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Aguirre-Sampieri S, Casañal A, Emsley P, Garza-Ramos G. Cryo-EM structure of bacterial nitrilase reveals insight into oligomerization, substrate recognition, and catalysis. J Struct Biol 2024; 216:108093. [PMID: 38615726 PMCID: PMC7616060 DOI: 10.1016/j.jsb.2024.108093] [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: 01/17/2024] [Revised: 03/26/2024] [Accepted: 04/12/2024] [Indexed: 04/16/2024]
Abstract
Many enzymes can self-assemble into higher-order structures with helical symmetry. A particularly noteworthy example is that of nitrilases, enzymes in which oligomerization of dimers into spiral homo-oligomers is a requirement for their enzymatic function. Nitrilases are widespread in nature where they catalyze the hydrolysis of nitriles into the corresponding carboxylic acid and ammonia. Here, we present the Cryo-EM structure, at 3 Å resolution, of a C-terminal truncate nitrilase from Rhodococcus sp. V51B that assembles in helical filaments. The model comprises a complete turn of the helical arrangement with a substrate-intermediate bound to the catalytic cysteine. The structure was solved having added the substrate to the protein. The length and stability of filaments was made more substantial in the presence of the aromatic substrate, benzonitrile, but not for aliphatic nitriles or dinitriles. The overall structure maintains the topology of the nitrilase family, and the filament is formed by the association of dimers in a chain-like mechanism that stabilizes the spiral. The active site is completely buried inside each monomer, while the substrate binding pocket was observed within the oligomerization interfaces. The present structure is in a closed configuration, judging by the position of the lid, suggesting that the intermediate is one of the covalent adducts. The proximity of the active site to the dimerization and oligomerization interfaces, allows the dimer to sense structural changes once the benzonitrile was bound, and translated to the rest of the filament, stabilizing the helical structure.
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Affiliation(s)
- Sergio Aguirre-Sampieri
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Bioquímica, Circuito Escolar S/N, Ciudad Universitaria, CDMX, Mexico
| | - Ana Casañal
- Human Technopole, Palazzo Italia, Viale Rita Levi‑Montalcini, 1, 20157 Milan, Italy
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Structural Studies Division, Francis Crick Avenue, CB2 0QH Cambridge, England
| | - Georgina Garza-Ramos
- Universidad Nacional Autónoma de México, Facultad de Medicina, Departamento de Bioquímica, Circuito Escolar S/N, Ciudad Universitaria, CDMX, Mexico.
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2
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Zhou SP, Xue YP, Zheng YG. Maximizing the potential of nitrilase: Unveiling their diversity, catalytic proficiency, and versatile applications. Biotechnol Adv 2024; 72:108352. [PMID: 38574900 DOI: 10.1016/j.biotechadv.2024.108352] [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: 11/21/2023] [Revised: 03/10/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024]
Abstract
Nitrilases represent a distinct class of enzymes that play a pivotal role in catalyzing the hydrolysis of nitrile compounds, leading to the formation of corresponding carboxylic acids. These enzymatic entities have garnered significant attention across a spectrum of industries, encompassing pharmaceuticals, agrochemicals, and fine chemicals. Moreover, their significance has been accentuated by mounting environmental pressures, propelling them into the forefront of biodegradation and bioremediation endeavors. Nevertheless, the natural nitrilases exhibit intrinsic limitations such as low thermal stability, narrow substrate selectivity, and inadaptability to varying environmental conditions. In the past decade, substantial efforts have been made in elucidating the structural underpinnings and catalytic mechanisms of nitrilase, providing basis for engineering of nitrilases. Significant breakthroughs have been made in the regulation of nitrilases with ideal catalytic properties and application of the enzymes for industrial productions. This review endeavors to provide a comprehensive discourse and summary of recent research advancements related to nitrilases, with a particular emphasis on the elucidation of the structural attributes, catalytic mechanisms, catalytic characteristics, and strategies for improving catalytic performance of nitrilases. Moreover, the exploration extends to the domain of process engineering and the multifarious applications of nitrilases. Furthermore, the future development trend of nitrilases is prospected, providing important guidance for research and application in the related fields.
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Affiliation(s)
- Shi-Peng Zhou
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, 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
| | - Ya-Ping Xue
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, 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
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, 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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3
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Bhalla TC, Thakur N, Kumar V. Arylacetonitrilases: Potential Biocatalysts for Green Chemistry. Appl Biochem Biotechnol 2024; 196:1769-1785. [PMID: 37453025 DOI: 10.1007/s12010-023-04643-2] [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] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
Nitrilases are the enzymes that catalyze the hydrolysis of nitriles to corresponding carboxylic acid and ammonia. They are broadly categorized into aromatic, aliphatic, and arylacetonitrilases based on their substrate specificity. Most of the studies pertaining to these enzymes in the literature have focused on aromatic and aliphatic nitrilases. However, arylacetonitrilases have attracted the attention of academia and industry in the last several years due to their aryl specificity and enantioselectivity. They have emerged as interesting biocatalytic tools in green chemistry to synthesize useful aryl acids such as mandelic acid and derivatives of phenylacetic acid. The aim of the present review is to collate information on the arylacetonitrilases and their catalytic properties including enantioselectivity and potential applications in organic synthesis.
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Affiliation(s)
- Tek Chand Bhalla
- Department of Biotechnology, Himachal Pradesh University, Himachal Pradesh, Gyan-Path, Shimla, 171005, India.
| | - Neerja Thakur
- Department of Biotechnology, Himachal Pradesh University, Himachal Pradesh, Gyan-Path, Shimla, 171005, India
- Department of Biotechnology and Microbiology, Himachal Pradesh, Rajkiya Kanya Mahavidyalaya, Longwood, Shimla, 171001, India
| | - Vijay Kumar
- Department of Biotechnology, Himachal Pradesh University, Himachal Pradesh, Gyan-Path, Shimla, 171005, India
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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4
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Son Y, Jeong D, Kim K, Cho J. Mechanistic Insights into Nitrile Activation by Cobalt(III)-Hydroperoxo Intermediates: The Influence of Ligand Basicity. JACS AU 2023; 3:3204-3212. [PMID: 38034966 PMCID: PMC10685436 DOI: 10.1021/jacsau.3c00532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 12/02/2023]
Abstract
The versatile applications of nitrile have led to the widespread use of nitrile activation in the synthesis of pharmacologically and industrially valuable compounds. We reported the activation of nitriles using mononuclear cobalt(III)-hydroperoxo complexes, [CoIII(Me3-TPADP)(O2H)(RCN)]2+ [R = Me (2) and Ph (2Ph)], to form cobalt(III)-peroxyimidato complexes, [CoIII(Me3-TPADP)(R-C(=NH)O2)]2+ [R = Me (3) and Ph (3Ph)]. The independence of the rate on the nitrile concentration and the positive Hammett value of 3.2(2) indicated that the reactions occur via an intramolecular nucleophilic attack of the hydroperoxide ligand to the coordinated nitrile carbon atom. In contrast, the previously reported cobalt(III)-hydroperoxo complex, [CoIII(TBDAP)(O2H)(CH3CN)]2+ (2TBDAP), exhibited the deficiency of reactivity toward nitrile. The comparison of pKa values and redox potentials of 2 and 2TBDAP showed that Me3-TPADP had a stronger ligand field strength than that of TBDAP. The density functional theory calculations for 2 and 2TBDAP support that the strengthened ligand field in 2 is mainly due to the replacement of two tert-butyl amine donors in TBDAP with methyl groups in Me3-TPADP, resulting in the compression of the Co-Nax bond lengths. These results provide mechanistic evidence of nitrile activation by the cobalt(III)-hydroperoxo complex and indicate that the basicity dependent on the ligand framework contributes to the ability of nitrile activation.
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Affiliation(s)
- Yeongjin Son
- Department
of Chemistry, Ulsan National Institute of
Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department
of Emerging Materials Science, Daegu Gyeongbuk
Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Donghyun Jeong
- Department
of Chemistry, Ulsan National Institute of
Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyungmin Kim
- Department
of Chemistry, Ulsan National Institute of
Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department
of Emerging Materials Science, Daegu Gyeongbuk
Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Jaeheung Cho
- Department
of Chemistry, Ulsan National Institute of
Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Graduate
School of Carbon Neutrality, Ulsan National
Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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Abdel-Massih RM, Debs E, Othman L, Attieh J, Cabrerizo FM. Glucosinolates, a natural chemical arsenal: More to tell than the myrosinase story. Front Microbiol 2023; 14:1130208. [PMID: 37089539 PMCID: PMC10114928 DOI: 10.3389/fmicb.2023.1130208] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/13/2023] [Indexed: 04/08/2023] Open
Abstract
Glucosinolates are a group of thioglucosides that belong to the class of plant nitrogen-containing natural products. So far, very little biological activity has been associated with intact glucosinolates. The hydrolysis of glucosinolates has, for long, attracted attention because of the potent biological activity of the hydrolysis products. From allelopathic to antiparasitic, antimicrobial and antineoplastic effects, the activity spectrum of the degradation products of typical glucosinolates has been the subject of much research. The present review seeks to address the various means of glucosinolate degradation (thermal, enzymatic, or chemical degradation) and the ensuing products. It also aims to draw a comparative profile of the various antimicrobial effects of these degradation products to provide a further understanding of the biological function of these important compounds.
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Affiliation(s)
| | - Espérance Debs
- Department of Biology, Faculty of Arts and Sciences, University of Balamand, El-Koura, Lebanon
| | - Leen Othman
- Faculty of Medicine and Medical Sciences, University of Balamand, El-Koura, Lebanon
| | - Jihad Attieh
- Department of Biology, Faculty of Arts and Sciences, University of Balamand, El-Koura, Lebanon
| | - Franco M. Cabrerizo
- Instituto Tecnológico de Chascomús, National Scientific and Technical Research Council – National University of General San Martín, Chascomús, Argentina
- Escuela de Bio y Nanotecnologías, National University of General San Martín, Buenos Aires, Argentina
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Salwan R, Sharma V, Das S. Phylogenetic and Structural Analysis of Bacterial Nitrilases for the Biodegradation of Nitrile Compounds. Curr Protein Pept Sci 2022; 23:874-882. [PMID: 36154580 DOI: 10.2174/1389203723666220921154409] [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: 02/20/2022] [Revised: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND Microbial nitrilases play a vital role in the biodegradation of nitrilecontaining pollutants, effluent treatments in chemical and textile industries, and the biosynthesis of Indole-3-acetic acid (IAA) from tryptophan in plants. However, the lack of structural information limits the correlation between its activity and substrate specificity. METHODS The present study involves the genome mining of bacteria for the distribution and diversity of nitrilases, their phylogenetic analysis and structural characterization for motifs/ domains, followed by interaction with substrates. RESULTS Here, we mined the bacterial genomes for nitrilases and correlated their functions to hypothetical, uncharacterized, or putative ones. The comparative genomics revealed four AcNit, As7Nit, Cn5Nit and Cn9Nit predicted nitrilases encoding genes as uncharacterized subgroups of the nitrilase superfamily. The annotation of these nitrilases encoding genes revealed relatedness with nitrilase hydratases and cyanoalanine hydratases. At the proteomics level, the motif analysis of these protein sequences predicted a single motif of 20-28 aa, with glutamate (E), lysine (K) and cysteine (C) residues as a part of catalytic triad along with several other residues at the active site. The structural analysis of the nitrilases revealed geometrical and close conformation in the form of α-helices and β-sheets arranged in a sandwich structure. The catalytic residues constituted the substrate binding pocket and exhibited the broad nitrile substrate spectra for aromatic and aliphatic nitriles-containing compounds. The aromatic amino acid residues Y159 in the active site were predicted to be responsible for substrate specificity. The substitution of non-aromatic alanine residue in place of Y159 completely disrupted the catalytic activity for indole-3-acetonitrile (IAN). CONCLUSION The present study reports genome mining and simulation of structure-function relationship for uncharacterized bacterial nitrilases and their role in the biodegradation of pollutants and xenobiotics, which could be of applications in different industrial sectors.
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Affiliation(s)
- Richa Salwan
- College of Horticulture and Forestry (Dr. YS Parmar University of Horticulture and Forestry), Neri, Hamirpur (HP)- 177 001, India
| | - Vivek Sharma
- University Centre for Research and Development, Chandigarh University (PB)-140413, India
| | - Surajit Das
- Department of Life Science, Laboratory of Environmental Microbiology and Ecology (LEnME), National Institute of Technology Rourkela, Rourkela- 769 008, Odisha, India
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7
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The structures of the C146A variant of the amidase from Pyrococcus horikoshii bound to glutaramide and acetamide suggest the basis of amide recognition. J Struct Biol 2022; 214:107859. [DOI: 10.1016/j.jsb.2022.107859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022]
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8
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Amrutha M, Nampoothiri KM. In silico analysis of nitrilase-3 protein from Corynebacterium glutamicum for bioremediation of nitrile herbicides. J Genet Eng Biotechnol 2022; 20:51. [PMID: 35348933 PMCID: PMC8964915 DOI: 10.1186/s43141-022-00332-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/09/2022] [Indexed: 01/01/2023]
Abstract
Background The nitrile compounds are produced either naturally or synthetically and are highly used in many manufacturing industries such as pharmaceuticals, pesticides, chemicals, and polymers. However, the extensive use and accumulation of these nitrile compounds have caused severe environmental pollution. Nitrilated herbicides are one such toxic substance that will persist in the soil for a long time. Therefore, effective measures must be taken to avoid its pollution to the environment. A variety of nitrile-converting bacterial species have the ability to convert these toxic substances into less toxic ones by using enzymatic processes. Among the bacterial groups, actinobacteria family members show good degradation capacity on these pollutants. The soil-dwelling Gram-positive industrial microbe Corynebacterium glutamicum is one such family member and its nitrile-degradation pathway is not well studied yet. In order to understand the effectiveness of using C. glutamicum for the degradation of such nitrile herbicides, an in silico approach has been done. In this perspective, this work focus on the structural analysis and molecular docking studies of C. glutamicum with nitrilated herbicides such as dichlobenil, bromoxynil, and chloroxynil. Results The bioinformatics analysis using different tools and software helped to confirm that the genome of C. glutamicum ATCC 13032 species have genes (cg 3093) codes for carbon-nitrogen hydrolase enzyme, which specifically act on non-peptide bond present in the nitrile compounds. The conserved domain analysis indicated that this protein sequence was nitrilase-3 and comes under the nitrilase superfamily. The multiple sequence alignment analysis confirmed that the conserved catalytic triad residues were 40E, 115K, and 151C, and the existence of nitrilase-3 protein in the genome of Corynebacterium sp. was evaluated by a phylogenetic tree. The analysis of physico-chemical properties revealed that alanine is the most abounded amino acid (10.20%) in the nitrilase-3 protein, and these properties influence the substrate specificity of aliphatic and aromatic nitrile compounds. The homology modelled protein showed better affinity towards nitrile herbicides such as 2,6-dichlorobenzamide (BAM) and 3,5-dichloro-4-hydroxy-benzamide (CIAM) with the affinity value of − 5.8 and − 5.7 kcal/mol respectively. Conclusions The in silico studies manifested that C. glutamicum ATCC 13032 is one of the promising strains for the bioremediation of nitrilated herbicides contaminated soil.
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Affiliation(s)
- M Amrutha
- Microbial Processes and Technology Division (MPTD), CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum, Kerala, 695019, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - K Madhavan Nampoothiri
- Microbial Processes and Technology Division (MPTD), CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum, Kerala, 695019, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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9
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Phelan RM, Abrahamson MJ, Brown JTC, Zhang RK, Zwick CR. Development of Scalable Processes with Underutilized Biocatalyst Classes. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryan M. Phelan
- Process Research and Development, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Michael J. Abrahamson
- Operations Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Jesse T. C. Brown
- Process Research and Development, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Ruijie K. Zhang
- Discovery Chemistry and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Christian R. Zwick
- Process Research and Development, AbbVie Inc., North Chicago, Illinois 60064, United States
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10
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Rational regulation of reaction specificity of nitrilase for efficient biosynthesis of 2-chloronicotinic acid through a single site mutation. Appl Environ Microbiol 2022; 88:e0239721. [PMID: 35020449 DOI: 10.1128/aem.02397-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrilase-catalyzed hydrolysis of 2-chloronicotinonitrile (2-CN) is a promising approach for efficient synthesis of 2-chloronicotinic acid (2-CA). Development of nitrilase with ideal catalytic properties is crucial for the biosynthetic route with industrial potentail. Herein, a nitrilase from Rhodococcus zopfii (RzNIT), which showed much higher hydration activity than hydrolysis activity, was designed for efficient hydrolysis of 2-CN. Two residues (N165 and W167) significantly affecting the reaction specificity were precisely identified. By tuning these two residues, a single mutation of W167G with abolished hydration activity and 20-fold improved hydrolysis activity was obtained. Molecular dynamics simulation and molecular docking revealed that the mutation generated a larger binding pocket, causing the substrate 2-CN bound more deeply in the pocket and the formation of delocalized π bond between the residues W190 and Y196, which reduced the negative influence of steric hindrance and electron effect caused by chlorine substituent. With mutant W167G as biocatalyst, 100 mM 2-CN was exclusively converted into 2-CA within 16 h. The study provides useful guidance in nitrilase engineering for simultaneous improvement of reaction specificity and catalytic activity, which are highly desirable in value-added carboxylic acids production from nitriles hydrolysis. Importance 2-CA is an important building block for agrochemicals and pharmaceuticals with rapid increase in demand in recent years. It is currently manufactured from 3-cyanopyridine by chemical methods. However, during the final step of 2-CN hydrolysis under high temperature and strong alkaline conditions, by-product 2-CM was generated except for the target product, leading to low yield and tedious separation steps. Nitrilase-mediated hydrolysis is regarded as a promising alternative for 2-CA production, which proceeds under mild conditions. Nevertheless, nitrilase capable of efficient hydrolysis of 2-CN was not reported till now, since the enzymes showed either extremely low activity or surprisingly high hydration activity towards 2-CN. Herein, the reaction specificity of RzNIT was precisely tuned through a single site mutation. The mutant exhibited remarkably enhanced hydrolysis activity without formation of by-products, providing a robust biocatalyst for 2-CA biosynthesis with industrial potential.
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Epova EY, Shevelev AB, Shurubor YI, Cooper AJL, Biryukova YK, Bogdanova ES, Tyno YY, Lebedeva AA, Krasnikov BF. A novel efficient producer of human ω-amidase (Nit2) in Escherichia coli. Anal Biochem 2021; 632:114332. [PMID: 34391728 DOI: 10.1016/j.ab.2021.114332] [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: 04/10/2021] [Revised: 07/09/2021] [Accepted: 08/06/2021] [Indexed: 11/25/2022]
Abstract
Nit2/ω-amidase catalyzes the hydrolysis of α-ketoglutaramate (KGM, the α-keto acid analogue of glutamine) to α-ketoglutarate and ammonia. The enzyme also catalyzes the amide hydrolysis of monoamides of 4- and 5-C-dicarboxylates, including α-ketosuccinamate (KSM, the α-keto acid analogue of asparagine) and succinamate (SM). Here we describe an inexpensive procedure for high-yield expression of human Nit2 (hNit2) in Escherichia coli and purification of the expressed protein. This work includes: 1) the design of a genetic construct (pQE-Nit22) obtained from the previously described construct (pQE-Nit2) by replacing rare codons within an 81 bp-long DNA fragment "preferred" by E. coli near the translation initiation site; 2) methods for producing and maintaining the pQE-Nit22 construct; 3) purification of recombinant hNit2; and 4) activity measurements of the purified enzyme with KGM and SM. Important features of the hNit2 gene within the pQE-Nit22 construct are: 1) optimized codon composition, 2) the presence of an N-terminus His6 tag immediately after the initiating codon ATG (Met) that permits efficient purification of the end-product on a Ni-NTA-agarose column. We anticipate that the availability of high yield hNit2/ω-amidase will be helpful in elucidating the normal and pathological roles of this enzyme and in the design of specific inhibitors.
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Affiliation(s)
- Ekaterina Yu Epova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexei B Shevelev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Arthur J L Cooper
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA
| | - Yulia K Biryukova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elena S Bogdanova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Plekhanov Russian University of Economics, Moscow, Russia
| | - Yaroslav Ya Tyno
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Anna A Lebedeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Boris F Krasnikov
- Centre for Strategic Planning of FMBA of the Russian Federation, Moscow, Russia; Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA.
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12
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Cavalieri V. The Expanding Constellation of Histone Post-Translational Modifications in the Epigenetic Landscape. Genes (Basel) 2021; 12:genes12101596. [PMID: 34680990 PMCID: PMC8535662 DOI: 10.3390/genes12101596] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/02/2021] [Accepted: 10/05/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a nucleosome-based chromatin structure accompanied the evolutionary transition from prokaryotes to eukaryotes. In this scenario, histones became the heart of the complex and precisely timed coordination between chromatin architecture and functions during adaptive responses to environmental influence by means of epigenetic mechanisms. Notably, such an epigenetic machinery involves an overwhelming number of post-translational modifications at multiple residues of core and linker histones. This review aims to comprehensively describe old and recent evidence in this exciting field of research. In particular, histone post-translational modification establishing/removal mechanisms, their genomic locations and implication in nucleosome dynamics and chromatin-based processes, as well as their harmonious combination and interdependence will be discussed.
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Affiliation(s)
- Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
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13
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Scott ME, Wang X, Humphreys LD, Geier MJ, Kannan B, Chan J, Brown G, Dourado DFAR, Gray D, Mix S, Pukin A. Enzyme Optimization and Process Development for a Scalable Synthesis of (R)-2-Methoxymandelic Acid. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.1c00250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mark E. Scott
- Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta, Canada, T6S 1A1
| | - Xiaotian Wang
- Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta, Canada, T6S 1A1
| | - Luke D. Humphreys
- Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta, Canada, T6S 1A1
| | - Michael J. Geier
- Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta, Canada, T6S 1A1
| | - Balamurali Kannan
- Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, Alberta, Canada, T6S 1A1
| | - Johann Chan
- Gilead Sciences, Inc, 333 Lakeside Drive, Foster City, California 94404, United States
| | - Gareth Brown
- Almac Sciences, 20 Seagoe Industrial Est., Craigavon BT63 5QD, U.K
| | | | - Darren Gray
- Almac Sciences, 20 Seagoe Industrial Est., Craigavon BT63 5QD, U.K
| | - Stefan Mix
- Almac Sciences, 20 Seagoe Industrial Est., Craigavon BT63 5QD, U.K
| | - Aliaksei Pukin
- Almac Sciences, 20 Seagoe Industrial Est., Craigavon BT63 5QD, U.K
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14
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Silva Teixeira CS, Sousa SF, Cerqueira NMFSA. An Unsual Cys-Glu-Lys Catalytic Triad is Responsible for the Catalytic Mechanism of the Nitrilase Superfamily: A QM/MM Study on Nit2. Chemphyschem 2021; 22:796-804. [PMID: 33463886 DOI: 10.1002/cphc.202000751] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/13/2021] [Indexed: 12/29/2022]
Abstract
Nitrilase 2 (Nit2) is a representative member of the nitrilase superfamily that catalyzes the hydrolysis of α-ketosuccinamate into oxaloacetate. It has been associated with the metabolism of rapidly dividing cells like cancer cells. The catalytic mechanism of Nit2 employs a catalytic triad formed by Cys191, Glu81 and Lys150. The Cys191 and Glu81 play an active role during the catalytic process while the Lys150 is shown to play only a secondary role. The results demonstrate that the catalytic mechanism of Nit2 involves four steps. The nucleophilic attack of Cys191 to the α-ketosuccinamate, the formation of two tetrahedral enzyme adducts and the hydrolysis of a thioacyl-enzyme intermediate, from which results the formation of oxaloacetate and enzymatic turnover. The rate limiting step of the catalytic process is the formation of the first tetrahedral intermediate with a calculated activation free energy of 18.4 kcal/mol, which agrees very well with the experimental kcat (17.67 kcal/mol).
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Affiliation(s)
- Carla S Silva Teixeira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, 4200-319, Portugal
| | - Sérgio F Sousa
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, 4200-319, Portugal
| | - Nuno M F S A Cerqueira
- UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, Porto, 4200-319, Portugal
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15
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Jones LB, Wang X, Gullapalli JS, Kunz DA. Characterization of the Nit6803 nitrilase homolog from the cyanotroph Pseudomonas fluorescens NCIMB 11764. Biochem Biophys Rep 2021; 25:100893. [PMID: 33506113 PMCID: PMC7815647 DOI: 10.1016/j.bbrep.2020.100893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 11/01/2022] Open
Abstract
We report the purification and characterization of a nitrilase (E.C. 3.5.5.1) (Nit11764) essential for the assimilation of cyanide as the sole nitrogen source by the cyanotroph, Pseudomonas fluorescens NCIMB 11764. Nit11764, is a member of a family of homologous proteins (nitrile_sll0784) for which the genes typically reside in a conserved seven-gene cluster known as Nit1C. The physical properties and substrate specificity of Nit11764 resemble those of Nit6803, the current reference protein for the family, and the only true nitrilase that has been crystallized. The substrate binding pocket of the two enzymes places the substrate in direct proximity to the active site nucleophile (C160) and conserved catalytic triad (Glu44, Lys126). The two enzymes exhibit a similar substrate profile, however, for Nit11764, cinnamonitrile, was found to be an even better substrate than fumaronitrile the best substrate previously identified for Nit6803. A higher affinity for cinnamonitrile (Km 1.27 mM) compared to fumaronitrile (Km 8.57 mM) is consistent with docking studies predicting a more favorable interaction with hydrophobic residues lining the binding pocket. By comparison, 3,4-dimethoxycinnamonitrile was a poorer substrate the substituted methoxyl groups apparently hindering entry into the binding pocket. in situ 1H NMR studies revealed that only one of the two nitrile substituents in the dinitrile, fumaronitrile, was attacked yielding trans-3-cyanoacrylate (plus ammonia) as a product. The essentiality of Nit11764 for cyanotrophy remains uncertain given that cyanide itself is a poor substrate and the catalytic efficiencies for even the best of nitrile substrates (~5 × 103 M-1 s-1) is less than stellar.
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Affiliation(s)
- Lauren B Jones
- Division of Biochemistry and Molecular Biology, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Xiaoqiang Wang
- Division of Biochemistry and Molecular Biology, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA.,BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Jaya S Gullapalli
- Division of Biochemistry and Molecular Biology, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Daniel A Kunz
- Division of Biochemistry and Molecular Biology, Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
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16
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Chen Z, Wang H, Yang L, Jiang S, Wei D. Significantly enhancing the stereoselectivity of a regioselective nitrilase for the production of ( S)-3-cyano-5-methylhexanoic acid using an MM/PBSA method. Chem Commun (Camb) 2021; 57:931-934. [PMID: 33398309 DOI: 10.1039/d0cc07106d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The present investigation describes the successful molecular modification of a regio- and stereo-specific nitrilase toward rac-ISBN to (S)-CMHA, a critical intermediate in the preparation of optically pure pregabalin. Two hotspots of Trp57 and Val134 were identified based on the classical binding free energy molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) calculation method. Mutants W57F/V134M and W57Y/V134M were successfully obtained with high enantioselectivity (E >300). Furthermore, these two mutants were efficiently capable of kinetic resolution of rac-ISBN to (S)-CMHA, with both exhibiting a high e.e. (>99.9%), as well as conversion ratios of 43.8% and 40.9%, respectively. Docking and molecular dynamics simulation analysis clarified that the underlying mechanisms were related to a DC-S switch and the formation of a hydrogen bond in the active center of nitrilase. The successful utilization of the MM/PBSA method for identifying hotspots that modulate the stereoselectivity in our study could provide guidelines for the molecular modification of nitrilases, and the mutants obtained could be potentially utilized for the industrial preparation of optically pure pregabalin.
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Affiliation(s)
- Zhi Chen
- 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.
| | - Lin Yang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| | - Shuiqing Jiang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, 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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17
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Toprak A, Tükel SS, Yildirim D. Stabilization of multimeric nitrilase via different immobilization techniques for hydrolysis of acrylonitrile to acrylic acid. BIOCATAL BIOTRANSFOR 2021. [DOI: 10.1080/10242422.2020.1869217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Ali Toprak
- Vocational School of Acigol, University of Nevsehir Haci Bektas Veli, Nevsehir, Turkey
- Department of Chemistry, Faculty of Science and Letters, University of Cukurova, Adana, Turkey
| | - S. Seyhan Tükel
- Department of Chemistry, Faculty of Science and Letters, University of Cukurova, Adana, Turkey
| | - Deniz Yildirim
- Department of Chemical Engineering, Faculty of Ceyhan Engineering, University of Cukurova, Adana, Turkey
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18
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Terada A, Komatsu D, Ogawa T, Flamandita D, Sahlan M, Nishimura M, Yohda M. Isolation of cyanide-degrading bacteria and molecular characterization of its cyanide-degrading nitrilase. Biotechnol Appl Biochem 2020; 69:183-189. [PMID: 33377552 DOI: 10.1002/bab.2095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/25/2020] [Indexed: 11/07/2022]
Abstract
Hydrogen cyanide is an industrially important chemical, and its annual production is more than 1.5 million tons. Because of its toxicity, the cyanide-containing effluents from industries have caused many environmental problems. Among various methods to treat the contaminated soils or water, the biological degradation is regarded to be promising. We isolated two cyanide-degrading microorganisms, Pedobacter sp. EBE-1 and Bacillus sp. EBE-2, from soil contaminated with cyanide. Among these bacteria, Bacillus sp. EBE-2 exhibited significantly a high cyanide-degrading ability. Bacillus sp. EBE-2 might be used for the remediation of cyanide contaminated water or soil. A nitrilase gene was cloned from Bacillus sp. EBE-2. Bacillus nitrilase was expressed in Escherichia coli and purified. Bacillus nitrilase exhibited cyanide-degrading activity as a large oligomer. Since formic acid formation from cyanide was observed, Bacillus nitrilase is likely to be a cyanide hydrolase. Although there exist various homologous enzymes annotated as carbon-nitrogen family hydrolases, this is the first report on the cyanide degrading activity. The structure and catalytic site of Bacillus nitrilase were studied by homology modeling and molecular docking simulation.
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Affiliation(s)
- Ayane Terada
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Daisuke Komatsu
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
- EnBio Engineering, Chiyoda, Tokyo, Japan
| | - Takahiro Ogawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Darin Flamandita
- Department of Chemical Engineering, Universitas Indonesia, Depok, Indonesia
| | - Muhamad Sahlan
- Department of Chemical Engineering, Universitas Indonesia, Depok, Indonesia
| | | | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
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19
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Gurung AB, Bhutia JT, Bhattacharjee A. High-throughput virtual screening of novel potent inhibitor(s) for Human Vanin-1 enzyme. J Biomol Struct Dyn 2020; 40:4208-4223. [PMID: 33289461 DOI: 10.1080/07391102.2020.1854857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Vanin-1 (VNN1) is a glycosylphosphatidylinositol (GPI)-anchored ectoenzyme which hydrolyzes pantetheine to pantothenic acid and cysteamine. It has emerged as a promising drug target for many human diseases associated with oxidative stress and inflammatory pathways. In the present study we used structure-based virtual screening approach for the identification of small molecule inhibitors of vanin-1. A chemical library consisting of natural compounds, synthetic compounds and RRV analogs were screened for drug-like molecules. The filtered molecules were subjected to molecular docking studies. Three potential hits-ZINC04073864 (Natural compound), CID227017 (synthetic compound) and CID129558381 (RRV analog)-were identified for the target enzyme. The molecules form good number of hydrogen bonds with the catalytic residues such as Glu79, Lys178 and Cys211. The apo-VNN1 and VNN1-ligand complexes were subjected to molecular dynamics (MD) simulation for 30 ns. The geometric properties such as root mean square deviation, radius of gyration, solvent accessible surface area, number of hydrogen bonds and the distance between the catalytic triad residues-Glu79, Lys178 and Cys211 were altered upon binding of the compounds. Essential dynamics and entropic studies further confirmed that the fluctuations in VNN1 decrease upon binding of the compounds. The lead molecules were stable throughout the simulation time period. Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) studies showed that Van der Waals interaction energy contributes significantly to the total binding free energy. Thus, our study reveals three lead molecules-ZINC04073864, CID227017 and CID129558381 as potential inhibitors of Vanin-1 which can be validated through further studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arun Bahadur Gurung
- Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India.,Department of Basic Sciences and Social Sciences, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Jigmi Tshering Bhutia
- Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Atanu Bhattacharjee
- Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
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20
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Phe-140 Determines the Catalytic Efficiency of Arylacetonitrilase from Alcaligenes faecalis. Int J Mol Sci 2020; 21:ijms21217859. [PMID: 33113984 PMCID: PMC7660301 DOI: 10.3390/ijms21217859] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/03/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
Arylacetonitrilase from Alcaligenes faecalis ATCC8750 (NitAF) hydrolyzes various arylacetonitriles to the corresponding carboxylic acids. A systematic strategy of amino acid residue screening through sequence alignment, followed by homology modeling and biochemical confirmation was employed to elucidate the determinant of NitAF catalytic efficiency. Substituting Phe-140 in NitAF (wild-type) to Trp did not change the catalytic efficiency toward phenylacetonitrile, an arylacetonitrile. The mutants with nonpolar aliphatic amino acids (Ala, Gly, Leu, or Val) at location 140 had lower activity, and those with charged amino acids (Asp, Glu, or Arg) exhibited nearly no activity for phenylacetonitrile. Molecular modeling showed that the hydrophobic benzene ring at position 140 supports a mechanism in which the thiol group of Cys-163 carries out a nucleophilic attack on a cyanocarbon of the substrate. Characterization of the role of the Phe-140 residue demonstrated the molecular determinant for the efficient formation of arylcarboxylic acids.
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21
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Shen JD, Cai X, Liu ZQ, Zheng YG. Nitrilase: a promising biocatalyst in industrial applications for green chemistry. Crit Rev Biotechnol 2020; 41:72-93. [PMID: 33045860 DOI: 10.1080/07388551.2020.1827367] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nitrilases are widely distributed in nature and are able to hydrolyze nitriles into their corresponding carboxylic acids and ammonia. In industry, nitrilases have been used as green biocatalysts for the production of high value-added products. To date, biocatalysts are considered to be important alternatives to chemical catalysts due to increasing environmental problems and resource scarcity. This review provides an overview of recent advances of nitrilases in aspects of distribution, enzyme screening, molecular structure and catalytic mechanism, protein engineering, and their potential applications in industry.
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Affiliation(s)
- Ji-Dong Shen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
| | - Xue Cai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, P.R. China
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22
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Plant Nitrilase Homologues in Fungi: Phylogenetic and Functional Analysis with Focus on Nitrilases in Trametes versicolor and Agaricus bisporus. Molecules 2020; 25:molecules25173861. [PMID: 32854275 PMCID: PMC7503981 DOI: 10.3390/molecules25173861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/15/2020] [Accepted: 08/16/2020] [Indexed: 11/17/2022] Open
Abstract
Fungi contain many plant-nitrilase (NLase) homologues according to database searches. In this study, enzymes NitTv1 from Trametes versicolor and NitAb from Agaricus bisporus were purified and characterized as the representatives of this type of fungal NLase. Both enzymes were slightly more similar to NIT4 type than to NIT1/NIT2/NIT3 type of plant NLases in terms of their amino acid sequences. Expression of the synthetic genes in Escherichia coli Origami B (DE3) was induced with 0.02 mM isopropyl β-D-1-thiogalactopyranoside at 20 °C. Purification of NitTv1 and NitAb by cobalt affinity chromatography gave ca. 6.6 mg and 9.6 mg of protein per 100 mL of culture medium, respectively. Their activities were determined with 25 mM of nitriles in 50 mM Tris/HCl buffer, pH 8.0, at 30 °C. NitTv1 and NitAb transformed β-cyano-L-alanine (β-CA) with the highest specific activities (ca. 132 and 40 U mg−1, respectively) similar to plant NLase NIT4. β-CA was transformed into Asn and Asp as in NIT4 but at lower Asn:Asp ratios. The fungal NLases also exhibited significant activities for (aryl)aliphatic nitriles such as 3-phenylpropionitrile, cinnamonitrile and fumaronitrile (substrates of NLase NIT1). NitTv1 was more stable than NitAb (at pH 5–9 vs. pH 5–7). These NLases may participate in plant–fungus interactions by detoxifying plant nitriles and/or producing plant hormones. Their homology models elucidated the molecular interactions with various nitriles in their active sites.
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23
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Lauder K, Anselmi S, Finnigan JD, Qi Y, Charnock SJ, Castagnolo D. Enantioselective Synthesis of α-Thiocarboxylic Acids by Nitrilase Biocatalysed Dynamic Kinetic Resolution of α-Thionitriles. Chemistry 2020; 26:10422-10426. [PMID: 32239730 PMCID: PMC7496879 DOI: 10.1002/chem.202001108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/01/2020] [Indexed: 11/14/2022]
Abstract
The enantioselective synthesis of α-thiocarboxylic acids by biocatalytic dynamic kinetic resolution (DKR) of nitrile precursors exploiting nitrilase enzymes is described. A panel of 35 nitrilase biocatalysts were screened and enzymes Nit27 and Nit34 were found to catalyse the DKR of racemic α-thionitriles under mild conditions, affording the corresponding carboxylic acids with high conversions and good-to-excellent ee. The ammonia produced in situ during the biocatalytic transformation favours the racemization of the nitrile enantiomers and, in turn, the DKR without the need of any external additive base.
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Affiliation(s)
- Kate Lauder
- School of Cancer and Pharmaceutical SciencesKing's College London150 Stamford StreetSE1 9NHLondonUK
| | - Silvia Anselmi
- School of Cancer and Pharmaceutical SciencesKing's College London150 Stamford StreetSE1 9NHLondonUK
| | - James D. Finnigan
- Prozomix LimitedWest End Industrial Estate, HaltwhistleNorthumberlandNE49 9HAUK
| | - Yuyin Qi
- Prozomix LimitedWest End Industrial Estate, HaltwhistleNorthumberlandNE49 9HAUK
| | - Simon J. Charnock
- Prozomix LimitedWest End Industrial Estate, HaltwhistleNorthumberlandNE49 9HAUK
| | - Daniele Castagnolo
- School of Cancer and Pharmaceutical SciencesKing's College London150 Stamford StreetSE1 9NHLondonUK
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24
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Dong A, Yang Y, Liu S, Zenda T, Liu X, Wang Y, Li J, Duan H. Comparative proteomics analysis of two maize hybrids revealed drought-stress tolerance mechanisms. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1805015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Anyi Dong
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, PR China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, Hebei, PR China
| | - Yatong Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, PR China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, Hebei, PR China
| | - Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, PR China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, Hebei, PR China
| | - Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, PR China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, Hebei, PR China
| | - Xinyue Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, PR China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, Hebei, PR China
| | - Yafei Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, PR China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, Hebei, PR China
| | - Jiao Li
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, PR China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, Hebei, PR China
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, PR China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, Hebei, PR China
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25
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Wang SZ, Wang ZK, Gong JS, Qin J, Dong TT, Xu ZH, Shi JS. Improving the biocatalytic performance of co-immobilized cells harboring nitrilase via addition of silica and calcium carbonate. Bioprocess Biosyst Eng 2020; 43:2201-2207. [PMID: 32661565 DOI: 10.1007/s00449-020-02405-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/07/2020] [Indexed: 11/27/2022]
Abstract
To improve nicotinic acid (NA) yield and meet industrial application requirements of sodium alginate-polyvinyl alcohol (SA-PVA) immobilized cells of Pseudomonas putida mut-D3 harboring nitrilase, inorganic materials were added to the SA-PVA immobilized cells to improve mechanical strength and mass transfer performance. The concentrations of inorganic materials were optimized to be 2.0% silica and 0.6% CaCO3. The optimal pH and temperature for SA-PVA immobilized cells and composite immobilized cells were both 8.0 and 45 °C, respectively. The half-lives of composite immobilized cells were 271.48, 150.92, 92.92 and 33.12 h, which were 1.40-, 1.35-, 1.22- and 1.63-fold compared to SA-PVA immobilized cells, respectively. The storage stability of the composite immobilized cells was slightly increased. The composite immobilized cells could convert 14 batches of 3-cyanopyridine with feeding concentration of 250 mM and accumulate 418 g ·L-1 nicotinic acid, while the SA-PVA immobilized cells accumulated 346 g L-1 nicotinic acid.
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Affiliation(s)
- Shun-Zhi Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Zi-Kai Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, People's Republic of China.
| | - Jiufu Qin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Ting-Ting Dong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Zheng-Hong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, People's Republic of China.
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26
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Kumari P, Poddar R. Computational modeling for mutational analysis of nitrilase enzyme towards enhancement of binding empathy. J Biomol Struct Dyn 2020; 39:2289-2301. [PMID: 32216606 DOI: 10.1080/07391102.2020.1747546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Nitrilase enzyme (a green catalyst) is an industrially important enzyme which hydrolyses various nitrile compounds (containing -CN functional group) into amides and corresponding carboxylic acids. The current study explored the binding affinity and a method to enhance the catalysis activity of the enzyme using computational approaches. Four mutants were generated using sequential site-directed mutagenesis aiming that an increase in hydrogen bonds that will further increase binding efficiency towards the ligand. Molecular dynamics simulation was rigorously performed to check the stability of those mutants followed by docking to verify its interaction with the ligand. Various statistical dynamics analyses were performed to validate the structure. All the studies predict that built mutants are stable. Mutants 2 and 3 showed a better affinity towards acrylamide by forming the highest number of hydrogen bonds implying better catalysis. The binding affinity values of the Mutant 2 and Mutant 3 with acrylamide are -7.44 kcal/mol and -7.17 kcal/mol, respectively. This study may prove useful for the industry to develop efficient nitrilase enzymes with improved catalytic activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priya Kumari
- Department of Bioengineering, Birla Institute of Technology-Mesra, Ranchi, JH, India
| | - Raju Poddar
- Department of Bioengineering, Birla Institute of Technology-Mesra, Ranchi, JH, India
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Chuenchor W, Doukov TI, Chang KT, Resto M, Yun CS, Gerratana B. Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD + synthetases. Nat Commun 2020; 11:16. [PMID: 31911602 PMCID: PMC6946656 DOI: 10.1038/s41467-019-13845-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/03/2019] [Indexed: 12/15/2022] Open
Abstract
NAD+ synthetase is an essential enzyme of de novo and recycling pathways of NAD+ biosynthesis in Mycobacterium tuberculosis but not in humans. This bifunctional enzyme couples the NAD+ synthetase and glutaminase activities through an ammonia tunnel but free ammonia is also a substrate. Here we show that the Homo sapiens NAD+ synthetase (hsNadE) lacks substrate specificity for glutamine over ammonia and displays a modest activation of the glutaminase domain compared to tbNadE. We report the crystal structures of hsNadE and NAD+ synthetase from M. tuberculosis (tbNadE) with synthetase intermediate analogues. Based on the observed exclusive arrangements of the domains and of the intra- or inter-subunit tunnels we propose a model for the inter-domain communication mechanism for the regulation of glutamine-dependent activity and NH3 transport. The structural and mechanistic comparison herein reported between hsNadE and tbNadE provides also a starting point for future efforts in the development of anti-TB drugs.
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Affiliation(s)
- Watchalee Chuenchor
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Tzanko I Doukov
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, 94025, USA
| | - Kai-Ti Chang
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Melissa Resto
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Chang-Soo Yun
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Barbara Gerratana
- Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
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A comparative multivariate analysis of nitrilase enzymes: An ensemble based computational approach. Comput Biol Chem 2019; 83:107095. [DOI: 10.1016/j.compbiolchem.2019.107095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/20/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022]
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Comparative Analysis of the Conversion of Mandelonitrile and 2-Phenylpropionitrile by a Large Set of Variants Generated from a Nitrilase Originating from Pseudomonas fluorescens EBC191. Molecules 2019; 24:molecules24234232. [PMID: 31766372 PMCID: PMC6930498 DOI: 10.3390/molecules24234232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 11/17/2022] Open
Abstract
The arylacetonitrilase from the bacterium Pseudomonas fluorescens EBC191 has been intensively studied as a model to understand the molecular basis for the substrate-, reaction-, and enantioselectivity of nitrilases. The nitrilase converts various aromatic and aliphatic nitriles to the corresponding acids and varying amounts of the corresponding amides. The enzyme has been analysed by site-specific mutagenesis and more than 50 different variants have been generated and analysed for the conversion of (R,S)-mandelonitrile and (R,S)-2-phenylpropionitrile. These comparative analyses demonstrated that single point mutations are sufficient to generate enzyme variants which hydrolyse (R,S)-mandelonitrile to (R)-mandelic acid with an enantiomeric excess (ee) of 91% or to (S)-mandelic acid with an ee-value of 47%. The conversion of (R,S)-2-phenylpropionitrile by different nitrilase variants resulted in the formation of either (S)- or (R)-2-phenylpropionic acid with ee-values up to about 80%. Furthermore, the amounts of amides that are produced from (R,S)-mandelonitrile and (R,S)-2-phenylpropionitrile could be changed by single point mutations between 2%–94% and <0.2%–73%, respectively. The present study attempted to collect and compare the results obtained during our previous work, and to obtain additional general information about the relationship of the amide forming capacity of nitrilases and the enantiomeric composition of the products.
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Zhang Q, Lu X, Zhang Y, Tang X, Zheng R, Zheng Y. Development of a robust nitrilase by fragment swapping and semi‐rational design for efficient biosynthesis of pregabalin precursor. Biotechnol Bioeng 2019; 117:318-329. [DOI: 10.1002/bit.27203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/06/2019] [Accepted: 10/13/2019] [Indexed: 01/20/2023]
Affiliation(s)
- Qin Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Xia‐Feng Lu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Yan Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Xiao‐Ling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Ren‐Chao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
| | - Yu‐Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and BioengineeringZhejiang University of TechnologyHangzhou China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of EducationZhejiang University of TechnologyHangzhou China
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Li J, Jia Y, Lin A, Hanna M, Chelico L, Xiao W, Moore SA. Structure of Ddi2, a highly inducible detoxifying metalloenzyme from Saccharomyces cerevisiae. J Biol Chem 2019; 294:10674-10685. [PMID: 31152065 PMCID: PMC6615675 DOI: 10.1074/jbc.ra118.006394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/21/2019] [Indexed: 11/06/2022] Open
Abstract
Cyanamide (H2N-CN) is used to break bud dormancy in woody plants and to deter alcohol use in humans. The biological effects of cyanamide in both these cases require the enzyme catalase. We previously demonstrated that Saccharomyces cerevisiae exposed to cyanamide resulted in strong induction of DDI2 gene expression. Ddi2 enzymatically hydrates cyanamide to urea and belongs to the family of HD-domain metalloenzymes (named after conserved active-site metal-binding His and Asp residues). Here, we report the X-ray structure of yeast Ddi2 to 2.6 Å resolution, revealing that Ddi2 is a dimeric zinc metalloenzyme. We also confirm that Ddi2 shares structural similarity with other known HD-domain proteins. HD residues His-55, His-88, and Asp-89 coordinate the active-site zinc, and the fourth zinc ligand is a water/hydroxide molecule. Other HD domain enzymes have a second aspartate metal ligand, but in Ddi2 this residue (Thr-157) does not interact with the zinc ion. Several Ddi2 active-site point mutations exhibited reduced catalytic activity. We kinetically and structurally characterized H137N and T157V mutants of Ddi2. A cyanamide soak of the Ddi2-T157V enzyme revealed cyanamide bound directly to the Zn2+ ion, having displaced the zinc-bound water molecule. The mode of cyanamide binding to Ddi2 resembles cyanamide binding to the active-site zinc of carbonic anhydrase, a known cyanamide hydratase. Finally, we observed that the sensitivity of ddi2Δ ddi3Δ to cyanamide was not rescued by plasmids harboring ddi2-H137N or ddi2-TI57V variants, demonstrating that yeast cells require a functioning cyanamide hydratase to overcome cyanamide-induced growth defects.
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Affiliation(s)
- Jia Li
- From the Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada and
| | - Yunhua Jia
- From the Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada and
| | - Aiyang Lin
- From the Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada and
- the Beijing Key Laboratory of DNA Damage Responses, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Michelle Hanna
- From the Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada and
| | - Linda Chelico
- From the Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada and
| | - Wei Xiao
- From the Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada and
- the Beijing Key Laboratory of DNA Damage Responses, College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Stanley A Moore
- From the Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada and
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Chen Z, Zhao J, Jiang S, Wei D. Recent research advancements on regioselective nitrilase: fundamental and applicative aspects. Appl Microbiol Biotechnol 2019; 103:6393-6405. [PMID: 31236614 DOI: 10.1007/s00253-019-09915-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 11/29/2022]
Abstract
Nitrilase-mediated biocatalysis reactions have been continuously arousing wide interests by scholars and entrepreneurs in organic synthesis over the past six decades. Since regioselective nitrilases could hydrolyze only one cyano group of dinitriles into corresponding cyanocarboxylic acids, which are virtually impossible by chemical hydrolysis and of interest for a variety of applications, it becomes particularly appealing to synthetic chemists. The aim of the current review is to summarize the recent advancements on regioselective nitrilases concerning their fundamental researches and applications in synthesis of a series of high-value fine chemicals and pharmaceuticals. Carbon chain lengths and substituent group positions of substrates are found to be two crucial factors in affecting regioselectivity of nitrilase. Practical applications of regioselective nitrilases in synthesis of 1,5-dimethyl-2-piperidone (1,5-DMPD), atorvastatin, gabapentin, (R)-baclofen, and (S)-pregabalin were systematically reviewed. Future perspectives clearly elucidating the mechanism of regioselectivity and further molecular modifications of regioselective nitrilases integrating within silico technology for industrial applications were discussed.
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Affiliation(s)
- Zhi Chen
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiang Zhao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Shuiqing Jiang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, 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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Chhiba-Govindjee VP, van der Westhuyzen CW, Bode ML, Brady D. Bacterial nitrilases and their regulation. Appl Microbiol Biotechnol 2019; 103:4679-4692. [DOI: 10.1007/s00253-019-09776-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/25/2022]
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Atalah J, Cáceres-Moreno P, Espina G, Blamey JM. Thermophiles and the applications of their enzymes as new biocatalysts. BIORESOURCE TECHNOLOGY 2019; 280:478-488. [PMID: 30826176 DOI: 10.1016/j.biortech.2019.02.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 05/20/2023]
Abstract
Ecological and efficient alternatives to industrial processes have sparked interest for using microorganisms and enzymes as biocatalysts. One of the difficulties is finding candidates capable of resisting the harsh conditions in which industrial processes usually take place. Extremophiles, microorganisms naturally found in "extreme" ecological niches, produce robust enzymes for bioprocesses and product development. Thermophiles like Geobacillus, Alyciclobacillus, Anoxybacillus, Pyrococcus and Thermoccocus are some of the extremophiles containing enzymes showing special promise for biocatalysis. Glutamate dehydrogenase used in food processes, laccases and xylanases in pulp and paper processes, nitrilases and transaminases for pharmaceutical drug synthesis and lipases present in detergents, are examples of the increasing use of enzymes for biocatalytic synthesis from thermophilic microorganisms. Some of these enzymes from thermophiles have been expressed as recombinant enzymes and are already in the market. Here we will review recent discoveries of thermophilic enzymes and their current and potential applications in industry.
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Affiliation(s)
- Joaquín Atalah
- Fundación Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago, Chile
| | | | - Giannina Espina
- Fundación Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago, Chile
| | - Jenny M Blamey
- Fundación Biociencia, José Domingo Cañas 2280, Ñuñoa, Santiago, Chile; Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Estación Central, Santiago, Chile.
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Thakur N, Sharma NK, Thakur S, Monika, Bhalla TC. Bioprocess Development for the Synthesis of 4-Aminophenylacetic Acid Using Nitrilase Activity of Whole Cells of Alcaligenes faecalis MTCC 12629. Catal Letters 2019. [DOI: 10.1007/s10562-019-02762-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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36
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Lauritano C, De Luca D, Amoroso M, Benfatto S, Maestri S, Racioppi C, Esposito F, Ianora A. New molecular insights on the response of the green alga Tetraselmis suecica to nitrogen starvation. Sci Rep 2019; 9:3336. [PMID: 30833632 PMCID: PMC6399242 DOI: 10.1038/s41598-019-39860-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/01/2019] [Indexed: 12/20/2022] Open
Abstract
Microalgae are currently considered one of the most promising resources for biofuel production, aquaculture feedstock and new pharmaceuticals. Among them, green algae of the genus Tetraselmis are extensively studied for their lipid accumulation in nutrient-starvation conditions. In this paper, we present the full-transcriptome of Tetraselmis suecica and differential expression analysis between nitrogen-starved and -repleted conditions (at stationary phase) focusing not only on lipid metabolism but giving new insights on nutrient starvation responses. Transcripts involved in signal transduction pathways, stress and antioxidant responses and solute transport were strongly up-regulated when T. suecica was cultured under nitrogen starvation. On the contrary, transcripts involved in amino acid synthesis, degradation of sugars, secondary metabolite synthesis, as well as photosynthetic activity were down-regulated under the same conditions. Among differentially expressed transcripts, a polyketide synthase and three lipoxygenases (involved in the synthesis of secondary metabolites with antipredator, anticancer and anti-infective activities) were identified, suggesting the potential synthesis of bioactive compounds by this microalga. In addition, the transcript for a putative nitrilase, enzyme used in nitrile bioremediation, is here reported for the first time for T. suecica. These findings give new insights on T. suecica responses to nutrient starvation and on possible biotechnological applications for green algae.
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Affiliation(s)
- Chiara Lauritano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - Daniele De Luca
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Mariano Amoroso
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Salvatore Benfatto
- Università degli Studi di Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Simone Maestri
- Università degli Studi di Verona, Ca' Vignal 1, Strada Le Grazie 15, 37134, Verona, Italy
| | - Claudia Racioppi
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.,Center for Developmental Genetics, Department of Biology, College of Arts and Science, New York University, New York, USA
| | - Francesco Esposito
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Adrianna Ianora
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
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Martínková L. Nitrile metabolism in fungi: A review of its key enzymes nitrilases with focus on their biotechnological impact. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Martínez-Rodríguez S, Conejero-Muriel M, Gavira JA. A novel cysteine carbamoyl-switch is responsible for the inhibition of formamidase, a nitrilase superfamily member. Arch Biochem Biophys 2019; 662:151-159. [PMID: 30528776 DOI: 10.1016/j.abb.2018.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 11/25/2022]
Abstract
Formamidases (EC 3.5.1.49) and amidases (EC 3.5.1.4) are paralogous cysteine-dependent enzymes which catalyze the conversion of amide substrates to ammonia and the corresponding carboxylic acid. Both enzymes have been suggested as an alternative pathway for ammonia production during urea shortage. Urea was proved key in the transcriptional regulation of formamidases/amidases, connecting urea level to amide metabolism. In addition, different amidases have also been shown to be inhibited by urea, pointing to urea-regulation at the enzymatic level. Although amidases have been widely studied due to its biotechnological application in the hydrolysis of aliphatic amides, up to date, only two formamidases have been extensively characterized, belonging to Helicobacter pylori (HpyAmiF) and Bacillus cereus (BceAmiF). In this work, we report the first structure of an acyl-intermediate of BceAmiF. We also report the inhibition of BceAmiF by urea, together with mass spectrometry studies confirming the S-carbamoylation of BceAmiF after urea treatment. X-ray studies of urea-soaked BceAmiF crystals showed short- and long-range rearrangements affecting oligomerization interfaces. Since cysteine-based switches are known to occur in the regulation of different metabolic and signaling pathways, our results suggest a novel S-carbamoylation-switch for the regulation of BceAmiF. This finding could relate to previous observations of unexplained modifications in the catalytic cysteine of different nitrilase superfamily members and therefore extending this regulation mechanism to the whole nitrilase superfamily.
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Affiliation(s)
- Sergio Martínez-Rodríguez
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada (Campus de Melilla), 52071, Melilla, Spain; Laboratorio de Estudios Cristalográficos, CSIC-UGR, 18100, Granada, Spain.
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Jung J, Braun J, Czabany T, Nidetzky B. Interplay of nucleophilic catalysis with proton transfer in the nitrile reductase QueF from Escherichia coli. Catal Sci Technol 2019. [DOI: 10.1039/c8cy02331j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proton relay through an active-site network of hydrogen bonds promotes enzymatic nitrile reduction to amine via a covalent thioimidate enzyme intermediate.
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Affiliation(s)
- Jihye Jung
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- A-8010 Graz
- Austria
| | - Jan Braun
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- A-8010 Graz
- Austria
| | - Tibor Czabany
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- A-8010 Graz
- Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering
- Graz University of Technology
- NAWI Graz
- A-8010 Graz
- Austria
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Dimethylformamide is a novel nitrilase inducer in Rhodococcus rhodochrous. Appl Microbiol Biotechnol 2018; 102:10055-10065. [DOI: 10.1007/s00253-018-9367-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/20/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
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Urbancsok J, Bones AM, Kissen R. Benzyl Cyanide Leads to Auxin-Like Effects Through the Action of Nitrilases in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:1240. [PMID: 30197652 PMCID: PMC6117430 DOI: 10.3389/fpls.2018.01240] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/06/2018] [Indexed: 05/19/2023]
Abstract
Plants within the Brassicales order generate glucosinolate hydrolysis products that can exert different biological effects on several organisms. Here, we evaluated the physiological effects of one of these compounds, benzyl cyanide (phenylacetonitrile), when exogenously applied on Arabidopsis thaliana. Treatment with benzyl cyanide led to a dose-dependent reduction of primary root length and total biomass. Further morphological changes like elongated hypocotyls, epinastic cotyledons, and increased formation of adventitious roots resembled a severe auxin-overproducer phenotype. The elevated auxin response was confirmed by histochemical staining and gene expression analysis of auxin-responsive genes. Nitriles are converted by specific enzymes, nitrilases (NIT1-3), to their corresponding carboxylic acids. The nitrilase mutants nit1 and nit2 tolerated benzyl cyanide treatments better than the wild type, with nit2 being less resistant than nit1. A NIT2RNAi line suppressing several nitrilases was resistant to all tested benzyl cyanide concentrations. When exposed to phenylacetic acid (PAA) - the corresponding carboxylic acid of benzyl cyanide - wild type and mutant seedlings were, however, equally susceptible and showed a more severe auxin phenotype than upon cyanide treatment. Here, we demonstrate that the auxin-like effects triggered by benzyl cyanide on Arabidopsis are due to its nitrilase-mediated conversion to the natural auxin PAA.
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Affiliation(s)
| | | | - Ralph Kissen
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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Conversion of aliphatic nitriles by the arylacetonitrilase from Pseudomonas fluorescens EBC191. World J Microbiol Biotechnol 2018; 34:91. [PMID: 29896645 DOI: 10.1007/s11274-018-2477-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/08/2018] [Indexed: 10/14/2022]
Abstract
The conversion of aliphatic nitriles by the arylacetonitrilase from Pseudomonas fluorescens EBC191 (NitA) was analyzed. The nitrilase hydrolysed a wide range of aliphatic mono- and dinitriles and showed a preference for unsaturated aliphatic substrates containing 5-6 carbon atoms. In addition, increased reaction rates were also found for aliphatic nitriles carrying electron withdrawing substituents (e.g. chloro- or hydroxy-groups) close to the nitrile group. Aliphatic dinitriles were attacked only at one of the nitrile groups and with most of the tested dinitriles the monocarboxylates were detected as major products. In contrast, fumarodinitrile was converted to the monocarboxylate and the monocarboxamide in a ratio of about 65:35. Significantly different relative amounts of the two products were observed with two nitrilase variants with altered reaction specifities. NitA converted some aliphatic substrates with higher rates than 2-phenylpropionitrile, which is one of the standard substrates for arylacetonitrilases. This indicated that the traditional classification of nitrilases as "arylacetonitrilases", "aromatic" or "aliphatic" nitrilases might require some corrections. This was also suggested by the construction of some variants of NitA which were modified in an amino acid residue which was previously suggested to be essential for the conversion of aliphatic substrates by a homologous nitrilase.
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Santos ARS, Gerhardt ECM, Moure VR, Pedrosa FO, Souza EM, Diamanti R, Högbom M, Huergo LF. Kinetics and structural features of dimeric glutamine-dependent bacterial NAD + synthetases suggest evolutionary adaptation to available metabolites. J Biol Chem 2018; 293:7397-7407. [PMID: 29581233 DOI: 10.1074/jbc.ra118.002241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/11/2018] [Indexed: 01/09/2023] Open
Abstract
NADH (NAD+) and its reduced form NADH serve as cofactors for a variety of oxidoreductases that participate in many metabolic pathways. NAD+ also is used as substrate by ADP-ribosyl transferases and by sirtuins. NAD+ biosynthesis is one of the most fundamental biochemical pathways in nature, and the ubiquitous NAD+ synthetase (NadE) catalyzes the final step in this biosynthetic route. Two different classes of NadE have been described to date: dimeric single-domain ammonium-dependent NadENH3 and octameric glutamine-dependent NadEGln, and the presence of multiple NadE isoforms is relatively common in prokaryotes. Here, we identified a novel dimeric group of NadEGln in bacteria. Substrate preferences and structural analyses suggested that dimeric NadEGln enzymes may constitute evolutionary intermediates between dimeric NadENH3 and octameric NadEGln The characterization of additional NadE isoforms in the diazotrophic bacterium Azospirillum brasilense along with the determination of intracellular glutamine levels in response to an ammonium shock led us to propose a model in which these different NadE isoforms became active accordingly to the availability of nitrogen. These data may explain the selective pressures that support the coexistence of multiple isoforms of NadE in some prokaryotes.
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Affiliation(s)
| | | | | | | | | | - Riccardo Diamanti
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Luciano Fernandes Huergo
- Department of Biochemistry and Molecular Biology, Curitiba, PR, 512 Brazil; Setor Litoral, Universidade Federal do Paraná (UFPR), Curitiba, PR, 512 Brazil.
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Lin C, Zhang J, Lu Y, Li X, Zhang W, Zhang W, Lin W, Zheng L, Li X. NIT1 suppresses tumour proliferation by activating the TGFβ1-Smad2/3 signalling pathway in colorectal cancer. Cell Death Dis 2018; 9:263. [PMID: 29449642 PMCID: PMC5833788 DOI: 10.1038/s41419-018-0333-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 12/19/2022]
Abstract
NIT1 protein has been reported to be a potential tumour suppressor in tumour progression. However, little is known about the specific role of NIT1 in tumour development and progression. In this study, we confirmed the specific effects of NIT1 in the regulation of colorectal carcinoma cell proliferation. Here, we showed that NIT1 was significantly downregulated in colorectal cancer tissues compared with that in adjacent normal tissues. The decreased expression of NIT1 was significantly correlated with poor differentiation and more serosal invasion. Functional experiments showed that NIT1 inhibited CRC cell growth both in vitro and in vivo. NIT1 induced cell cycle arrest and apoptosis. Furthermore, NIT1 recruited Smad2/3 to the TGFβ receptor and activated the TGFβ–Smad2/3 pathway by interacting with SARA and SMAD2/3 in CRC. Further study has shown that SMAD3 directly binds to the promoter regions of NIT1 and enhances the transcription of NIT1. Together, our findings indicate that NIT1 suppresses CRC proliferation through a positive feedback loop between NIT1 and activation of the TGFβ–Smad signalling pathway. This study might provide a new promising strategy for CRC.
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Affiliation(s)
- Chun Lin
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jianming Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanxia Lu
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiaomin Li
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenjuan Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Zhang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Weihao Lin
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Lin Zheng
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xuenong Li
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
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Noh H, Jeong D, Ohta T, Ogura T, Valentine JS, Cho J. Distinct Reactivity of a Mononuclear Peroxocobalt(III) Species toward Activation of Nitriles. J Am Chem Soc 2017; 139:10960-10963. [PMID: 28758392 DOI: 10.1021/jacs.7b04479] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A mononuclear side-on peroxocobalt(III) complex with a tetradentate macrocyclic ligand, [CoIII(TBDAP)(O2)]+ (1), shows a novel and facile mode of dioxygenase-like reactivity with nitriles (R-C≡N; R = Me, Et, and Ph) to produce the corresponding mononuclear hydroximatocobalt(III) complexes, [CoIII(TBDAP)(R-C(═NO)O)]+, in which the nitrile moiety is oxidized by two oxygen atoms of the peroxo group. The overall reaction proceeds in one-pot under ambient conditions (ca. 1 h, 40 °C). 18O-Labeling experiments confirm that both oxygen atoms are derived from the peroxo ligand. The structures of all products, hydroximatocobalt(III) complexes, were confirmed by X-ray crystallography and various spectroscopic techniques. Kinetic studies including the Hammett analysis and isotope labeling experiments suggest that the mechanistic mode of 1 for activation of nitriles occurs via a concerted mechanism. This novel reaction would be significantly valuable for expanding the chemistry for nitrile activation and utilization.
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Affiliation(s)
- Hyeonju Noh
- Department of Emerging Materials Science, DGIST , Daegu 42988, Korea
| | - Donghyun Jeong
- Department of Emerging Materials Science, DGIST , Daegu 42988, Korea
| | - Takehiro Ohta
- Picobiology Institute, Graduate School of Life Science, University of Hyogo , RSC-UH LP Center, Hyogo 679-5148, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo , RSC-UH LP Center, Hyogo 679-5148, Japan
| | | | - Jaeheung Cho
- Department of Emerging Materials Science, DGIST , Daegu 42988, Korea
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Krasnikov BF, Deryabina YI, Isakova EP, Biriukova IK, Shevelev AB, Antipov AN. New recombinant producer of human ω-amidase based on Escherichia coli. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817030115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Bioengineering of Nitrilases Towards Its Use as Green Catalyst: Applications and Perspectives. Indian J Microbiol 2017; 57:131-138. [PMID: 28611489 DOI: 10.1007/s12088-017-0645-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/20/2017] [Indexed: 10/19/2022] Open
Abstract
Nitrilases are commercial biocatalysts used for the synthesis of plastics, paints, fibers in the chemical industries, pharmaceutical drugs and herbicides for agricultural uses. Nitrilase hydrolyses the nitriles and dinitriles to their corresponding carboxylic acids and ammonia. They have a broad range of substrate specificities as well as enantio-, regio- and chemo-selective properties which make them useful for biotransformation of nitriles to important compounds because of which they are considered as 'Green Catalysts'. Nitriles are widespread in nature and synthesized as a consequence of anthropogenic and biological activities. These are also present in certain plant species and are known to cause environmental pollution. Biotransformation using native organisms as catalysts tends to be insufficient since the enzyme of interest has very low amount in the total cellular protein, rate of reaction is slow along with the instability of enzymes. Therefore, to overcome these limitations, bioengineering offers an alternative approach to alter the properties of enzymes to enhance the applicability and stability. The present review highlights the aspects of producing the recombinant microorganisms and overexpressing the enzyme of interest for the enhanced stability at high temperatures, immobilization techniques, extremes of pH, organic solvents and hydrolysing dintriles to chiral compounds which may enhance the possibilities for creating specific enzymes for biotransformation.
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Nielsen LJ, Stuart P, Pičmanová M, Rasmussen S, Olsen CE, Harholt J, Møller BL, Bjarnholt N. Dhurrin metabolism in the developing grain of Sorghum bicolor (L.) Moench investigated by metabolite profiling and novel clustering analyses of time-resolved transcriptomic data. BMC Genomics 2016; 17:1021. [PMID: 27964718 PMCID: PMC5154151 DOI: 10.1186/s12864-016-3360-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/28/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The important cereal crop Sorghum bicolor (L.) Moench biosynthesize and accumulate the defensive compound dhurrin during development. Previous work has suggested multiple roles for the compound including a function as nitrogen storage/buffer. Crucial for this function is the endogenous turnover of dhurrin for which putative pathways have been suggested but not confirmed. RESULTS In this study, the biosynthesis and endogenous turnover of dhurrin in the developing sorghum grain was studied by metabolite profiling and time-resolved transcriptome analyses. Dhurrin was found to accumulate in the early phase of grain development reaching maximum amounts 25 days after pollination. During the subsequent maturation period, the dhurrin content was turned over, resulting in only negligible residual dhurrin amounts in the mature grain. Dhurrin accumulation correlated with the transcript abundance of the three genes involved in biosynthesis. Despite the accumulation of dhurrin, the grains were acyanogenic as demonstrated by the lack of hydrogen cyanide release from macerated grain tissue and by the absence of transcripts encoding dhurrinases. With the missing activity of dhurrinases, the decrease in dhurrin content in the course of grain maturation represents the operation of hitherto uncharacterized endogenous dhurrin turnover pathways. Evidence for the operation of two such pathways was obtained by metabolite profiling and time-resolved transcriptome analysis. By combining cluster- and phylogenetic analyses with the metabolite profiling, potential gene candidates of glutathione S-transferases, nitrilases and glycosyl transferases involved in these pathways were identified. The absence of dhurrin in the mature grain was replaced by a high content of proanthocyanidins. Cluster- and phylogenetic analyses coupled with metabolite profiling, identified gene candidates involved in proanthocyanidin biosynthesis in sorghum. CONCLUSIONS The results presented in this article reveal the existence of two endogenous dhurrin turnover pathways in sorghum, identify genes putatively involved in these transformations and show that dhurrin in addition to its insect deterrent properties may serve as a storage form of reduced nitrogen. In the course of sorghum grain maturation, proanthocyanidins replace dhurrin as a defense compound. The lack of cyanogenesis in the developing sorghum grain renders this a unique experimental system to study CNglc synthesis as well as endogenous turnover.
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Affiliation(s)
| | - Peter Stuart
- Seedtek, 12 Kestrel Court, Toowoomba, 4350 Australia
| | - Martina Pičmanová
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871 Denmark
- VILLUM Research Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871 Denmark
- Center for Synthetic Biology ‘bioSYNergy’, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Department of Systems Biology, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Carl Erik Olsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871 Denmark
| | - Jesper Harholt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871 Denmark
- VILLUM Research Center for Plant Plasticity, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871 Denmark
- Center for Synthetic Biology ‘bioSYNergy’, University of Copenhagen, Copenhagen, Denmark
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
| | - Nanna Bjarnholt
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871 Denmark
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Decuyper L, Piens N, Mincke J, Bomon J, De Schrijver B, Mollet K, De Winter K, Desmet T, D'hooghe M. A nitrilase-mediated entry to 4-carboxymethyl-β-lactams from chemically prepared 4-(cyanomethyl)azetidin-2-ones. RSC Adv 2016. [DOI: 10.1039/c6ra08213k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
4-(Cyanomethyl)azetidin-2-ones were efficiently prepared from 1,2:5,6-di-O-isopropylidene-d-mannitol, followed by a nitrilase-catalyzed hydrolysis to 4-carboxymethyl β-lactams without affecting the sensitive four-membered ring system.
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Affiliation(s)
- Lena Decuyper
- SynBioC Research Group
- Department of Sustainable Organic Chemistry and Technology
- Faculty of Bioscience Engineering
- Ghent University
- B-9000 Ghent
| | - Nicola Piens
- SynBioC Research Group
- Department of Sustainable Organic Chemistry and Technology
- Faculty of Bioscience Engineering
- Ghent University
- B-9000 Ghent
| | - Jens Mincke
- SynBioC Research Group
- Department of Sustainable Organic Chemistry and Technology
- Faculty of Bioscience Engineering
- Ghent University
- B-9000 Ghent
| | - Jeroen Bomon
- SynBioC Research Group
- Department of Sustainable Organic Chemistry and Technology
- Faculty of Bioscience Engineering
- Ghent University
- B-9000 Ghent
| | - Bert De Schrijver
- SynBioC Research Group
- Department of Sustainable Organic Chemistry and Technology
- Faculty of Bioscience Engineering
- Ghent University
- B-9000 Ghent
| | - Karen Mollet
- SynBioC Research Group
- Department of Sustainable Organic Chemistry and Technology
- Faculty of Bioscience Engineering
- Ghent University
- B-9000 Ghent
| | - Karel De Winter
- Department of Biochemical and Microbial Technology
- Faculty of Bioscience Engineering
- Ghent University
- B-9000 Ghent
- Belgium
| | - Tom Desmet
- Department of Biochemical and Microbial Technology
- Faculty of Bioscience Engineering
- Ghent University
- B-9000 Ghent
- Belgium
| | - Matthias D'hooghe
- SynBioC Research Group
- Department of Sustainable Organic Chemistry and Technology
- Faculty of Bioscience Engineering
- Ghent University
- B-9000 Ghent
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50
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Chang HC, Hsu YC, Chen CH, Kuo TS, Lee WZ. Thioiminium and thiaphospholanium derived from acetonitrile via nickel(II)-(2-mercaptophenyl)phosphine complexation. Dalton Trans 2015; 44:20808-11. [PMID: 26549142 DOI: 10.1039/c5dt03316k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
[Ni(P(o-C6H4S)(o-C6H4SC(CH3)=NH2)(C6H5))2](ClO4)2 (2) with two thioiminium functionalities is derived from CH3CN solvent under anhydrous conditions. Moreover, thiaphospholanium salts, [(C6H5)P(C6H4SC(CH3)(NHCOCH3))(o-C6H4SH)](ClO4) (3) and [(C6H5)2-P(C6H4SC(CH3)(NH3))](ClO4)2 (5), can be obtained through a similar Pinner-type nitrile activation. These results demonstrate the possible intermediate of enzymatic nitrile transformation and also provide an approach to the preparation of 2-amino-1,3-benzothiaphospholanium derivatives.
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Affiliation(s)
- Hao-Ching Chang
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan.
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