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Miller C, Huntoon D, Kaley N, Ogutu I, Fiedler AT, Bennett B, Liu D, Holz R. Role of second-sphere arginine residues in metal binding and metallocentre assembly in nitrile hydratases. J Inorg Biochem 2024; 256:112565. [PMID: 38677005 DOI: 10.1016/j.jinorgbio.2024.112565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024]
Abstract
Two conserved second-sphere βArg (R) residues in nitrile hydratases (NHase), that form hydrogen bonds with the catalytically essential sulfenic and sulfinic acid ligands, were mutated to Lys and Ala residues in the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) and the Fe-type NHase from Rhodococcus equi TG328-2 (ReNHase). Only five of the eight mutants (PtNHase βR52A, βR52K, βR157A, βR157K and ReNHase βR61A) were successfully expressed and purified. Apart from the PtNHase βR52A mutant that exhibited no detectable activity, the kcat values obtained for the PtNHase and ReNHase βR mutant enzymes were between 1.8 and 12.4 s-1 amounting to <1% of the kcat values observed for WT enzymes. The metal content of each mutant was also significantly decreased with occupancies ranging from ∼10 to ∼40%. UV-Vis spectra coupled with EPR data obtained on the ReNHase mutant enzyme, suggest a decrease in the Lewis acidity of the active site metal ion. X-ray crystal structures of the four PtNHase βR mutant enzymes confirmed the mutation and the low active site metal content, while also providing insight into the active site hydrogen bonding network. Finally, DFT calculations suggest that the equatorial sulfenic acid ligand, which has been shown to be the catalytic nucleophile, is protonated in the mutant enzyme. Taken together, these data confirm the necessity of the conserved second-sphere βR residues in the proposed subunit swapping process and post-translational modification of the α-subunit in the α activator complex, along with stabilizing the catalytic sulfenic acid in its anionic form.
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Affiliation(s)
- Callie Miller
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Delanie Huntoon
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Nicholas Kaley
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Irene Ogutu
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA
| | - Adam T Fiedler
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, WI 53233, USA
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA
| | - Richard Holz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO 80401, USA.
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2
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Vaccaro FA, Drennan CL. The role of nucleoside triphosphate hydrolase metallochaperones in making metalloenzymes. Metallomics 2022; 14:6575898. [PMID: 35485745 PMCID: PMC9164220 DOI: 10.1093/mtomcs/mfac030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022]
Abstract
Metalloenzymes catalyze a diverse set of challenging chemical reactions that are essential for life. These metalloenzymes rely on a wide range of metallocofactors, from single metal ions to complicated metallic clusters. Incorporation of metal ions and metallocofactors into apo-proteins often requires the assistance of proteins known as metallochaperones. Nucleoside triphosphate hydrolases (NTPases) are one important class of metallochaperones and are found widely distributed throughout the domains of life. These proteins use the binding and hydrolysis of nucleoside triphosphates, either adenosine triphosphate (ATP) or guanosine triphosphate (GTP), to carry out highly specific and regulated roles in the process of metalloenzyme maturation. Here, we review recent literature on NTPase metallochaperones and describe the current mechanistic proposals and available structural data. By using representative examples from each type of NTPase, we also illustrate the challenges in studying these complicated systems. We highlight open questions in the field and suggest future directions. This minireview is part of a special collection of articles in memory of Professor Deborah Zamble, a leader in the field of nickel biochemistry.
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Affiliation(s)
- Francesca A Vaccaro
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
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3
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Ma D, Cheng Z, Peplowski L, Han L, Xia Y, Hou X, Guo J, Yin D, Rao Y, Zhou Z. Insight into the broadened substrate scope of nitrile hydratase by static and dynamic structure analysis. Chem Sci 2022; 13:8417-8428. [PMID: 35919716 PMCID: PMC9297474 DOI: 10.1039/d2sc02319a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/28/2022] [Indexed: 11/21/2022] Open
Abstract
Mutations of two gating residues at the substrate access tunnel entrance direct the substrate scope of NHases.
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Affiliation(s)
- Dong Ma
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiaodong Hou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Junling Guo
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Dejing Yin
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yijian Rao
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao, Jiangsu, China
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4
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Edmonds KA, Jordan MR, Giedroc DP. COG0523 proteins: a functionally diverse family of transition metal-regulated G3E P-loop GTP hydrolases from bacteria to man. Metallomics 2021; 13:6327566. [PMID: 34302342 PMCID: PMC8360895 DOI: 10.1093/mtomcs/mfab046] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 01/13/2023]
Abstract
Transition metal homeostasis ensures that cells and organisms obtain sufficient metal to meet cellular demand while dispensing with any excess so as to avoid toxicity. In bacteria, zinc restriction induces the expression of one or more Zur (zinc-uptake repressor)-regulated Cluster of Orthologous Groups (COG) COG0523 proteins. COG0523 proteins encompass a poorly understood sub-family of G3E P-loop small GTPases, others of which are known to function as metallochaperones in the maturation of cobalamin (CoII) and NiII cofactor-containing metalloenzymes. Here, we use genomic enzymology tools to functionally analyse over 80 000 sequences that are evolutionarily related to Acinetobacter baumannii ZigA (Zur-inducible GTPase), a COG0523 protein and candidate zinc metallochaperone. These sequences segregate into distinct sequence similarity network (SSN) clusters, exemplified by the ZnII-Zur-regulated and FeIII-nitrile hydratase activator CxCC (C, Cys; X, any amino acid)-containing COG0523 proteins (SSN cluster 1), NiII-UreG (clusters 2, 8), CoII-CobW (cluster 4), and NiII-HypB (cluster 5). A total of five large clusters that comprise ≈ 25% of all sequences, including cluster 3 which harbors the only structurally characterized COG0523 protein, Escherichia coli YjiA, and many uncharacterized eukaryotic COG0523 proteins. We also establish that mycobacterial-specific protein Y (Mpy) recruitment factor (Mrf), which promotes ribosome hibernation in actinomycetes under conditions of ZnII starvation, segregates into a fifth SSN cluster (cluster 17). Mrf is a COG0523 paralog that lacks all GTP-binding determinants as well as the ZnII-coordinating Cys found in CxCC-containing COG0523 proteins. On the basis of this analysis, we discuss new perspectives on the COG0523 proteins as cellular reporters of widespread nutrient stress induced by ZnII limitation.
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Affiliation(s)
- Katherine A Edmonds
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Matthew R Jordan
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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5
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Shen JD, Cai X, Wang M, Liu ZQ, Zheng YG. Proposed mechanism for post-translational self-modification of Co-NHase based on Co 2+ diffusion limitation. Biotechnol J 2021; 16:e2100103. [PMID: 34363653 DOI: 10.1002/biot.202100103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/14/2021] [Accepted: 07/27/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Nitrile hydratase (NHase), was an excellent biocatalyst for the synthesis of amide compounds. NHase was typical heterodimeric metalloprotein, required of the assistance of activator for active expressions. In this work, we found a special Co-NHase HBA from Caldalkalibacillus thermarum, which had the ability of post-translational self-modification and could incorporate Co2+ into the catalytic center in the absence of activator. METHOD AND RESULTS We simulated the movement of Co2+ in silico and established a hypothetical model to predict the Co2+ incorporation efficiency (XCo ) of NHases. According to the simulation results, NHase mutants with different positive charge distribution were constructed. Compared with wild-type, the Co2+ incorporation efficiency of K1 (M10K) was increased by 2.1-fold from 0.36 to 0.76, and the specific activity was increased by 3.2-fold from 136.3 to 432.0 U/mg, while mutant K1H1 (M10K, D11H) and K2H2 (M10K, D11H, E20K, N21H) lost the ability of post-translation self-modification. CONCLUSIONS AND IMPLICATIONS The interactions of positively charged residues near the catalytic center, such as lysine with strong electrostatic repulsive interaction, arginine with weak electrostatic repulsive interaction and histidine with metal affinity, could limit the free diffusion of Co2+ in NHase and affect the efficiency of post-translational self-modification. This work also provided an effective strategy for protein engineering of NHases and other metalloenzymes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ji-Dong Shen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ming Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
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6
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Lankathilaka KPW, Bennett B, Holz RC. The Fe-type nitrile hydratase from Rhodococcus equi TG328-2 forms an alpha-activator protein complex. J Biol Inorg Chem 2020; 25:903-911. [DOI: 10.1007/s00775-020-01806-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
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7
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Guo L, Cheng X, Jiang HY, Dai YJ. Maturation Mechanism of Nitrile Hydratase From Streptomyces canus CGMCC 13662 and Its Structural Character. Front Microbiol 2020; 11:1419. [PMID: 32670250 PMCID: PMC7329996 DOI: 10.3389/fmicb.2020.01419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/02/2020] [Indexed: 11/13/2022] Open
Abstract
Nitrile hydratases have received significant interest both in the large-scale industrial production of acrylamide and nicotinamide, and the remediation of environmental contamination with nitrile-containing pollutants. Almost all known nitrile hydratases include an α-subunit (AnhA) and β-subunit (AnhB), and a specific activator protein is crucial for their maturation and catalytic activity. Many studies exist on nitrile hydratase characteristics and applications, but few have reported their metal insertion and post-translational maturation mechanism. In this study, we investigated the cobalt insertion and maturation mechanism of nitrile hydratase from Streptomyces canus CGMCC 13662 (ScNHase) bearing three subunits (AnhD, AnhE, and AnhA). ScNHase subunits were purified, and the cobalt content and nitrile hydratase activity of the ScNHase subunits were detected. We discovered that cobalt could insert into the cobalt-free AnhA of ScNHase in the absence of activator protein under reduction agent DL-dithiothreitol (DTT) environment. AnhD not only performed the function of AnhB of NHase, but also acted as a metal ion chaperone and self-subunit swapping chaperone, while AnhE did not act as similar performance. A cobalt direct-insertion under reduction condition coordinated self-subunit swapping mechanism is responsible for ScNHase post-translational maturation. Molecular docking of ScNHase and substrates suggested that the substrate specificity of ScNHase was correlated with its structure. ScNHase had a weak hydrophobic interaction with IAN through protein-ligand interaction analysis and, therefore, had no affinity with indole-3-acetonitrile (IAN). The post-translational maturation mechanism and structure characteristics of ScNHase could help guide research on the environmental remediation of nitrile-containing waste contamination and three-subunit nitrile hydratase.
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Affiliation(s)
- Ling Guo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Xi Cheng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Huo-Yong Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Yi-Jun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China
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8
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Cheng Z, Xia Y, Zhou Z. Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications. Front Bioeng Biotechnol 2020; 8:352. [PMID: 32391348 PMCID: PMC7193024 DOI: 10.3389/fbioe.2020.00352] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.
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Affiliation(s)
| | | | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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9
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Lankathilaka KPW, Stein N, Holz RC, Bennett B. Cellular maturation of an iron-type nitrile hydratase interrogated using EPR spectroscopy. J Biol Inorg Chem 2019; 24:1105-1113. [PMID: 31549242 DOI: 10.1007/s00775-019-01720-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/13/2019] [Indexed: 11/24/2022]
Abstract
Nitrile hydratase (NHase) is a non-heme iron-containing enzyme that has applications in commodity chemical synthesis, pharmaceutical intermediate synthesis, and reclamation of nitrile-(bromoxynil) contaminated land. Mechanistic study of the enzyme has been complicated by the expression of multiple overlapping Fe(III) EPR signals. The individual signals were recently assigned to distinct chemical species with the assistance of DFT calculations. Here, the origins and evolution of the EPR signals from cells overexpressing the enzyme were investigated, with the aims of optimizing the preparation of homogeneous samples of NHase for study and investigating the application of E. coli overexpressing the enzyme for "green" chemistry. It was revealed that nitrile hydratase forms two sets of inactive complexes in vivo over time. One is due to reversible complexation with endogenous carboxylic acids, while the second is due to irreversibly inactivating oxidation of an essential cysteine sulfenic acid. It was shown that the homogeneity of preparations can be improved by employing an anaerobic protocol. The ability of the substrates acrylonitrile and acetonitrile to be taken up by cells and hydrated to the corresponding amides by NHase was demonstrated by EPR identification of the product complexes of NHase in intact cells. The inhibitors butyric acid and butane boronic acid were also taken up by E. coli and formed complexes with NHase in vivo, indicating that care must be taken with environmental variables when attempting microbially assisted synthesis and reclamation.
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Affiliation(s)
| | - Natalia Stein
- Department of Physics, Marquette University, 1420 W. Clybourn St., Milwaukee, WI, 53233, USA
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI, 53226, USA
| | - Richard C Holz
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI, 53201-1881, USA.
- Department of Chemistry, Colorado School of Mines, Golden, CO, 80401, USA.
| | - Brian Bennett
- Department of Physics, Marquette University, 1420 W. Clybourn St., Milwaukee, WI, 53233, USA.
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10
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Advances in cloning, structural and bioremediation aspects of nitrile hydratases. Mol Biol Rep 2019; 46:4661-4673. [DOI: 10.1007/s11033-019-04811-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/10/2019] [Indexed: 01/09/2023]
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11
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Guo L, Fang WW, Guo LL, Yao CF, Zhao YX, Ge F, Dai YJ. Biodegradation of the Neonicotinoid Insecticide Acetamiprid by Actinomycetes Streptomyces canus CGMCC 13662 and Characterization of the Novel Nitrile Hydratase Involved. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5922-5931. [PMID: 31067049 DOI: 10.1021/acs.jafc.8b06513] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Neonicotinoid insecticide pollution in soil and water poses serious environmental risks. Microbial biodegradation is an important neonicotinoid insecticide degradation pathway in the environment. In this study, 70.0% of the acetamiprid in a 200 mg/L solution was degraded by actinomycetes Streptomyces canus CGMCC 13662 (isolated from soil) in 48 h, and the acetamiprid degradation half-life was 27.7 h. Acetamiprid was degraded to IM-1-2 (( E)-1-(1-(((6-chloropyridin-3-yl)methyl)(methyl) amino)ethylidene)urea) through hydrolysis of the cyanoimine moiety. Gene cloning and overexpression indicated that a novel nitrile hydratase with three unusual subunits (AnhD, AnhE, and AnhA) without accessory protein mediated IM-1-2 formation. The purified nitrile hydratase responsible for degrading acetamiprid had a Km of 5.85 mmol/L and a Vmax of 15.99 U/mg. A homology model suggested that AnhD-Glu56 and AnhE-His21 play important roles in the catalytic efficiency of the nitrile hydratase. S. canus CGMCC 13662 could be used to remediate environments contaminated with acetamiprid.
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Affiliation(s)
- Ling Guo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science , Nanjing Normal University , Nanjing 210023 , People's Republic of China
| | - Wen-Wan Fang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science , Nanjing Normal University , Nanjing 210023 , People's Republic of China
| | - Lei-Lei Guo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science , Nanjing Normal University , Nanjing 210023 , People's Republic of China
| | - Chuan-Fei Yao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science , Nanjing Normal University , Nanjing 210023 , People's Republic of China
| | - Yun-Xiu Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science , Nanjing Normal University , Nanjing 210023 , People's Republic of China
| | - Feng Ge
- Ministry of Environmental Protection , Nanjing Institute of Environmental Sciences , Nanjing 210042 , People's Republic of China
| | - Yi-Jun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science , Nanjing Normal University , Nanjing 210023 , People's Republic of China
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12
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Lavrov KV, Shemyakina AO, Grechishnikova EG, Novikov AD, Kalinina TI, Yanenko AS. In vivo metal selectivity of metal-dependent biosynthesis of cobalt-type nitrile hydratase in Rhodococcus bacteria: a new look at the nitrile hydratase maturation mechanism? Metallomics 2019; 11:1162-1171. [DOI: 10.1039/c8mt00129d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Metal-dependent cblA-mediated mechanism of transcription regulation of NHase could not discriminate Ni and Co, but mechanism of NHase enzyme maturation could do this.
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Affiliation(s)
- Konstantin V. Lavrov
- Laboratory of Molecular Biotechnology
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”
- Moscow
- Russia
| | - Anna O. Shemyakina
- Laboratory of Molecular Biotechnology
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”
- Moscow
- Russia
| | - Elena G. Grechishnikova
- Laboratory of Molecular Biotechnology
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”
- Moscow
- Russia
| | - Andrey D. Novikov
- Laboratory of Molecular Biotechnology
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”
- Moscow
- Russia
| | - Tatyana I. Kalinina
- Laboratory of Molecular Biotechnology
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”
- Moscow
- Russia
| | - Alexander S. Yanenko
- Laboratory of Molecular Biotechnology
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”
- Moscow
- Russia
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13
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Yang X, Bennett B, Holz RC. Analyzing the function of the insert region found between the α and β-subunits in the eukaryotic nitrile hydratase from Monosiga brevicollis. Arch Biochem Biophys 2018; 657:1-7. [PMID: 30205086 PMCID: PMC6201762 DOI: 10.1016/j.abb.2018.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
Abstract
The functional roles of the (His)17 region and an insert region in the eukaryotic nitrile hydratase (NHase, EC 4.2.1.84) from Monosiga brevicollis (MbNHase), were examined. Two deletion mutants, MbNHaseΔ238-257 and MbNHaseΔ219-272, were prepared in which the (His)17 sequence and the entire insert region were removed. Each of these MbNHase enzymes provided an α2β2 heterotetramer, identical to that observed for prokaryotic NHases and contains their full complement of cobalt ions. Deletion of the (His)17 motif provides an MbNHase enzyme that is ∼55% as active as the WT enzyme when expressed in the absence of the Co-type activator (ε) protein from Pseudonocardia thermophila JCM 3095 (PtNHaseact) but ∼28% more active when expressed in the presence of PtNHaseact. MbNHaseΔ219-272 exhibits ∼55% and ∼89% of WT activity, respectively, when expressed in the absence or presence of PtNHaseact. Proteolytic cleavage of MbNHase provides an α2β2 heterotetramer that is modestly more active compared to WT MbNHase (kcat = 163 ± 4 vs 131 ± 3 s-1). Combination of these data establish that neither the (His)17 nor the insert region are required for metallocentre assembly and maturation, suggesting that Co-type eukaryotic NHases utilize a different mechanism for metal ion incorporation and post-translational activation compared to prokaryotic NHases.
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Affiliation(s)
- Xinhang Yang
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI, 53201, USA
| | - Brian Bennett
- Department of Physics, Marquette University, PO Box 1881, Milwaukee, WI, 53201-1881, USA
| | - Richard C Holz
- Department of Chemistry, Marquette University, PO Box 1881, Milwaukee, WI, 53201, USA.
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Lavrov KV, Shemyakina AO, Grechishnikova EG, Novikov AD, Derbikov DD, Kalinina TI, Yanenko AS. New cblA gene participates in regulation of cobalt-dependent transcription of nitrile hydratase genes in Rhodococcus rhodochrous. Res Microbiol 2018; 169:227-236. [DOI: 10.1016/j.resmic.2018.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/10/2018] [Accepted: 03/13/2018] [Indexed: 11/29/2022]
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15
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Prejanò M, Marino T, Rizzuto C, Madrid Madrid JC, Russo N, Toscano M. Reaction Mechanism of Low-Spin Iron(III)- and Cobalt(III)-Containing Nitrile Hydratases: A Quantum Mechanics Investigation. Inorg Chem 2017; 56:13390-13400. [DOI: 10.1021/acs.inorgchem.7b02121] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mario Prejanò
- Department of Chemistry
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Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Tiziana Marino
- Department of Chemistry
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Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Carmen Rizzuto
- Department of Chemistry
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Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Josè Carlos Madrid Madrid
- Department of Chemistry
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Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Nino Russo
- Department of Chemistry
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Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Marirosa Toscano
- Department of Chemistry
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Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
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Abstract
Nitrile hydratase (NHase) from Rhodococcus rhodochrous J1 is widely used for industrial production of acrylamide and nicotinamide. However, the two types of NHases (L-NHase and H-NHase) from R. rhodochrous J1 were only slightly expressed in E. coli by routine methods, which limits the comprehensive and systematic characterization of the enzyme properties. We successfully expressed the two types of recombinant NHases in E. coli by codon-optimization, engineering of Ribosome Binding Site (RBS) and spacer sequences. The specific activity of the purified L-NHase and H-NHase were 400 U/mg and 234 U/mg, respectively. The molecular mass of L-NHase and H-NHase was identified to be 94 kDa and 504 kDa, respectively, indicating that the quaternary structure of the two types of NHases was the same as those in R. rhodochrous J1. H-NHase exhibited higher substrate and product tolerance than L-NHase. Moreover, higher activity and shorter culture time were achieved in recombinant E. coli, and the whole cell catalyst of recombinant E. coli harboring H-NHase has equivalent efficiency in tolerance to the high-concentration product relative to that in R. rhodochrous J1. These results indicate that biotransformation of nitrile by R. rhodochrous J1 represents a potential alternative to NHase-producing E. coli.
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Pei X, Yang Z, Wang A, Yang L, Wu J. Identification and functional analysis of the activator gene involved in the biosynthesis of Co-type nitrile hydratase from Aurantimonas manganoxydans. J Biotechnol 2017; 251:38-46. [DOI: 10.1016/j.jbiotec.2017.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/05/2017] [Accepted: 03/14/2017] [Indexed: 11/15/2022]
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Zhang H, Li M, Li J, Wang G, Li F, Xiong M. Chaperone-assisted maturation of the recombinant Fe-type nitrile hydratase is insufficient for fully active expression in Escherichia coli. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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A cobalt-containing eukaryotic nitrile hydratase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:107-112. [DOI: 10.1016/j.bbapap.2016.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/17/2016] [Accepted: 09/22/2016] [Indexed: 11/18/2022]
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The iron-type nitrile hydratase activator protein is a GTPase. Biochem J 2016; 474:247-258. [PMID: 27807009 DOI: 10.1042/bcj20160884] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/27/2016] [Accepted: 11/02/2016] [Indexed: 01/01/2023]
Abstract
The Fe-type nitrile hydratase activator protein from Rhodococcus equi TG328-2 (ReNHase TG328-2) was successfully expressed and purified. Sequence analysis and homology modeling suggest that it is a G3E P-loop guanosine triphosphatase (GTPase) within the COG0523 subfamily. Kinetic studies revealed that the Fe-type activator protein is capable of hydrolyzing GTP to GDP with a kcat value of 1.2 × 10-3 s-1 and a Km value of 40 μM in the presence of 5 mM MgCl2 in 50 mM 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid at a pH of 8.0. The addition of divalent metal ions, such as Co(II), which binds to the ReNHase TG328-2 activator protein with a Kd of 2.9 μM, accelerated the rate of GTP hydrolysis, suggesting that GTP hydrolysis is potentially connected to the proposed metal chaperone function of the ReNHase TG328-2 activator protein. Circular dichroism data reveal a significant conformational change upon the addition of GTP, which may be linked to the interconnectivity of the cofactor binding sites, resulting in an activator protein that can be recognized and can bind to the NHase α-subunit. A combination of these data establishes, for the first time, that the ReNHase TG328-2 activator protein falls into the COG0523 subfamily of G3E P-loop GTPases, many of which play a role in metal homeostasis processes.
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Activity Enhancement Based on the Chemical Equilibrium of Multiple-Subunit Nitrile Hydratase from Bordetella petrii. Appl Biochem Biotechnol 2016; 180:3-9. [PMID: 27075457 DOI: 10.1007/s12010-016-2079-7] [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: 12/17/2015] [Accepted: 04/06/2016] [Indexed: 10/22/2022]
Abstract
The maturation mechanism of nitrile hydratase (NHase) of Pseudomonas putida NRRL-18668 was discovered and named as "self-subunit swapping." Since the NHase of Bordetella petrii DSM 12804 is similar to that of P. putida, the NHase maturation of B. petrii is proposed to be the same as that of P. putida. However, there is no further information on the application of NHase according to these findings. We successfully rapidly purified NHase and its activator through affinity his tag, and found that the cell extracts of NHase possessed multiple types of protein ingredients including α, β, α2β2, and α(P14K)2 who were in a state of chemical equilibrium. Furthermore, the activity was significantly enhanced through adding extra α(P14K)2 to the cell extracts of NHase according to the chemical equilibrium. Our findings are useful for the activity enhancement of multiple-subunit enzyme and for the first time significantly increased the NHase activity according to the chemical equilibrium.
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Sun W, Zhu L, Chen X, Chen P, Yang L, Ding W, Zhou Z, Liu Y. Successful expression of the Bordetella petrii nitrile hydratase activator P14K and the unnecessary role of Ser115. BMC Biotechnol 2016; 16:21. [PMID: 26897378 PMCID: PMC4761151 DOI: 10.1186/s12896-016-0252-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 02/15/2016] [Indexed: 11/28/2022] Open
Abstract
Background The activator P14K is necessary for the activation of nitrile hydratase (NHase). However, it is hard to be expressed heterogeneously. Although an N-terminal strep tagged P14K could be successfully expressed from Pseudomonas putida, various strategies for the over-expression of P14K are needed to facilitate further application of NHase. Results P14K was successfully expressed through fusing a his tag (his-P14K), and was over-expressed through fusing a gst tag (gst-P14K) at its N-terminus in the NHase of Bordetella petrii DSM 12804. The stability of gst-P14K was demonstrated to be higher than that of the his-P14K. In addition, the Ser115 in the characteristic motif CXLC-Ser115-C of the active center of NHase was found to be unnecessary for NHase maturation. Conclusions Our results are not only useful for the NHase activator expression and the understanding of the role of Ser115 during NHase activation, but also helpful for other proteins with difficulty in heterologous expression.
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Affiliation(s)
- Weifeng Sun
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Longbao Zhu
- School of Biochemical Engineering, Anhui Polytechnic University, Anhui, 241000, China.
| | - Xianggui Chen
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Ping Chen
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Lingling Yang
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Wenwu Ding
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Yi Liu
- Key Laboratory of Food and Biotechnology, School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
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Xia Y, Cui W, Liu Z, Zhou L, Cui Y, Kobayashi M, Zhou Z. Construction of a subunit-fusion nitrile hydratase and discovery of an innovative metal ion transfer pattern. Sci Rep 2016; 6:19183. [PMID: 26755342 PMCID: PMC4709657 DOI: 10.1038/srep19183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 12/07/2015] [Indexed: 01/10/2023] Open
Abstract
Metallochaperones are metal-binding proteins designed to deliver the appropriate metal to a target protein. The metal is usually transferred between different proteins. In this study, we discovered that metal was transferred between the same subunit of a mutant nitrile hydratase (NHase). Various “activator proteins” mediate the trafficking of metal ions into NHases. We constructed fusion NHases by fusing the β- and α-subunits and/or the “activator proteins” of the NHase from Pseudomonas putida. The fusion NHases exhibited higher thermostability and tolerance to high concentrations of the product amide. The mechanism of the cobalt incorporation changed from a self-subunit swapping pattern to an apoprotein-specific molecular chaperone pattern in vivo and a metallochaperone pattern in vitro. Notably, the cobalt transfer occurred between the same α-subunit in the metallochaperone pattern. These results not only demonstrated the superiority of fusion-type NHases, but also revealed an innovative metal ion transfer pattern in metalloprotein biosynthesis.
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Affiliation(s)
- Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Li Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Youtian Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Gong JS, Shi JS, Lu ZM, Li H, Zhou ZM, Xu ZH. Nitrile-converting enzymes as a tool to improve biocatalysis in organic synthesis: recent insights and promises. Crit Rev Biotechnol 2015; 37:69-81. [DOI: 10.3109/07388551.2015.1120704] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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25
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Enhancement of thermo-stability and product tolerance of Pseudomonas putida nitrile hydratase by fusing with self-assembling peptide. J Biosci Bioeng 2014; 118:249-52. [DOI: 10.1016/j.jbiosc.2014.02.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 10/25/2022]
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26
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Chivers PT. Cobalt and Nickel. BINDING, TRANSPORT AND STORAGE OF METAL IONS IN BIOLOGICAL CELLS 2014. [DOI: 10.1039/9781849739979-00381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cobalt and nickel play key roles in biological systems as cofactors in a small number of important enzymes. The majority of these are found in microbes. Evidence for direct roles for Ni(II) and Co(II) enzymes in higher organisms is limited, with the exception of the well-known requirement for the cobalt-containing vitamin B12 cofactor and the Ni-dependent urease in plants. Nonetheless, nickel in particular plays a key role in human health because of its essential role in microbes that inhabit various growth niches within the body. These roles can be beneficial, as can be seen with the anaerobic production and consumption of H2 in the digestive tract by bacteria and archaea that results in increased yields of short-chain fatty acids. In other cases, nickel has an established role in the establishment of pathogenic infection (Helicobacter pylori urease and colonization of the stomach). The synthesis of Co- and Ni-containing enzymes requires metal import from the extracellular milieu followed by the targeting of these metals to the appropriate protein and enzymes involved in metallocluster or cofactor biosynthesis. These metals are toxic in excess so their levels must be regulated carefully. This complex pathway of metalloenzyme synthesis and intracellular homeostasis requires proteins that can specifically recognize these metals in a hierarchical manner. This chapter focuses on quantitative and structural details of the cobalt and nickel binding sites in transport, trafficking and regulatory proteins involved in cobalt and nickel metabolism in microbes.
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Affiliation(s)
- Peter T. Chivers
- Department of Chemistry, School of Biological and Biomedical Sciences, and Biophysical Sciences Institute, Durham University Durham UK
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27
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Liu Y, Cui W, Liu Z, Cui Y, Xia Y, Kobayashi M, Zhou Z. Effect of flexibility and positive charge of the C-terminal domain on the activator P14K function for nitrile hydratase inPseudomonas putida. FEMS Microbiol Lett 2014; 352:38-44. [DOI: 10.1111/1574-6968.12376] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 12/31/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yi Liu
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
| | - Youtian Cui
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
| | - Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry; The University of Tsukuba; Tsukuba Ibaraki Japan
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology; School of Biotechnology; Jiangnan University; Wuxi China
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Liu Y, Cui W, Fang Y, Yu Y, Cui Y, Xia Y, Kobayashi M, Zhou Z. Strategy for successful expression of the Pseudomonas putida nitrile hydratase activator P14K in Escherichia coli. BMC Biotechnol 2013; 13:48. [PMID: 23731949 PMCID: PMC3680314 DOI: 10.1186/1472-6750-13-48] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/30/2013] [Indexed: 11/10/2022] Open
Abstract
Background Activators of Nitrile hydratase (NHase) are essential for functional NHase biosynthesis. However, the activator P14K in P. putida is difficult to heterogeneously express, which retards the clarification of the mechanism of P14K involved in the maturation of NHase. Although a strep tag containing P14K (strep-P14K) was over-expressed, its low expression level and low stability affect the further analysis. Results We successfully expressed P14K through genetic modifications according to N-end rule and analyzed the mechanism for its difficult expression. We found that mutation of the second N-terminal amino-acid of the protein from lysine to alanine or truncating the N-terminal 16 amino-acid sequence resulted in successful expression of P14K. Moreover, fusion of a pelB leader and strep tag together (pelB-strep-P14K) at the N-terminus increased P14K expression. In addition, the pelB-strep-P14K was more stable than the strep-P14K. Conclusions Our results are not only useful for clarification of the role of P14K involved in the NHase maturation, but also helpful for heterologous expression of other difficult expression proteins.
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Affiliation(s)
- Yi Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Peoples Republic of China
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Dutta A, Flores M, Roy S, Schmitt JC, Hamilton GA, Hartnett HE, Shearer J, Jones AK. Sequential oxidations of thiolates and the cobalt metallocenter in a synthetic metallopeptide: implications for the biosynthesis of nitrile hydratase. Inorg Chem 2013; 52:5236-45. [PMID: 23587023 PMCID: PMC4046696 DOI: 10.1021/ic400171z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cobalt nitrile hydratases (Co-NHase) contain a catalytic cobalt(III) ion coordinated in an N2S3 first coordination sphere composed of two amidate nitrogens and three cysteine-derived sulfur donors: a thiolate (-SR), a sulfenate (-S(R)O(-)), and a sulfinate (-S(R)O2(-)). The sequence of biosynthetic reactions that leads to the post-translational oxidations of the metal and the sulfur ligands is unknown, but the process is believed to be initiated directly by oxygen. Herein we utilize cobalt bound in an N2S2 first coordination sphere by a seven amino acid peptide known as SODA (ACDLPCG) to model this oxidation process. Upon exposure to oxygen, Co-SODA is oxidized in two steps. In the first fast step (seconds), magnetic susceptibility measurements demonstrated that the metallocenter remains paramagnetic, that is, Co(2+), and sulfur K-edge X-ray absorption spectroscopy (XAS) is used to show that one of the thiolates is oxidized to sulfinate. In a second process on a longer time scale (hours), magnetic susceptibility measurements and Co K-edge XAS show that the metal is oxidized to Co(3+). Unlike other model complexes, additional slow oxidation of the second thiolate in Co-SODA is not observed, and a catalytically active complex is never formed. The likely reason is the absence of the axial thiolate ligand. In essence, the reactivity of Co-SODA can be described as between previously described models which either quickly convert to final product or are stable in air, and it offers a first glimpse into a possible oxidation pathway for nitrile hydratase biosynthesis.
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Affiliation(s)
- Arnab Dutta
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, AZ 85287
| | - Marco Flores
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
| | - Souvik Roy
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, AZ 85287
| | | | | | - Hilairy E. Hartnett
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- School of Earth and Space Exploration; Arizona State University, Tempe, AZ 85287
| | - Jason Shearer
- Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Anne K. Jones
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, AZ 85287
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Liu Y, Cui W, Xia Y, Cui Y, Kobayashi M, Zhou Z. Self-subunit swapping occurs in another gene type of cobalt nitrile hydratase. PLoS One 2012; 7:e50829. [PMID: 23226397 PMCID: PMC3511329 DOI: 10.1371/journal.pone.0050829] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 10/25/2012] [Indexed: 11/30/2022] Open
Abstract
Self-subunit swapping is one of the post-translational maturation of the cobalt-containing nitrile hydratase (Co-NHase) family of enzymes. All of these NHases possess a gene organization of <β-subunit> <α-subunit> <activator protein>, which allows the activator protein to easily form a mediatory complex with the α-subunit of the NHase after translation. Here, we discovered that the incorporation of cobalt into another type of Co-NHase, with a gene organization of <α-subunit> <β-subunit> <activator protein>, was also dependent on self-subunit swapping. We successfully isolated a recombinant NHase activator protein (P14K) of Pseudomonas putida NRRL-18668 by adding a Strep-tag N-terminal to the P14K gene. P14K was found to form a complex [α(StrepP14K)2] with the α-subunit of the NHase. The incorporation of cobalt into the NHase of P. putida was confirmed to be dependent on the α-subunit substitution between the cobalt-containing α(StrepP14K)2 and the cobalt-free NHase. Cobalt was inserted into cobalt-free α(StrepP14K)2 but not into cobalt-free NHase, suggesting that P14K functions not only as a self-subunit swapping chaperone but also as a metallochaperone. In addition, NHase from P. putida was also expressed by a mutant gene that was designed with a <β-subunit> <α-subunit> <P14K> order. Our findings expand the general features of self-subunit swapping maturation.
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Affiliation(s)
- Yi Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Youtian Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
- * E-mail: (MK); (ZMZ)
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- * E-mail: (MK); (ZMZ)
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Engineering of Rhodococcus cell catalysts for tolerance improvement by sigma factor mutation and active plasmid partition. ACTA ACUST UNITED AC 2012; 39:1421-30. [DOI: 10.1007/s10295-012-1146-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022]
Abstract
Abstract
Tolerance to various stresses is a key phenotype for cell catalysts, which are used widely in bioproduction of diverse valuable chemicals. Using the Rhodococcus ruber TH strain, which exhibits high nitrile hydratase activity, as the target cell catalyst for acrylamide production, we established a method to improve cell tolerance by stably introducing global transcription perturbation. The σ70 gene (sigA) of R. ruber was cloned and randomly mutated. An R. ruber TH3/pNV-sigAM library containing additional sigA mutants was constructed and used for survival selection. The TH3/M4N1-59 mutant was selected by acrylonitrile/acrylamide double stress and exhibited a 160 % extension of the half-life of nitrile hydratase upon exposure to 40 % acrylamide. A redesigned parDEM gene was introduced to Rhodococcus to accomplish stable inheritance of plasmids. A two-batch acrylonitrile hydration reaction was performed using the engineered cells as a catalyst. Compared to TH3, the acrylamide productivity of TH3/M4N1-59DEM catalysis increased by 27.8 and 37.5 % in the first and second bioreaction batches, respectively. These data suggest a novel method for increasing the bioconversion productivity of target chemicals through sigA mutation of the cell catalyst.
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The Fe-type nitrile hydratase from Comamonas testosteroni Ni1 does not require an activator accessory protein for expression in Escherichia coli. Biochem Biophys Res Commun 2012; 424:365-70. [DOI: 10.1016/j.bbrc.2012.06.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 06/11/2012] [Indexed: 11/23/2022]
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Yukl ET, Wilmot CM. Cofactor biosynthesis through protein post-translational modification. Curr Opin Chem Biol 2012; 16:54-9. [PMID: 22387133 DOI: 10.1016/j.cbpa.2012.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 02/09/2012] [Accepted: 02/10/2012] [Indexed: 11/25/2022]
Abstract
Post-translational modifications of amino acids can be used to generate novel cofactors capable of chemistries inaccessible to conventional amino acid side chains. The biosynthesis of these sites often requires one or more enzyme or protein accessory factors, the functions of which are quite diverse and often difficult to isolate in cases where multiple enzymes are involved. Herein is described the current knowledge of the biosynthesis of urease and nitrile hydratase metal centers, pyrroloquinoline quinone, hypusine, and tryptophan tryptophylquinone cofactors along with the most recent work elucidating the functions of individual accessory factors in these systems. These examples showcase the breadth and diversity of this continually expanding field.
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Affiliation(s)
- Erik T Yukl
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, United States
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Abstract
Cobalt is an essential trace element in both prokaryotes and eukaryotes. Nevertheless, it occurs less frequently in metalloproteins than other transition metals. This low occurrence appears to be due to the metal's low abundance in nature as well as its competition with iron, whose biologically critical functions include respiration and photosynthesis. In this review, we discuss the biological role of cobalt, the major effects of cobalt on iron utilization, as well as several mechanisms that cells have developed to circumvent the toxicity of cobalt while still exploiting its chemistry.
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Affiliation(s)
- Sachi Okamoto
- University of British Columbia - Microbiology and Immunology, Vancouver, British Columbia, Canada
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