1
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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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Luo J, Song C, Cui W, Han L, Zhou Z. Counteraction of stability-activity trade-off of Nattokinase through flexible region shifting. Food Chem 2023; 423:136241. [PMID: 37178594 DOI: 10.1016/j.foodchem.2023.136241] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The widespread trade-off between stability and activity severely limits enzyme evolution. Although some progresses have been made to overcome this limitation, the counteraction mechanism for enzyme stability-activity trade-off remains obscure. Here, we clarified the counteraction mechanism of the Nattokinase stability-activity trade-off. A combinatorial mutant M4 was obtained by multi-strategy engineering, exhibiting a 20.7-fold improved half-life; meanwhile, the catalytic efficiency was doubled. Molecular dynamics simulation revealed that an obvious flexible region shifting in the structure of mutant M4 was occurred. The flexible region shifting which contributed to maintain the global structural flexibility, was considered to be the key factor for counteracting the stability-activity trade-off. Further analysis illustrated that the flexible region shifting was driven by region dynamical networks reshaping. This work provided deep insight into the counteraction mechanism of enzyme stability-activity trade-off, suggesting that flexible region shifting would be an effective strategy for enzyme evolution through computational protein engineering.
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Affiliation(s)
- Jie Luo
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Chenshuo Song
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Laichuang Han
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
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3
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Xia Y, Cheng Z, Hou C, Peplowski L, Zhou Z, Chen X. Discovery of the ATPase Activity of a Cobalt-Type Nitrile Hydratase Activator and Its Promoting Effect on Enzyme Maturation. Biochemistry 2022; 61:2940-2947. [PMID: 35673797 DOI: 10.1021/acs.biochem.2c00167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An activator protein and a metal ion are two factors known to be indispensable for the maturation of nitrile hydratase (NHase). Here, the third key factor, adenosine triphosphate (ATP), was identified to play an important role in the activation of Co-type NHase. Free phosphate measurements revealed that the Co-type activator protein can hydrolyze ATP/GTP with appreciable performance and that such catalytic performance is related to NHase activity. Computational analysis and site-directed mutagenesis identified several potential hot spot residues involved in the binding of ATP to Co-type activator protein, and an E60A/W61A/D62A/I139A/T141A combinatorial variant reduced the ATPase activity to 18% of its original level. Further NHase activation studies using the combinatorial variant demonstrated that although the ATPase activity of the Co-type activator protein correlated with NHase activity, a low ATP concentration of 0.5 mmol/L was optimal for NHase activation, with higher ATP concentrations potentially inhibiting NHase activity.
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Affiliation(s)
- Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Chen Hou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xianzhong Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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4
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Cheng Z, Jiang S, Zhou Z. Substrate access tunnel engineering for improving the catalytic activity of a thermophilic nitrile hydratase toward pyridine and pyrazine nitriles. Biochem Biophys Res Commun 2021; 575:8-13. [PMID: 34454178 DOI: 10.1016/j.bbrc.2021.08.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 10/20/2022]
Abstract
Nitrile hydratase (NHase) is able to bio-transform nitriles into amides. As nitrile hydration being an exothermic reaction, a NHase with high activity and stability is needed for amide production. However, the widespread use of NHase for amide bio-production is limited by an activity-stability trade-off. In this study, through the combination of substrate access tunnel calculation, residue conservative analysis and site-saturation mutagenesis, a residue located at the substrate access tunnel entrance of the thermophilic NHase from extremophile Caldalkalibacillus thermarum TA2. A1, βLeu48, was semi-rationally identified as a potential gating residue that directs the enzymatic activity toward various pyridine and pyrazine nitriles. The specific activity of the corresponding mutant βL48H towards 3-cyanopyridine, 2-cyanopyridine and cyanopyrazine were 2.4-fold, 2.8-fold and 3.1-fold higher than that of its parent enzyme, showing a great potential in the industrial production of high-value pyridine and pyrazine carboxamides. Further structural analysis demonstrated that the βHis48 could form a long-lasting hydrogen bond with αGlu166, which contributes to the expansion of the entrance of substrate access tunnel and accelerate substrate migration.
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Affiliation(s)
- Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Shijin Jiang
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (Ministry of Education), School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China; Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao, 226500, China.
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5
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Maruyama S, Sawano K, Amaki S, Suzuki T, Narita S, Kimura K, Arakawa T, Yamada C, Ito Y, Dohmae N, Fujita K, Ishiwata A, Fushinobu S. Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase. Glycobiology 2021; 32:171-180. [PMID: 34735571 DOI: 10.1093/glycob/cwab103] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/16/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
β-l-Arabinofuranosidase HypBA1 from Bifidobacterium longum belongs to the glycoside hydrolase family 127. At the active site of HypBA1, a cysteine residue (Cys417) coordinates with a Zn2+ atom and functions as the catalytic nucleophile for the anomer-retaining hydrolytic reaction. In this study, the role of Zn2+ ion and cysteine in catalysis as well as the substrate-bound structure were studied based on biochemical and crystallographic approaches. The enzymatic activity of HypBA1 decreased after dialysis in the presence of EDTA and guanidine hydrochloride and was then recovered by the addition of Zn2+. The Michaelis complex structure was determined using a crystal of a mutant at the acid/base catalyst residue (E322Q) soaked in a solution containing the substrate p-nitrophenyl-β-l-arabinofuranoside. To investigate the covalent thioglycosyl enzyme intermediate structure, synthetic inhibitors of l-arabinofuranosyl haloacetamide derivatives with different anomer configurations were used to target the nucleophilic cysteine. In the crystal structure of HypBA1, β-configured l-arabinofuranosylamide formed a covalent link with Cys417, whereas α-configured l-arabinofuranosylamide was linked to a noncatalytic residue Cys415. Mass spectrometric analysis indicated that Cys415 was also reactive with the probe molecule. With the β-configured inhibitor, the arabinofuranoside moiety was correctly positioned at the subsite and the active site integrity was retained to successfully mimic the covalent intermediate state.
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Affiliation(s)
- Shun Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kota Sawano
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoko Amaki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takehiro Suzuki
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Satoru Narita
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma, Saitama 337-8570, Japan
| | - Kenta Kimura
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma, Saitama 337-8570, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chihaya Yamada
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yukishige Ito
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Science, Osaka University, 1-1 Machikaneyamacho, Toyonaka, Osaka 560-0043, Japan
| | - Naoshi Dohmae
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Akihiro Ishiwata
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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6
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Sun S, Zhou J, Jiang J, Dai Y, Sheng M. Nitrile Hydratases: From Industrial Application to Acetamiprid and Thiacloprid Degradation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10440-10449. [PMID: 34469128 DOI: 10.1021/acs.jafc.1c03496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The widespread application of neonicotinoid insecticides (NEOs) in agriculture causes a series of environmental and ecological problems. Microbial remediation is a popular approach to relieve these negative impacts, but the associated molecular mechanisms are rarely explored. Nitrile hydratase (NHase), an enzyme commonly used in industry for amide production, was discovered to be responsible for the degradation of acetamiprid (ACE) and thiacloprid (THI) by microbes. Since then, research into NHases in NEO degradation has attracted increasing attention. In this review, microbial degradation of ACE and THI is briefly described. We then focus on NHase evolution, gene composition, maturation mechanisms, expression, and biochemical properties with regard to application of NHases in NEO degradation for bioremediation.
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Affiliation(s)
- Shilei Sun
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jiangsheng Zhou
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Yijun 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
| | - Miaomiao Sheng
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 310053, People's Republic of China
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7
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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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8
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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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9
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Ogutu IRAM, Holz RC, Bennett B. Insight into the Maturation Process of the Nitrile Hydratase Active Site. Inorg Chem 2021; 60:5432-5435. [PMID: 33779143 DOI: 10.1021/acs.inorgchem.0c02924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The metal binding motif of all nitrile hydratases (NHases, EC 4.2.1.84) is highly conserved (CXXCSCX) in the α-subunit. Accordingly, an eight amino acid peptide (VCTLCSCY), based on the metal binding motif of the Co-type NHase from Pseudonocardia thermophilia (PtNHase), was synthesized and shown to coordinate Fe(II) under anaerobic conditions. Parallel-mode EPR data on the mononuclear Fe(II)-peptide complex confirmed an integer-spin signal at g' ∼ 9, indicating an S = 2 system with unusually small axial ZFS, D = 0.29 cm-1 Exposure to air yielded a transient high-spin EPR signal most consistent with an intermediate/admixed S = 3/2 spin state, while the integer-spin signal was extinguished. Prolonged exposure to air resulted in the observation of EPR signals at g = 2.04, 2.16, and 2.20, consistent with the formation of a low-spin Fe(III)-peptide complex with electronic and structural similarity to the NHase from Rhodococcus equi TG328-2 (ReNHase). Coupled with MS data, these data support a progression for iron oxidation in NHases that proceeds from a reduced high spin to an oxidized high spin followed by formation of an oxidized low-spin iron center, something that heretofore has not been observed.
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Affiliation(s)
- Irene R A M Ogutu
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States.,Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Richard C Holz
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States.,Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, Wisconsin 53201-1881, United States
| | - Brian Bennett
- Department of Physics, Marquette University, 1420 W. Clybourn Street, Milwaukee, Wisconsin 53233, United States
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10
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Effect and mechanism analysis of different linkers on efficient catalysis of subunit-fused nitrile hydratase. Int J Biol Macromol 2021; 181:444-451. [PMID: 33753198 DOI: 10.1016/j.ijbiomac.2021.03.103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 11/21/2022]
Abstract
Protein fusion using a linker plays an important role for protein evolution. However, designing suitable linkers for protein evolution is yet challenging and under-explored. To further clarify the regular pattern of suitable type of linker for fusion proteins, one nitrile hydratase (NHase) was used as a target protein and subunit fusion strategy was carried out to improve its efficient catalysis. Subunit-fused variants with three different types of linkers were constructed and characterized. All variants exhibited higher stability than that of the wild type. The longer the linker was, the higher stability NHase showed, however, too long linker affected NHase activity and expression. Among the three types of linkers, the α-helical linker seemed more suitable for NHase than flexible or rigid linkers. Though it is not clear how the linkers affecting the activity, structure analysis indicated that the stability improvement is dependent on the additional salt bridge, H-bond, and the subunit interface area increasing due to the linker insertion, among which the additional salt bridge and interface area were more important factors. The results described here may be useful for redesigning other enzymes through subunit fusion.
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11
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Wu Z, Zhang Z, Cai S, Zheng R, Zheng Y. High-level expression of nitrile hydratase from Pantoea sp. At-9b in Escherichia coli. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.11.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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12
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Hashimoto Y, Ube Y, Doi S, Kumano T, Kobayashi M. Metal chaperone, NhpC, involved in the metallocenter biosynthesis of nitrile hydratase. J GEN APPL MICROBIOL 2021; 67:24-32. [DOI: 10.2323/jgam.2020.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yoshiteru Hashimoto
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), The University of Tsukuba
| | - Yuko Ube
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
| | - Shiori Doi
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
| | - Takuto Kumano
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), The University of Tsukuba
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry and Graduate School of Life and Environmental Sciences, The University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), The University of Tsukuba
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13
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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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14
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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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15
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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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16
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Han L, Cui W, Lin Q, Chen Q, Suo F, Ma K, Wang Y, Hao W, Cheng Z, Zhou Z. Efficient Overproduction of Active Nitrile Hydratase by Coupling Expression Induction and Enzyme Maturation via Programming a Controllable Cobalt-Responsive Gene Circuit. Front Bioeng Biotechnol 2020; 8:193. [PMID: 32266230 PMCID: PMC7105576 DOI: 10.3389/fbioe.2020.00193] [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: 12/04/2019] [Accepted: 02/27/2020] [Indexed: 11/13/2022] Open
Abstract
A robust and portable expression system is of great importance in enzyme production, metabolic engineering, and synthetic biology, which maximizes the performance of the engineered system. In this study, a tailor-made cobalt-induced expression system (CIES) was developed for low-cost and eco-friendly nitrile hydratase (NHase) production. First, the strong promoter Pveg from Bacillus subtilis, the Ni(II)/Co(II) responsive repressor RcnR, and its operator were reorganized to construct a CIES. In this system, the expression of reporter green fluorescent protein (GFP) was specifically triggered by Co(II) over a broad range of concentration. The performance of the cobalt-induced system was evolved to version 2.0 (CIES 2.0) for adaptation to different concentrations of Co(II) through programming a homeostasis system that rebalances cobalt efflux and influx with RcnA and NiCoT, respectively. Harnessing these synthetic platforms, the induced expression of NHase was coupled with enzyme maturation by Co(II) in a synchronizable manner without requiring additional inducers, which is a unique feature relative to other induced systems for production of NHase. The yield of NHase was 111.2 ± 17.9 U/ml using CIES and 114.9 ± 1.4 U/ml using CIES 2.0, which has a producing capability equivalent to that of commonly used isopropyl thiogalactoside (IPTG)-induced systems. In a scale-up system using a 5-L fermenter, the yielded enzymatic activity reached 542.2 ± 42.8 U/ml, suggesting that the designer platform for NHase is readily applied to the industry. The design of CIES in this study not only provided a low-cost and eco-friendly platform to overproduce NHase but also proposed a promising pipeline for development of synthetic platforms for expression of metalloenzymes.
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Affiliation(s)
- Laichuang Han
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Qiao Lin
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Qiaoqing Chen
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Feiya Suo
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Ke Ma
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Yang Wang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Wenliang Hao
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Jiangnan University, Jiangsu, China
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17
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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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18
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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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19
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Xia Y, Peplowski L, Cheng Z, Wang T, Liu Z, Cui W, Kobayashi M, Zhou Z. Metallochaperone function of the self‐subunit swapping chaperone involved in the maturation of subunit‐fused cobalt‐type nitrile hydratase. Biotechnol Bioeng 2019; 116:481-489. [DOI: 10.1002/bit.26865] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/24/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus UniversityTorun Poland
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
| | - Tianyi Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, TennodaiTsukuba Ibaraki Japan
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan UniversityWuxi China
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20
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Yu H, Jiao S, Wang M, Liang Y, Tang L. Biodegradation of Nitriles by Rhodococcus. BIOLOGY OF RHODOCOCCUS 2019. [DOI: 10.1007/978-3-030-11461-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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21
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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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22
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Yang Z, Pei X, Xu G, Wu J, Yang L. N-terminal engineering of overlapping genes in the nitrile hydratase gene cluster improved its activity. Enzyme Microb Technol 2018; 117:9-14. [PMID: 30037557 DOI: 10.1016/j.enzmictec.2018.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 01/06/2023]
Abstract
Nitrile hydratase which catalyzes the hydration of nitriles to the corresponding amides is operon-encoded. However, when heterologously expressed, genes in the same operon are usually not equally expressed, and the ratio needs to be fine-tuned. A gene cluster of three genes (corresponding to α-subunit, β-subunit and activator) encoding the nitrile hydratase was cloned from Aurantimonas manganoxydans ATCC BAA-1229 and expressed in Escherichia coli. However, difficulty was encountered in heterologous expression of the activator and the expression level of β-subunit was lower than that of α-subunit, which together resulted in low catalytic efficiency. To improve the expression of activator, a set of SKIK tags were fused to the N-terminus of the activator. To elevate the expression level of β-subunit, a silent mutation strategy was applied in the overlapping sequence with α-subunit around its translation initial region. Finally, the expression of β-subunit and activator were improved and the maximum activity of NHase1229 was doubled, reaching 160 U/mL towards 3-cyanopyridine. These results indicate that N-terminal engineering is an efficient strategy for optimizing the expression of multiple genes in operons.
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Affiliation(s)
- Zhengfei Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 310012, China
| | - Gang Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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23
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Xia Y, Cui W, Cheng Z, Peplowski L, Liu Z, Kobayashi M, Zhou Z. Improving the Thermostability and Catalytic Efficiency of the Subunit-Fused Nitrile Hydratase by Semi-Rational Engineering. ChemCatChem 2018. [DOI: 10.1002/cctc.201701374] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi 214122 P.R. China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi 214122 P.R. China
| | - Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi 214122 P.R. China
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics; Nicolaus Copernicus University; Grudziadzka 5 87-100 Torun Poland
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi 214122 P.R. China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry and the Graduate School of Life, and Environment Sciences; University of Tsukuba; Ibaraki 305-8572 Japan
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi 214122 P.R. China
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24
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Cheng Z, Cui W, Xia Y, Peplowski L, Kobayashi M, Zhou Z. Modulation of Nitrile Hydratase Regioselectivity towards Dinitriles by Tailoring the Substrate Binding Pocket Residues. ChemCatChem 2017. [DOI: 10.1002/cctc.201701170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhongyi Cheng
- Key laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi 214122 P.R. China
| | - Wenjing Cui
- Key laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi 214122 P.R. China
| | - Yuanyuan Xia
- Key laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi 214122 P.R. China
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics; Nicolaus Copernicus University; Grudziadzka 5 87-100 Torun Poland
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry and the Graduate School of Life, and Environment Sciences; The University of Tsukuba; Ibaraki 305-8572 Japan
| | - Zhemin Zhou
- Key laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi 214122 P.R. China
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25
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Cheng Z, Peplowski L, Cui W, Xia Y, Liu Z, Zhang J, Kobayashi M, Zhou Z. Identification of key residues modulating the stereoselectivity of nitrile hydratase toward rac-mandelonitrile by semi-rational engineering. Biotechnol Bioeng 2017; 115:524-535. [DOI: 10.1002/bit.26484] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/19/2017] [Accepted: 10/22/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi China
| | - Lukasz Peplowski
- Faculty of Physics; Institute of Physics; Astronomy and Informatics; Nicolaus. Copernicus University; Grudziadzka 5 Torun Poland
| | - 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
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi China
| | - Jialei Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry and the Graduate School of Life and Environmental Sciences; The University of Tsukuba; Tsukuba Ibaraki Japan
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; Jiangnan University; Wuxi China
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26
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Matoba Y, Kihara S, Muraki Y, Bando N, Yoshitsu H, Kuroda T, Sakaguchi M, Kayama K, Tai H, Hirota S, Ogura T, Sugiyama M. Activation Mechanism of the Streptomyces Tyrosinase Assisted by the Caddie Protein. Biochemistry 2017; 56:5593-5603. [DOI: 10.1021/acs.biochem.7b00635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yasuyuki Matoba
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Shogo Kihara
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Yoshimi Muraki
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Naohiko Bando
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Hironari Yoshitsu
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Teruo Kuroda
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
| | - Miyuki Sakaguchi
- Picobiology
Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Koto 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kure’e Kayama
- Picobiology
Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Koto 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Hulin Tai
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama,
Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate
School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama,
Ikoma, Nara 630-0192, Japan
| | - Takashi Ogura
- Picobiology
Institute, Graduate School of Life Science, University of Hyogo, RSC-UH Leading Program Center, Koto 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Masanori Sugiyama
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Kasumi 1-2-3, Minami-ku, Hiroshima 734-8551, Japan
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27
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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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28
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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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29
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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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30
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Wang Z, Liu Z, Cui W, Zhou Z. Establishment of Bioprocess for Synthesis of Nicotinamide by Recombinant Escherichia coli Expressing High-Molecular-Mass Nitrile Hydratase. Appl Biochem Biotechnol 2017; 182:1458-1466. [PMID: 28150192 DOI: 10.1007/s12010-017-2410-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/13/2017] [Indexed: 10/20/2022]
Abstract
Application of engineered bacteria expressing nitrile hydratase for the production of amide is getting tremendous attention due to the rapid development of recombinant DNA technique. This study evaluated the effect of 3-cyanopyridine concentrations on nicotinamide production using recombinant Escherichia coli strain (BAG) expressing high-molecular-mass nitrile hydratase from Rhodococcus rhodochrous J1, and established proper process of whole-cell catalysis of 3-cyanopyridine and high cell-density cultivation. The process of substrate fed-batch was applied in the production of nicotinamide, and the concentration of product reached 390 g/L under the condition of low cell-density. After the high cell-density cultivation of BAG in 5 L bioreactor, the OD600 of cell attained 200 and the total activity reached 2813 U/mL. Different high density of BAG after fermentation in the tank was used to catalyze 3-cyanopyridine, and the concentration of nicotinamide reached to 508 g/L in just 60 min. The productivity of BAG was 212% higher than that of R. rhodochrous J1, and it is possible that BAG is able to achieve industrial production of nicotinamide.
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Affiliation(s)
- Zhe Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Wenjing Cui
- 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.
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31
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Jiang S, Zhang L, Yao Z, Gao B, Wang H, Mao X, Wei D. Switching a nitrilase from Syechocystis sp. PCC6803 to a nitrile hydratase by rationally regulating reaction pathways. Catal Sci Technol 2017. [DOI: 10.1039/c7cy00060j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Based on this mechanism, a nitrilase was engineered to shift the reaction pathway from formation of acid to formation of amide.
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Affiliation(s)
- Shuiqin Jiang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Lujia Zhang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Zhiqiang Yao
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Xiangzhao Mao
- Ocean Univ China
- Coll Food Sci & Engn
- Qingdao 266003
- China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- China
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32
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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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Abe T, Hashimoto Y, Sugimoto S, Kobayashi K, Kumano T, Kobayashi M. Amide compound synthesis by adenylation domain of bacillibactin synthetase. J Antibiot (Tokyo) 2016; 70:435-442. [DOI: 10.1038/ja.2016.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 07/07/2016] [Accepted: 08/29/2016] [Indexed: 11/09/2022]
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34
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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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35
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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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37
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Sun SL, Lu TQ, Yang WL, Guo JJ, Rui X, Mao SY, Zhou LY, Dai YJ. Characterization of a versatile nitrile hydratase of the neonicotinoid thiacloprid-degrading bacterium Ensifer meliloti CGMCC 7333. RSC Adv 2016. [DOI: 10.1039/c5ra27966f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The nitrogen-fixing bacterium Ensifer meliloti CGMCC 7333 and its nitrile hydratase (NHase) degrade the neonicotinoid insecticides, thiacloprid (THI) and acetamiprid (ACE), to their corresponding amide metabolites.
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Affiliation(s)
- Shi-Lei Sun
- 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
| | - Tian-Qi Lu
- 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
| | - Wen-Long Yang
- 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
| | - Jing-Jing 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
| | - Xue Rui
- 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
| | - Shi-Yun Mao
- 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
| | - Ling-Yan Zhou
- 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
| | - 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
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38
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Kumano T, Takizawa Y, Shimizu S, Kobayashi M. Nitrile-synthesizing enzyme: Gene cloning, overexpression and application for the production of useful compounds. J GEN APPL MICROBIOL 2016; 62:174-80. [DOI: 10.2323/jgam.2016.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Takuto Kumano
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Yuko Takizawa
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University
| | - Sakayu Shimizu
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, University of Tsukuba
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39
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Kumano T, Suzuki T, Shimizu S, Kobayashi M. Nitrile-synthesizing enzyme: Screening, purification and characterization. J GEN APPL MICROBIOL 2016; 62:167-73. [DOI: 10.2323/jgam.2016.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Takuto Kumano
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Takahisa Suzuki
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University
| | - Sakayu Shimizu
- Division of Applied Life Science, Graduate School of Agriculture, Kyoto University
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, University of Tsukuba
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40
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The Stability Enhancement of Nitrile Hydratase from Bordetella petrii by Swapping the C-terminal Domain of β subunit. Appl Biochem Biotechnol 2015; 178:1481-7. [DOI: 10.1007/s12010-015-1961-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
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41
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Pei X, Wang Q, Meng L, Li J, Yang Z, Yin X, Yang L, Chen S, Wu J. Chaperones-assisted soluble expression and maturation of recombinant Co-type nitrile hydratase in Escherichia coli to avoid the need for a low induction temperature. J Biotechnol 2015; 203:9-16. [PMID: 25796588 DOI: 10.1016/j.jbiotec.2015.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/03/2015] [Accepted: 03/07/2015] [Indexed: 11/28/2022]
Abstract
Nitrile hydratase (NHase) is an important industrial enzyme that biosynthesizes high-value amides. However, most of NHases expressed in Escherichia coli easily aggregate to inactive inclusion bodies unless the induction temperature is reduced to approximately 20°C. The NHase from Aurantimonas manganoxydans has been functionally expressed in E. coli, and exhibits considerable potential for the production of nicotinamide in industrial application. In this study, the effects of chaperones including GroEL/ES, Dnak/J-GrpE and trigger factor on the expression of the recombinant Co-type NHase were investigated. The results indicate that three chaperones can significantly promote the active expression of the recombinant NHase at 30°C. The total NHase activities reached to 263 and 155U/ml in shake flasks when the NHase was co-expressed with GroEL/ES and DnaK/J-GrpE, which were 52- and 31-fold higher than the observed activities without chaperones, respectively. This increase is possibly due to the soluble expression of the recombinant NHase assisted by molecular chaperones. Furthermore, GroEL/ES and DnaK/J-GrpE were determined to promote the maturation of the Co-type NHase in E. coli under the absence of the parental activator gene. These knowledge regarding the chaperones effect on the NHase expression are useful for understanding the biosynthesis of Co-type NHase.
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Affiliation(s)
- Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 310012, PR China
| | - Qiuyan Wang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 310012, PR China
| | - Lijun Meng
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310028, PR China
| | - Jing Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310028, PR China
| | - Zhengfen Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310028, PR China
| | - Xiaopu Yin
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou, 310012, PR China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310028, PR China
| | - Shaoyun Chen
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053, PR China.
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310028, PR China.
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42
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Natural low-molecular mass organic compounds with oxidase activity as organocatalysts. Proc Natl Acad Sci U S A 2014; 111:17152-7. [PMID: 25411318 DOI: 10.1073/pnas.1417941111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Organocatalysts, low-molecular mass organic compounds composed of nonmetallic elements, are often used in organic synthesis, but there have been no reports of organocatalysts of biological origin that function in vivo. Here, we report that actinorhodin (ACT), a natural product derived from Streptomyces coelicolor A3(2), acts as a biocatalyst. We purified ACT and assayed its catalytic activity in the oxidation of L-ascorbic acid and L-cysteine as substrates by analytical methods for enzymes. Our findings were as follows: (i) oxidation reactions producing H2O2 proceeded upon addition of ACT to the reaction mixture; (ii) ACT was not consumed during the reactions; and (iii) a small amount (catalytic amount) of ACT consumed an excess amount of the substrates. Even at room temperature, atmospheric pressure, and neutral pH, ACT showed catalytic activity in aqueous solution, and ACT exhibited substrate specificity in the oxidation reactions. These findings reveal ACT to be an organocatalyst. ACT is known to show antibiotic activity, but its mechanism of action remains unknown. On the basis of our results, we propose that ACT kills bacteria by catalyzing the production of toxic levels of H2O2. We also screened various other natural products of bacterial, plant, and animal origins and found that several of the compounds exhibited catalytic activity, suggesting that living organisms produce and use these compounds as biocatalysts in nature.
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43
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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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44
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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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45
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Improvement of stability of nitrile hydratase via protein fragment swapping. Biochem Biophys Res Commun 2014; 450:401-8. [DOI: 10.1016/j.bbrc.2014.05.127] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 05/27/2014] [Indexed: 11/21/2022]
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46
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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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47
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Discovery of a new Fe-type nitrile hydratase efficiently hydrating aliphatic and aromatic nitriles by genome mining. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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48
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Pei X, Zhang H, Meng L, Xu G, Yang L, Wu J. Efficient cloning and expression of a thermostable nitrile hydratase in Escherichia coli using an auto-induction fed-batch strategy. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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49
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A new synthetic route to N-benzyl carboxamides through the reverse reaction of N-substituted formamide deformylase. Appl Environ Microbiol 2013; 80:61-9. [PMID: 24123742 DOI: 10.1128/aem.02429-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, we isolated a new enzyme, N-substituted formamide deformylase, that catalyzes the hydrolysis of N-substituted formamide to the corresponding amine and formate (H. Fukatsu, Y. Hashimoto, M. Goda, H. Higashibata, and M. Kobayashi, Proc. Natl. Acad. Sci. U. S. A. 101:13726-13731, 2004, doi:10.1073/pnas.0405082101). Here, we discovered that this enzyme catalyzed the reverse reaction, synthesizing N-benzylformamide (NBFA) from benzylamine and formate. The reverse reaction proceeded only in the presence of high substrate concentrations. The effects of pH and inhibitors on the reverse reaction were almost the same as those on the forward reaction, suggesting that the forward and reverse reactions are both catalyzed at the same catalytic site. Bisubstrate kinetic analysis using formate and benzylamine and dead-end inhibition studies using a benzylamine analogue, aniline, revealed that the reverse reaction of this enzyme proceeds via an ordered two-substrate, two-product (bi-bi) mechanism in which formate binds first to the enzyme active site, followed by benzylamine binding and the subsequent release of NBFA. To our knowledge, this is the first report of the reverse reaction of an amine-forming deformylase. Surprisingly, analysis of the substrate specificity for acids demonstrated that not only formate, but also acetate and propionate (namely, acids with numbers of carbon atoms ranging from C1 to C3), were active as acid substrates for the reverse reaction. Through this reaction, N-substituted carboxamides, such as NBFA, N-benzylacetamide, and N-benzylpropionamide, were synthesized from benzylamine and the corresponding acid substrates.
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Lipowicz B, Hanekop N, Schmitt L, Proksch P. An aeroplysinin-1 specific nitrile hydratase isolated from the marine sponge Aplysina cavernicola. Mar Drugs 2013; 11:3046-67. [PMID: 23966036 PMCID: PMC3766881 DOI: 10.3390/md11083046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 11/24/2022] Open
Abstract
A nitrile hydratase (NHase) that specifically accepts the nitrile aeroplysinin-1 (1) as a substrate and converts it into the dienone amide verongiaquinol (7) was isolated, partially purified and characterized from the Mediterranean sponge Aplysina cavernicola; although it is currently not known whether the enzyme is of sponge origin or produced by its symbiotic microorganisms. The formation of aeroplysinin-1 and of the corresponding dienone amide is part of the chemical defence system of A. cavernicola. The latter two compounds that show strong antibiotic activity originate from brominated isoxazoline alkaloids that are thought to protect the sponges from invasion of bacterial pathogens. The sponge was shown to contain at least two NHases as two excised protein bands from a non denaturating Blue Native gel showed nitrile hydratase activity, which was not observed for control samples. The enzymes were shown to be manganese dependent, although cobalt and nickel ions were also able to recover the activity of the nitrile hydratases. The temperature and pH optimum of the studied enzymes were found at 41 °C and pH 7.8. The enzymes showed high substrate specificity towards the physiological substrate aeroplysinin-1 (1) since none of the substrate analogues that were prepared either by partial or by total synthesis were converted in an in vitro assay. Moreover de-novo sequencing by mass spectrometry was employed to obtain information about the primary structure of the studied NHases, which did not reveal any homology to known NHases.
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Affiliation(s)
- Bartosz Lipowicz
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine University, Universitaetsstrasse 1, Bldg. 26.23, 40225 Duesseldorf, Germany; E-Mail:
| | - Nils Hanekop
- Institute of Biochemistry, Heinrich-Heine University, Universitaetsstrasse 1, Bldg. 26.42, 40225 Duesseldorf, Germany; E-Mail:
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine University, Universitaetsstrasse 1, Bldg. 26.42, 40225 Duesseldorf, Germany; E-Mail:
| | - Peter Proksch
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine University, Universitaetsstrasse 1, Bldg. 26.23, 40225 Duesseldorf, Germany; E-Mail:
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