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Dusíková A, Baranová T, Krahulec J, Dakošová O, Híveš J, Naumowicz M, Gál M. Electrochemical Impedance Spectroscopy for the Sensing of the Kinetic Parameters of Engineered Enzymes. SENSORS (BASEL, SWITZERLAND) 2024; 24:2643. [PMID: 38676260 PMCID: PMC11054234 DOI: 10.3390/s24082643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
The study presents a promising approach to enzymatic kinetics using Electrochemical Impedance Spectroscopy (EIS) to assess fundamental parameters of modified enteropeptidases. Traditional methods for determining these parameters, while effective, often lack versatility and convenience, especially under varying environmental conditions. The use of EIS provides a novel approach that overcomes these limitations. The enteropeptidase underwent genetic modification through the introduction of single amino acid modifications to assess their effect on enzyme kinetics. However, according to the one-sample t-test results, the difference between the engineered enzymes and hEKL was not statistically significant by conventional criteria. The kinetic parameters were analyzed using fluorescence spectroscopy and EIS, which was found to be an effective tool for the real-time measurement of enzyme kinetics. The results obtained through EIS were not significantly different from those obtained through traditional fluorescence spectroscopy methods (p value >> 0.05). The study validates the use of EIS for measuring enzyme kinetics and provides insight into the effects of specific amino acid changes on enteropeptidase function. These findings have potential applications in biotechnology and biochemical research, suggesting a new method for rapidly assessing enzymatic activity.
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Affiliation(s)
- Adriána Dusíková
- Department of Molecular Biology, Faculty of Natural Sciences, Commenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia; (A.D.); (J.K.)
| | - Timea Baranová
- Department of Inorganic Technology, Faculty of Chemical and Food Technology STU in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia; (T.B.); (O.D.); (J.H.)
| | - Ján Krahulec
- Department of Molecular Biology, Faculty of Natural Sciences, Commenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia; (A.D.); (J.K.)
| | - Olívia Dakošová
- Department of Inorganic Technology, Faculty of Chemical and Food Technology STU in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia; (T.B.); (O.D.); (J.H.)
| | - Ján Híveš
- Department of Inorganic Technology, Faculty of Chemical and Food Technology STU in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia; (T.B.); (O.D.); (J.H.)
| | - Monika Naumowicz
- Faculty of Chemistry, University of Białystok, ul. K. Ciołkowskiego 1K, 15-245 Białystok, Poland;
| | - Miroslav Gál
- Department of Inorganic Technology, Faculty of Chemical and Food Technology STU in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia; (T.B.); (O.D.); (J.H.)
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Trier NH, Houen G. Sequential Double Immunoblotting with Peptide Antibodies. Methods Mol Biol 2024; 2821:237-248. [PMID: 38997494 DOI: 10.1007/978-1-0716-3914-6_19] [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] [Indexed: 07/14/2024]
Abstract
Immunoblotting, also termed western blotting, is a powerful method for detection and characterization of proteins separated by various electrophoretic techniques. The combination of sodium dodecyl sulfate-poly acrylamide gel electrophoresis (SDS-PAGE), having high separating power, immunoblotting to synthetic membranes, and detection with highly specific peptide antibodies, is especially useful for studying individual proteins in relation to cellular processes, disease mechanisms, etc. Here, we describe a protocol for the sequential detection of various forms of an individual protein using peptide antibodies, exemplified by the characterization of antibody specificity for different forms of the protein calreticulin by double SDS-PAGE immunoblotting.
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Affiliation(s)
- Nicole Hartwig Trier
- Department of Neurology and Institute of Translational Research, Rigshospitalet, Glostrup, Denmark.
| | - Gunnar Houen
- Department of Neurology and Translational Research Center, Rigshospitalet, Glostrup, Denmark
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3
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Whitham D, Bruno P, Haaker N, Arcaro KF, Pentecost BT, Darie CC. Deciphering a proteomic signature for the early detection of breast cancer from breast milk: the role of quantitative proteomics. Expert Rev Proteomics 2024; 21:81-98. [PMID: 38376826 DOI: 10.1080/14789450.2024.2320158] [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: 09/05/2023] [Accepted: 12/26/2023] [Indexed: 02/21/2024]
Abstract
INTRODUCTION Breast cancer is one of the most prevalent cancers among women in the United States. Current research regarding breast milk has been focused on the composition and its role in infant growth and development. There is little information about the proteins, immune cells, and epithelial cells present in breast milk which can be indicative of the emergence of BC cells and tumors. AREAS COVERED We summarize all breast milk studies previously done in our group using proteomics. These studies include 1D-PAGE and 2D-PAGE analysis of breast milk samples, which include within woman and across woman comparisons to identify dysregulated proteins in breast milk and the roles of these proteins in both the development of BC and its diagnosis. Our projected outlook for the use of milk for cancer detection is also discussed. EXPERT OPINION Analyzing the samples by multiple methods allows one to interrogate a set of samples with various biochemical methods that complement each other, thus providing a more comprehensive proteome. Complementing methods like 1D-PAGE, 2D-PAGE, in-solution digestion and proteomics analysis with PTM-omics, peptidomics, degradomics, or interactomics will provide a better understanding of the dysregulated proteins, but also the modifications or interactions between these proteins.
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Affiliation(s)
- Danielle Whitham
- Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, USA
| | - Pathea Bruno
- Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, USA
| | - Norman Haaker
- Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, USA
| | - Kathleen F Arcaro
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Brian T Pentecost
- Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, USA
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Costel C Darie
- Department of Chemistry and Biochemistry, Clarkson University, Potsdam, NY, USA
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4
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Rosmeita CN, Budiarti S, Mustopa AZ, Novianti E, Swasthikawati S, Chairunnisa S, Hertati A, Nurfatwa M, Ekawati N, Hasan N. Expression, purification, and characterization of self-assembly virus-like particles of capsid protein L1 HPV 52 in Pichia pastoris GS115. J Genet Eng Biotechnol 2023; 21:126. [PMID: 37981617 PMCID: PMC10657913 DOI: 10.1186/s43141-023-00571-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/26/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Cervical cancer caused by the human papillomavirus (HPV) is one of the most frequent malignances globally. HPV 52 is a high-risk cancer-causing genotype that has been identified as the most prevalent type in Indonesia. Virus-like particles (VLP)-based vaccinations against HPV infection could benefit from self-assembled VLP of L1 capsid protein. RESULT The recombinant HPV 52 L1 was expressed in Pichia pastoris on a shake-flask scale with 0.5% methanol induction in this study. The copy number was used to compare the expression level and stability. The colony that survived on a solid medium containing 2000 μg/ml of Zeocin was selected and cultured to express HPV 52 L1. DNA was extracted from the chosen colony, and the copy was determined using qPCR. HPV 52 L1 protein was then purified through fast performance liquid chromatography. Transmission electron microscopy (TEM) evaluation confirmed the VLP self-assembly. The genomic DNA remained intact after 100 generations of serial cultivation under no selective pressure medium conditions, and the protein produced was relatively stable. However, the band intensity was slightly lower than in the parental colony. In terms of copy number, a low copy transformant resulted in low expression but produced a highly stable recombinant clone. Eventually, the L1 protein expressed in Pichia pastoris can self-assemble into VLP. Therefore, recombinant HPV possesses a stable clone and the ability to self-assemble into VLP. CONCLUSION The recombinant L1 HPV 52 protein is successfully expressed in P. pastoris within a size range of approximately 55 kDa and demonstrated favorable stability. The L1 protein expressed in Pichia pastoris successful self-assembled of HPV VLPs, thereby establishing their potential efficacy as a prophylactic vaccine.
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Affiliation(s)
- Chindy Nur Rosmeita
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
- Program of Biotechnology, Graduate School, IPB University, Bogor, Indonesia
| | - Sri Budiarti
- Program of Biotechnology, Graduate School, IPB University, Bogor, Indonesia
- Indonesia Research Center for Bioresources and Biotechnology, IPB University, Bogor, Indonesia
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia.
| | - Ela Novianti
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Sri Swasthikawati
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Sheila Chairunnisa
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Ai Hertati
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Maritsa Nurfatwa
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Nurlaili Ekawati
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
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5
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Sule R, Rivera G, Gomes AV. Western blotting (immunoblotting): history, theory, uses, protocol and problems. Biotechniques 2023; 75:99-114. [PMID: 36971113 DOI: 10.2144/btn-2022-0034] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Western blotting (immunoblotting) is a powerful and commonly used technique that is capable of detecting or semiquantifying an individual protein from complex mixtures of proteins extracted from cells or tissues. The history surrounding the origin of western blotting, the theory behind the western blotting technique, a comprehensive protocol and the uses of western blotting are presented. Lesser known and significant problems in the western blotting field and troubleshooting of common problems are highlighted and discussed. This work is a comprehensive primer and guide for new western blotting researchers and those interested in a better understanding of the technique or getting better results.
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Affiliation(s)
- Rasheed Sule
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Gabriela Rivera
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
- Department of Physiology & Membrane Biology, University of California, Davis, Davis, CA 95616, USA
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6
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Khochare S, Senji Laxme RR, Jaikumar P, Kaur N, Attarde S, Martin G, Sunagar K. Fangs in the Ghats: Preclinical Insights into the Medical Importance of Pit Vipers from the Western Ghats. Int J Mol Sci 2023; 24:ijms24119516. [PMID: 37298463 DOI: 10.3390/ijms24119516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 06/12/2023] Open
Abstract
The socioeconomic impact of snakebites in India is largely attributed to a subset of snake species commonly known as the 'big four'. However, envenoming by a range of other clinically important yet neglected snakes, a.k.a. the 'neglected many', also adds to this burden. The current approach of treating bites from these snakes with the 'big four' polyvalent antivenom is ineffective. While the medical significance of various species of cobras, saw-scaled vipers, and kraits is well-established, the clinical impact of pit vipers from regions such as the Western Ghats, northeastern India, and the Andaman and Nicobar Islands remains poorly understood. Amongst the many species of snakes found in the Western Ghats, the hump-nosed (Hypnale hypnale), Malabar (Craspedocephalus malabaricus), and bamboo (Craspedocephalus gramineus) pit vipers can potentially inflict severe envenoming. To evaluate the severity of toxicity inflicted by these snakes, we characterised their venom composition, biochemical and pharmacological activities, and toxicity- and morbidity-inducing potentials, including their ability to damage kidneys. Our findings highlight the therapeutic inadequacies of the Indian and Sri Lankan polyvalent antivenoms in neutralising the local and systemic toxicity resulting from pit viper envenomings.
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Affiliation(s)
- Suyog Khochare
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - R R Senji Laxme
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Priyanka Jaikumar
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Navneet Kaur
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Saurabh Attarde
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Gerard Martin
- The Liana Trust, Survey #1418/1419, Rathnapuri, Hunsur 571189, India
| | - Kartik Sunagar
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
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Karaiyan P, Chang CCH, Chan ES, Tey BT, Ramanan RN, Ooi CW. In silico screening and heterologous expression of soluble dimethyl sulfide monooxygenases of microbial origin in Escherichia coli. Appl Microbiol Biotechnol 2022; 106:4523-4537. [PMID: 35713659 PMCID: PMC9259527 DOI: 10.1007/s00253-022-12008-8] [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: 02/20/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022]
Abstract
Abstract Sequence-based screening has been widely applied in the discovery of novel microbial enzymes. However, majority of the sequences in the genomic databases were annotated using computational approaches and lacks experimental characterization. Hence, the success in obtaining the functional biocatalysts with improved characteristics requires an efficient screening method that considers a wide array of factors. Recombinant expression of microbial enzymes is often hampered by the undesirable formation of inclusion body. Here, we present a systematic in silico screening method to identify the proteins expressible in soluble form and with the desired biological properties. The screening approach was adopted in the recombinant expression of dimethyl sulfide (DMS) monooxygenase in Escherichia coli. DMS monooxygenase, a two-component enzyme consisting of DmoA and DmoB subunits, was used as a model protein. The success rate of producing soluble and active DmoA is 71% (5 out of 7 genes). Interestingly, the soluble recombinant DmoA enzymes exhibited the NADH:FMN oxidoreductase activity in the absence of DmoB (second subunit), and the cofactor FMN, suggesting that DmoA is also an oxidoreductase. DmoA originated from Janthinobacterium sp. AD80 showed the maximum NADH oxidation activity (maximum reaction rate: 6.6 µM/min; specific activity: 133 µM/min/mg). This novel finding may allow DmoA to be used as an oxidoreductase biocatalyst for various industrial applications. The in silico gene screening methodology established from this study can increase the success rate of producing soluble and functional enzymes while avoiding the laborious trial and error involved in the screening of a large pool of genes available. Key points • A systematic gene screening method was demonstrated. • DmoA is also an oxidoreductase capable of oxidizing NADH and reducing FMN. • DmoA oxidizes NADH in the absence of external FMN. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12008-8.
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Affiliation(s)
- Prasanth Karaiyan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Catherine Ching Han Chang
- Arkema Thiochemicals Sdn. Bhd., Jalan PJU 1A/7A OASIS Ara Damansara, 47301, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Eng-Seng Chan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Beng Ti Tey
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.,Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia
| | - Ramakrishnan Nagasundara Ramanan
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia. .,Arkema Thiochemicals Sdn. Bhd., Jalan PJU 1A/7A OASIS Ara Damansara, 47301, Petaling Jaya, Selangor Darul Ehsan, Malaysia.
| | - Chien Wei Ooi
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia. .,Advanced Engineering Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.
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Identification of the Talaromyces cellulolyticus Gene Encoding an Extracellular Enzyme with β-galactosidase Activity and Testing it as a Reporter for Gene Expression Assays. Mol Biotechnol 2022; 64:637-649. [PMID: 35059977 DOI: 10.1007/s12033-022-00453-9] [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: 06/23/2021] [Accepted: 01/11/2022] [Indexed: 10/19/2022]
Abstract
The filamentous fungus Talaromyces cellulolyticus (formerly Acremonium cellulolyticus) is currently being intensively studied as a promising industrial producer of a number of secreted cellulolytic enzymes. In this study, the T. cellulolyticus gene lacA, which encodes a protein orthologous to the fungal extracellular β-galactosidases of family 35, was identified. The substitution of the lacA upstream region with a constitutive promoter demonstrated that the product of this gene is effectively secreted and possesses β-galactosidase activity. The optimal pH and temperature values for the hydrolysis of o-nitrophenyl-β-D-galactopyranoside by this enzyme were determined to be pH 4.5-5.5 and 50 °C, respectively. The negligible production of β-galactosidase activity by strains expressing lacA under native regulation raises the possibility of using lacA as a reporter gene. To test this hypothesis, the native promoter of lacA was replaced with the strong inducible promoter of the T. cellulolyticus cellobiohydrolase I gene. The cultivation of the resulting strain in various media showed that the β-galactosidase activity depends on cultivation conditions similar to the cellobiohydrolase activity. Thus, the suitability of lacA as a reporter for evaluating promoters with a wide range of expression profiles was demonstrated.
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9
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Spiegel H, Schillberg S, Nölke G. Production of Recombinant Proteins by Agrobacterium-Mediated Transient Expression. Methods Mol Biol 2022; 2480:89-102. [PMID: 35616859 DOI: 10.1007/978-1-0716-2241-4_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The agroinfiltration of plant tissue is a robust method that allows the rapid and transient expression of recombinant proteins. Using wild-type plants as biomass, agroinfiltration exploits the ability of plants to synthesize even complex multimeric proteins that require oxidative folding and/or post-translational modifications, while avoiding the expensive and time-consuming creation of stably transformed plant lines. Here we describe a generic method for the transient expression of recombinant proteins in Nicotiana benthamiana at the small to medium laboratory scale, including appropriate binary vectors, the design and cloning of expression constructs, the transformation, selection, and cultivation of recombinant Agrobacterium tumefaciens, the infiltration of plants using a syringe or vacuum device, and finally the extraction of recombinant proteins from plant tissues.
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Affiliation(s)
- Holger Spiegel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany.
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Department of Phytopathology, Justus Liebig University Giessen, Giessen, Germany
| | - Greta Nölke
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
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10
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Attarde S, Khochare S, Iyer A, Dam P, Martin G, Sunagar K. Venomics of the Enigmatic Andaman Cobra ( Naja sagittifera) and the Preclinical Failure of Indian Antivenoms in Andaman and Nicobar Islands. Front Pharmacol 2021; 12:768210. [PMID: 34759827 PMCID: PMC8573199 DOI: 10.3389/fphar.2021.768210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
The Andaman and Nicobar Islands are an abode to a diversity of flora and fauna, including the many endemic species of snakes, such as the elusive Andaman cobra (Naja sagittifera). However, the ecology and evolution of venomous snakes inhabiting these islands have remained entirely uninvestigated. This study aims to bridge this knowledge gap by investigating the evolutionary history of N. sagittifera and its venom proteomic, biochemical and toxicity profile. Phylogenetic reconstructions confirmed the close relationship between N. sagittifera and the Southeast Asian monocellate cobra (N. kaouthia). Overlooking this evolutionary history, a polyvalent antivenom manufactured using the venom of the spectacled cobra (N. naja) from mainland India is used for treating N. sagittifera envenomations. Comparative evaluation of venoms of these congeners revealed significant differences in their composition, functions and potencies. Given the close phylogenetic relatedness between N. sagittifera and N. kaouthia, we further assessed the cross-neutralising efficacy of Thai monovalent N. kaouthia antivenom against N. sagittifera venoms. Our findings revealed the inadequate preclinical performance of the Indian polyvalent and Thai monovalent antivenoms in neutralising N. sagittifera venoms. Moreover, the poor efficacy of the polyvalent antivenom against N. naja venom from southern India further revealed the critical need to manufacture region-specific Indian antivenoms.
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Affiliation(s)
- Saurabh Attarde
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Suyog Khochare
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Ashwin Iyer
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Paulomi Dam
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | | | - Kartik Sunagar
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
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11
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Avula B, Parveen I, Zhao J, Wang M, Techen N, Wang YH, Riaz M, Bae JY, Shami AA, Chittiboyina AG, Khan IA, Sharp JS. A Comprehensive Workflow for the Analysis of Bio-Macromolecular Supplements: Case Study of 20 Whey Protein Products. J Diet Suppl 2021; 19:515-533. [PMID: 33764265 DOI: 10.1080/19390211.2021.1897724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The presence of bio-macromolecules as major ingredients is a primary factor in marketing many biologically derived macromolecular supplements. Workflows for analyzing these supplements for quality assurance, adulteration, and other supply-chain difficulties must include a qualitative assessment of small-molecule and macromolecular components; however, no such integrated protocol has been reported for these bio-macromolecular supplements. Twenty whey protein supplements were analyzed using an integrated workflow to identify protein content, protein adulteration, inorganic elemental content, and macromolecular and small-molecule profiles. Orthogonal analytical methods were employed, including NMR profiling, LC-DAD-QToF analysis of small-molecule components, ICP-MS analysis of inorganic elements, determination of total protein content by a Bradford assay, SDS-PAGE protein profiling, and bottom-up shotgun proteomic analysis using LC-MS-MS. All 20 supplements showed a reduced protein content compared to the claimed content but no evidence of adulteration with protein from an unclaimed source. Many supplements included unlabeled small-molecule additives (but nontoxic) and significant deviations in metal content, highlighting the importance of both macromolecular and small-molecule analysis in the comprehensive profiling of macromolecular supplements. An orthogonal, integrated workflow allowed the detection of crucial product characteristics that would have remained unidentified using traditional workflows involving either analysis of small-molecule nutritional supplements or protein analysis.
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Affiliation(s)
- Bharathi Avula
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA
| | - Iffat Parveen
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA
| | - Jianping Zhao
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA
| | - Mei Wang
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA
| | - Natascha Techen
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA
| | - Yan-Hong Wang
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA
| | - Mohammad Riaz
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, MS, USA University
| | - Ji-Yeong Bae
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA.,College of Pharmacy, Jeju National University, Jeju, South Korea
| | - Anter A Shami
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, MS, USA University
| | - Amar G Chittiboyina
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA
| | - Ikhlas A Khan
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA.,Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, MS, USA University
| | - Joshua S Sharp
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, MS, USA University.,Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA
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12
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Senji Laxme RR, Khochare S, Attarde S, Suranse V, Iyer A, Casewell NR, Whitaker R, Martin G, Sunagar K. Biogeographic venom variation in Russell's viper (Daboia russelii) and the preclinical inefficacy of antivenom therapy in snakebite hotspots. PLoS Negl Trop Dis 2021; 15:e0009247. [PMID: 33764996 PMCID: PMC7993602 DOI: 10.1371/journal.pntd.0009247] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Snakebite in India results in over 58,000 fatalities and a vast number of morbidities annually. The majority of these clinically severe envenomings are attributed to Russell's viper (Daboia russelii), which has a near pan-India distribution. Unfortunately, despite its medical significance, the influence of biogeography on the composition and potency of venom from disparate D. russelii populations, and the repercussions of venom variation on the neutralisation efficacy of marketed Indian antivenoms, remain elusive. METHODS Here, we employ an integrative approach comprising proteomic characterisation, biochemical analyses, pharmacological assessment, and venom toxicity profiling to elucidate the influence of varying ecology and environment on the pan-Indian populations of D. russelii. We then conducted in vitro venom recognition experiments and in vivo neutralisation assays to evaluate the efficacy of the commercial Indian antivenoms against the geographically disparate D. russelii populations. FINDINGS We reveal significant intraspecific variation in the composition, biochemical and pharmacological activities and potencies of D. russelii venoms sourced from five distinct biogeographic zones across India. Contrary to our understanding of the consequences of venom variation on the effectiveness of snakebite therapy, commercial antivenom exhibited surprisingly similar neutralisation potencies against the majority of the investigated populations, with the exception of low preclinical efficacy against the semi-arid population from northern India. However, the ability of Indian antivenoms to counter the severe morbid effects of Daboia envenoming remains to be evaluated. CONCLUSION The concerning lack of antivenom efficacy against the north Indian population of D. russelii, as well as against two other 'big four' snake species in nearby locations, underscores the pressing need to develop pan-India effective antivenoms with improved efficacy in high snakebite burden locales.
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Affiliation(s)
- R. R. Senji Laxme
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Suyog Khochare
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Saurabh Attarde
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Vivek Suranse
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Ashwin Iyer
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | - Romulus Whitaker
- Madras Crocodile Bank Trust/Centre for Herpetology. East Coast Road, Mamallapuram, Tamil Nadu, India
| | - Gerard Martin
- The Liana Trust. Survey #1418/1419 Rathnapuri, Hunsur, Karnataka, India
| | - Kartik Sunagar
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
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Senji Laxme RR, Attarde S, Khochare S, Suranse V, Martin G, Casewell NR, Whitaker R, Sunagar K. Biogeographical venom variation in the Indian spectacled cobra (Naja naja) underscores the pressing need for pan-India efficacious snakebite therapy. PLoS Negl Trop Dis 2021; 15:e0009150. [PMID: 33600405 PMCID: PMC7924803 DOI: 10.1371/journal.pntd.0009150] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 03/02/2021] [Accepted: 01/18/2021] [Indexed: 01/08/2023] Open
Abstract
Background Snake venom composition is dictated by various ecological and environmental factors, and can exhibit dramatic variation across geographically disparate populations of the same species. This molecular diversity can undermine the efficacy of snakebite treatments, as antivenoms produced against venom from one population may fail to neutralise others. India is the world’s snakebite hotspot, with 58,000 fatalities and 140,000 morbidities occurring annually. Spectacled cobra (Naja naja) and Russell’s viper (Daboia russelii) are known to cause the majority of these envenomations, in part due to their near country-wide distributions. However, the impact of differing ecologies and environment on their venom compositions has not been comprehensively studied. Methods Here, we used a multi-disciplinary approach consisting of venom proteomics, biochemical and pharmacological analyses, and in vivo research to comparatively analyse N. naja venoms across a broad region (>6000 km; seven populations) covering India’s six distinct biogeographical zones. Findings By generating the most comprehensive pan-Indian proteomic and toxicity profiles to date, we unveil considerable differences in the composition, pharmacological effects and potencies of geographically-distinct venoms from this species and, through the use of immunological assays and preclinical experiments, demonstrate alarming repercussions on antivenom therapy. We find that commercially-available antivenom fails to effectively neutralise envenomations by the pan-Indian populations of N. naja, including a complete lack of neutralisation against the desert Naja population. Conclusion Our findings highlight the significant influence of ecology and environment on snake venom composition and potency, and stress the pressing need to innovate pan-India effective antivenoms to safeguard the lives, limbs and livelihoods of the country’s 200,000 annual snakebite victims. Annually, India is burdened by the highest number of snake envenomations across the globe, with over 58,000 fatalities and three times the number of morbidities, predominantly affecting the rural agrarian communities. The spectacled cobra (Naja naja) and Russell’s viper (Daboia russelii) are responsible for the vast majority of envenomations in the country, in part, due to their near country-wide distributions. In this study, we unveil the astounding differences in venom composition of N. naja from six different biogeographical zones across the country (>6000 km). We provide a comprehensive account of their disparate venom proteomic profiles, biochemical and pharmacological effects, and the associated potencies. Our study uncovers alarming differences in the efficacy of the marketed polyvalent antivenoms in neutralising these venoms, thereby, emphasising the pressing need to develop dose-efficacious and pan-India effective antivenoms for the treatment of snakebites in the country. This study also highlights the significant influence of ecology and diverse environments on the venom variability, insinuating the necessity for innovating cost-effective and pan-India efficacious solutions to safeguard the lives, limbs and livelihoods of India’s two hundred thousand annual snakebite victims.
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Affiliation(s)
- R. R. Senji Laxme
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Saurabh Attarde
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Suyog Khochare
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Vivek Suranse
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Gerard Martin
- The Liana Trust, Survey #1418/1419 Rathnapuri, Hunsur, Karnataka, India
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | - Romulus Whitaker
- Madras Crocodile Bank Trust/Centre for Herpetology, Mamallapuram, Tamil Nadu, India
| | - Kartik Sunagar
- Evolutionary Venomics Lab. Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
- * E-mail:
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El-Sheikh SMA, Youssef FM, Mohamed HI, El-Saber Batiha G, Albrakati A, Galal AAA. Efficacy of grape seed hydro-alcoholic extract in the treatment of experimentally Pasteurella multocida infected rabbits. Vet Med Sci 2021; 7:923-934. [PMID: 33590677 PMCID: PMC8136928 DOI: 10.1002/vms3.446] [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: 10/13/2020] [Revised: 01/07/2021] [Accepted: 01/23/2021] [Indexed: 12/14/2022] Open
Abstract
Pasteurellosis is one of the rabbit's most bacterial severe diseases and leads to considerable financial damages in large production systems worldwide. Antibiotic use in animals may lead to antibiotic residues in animal products, including meat. Therefore, this study was designed to evaluate the potential role of grape seed extract (GSE) in treating Pasteurella multocida infection in rabbits. For this purpose, 45 weaned male New Zealand rabbits were divided into three groups; control, infected and infected-GSE treated. Experimental P. multocida infection in rabbits induced a remarkable decrease in body weight, body weight gain, as well as microcytic hypochromic anaemia, leucocytosis, neutrophilia and lymphocytopenia. Also, a significant increase in the hepatic and renal injury biomarkers, in interleukin-6, total globulin, α, β and γ globulins, as well as a marked reduction in total protein and albumin, were recorded in the P. multocida-infected rabbits. Treatment of infected rabbits with GSE modulated most of these altered parameters. This study endorses the administration of GSE for the treatment of Pasteurellosis in rabbits. Further studies are required to identify the possible additional effects, appropriate doses and duration of the GSE therapy in rabbits Pasteurellosis.
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Affiliation(s)
- Sawsan M A El-Sheikh
- Department of Pharmacology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Fatma M Youssef
- Department of Clinical Pathology, Animal Health Research Institute, Ismailia, Egypt
| | - Haidi I Mohamed
- Department of Pharmacology, Animal Health Research Institute, Ismailia, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicines, Damanhour University, Damanhour, Egypt
| | - Ashraf Albrakati
- Department of Human Anatomy, College of Medicine, Taif University, Taif, Saudi Arabia
| | - Azza A A Galal
- Department of Pharmacology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
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Le HTN, Cho S. Deciphering the Disaggregation Mechanism of Amyloid Beta Aggregate by 4-(2-Hydroxyethyl)-1-Piperazinepropanesulfonic Acid Using Electrochemical Impedance Spectroscopy. SENSORS 2021; 21:s21030788. [PMID: 33503934 PMCID: PMC7865397 DOI: 10.3390/s21030788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 12/18/2022]
Abstract
Aggregation of amyloid-β (aβ) peptides into toxic oligomers, fibrils, and plaques is central in the molecular pathogenesis of Alzheimer’s disease (AD) and is the primary focus of AD diagnostics. Disaggregation or elimination of toxic aβ aggregates in patients is important for delaying the progression of neurodegenerative disorders in AD. Recently, 4-(2-hydroxyethyl)-1-piperazinepropanesulfonic acid (EPPS) was introduced as a chemical agent that binds with toxic aβ aggregates and transforms them into monomers to reduce the negative effects of aβ aggregates in the brain. However, the mechanism of aβ disaggregation by EPPS has not yet been completely clarified. In this study, an electrochemical impedimetric immunosensor for aβ diagnostics was developed by immobilizing a specific anti-amyloid-β (aβ) antibody onto a self-assembled monolayer functionalized with a new interdigitated chain-shaped electrode (anti-aβ/SAM/ICE). To investigate the ability of EPPS in recognizing AD by extricating aβ aggregation, commercially available aβ aggregates (aβagg) were used. Electrochemical impedance spectroscopy was used to probe the changes in charge transfer resistance (Rct) of the immunosensor after the specific binding of biosensor with aβagg. The subsequent incubation of the aβagg complex with a specific concentration of EPPS at different time intervals divulged AD progression. The decline in the Rct of the immunosensor started at 10 min of EPPS incubation and continued to decrease gradually from 20 min, indicating that the accumulation of aβagg on the surface of the anti-aβ/SAM/ICE sensor has been extricated. Here, the kinetic disaggregation rate k value of aβagg was found to be 0.038. This innovative study using electrochemical measurement to investigate the mechanism of aβagg disaggregation by EPPS could provide a new perspective in monitoring the disaggregation periods of aβagg from oligomeric to monomeric form, and then support for the prediction and handling AD symptoms at different stages after treatment by a drug, EPPS.
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Affiliation(s)
- Hien T. Ngoc Le
- Department of Electronic Engineering, Gachon University, Seongnam-si, Gyeonggi-do 13120, Korea;
| | - Sungbo Cho
- Department of Electronic Engineering, Gachon University, Seongnam-si, Gyeonggi-do 13120, Korea;
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Korea
- Correspondence: ; Tel.: +82-(31)-750-5321
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Delmez V, Degand H, Poleunis C, Moshkunov K, Chundak M, Dupont-Gillain C, Delcorte A. Deposition of Intact and Active Proteins In Vacuo Using Large Argon Cluster Ion Beams. J Phys Chem Lett 2021; 12:952-957. [PMID: 33443416 DOI: 10.1021/acs.jpclett.0c02510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Providing inert materials with a biochemical function, for example using proteins, is a cornerstone technology underlying many applications. However, the controlled construction of protein thin films remains a major challenge. Here, an innovative solvent-free approach for protein deposition is reported, using lysozyme as a model. By diverting a time-of-flight secondary ion mass spectrometer (ToF-SIMS) from its standard analytical function, large argon clusters were used to achieve protein transfer. A target consisting of a pool of proteins was bombarded with 10 keV Ar5000+ ions, and the ejected proteins were collected on a silicon wafer. The ellipsoidal deposition pattern was evidenced by ToF-SIMS analysis, while SDS-PAGE electrophoresis confirmed the presence of intact lysozyme on the collector. Finally, enzymatic activity assays demonstrated the preservation of the three-dimensional structure of the transferred proteins. These results pave the way to well-controlled protein deposition using ion beams and to the investigation of more complex multilayer architectures.
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Affiliation(s)
- Vincent Delmez
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| | - Hervé Degand
- Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Université catholique de Louvain, Croix du Sud 4-5, B-1348 Louvain-la-Neuve, Belgium
| | - Claude Poleunis
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| | - Konstantin Moshkunov
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| | - Mykhailo Chundak
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| | - Christine Dupont-Gillain
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
| | - Arnaud Delcorte
- Institute of Condensed Matter and Nanosciences-Bio & Soft Matter, Université catholique de Louvain, Place Louis Pasteur, 1 bte L4.01.10, B-1348 Louvain-la-Neuve, Belgium
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Sittipol D, Rodpan S, Ajingi YS, Lohnoo T, Lerksuthirat T, Kumsang Y, Yingyong W, Khunrae P, Rattanarojpong T, Pattanapanyasat K, Jongruja N. Identification, overexpression, purification, and biochemical characterization of a novel hyperthermostable keratinase from Geoglobus acetivorans. 3 Biotech 2021; 11:2. [PMID: 33269186 DOI: 10.1007/s13205-020-02538-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/30/2020] [Indexed: 01/19/2023] Open
Abstract
The goal of this study was to identify and biochemically characterize a novel hyperthermostable keratinase from microorganisms for feather waste degradation. Here, a hyperthermophilic Geoglobus acetivorans keratinase (GacK) gene was chosen based on a search of a sequence database. The selected GacK gene was synthesized, cloned, and successfully expressed without a signal peptide in the E. coli system. A monomer of approximately 58 kDa was obtained in a soluble form and purified. The recombinant GacK displayed the highest activity at an optimum temperature of 100 °C and a pH of 10. The hyperthermostable GacK enzymatic performance remained high even after incubation in nonionic surfactants and the chelating agent EDTA. The residual and keratinolytic activities of GacK, as determined with azocasein and keratin azure used as substrates, remained significantly greater than 80% at 130 °C for 7 h. The kinetic parameters Km and Vmax for azure keratin were 0.41 mg/ml and 875.14 unit/mg, respectively, while those for azocasein were 1.51 mg/ml and 505.32 unit/mg, respectively. The results suggest that the enzyme is among the most hyperthermostable keratinases. Because of its enzymatic characteristics to degrade keratin azure at high temperatures, GacK may potentially be utilized in future industrial applications.
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Speciale I, Laugieri ME, Noel E, Lin S, Lowary TL, Molinaro A, Duncan GA, Agarkova IV, Garozzo D, Tonetti MG, Van Etten JL, De Castro C. Chlorovirus PBCV-1 protein A064R has three of the transferase activities necessary to synthesize its capsid protein N-linked glycans. Proc Natl Acad Sci U S A 2020; 117:28735-28742. [PMID: 33139538 PMCID: PMC7682578 DOI: 10.1073/pnas.2016626117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Paramecium bursaria chlorella virus-1 (PBCV-1) is a large double-stranded DNA (dsDNA) virus that infects the unicellular green alga Chlorella variabilis NC64A. Unlike many other viruses, PBCV-1 encodes most, if not all, of the enzymes involved in the synthesis of the glycans attached to its major capsid protein. Importantly, these glycans differ from those reported from the three domains of life in terms of structure and asparagine location in the sequon of the protein. Previous data collected from 20 PBCV-1 spontaneous mutants (or antigenic variants) suggested that the a064r gene encodes a glycosyltransferase (GT) with three domains, each with a different function. Here, we demonstrate that: domain 1 is a β-l-rhamnosyltransferase; domain 2 is an α-l-rhamnosyltransferase resembling only bacterial proteins of unknown function, and domain 3 is a methyltransferase that methylates the C-2 hydroxyl group of the terminal α-l-rhamnose (Rha) unit. We also establish that methylation of the C-3 hydroxyl group of the terminal α-l-Rha is achieved by another virus-encoded protein A061L, which requires an O-2 methylated substrate. This study, thus, identifies two of the glycosyltransferase activities involved in the synthesis of the N-glycan of the viral major capsid protein in PBCV-1 and establishes that a single protein A064R possesses the three activities needed to synthetize the 2-OMe-α-l-Rha-(1→2)-β-l-Rha fragment. Remarkably, this fragment can be attached to any xylose unit.
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Affiliation(s)
- Immacolata Speciale
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
- Department of Agricultural Sciences, University of Napoli Federico II, 80055 Portici NA, Italy
| | - Maria Elena Laugieri
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy
| | - Eric Noel
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118
| | - Sicheng Lin
- Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, AB T6G 2G2 , Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Gunning-Lemieux Chemistry Centre, Edmonton, AB T6G 2G2 , Canada
- Institute of Biological Chemistry, Academia Sinica, Nangang, 11529 Taipei, Taiwan
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, 80126 Napoli, Italy
| | - Garry A Duncan
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
| | - Irina V Agarkova
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0722
| | - Domenico Garozzo
- CNR, Institute for Polymers, Composites and Biomaterials, 95126 Catania, Italy
| | - Michela G Tonetti
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, 16132 Genova, Italy;
| | - James L Van Etten
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900;
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583-0722
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli Federico II, 80055 Portici NA, Italy;
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Dynamic modulations of the MDA-MB-231 secretions at low dose radiation. J Radioanal Nucl Chem 2020. [DOI: 10.1007/s10967-020-07139-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Beyond the 'big four': Venom profiling of the medically important yet neglected Indian snakes reveals disturbing antivenom deficiencies. PLoS Negl Trop Dis 2019; 13:e0007899. [PMID: 31805055 PMCID: PMC6894822 DOI: 10.1371/journal.pntd.0007899] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/01/2019] [Indexed: 11/19/2022] Open
Abstract
Background Snakebite in India causes the highest annual rates of death (46,000) and disability (140,000) than any other country. Antivenom is the mainstay treatment of snakebite, whose manufacturing protocols, in essence, have remained unchanged for over a century. In India, a polyvalent antivenom is produced for the treatment of envenomations from the so called ‘big four’ snakes: the spectacled cobra (Naja naja), common krait (Bungarus caeruleus), Russell’s viper (Daboia russelii), and saw-scaled viper (Echis carinatus). In addition to the ‘big four’, India is abode to many other species of venomous snakes that have the potential to inflict severe clinical or, even, lethal envenomations in their human bite victims. Unfortunately, specific antivenoms are not produced against these species and, instead, the ‘big four’ antivenom is routinely used for the treatment. Methods We characterized the venom compositions, biochemical and pharmacological activities and toxicity profiles (mouse model) of the major neglected yet medically important Indian snakes (E. c. sochureki, B. sindanus, B. fasciatus, and two populations of N. kaouthia) and their closest ‘big four’ congeners. By performing WHO recommended in vitro and in vivo preclinical assays, we evaluated the efficiencies of the commercially marketed Indian antivenoms in recognizing venoms and neutralizing envenomations by these neglected species. Findings As a consequence of dissimilar ecologies and diet, the medically important snakes investigated exhibited dramatic inter- and intraspecific differences in their venom profiles. Currently marketed antivenoms were found to exhibit poor dose efficacy and venom recognition potential against the ‘neglected many’. Premium Serums antivenom failed to neutralise bites from many of the neglected species and one of the ‘big four’ snakes (North Indian population of B. caeruleus). Conclusions This study unravels disturbing deficiencies in dose efficacy and neutralisation capabilities of the currently marketed Indian antivenoms, and emphasises the pressing need to develop region-specific snakebite therapy for the ‘neglected many’. Snakebite is a ‘neglected tropical disease’ that majorly affects the rural populations in developing countries. India bears the brunt of snakebites with over 46,000 deaths and 140,000 disabilities, annually. A significant number of these bites are attributed to the widely distributed ‘big four’ snakes, namely spectacled cobra (Naja naja), common krait (Bungarus caeruleus), Russell’s viper (Daboia russelii), and saw-scaled viper (Echis carinatus). The commercial antivenoms marketed in India are only manufactured against these four species, while neglecting many other medically relevant snakes with restricted geographic distribution. Snakebite pathology is dependent on the venom composition of the population/species, which can, in turn, vary intra- and inter-specifically. Though this variation severely limits the cross-population/species antivenom efficacy, envenomations by the neglected snakes in India are treated with the ‘big four’ antivenom. Therefore, to unravel the underlying venom variability, we investigated venom proteomic, biochemical/pharmacological and toxicity profiles of the major neglected Indian snakes and their ‘big four’ relatives. To assess the effectiveness of the ‘big four’ antivenom in treating bites from these neglected snakes, we performed preclinical experiments, which revealed alarming inadequacies of the commercial antivenoms. Our findings accentuate the compelling necessity for the innovation of highly efficacious next-generation snakebite therapy in India.
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Purification and Characterization of A New Cold-Adapted and Thermo-Tolerant Chitosanase from Marine Bacterium Pseudoalteromonas sp. SY39. Molecules 2019; 24:molecules24010183. [PMID: 30621320 PMCID: PMC6337222 DOI: 10.3390/molecules24010183] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/18/2018] [Accepted: 12/29/2018] [Indexed: 12/20/2022] Open
Abstract
Chitosanases play an important role in chitosan degradation, forming enzymatic degradation products with several biological activities. Although many chitosanases have been discovered and studied, the enzymes with special characteristics are still rather rare. In this study, a new chitosanase, CsnM, with an apparent molecular weight of 28 kDa was purified from the marine bacterium Pseudoalteromonas sp. SY39. CsnM is a cold-adapted enzyme, which shows highest activity at 40 °C and exhibits 30.6% and 49.4% of its maximal activity at 10 and 15 °C, respectively. CsnM is also a thermo-tolerant enzyme that recovers 95.2%, 89.1% and 88.1% of its initial activity after boiling for 5, 10 and 20 min, respectively. Additionally, CsnM is an endo-type chitosanase that yields chitodisaccharide as the main product (69.9% of the total product). It’s cold-adaptation, thermo-tolerance and high chitodisaccharide yield make CsnM a superior candidate for biotechnological application to produce chitooligosaccharides.
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Reif A, Chiki A, Ricci J, Lashuel HA. Generation of Native, Untagged Huntingtin Exon1 Monomer and Fibrils Using a SUMO Fusion Strategy. J Vis Exp 2018. [PMID: 30010666 PMCID: PMC6102005 DOI: 10.3791/57506] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Huntington's Disease (HD) is an inherited fatal neurodegenerative disease caused by a CAG expansion (≥36) in the first exon of the HD gene, resulting in the expression of the Huntingtin protein (Htt) or N-terminal fragments thereof with an expanded polyglutamine (polyQ) stretch. The exon1 of the Huntingtin protein (Httex1) is the smallest Htt fragment that recapitulates many of the features of HD in cellular and animal models and is one of the most widely studied fragments of Htt. The small size of Httex1 makes it experimentally more amenable to biophysical characterization using standard and high-resolution techniques in comparison to longer fragments or full-length Htt. However, the high aggregation propensity of mutant Httex1 (mHttex1) with increased polyQ content (≥42) has made it difficult to develop efficient expression and purification systems to produce these proteins in sufficient quantities and make them accessible to scientists from different disciplines without the use of fusion proteins or other strategies that alter the native sequence of the protein. We present here a robust and optimized method for the production of milligram quantities of native, tag-free Httex1 based on the transient fusion of small ubiquitin related modifier (SUMO). The simplicity and efficiency of the strategy will eliminate the need to use non-native sequences of Httex1, thus making this protein more accessible to researchers and improving the reproducibility of experiments across different laboratories. We believe that these advances will also facilitate future studies aimed at elucidating the structure-function relationship of Htt as well as developing novel diagnostic tools and therapies to treat or slow the progression of HD.
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Affiliation(s)
- Andreas Reif
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne (EPFL)
| | - Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne (EPFL)
| | - Jonathan Ricci
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne (EPFL)
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne (EPFL);
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23
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Bass JJ, Wilkinson DJ, Rankin D, Phillips BE, Szewczyk NJ, Smith K, Atherton PJ. An overview of technical considerations for Western blotting applications to physiological research. Scand J Med Sci Sports 2017; 27:4-25. [PMID: 27263489 PMCID: PMC5138151 DOI: 10.1111/sms.12702] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2016] [Indexed: 12/11/2022]
Abstract
The applications of Western/immunoblotting (WB) techniques have reached multiple layers of the scientific community and are now considered routine procedures in the field of physiology. This is none more so than in relation to skeletal muscle physiology (i.e., resolving the mechanisms underpinning adaptations to exercise). Indeed, the inclusion of WB data is now considered an essential aspect of many such physiological publications to provide mechanistic insight into regulatory processes. Despite this popularity, and due to the ubiquitous and relatively inexpensive availability of WB equipment, the quality of WB in publications and subsequent analysis and interpretation of the data can be variable, perhaps resulting in spurious conclusions. This may be due to poor laboratory technique and/or lack of comprehension of the critical steps involved in WB and what quality control procedures should be in place to ensure robust data generation. The present review aims to provide a detailed description and critique of WB procedures and technicalities, from sample collection through preparation, blotting and detection, to analysis of the data collected. We aim to provide the reader with improved expertise to critically conduct, evaluate, and troubleshoot the WB process, to produce reproducible and reliable blots.
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Affiliation(s)
- J J Bass
- MRC/ARUK Centre of Excellence for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, UK
| | - D J Wilkinson
- MRC/ARUK Centre of Excellence for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, UK
| | - D Rankin
- MRC/ARUK Centre of Excellence for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, UK
| | - B E Phillips
- MRC/ARUK Centre of Excellence for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, UK
| | - N J Szewczyk
- MRC/ARUK Centre of Excellence for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, UK
| | - K Smith
- MRC/ARUK Centre of Excellence for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, UK
| | - P J Atherton
- MRC/ARUK Centre of Excellence for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, UK
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24
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Joshi M, Nerurkar M, Adivarekar R. Characterization, Kinetic, and Thermodynamic Studies of Marine Pectinase FromBacillus subtilis. Prep Biochem Biotechnol 2014; 45:205-20. [DOI: 10.1080/10826068.2014.907181] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Contreras Esquivel JC, Voget CE. Purification and partial characterization of an acidic polygalacturonase from Aspergillus kawachii. J Biotechnol 2005; 110:21-8. [PMID: 15099902 DOI: 10.1016/j.jbiotec.2004.01.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2002] [Revised: 10/01/2003] [Accepted: 01/16/2004] [Indexed: 11/27/2022]
Abstract
An endo-polygalacturonase, named PGI, was purified to homogeneity from the culture filtrate of Aspergillus kawachii IFO 4033 grown in a glucose-tryptone medium. The molecular mass of PGI was estimated to be 60 kDa by SDS-PAGE and 40 kDa by gel filtration on Sephacryl S-100. The isoelectric point was 3.55 as determined by isoelectic focusing. PGI exhibited binding properties to ConA-Sepharose suggesting that the protein is glycosylated. The N-terminal amino acid sequence was also determined as S-T-C-T-F-T-D-A-A-T-A-S-E-S-K. The remarkable property of PGI was its high activity in the pH range 2.0-3.0 towards soluble and insoluble substrates, while being inactive at pH 5.0. Enzyme stability at low pHs was markedly enhanced by different compounds, such as proteins, polysaccharides, simple sugars and the substrate pectin. PGI was very efficient to extract pectin from lemmon protopectin and to macerate carrot tissues at pH 2.0. These properties make PGI an interesting biocatalyst for industrial applications under highly acidic conditions.
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Affiliation(s)
- J C Contreras Esquivel
- Departamento de Investigación en Alimentos, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, P.O. Box 252-21P-25000, Saltillo, Coahuila, Mexico
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26
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Pioszak AA, Ninfa AJ. Mutations altering the N-terminal receiver domain of NRI (NtrC) That prevent dephosphorylation by the NRII-PII complex in Escherichia coli. J Bacteriol 2004; 186:5730-40. [PMID: 15317778 PMCID: PMC516846 DOI: 10.1128/jb.186.17.5730-5740.2004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phosphorylated form of NRI is the transcriptional activator of nitrogen-regulated genes in Escherichia coli. NRI approximately P displays a slow autophosphatase activity and is rapidly dephosphorylated by the complex of the NRII and PII signal transduction proteins. Here we describe the isolation of two mutations, causing the alterations DeltaD10 and K104Q in the receiver domain of NRI, that were selected as conferring resistance to dephosphorylation by the NRII-PII complex. The mutations, which alter highly conserved residues near the D54 site of phosphorylation in the NRI receiver domain, resulted in elevated expression of nitrogen-regulated genes under nitrogen-rich conditions. The altered NRI receiver domains were phosphorylated by NRII in vitro but were defective in dephosphorylation. The DeltaD10 receiver domain retained normal autophosphatase activity but was resistant to dephosphorylation by the NRII-PII complex. The K104Q receiver domain lacked both the autophosphatase activity and the ability to be dephosphorylated by the NRII-PII complex. The properties of these altered proteins are consistent with the hypothesis that the NRII-PII complex is not a true phosphatase but rather collaborates with NRI approximately P to bring about its dephosphorylation.
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Affiliation(s)
- Augen A Pioszak
- Department of Biological Chemistry, University of Michigan Medical School, 1301 E. Catherine, Ann Arbor, MI 48109-0606, USA
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27
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Hikawa N, Takenaka T. Mature sensory neuron-derived hybrid cell line expressing NGF-dependent neurite extension. Brain Res 1997; 774:225-8. [PMID: 9452214 DOI: 10.1016/s0006-8993(97)81709-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We established a hybrid cell line which extended neurites in the presence of nerve growth factor by fusion between adult mouse sensory neurons and neuroblastoma C1300 cells using emetine and actinomycin D. The serine-phosphorylated 200 and 160 kDa neurofilament proteins were detected in the hybrid cells. In comparison, C1300 cells expressed both subunit of non-phosphorylated neurofilaments at serine residues.
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Affiliation(s)
- N Hikawa
- Department of Physiology, School of Medicine, Yokohama City University, Yokohama, Japan
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28
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Ninfa EG, Atkinson MR, Kamberov ES, Ninfa AJ. Mechanism of autophosphorylation of Escherichia coli nitrogen regulator II (NRII or NtrB): trans-phosphorylation between subunits. J Bacteriol 1993; 175:7024-32. [PMID: 8226644 PMCID: PMC206830 DOI: 10.1128/jb.175.21.7024-7032.1993] [Citation(s) in RCA: 129] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Nitrogen regulator II (NRII or NtrB) is a homodimeric signal-transducing protein kinase/phosphatase responsible for the transcriptional regulation of the Ntr regulon in Escherichia coli. NRII is a member of a large family of proteins that are part of the related two-component signal transduction systems. We studied the mechanism of NRII autophosphorylation by using purified components. Alteration of the site of NRII autophosphorylation to asparagine (H-139-->N [H139N]) or deletion of the C-terminal 59 amino acids of NRII (ter291) resulted in proteins that were not autophosphorylated upon incubation with ATP. Alteration of glycine 313 to alanine resulted in a protein (G313A) that was phosphorylated to a lesser extent than the wild-type protein. Unlike wild-type NRII and H139N, G313A could not be efficiently cross-linked to [alpha-32P]ATP, suggesting that the G313A mutation affects nucleotide binding. Fusion of maltose-binding protein (MBP) to the N-terminal end of NRII resulted in a protein (MBP-NRII) that autophosphorylated normally. We developed a procedure for forming mixed dimers in vitro from these proteins. In mixed dimers consisting of MBP-NRII and H139N, only the MBP-NRII subunit is phosphorylated. In contrast, in mixed dimers consisting of MBP-NRII and G313A, phosphorylation is predominantly on the G313A subunit. We also demonstrated that the G313A and H139N proteins could complement for the autophosphorylation reaction when they were treated so as to permit the formation of mixed dimers and that the wild-type and H139N proteins could phosphorylate the ter291 protein. These results indicate that the autophosphorylation reaction occurs within the dimer by a trans, intersubunit mechanism in which one subunit binds ATP and phosphorylates the other subunit.
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Affiliation(s)
- E G Ninfa
- Department of Biochemistry, Wayne State University School of Medicine, Detroit, Michigan 48201
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29
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Morales P, Madarro A, Pérez-González JA, Sendra JM, Piñaga F, Flors A. Purification and Characterization of Alkaline Xylanases from
Bacillus polymyxa. Appl Environ Microbiol 1993; 59:1376-82. [PMID: 16348932 PMCID: PMC182092 DOI: 10.1128/aem.59.5.1376-1382.1993] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By applying different classical and fast protein liquid chromatographic techniques, three xylanases (β-1,4-
d
-xylan xylanhydrolase) were purified to homogeneity from the extracellular enzymatic complex of
Bacillus polymyxa
. The three enzymes (X
34
C, X
34
E, and X
22
) were small proteins of 34, 34, and 22 kDa and basic pIs 9.3, >9.3, and 9.0, respectively. X
34
C and X
34
E are closely related and seem to be isoforms of the same enzyme. However, they differ in some characteristics. The three enzymes had different pH and temperature optima. One of them, X
34
E, showed a high thermal stability. The
V
max
values determined for X
34
C, X
34
E, and X
22
enzymes on oat spelts xylan were 14.9, 85.5, and 64.0 U mg
-1
, respectively, and 16.1, 62.0, and 150.6 U mg
-1
on birchwood xylan. When oat spelts xylan was the substrate used,
K
m
values of 3.4, 2.4, and 1.9 mg ml
-1
were obtained for X
34
C, X
34
E, and X
22
enzymes, respectively, and 0.65, 6.3, and 0.32 mg ml
-1
were the respective
K
m
values determined with birchwood xylan as the substrate. The enzymes were nondebranching endo-β-xylanases. Xylose was one of the products of xylan hydrolysis by xylanases X
34
C and X
34
E, but this monosaccharide was not released by X
22
enzyme. However, neither of the enzymes was able to degrade xylobiose.
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Affiliation(s)
- P Morales
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010 Valencia, Spain
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