1
|
Ndochinwa OG, Wang QY, Amadi OC, Nwagu TN, Nnamchi CI, Okeke ES, Moneke AN. Current status and emerging frontiers in enzyme engineering: An industrial perspective. Heliyon 2024; 10:e32673. [PMID: 38912509 PMCID: PMC11193041 DOI: 10.1016/j.heliyon.2024.e32673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024] Open
Abstract
Protein engineering mechanisms can be an efficient approach to enhance the biochemical properties of various biocatalysts. Immobilization of biocatalysts and the introduction of new-to-nature chemical reactivities are also possible through the same mechanism. Discovering new protocols that enhance the catalytic active protein that possesses novelty in terms of being stable, active, and, stereoselectivity with functions could be identified as essential areas in terms of concurrent bioorganic chemistry (synergistic relationship between organic chemistry and biochemistry in the context of enzyme engineering). However, with our current level of knowledge about protein folding and its correlation with protein conformation and activities, it is almost impossible to design proteins with specific biological and physical properties. Hence, contemporary protein engineering typically involves reprogramming existing enzymes by mutagenesis to generate new phenotypes with desired properties. These processes ensure that limitations of naturally occurring enzymes are not encountered. For example, researchers have engineered cellulases and hemicellulases to withstand harsh conditions encountered during biomass pretreatment, such as high temperatures and acidic environments. By enhancing the activity and robustness of these enzymes, biofuel production becomes more economically viable and environmentally sustainable. Recent trends in enzyme engineering have enabled the development of tailored biocatalysts for pharmaceutical applications. For instance, researchers have engineered enzymes such as cytochrome P450s and amine oxidases to catalyze challenging reactions involved in drug synthesis. In addition to conventional methods, there has been an increasing application of machine learning techniques to identify patterns in data. These patterns are then used to predict protein structures, enhance enzyme solubility, stability, and function, forecast substrate specificity, and assist in rational protein design. In this review, we discussed recent trends in enzyme engineering to optimize the biochemical properties of various biocatalysts. Using examples relevant to biotechnology in engineering enzymes, we try to expatiate the significance of enzyme engineering with how these methods could be applied to optimize the biochemical properties of a naturally occurring enzyme.
Collapse
Affiliation(s)
- Obinna Giles Ndochinwa
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | - Qing-Yan Wang
- State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Oyetugo Chioma Amadi
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | - Tochukwu Nwamaka Nwagu
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | | | - Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences & Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety, Jiangsu University, 301 Xuefu Rd., 212013, Zhenjiang, Jiangsu, China
| | - Anene Nwabu Moneke
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| |
Collapse
|
2
|
Recent Progress in the Production of Cyanide-Converting Nitrilases—Comparison with Nitrile-Hydrolyzing Enzymes. Catalysts 2023. [DOI: 10.3390/catal13030500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
Nitrilases have a high potential for application in organic chemistry, environmental technology, and analytics. However, their industrial uses require that they are produced in highly active and robust forms at a reasonable cost. Some organic syntheses catalyzed by nitrilases have already reached a high level of technological readiness. This has been enabled by the large-scale production of recombinant catalysts. Despite some promising small-scale methods being proposed, the production of cyanide-converting nitrilases (cyanide hydratase and cyanide dihydratase) is lagging in this regard. This review focuses on the prospects of cyanide(di)hydratase-based catalysts. The current knowledge of these enzymes is summarized and discussed in terms of the origin and distribution of their sequences, gene expression, structure, assays, purification, immobilization, and uses. Progresses in the production of other nitrilase catalysts are also tackled, as it may inspire the development of the preparation processes of cyanide(di)hydratases.
Collapse
|
3
|
Genomic Characterization of Bacillus safensis Isolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD. Appl Environ Microbiol 2022; 88:e0091622. [PMID: 35762789 PMCID: PMC9317851 DOI: 10.1128/aem.00916-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Understanding the biochemistry and metabolic pathways of cyanide degradation is necessary to improve the efficacy of cyanide bioremediation processes and industrial requirements. We have isolated and sequenced the genome of a cyanide-degrading Bacillus strain from water in contact with mine tailings from Lima, Peru. This strain was classified as Bacillus safensis based on 16S rRNA gene sequencing and core genome analyses and named B. safensis PER-URP-08. We searched for possible cyanide-degradation enzymes in the genome of this strain and identified a putative cyanide dihydratase (CynD) gene similar to a previously characterized CynD from Bacillus pumilus C1. Sequence analysis of CynD from B. safensis and B. pumilus allow us to identify C-terminal residues that differentiate both CynDs. We then cloned, expressed in Escherichia coli, and purified recombinant CynD from B. safensis PER-URP-08 (CynDPER-URP-08) and showed that in contrast to CynD from B. pumilus C1, this recombinant CynD remains active at up to pH 9. We also showed that oligomerization of CynDPER-URP-08 decreases as a function of increased pH. Finally, we demonstrated that transcripts of CynDPER-URP-08 in B. safensis PER-URP-08 are strongly induced in the presence of cyanide. Our results suggest that the use of B. safensis PER-URP-08 and CynDPER-URP-08 as potential tool for cyanide bioremediation warrants further investigation. IMPORTANCE Despite being of environmental concern around the world due to its toxicity, cyanide continues to be used in many important industrial processes. Thus, searching for cyanide bioremediation methods is a matter of societal concern and must be present on the political agenda of all governments. Here, we report the isolation, genome sequencing and characterization of cyanide degradation capacity of a bacterial strain isolated from an industrial mining site in Peru. We characterize a cyanide dehydratase (CynD) homolog from one of these bacteria, Bacillus safensis PER-URP-08.
Collapse
|
4
|
Zhang H, Zhang H, Qin X, Wang X, Wang Y, Tu T, Wang Y, Yao B, Huang H, Luo H. Biodegradation of nitriles derived from glucosinolates in rapeseed meal by BnNIT2: a nitrilase from Brassica napus with wide substrate specificity. Appl Microbiol Biotechnol 2022; 106:2445-2454. [PMID: 35262786 DOI: 10.1007/s00253-022-11844-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 11/02/2022]
Abstract
Nitriles derived from glucosinolates (GSLs) in rapeseed meal (RSM) can cause lesions on animal liver and kidneys. Nitrilase converts nitriles to carboxylic acids and NH3, eliminating their toxicity. Here we describe a nitrilase, BnNIT2, from Brassica napus (optimal temperature, 45 °C; pH, 7.0) that is stable at 40 °C and has a wide substrate specificity. Recombinant BnNIT2 converted the three main nitriles from GSLs (3-hydroxy-4-pentenenitrile, 3-butenenitrile, and 4-pentenenitrile), with the highest specific activity (58.6 U/mg) for 4-pentenenitrile. We used mutagenesis to improve the thermostability of BnNIT2; the resulting mutant BnNIT2-H90M had an ~ 14.5% increase in residual activity at 50 °C for 1 h. To verify the functionality of BnNIT2, GSLs were extracted from RSM and converted into nitriles at pH 5.0 in the presence of Fe2+. Then, BnNIT2 was used to degrade the nitriles from GSLs; ultimately, ~ 80% of nitriles were removed. Thus BnNIT2 is a potential enzyme for detoxification of RSM. KEY POINTS: • Functional identification of the plant nitrilase BnNIT2. • Identified a mutant, H90M, with improved thermostability. • BnNIT2 was capable of degrading nitriles from transformed GSLs.
Collapse
Affiliation(s)
- Heng Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Honghai Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| |
Collapse
|
5
|
Application Potential of Cyanide Hydratase from Exidia glandulosa: Free Cyanide Removal from Simulated Industrial Effluents. Catalysts 2021. [DOI: 10.3390/catal11111410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Industries such as mining, cokemaking, (petro)chemical and electroplating produce effluents that contain free cyanide (fCN = HCN + CN−). Currently, fCN is mainly removed by (physico)chemical methods or by biotreatment with activated sludge. Cyanide hydratases (CynHs) (EC 4.2.1.66), which convert fCN to the much less toxic formamide, have been considered for a mild approach to wastewater decyanation. However, few data are available to evaluate the application potential of CynHs. In this study, we used a new CynH from Exidia glandulosa (protein KZV92691.1 designated NitEg by us), which was overproduced in Escherichia coli. The purified NitEg was highly active for fCN with 784 U/mg protein, kcat 927/s and kcat/KM 42/s/mM. It exhibited optimal activities at pH approximately 6–9 and 40–45 °C. It was quite stable in this pH range, and retained approximately 40% activity at 37 °C after 1 day. Silver and copper ions (1 mM) decreased its activity by 30–40%. The removal of 98–100% fCN was achieved for 0.6–100 mM fCN. Moreover, thiocyanate, sulfide, ammonia or phenol added in amounts typical of industrial effluents did not significantly reduce the fCN conversion, while electroplating effluents may need to be diluted due to high fCN and metal content. The ease of preparation of NitEg, its high specific activity, robustness and long shelf life make it a promising biocatalyst for the detoxification of fCN.
Collapse
|
6
|
Victorino da Silva Amatto I, Gonsales da Rosa-Garzon N, Antônio de Oliveira Simões F, Santiago F, Pereira da Silva Leite N, Raspante Martins J, Cabral H. Enzyme engineering and its industrial applications. Biotechnol Appl Biochem 2021; 69:389-409. [PMID: 33555054 DOI: 10.1002/bab.2117] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 01/03/2023]
Abstract
Recently, there has been an increase in the demand for enzymes with modified activity, specificity, and stability. Enzyme engineering is an important tool to meet the demand for enzymes adjusted to different industrial processes. Knowledge of the structure and function of enzymes guides the choice of the best strategy for engineering enzymes. Each enzyme engineering strategy, such as rational design, directed evolution, and semi-rational design, has specific applications, as well as limitations, which must be considered when choosing a suitable strategy. Engineered enzymes can be optimized for different industrial applications by choosing the appropriate strategy. This review features engineered enzymes that have been applied in food, animal feed, pharmaceuticals, medical applications, bioremediation, biofuels, and detergents.
Collapse
Affiliation(s)
- Isabela Victorino da Silva Amatto
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Nathalia Gonsales da Rosa-Garzon
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Flávio Antônio de Oliveira Simões
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Pharmaceutical Sciences Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Fernanda Santiago
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Nathália Pereira da Silva Leite
- Pharmaceutical Sciences Program, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, XUniversity of São Paulo, Ribeirão Preto, SP, Brazil
| | - Júlia Raspante Martins
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Pharmaceutical Sciences Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| |
Collapse
|
7
|
Razanamahandry LC, Onwordi CT, Saban W, Bashir AKH, Mekuto L, Malenga E, Manikandan E, Fosso-Kankeu E, Maaza M, Ntwampe SKO. Performance of various cyanide degrading bacteria on the biodegradation of free cyanide in water. JOURNAL OF HAZARDOUS MATERIALS 2019; 380:120900. [PMID: 31326841 DOI: 10.1016/j.jhazmat.2019.120900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/07/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
This study reports on the biodegradation of free cyanide (FCN) by cyanide degrading bacteria (CDB) that were isolated from mining wastewater and thiocyanate containing wastewater. The performance of these isolates was compared to cryopreserved CDBs that were used in previous studies. The performance of the isolates to degrade FCN was studied in batch cultures. It was observed that the CDB from the thiocyanate wastewater showed higher biodegradation rates (2.114 g CN-. L-1.O.D600 nm-1.h-1) compared to the isolates from the mining wastewater. The isolates from the cryopreserved CDBs and from the mining wastewater achieved a biodegradation rate of 1.285 g CN- L-1.O.D600 nm-1.h-1 and 1.209 g CN-.L-1.O.D600 nm-1.h-1, respectively. This study demonstrated that the source of the organisms plays a significant role on FCN biodegradation.
Collapse
Affiliation(s)
- L C Razanamahandry
- UNESCO UNISA Africa Chair in Nanoscience's/Nanotechnology Laboratories (U2AC2N), College of Graduate Studies, University of South Africa (UNISA), Muckleneuk Ridge, P.O. Box 392, Pretoria, South Africa; Nanosciences African network (NANOAFNET), Materials Research Group (MRG), iThemba LABS-National Research Foundation (NRF), 1 Old Faure Road, 7129, P.O. Box 722, Somerset West, Western Cape Province, Cape Town, South Africa.
| | - C T Onwordi
- University of Western Cape, Environmental and Nano Sciences, Department of Chemistry, Faculty of Natural Sciences, Bellville, Private mail Bag X17, Cape Town, 7535, South Africa
| | - W Saban
- UNESCO UNISA Africa Chair in Nanoscience's/Nanotechnology Laboratories (U2AC2N), College of Graduate Studies, University of South Africa (UNISA), Muckleneuk Ridge, P.O. Box 392, Pretoria, South Africa; Nanosciences African network (NANOAFNET), Materials Research Group (MRG), iThemba LABS-National Research Foundation (NRF), 1 Old Faure Road, 7129, P.O. Box 722, Somerset West, Western Cape Province, Cape Town, South Africa
| | - A K H Bashir
- UNESCO UNISA Africa Chair in Nanoscience's/Nanotechnology Laboratories (U2AC2N), College of Graduate Studies, University of South Africa (UNISA), Muckleneuk Ridge, P.O. Box 392, Pretoria, South Africa; Nanosciences African network (NANOAFNET), Materials Research Group (MRG), iThemba LABS-National Research Foundation (NRF), 1 Old Faure Road, 7129, P.O. Box 722, Somerset West, Western Cape Province, Cape Town, South Africa
| | - L Mekuto
- University of Johannesburg, Department of Chemical Engineering, Johannesburg, South Africa
| | - E Malenga
- Water Pollution Monitoring and Remediation Initiatives Research Group, School of Chemical and Minerals Engineering, North-West University, Private Bag X1290, Potchefstroom, 2520, South Africa
| | - E Manikandan
- UNESCO UNISA Africa Chair in Nanoscience's/Nanotechnology Laboratories (U2AC2N), College of Graduate Studies, University of South Africa (UNISA), Muckleneuk Ridge, P.O. Box 392, Pretoria, South Africa; Nanosciences African network (NANOAFNET), Materials Research Group (MRG), iThemba LABS-National Research Foundation (NRF), 1 Old Faure Road, 7129, P.O. Box 722, Somerset West, Western Cape Province, Cape Town, South Africa; Thiruvalluvar University, Department of Physics, TUCAS Campus, Thennangur, 604408, Vellore, India
| | - E Fosso-Kankeu
- Water Pollution Monitoring and Remediation Initiatives Research Group, School of Chemical and Minerals Engineering, North-West University, Private Bag X1290, Potchefstroom, 2520, South Africa
| | - M Maaza
- UNESCO UNISA Africa Chair in Nanoscience's/Nanotechnology Laboratories (U2AC2N), College of Graduate Studies, University of South Africa (UNISA), Muckleneuk Ridge, P.O. Box 392, Pretoria, South Africa; Nanosciences African network (NANOAFNET), Materials Research Group (MRG), iThemba LABS-National Research Foundation (NRF), 1 Old Faure Road, 7129, P.O. Box 722, Somerset West, Western Cape Province, Cape Town, South Africa
| | - S K O Ntwampe
- Bioresource Engineering Research Group (BioERG), Cape Peninsula University of Technology, P.O. Box 652, Cape Town 8000, South Africa; Department of Chemical Engineering, Faculty of Engineering and the Built Environment, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, Cape Town, South Africa
| |
Collapse
|
8
|
Sharma M, Akhter Y, Chatterjee S. A review on remediation of cyanide containing industrial wastes using biological systems with special reference to enzymatic degradation. World J Microbiol Biotechnol 2019; 35:70. [DOI: 10.1007/s11274-019-2643-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/08/2019] [Indexed: 11/24/2022]
|
9
|
Park JM, Trevor Sewell B, Benedik MJ. Cyanide bioremediation: the potential of engineered nitrilases. Appl Microbiol Biotechnol 2017; 101:3029-3042. [PMID: 28265723 DOI: 10.1007/s00253-017-8204-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/29/2022]
Abstract
The cyanide-degrading nitrilases are of notable interest for their potential to remediate cyanide contaminated waste streams, especially as generated in the gold mining, pharmaceutical, and electroplating industries. This review provides a brief overview of cyanide remediation in general but with a particular focus on the cyanide-degrading nitrilases. These are of special interest as the hydrolysis reaction does not require secondary substrates or cofactors, making these enzymes particularly good candidates for industrial remediation processes. The genetic approaches that have been used to date for engineering improved enzymes are described; however, recent structural insights provide a promising new approach.
Collapse
Affiliation(s)
- Jason M Park
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA
| | - B Trevor Sewell
- Structural Biology Research Unit, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA.
| |
Collapse
|
10
|
Recent advances and challenges in the heterologous production of microbial nitrilases for biocatalytic applications. World J Microbiol Biotechnol 2016; 33:8. [DOI: 10.1007/s11274-016-2173-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/05/2016] [Indexed: 01/21/2023]
|
11
|
Crum MA, Sewell BT, Benedik MJ. Bacillus pumilus Cyanide Dihydratase Mutants with Higher Catalytic Activity. Front Microbiol 2016; 7:1264. [PMID: 27570524 PMCID: PMC4981594 DOI: 10.3389/fmicb.2016.01264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/02/2016] [Indexed: 11/24/2022] Open
Abstract
Cyanide degrading nitrilases are noted for their potential to detoxify industrial wastewater contaminated with cyanide. However, such application would benefit from an improvement to characteristics such as their catalytic activity and stability. Following error-prone PCR for random mutagenesis, several cyanide dihydratase mutants from Bacillus pumilus were isolated based on improved catalysis. Four point mutations, K93R, D172N, A202T, and E327K were characterized and their effects on kinetics, thermostability and pH tolerance were studied. K93R and D172N increased the enzyme’s thermostability whereas E327K mutation had a less pronounced effect on stability. The D172N mutation also increased the affinity of the enzyme for its substrate at pH 7.7 but lowered its kcat. However, the A202T mutation, located in the dimerization or the A surface, destabilized the protein and abolished its activity. No significant effect on activity at alkaline pH was observed for any of the purified mutants. These mutations help confirm the model of CynD and are discussed in the context of the protein–protein interfaces leading to the protein quaternary structure.
Collapse
Affiliation(s)
- Mary A Crum
- Department of Biology, Texas A&M University, College Station TX, USA
| | - B Trevor Sewell
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station TX, USA
| |
Collapse
|
12
|
Park JM, Mulelu A, Sewell BT, Benedik MJ. Probing an Interfacial Surface in the Cyanide Dihydratase from Bacillus pumilus, A Spiral Forming Nitrilase. Front Microbiol 2016; 6:1479. [PMID: 26779137 PMCID: PMC4700190 DOI: 10.3389/fmicb.2015.01479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/08/2015] [Indexed: 11/13/2022] Open
Abstract
Nitrilases are of significant interest both due to their potential for industrial production of valuable products as well as degradation of hazardous nitrile-containing wastes. All known functional members of the nitrilase superfamily have an underlying dimer structure. The true nitrilases expand upon this basic dimer and form large spiral or helical homo-oligomers. The formation of this larger structure is linked to both the activity and substrate specificity of these nitrilases. The sequences of the spiral nitrilases differ from the non-spiral forming homologs by the presence of two insertion regions. Homology modeling suggests that these regions are responsible for associating the nitrilase dimers into the oligomer. Here we used cysteine scanning across these two regions, in the spiral forming nitrilase cyanide dihydratase from Bacillus pumilus (CynD), to identify residues altering the oligomeric state or activity of the nitrilase. Several mutations were found to cause changes to the size of the oligomer as well as reduction in activity. Additionally one mutation, R67C, caused a partial defect in oligomerization with the accumulation of smaller oligomer variants. These results support the hypothesis that these insertion regions contribute to the unique quaternary structure of the spiral microbial nitrilases.
Collapse
Affiliation(s)
- Jason M Park
- Department of Biology, Texas A&M University, College Station TX, USA
| | - Andani Mulelu
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - B Trevor Sewell
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute for Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Michael J Benedik
- Department of Biology, Texas A&M University, College Station TX, USA
| |
Collapse
|
13
|
Cyanide hydratases and cyanide dihydratases: emerging tools in the biodegradation and biodetection of cyanide. Appl Microbiol Biotechnol 2015; 99:8875-82. [DOI: 10.1007/s00253-015-6899-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 11/27/2022]
|
14
|
Crum M, Park J, Sewell B, Benedik M. C-terminal hybrid mutant of Bacillus pumilus
cyanide dihydratase dramatically enhances thermal stability and pH tolerance by reinforcing oligomerization. J Appl Microbiol 2015; 118:881-9. [DOI: 10.1111/jam.12754] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/06/2015] [Accepted: 01/08/2015] [Indexed: 01/27/2023]
Affiliation(s)
- M.A. Crum
- Department of Biology; Texas A&M University; College Station TX USA
| | - J.M. Park
- Department of Biology; Texas A&M University; College Station TX USA
| | - B.T. Sewell
- Structural Biology Research Unit; Division of Medical Biochemistry; Institute of Infectious Disease and Molecular Medicine; University of Cape Town; Cape Town South Africa
| | - M.J. Benedik
- Department of Biology; Texas A&M University; College Station TX USA
| |
Collapse
|
15
|
Crum MAN, Park JM, Mulelu AE, Sewell BT, Benedik MJ. Probing C-terminal interactions of the Pseudomonas stutzeri cyanide-degrading CynD protein. Appl Microbiol Biotechnol 2014; 99:3093-102. [PMID: 25549622 DOI: 10.1007/s00253-014-6335-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/10/2014] [Accepted: 12/14/2014] [Indexed: 12/01/2022]
Abstract
The cyanide dihydratases from Bacillus pumilus and Pseudomonas stutzeri share high amino acid sequence similarity throughout except for their highly divergent C-termini. However, deletion or exchange of the C-termini had different effects upon each enzyme. Here we extended previous studies and investigated how the C-terminus affects the activity and stability of three nitrilases, the cyanide dihydratases from B. pumilus (CynDpum) and P. stutzeri (CynDstut) and the cyanide hydratase from Neurospora crassa. Enzymes in which the C-terminal residues were deleted decreased in both activity and thermostability with increasing deletion lengths. However, CynDstut was more sensitive to such truncation than the other two enzymes. A domain of the P. stutzeri CynDstut C-terminus not found in the other enzymes, 306GERDST311, was shown to be necessary for functionality and explains the inactivity of the previously described CynDstut-pum hybrid. This suggests that the B. pumilus C-terminus, which lacks this motif, may have specific interactions elsewhere in the protein, preventing it from acting in trans on a heterologous CynD protein. We identify the dimerization interface A-surface region 195-206 (A2) from CynDpum as this interaction site. However, this A2 region did not rescue activity in C-terminally truncated CynDstutΔ302 or enhance the activity of full-length CynDstut and therefore does not act as a general stability motif.
Collapse
Affiliation(s)
- Mary Abou-Nader Crum
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA
| | | | | | | | | |
Collapse
|