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Guo Y, Li J, Zhang S, Song Y, Chen G, He L, Wang L, Liang C. Significant Enhancement Catalytic Activity of Nitrile Hydratase by Balancing the Subunits Expression. Chembiochem 2024; 25:e202400526. [PMID: 39617726 DOI: 10.1002/cbic.202400526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 11/22/2024] [Accepted: 11/27/2024] [Indexed: 12/11/2024]
Abstract
Escherichia coli (E. coli) is the most commonly used bacterial recombinant protein production system due to its easy genetic modification properties. In our previous study, a recombinant plasmid expressing the Fe-type nitrile hydratase derived from Rhodococcus erythropolis CCM2595 (ReNHase) was successfully constructed and the recombinant ReNHase exerted an excellent catalytic effect on dinitrile compounds. Nevertheless, the ReNHases were confronted with imbalanced subunit expression during heterologous expression, which restricted the enzymes assemble functionally. In this study, the secondary structure of mRNA in the ribosome binding sequence region of the β-subunit was optimized to elevate the translation efficiency of the β-subunit gene and balance the expression of α- and β-subunits in ReNHase. The optimized ReNHase showed a 12-fold increase in specific enzyme activity over wild-type ReNHase. To further enhance the soluble expression of ReNHase, the ReNHase was labeled using three different fusion tags, resulting in three new recombinant ReNHases. In these recombinant ReNHases, some of the fusion tags promoted the soluble expression of ReNHase, but also affected the balance of α-/β-subunit expression and the secondary structure of the ReNHase, and reduced the enzyme activity. In conclusion, our results provide an optimized strategy for the heterologous expression of multi-subunit proteins.
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Affiliation(s)
- Yi Guo
- School of Chemical Engineering, Laboratory of Advanced Materials and Catalytic Engineering, Dalian University of Technology, Dalian, 116024, China
- Laboratory of Synthetic Biology and Biotransformation, Chengdu Research Institute of Dalian University of Technology, Chengdu, 611939, China
| | - Jiaxin Li
- School of Chemical Engineering, Laboratory of Advanced Materials and Catalytic Engineering, Dalian University of Technology, Dalian, 116024, China
- Laboratory of Synthetic Biology and Biotransformation, Chengdu Research Institute of Dalian University of Technology, Chengdu, 611939, China
| | - Song Zhang
- School of Chemical Engineering Ocean and Life Science, Dalian University of Technology, Panjin, 124221, China
| | - Yingjie Song
- School of Chemical Engineering Ocean and Life Science, Dalian University of Technology, Panjin, 124221, China
| | - Guobing Chen
- School of Chemical Engineering Ocean and Life Science, Dalian University of Technology, Panjin, 124221, China
| | - Leiyu He
- School of Chemical Engineering Ocean and Life Science, Dalian University of Technology, Panjin, 124221, China
| | - Li Wang
- School of Chemical Engineering Ocean and Life Science, Dalian University of Technology, Panjin, 124221, China
- Laboratory of Synthetic Biology and Biotransformation, Chengdu Research Institute of Dalian University of Technology, Chengdu, 611939, China
| | - Changhai Liang
- School of Chemical Engineering, Laboratory of Advanced Materials and Catalytic Engineering, Dalian University of Technology, Dalian, 116024, China
- Laboratory of Synthetic Biology and Biotransformation, Chengdu Research Institute of Dalian University of Technology, Chengdu, 611939, China
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Moraes MI, Iglesias C, Teixeira IS, Milagre HM, Giordano SR, Milagre CD. Biotransformations of nitriles mediated by in vivo nitrile hydratase of Rhodococcus erythropolis ATCC 4277 heterologously expressed in E. Coli. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2022.100760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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3
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Chen Y, Jiao S, Wang M, Chen J, Yu H. A novel molecular chaperone GroEL2 from Rhodococcus ruber and its fusion chimera with nitrile hydratase for co-enhanced activity and stability. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2018.07.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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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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5
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Pratush A, Seth A, Bhalla TC. Expression of nitrile hydratase gene of mutant 4D strain of Rhodococcus rhodochrous PA 34 in Pichia pastoris. BIOCATAL BIOTRANSFOR 2016. [DOI: 10.1080/10242422.2016.1247831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Amit Pratush
- Department of Bioengineering, School of life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China,
| | - Amit Seth
- Department of Bioengineering, Shoolini University of Biotechnology and management Sciences, Solan, India, and
| | - Tek Chand Bhalla
- Department of Biotechnology, Himachal Pradesh University, Shimla, India
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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: 1.4] [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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Duca D, Lorv J, Patten CL, Rose D, Glick BR. Indole-3-acetic acid in plant-microbe interactions. Antonie van Leeuwenhoek 2014; 106:85-125. [PMID: 24445491 DOI: 10.1007/s10482-013-0095-y] [Citation(s) in RCA: 354] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/07/2013] [Indexed: 01/04/2023]
Abstract
Indole-3-acetic acid (IAA) is an important phytohormone with the capacity to control plant development in both beneficial and deleterious ways. The ability to synthesize IAA is an attribute that many bacteria including both plant growth-promoters and phytopathogens possess. There are three main pathways through which IAA is synthesized; the indole-3-pyruvic acid, indole-3-acetamide and indole-3-acetonitrile pathways. This chapter reviews the factors that effect the production of this phytohormone, the role of IAA in bacterial physiology and in plant-microbe interactions including phytostimulation and phytopathogenesis.
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Affiliation(s)
- Daiana Duca
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada,
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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: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Cloning, sequencing, and expression of nitrile hydratase gene of mutant 4D strain of Rhodococcus rhodochrous PA 34 in E. coli. Appl Biochem Biotechnol 2012; 168:465-86. [PMID: 22833401 DOI: 10.1007/s12010-012-9790-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 07/03/2012] [Indexed: 10/28/2022]
Abstract
The NHase encoding gene of mutant 4D was isolated by PCR amplification. The NHase gene of mutant 4D was successfully cloned and expressed in Escherichia coli by using Ek/LIC Duet cloning kits (Novagen). For the active expression of the NHase gene, the co-expression of small cobalt transporter gene (P-protein gene) has also been co-expressed with NHase gene E. coli. The nucleotide sequence of this NHase gene revealed high homology with the H-NHase of Rhodococcus rhodochrous J1. The recombinant E. coli cells showed higher NHase activity (5.9 U/mg dcw) as compared to the wild (4.1 U/mg dcw) whereas it is less than the mutant strain (8.4 U/mg dcw). Addition of cobalt ion in Luria-Bertani medium is needed up to a very small concentration (0.4 mM) for NHase activity. The recombinant E. coli exhibited maximum NHase activity at 6 h of incubation and was purified with a yield of 56 % with specific activity of 37.1 U/mg protein.
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van Pelt S, Zhang M, Otten LG, Holt J, Sorokin DY, van Rantwijk F, Black GW, Perry JJ, Sheldon RA. Probing the enantioselectivity of a diverse group of purified cobalt-centred nitrile hydratases. Org Biomol Chem 2011; 9:3011-9. [DOI: 10.1039/c0ob01067g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Nitrile hydratases (NHases): At the interface of academia and industry. Biotechnol Adv 2010; 28:725-41. [DOI: 10.1016/j.biotechadv.2010.05.020] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 05/16/2010] [Accepted: 05/17/2010] [Indexed: 11/19/2022]
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13
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Leng DH, Wang DX, Huang ZT, Wang MX. Highly efficient and enantioselective biotransformations of β-lactam carbonitriles and carboxamides and their synthetic applications. Org Biomol Chem 2010; 8:4736-43. [PMID: 20721414 DOI: 10.1039/c0ob00198h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalyzed by Rhodococcus erythropolis AJ270, a nitrile hydratase and amidase containing microbial whole cell catalyst, a number of racemic 1-arylmethyl- and 1-allyl-4-oxoazetidine-2-carbonitriles and carboxamides underwent efficient transformations under very mild conditions to produce enantiopure functionalized S-amide and R-acid products in excellent yields. While the nitrile hydratase showed good enzyme activity but virtually no enantioselectivity, the amidase displayed high R-enantioselectivity against almost all amide substrates tested. The synthetic applications of the resulting functionalized chiral β-lactam derivatives were demonstrated by the facile preparation of β-lactam-fused heterocyclic compounds.
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Affiliation(s)
- Dong-Hui Leng
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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Coffey L, Owens E, Tambling K, O'Neill D, O'Connor L, O'Reilly C. Real-time PCR detection of Fe-type nitrile hydratase genes from environmental isolates suggests horizontal gene transfer between multiple genera. Antonie van Leeuwenhoek 2010; 98:455-63. [PMID: 20502965 DOI: 10.1007/s10482-010-9459-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 05/14/2010] [Indexed: 11/25/2022]
Abstract
Nitriles are widespread in the environment as a result of biological and industrial activity. Nitrile hydratases catalyse the hydration of nitriles to the corresponding amide and are often associated with amidases, which catalyze the conversion of amides to the corresponding acids. Nitrile hydratases have potential as biocatalysts in bioremediation and biotransformation applications, and several successful examples demonstrate the advantages. In this work a real-time PCR assay was designed for the detection of Fe-type nitrile hydratase genes from environmental isolates purified from nitrile-enriched soils and seaweeds. Specific PCR primers were also designed for amplification and sequencing of the genes. Identical or highly homologous nitrile hydratase genes were detected from isolates of numerous genera from geographically diverse sites, as were numerous novel genes. The genes were also detected from isolates of genera not previously reported to harbour nitrile hydratases. The results provide further evidence that many bacteria have acquired the genes via horizontal gene transfer. The real-time PCR assay should prove useful in searching for nitrile hydratases that could have novel substrate specificities and therefore potential in industrial applications.
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Affiliation(s)
- Lee Coffey
- Pharmaceutical & Molecular Biotechnology Research Centre, Chemical & Life Sciences Department, Waterford Institute of Technology, Ireland.
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15
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Coffey L, Clarke A, Duggan P, Tambling K, Horgan S, Dowling D, O'Reilly C. Isolation of identical nitrilase genes from multiple bacterial strains and real-time PCR detection of the genes from soils provides evidence of horizontal gene transfer. Arch Microbiol 2009; 191:761-71. [PMID: 19730817 DOI: 10.1007/s00203-009-0507-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 08/19/2009] [Accepted: 08/20/2009] [Indexed: 10/20/2022]
Abstract
Bacterial enzymes capable of nitrile hydrolysis have significant industrial potential. Microbacterium sp. AJ115, Rhodococcus erythropolis AJ270 and AJ300 were isolated from the same location in England and harbour identical nitrile hydratase/amidase gene clusters. Strain AJ270 has been well studied due to its nitrile hydratase and amidase activity. R. erythropolis ITCBP was isolated from Denmark and carries a very similar nitrile hydratase/amidase gene cluster. In this study, an identical nitrilase gene (nit1) was isolated from the four strains, and the nitrilase from strain AJ270 cloned and expressed in Escherichia coli. Analysis of the recombinant nitrilase has shown it to be functional with activity demonstrated towards phenylacetonitrile. A real-time PCR TaqMan assay was developed that allowed nit1 detection directly from soil enrichment cultures without DNA extraction, with nit1 detected in all samples tested. Real-time PCR screening of isolates from these soils resulted in the isolation of nit1 and also very similar nitrilase gene nit2 from a number of Burkholderia sp. The genes nit1 and nit2 have also been detected in many bacteria of different genera but are unstable in these isolates. It is likely that the genes were acquired by horizontal gene transfer and may be wide-spread in the environment.
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Affiliation(s)
- Lee Coffey
- Department of Chemical and Life Sciences, Waterford Institute of Technology, Waterford, Ireland.
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Cloning and functional expression of a nitrile hydratase (NHase) from Rhodococcus equi TG328-2 in Escherichia coli, its purification and biochemical characterisation. Appl Microbiol Biotechnol 2009; 85:1417-25. [DOI: 10.1007/s00253-009-2153-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/10/2009] [Accepted: 07/15/2009] [Indexed: 10/20/2022]
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17
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Martínez-Alonso M, González-Montalbán N, García-Fruitós E, Villaverde A. Learning about protein solubility from bacterial inclusion bodies. Microb Cell Fact 2009; 8:4. [PMID: 19133126 PMCID: PMC2630952 DOI: 10.1186/1475-2859-8-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 01/08/2009] [Indexed: 11/30/2022] Open
Abstract
The progressive solving of the conformation of aggregated proteins and the conceptual understanding of the biology of inclusion bodies in recombinant bacteria is providing exciting insights on protein folding and quality. Interestingly, newest data also show an unexpected functional and structural complexity of soluble recombinant protein species and picture the whole bacterial cell factory scenario as more intricate than formerly believed.
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Affiliation(s)
- Mónica Martínez-Alonso
- Institute for Biotechnology and Biomedicine and Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain.
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