction, M. abscessus grew on both steroids. In contrast to M. tuberculosis, Rhodococcus jostii RHA1, and other Actinobacteria, the cholesterol and 4-AD catabolic gene clusters of the M. abscessus complex lack genes encoding HsaD, the meta-cleavage product (MCP) hydrolase. However, M. abscessus ATCC 19977 harbors two hsaD homologs elsewhere in its genome. Only one of the encoded enzymes detectably transformed steroid metabolites. Among tested substrates, HsaDMab and HsaDMtb of M. tuberculosis had highest substrate specificities for MCPs with partially degraded side chains thioesterified with coenzyme A (kcat/KM = 1.9 × 104 and 5.7 × 103 mM-1s-1, respectively). Consistent with a dual role in cholesterol and 4-AD catabolism, HsaDMab also transformed nonthioesterified substrates efficiently, and a ΔhsaD mutant of M. abscessus grew on neither steroid. Interestingly, both steroids prevented growth of the mutant on acetate. The ΔhsaD mutant of M. abscessus excreted cholesterol metabolites with a fully degraded side chain, while the corresponding RHA1 mutant excreted metabolites with partially degraded side chains. Finally, the ΔhsaD mutant was not viable in macrophages. Overall, our data establish that the cholesterol and 4-AD catabolic pathways of M. abscessus are unique in that they converge upstream of where this occurs in characterized steroid-catabolizing bacteria. The data further indicate that cholesterol is a substrate for intracellular bacteria and that cholesterol-dependent toxicity is not strictly dependent on coenzyme A sequestration.
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Navas LE, Zahn M, Bajwa H, Grigg JC, Wolf ME, Chan ACK, Murphy MEP, McGeehan JE, Eltis LD. Characterization of a phylogenetically distinct extradiol dioxygenase involved in the bacterial catabolism of lignin-derived aromatic compounds. J Biol Chem 2022; 298:101871. [PMID: 35346686 PMCID: PMC9062432 DOI: 10.1016/j.jbc.2022.101871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 10/28/2022] Open
Abstract
The actinobacterium Rhodococcus jostii RHA1 grows on a remarkable variety of aromatic compounds and has been studied for applications ranging from the degradation of polychlorinated biphenyls to the valorization of lignin, an underutilized component of biomass. In RHA1, the catabolism of two classes of lignin-derived compounds, alkylphenols and alkylguaiacols, involves a phylogenetically distinct extradiol dioxygenase, AphC, previously misannotated as BphC, an enzyme involved in biphenyl catabolism. To better understand the role of AphC in RHA1 catabolism, we first showed that purified AphC had highest apparent specificity for 4-propylcatechol (kcat/KM ∼106 M-1 s-1), and its apparent specificity for 4-alkylated substrates followed the trend for alkylguaiacols: propyl > ethyl > methyl > phenyl > unsubstituted. We also show AphC only poorly cleaved 3-phenylcatechol, the preferred substrate of BphC. Moreover, AphC and BphC cleaved 3-phenylcatechol and 4-phenylcatechol with different regiospecificities, likely due to the substrates' binding mode. A crystallographic structure of the AphC·4-ethylcatechol binary complex to 1.59 Å resolution revealed that the catechol is bound to the active site iron in a bidentate manner and that the substrate's alkyl side chain is accommodated by a hydrophobic pocket. Finally, we show RHA1 grows on a mixture of 4-ethylguaiacol and guaiacol, simultaneously catabolizing these substrates through meta-cleavage and ortho-cleavage pathways, respectively, suggesting that the specificity of AphC helps to prevent the routing of catechol through the Aph pathway. Overall, this study contributes to our understanding of the bacterial catabolism of aromatic compounds derived from lignin, and the determinants of specificity in extradiol dioxygenases.
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Affiliation(s)
- Laura E Navas
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Michael Zahn
- Centre for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Harbir Bajwa
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Jason C Grigg
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Megan E Wolf
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - John E McGeehan
- Centre for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada.
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Ines P, Vlasta D, Sanja F, Ana BK, Dubravka H, Fabrice ML, Nikolina UK. Unraveling metabolic flexibility of rhodococci in PCB transformation. CHEMOSPHERE 2021; 282:130975. [PMID: 34111638 DOI: 10.1016/j.chemosphere.2021.130975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/17/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Even though the genetic attributes suggest presence of multiple degradation pathways, most of rhodococci are known to transform PCBs only via regular biphenyl (bph) pathway. Using GC-MS analysis, we monitored products formed during transformation of 2,4,4'-trichlorobiphenyl (PCB-28), 2,2',5,5'-tetrachlorobiphenyl (PCB-52) and 2,4,3'-trichlorobiphenyl (PCB-25) by previously characterized PCB-degrading rhodococci Z6, T6, R2, and Z57, with the aim to explore their metabolic pleiotropy in PCB transformations. A striking number of different transformation products (TPs) carrying a phenyl ring as a substituent, both those generated as a part of the bph pathway and an array of unexpected TPs, implied a curious transformation ability. We hypothesized that studied rhodococcal isolates, besides the regular one, use at least two alternative pathways for PCB transformation, including the pathway leading to acetophenone formation (via 3,4 (4,5) dioxygenase attack on the molecule), and a third sideway pathway that includes stepwise oxidative decarboxylation of the aliphatic side chain of the 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate. Structure of the identified chlorinated benzoic acids and acetophenones allowed us to hypothesize that the first two pathways were the outcome of a ring-hydroxylating dioxygenase with the ability to attack both the 2,3 (5,6) and the 3,4 (4,5) positions of the biphenyl ring as well as dechlorination activity at both, -ortho and -para positions. We propose that several TPs produced by the bph pathway could have caused the triggering of the third sideway pathway. In conclusion, this study proposed ability of rhodococci to use different strategies in PCB transformation, which allows them to circumvent potential negative aspect of TPs on the overall transformation pathway.
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Affiliation(s)
- Petrić Ines
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia.
| | - Drevenkar Vlasta
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | - Fingler Sanja
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | | | - Hršak Dubravka
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia
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Differential Roles of Three Different Upper Pathway meta Ring Cleavage Product Hydrolases in the Degradation of Dibenzo- p-Dioxin and Dibenzofuran by Sphingomonas wittichii Strain RW1. Appl Environ Microbiol 2021; 87:e0106721. [PMID: 34469199 DOI: 10.1128/aem.01067-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphingomonas wittichii RW1 grows on the two related compounds dibenzofuran (DBF) and dibenzo-p-dioxin (DXN) as the sole source of carbon. Previous work by others (P. V. Bunz, R. Falchetto, and A. M. Cook, Biodegradation 4:171-178, 1993, https://doi/org/10.1007/BF00695119) identified two upper pathway meta cleavage product hydrolases (DxnB1 and DxnB2) active on the DBF upper pathway metabolite 2-hydroxy-6-oxo-6-(2-hydroxyphenyl)-hexa-2,4-dienoate. We took a physiological approach to determine the role of these two enzymes in the degradation of DBF and DXN by RW1. Single knockouts of either plasmid-located dxnB1 or chromosome-located dxnB2 had no effect on RW1 growth on either DBF or DXN. However, a double-knockout strain lost the ability to grow on DBF but still grew normally on DXN, demonstrating that DxnB1 and DxnB2 are the only hydrolases involved in the DBF upper pathway. Using a transcriptomics-guided approach, we identified a constitutively expressed third hydrolase encoded by the chromosomally located SWIT0910 gene. Knockout of SWIT0910 resulted in a strain that no longer grows on DXN but still grows normally on DBF. Thus, the DxnB1 and DxnB2 hydrolases function in the DBF but not the DXN catabolic pathway, and the SWIT0190 hydrolase functions in the DXN but not the DBF catabolic pathway. IMPORTANCE S. wittichii RW1 is one of only a few strains known to grow on DXN as the sole source of carbon. Much of the work deciphering the related RW1 DXN and DBF catabolic pathways has involved genome gazing, transcriptomics, proteomics, heterologous expression, and enzyme purification and characterization. Very little research has utilized physiological techniques to precisely dissect the genes and enzymes involved in DBF and DXN degradation. Previous work by others identified and extensively characterized two RW1 upper pathway hydrolases. Our present work demonstrates that these two enzymes are involved in DBF but not DXN degradation. In addition, our work identified a third constitutively expressed hydrolase that is involved in DXN but not DBF degradation. Combined with our previous work (T. Y. Mutter and G. J. Zylstra, Appl Environ Microbiol 87:e02464-20, 2021, https://doi.org/10.1128/AEM.02464-20), this means that the RW1 DXN upper pathway involves genes from three very different locations in the genome, including an initial plasmid-encoded dioxygenase and a ring cleavage enzyme and hydrolase encoded on opposite sides of the chromosome.
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Li M, He W, Yang H, Sun S, Li Y. Potential Environmental Risk Characteristics of PCB Transformation Products in the Environmental Medium. TOXICS 2021; 9:toxics9090213. [PMID: 34564364 PMCID: PMC8472189 DOI: 10.3390/toxics9090213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022]
Abstract
The complementary construction of polychlorinated biphenyl (PCB) phytotoxicity and the biotoxicity 3D-QSAR model, combined with the constructed PCB environmental risk characterization model, was carried out to evaluate the persistent organic pollutant (POP) properties (toxicity (phytotoxicity and biotoxicity), bioconcentration, migration, and persistence) of PCBs and their corresponding transformation products (phytodegradation, microbial degradation, biometabolism, and photodegradation). The transformation path with a significant increase in environmental risks was analyzed. Some environmentally friendly PCB derivatives, exhibiting a good modification effect, and their parent molecules were selected as precursor molecules. Their transformation processes were simulated and evaluated for assessing the environmental risks. Some transformation products displayed increased environmental risks. The environmental risks of plant degradation products of the PCBs in the environmental media showed the maximum risk, indicating that the potential risks of the transformation products of the PCBs and their environmentally friendly derivatives could not be neglected. It is essential to further improve the ability of plants to degrade their transformation products. The improvement of some degradation products for environmentally friendly PCB derivatives indicates that the theoretical modification of a single environmental feature cannot completely control the potential environmental risks of molecules. In addition, this method can be used to analyze and evaluate environmentally friendly PCB derivatives to avoid and reduce the potential environmental and human health risks caused by environmentally friendly PCB derivatives.
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Affiliation(s)
- Minghao Li
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China; (M.L.); (W.H.); (H.Y.)
- School of Emergency Science and Engineering, Jilin Jianzhu University, Changchun 130119, China
| | - Wei He
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China; (M.L.); (W.H.); (H.Y.)
| | - Hao Yang
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China; (M.L.); (W.H.); (H.Y.)
| | - Shimei Sun
- School of Emergency Science and Engineering, Jilin Jianzhu University, Changchun 130119, China
- Correspondence: (S.S.); (Y.L.)
| | - Yu Li
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China; (M.L.); (W.H.); (H.Y.)
- Correspondence: (S.S.); (Y.L.)
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Selective pressure of biphenyl/polychlorinated biphenyls on the formation of aerobic bacterial associations and their biodegradative potential. Folia Microbiol (Praha) 2021; 66:659-676. [PMID: 33966251 DOI: 10.1007/s12223-021-00873-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Unique bacterial associations were formed in the polluted soils from territory of the industrial factories Open Joint Stock Company "The Middle Volga Chemical Plant," Chapaevsk, Russia and Open Joint Stock Company "Lubricant Producing Plant," Perm, Russia. This study evaluates the influence of the biphenyl/polychlorinated biphenyls (PCB) on the formation of aerobic bacterial associations and their biodegradative potential. Enrichment cultivation of the soil samples from the territories of these industrial factories with PCB (commercial mixture Sovol) was lead for forming aerobic bacterial enrichment cultures showing a unique composition. The dominating in these bacterial cultures was the phylum Proteobacteria (Beta- and Gammaproteobacteria). Using biphenyl as a carbon source led to decrease of biodiversity in the final stable bacterial associations. Periodic cultivation experiments demonstrated that the association PN2-B has a high degradative potential among the six studied bacterial associations. PN2-B degraded 100% mono-chlorobiphenyls (94.5 mg/L), 86.2% di-chlorobiphenyls (22.3 mg/L), 50.9% Sovol, and 38.4% Delor 103 (13.8 mg/L). Qualitative analysis of metabolites showed that association performed transformation of chlorobenzoic acids (PCB degradation intermediates) into metabolites of citrate cycle. Twelve individual strain-destructors were isolated. The strains were found to degrade 17.7-100% PCB1, 36.2-100% PCB2, 18.8-100% PCB3 (94.5 mg/L), and 15.7-78.2% PCB8 (22.3 mg/L). The strains were shown to metabolize chlorobenzoic acids formed during degradation of chlorobiphenyls. A unique ability of strains Micrococcus sp. PNS1 and Stenotrophomonas sp. PNS6 to degrade ortho-, meta-, and para-monosubstituted chlorobenzoic acids was revealed. Our results suggest that PN2-B and individual bacterial strains will be perspective for cleaning of the environment from polychlorinated biphenyls.
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Khalid F, Hashmi MZ, Jamil N, Qadir A, Ali MI. Microbial and enzymatic degradation of PCBs from e-waste-contaminated sites: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:10474-10487. [PMID: 33411303 DOI: 10.1007/s11356-020-11996-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/07/2020] [Indexed: 05/21/2023]
Abstract
Electronic waste is termed as e-waste and on recycling it produces environmental pollution. Among these e-waste pollutants, polychlorinated biphenyls (PCBs) are significantly important due to ubiquitous, organic in nature and serious health and environmental hazards. PCBs are used in different electrical equipment such as in transformers and capacitors for the purposes of exchange of heat and hydraulic fluids. Bioremediation is a reassuring technology for the elimination of the PCBs from the environment. In spite of their chemical stability, there are several microbes which can bio-transform or mineralize the PCBs aerobically or anaerobically. In this review paper, our objective was to summarize the information regarding PCB-degrading enzymes and microbes. The review suggested that the most proficient PCB degraders during anaerobic condition are Dehalobacter, Dehalococcoides, and Desulfitobacterium and in aerobic condition are Burkholderia, Achromobacter, Comamonas, Ralstonia, Pseudomonas, Bacillus, and Alcaligenes etc., showing the broadest substrate among bacterial strains. Enzymes found in soil such as dehydrogenases and fluorescein diacetate (FDA) esterases have the capability to breakdown PCBs. Biphenyl upper pathway involves four enzymes: dehydrogenase (bphB), multicomponent dioxygenase (bphA, E, F, and G), second dioxygenase (bphC), hydrolase, and (bphD). Biphenyl dioxygenase is considered as the foremost enzyme used for aerobic degradation of PCBs in metabolic pathway. It has been proved that several micro-organisms are responsible for the PCB metabolization. The review provides novel strategies for e-waste-contaminated soil management.
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Affiliation(s)
- Foqia Khalid
- College of Earth and Environmental Science, University of the Punjab, Lahore, Pakistan
| | - Muhammad Zaffar Hashmi
- Department of Chemistry, COMSATS University Islamabad, Islamabad, 44000, Pakistan.
- Pakistan Academy of Science, 3-Constitution Avenue Sector G-5/2, Islamabad, Pakistan.
| | - Nadia Jamil
- College of Earth and Environmental Science, University of the Punjab, Lahore, Pakistan
| | - Abdul Qadir
- College of Earth and Environmental Science, University of the Punjab, Lahore, Pakistan
| | - Muhammad Ishtiaq Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
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Bako CM, Mattes TE, Marek RF, Hornbuckle KC, Schnoor JL. Biodegradation of PCB congeners by Paraburkholderia xenovorans LB400 in presence and absence of sediment during lab bioreactor experiments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116364. [PMID: 33412450 PMCID: PMC8183161 DOI: 10.1016/j.envpol.2020.116364] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/04/2020] [Accepted: 12/19/2020] [Indexed: 05/21/2023]
Abstract
Experiments were conducted to measure biodegradation of polychlorinated biphenyl (PCB) congeners contained in mixture Aroclor 1248 and congeners present in wastewater lagoon sediment contaminated decades earlier at Altavista, Virginia. A well-characterized strain of aerobic PCB-degrading bacteria, Paraburkholderia xenovorans LB400 was incubated in laboratory bioreactors with PCB-contaminated sediment collected at the site. The experiments evaluated strain LB400's ability to degrade PCBs in absence of sediment and in PCB-contaminated sediment slurry. In absence of sediment, LB400 transformed 76% of Aroclor 1248 within seven days, spanning all homolog groups present in the mixture. In sediment slurry, only mono- and di-chlorinated PCB congeners were transformed. These results show that LB400 is capable of rapidly biodegrading most PCB congeners when they are freely dissolved in liquid but cannot degrade PCB congeners having three or more chlorine substituents in sediment slurry. Finally, using GC/MS-MS triple quadrupole spectrometry, this work distinguishes between physical (sorption to cells) and biological removal mechanisms, illuminates the process by which microorganisms with LB400-type congener specificity can selectively transform lower-chlorinated congeners over time, and makes direct comparisons to other studies where individual congener data is reported.
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Affiliation(s)
- Christian M Bako
- The Department of Civil & Environmental Engineering, 4105 Seamans Center for the Engineering Arts & Sciences, University of Iowa, Iowa City, IA, USA, 52245
| | - Timothy E Mattes
- The Department of Civil & Environmental Engineering, 4105 Seamans Center for the Engineering Arts & Sciences, University of Iowa, Iowa City, IA, USA, 52245
| | - Rachel F Marek
- The Department of Civil & Environmental Engineering, 4105 Seamans Center for the Engineering Arts & Sciences, University of Iowa, Iowa City, IA, USA, 52245
| | - Keri C Hornbuckle
- The Department of Civil & Environmental Engineering, 4105 Seamans Center for the Engineering Arts & Sciences, University of Iowa, Iowa City, IA, USA, 52245
| | - Jerald L Schnoor
- The Department of Civil & Environmental Engineering, 4105 Seamans Center for the Engineering Arts & Sciences, University of Iowa, Iowa City, IA, USA, 52245.
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11
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Jia Y, Wang J, Ren C, Nahurira R, Khokhar I, Wang J, Fan S, Yan Y. Identification and characterization of a meta-cleavage product hydrolase involved in biphenyl degradation from Arthrobacter sp. YC-RL1. Appl Microbiol Biotechnol 2019; 103:6825-6836. [PMID: 31240368 DOI: 10.1007/s00253-019-09956-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/27/2022]
Abstract
Polychlorinated biphenyls (PCBs) are a group of persistent organic pollutants (POPs) widely existing in the environment. Arthrobacter sp. YC-RL1 is a biphenyl-degrading bacterium that shows metabolic versatility towards aromatic compounds. A 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate (HOPDA) hydrolase (BphD) gene involved in the biodegradation of biphenyl was cloned from strain YC-RL1 and heterologously expressed in Escherichia coli BL21 (DE3). The recombinant BphDYC-RL1 was purified and characterized. BphDYC-RL1 showed the highest activity at 45 °C and pH 7. It was stable under a wide range of temperature (20-50 °C). The enzyme had a Km value of 0.14 mM, Kcat of 11.61 s-1, and Vmax of 0.027 U/mg. Temperature dependence catalysis exhibited a biphasic Arrhenius Plot with a transition at 20 °C. BphDYC-RL1 was inactivated by SDS, Tween 20, Tween 80, Trition X-100, DTT, CHAPS, NBS, PMSF, and DEPC, but insensitive to EDTA. Site-directed mutagenesis of the active-site residues revealed that the catalytic triad residues (Ser115, His275, and Asp247) of BphDYC-RL1 were necessary for its activity. The investigation of BphDYC-RL1 not only provides new potential enzyme resource for the biodegradation of biphenyl but also helps deepen our understanding on the catalytic process and mechanism.
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Affiliation(s)
- Yang Jia
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Junhuan Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chao Ren
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruth Nahurira
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ibatsam Khokhar
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiayi Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuanghu Fan
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanchun Yan
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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12
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Kuatsjah E, Chan ACK, Hurst TE, Snieckus V, Murphy MEP, Eltis LD. Metal- and Serine-Dependent Meta-Cleavage Product Hydrolases Utilize Similar Nucleophile-Activation Strategies. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02955] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - Timothy E. Hurst
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Victor Snieckus
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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13
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Nerdinger S, Kuatsjah E, Hurst TE, Schlapp-Hackl I, Kahlenberg V, Wurst K, Eltis LD, Snieckus V. Bacterial Catabolism of Biphenyls: Synthesis and Evaluation of Analogues. Chembiochem 2018; 19:1771-1778. [PMID: 29905982 DOI: 10.1002/cbic.201800231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Indexed: 12/31/2022]
Abstract
A series of alkylated 2,3-dihydroxybiphenyls has been prepared on the gram scale by using an effective Directed ortho Metalation-Suzuki-Miyaura cross-coupling strategy. These compounds have been used to investigate the substrate specificity of the meta-cleavage dioxygenase BphC, a key enzyme in the microbial catabolism of biphenyl. Isolation and characterization of the meta-cleavage products will allow further study of related processes, including the catabolism of lignin-derived biphenyls.
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Affiliation(s)
- Sven Nerdinger
- Global Commercial Operations, Sandoz GmbH, Biochemiestrasse 10, 6250, Kundl, Austria
| | - Eugene Kuatsjah
- Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Timothy E Hurst
- Department of Chemistry, Queen's University, Chernoff Hall, Kingston, ON, K7L 3N6, Canada
| | - Inge Schlapp-Hackl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Center for Chemistry and Biomedicine, Innrain 80-82, 6020, Innsbruck, Austria
| | - Volker Kahlenberg
- Institute of Mineralogy and Petrography, University of Innsbruck, Innrain 52, 6020, Innsbruck, Austria
| | - Klaus Wurst
- Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Lindsay D Eltis
- Life Sciences Centre, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Victor Snieckus
- Department of Chemistry, Queen's University, Chernoff Hall, Kingston, ON, K7L 3N6, Canada
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14
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Kuatsjah E, Chan ACK, Kobylarz MJ, Murphy MEP, Eltis LD. The bacterial meta-cleavage hydrolase LigY belongs to the amidohydrolase superfamily, not to the α/β-hydrolase superfamily. J Biol Chem 2017; 292:18290-18302. [PMID: 28935670 DOI: 10.1074/jbc.m117.797696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/15/2017] [Indexed: 01/27/2023] Open
Abstract
Strain SYK-6 of the bacterium Sphingobium sp. catabolizes lignin-derived biphenyl via a meta-cleavage pathway. In this pathway, LigY is proposed to catalyze the hydrolysis of the meta-cleavage product (MCP) 4,11-dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenyl-hexa-2,4-dienoate. Here, we validated this reaction by identifying 5-carboxyvanillate and 4-carboxy-2-hydroxypenta-2,4-dienoate as the products and determined the kcat and kcat/Km values as 9.3 ± 0.6 s-1 and 2.5 ± 0.2 × 107 m-1 s-1, respectively. Sequence analyses and a 1.9 Å resolution crystal structure established that LigY belongs to the amidohydrolase superfamily, unlike previously characterized MCP hydrolases, which are serine-dependent enzymes of the α/β-hydrolase superfamily. The active-site architecture of LigY resembled that of α-amino-β-carboxymuconic-ϵ-semialdehyde decarboxylase, a class III amidohydrolase, with a single zinc ion coordinated by His-6, His-8, His-179, and Glu-282. Interestingly, we found that LigY lacks the acidic residue proposed to activate water for hydrolysis in other class III amidohydrolases. Moreover, substitution of His-223, a conserved residue proposed to activate water in other amidohydrolases, reduced the kcat to a much lesser extent than what has been reported for other amidohydrolases, suggesting that His-223 has a different role in LigY. Substitution of Arg-72, Tyr-190, Arg-234, or Glu-282 reduced LigY activity over 100-fold. On the basis of these results, we propose a catalytic mechanism involving substrate tautomerization, substrate-assisted activation of water for hydrolysis, and formation of a gem-diol intermediate. This last step diverges from what occurs in serine-dependent MCP hydrolases. This study provides insight into C-C-hydrolyzing enzymes and expands the known range of reactions catalyzed by the amidohydrolase superfamily.
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Affiliation(s)
| | - Anson C K Chan
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Marek J Kobylarz
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E P Murphy
- the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- From the Genome Science and Technology Program and .,the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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15
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A water-assisted nucleophilic mechanism utilized by BphD, the meta-cleavage product hydrolase in biphenyl degradation. J Mol Graph Model 2017; 76:448-455. [DOI: 10.1016/j.jmgm.2017.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 11/22/2022]
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16
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Kuatsjah E, Chen HM, Withers SG, Eltis LD. Characterization of an extradiol dioxygenase involved in the catabolism of lignin-derived biphenyl. FEBS Lett 2017; 591:1001-1009. [DOI: 10.1002/1873-3468.12611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 02/22/2017] [Accepted: 02/23/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Eugene Kuatsjah
- Genome Science and Technology Program; The University of British Columbia; Vancouver BC Canada
| | - Hong-Ming Chen
- Department of Chemistry; The University of British Columbia; Vancouver BC Canada
| | - Stephen G. Withers
- Genome Science and Technology Program; The University of British Columbia; Vancouver BC Canada
- Department of Chemistry; The University of British Columbia; Vancouver BC Canada
- Department of Biochemistry; Life Sciences Institute; The University of British Columbia; Vancouver BC Canada
| | - Lindsay D. Eltis
- Genome Science and Technology Program; The University of British Columbia; Vancouver BC Canada
- Department of Biochemistry; Life Sciences Institute; The University of British Columbia; Vancouver BC Canada
- Department of Microbiology and Immunology; Life Sciences Institute; The University of British Columbia; Vancouver BC Canada
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17
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Devamani T, Rauwerdink AM, Lun-zer M, Jones BJ, Mooney JL, Tan MAO, Zhang ZJ, Xu JH, Dean AM, Kazlauskas RJ. Catalytic Promiscuity of Ancestral Esterases and Hydroxynitrile Lyases. J Am Chem Soc 2016; 138:1046-56. [PMID: 26736133 PMCID: PMC5466365 DOI: 10.1021/jacs.5b12209] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Catalytic promiscuity is a useful, but accidental, enzyme property, so finding catalytically promiscuous enzymes in nature is inefficient. Some ancestral enzymes were branch points in the evolution of new enzymes and are hypothesized to have been promiscuous. To test the hypothesis that ancestral enzymes were more promiscuous than their modern descendants, we reconstructed ancestral enzymes at four branch points in the divergence hydroxynitrile lyases (HNL's) from esterases ∼ 100 million years ago. Both enzyme types are α/β-hydrolase-fold enzymes and have the same catalytic triad, but differ in reaction type and mechanism. Esterases catalyze hydrolysis via an acyl enzyme intermediate, while lyases catalyze an elimination without an intermediate. Screening ancestral enzymes and their modern descendants with six esterase substrates and six lyase substrates found higher catalytic promiscuity among the ancestral enzymes (P < 0.01). Ancestral esterases were more likely to catalyze a lyase reaction than modern esterases, and the ancestral HNL was more likely to catalyze ester hydrolysis than modern HNL's. One ancestral enzyme (HNL1) along the path from esterase to hydroxynitrile lyases was especially promiscuous and catalyzed both hydrolysis and lyase reactions with many substrates. A broader screen tested mechanistically related reactions that were not selected for by evolution: decarboxylation, Michael addition, γ-lactam hydrolysis and 1,5-diketone hydrolysis. The ancestral enzymes were more promiscuous than their modern descendants (P = 0.04). Thus, these reconstructed ancestral enzymes are catalytically promiscuous, but HNL1 is especially so.
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Affiliation(s)
- Titu Devamani
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Alissa M. Rauwerdink
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Mark Lun-zer
- University of Minnesota, Department of Ecology, Evolution & Behavior and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Bryan J. Jones
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Joanna L. Mooney
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | | | - Zhi-Jun Zhang
- East China University of Science and Technology, School of Biotechnology, Meilong Road 130, Shanghai 200237 P. R. China
| | - Jian-He Xu
- East China University of Science and Technology, School of Biotechnology, Meilong Road 130, Shanghai 200237 P. R. China
| | - Antony M. Dean
- University of Minnesota, Department of Ecology, Evolution & Behavior and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
- Sun Yat-sen University, Institute of Ecology and Evolution, No.135, Xinggang West Road, Guangzhou, 510275 P. R. China
| | - Romas J. Kazlauskas
- University of Minnesota, Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
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18
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Rauwerdink A, Kazlauskas RJ. How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: the Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes. ACS Catal 2015; 5:6153-6176. [PMID: 28580193 DOI: 10.1021/acscatal.5b01539] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes within a family often catalyze different reactions. In some cases, this variety stems from different catalytic machinery, but in other cases the machinery is identical; nevertheless, the enzymes catalyze different reactions. In this review, we examine the subset of α/β-hydrolase fold enzymes that contain the serine-histidine-aspartate catalytic triad. In spite of having the same protein fold and the same core catalytic machinery, these enzymes catalyze seventeen different reaction mechanisms. The most common reactions are hydrolysis of C-O, C-N and C-C bonds (Enzyme Classification (EC) group 3), but other enzymes are oxidoreductases (EC group 1), acyl transferases (EC group 2), lyases (EC group 4) or isomerases (EC group 5). Hydrolysis reactions often follow the canonical esterase mechanism, but eight variations occur where either the formation or cleavage of the acyl enzyme intermediate differs. The remaining eight mechanisms are lyase-type elimination reactions, which do not have an acyl enzyme intermediate and, in four cases, do not even require the catalytic serine. This diversity of mechanisms from the same catalytic triad stems from the ability of the enzymes to bind different substrates, from the requirements for different chemical steps imposed by these new substrates and, only in about half of the cases, from additional hydrogen bond partners or additional general acids/bases in the active site. This detailed analysis shows that binding differences and non-catalytic residues create new mechanisms and are essential for understanding and designing efficient enzymes.
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Affiliation(s)
- Alissa Rauwerdink
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
| | - Romas J. Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
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19
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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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20
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Li Y, Zhang R, Du L, Zhang Q, Wang W. Insight into the catalytic mechanism of meta-cleavage product hydrolase BphD: a quantum mechanics/molecular mechanics study. RSC Adv 2015. [DOI: 10.1039/c5ra09939k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The catalytic mechanism of BphD (the fourth enzyme of the biphenyl catabolic pathway) toward its natural substrate 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) was investigated in atomistic detail by QM/MM approach.
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Affiliation(s)
- Yanwei Li
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Ruiming Zhang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Likai Du
- Key Laboratory of Bio-based Materials
- Qingdao Institute of Bio-energy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- P. R. China
| | - Qingzhu Zhang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
| | - Wenxing Wang
- Environment Research Institute
- Shandong University
- Jinan 250100
- P. R. China
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21
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Passatore L, Rossetti S, Juwarkar AA, Massacci A. Phytoremediation and bioremediation of polychlorinated biphenyls (PCBs): state of knowledge and research perspectives. JOURNAL OF HAZARDOUS MATERIALS 2014; 278:189-202. [PMID: 24976127 DOI: 10.1016/j.jhazmat.2014.05.051] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 05/20/2023]
Abstract
This review summarizes the bioremediation and phytoremediation technologies proposed so far to detoxify PCB-contaminated sites. A critical analysis about the potential and limits of the PCB pollution treatment strategies by means of plants, fungi and bacteria are elucidated, including the new insights emerged from recent studies on the rhizosphere potential and on the implementation of simultaneous aerobic and anaerobic biodegradation processes. The review describes the biodegradation and phytoremediation processes and elaborates on the environmental variables affecting contaminant degradation rates, summarizing the amendments recommended to enhance PCB degradation. Additionally, issues connected with PCB toxicology, actual field remediation strategies and economical evaluation are discussed.
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Affiliation(s)
- Laura Passatore
- Institute of Agro-environment and Forest Biology (IBAF), National Research Council (CNR), Via Salaria Km 29.300, 00015 Monterotondo (Rome), Italy; Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria Km 29.300, 00015 Monterotondo (Rome), Italy
| | - Asha A Juwarkar
- Environmental Biotechnology Division, National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440 020, India
| | - Angelo Massacci
- Institute of Agro-environment and Forest Biology (IBAF), National Research Council (CNR), Via Salaria Km 29.300, 00015 Monterotondo (Rome), Italy.
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22
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Catalytic transformation of HODAs using an efficient meta-cleavage product hydrolase-spore surface display system. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Qin H, Brookes PC, Xu J. Cucurbita spp. and Cucumis sativus enhance the dissipation of polychlorinated biphenyl congeners by stimulating soil microbial community development. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2014; 184:306-312. [PMID: 24077568 DOI: 10.1016/j.envpol.2013.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 08/28/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
A number of Cucurbita species have the potential to extract polychlorinated biphenyls (PCBs) from soil, but their impact on the soil microbial communities responsible for PCB degradation remains unclear. A greenhouse experiment was conducted to investigate the effect of three Cucurbita and one Cucumis species on PCB dissipation and soil microbial community structure. Compared to the unplanted control, enhanced losses of PCBs (19.5%-42.7%) were observed in all planted soils. Cucurbita pepo and Cucurbita moschata treatments were more efficient in PCB dissipation, and have similar patterns of soil phospholipid fatty acids (PLFAs) and PCB congener profiles. Cucurbita treatments tend to have higher soil microbial biomass than Cucumis. Gram-negative (G(-)) bacteria were significantly correlated with PCB degradation rates (R(2) = 0.719, p < 0.001), while fungi and G(-) bacteria were correlated with dissipation of the penta homologue group (R(2) = 0.590, p < 0.01). Therefore, Cucurbita related soil microorganisms could play an important role in remediation of PCB contaminated soils.
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Affiliation(s)
- Hua Qin
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China; School of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an 311300, China
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24
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Single residues dictate the co-evolution of dual esterases: MCP hydrolases from the α/β hydrolase family. Biochem J 2013; 454:157-66. [PMID: 23750508 DOI: 10.1042/bj20130552] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Several members of the C-C MCP (meta-cleavage product) hydrolase family demonstrate an unusual ability to hydrolyse esters as well as the MCPs (including those from mono- and bi-cyclic aromatics). Although the molecular mechanisms responsible for such substrate promiscuity are starting to emerge, the full understanding of these complex enzymes is far from complete. In the present paper, we describe six distinct α/β hydrolases identified through genomic approaches, four of which demonstrate the unprecedented characteristic of activity towards a broad spectrum of substrates, including p-nitrophenyl, halogenated, fatty acyl, aryl, glycerol, cinnamoyl and carbohydrate esters, lactones, 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate and 2-hydroxy-6-oxohepta-2,4-dienoate. Using structural analysis and site-directed mutagenesis we have identified the three residues (Ser32, Val130 and Trp144) that determine the unusual substrate specificity of one of these proteins, CCSP0084. The results may open up new research avenues into comparative catalytic models, structural and mechanistic studies, and biotechnological applications of MCP hydrolases.
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Ruzzini AC, Bhowmik S, Ghosh S, Yam KC, Bolin JT, Eltis LD. A substrate-assisted mechanism of nucleophile activation in a Ser-His-Asp containing C-C bond hydrolase. Biochemistry 2013; 52:7428-38. [PMID: 24067021 DOI: 10.1021/bi401156a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The meta-cleavage product (MCP) hydrolases utilize a Ser-His-Asp triad to hydrolyze a carbon-carbon bond. Hydrolysis of the MCP substrate has been proposed to proceed via an enol-to-keto tautomerization followed by a nucleophilic mechanism of catalysis. Ketonization involves an intermediate, ES(red), which possesses a remarkable bathochromically shifted absorption spectrum. We investigated the catalytic mechanism of the MCP hydrolases using DxnB2 from Sphingomonas wittichii RW1. Pre-steady-state kinetic and LC ESI/MS evaluation of the DxnB2-mediated hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid to 2-hydroxy-2,4-pentadienoic acid and benzoate support a nucleophilic mechanism catalysis. In DxnB2, the rate of ES(red) decay and product formation showed a solvent kinetic isotope effect of 2.5, indicating that a proton transfer reaction, assigned here to substrate ketonization, limits the rate of acylation. For a series of substituted MCPs, this rate was linearly dependent on MCP pKa2 (βnuc ∼ 1). Structural characterization of DxnB2 S105A:MCP complexes revealed that the catalytic histidine is displaced upon substrate-binding. The results provide evidence for enzyme-catalyzed ketonization in which the catalytic His-Asp pair does not play an essential role. The data further suggest that ES(red) represents a dianionic intermediate that acts as a general base to activate the serine nucleophile. This substrate-assisted mechanism of nucleophilic catalysis distinguishes MCP hydrolases from other serine hydrolases.
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Affiliation(s)
- Antonio C Ruzzini
- Departments of †Biochemistry & Molecular Biology and ‡Microbiology & Immunology, The University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
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26
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Ruzzini AC, Bhowmik S, Yam KC, Ghosh S, Bolin JT, Eltis LD. The lid domain of the MCP hydrolase DxnB2 contributes to the reactivity toward recalcitrant PCB metabolites. Biochemistry 2013; 52:5685-5695. [PMID: 23879719 PMCID: PMC3903462 DOI: 10.1021/bi400774m] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DxnB2 and BphD are meta-cleavage product (MCP) hydrolases that catalyze C-C bond hydrolysis of the biphenyl metabolite 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA). BphD is a bottleneck in the bacterial degradation of polychlorinated biphenyls (PCBs) by the Bph catabolic pathway due in part to inhibition by 3-Cl HOPDAs. By contrast, DxnB2 from Sphingomonas wittichii RW1 catalyzes the hydrolysis of 3-Cl HOPDAs more efficiently. X-ray crystallographic studies of the catalytically inactive S105A variant of DxnB2 complexed with 3-Cl HOPDA revealed a binding mode in which C1 through C6 of the dienoate are coplanar. The chlorine substituent is accommodated by a hydrophobic pocket that is larger than the homologous site in BphDLB400 from Burkholderia xenovorans LB400. The planar binding mode observed in the crystalline complex was consistent with the hyper- and hypsochromically shifted absorption spectra of 3-Cl and 3,9,11-triCl HOPDA, respectively, bound to S105A in solution. Moreover, ES(red), an intermediate possessing a bathochromically shifted spectrum observed in the turnover of HOPDA, was not detected, suggesting that substrate destabilization was rate-limiting in the turnover of these PCB metabolites. Interestingly, electron density for the first α-helix of the lid domain was poorly defined in the dimeric DxnB2 structures, unlike in the tetrameric BphDLB400. Structural comparison of MCP hydrolases identified the NC-loop, connecting the lid to the α/β-hydrolase core domain, as a determinant in the oligomeric state and suggests its involvement in catalysis. Finally, an increased mobility of the DxnB2 lid may contribute to the enzyme's ability to hydrolyze PCB metabolites, highlighting how lid architecture contributes to substrate specificity in α/β-hydrolases.
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Affiliation(s)
- Antonio C. Ruzzini
- Department of Biochemistry and Molecular Biology, University of British Columbia, BC, Canada
| | - Shiva Bhowmik
- Purdue Cancer Research Center and Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Katherine C. Yam
- Department of Biochemistry and Molecular Biology, University of British Columbia, BC, Canada
| | - Subhangi Ghosh
- Purdue Cancer Research Center and Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Jeffrey T. Bolin
- Purdue Cancer Research Center and Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Lindsay D. Eltis
- Department of Biochemistry and Molecular Biology, University of British Columbia, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, BC, Canada
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27
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Hernández-Sánchez V, Lang E, Wittich RM. The Three-Species Consortium of Genetically Improved Strains Cupriavidus necator RW112, Burkholderia xenovorans RW118, and Pseudomonas pseudoalcaligenes RW120 Grows with Technical Polychlorobiphenyl, Aroclor 1242. Front Microbiol 2013; 4:90. [PMID: 23658554 PMCID: PMC3647243 DOI: 10.3389/fmicb.2013.00090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 03/08/2013] [Indexed: 12/03/2022] Open
Abstract
Burkholderia xenovorans LB400, Cupriavidus necator H850, and Pseudomonas pseudoalcaligenes KF707 are bacterial strains able to mineralize biphenyl and to co-oxidize many of its halogenated derivatives (PCBs). Only strain LB400 also mineralizes a few mono- and dichlorobiphenyls, due to the presence of a functioning chlorocatechol pathway. Here, we used a Tn5-based minitransposon shuttle system to chromosomically introduce genes tcbRCDEF, encoding the chlorocatechol pathway into KF707, and genes cbdABC encoding a 2-chlorobenzoate 1,2-dioxygenase into KF707 and LB400, as well as transposon Tn4653 from the TOL plasmid, providing genes xylXYZL, encoding a broad-range toluate (methylbenzoate) dioxygenase and its dihydrodiol dehydrogenase, to extend the range for the mineralization of halogenated benzoates in LB400 and in KF707 through co-oxidation of halobenzoates into chlorocatechols. The engineered derivatives of LB400 and KF707 thus gained the ability for the mineralization of all isomeric monochloro- and bromobenzoates of the so-called lower pathway which, consequently, also allowed the mineralization of all monochlorobiphenyls and a number of di- and trichlorobiphenyls, thus preventing the accumulation of halobenzoates and of catabolites thereof. LB400 and KF707 also grow with the two commercial PCB formulations, Aroclor 1221 and Aroclor 1232, as the sole carbon and energy sources, but not with higher halogenated PCB mixtures, similar to the already published strain RW112. Repeated exposition of the modified LB400 to short pulses of UV light, over a prolonged period of time, allowed the isolation of a derivative of LB400, termed RW118, capable of growth with Aroclor 1016 still containing only traces of biphenyl, and in co-culture with modified KF707 termed RW120, and modified H850 (RW112) with Aroclor 1242, the commercial mixture already void of biphenyl and monochlorobiphenyls.
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Affiliation(s)
- Verónica Hernández-Sánchez
- Department of Environmental Protection, Experimental Station of the Zaidín, Spanish High Council for Scientific Research Granada, Spain
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28
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Sylvestre M. Prospects for using combined engineered bacterial enzymes and plant systems to rhizoremediate polychlorinated biphenyls. Environ Microbiol 2012; 15:907-15. [PMID: 23106850 DOI: 10.1111/1462-2920.12007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 09/06/2012] [Accepted: 09/26/2012] [Indexed: 01/17/2023]
Abstract
The fate of polychlorinated biphenyls (PCBs) in soil is driven by a combination of interacting biological processes. Several investigations have brought evidence that the rhizosphere provides a remarkable ecological niche to enhance the PCB degradation process by rhizobacteria. The bacterial oxidative enzymes involved in PCB degradation have been investigated extensively and novel engineered enzymes exhibiting enhanced catalytic activities toward more persistent PCBs have been described. Furthermore, recent studies suggest that approaches involving processes based on plant-microbe associations are very promising to remediate PCB-contaminated sites. In this review emphasis will be placed on the current state of knowledge regarding the strategies that are proposed to engineer the enzymes of the PCB-degrading bacterial oxidative pathway and to design PCB-degrading plant-microbe systems to remediate PCB-contaminated soil.
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Affiliation(s)
- Michel Sylvestre
- Institut National de la Recherche Scientifique, INRS-Instittut Armand-Frappier, Laval, Quebec, Canada, H7V1B7.
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29
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Ruzzini AC, Horsman GP, Eltis LD. The Catalytic Serine of meta-Cleavage Product Hydrolases Is Activated Differently for C–O Bond Cleavage Than for C–C Bond Cleavage. Biochemistry 2012; 51:5831-40. [DOI: 10.1021/bi300663r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antonio C. Ruzzini
- Department of Biochemistry
and Molecular Biology and
Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver,
British Columbia V6T 1Z3, Canada
| | - Geoff P. Horsman
- Department of Biochemistry
and Molecular Biology and
Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver,
British Columbia V6T 1Z3, Canada
| | - Lindsay D. Eltis
- Department of Biochemistry
and Molecular Biology and
Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver,
British Columbia V6T 1Z3, Canada
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30
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Ruzzini AC, Ghosh S, Horsman GP, Foster LJ, Bolin JT, Eltis LD. Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad. J Am Chem Soc 2012; 134:4615-24. [DOI: 10.1021/ja208544g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antonio C. Ruzzini
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Subhangi Ghosh
- Purdue Cancer Research Center
and Markey Center for Structural Biology, Department of Biological
Sciences, Purdue University, West Lafayette,
Indiana 47907, United States
| | - Geoff P. Horsman
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Leonard J. Foster
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Jeffrey T. Bolin
- Purdue Cancer Research Center
and Markey Center for Structural Biology, Department of Biological
Sciences, Purdue University, West Lafayette,
Indiana 47907, United States
| | - Lindsay D. Eltis
- Department
of Biochemistry and
Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
- Department of Microbiology and
Immunology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
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31
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Characterization of biphenyl dioxygenase sequences and activities encoded by the metagenomes of highly polychlorobiphenyl-contaminated soils. Appl Environ Microbiol 2012; 78:2706-15. [PMID: 22327590 DOI: 10.1128/aem.07381-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Total extracted DNA from two heavily polychlorobiphenyl-contaminated soils was analyzed with respect to biphenyl dioxygenase sequences and activities. This was done by PCR amplification and cloning of a DNA segment encoding the active site of the enzyme. The translated sequences obtained fell into three similarity clusters (I to III). Sequence identities were high within but moderate or low between the clusters. Members of clusters I and II showed high sequence similarities with well-known biphenyl dioxygenases. Cluster III showed low (43%) sequence identity with a biphenyl dioxygenase from Rhodococcus jostii RHA1. Amplicons from the three clusters were used to reconstitute and express complete biphenyl dioxygenase operons. In most cases, the resulting hybrid dioxygenases were detected in cell extracts of the recombinant hosts. At least 83% of these enzymes were catalytically active. Several amino acid exchanges were identified that critically affected activity. Chlorobiphenyl turnover by the enzymes containing the prototype sequences of clusters I and II was characterized with 10 congeners that were major, minor, or not constituents of the contaminated soils. No direct correlations were observed between on-site concentrations and rates of productive dioxygenations of these chlorobiphenyls. The prototype enzymes displayed markedly different substrate and product ranges. The cluster II dioxygenase possessed a broader substrate spectrum toward the assayed congeners, whereas the cluster I enzyme was superior in the attack of ortho-chlorinated aromatic rings. These results demonstrate the feasibility of the applied approach to functionally characterize dioxygenase activities of soil metagenomes via amplification of incomplete genes.
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32
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George KW, Kagle J, Junker L, Risen A, Hay AG. Growth of Pseudomonas putida F1 on styrene requires increased catechol-2,3-dioxygenase activity, not a new hydrolase. Microbiology (Reading) 2011; 157:89-98. [DOI: 10.1099/mic.0.042531-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas putida F1 cannot grow on styrene despite being able to degrade it through the toluene degradation (tod) pathway. Previous work had suggested that this was because TodF, the meta-fission product (MFP) hydrolase, was unable to metabolize the styrene MFP 2-hydroxy-6-vinylhexa-2,4-dienoate. Here we demonstrate via kinetic and growth analyses that the substrate specificity of TodF is not the limiting factor preventing F1 from growing on styrene. Rather, we found that the metabolite 3-vinylcatechol accumulated during styrene metabolism and that micromolar concentrations of this intermediate inactivated TodE, the catechol-2,3-dioxygenase (C23O) responsible for its cleavage. Analysis of cells growing on styrene suggested that inactivation of TodE and the subsequent accumulation of 3-vinylcatechol resulted in toxicity and cell death. We found that simply overexpressing TodE on a plasmid (pTodE) was all that was necessary to allow F1 to grow on styrene. Similar results were also obtained by expressing a related C23O, DmpB from Pseudomonas sp. CF600, in tandem with its plant-like ferredoxin, DmpQ (pDmpQB). Further analysis revealed that the ability of F1 (pDmpQB) and F1 (pTodE) to grow on styrene correlated with increased C23O activity as well as resistance of the enzyme to 3-vinylcatechol-mediated inactivation. Although TodE inactivation by 3-halocatechols has been studied before, to our knowledge, this is the first published report demonstrating inactivation by a 3-vinylcatechol. Given the ubiquity of catechol intermediates in aromatic hydrocarbon metabolism, our results further demonstrate the importance of C23O inactivation as a determinant of growth substrate specificity.
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Affiliation(s)
- Kevin W. George
- Department of Microbiology, Cornell University Ithaca, NY 14850, USA
- Field of Environmental Toxicology, Cornell University Ithaca, NY 14850, USA
| | - Jeanne Kagle
- Department of Microbiology, Cornell University Ithaca, NY 14850, USA
| | - Lauren Junker
- Department of Microbiology, Cornell University Ithaca, NY 14850, USA
| | - Amy Risen
- Department of Microbiology, Cornell University Ithaca, NY 14850, USA
- Field of Environmental Toxicology, Cornell University Ithaca, NY 14850, USA
| | - Anthony G. Hay
- Department of Microbiology, Cornell University Ithaca, NY 14850, USA
- Field of Environmental Toxicology, Cornell University Ithaca, NY 14850, USA
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33
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Saavedra JM, Acevedo F, González M, Seeger M. Mineralization of PCBs by the genetically modified strain Cupriavidus necator JMS34 and its application for bioremediation of PCBs in soil. Appl Microbiol Biotechnol 2010; 87:1543-54. [DOI: 10.1007/s00253-010-2575-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 03/18/2010] [Accepted: 03/18/2010] [Indexed: 11/29/2022]
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34
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Lack NA, Yam KC, Lowe ED, Horsman GP, Owen RL, Sim E, Eltis LD. Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. J Biol Chem 2010; 285:434-43. [PMID: 19875455 PMCID: PMC2804191 DOI: 10.1074/jbc.m109.058081] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 09/25/2009] [Indexed: 11/06/2022] Open
Abstract
In the recently identified cholesterol catabolic pathway of Mycobacterium tuberculosis, 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (HsaD) is proposed to catalyze the hydrolysis of a carbon-carbon bond in 4,5-9,10-diseco-3-hydroxy-5,9,17-tri-oxoandrosta-1(10),2-diene-4-oic acid (DSHA), the cholesterol meta-cleavage product (MCP) and has been implicated in the intracellular survival of the pathogen. Herein, purified HsaD demonstrated 4-33 times higher specificity for DSHA (k(cat)/K(m) = 3.3 +/- 0.3 x 10(4) m(-1) s(-1)) than for the biphenyl MCP 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) and the synthetic analogue 8-(2-chlorophenyl)-2-hydroxy-5-methyl-6-oxoocta-2,4-dienoic acid (HOPODA), respectively. The S114A variant of HsaD, in which the active site serine was substituted with alanine, was catalytically impaired and bound DSHA with a K(d) of 51 +/- 2 mum. The S114A.DSHA species absorbed maximally at 456 nm, 60 nm red-shifted versus the DSHA enolate. Crystal structures of the variant in complex with HOPDA, HOPODA, or DSHA to 1.8-1.9 Aindicate that this shift is due to the enzyme-induced strain of the enolate. These data indicate that the catalytic serine catalyzes tautomerization. A second role for this residue is suggested by a solvent molecule whose position in all structures is consistent with its activation by the serine for the nucleophilic attack of the substrate. Finally, the alpha-helical lid covering the active site displayed a ligand-dependent conformational change involving differences in side chain carbon positions of up to 6.7 A, supporting a two-conformation enzymatic mechanism. Overall, these results provide novel insights into the determinants of specificity in a mycobacterial cholesterol-degrading enzyme as well as into the mechanism of MCP hydrolases.
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Affiliation(s)
| | - Katherine C. Yam
- the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada, and
| | - Edward D. Lowe
- Molecular Biophysics, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Geoff P. Horsman
- the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada, and
| | - Robin L. Owen
- the Swiss Light Source, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Edith Sim
- From the Departments of Pharmacology and
| | - Lindsay D. Eltis
- the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada, and
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35
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Huitema C, Zhang J, Yin J, James MNG, Vederas JC, Eltis LD. Heteroaromatic ester inhibitors of hepatitis A virus 3C proteinase: Evaluation of mode of action. Bioorg Med Chem 2008; 16:5761-77. [PMID: 18407505 PMCID: PMC7125897 DOI: 10.1016/j.bmc.2008.03.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 03/24/2008] [Indexed: 11/23/2022]
Abstract
The related 3C and 3C-like proteinase (3C(pro) and 3CL(pro)) of picornaviruses and coronaviruses, respectively, are good drug targets. As part of an effort to generate broad-spectrum inhibitors of these enzymes, we screened a library of inhibitors based on a halopyridinyl ester from a previous study of the severe acute respiratory syndrome (SARS) 3CL proteinase against Hepatitis A virus (HAV) 3C(pro). Three of the compounds, which also had furan rings, inhibited the cleavage activity of HAV 3C(pro) with K(ic)s of 120-240nM. HPLC-based assays revealed that the inhibitors were slowly hydrolyzed by both HAV 3C(pro) and SARS 3CL(pro), confirming the identity of the expected products. Mass spectrometric analyses indicated that this hydrolysis proceeded via an acyl-enzyme intermediate. Modeling studies indicated that the halopyridinyl moiety of the inhibitor fits tightly into the S1-binding pocket, consistent with the lack of tolerance of the inhibitors to modification in this portion of the molecule. These compounds are among the most potent non-peptidic inhibitors reported to date against a 3C(pro).
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Affiliation(s)
- Carly Huitema
- Department of Microbiology, University of British Columbia, 2350 Health Science Mall, Vancouver, British Columbia, Canada V6T 1Z3
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36
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Furukawa K, Fujihara H. Microbial degradation of polychlorinated biphenyls: Biochemical and molecular features. J Biosci Bioeng 2008; 105:433-49. [PMID: 18558332 DOI: 10.1263/jbb.105.433] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 02/04/2008] [Indexed: 11/17/2022]
Affiliation(s)
- Kensuke Furukawa
- Depatment of Food and Bioscience, Faculty of Food and Nutrition, Beppu University, Beppu, Ohita 874-8501, Japan.
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37
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Kim SJ, Kweon O, Jones RC, Edmondson RD, Cerniglia CE. Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 2008; 19:859-81. [PMID: 18421421 DOI: 10.1007/s10532-008-9189-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 03/28/2008] [Indexed: 11/29/2022]
Abstract
Mycobacterium vanbaalenii PYR-1 is well known for its ability to degrade a wide range of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs). The genome of this bacterium has recently been sequenced, allowing us to gain insights into the molecular basis for the degradation of PAHs. The 6.5 Mb genome of PYR-1 contains 194 chromosomally encoded genes likely associated with degradation of aromatic compounds. The most distinctive feature of the genome is the presence of a 150 kb major catabolic region at positions 494 approximately 643 kb (region A), with an additional 31 kb region at positions 4,711 approximately 4,741 kb (region B), which is predicted to encode most enzymes for the degradation of PAHs. Region A has an atypical mosaic structure made of several gene clusters in which the genes for PAH degradation are complexly arranged and scattered around the clusters. Significant differences in the gene structure and organization as compared to other well-known aromatic hydrocarbon degraders including Pseudomonas and Burkholderia were revealed. Many identified genes were enriched with multiple paralogs showing a remarkable range of diversity, which could contribute to the wide variety of PAHs degraded by M. vanbaalenii PYR-1. The PYR-1 genome also revealed the presence of 28 genes involved in the TCA cycle. Based on the results, we proposed a pathway in which HMW PAHs are degraded into the beta-ketoadipate pathway through protocatechuate and then mineralized to CO2 via TCA cycle. We also identified 67 and 23 genes involved in PAH degradation and TCA cycle pathways, respectively, to be expressed as proteins.
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Affiliation(s)
- Seong-Jae Kim
- Division of Microbiology, National Center for Toxicological Research/U.S. FDA, Jefferson, AR 72079, USA
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38
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Khajamohiddin S, Repalle ER, Pinjari AB, Merrick M, Siddavattam D. Biodegradation of aromatic compounds: an overview of meta-fission product hydrolases. Crit Rev Microbiol 2008; 34:13-31. [PMID: 18259978 DOI: 10.1080/10408410701683656] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Meta fission product (MFP) hydrolases catalyze hydrolysis of a low reactive carbon-carbon bond found in meta-fission products, generated during biodegradation of various aromatic compounds. These enzymes belong to the alpha/beta hydrolase super family and show structural conservation despite having poor sequence similarity. MFP-hydrolases are substrate specific and studies have indicated that this substrate specificity plays a key role in the determination of the organism's ability to degrade a particular substrate. In this concise review of MFP-hydrolases we discuss their classification, biochemical properties, the molecular basis of their substrate specificity, their catalytic mechanism, and evolutionary significance.
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Affiliation(s)
- Syed Khajamohiddin
- Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Lambo AJ, Patel TR. Biodegradation of polychlorinated biphenyls in Aroclor 1232 and production of metabolites from 2,4,4'-trichlorobiphenyl at low temperature by psychrotolerant Hydrogenophaga sp. strain IA3-A. J Appl Microbiol 2008; 102:1318-29. [PMID: 17448167 DOI: 10.1111/j.1365-2672.2006.03268.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS To determine the extent and pattern of degradation of polychlorinated biphenyls (PCBs) in Aroclor 1232 at 5 degrees C by a psychrotolerant bacterium, and to confirm the formation of intermediates of PCB metabolism at low temperature using 2,4,4'-trichlorobiphenyl (2,4,4'-TCB). METHODS AND RESULTS 10 ppm of Aroclor 1232 or 100 micromol l(-1) 2,4,4'-TCB was incubated with biphenyl-grown cells at 5 degrees C or 30 degrees C for 48 or 72 h. Degradation of PCBs and the products of metabolism of 2,4,4'-TCB were confirmed by gas chromatography and mass spectrometry. Extents of degradation of many of the PCBs were similar at 5 degrees C and 30 degrees C. The extent of biodegradation of PCBs in Aroclor 1232 at 5 degrees C was dependent on chlorination pattern. The 14 chlorine-containing intermediates of 2,4,4'-TCB metabolism, which were detected, include several isomers of dihydrodiols, dihydroxy compounds and meta-cleavage compounds. CONCLUSIONS The bacterium will be useful for bioremediation of PCB-contaminated sites in cold climates; however, knowledge of the products of PCB metabolism is necessary, as they could be more toxic than the parent compounds. SIGNIFICANCE AND IMPACT OF THE STUDY Substantial degradation of some PCBs in Aroclor 1232 was demonstrated at low temperature within 48 h. The detection of several isomeric intermediates suggests that multiple pathways are used to transform PCBs in this strain. For the first time, formation of metabolic products from 2,4,4'-TCB at low temperature is confirmed.
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Affiliation(s)
- A J Lambo
- Department of Biology, Applied Microbiology and Biotechnology Laboratory, Memorial University of Newfoundland, St John's, NF, Canada.
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40
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Adebusoye SA, Ilori MO, Picardal FW, Amund OO. Metabolism of chlorinated biphenyls: use of 3,3'- and 3,5-dichlorobiphenyl as sole sources of carbon by natural species of Ralstonia and Pseudomonas. CHEMOSPHERE 2008; 70:656-63. [PMID: 17706746 DOI: 10.1016/j.chemosphere.2007.06.079] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 06/26/2007] [Accepted: 06/26/2007] [Indexed: 05/16/2023]
Abstract
Ralstonia sp. SA-3, Ralstonia sp. SA-4 and Pseudomonas sp. SA-6 are natural strains with a novel capacity to utilize meta-substituted dichlorobiphenyls (diCBs) hitherto not known to serve as a sole source of carbon and energy for polychlorobiphenyl-degraders. In growth experiments, axenic cultures of isolates grew logarithmically on 3,3'-diCB with generation times that ranged insignificantly (t-test, P>0.05) from 30.4 to 33.8 h. Both 3-chlorobenzoate (3-CBA) and chloride produced as metabolites were recovered in non-stoichiometric quantities. The release of chloride by the cultures lagged substantially, indicating that the initial dioxygenase attack preceded cleavage of carbon-chloride bonds and that chloride must have been released from the chlorinated hydroxypentadienoate. In the case of 3,5-diCB, SA-3 and SA-6 metabolised this substrate primarily to 3,5-CBA. The lack of chloride in the culture media coupled with stoichiometric recovery of 3,5-CBA suggests that growth by these strains occurred predominantly at the expense of the unsubstituted phenyl ring. The unique metabolic properties of these three aerobic isolates point to their potential usefulness as seeds for bioremediation of PCBs polluted environments without the need for repeated inoculation or supplementation by a primary growth substrate such as biphenyl.
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Affiliation(s)
- Sunday A Adebusoye
- Department of Botany and Microbiology, Faculty of Science, University of Lagos, Akoka, Yaba, Lagos, Nigeria.
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41
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Bhowmik S, Horsman GP, Bolin JT, Eltis LD. The molecular basis for inhibition of BphD, a C-C bond hydrolase involved in polychlorinated biphenyls degradation: large 3-substituents prevent tautomerization. J Biol Chem 2007; 282:36377-85. [PMID: 17932031 DOI: 10.1074/jbc.m707035200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The microbial degradation of polychlorinated biphenyls (PCBs) by the biphenyl catabolic (Bph) pathway is limited in part by the pathway's fourth enzyme, BphD. BphD catalyzes an unusual carbon-carbon bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA), in which the substrate is subject to histidine-mediated enol-keto tautomerization prior to hydrolysis. Chlorinated HOPDAs such as 3-Cl HOPDA inhibit BphD. Here we report that BphD preferentially hydrolyzed a series of 3-substituted HOPDAs in the order H>F>Cl>Me, suggesting that catalysis is affected by steric, not electronic, determinants. Transient state kinetic studies performed using wild-type BphD and the hydrolysis-defective S112A variant indicated that large 3-substituents inhibited His-265-catalyzed tautomerization by 5 orders of magnitude. Structural analyses of S112A.3-Cl HOPDA and S112A.3,10-diF HOPDA complexes revealed a non-productive binding mode in which the plane defined by the carbon atoms of the dienoate moiety of HOPDA is nearly orthogonal to that of the proposed keto tautomer observed in the S112A.HOPDA complex. Moreover, in the 3-Cl HOPDA complex, the 2-hydroxo group is moved by 3.6 A from its position near the catalytic His-265 to hydrogen bond with Arg-190 and access of His-265 is blocked by the 3-Cl substituent. Nonproductive binding may be stabilized by interactions involving the 3-substituent with non-polar side chains. Solvent molecules have poor access to C6 in the S112A.3-Cl HOPDA structure, more consistent with hydrolysis occurring via an acyl-enzyme than a gem-diol intermediate. These results provide insight into engineering BphD for PCB degradation.
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Affiliation(s)
- Shiva Bhowmik
- Purdue Cancer Center and Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-2054, USA
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42
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Nerdinger S, Kendall C, Cai X, Marchart R, Riebel P, Johnson MR, Yin CF, Hénaff N, Eltis LD, Snieckus V. Combined directed ortho Metalation/Suzuki-Miyaura cross-coupling strategies. Regiospecific synthesis of chlorodihydroxybiphenyls and polychlorinated biphenyls. J Org Chem 2007; 72:5960-7. [PMID: 17616228 DOI: 10.1021/jo062543i] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Directed ortho Metalation (DoM)/Suzuki-Miyaura cross-coupling strategy is applied for the regiospecific construction of all isomeric monochloro and selected dichloro and trichloro 2,3-dihydroxybiphenyls (DHBs). The combined methodology highlights iterative DoM processes, hindered Suzuki-Miyaura couplings, and advantages in diversity in approaches from commercial starting materials leading to provision of chloro-DHBs as single isomers in high purity and on a gram scale. The syntheis of several PCBs are also reported.
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Affiliation(s)
- S Nerdinger
- Sandoz GmbH, ATKU, B104/6/R703, Sandoz GmbH, Biochemiestrasse 10, A-6250 Kundl/Tirol, Austria
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43
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Horsman GP, Bhowmik S, Seah SYK, Kumar P, Bolin JT, Eltis LD. The Tautomeric Half-reaction of BphD, a C-C Bond Hydrolase. J Biol Chem 2007; 282:19894-904. [PMID: 17442675 DOI: 10.1074/jbc.m702237200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BphD of Burkholderia xenovorans LB400 catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to afford benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD). An enol-keto tautomerization has been proposed to precede hydrolysis via a gem-diol intermediate. The role of the canonical catalytic triad (Ser-112, His-265, Asp-237) in mediating these two half-reactions remains unclear. We previously reported that the BphD-catalyzed hydrolysis of HOPDA (lambda(max) is 434 nm for the free enolate) proceeds via an unidentified intermediate with a red-shifted absorption spectrum (lambda(max) is 492 nm) (Horsman, G. P., Ke, J., Dai, S., Seah, S. Y. K., Bolin, J. T., and Eltis, L. D. (2006) Biochemistry 45, 11071-11086). Here we demonstrate that the S112A variant generates and traps a similar intermediate (lambda(max) is 506 nm) with a similar rate, 1/tau approximately 500 s(-1). The crystal structure of the S112A:HOPDA complex at 1.8-A resolution identified this intermediate as the keto tautomer, (E)-2,6-dioxo-6-phenyl-hex-3-enoate. This keto tautomer did not accumulate in either the H265A or the S112A/H265A double variants, indicating that His-265 catalyzes tautomerization. Consistent with this role, the wild type and S112A enzymes catalyzed tautomerization of the product HPD, whereas H265A variants did not. This study thus identifies a keto intermediate, and demonstrates that the catalytic triad histidine catalyzes the tautomerization half-reaction, expanding the role of this residue from its purely hydrolytic function in other serine hydrolases. Finally, the S112A:HOPDA crystal structure is more consistent with hydrolysis occurring via an acyl-enzyme intermediate than a gem-diol intermediate as solvent molecules have poor access to C6, and the closest ordered water is 7 A away.
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Affiliation(s)
- Geoff P Horsman
- Department of Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Yang X, Liu X, Song L, Xie F, Zhang G, Qian S. Characterization and functional analysis of a novel gene cluster involved in biphenyl degradation in Rhodococcus sp. strain R04. J Appl Microbiol 2007; 103:2214-24. [DOI: 10.1111/j.1365-2672.2007.03461.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Gai Z, Yu B, Li L, Wang Y, Ma C, Feng J, Deng Z, Xu P. Cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading Sphingomonas sp. strain. Appl Environ Microbiol 2007; 73:2832-8. [PMID: 17337542 PMCID: PMC1892858 DOI: 10.1128/aem.02704-06] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 02/20/2007] [Indexed: 11/20/2022] Open
Abstract
A carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. The isolate, designated Sphingomonas sp. strain XLDN2-5, could utilize carbazole (CA) as the sole source of carbon, nitrogen, and energy. Washed cells of strain XLDN2-5 were shown to be capable of degrading dibenzofuran (DBF) and dibenzothiophene (DBT). Examination of metabolites suggested that XLDN2-5 degraded DBF to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently to salicylic acid through the angular dioxygenation pathway. In contrast to DBF, strain XLDN2-5 could transform DBT through the ring cleavage and sulfoxidation pathways. Sphingomonas sp. strain XLDN2-5 could cometabolically degrade DBF and DBT in the growing system using CA as a substrate. After 40 h of incubation, 90% of DBT was transformed, and CA and DBF were completely removed. These results suggested that strain XLDN2-5 might be useful in the bioremediation of environments contaminated by these compounds.
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Affiliation(s)
- Zhonghui Gai
- State Key Laboratory of Microbial Technology, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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46
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Seah SYK, Ke J, Denis G, Horsman GP, Fortin PD, Whiting CJ, Eltis LD. Characterization of a C-C bond hydrolase from Sphingomonas wittichii RW1 with novel specificities towards polychlorinated biphenyl metabolites. J Bacteriol 2007; 189:4038-45. [PMID: 17416660 PMCID: PMC1913379 DOI: 10.1128/jb.01950-06] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphingomonas wittichii RW1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins via meta cleavage. We used inverse PCR to amplify dxnB2, a gene encoding one of three meta-cleavage product (MCP) hydrolases identified in the organism that are homologues of BphD involved in biphenyl catabolism. Purified DxnB2 catalyzed the hydrolysis of 8-OH 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (HOPDA) approximately six times faster than for HOPDA at saturating substrate concentrations. Moreover, the specificity of DxnB2 for HOPDA (k(cat)/K(m) = 1.2 x 10(7) M(-1) s(-1)) was about half that of the BphDs of Burkholderia xenovorans LB400 and Rhodococcus globerulus P6, two potent polychlorinated biphenyl (PCB)-degrading strains. Interestingly, DxnB2 transformed 3-Cl and 4-OH HOPDAs, compounds that inhibit the BphDs and limit PCB degradation. DxnB2 had a higher specificity for 9-Cl HOPDA than for HOPDA but a lower specificity for 8-Cl HOPDA (k(cat)/K(m) = 1.7 x 10(6) M(-1) s(-1)), the chlorinated analog of 8-OH HOPDA produced during dibenzofuran catabolism. Phylogenetic analyses based on structure-guided sequence alignment revealed that DxnB2 belongs to a previously unrecognized class of MCP hydrolases, evolutionarily divergent from the BphDs although the physiological substrates of both enzyme types are HOPDAs. However, both classes of enzymes have mainly small hydrophobic residues lining the subsite that binds the C-6 phenyl of HOPDA, in contrast to the bulky hydrophobic residues (Phe106, Phe135, Trp150, and Phe197) found in the class II enzymes that prefer substrates possessing a C-6 alkyl. Thr196 and/or Asn203 appears to be an important determinant of specificity for DxnB2, potentially forming hydrogen bonds with the 8-OH substituent. This study demonstrates that the substrate specificities of evolutionarily divergent hydrolases may be useful for degrading mixtures of pollutants, such as PCBs.
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Lambo AJ, Patel TR. Temperature-dependent biotransformation of 2,4'-dichlorobiphenyl by psychrotolerant Hydrogenophaga strain IA3-A: higher temperatures prevent excess accumulation of problematic meta-cleavage products. Lett Appl Microbiol 2007; 44:447-53. [PMID: 17397486 DOI: 10.1111/j.1472-765x.2006.02070.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS The present work investigates the possibility that temperature could regulate the pattern of transformation of 2,4'-chlorobiphenyl (2,4'-CB) by psychrotolerant Hydrogenophaga sp. IA3-A. METHODS AND RESULTS Transformation of 2,4'-chlorobiphenyl to 2- and 4-chlorobenzoic acid (2- and 4-CBA), and meta-cleavage products by cells of strain IA3-A incubated at 10 degrees C, 25 degrees C, 37 degrees C or 45 degrees C were monitored by UV spectrometry, HPLC and GC-MS analyses. Cultures incubated at 10 degrees C, 25 degrees C or 37 degrees C produced low amounts of CBAs and excess levels of meta-cleavage products from 2,4'-CB. Cultures incubated at 45 degrees C transformed most of the degraded 2,4'-CB to CBAs and low level of meta-cleavage product. Culture extracts contained unusual varieties of isomeric hydroxylated metabolic products. CONCLUSIONS Efficient transformation of 2,4'-CB to CBAs was possible in cultures incubated at 45 degrees C. Evidence for the involvement of multiple pathways in the transformation of 2,4'-CB in strain IA3-A suggests that differential regulation of the pathways at different temperatures was likely responsible for the change in the pattern of transformation of 2,4'-CB in cultures incubated at 45 degrees C. SIGNIFICANCE AND IMPACT OF THE STUDY It may be possible to condition cells to transform chlorinated biphenyls more efficiently without accumulating excess level of toxic intermediates.
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Affiliation(s)
- A J Lambo
- Applied Microbiology and Biotechnology Laboratory, Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada.
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Cámara B, Seeger M, González M, Standfuss-Gabisch C, Kahl S, Hofer B. Generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls. Appl Environ Microbiol 2007; 73:2682-9. [PMID: 17322323 PMCID: PMC1855580 DOI: 10.1128/aem.02523-06] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, a sequence-based approach has been developed for the fast isolation and characterization of class II aryl-hydroxylating dioxygenase activities (S. Kahl and B. Hofer, Microbiology 149:1475-1481, 2003). It comprises the PCR amplification of segments of alpha subunit genes of unknown sequence that encode the catalytic center and their fusion with sequences of the bphA gene cluster of Burkholderia xenovorans LB400. One of the resulting chimeric enzymes, harboring the core segment of a dioxygenase from Pseudomonas sp. strain B4-Magdeburg, has now been characterized with respect to the oxidation of chlorobiphenyls (CBs). Its substrate and product specificities differed favorably from those of the parental dioxygenase of strain LB400. The hybrid possessed a higher regiospecificity and yielded less unproductive dioxygenations at meta and para carbons. It attacked ortho-, meta-, and para-chlorinated rings with comparable efficiencies. It gave significantly higher yields in ortho,meta-dioxygenation of recalcitrant congeners containing a doubly ortho-chlorinated ring. While the parental enzyme yielded mainly unproductive meta, para dioxygenation of 2,5,4'-CB, the hybrid predominantly converted this congener into an ortho,meta-dioxygenated product. The subsequent enzymes of the LB400 catabolic pathway were able to transform most of the metabolites formed by the novel dioxygenase, indicating that the substrate ranges of these biocatalysts are not adapted to that of their initial pathway enzyme. Some of the catabolites, however, were identified as problematic for further degradation. Our results demonstrate that the outlined approach can successfully be applied to obtain novel dioxygenase specificities that favorably complement or supplement known ones.
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Affiliation(s)
- Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotechnología Ambiental, Departamento de Química and Millennium Nucleus of Microbial Ecology and Environmental Microbiology and Biotechnology, Universidad Téchnica Federico Santa María, Valparaíso, Chile
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Adebusoye SA, Picardal FW, Ilori MO, Amund OO, Fuqua C, Grindle N. Growth on dichlorobiphenyls with chlorine substitution on each ring by bacteria isolated from contaminated African soils. Appl Microbiol Biotechnol 2007; 74:484-92. [PMID: 17047953 DOI: 10.1007/s00253-006-0651-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Revised: 08/28/2006] [Accepted: 09/04/2006] [Indexed: 10/24/2022]
Abstract
Until recently, it was generally believed that the presence of more than one chlorine substituent prevented chlorinated biphenyls from serving as a sole source of carbon and energy for aerobic bacteria. In this study, we report the isolation of three aerobic strains, identified as Enterobacter sp. SA-2, Ralstonia sp. SA-4, and Pseudomonas sp. SA-6 from Nigerian polluted soils, that were able to grow on a wide range of dichlorobiphenyls (diCBs). In addition to growing on all monochlorobiphenyls (monoCBs), the strains were all able to utilize 2,2'-, 2,4'-, and 2,3-diCB as a sole source of carbon and energy. With the exception of strain SA-2, growth was also sustainable on 3,3'-, and 3,5-diCB. Washed benzoate-grown cells were typically able to degrade 68 to 100% of the diCB (100 ppm) within 188 h, concomitant with a cell number increase of up to three orders-of-magnitude and elimination of varying amounts of chloride. In many cases, stoichiometric production of a chlorobenzoate (CBA) as a product was observed. During growth on 2,2'-, and 2,4'-diCB, organisms exclusively attacked an o-chlorinated ring resulting in the production of 2-CBA and 4-CBA, respectively. A gradual decline in the concentration of the latter was observed, which suggested that the product was being degraded further. In the case of 2,3-diCB, the unsubstituted ring was preferentially metabolized. Initial diCB degradation rates were greatest for 2,4'-diCB (11.2 +/- 0.91 to 30.3 +/- 7.8 nmol/min per 10(9) cells) and lowest for 2,2'-diCB (0.37 +/- 0.12 to 2.7 +/- 1.2 nmol/min per 10(9) cells).
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Affiliation(s)
- Sunday A Adebusoye
- Department of Botany and Microbiology, University of Lagos, Lagos, Nigeria
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Tocheva EI, Fortin PD, Eltis LD, Murphy MEP. Structures of Ternary Complexes of BphK, a Bacterial Glutathione S-Transferase That Reductively Dechlorinates Polychlorinated Biphenyl Metabolites. J Biol Chem 2006; 281:30933-40. [PMID: 16920719 DOI: 10.1074/jbc.m603125200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prokaryotic glutathione S-transferases are as diverse as their eukaryotic counterparts but are much less well characterized. BphK from Burkholderia xenovorans LB400 consumes two GSH molecules to reductively dehalogenate chlorinated 2-hydroxy-6-oxo-6-phenyl-2,4-dienoates (HOPDAs), inhibitory polychlorinated biphenyl metabolites. Crystallographic structures of two ternary complexes of BphK were solved to a resolution of 2.1A. In the BphK-GSH-HOPDA complex, GSH and HOPDA molecules occupy the G- and H-subsites, respectively. The thiol nucleophile of the GSH molecule is positioned for SN2 attack at carbon 3 of the bound HOPDA. The respective sulfur atoms of conserved Cys-10 and the bound GSH are within 3.0A, consistent with product release and the formation of a mixed disulfide intermediate. In the BphK-(GSH)2 complex, a GSH molecule occupies each of the two subsites. The three sulfur atoms of the two GSH molecules and Cys-10 are aligned suitably for a disulfide exchange reaction that would regenerate the resting enzyme and yield disulfide-linked GSH molecules. A second conserved residue, His-106, is adjacent to the thiols of Cys-10 and the GSH bound to the G-subsite and thus may stabilize a transition state in the disulfide exchange reaction. Overall, the structures support and elaborate a proposed dehalogenation mechanism for BphK and provide insight into the plasticity of the H-subsite.
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Affiliation(s)
- Elitza I Tocheva
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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