1
|
Siddiqui U, Khan AB, Ahmad T, Rehman AA, Jairajpuri MA. A common protein C inhibitor exosite partially controls the heparin induced activation and inhibition of serine proteases. Int J Biol Macromol 2024; 266:131065. [PMID: 38521329 DOI: 10.1016/j.ijbiomac.2024.131065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
Protein C inhibitor (PCI) maintains hemostasis by inhibiting both procoagulant and anticoagulant serine proteases, and plays important roles in coagulation, fibrinolysis, reproduction, and anti-angiogenesis. The reactive site loop of PCI traps and irreversibly inhibits the proteases like APC (activating protein C), thrombin (FIIa) and factor Xa (FXa). Previous studies on antithrombin (ATIII) had identified Tyr253 and Glu255 as functional exosites that interact and aid in the inhibition of factor IXa and FXa. Presence of exosite in PCI is not known, however a sequence comparison with the PCI from different vertebrate species and ATIII identified Glu239 to be absolutely conserved. PCI residues analogous to ATIII exosite residues were mutated to R238A and E239A. Purified variant PCI in the presence of heparin (10 μg/ml) showed a 2-4 fold decrease in the rate of inhibition of the proteases. However, the stoichiometry of inhibition of FIIa, APC, and FXa by native PCI, R238A and E239A variants were found to be close to 1.0, which also indicated the formation of stable complexes based on SDS-PAGE and western blot analysis with thrombin and APC. Our findings revealed the possible presence of an exosite in PCI that influences the protease inhibition rates.
Collapse
Affiliation(s)
- Urfi Siddiqui
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Abdul Burhan Khan
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Tahif Ahmad
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ahmed Abdur Rehman
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | | |
Collapse
|
2
|
Thakur S, Yasmin R, Malhotra A, Lalremsanga HT, Santra V, Giri S, Doley R. Isolation and Functional Characterization of Erythrofibrase: An Alfa-Fibrinogenase Enzyme from Trimeresurus erythrurus Venom of North-East India. Toxins (Basel) 2024; 16:201. [PMID: 38668626 PMCID: PMC11054993 DOI: 10.3390/toxins16040201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
Green pit viper bites induce mild toxicity with painful local swelling, blistering, cellulitis, necrosis, ecchymosis and consumptive coagulopathy. Several bite cases of green pit vipers have been reported in several south-east Asian countries including the north-eastern region of India. The present study describes isolation and characterization of a haemostatically active protein from Trimeresurus erythrurus venom responsible for coagulopathy. Using a two-step chromatographic method, a snake venom serine protease erythrofibrase was purified to homogeneity. SDS-PAGE of erythrofibrase showed a single band of ~30 kDa in both reducing and non-reducing conditions. The primary structure of erythrofibrase was determined by ESI LC-MS/MS, and the partial sequence obtained showed 77% sequence similarity with other snake venom thrombin-like enzymes (SVTLEs). The partial sequence obtained had the typical 12 conserved cysteine residues, as well as the active site residues (His57, Asp102 and Ser195). Functionally, erythrofibrase showed direct fibrinogenolytic activity by degrading the Aα chain of bovine fibrinogen at a slow rate, which might be responsible for causing hypofibrinogenemia and incoagulable blood for several days in envenomated patients. Moreover, the inability of Indian polyvalent antivenom (manufactured by Premium Serum Pvt. Ltd., Maharashtra, India) to neutralize the thrombin-like and plasmin-like activity of erythrofibrase can be correlated with the clinical inefficacy of antivenom therapy. This is the first study reporting an α-fibrinogenase enzyme erythrofibrase from T. erythrurus venom, which is crucial for the pathophysiological manifestations observed in envenomated victims.
Collapse
Affiliation(s)
- Susmita Thakur
- Molecular Toxinology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India; (S.T.); (R.Y.)
| | - Rafika Yasmin
- Molecular Toxinology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India; (S.T.); (R.Y.)
| | - Anita Malhotra
- Molecular Ecology and Evolution at Bangor, School of Environmental and Natural Sciences, Bangor University, Bangor LL57 2UW, UK;
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Aizawl 796004, Mizoram, India;
| | - Vishal Santra
- Society for Nature Conservation, Research and Community Engagement (CONCERN), Nalikul 712407, West Bengal, India;
- Captive and Field Herpetology, 13 Hirfron, Anglesey LL65 1YU, UK
- Shree Sainath Surgical and Maternity Hospital, Valsad 396050, Gujrat, India
| | - Surajit Giri
- Demow Government Community Health Centre, Raichai, Konwar Dihingia Gaon, Sivasagar 785662, Assam, India;
| | - Robin Doley
- Molecular Toxinology Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India; (S.T.); (R.Y.)
| |
Collapse
|
3
|
Teixeira EMGF, Kalume DE, Ferreira PF, Alves TA, Fontão APGA, Sampaio ALF, de Oliveira DR, Morgado-Díaz JA, Silva-López RE. A Novel Trypsin Kunitz-Type Inhibitor from Cajanus cajan Leaves and Its Inhibitory Activity on New Cancer Serine Proteases and Its Effect on Tumor Cell Growth. Protein J 2024; 43:333-350. [PMID: 38347326 DOI: 10.1007/s10930-023-10175-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2023] [Indexed: 05/01/2024]
Abstract
A novel trypsin inhibitor from Cajanus cajan (TIC) fresh leaves was partially purified by affinity chromatography. SDS-PAGE revealed one band with about 15 kDa with expressive trypsin inhibitor activity by zymography. TIC showed high affinity for trypsin (Ki = 1.617 μM) and was a competitive inhibitor for this serine protease. TIC activity was maintained after 24 h of treatment at 70 °C, after 1 h treatments with different pH values, and β-mercaptoethanol increasing concentrations, and demonstrated expressive structural stability. However, the activity of TIC was affected in the presence of oxidizing agents. In order to study the effect of TIC on secreted serine proteases, as well as on the cell culture growth curve, SK-MEL-28 metastatic human melanoma cell line and CaCo-2 colon adenocarcinoma was grown in supplemented DMEM, and the extracellular fractions were submitted salting out and affinity chromatography to obtain new secreted serine proteases. TIC inhibited almost completely, 96 to 89%, the activity of these serine proteases and reduced the melanoma and colon adenocarcinoma cells growth of 48 and 77% respectively. Besides, it is the first time that a trypsin inhibitor was isolated and characterized from C. cajan leaves and cancer serine proteases were isolated and partial characterized from SK-MEL-28 and CaCo-2 cancer cell lines. Furthermore, TIC shown to be potent inhibitor of tumor protease affecting cell growth, and can be one potential drug candidate to be employed in chemotherapy of melanoma and colon adenocarcinoma.
Collapse
Affiliation(s)
- Erika Maria Gomes Ferreira Teixeira
- Departament of Natural Products, Institute of Pharmaceuticals Technology, FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
- Laboratory of Bioprospection and Applied Ethnopharmacology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Dario Eluam Kalume
- Interdisciplinary Laboratory of Medical Research, IOC-Oswaldo Cruz Institute, FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, Rio de Janeiro, CEP 21045-900, Brazil
| | - Patrícia Fernandes Ferreira
- Departament of Natural Products, Institute of Pharmaceuticals Technology, FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Thayane Aparecida Alves
- Departament of Natural Products, Institute of Pharmaceuticals Technology, FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil
| | - Ana Paula G A Fontão
- Departament of Pharmacology, Institute of Pharmaceuticals Technology, FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, Rio de Janeiro, CEP 21045-900, Brazil
| | - André Luís Franco Sampaio
- Departament of Pharmacology, Institute of Pharmaceuticals Technology, FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, Rio de Janeiro, CEP 21045-900, Brazil
| | - Danilo Ribeiro de Oliveira
- Laboratory of Bioprospection and Applied Ethnopharmacology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - José Andrés Morgado-Díaz
- Cellular and Molecular Oncobiology Program, National Institute of Cancer (INCa), Rio de Janeiro, Brazil
| | - Raquel Elisa Silva-López
- Departament of Natural Products, Institute of Pharmaceuticals Technology, FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, Rio de Janeiro, 21045-900, Brazil.
| |
Collapse
|
4
|
Srivastava N, Shiburaj S, Khare SK. Improved production of alkaline and solvent-stable proteases from a halotolerant Exiguobacterium isolate through heterologous expression. Int J Biol Macromol 2024; 260:129507. [PMID: 38244731 DOI: 10.1016/j.ijbiomac.2024.129507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/31/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024]
Abstract
Halophiles are excellent sources of detergent proteases that are attributed to stability in alkaline pH, salts, surfactants, and hydrophobic solvents. The lower enzymatic yields and tedious downstream processes necessitate the search for newer halophilic sources. We have previously reported a halotolerant Exiguobacterium sp. TBG-PICH-001, which secretes solvent-tolerant alkaline protease/s. The present study describes the heterologous expression of two protease genes, namely, rsep metalloprotease (WP_195864791, 1.23 Kb) and tpa serine protease (WP_195864453, 0.879 Kb) genes. These were cloned into the pET 22b + plasmid vector and expressed in Escherichia coli BL21(DE3). The recombinant proteases rsep and tpa showed respective yields of 6.3 and 6.7 IU/mg, 11 and 12-fold higher than the crude native protease/s from TBG-PICH-001. These showed soluble expression at 46 and 32 KDa, respectively. These were purified to homogeneity through Ni-NTA-affinity chromatography. The purified proteases were characterized for properties like pH & temperature optima and stability, substrate specificity, kinetic parameters, and detergent attributes. They showed affinity towards various substrates with a respective Km of 392 and 301 μM towards casein. The recombinant proteases exhibited stability in the alkaline pH (7-10), surfactants, metal ions, detergents, and hydrophobic solvents, rendering their suitability as detergent additives.
Collapse
Affiliation(s)
- Nitin Srivastava
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Sugathan Shiburaj
- Department of Botany, University of Kerala, Palayam, Thiruvananthapuram, Kerala 695034, India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| |
Collapse
|
5
|
Detomasi TC, Batka AE, Valastyan JS, Hydorn MA, Craik CS, Bassler BL, Marletta MA. Proteases influence colony aggregation behavior in Vibrio cholerae. J Biol Chem 2023; 299:105386. [PMID: 37898401 PMCID: PMC10709122 DOI: 10.1016/j.jbc.2023.105386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/03/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Aggregation behavior provides bacteria protection from harsh environments and threats to survival. Two uncharacterized proteases, LapX and Lap, are important for Vibrio cholerae liquid-based aggregation. Here, we determined that LapX is a serine protease with a preference for cleavage after glutamate and glutamine residues in the P1 position, which processes a physiologically based peptide substrate with a catalytic efficiency of 180 ± 80 M-1s-1. The activity with a LapX substrate identified by a multiplex substrate profiling by mass spectrometry screen was 590 ± 20 M-1s-1. Lap shares high sequence identity with an aminopeptidase (termed VpAP) from Vibrio proteolyticus and contains an inhibitory bacterial prepeptidase C-terminal domain that, when eliminated, increases catalytic efficiency on leucine p-nitroanilide nearly four-fold from 5.4 ± 4.1 × 104 M-1s-1 to 20.3 ± 4.3 × 104 M-1s-1. We demonstrate that LapX processes Lap to its mature form and thus amplifies Lap activity. The increase is approximately eighteen-fold for full-length Lap (95.7 ± 5.6 × 104 M-1s-1) and six-fold for Lap lacking the prepeptidase C-terminal domain (11.3 ± 1.9 × 105 M-1s-1). In addition, substrate profiling reveals preferences for these two proteases that could inform in vivo function. Furthermore, purified LapX and Lap restore the timing of the V. cholerae aggregation program to a mutant lacking the lapX and lap genes. Both proteases must be present to restore WT timing, and thus they appear to act sequentially: LapX acts on Lap, and Lap acts on the substrate involved in aggregation.
Collapse
Affiliation(s)
- Tyler C Detomasi
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Allison E Batka
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Julie S Valastyan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; The Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Molly A Hydorn
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; The Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Michael A Marletta
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
| |
Collapse
|
6
|
Saggu SK, Bala R, Hora R, Mishra PC. Purification and characterization of a high molecular weight serine protease from Microbacterium paraoxydans sp. SKS10. Biotechnol Appl Biochem 2023; 70:1741-1753. [PMID: 37183365 DOI: 10.1002/bab.2472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/13/2023] [Indexed: 05/16/2023]
Abstract
Alkaline proteases from microbial sources have been found suitable for diverse industrial applications, with serine proteases being the most common enzymes used in the detergent industry. In the present study, we have purified and characterized an extracellular alkaline serine protease from Microbacterium paraoxydans sp. SKS10. The protease was purified using ammonium sulfate precipitation followed by different chromatography techniques (fold purification 6.919). Km and Vmax for the protease were determined to be 0.183 mg/mL and 4.904 U/mL, respectively. This enzyme is a thermostable high molecular weight (∼109.4 kDa) protease which has maximal activity at 60°C, and above pH 10. Inhibitor assays revealed the enzyme to be a serine protease whose activity increased by 2.5-fold in the presence of EDTA. This enzyme remained active in the presence of various metal salts and organic solvents and was compatible with commercially available laundry detergents highlighting its potential for use in the detergent industry.
Collapse
Affiliation(s)
- Sandeep Kaur Saggu
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, India
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, India
| | - Renu Bala
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, India
| | - Rachna Hora
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | | |
Collapse
|
7
|
Li N, Shen B, Liu Y, Weng P, Wu Z. Heterologous expression and characterization of Bacillus velezensis SW5 serine protease involved in the hydrolysis of anchovy protein. J Sci Food Agric 2023; 103:3468-3478. [PMID: 36807149 DOI: 10.1002/jsfa.12514] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Bacillus velezensis SW5, with good enzyme production ability, was isolated and identified in our laboratory from fermented fish sauce. Its galactosidase has been expressed in Escherichia coli, which could hydrolyze lactose in milk. The present study aims to express a novel serine protease gene (SPr-SW5) of this strain by Bacillus subtilis WB800N, and applies the expressed enzyme in hydrolysis of anchovy to prepare antioxidant substances, aiming to alleviate the waste of low-value fish resources. RESULTS SPr-SW5 with the open reading frame of 1353 bp encodes a serine protease (SPr-SW5) with 450 amino acids. The theoretical molecular weight and isoelectric point are 47.2 kDa and 5.22, respectively. The successful expression of SPr-SW5 in B. subtilis WB800N was confirmed by a skim milk plate test. Its optimal temperature and pH were 50 °C and 8.0, respectively. SPr-SW5 activity was increased by Ca2+ and Zn2+ , but inhibited by Fe3+ . Furthermore, SPr-SW5 was tolerant to 1% Tween-40 and Tween-80; however, its activity was strongly inhibited by 10 mm phenylmethylsulfonyl fluoride. Additionally, SPr-SW5 could be capable of hydrolyzing anchovy, the hydrolysate (AHP) at 10 g L-1 , with 2,2-diphenyl-1-picrylhydrazyl and hydroxyl (·OH) scavenging rates of 73.21% and 79.71%, displaying good antioxidant activity. CONCLUSION The novel SPr-SW5 was successfully expressed in B. subtilis WB800N. It exhibited excellent temperature stability and good tolerance to several metal ions. In addition, the anchovy hydrolyzed by expressed SPr-SW5 has good antioxidant ability. Overall, this research lays a good foundation for SPr-SW5 with respect to exploration and application in the food industry as enzyme preparation. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Na Li
- Collage of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Biao Shen
- Zhoushan Customs District, Zhoushan, Zhejiang, 316100, People's Republic of China
| | - Yang Liu
- Collage of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, People's Republic of China
| | - Peifang Weng
- Collage of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Zufang Wu
- Collage of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
| |
Collapse
|
8
|
Das M, Ghosh M. Screening, characterization, and kinetic studies of a serine alkaline protease from kitchen wastewater bacteria P2S1An and evaluation of its application in nutraceutical production. Water Environ Res 2023; 95:e10848. [PMID: 36813755 DOI: 10.1002/wer.10848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 01/11/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
This present investigation aimed at characterizing the biochemical potential and kinetic study of the protease isolated from kitchen wastewater bacteria, P2S1An. The enzymatic activity was optimum when incubated for 96 h, at 30°C and pH 9.0. The enzymatic activity of the purified protease (PrA) was 10.47-folds that of crude protease (S1). PrA was about 35 kDa in molecular weight. The broad pH and thermal stability, chelators, surfactants and solvent tolerance, and favorable thermodynamics suggested the potentiality of the extracted protease PrA. Thermal activity and stability were enhanced in presence of 1-mM Ca2+ ion at high temperatures. The protease was a serine one as its activity was completely diminished in presence of 1-mM PMSF. The Vmax , Km , and Kcat /Km suggested stability and catalytic efficiency of the protease. PrA hydrolyzes fish protein with 26.61 ± 0.16% of peptide bond cleavage after 240 min, comparable to Alcalase 2.4L (27.13 ± 0.31%). PRACTITIONER POINTS: A serine alkaline protease PrA was extracted from kitchen wastewater bacteria Bacillus tropicus Y14. Protease PrA showed significant activity and stability in a wide temperature and pH range. Protease showed great stability towards additives like metal ions, solvents, surfactants, polyols, and inhibitors. Kinetic study showed that the protease PrA had a prominent affinity and catalytic efficiency for the substrates. PrA hydrolysed fish proteins into short bioactive peptides which signify its potential in the formation of functional food ingredients.
Collapse
Affiliation(s)
- Madhushrita Das
- Department of Chemical Technology, University of Calcutta, Kolkata, West Bengal, India
| | - Mahua Ghosh
- Department of Chemical Technology, University of Calcutta, Kolkata, West Bengal, India
| |
Collapse
|
9
|
Ma J, Yang X, Fan W, Zhao C, Li W, Zhou D, Jiang S. Cloning and sequence analysis of a serine protease gene from Rhizoctonia solani Kühn AG5. Biotechnol Appl Biochem 2022; 69:2466-2474. [PMID: 34877711 DOI: 10.1002/bab.2296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022]
Abstract
The present study aimed to identify the subtilisin-like proteases (SLPs) of Rhizoctonia solani Kühn potentially involved in the virulence of this phytopathogenic fungus, which has 14 anastomosis groups (AGs) responsible for many crop diseases. Through mycelial microscope observation and strain identification of pathogenic fungus MS-3, it was determined to be R. solani AG-5. Both 5' and 3' rapid amplification of cDNA ends were used to clone the serine protease gene RsSLP from R. solani AG-5. The full-length obtained for RsSLP was 1714 bp with an open reading frame of 1587 bp, encoding a protein of 528 amino acids with a molecular mass of 55.8 kDa. This protein contained a predicted signal peptide for secretion but lacked a transmembrane domain or membrane anchor site. Bioinformatics analysis identified this protein as a serine protease with the Peptidase_S8 and Inhibitor_I9 characteristic domains of SLPs. Phylogenetic analysis suggested that frequent gene duplications of the SLPs occurred in R. solani (RsSLP), and RsSLP shares characteristic sequence features with virulence factors of other phytopathogenic fungi. Because the secretory serine protease RsSLP from R. solani AG5 is similar to the virulence factors of other phytopathogenic fungi, its identification will be helpful in studies considering the roles of these proteases in pathogen virulence.
Collapse
Affiliation(s)
- Jing Ma
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Xiling Yang
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Wenyan Fan
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Changjiang Zhao
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Wenshuai Li
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Di Zhou
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| | - Shujun Jiang
- Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China
| |
Collapse
|
10
|
Wu CY, Xiao KR, Wang LZ, Wang J, Song QS, Stanley D, Wei SJ, Zhu JY. Identification and expression profiling of serine protease-related genes in Tenebrio molitor. Arch Insect Biochem Physiol 2022; 111:e21963. [PMID: 36039637 DOI: 10.1002/arch.21963] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/23/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
In insects, serine proteases and serine protease homologs (SPs/SPHs) are involved in a variety of physiological processes including digestion, development, and immunity. Here, we identified 112 SP and 88 SPH genes in the genome of the yellow mealworm, Tenebrio molitor. Based on the features of domain structure, they were divided into "S" group containing single Tryp-SPc or Tryp-SPHc domain, "C" group containing 1-4 CLIP domain (CLIPA-D) and "M" group containing the CBD, CUB, EGF, Fz, Gd, LDLa, PAN, SEA, SR, Sushi, and TSP domains, and have 115, 48, and 37 gene members, respectively. According to the active sites in the catalytic triad, the putative trypsin, chymotrypsin, or elastase-like enzyme specificity of the identified SPs/SPHs were predicted. Phylogenetic and genomic location analyses revealed that gene duplication exists in the large amount of SPs/SPHs. Gene expression profiling using RNA-seq data along with real time reverse transcription-polymerase chain reaction analysis showed that most SP/SPH genes display life stage specific expression patterns, indicating their important roles in development. Many SP/SPH genes are specifically or highly expressed in the gut, salivary gland, fat body, hemocyte, ovary, and testis, suggesting that they participate in digestion, immunity, and reproduction. The findings lay the foundation for further functional characterization of SPs/SPHs in T. molitor.
Collapse
Affiliation(s)
- Chao-Yan Wu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Kai-Ran Xiao
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Long-Zhang Wang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jun Wang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Qi-Sheng Song
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
| | - David Stanley
- USDA/ARS Biological Control of Insects Research Laboratory, Columbia, Missouri, USA
| | - Shu-Jun Wei
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| |
Collapse
|
11
|
Merski M, Macedo-Ribeiro S, Wieczorek RM, Górna MW. The Repeating, Modular Architecture of the HtrA Proteases. Biomolecules 2022; 12:biom12060793. [PMID: 35740918 PMCID: PMC9221053 DOI: 10.3390/biom12060793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 02/04/2023] Open
Abstract
A conserved, 26-residue sequence [AA(X2)[A/G][G/L](X2)GDV[I/L](X2)[V/L]NGE(X1)V(X6)] and corresponding structure repeating module were identified within the HtrA protease family using a non-redundant set (N = 20) of publicly available structures. While the repeats themselves were far from sequence perfect, they had notable conservation to a statistically significant level. Three or more repetitions were identified within each protein despite being statistically expected to randomly occur only once per 1031 residues. This sequence repeat was associated with a six stranded antiparallel β-barrel module, two of which are present in the core of the structures of the PA clan of serine proteases, while a modified version of this module could be identified in the PDZ-like domains. Automated structural alignment methods had difficulties in superimposing these β-barrels, but the use of a target human HtrA2 structure showed that these modules had an average RMSD across the set of structures of less than 2 Å (mean and median). Our findings support Dayhoff’s hypothesis that complex proteins arose through duplication of simpler peptide motifs and domains.
Collapse
Affiliation(s)
- Matthew Merski
- Structural Biology Group, Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Correspondence: (M.M.); (M.W.G.); Tel.: +48-225-526-642 (M.M.)
| | - Sandra Macedo-Ribeiro
- Instituto de Investigação e Inovação em Saúde and Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal;
| | - Rafal M. Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Maria W. Górna
- Structural Biology Group, Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Correspondence: (M.M.); (M.W.G.); Tel.: +48-225-526-642 (M.M.)
| |
Collapse
|
12
|
Li X, Zhang Q, Xu Z, Jiang G, Gan L, Tian Y, Shi B. High-expression and characterization of a novel serine protease from Ornithinibacillus caprae L9 T with eco-friendly applications. Environ Sci Pollut Res Int 2022; 29:35996-36012. [PMID: 35060042 DOI: 10.1007/s11356-021-17495-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
In the current work, a novel thermophilic serine protease gene (P3862) from Ornithinibacillus caprae L9T was functionally expressed in Bacillus subtilis SCK6. The monomeric enzyme of about 29 kDa was purified to homogeneity with 43.91% of recovery and 2.81-folds of purification. Characterization of the purified protease revealed the optimum activity at pH 7 and 65 °C. The protease exhibited excellent activity and stability in the presence of Na+, Mg2+, Ca2+, ethanediol, n-hexane, Tween-20, Tween-80 and Triton X-100. P3862 displayed favorable caseinolytic activity, moderate keratinolytic activity but no collagenolytic activity. Besides, the homology model of P3862 possessed a globular configuration and characteristic of α/β hydrolase fold, and displayed stable interactions with casein, glycoprotein and keratin rather than collagen. Moreover, the crude enzyme could completely dehair goatskin within 6 h, resulting in decrease in BOD5, COD and TSS loads by 72.86, 74.07, and 73.79%, respectively, as compared with Na2S treatment. Biocatalytic applications revealed that it could effectively remove egg-stains from fabrics at 37 °C for 30 min with low supplementation (300 U/mL), and was able to degrade the feathers of duck and chicken. Overall, these outstanding properties make P3862 valuable in the development of environmentally friendly biotechnologies .
Collapse
Affiliation(s)
- Xiaoguang Li
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Qian Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education and College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Zhe Xu
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Guangyang Jiang
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Longzhan Gan
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Yongqiang Tian
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China.
| | - Bi Shi
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education and College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China.
| |
Collapse
|
13
|
Patil VS, Harish DR, Vetrivel U, Roy S, Deshpande SH, Hegde HV. Hepatitis C Virus NS3/4A Inhibition and Host Immunomodulation by Tannins from Terminalia chebula: A Structural Perspective. Molecules 2022; 27:molecules27031076. [PMID: 35164341 PMCID: PMC8839135 DOI: 10.3390/molecules27031076] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/15/2022] [Accepted: 01/22/2022] [Indexed: 01/27/2023] Open
Abstract
Terminalia chebula Retz. forms a key component of traditional folk medicine and is also reported to possess antihepatitis C virus (HCV) and immunomodulatory activities. However, information on the intermolecular interactions of phytochemicals from this plant with HCV and human proteins are yet to be established. Thus, by this current study, we investigated the HCV NS3/4A inhibitory and host immune-modulatory activity of phytocompounds from T. chebula through in silico strategies involving network pharmacology and structural bioinformatics techniques. To start with, the phytochemical dataset of T. chebula was curated from biological databases and the published literature. Further, the target ability of the phytocompounds was predicted using BindingDB for both HCV NS3/4A and other probable host targets involved in the immune system. Further, the identified targets were docked to the phytochemical dataset using AutoDock Vina executed through the POAP pipeline. The resultant docked complexes with significant binding energy were subjected to 50 ns molecular dynamics (MD) simulation in order to infer the stability of complex formation. During network pharmacology analysis, the gene set pathway enrichment of host targets was performed using the STRING and Reactome pathway databases. Further, the biological network among compounds, proteins, and pathways was constructed using Cytoscape 3.6.1. Furthermore, the druglikeness, side effects, and toxicity of the phytocompounds were also predicted using the MolSoft, ADVERpred, and PreADMET methods, respectively. Out of 41 selected compounds, 10 were predicted to target HCV NS3/4A and also to possess druglike and nontoxic properties. Among these 10 molecules, Chebulagic acid and 1,2,3,4,6-Pentagalloyl glucose exhibited potent HCV NS3/4A inhibitory activity, as these scored a lowest binding energy (BE) of −8.6 kcal/mol and −7.7 kcal/mol with 11 and 20 intermolecular interactions with active site residues, respectively. These findings are highly comparable with Asunaprevir (known inhibitor of HCV NS3/4A), which scored a BE of −7.4 kcal/mol with 20 key intermolecular interactions. MD studies also strongly suggest that chebulagic acid and 1,2,3,4,6-Pentagalloyl glucose as promising leads, as these molecules showed stable binding during 50 ns of production run. Further, the gene set enrichment and network analysis of 18 protein targets prioritized 10 compounds and were predicted to potentially modulate the host immune system, hemostasis, cytokine levels, interleukins signaling pathways, and platelet aggregation. On overall analysis, this present study predicts that tannins from T. chebula have a potential HCV NS3/4A inhibitory and host immune-modulatory activity. However, further experimental studies are required to confirm the efficacies.
Collapse
Affiliation(s)
- Vishal S. Patil
- ICMR-National Institute of Traditional Medicine, Nehru Nagar, Belagavi 590010, India; (V.S.P.); (U.V.); (S.H.D.); (H.V.H.)
| | - Darasaguppe R. Harish
- ICMR-National Institute of Traditional Medicine, Nehru Nagar, Belagavi 590010, India; (V.S.P.); (U.V.); (S.H.D.); (H.V.H.)
- Correspondence: (D.R.H.); (S.R.)
| | - Umashankar Vetrivel
- ICMR-National Institute of Traditional Medicine, Nehru Nagar, Belagavi 590010, India; (V.S.P.); (U.V.); (S.H.D.); (H.V.H.)
- ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai 600031, India
| | - Subarna Roy
- ICMR-National Institute of Traditional Medicine, Nehru Nagar, Belagavi 590010, India; (V.S.P.); (U.V.); (S.H.D.); (H.V.H.)
- Correspondence: (D.R.H.); (S.R.)
| | - Sanjay H. Deshpande
- ICMR-National Institute of Traditional Medicine, Nehru Nagar, Belagavi 590010, India; (V.S.P.); (U.V.); (S.H.D.); (H.V.H.)
- Regional Centre for Biotechnology, NCR-Biotech Science Cluster, Faridabad 121001, India
| | - Harsha V. Hegde
- ICMR-National Institute of Traditional Medicine, Nehru Nagar, Belagavi 590010, India; (V.S.P.); (U.V.); (S.H.D.); (H.V.H.)
| |
Collapse
|
14
|
Megale ÂAA, Magnoli FC, Guidolin FR, Godoi KS, Portaro FCV, Dias-da-Silva W. Bitis arietans Snake Venom and Kn-Ba, a Snake Venom Serine Protease, Induce the Production of Inflammatory Mediators in THP-1 Macrophages. Toxins (Basel) 2021; 13:toxins13120906. [PMID: 34941743 PMCID: PMC8705107 DOI: 10.3390/toxins13120906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/29/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Bitis arietans is a snake of medical importance found throughout sub-Saharan Africa and in savannas and pastures of Morocco and western Arabia. The effects of its venom are characterized by local and systemic alterations, such as inflammation and cardiovascular and hemostatic disturbances, which can lead to victims' death or permanent disability. To better characterize the inflammatory process induced by this snake's venom, the participation of eicosanoids and PAF (platelet- activating factor) in this response were demonstrated in a previous study. In addition, edema and early increased vascular permeability followed by an accumulation of polymorphonuclear (PMN) cells in the peritoneal cavity were accompanied by the production of the eicosanoids LTB4, LTC4, TXB2, and PGE2, and local and systemic production of IL-6 and MCP-1. In this context, the present study focused on the identification of inflammatory mediators produced by human macrophages derived from THP-1 cells in response to Bitis arietans venom (BaV), and Kn-Ba, a serine protease purified from this venom. Here, we show that Kn-Ba, and even the less intensive BaV, induced the production of the cytokine TNF and the chemokines RANTES and IL-8. Only Kn-Ba was able to induce the production of IL-6, MCP-1, and IP-10, whereas PGE2 was produced only in response to BaV. Finally, the release of IL-1β in culture supernatants suggests the activation of the inflammasomes by the venom of Bitis arietans and by Kn-Ba, which will be investigated in more detail in future studies.
Collapse
Affiliation(s)
- Ângela Alice Amadeu Megale
- Immunochemistry Laboratory, Butantan Institute, São Paulo 05503-900, Brazil; (F.C.M.); (F.R.G.); (K.S.G.)
- Correspondence: (Â.A.A.M.); (F.C.V.P.); (W.D.-d.-S.)
| | - Fabio Carlos Magnoli
- Immunochemistry Laboratory, Butantan Institute, São Paulo 05503-900, Brazil; (F.C.M.); (F.R.G.); (K.S.G.)
| | - Felipe Raimondi Guidolin
- Immunochemistry Laboratory, Butantan Institute, São Paulo 05503-900, Brazil; (F.C.M.); (F.R.G.); (K.S.G.)
| | - Kemily Stephanie Godoi
- Immunochemistry Laboratory, Butantan Institute, São Paulo 05503-900, Brazil; (F.C.M.); (F.R.G.); (K.S.G.)
| | - Fernanda Calheta Vieira Portaro
- Laboratory of Structure and Function of Biomolecules, Butantan Institute, São Paulo 05503-900, Brazil
- Correspondence: (Â.A.A.M.); (F.C.V.P.); (W.D.-d.-S.)
| | - Wilmar Dias-da-Silva
- Immunochemistry Laboratory, Butantan Institute, São Paulo 05503-900, Brazil; (F.C.M.); (F.R.G.); (K.S.G.)
- Correspondence: (Â.A.A.M.); (F.C.V.P.); (W.D.-d.-S.)
| |
Collapse
|
15
|
Sitprija S, Chanhome L, Reamtong O, Thiangtrongjit T, Vasaruchapong T, Khow O, Noiphrom J, Laoungbua P, Tubtimyoy A, Chaiyabutr N, Kumkate S. Proteomics and immunocharacterization of Asian mountain pit viper (Ovophis monticola) venom. PLoS One 2021; 16:e0260496. [PMID: 34851989 PMCID: PMC8635378 DOI: 10.1371/journal.pone.0260496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/10/2021] [Indexed: 01/06/2023] Open
Abstract
The venomic profile of Asian mountain pit viper Ovophis monticola is clarified in the present study. Using mass spectrometry-based proteomics, 247 different proteins were identified in crude venom of O. monticola found in Thailand. The most abundant proteins were snake venom metalloproteases (SVMP) (36.8%), snake venom serine proteases (SVSP) (31.1%), and phospholipases A2 (PLA2) (12.1%). Less abundant proteins included L-amino acid oxidase (LAAO) (5.7%), venom nerve growth factor (3.6%), nucleic acid degrading enzymes (3.2%), C-type lectins (CTL) (1.6%), cysteine-rich secretory proteins (CRISP) (1.2%) and disintegrin (1.2%). The immunoreactivity of this viper's venom to a monovalent antivenom against green pit viper Trimeresurus albolabris, or to a polyvalent antivenom against hemotoxic venom was investigated by indirect ELISA and two-dimensional (2D) immunoblotting. Polyvalent antivenom showed substantially greater reactivity levels than monovalent antivenom. A titer for the monovalent antivenom was over 1:1.28x107 dilution while that of polyvalent antivenom was 1:5.12x107. Of a total of 89 spots comprising 173 proteins, 40 spots of predominantly SVMP, SVSP and PLA2 were specific antigens for antivenoms. The 49 unrecognized spots containing 72 proteins were characterized as non-reactive proteins, and included certain types of CTLs and CRISPs. These neglected venom constituents could limit the effectiveness of antivenom-based therapy currently available for victims of pit viper envenomation.
Collapse
Affiliation(s)
- Siravit Sitprija
- Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, Thailand
| | - Lawan Chanhome
- Snake Farm, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
- * E-mail: (LC); (SK)
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Ratchathewi, Bangkok, Thailand
| | - Tipparat Thiangtrongjit
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Ratchathewi, Bangkok, Thailand
| | - Taksa Vasaruchapong
- Snake Farm, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
| | - Orawan Khow
- Department of Research and Development, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
| | - Jureeporn Noiphrom
- Department of Research and Development, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
| | - Panithi Laoungbua
- Snake Farm, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
| | - Arissara Tubtimyoy
- Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, Thailand
| | - Narongsak Chaiyabutr
- Snake Farm, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
- Department of Research and Development, Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok, Thailand
| | - Supeecha Kumkate
- Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, Thailand
- * E-mail: (LC); (SK)
| |
Collapse
|
16
|
Kriaa A, Jablaoui A, Rhimi S, Soussou S, Mkaouar H, Mariaule V, Gruba N, Gargouri A, Maguin E, Lesner A, Rhimi M. SP-1, a Serine Protease from the Gut Microbiota, Influences Colitis and Drives Intestinal Dysbiosis in Mice. Cells 2021; 10:2658. [PMID: 34685638 PMCID: PMC8534766 DOI: 10.3390/cells10102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/22/2021] [Accepted: 10/01/2021] [Indexed: 11/20/2022] Open
Abstract
Increased protease activity has been linked to the pathogenesis of IBD. While most studies have been focusing on host proteases in gut inflammation, it remains unclear how to address the potential contribution of their bacterial counterparts. In the present study, we report a functional characterization of a newly identified serine protease, SP-1, from the human gut microbiota. The serine protease repertoire of gut Clostridium was first explored, and the specificity of SP-1 was analyzed using a combinatorial chemistry method. Combining in vitro analyses and a mouse model of colitis, we show that oral administration of recombinant bacteria secreting SP-1 (i) compromises the epithelial barrier, (ii) alters the microbial community, and (ii) exacerbates colitis. These findings suggest that gut microbial protease activity may constitute a valuable contributor to IBD and could, therefore, represent a promising target for the treatment of the disease.
Collapse
Affiliation(s)
- Aicha Kriaa
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Amin Jablaoui
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Soufien Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Souha Soussou
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Héla Mkaouar
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Vincent Mariaule
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Natalia Gruba
- Faculty of Chemistry, University of Gdansk, Uniwersytet Gdanski, Chemistry, Wita Stwosza 63, PL80-308 Gdansk, Poland; (N.G.); (A.L.)
| | - Ali Gargouri
- Laboratory of Molecular Biotechnology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax, Sfax Bp ‘1177’ 3018, Tunisia;
| | - Emmanuelle Maguin
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Uniwersytet Gdanski, Chemistry, Wita Stwosza 63, PL80-308 Gdansk, Poland; (N.G.); (A.L.)
| | - Moez Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| |
Collapse
|
17
|
Hou Y, Yang L, Xu S, Zhang Y, Cheng Y, Li Y, Gong J, Xia Q. Trypsin-type serine protease p37k hydrolyzes CPAP3-type cuticle proteins in the molting fluid of the silkworm Bombyx mori. Insect Biochem Mol Biol 2021; 137:103610. [PMID: 34182106 DOI: 10.1016/j.ibmb.2021.103610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Cuticular proteins analogous to peritrophin 3 (CPAP3)-type cuticle proteins constitute a family of proteins with three chitin-binding domains (CBDs) that play an important role in cuticle formation by associating with chitin. In our previous study, we identified CPAP3-type cuticle proteins in the silkworm genome, of which we characterized CPAP3-A2 (BmCBP1), a protein highly expressed in the epidermis. In this study, to elucidate the digestion mechanism of CPAP3-type cuticle proteins, we incubated CPAP3-A2 with molting fluid in vitro and found that its hydrolysis, which was inhibited by serine and cysteine protease inhibitors, produced two major bands with a molecular weight of approximately 22 kD and 11 kD. A trypsin-type serine protease, p37k, was presumed to be responsible for hydrolyzing CPAP3-A2 based on liquid chromatography-tandem mass spectrometry analysis of naturally purified molting fluid. To verify this, p37k was subsequently expressed in Sf9 cells using the Bac-to-Bac baculovirus expression system. In its active form, the recombinant protease could successfully hydrolyze CPAP3-A2. Finally, we analyzed the CPAP3-A2 molting fluid digestion site. When arginine 169 of CPAP3-A2 was mutated to alanine, a weaker hydrolysis of mutant CPAP3-A2 was observed compared to that of normal CPAP3-A2. Collectively, we identified a trypsin-type serine protease that is involved in the degradation of CPAP3-type cuticle proteins, including CPAP3-A2, suggesting that this protease plays an important role during molting in Bombyx mori. These findings provide the basis for further elucidation of the mechanisms underlying insect molting and metamorphosis.
Collapse
Affiliation(s)
- Yong Hou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, 400716, China
| | - Lingzhen Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Shuping Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Yuhao Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Yuejing Cheng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Yi Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China
| | - Jing Gong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715, China; Biological Science Research Center, Southwest University, Beibei, Chongqing, 400715, China; Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, 400716, China.
| |
Collapse
|
18
|
Bocayuva Tavares GD, Fortes Aiub CA, Felzenszwalb I, Carrão Dantas EK, Araújo-Lima CF, Siqueira Júnior CL. In vitro biochemical characterization and genotoxicity assessment of Sapindus saponaria seed extract. J Ethnopharmacol 2021; 276:114170. [PMID: 33932515 DOI: 10.1016/j.jep.2021.114170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Sapindus saponaria, also popularly known as soapberry, has been used in folk medicinal values because of its therapeutic properties and several compounds in its composition, which represent a target in potential for drug discovery. However, few data about its potential toxicity has been reported. AIM OF THE STUDY Plant proteins can perform essential roles in survival, acting as defense mechanism, as well functioning as important molecular reserves for its natural metabolism. The aim of the current study was to investigate the in vitro toxicity profile of protein extract of S. saponaria and detect protein potentially involved in biological effects such as collagen hydrolysis and inhibition of viral proteases. MATERIALS AND METHODS Protein extract of soapberry seeds was investigated for its cytotoxic and genotoxic action using the Ames test. The protein extract was also subjected to a partial purification process of a protease and a protease inhibitor by gel chromatography filtration techniques and the partially isolated proteins were characterized biochemically. RESULTS Seed proteins extract of S. saponaria was evaluated until 100 μg/mL concentration, presenting cytotoxicity and mutagenicity in bacterial model mostly when exposed to exogenous metabolic system and causing cytotoxic and genotoxic effects in HepG2 cells. The purification and partial characterization of a serine protease (43 kDa) and a cysteine protease inhibitor (32.8 kDa) from protein extract of S. Saponaria, corroborate the idea of the biological use of the plant as an insecticide and larvicide. Although it shows cytotoxic, mutagenic and genotoxic effects. CONCLUSION The overall results of the present study provide supportive data on the potential use of proteins produced in S. saponaria seeds as pharmacological and biotechnological agents that can be further explored for the development of new drugs.
Collapse
Affiliation(s)
- Gustavo Duarte Bocayuva Tavares
- Laboratory of Biochemistry and Function of Plant Proteins, Department of Botany, Federal University of the State of Rio de Janeiro, Av. Pasteur, 458, Urca, Brazil.
| | - Claudia Alessandra Fortes Aiub
- Laboratory of Genotoxicity, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro, R. Frei Caneca, 94, Centro, Brazil.
| | - Israel Felzenszwalb
- Department of Biophysics and Biometrics, State University of Rio de Janeiro, Av. 28 de Setembro, 87, Pavilhão Américo Piquet Carneiro - 4o. Andar, Vila Isabel, Rio de Janeiro, RJ, Brazil.
| | - Eduardo Kennedy Carrão Dantas
- Department of Biophysics and Biometrics, State University of Rio de Janeiro, Av. 28 de Setembro, 87, Pavilhão Américo Piquet Carneiro - 4o. Andar, Vila Isabel, Rio de Janeiro, RJ, Brazil.
| | - Carlos Fernando Araújo-Lima
- Department of Biophysics and Biometrics, State University of Rio de Janeiro, Av. 28 de Setembro, 87, Pavilhão Américo Piquet Carneiro - 4o. Andar, Vila Isabel, Rio de Janeiro, RJ, Brazil.
| | - César Luis Siqueira Júnior
- Laboratory of Biochemistry and Function of Plant Proteins, Research Center on Agricultural Systems, Department of Botany, Federal University of the State of Rio de Janeiro, Av. Pasteur, 458, Urca, Brazil.
| |
Collapse
|
19
|
Elhusseiny SM, El-Mahdy TS, Awad MF, Elleboudy NS, Farag MMS, Yassein MA, Aboshanab KM. Proteome Analysis and In Vitro Antiviral, Anticancer and Antioxidant Capacities of the Aqueous Extracts of Lentinula edodes and Pleurotus ostreatus Edible Mushrooms. Molecules 2021; 26:4623. [PMID: 34361776 PMCID: PMC8348442 DOI: 10.3390/molecules26154623] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/16/2022] Open
Abstract
In this study, we examined aqueous extracts of the edible mushrooms Pleurotus ostreatus (oyster mushroom) and Lentinula edodes (shiitake mushroom). Proteome analysis was conducted using LC-Triple TOF-MS and showed the expression of 753 proteins by Pleurotus ostreatus, and 432 proteins by Lentinula edodes. Bioactive peptides: Rab GDP dissociation inhibitor, superoxide dismutase, thioredoxin reductase, serine proteinase and lectin, were identified in both mushrooms. The extracts also included promising bioactive compounds including phenolics, flavonoids, vitamins and amino acids. The extracts showed promising antiviral activities, with a selectivity index (SI) of 4.5 for Pleurotus ostreatus against adenovirus (Ad7), and a slight activity for Lentinula edodes against herpes simplex-II (HSV-2). The extracts were not cytotoxic to normal human peripheral blood mononuclear cells (PBMCs). On the contrary, they showed moderate cytotoxicity against various cancer cell lines. Additionally, antioxidant activity was assessed using DPPH radical scavenging, ABTS radical cation scavenging and ORAC assays. The two extracts showed potential antioxidant activities, with the maximum activity seen for Pleurotus ostreatus (IC50 µg/mL) = 39.46 ± 1.27 for DPPH; 11.22 ± 1.81 for ABTS; and 21.40 ± 2.20 for ORAC assays. This study encourages the use of these mushrooms in medicine in the light of their low cytotoxicity on normal PBMCs vis à vis their antiviral, antitumor and antioxidant capabilities.
Collapse
Affiliation(s)
- Shaza M. Elhusseiny
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ahram Canadian University (ACU), 4th Industrial Area, 6th of October City, Cairo 2566, Egypt; (S.M.E.); (T.S.E.-M.)
| | - Taghrid S. El-Mahdy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ahram Canadian University (ACU), 4th Industrial Area, 6th of October City, Cairo 2566, Egypt; (S.M.E.); (T.S.E.-M.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt
| | - Mohamed F. Awad
- Department of Biology, College of Science, Taif University, Taif 11099, Saudi Arabia;
| | - Nooran S. Elleboudy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Cairo 11566, Egypt; (N.S.E.); (M.A.Y.)
| | - Mohamed M. S. Farag
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo 11884, Egypt;
| | - Mahmoud A. Yassein
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Cairo 11566, Egypt; (N.S.E.); (M.A.Y.)
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Cairo 11566, Egypt; (N.S.E.); (M.A.Y.)
| |
Collapse
|
20
|
Gurunathan R, Huang B, Ponnusamy VK, Hwang JS, Dahms HU. Novel recombinant keratin degrading subtilisin like serine alkaline protease from Bacillus cereus isolated from marine hydrothermal vent crabs. Sci Rep 2021; 11:12007. [PMID: 34099743 PMCID: PMC8185006 DOI: 10.1038/s41598-021-90375-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/20/2021] [Indexed: 11/25/2022] Open
Abstract
Microbial secondary metabolites from extreme environments like hydrothermal vents are a promising source for industrial applications. In our study the protease gene from Bacillus cereus obtained from shallow marine hydrothermal vents in the East China Sea was cloned, expressed and purified. The protein sequence of 38 kDa protease SLSP-k was retrieved from mass spectrometry and identified as a subtilisin serine proteinase. The novel SLSP-k is a monomeric protein with 38 amino acid signal peptides being active over wide pH (7-11) and temperature (40-80 °C) ranges, with maximal hydrolytic activities at pH 10 and at 50 °C temperature. The hydrolytic activity is stimulated by Ca2+, Co2+, Mn2+, and DTT. It is inhibited by Fe2+, Cd2+, Cu2+, EDTA, and PMSF. The SLSP-k is stable in anionic, non-anionic detergents, and solvents. The ability to degrade keratin in chicken feather and hair indicates that this enzyme is suitable for the degradation of poultry waste without the loss of nutritionally essential amino acids which otherwise are lost in hydrothermal processing. Therefore, the proteinase is efficient in environmental friendly bioconversion of animal waste into fertilizers or value added products such as secondary animal feedstuffs.
Collapse
Affiliation(s)
- Revathi Gurunathan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan
| | - Bin Huang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan
| | - Vinoth Kumar Ponnusamy
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan
| | - Jiang-Shiou Hwang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan.
- Center of Excellence for Ocean Engineering, National Taiwan Ocean University, Keelung, 20224, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 20224, Taiwan.
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan.
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan.
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan.
| |
Collapse
|
21
|
Mkaouar H, Mariaule V, Rhimi S, Hernandez J, Kriaa A, Jablaoui A, Akermi N, Maguin E, Lesner A, Korkmaz B, Rhimi M. Gut Serpinome: Emerging Evidence in IBD. Int J Mol Sci 2021; 22:ijms22116088. [PMID: 34200095 PMCID: PMC8201313 DOI: 10.3390/ijms22116088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/11/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are incurable disorders whose prevalence and global socioeconomic impact are increasing. While the role of host genetics and immunity is well documented, that of gut microbiota dysbiosis is increasingly being studied. However, the molecular basis of the dialogue between the gut microbiota and the host remains poorly understood. Increased activity of serine proteases is demonstrated in IBD patients and may contribute to the onset and the maintenance of the disease. The intestinal proteolytic balance is the result of an equilibrium between the proteases and their corresponding inhibitors. Interestingly, the serine protease inhibitors (serpins) encoded by the host are well reported; in contrast, those from the gut microbiota remain poorly studied. In this review, we provide a concise analysis of the roles of serine protease in IBD physiopathology and we focus on the serpins from the gut microbiota (gut serpinome) and their relevance as a promising therapeutic approach.
Collapse
Affiliation(s)
- Héla Mkaouar
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Vincent Mariaule
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Soufien Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Juan Hernandez
- Department of Clinical Sciences, Nantes-Atlantic College of Veterinary Medicine and Food Sciences (Oniris), University of Nantes, 101 Route de Gachet, 44300 Nantes, France;
| | - Aicha Kriaa
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Amin Jablaoui
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Nizar Akermi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Emmanuelle Maguin
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Uniwersytet Gdanski, Chemistry, Wita Stwosza 63, PL80-308 Gdansk, Poland;
| | - Brice Korkmaz
- INSERM UMR-1100, “Research Center for Respiratory Diseases” and University of Tours, 37032 Tours, France;
| | - Moez Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France; (H.M.); (V.M.); (S.R.); (A.K.); (A.J.); (N.A.); (E.M.)
- Correspondence:
| |
Collapse
|
22
|
Abstract
Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.
Collapse
Affiliation(s)
| | - Peter Goettig
- Structural Biology Group, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria;
| |
Collapse
|
23
|
Arbita AA, Paul NA, Cox J, Zhao J. Extraction, partial purification and characterization of proteases from the red seaweed Gracilaria edulis with similar cleavage sites on κ-casein as calf rennet. Food Chem 2020; 330:127324. [PMID: 32569938 DOI: 10.1016/j.foodchem.2020.127324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 05/26/2020] [Accepted: 06/10/2020] [Indexed: 11/18/2022]
Abstract
Enzymes currently used in cheesemaking have various drawbacks, and there is a continual need to find new coagulants. This study describes the extraction and biochemical characterization of two proteases from the red alga Gracilaria edulis. The proteases were extracted with phosphate buffer and partially purified by ammonium sulphate precipitation and dialysis. The enzymes exhibited optimum caseinolytic activity at 60 °C and a pH range of 6-8. They showed a high ratio of milk-clotting over caseinolytic activity, indicating they had an excellent milk-clotting ability. The proteases were confirmed to be serine protease and metalloprotease with molecular weight (MW) of 44 and 108 kDa. They exhibited high hydrolytic activity on κ-caseins, cleaving κ-casein at four main sites, one of which being the same as that of calf rennet, which is the first reported for an algal protease. The findings demonstrated that the proteases could potentially be used as a milk coagulant in cheesemaking.
Collapse
Affiliation(s)
- Ariestya Arlene Arbita
- Food Science and Technology, School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia; School of Chemical Engineering, Faculty of Industrial and Technology, Parahyangan Catholic University, Ciumbuleuit 94, Bandung 40141, Indonesia
| | - Nicholas A Paul
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4558, Australia
| | - Julian Cox
- Food Science and Technology, School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Jian Zhao
- Food Science and Technology, School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia.
| |
Collapse
|
24
|
Tekin A, Uzuner U, Sezen K. Homology modeling and heterologous expression of highly alkaline subtilisin-like serine protease from Bacillus halodurans C-125. Biotechnol Lett 2020; 43:479-494. [PMID: 33047274 DOI: 10.1007/s10529-020-03025-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/06/2020] [Indexed: 01/22/2023]
Abstract
Here we report heterologous expression, enzymatic characterization and structure homology modeling of a subtilisin-like alkaline serine protease (ASP) from Bacillus halodurans C-125. Encoding gene was successfully obtained by PCR and cloned into pMA0911 shuttle vector under the control of strong HpaII promoter and expressed extracellularly. ASP enzyme was successfully expressed in B. subtilis WB800 cell line lacking eight extracellular proteases and produced extracellularly in the culture medium. Km, Vmax and specific activity parameters of the recombinantly produced ASP were identified as 0.2899 mg/ml, 76.12 U/ml and 9500 U/mg, respectively. The purified enzyme revealed remarkable proteolytic activity at highly alkaline conditions with a pH optimum 12.0 and notable thermostability with temperature optimum at 60 °C. Furthermore, substrate-free enzyme revealed remarkable pH stability at pH 12.0 and maintained 93% of its initial activity when incubated at 37 °C for 24 h and 60% of its initial activity upon incubation at 60 °C for 1 h. Theoretically calculated molecular mass of ASP protein was confirmed through SDS-PAGE and western blot analysis (Mw: 28.3 kDa). The secondary and tertiary structures of ASP protein were also identified through homology modeling and further examined in detail. ASP harbors a typical S8/S53 peptidase domain comprising 17 β-sheets and 9 α-helixes within its secondary structure. The structure dynamics analysis of modeled 3D structure further revealed that transient inactivating propeptide chain is the most dynamic region of ASP enzyme with 8.52 Å2 β-Factor value. Additional residue-dependent fluctuation plot analysis also confirmed the elevated structure dynamics patterning of ASP N-terminus which could be the potential prerequisite for the autonomous propeptide removal of alkaline serine peptidases. Yet the functional domain of ASP becomes quite stable after autonomous exclusion of its propeptide. Although the sequence homology between ASP and commercial detergent additive B. lentus protease (PDB ID:1GCI) was moderate (65.4% sequence similarity), their overlaid 3D structures revealed much higher similarity (98.14%) within 0.80 Å RMSD. In conclusions, with remarkable pH stability, notable thermostability and particularly high specific activity at extreme alkaline conditions, the unveiled ASP protein stands out as a novel protease candidate for various industrial sectors such as textile, detergent, leather, feed, waste, pharmaceutical and others.
Collapse
Affiliation(s)
- Aşkın Tekin
- Department of Medical Services and Techniques, Şebinkarahisar Social Sciences Vocational School, 28400, Şebinkarahisar, Giresun, Turkey
| | - Ugur Uzuner
- Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey.
| | - Kazım Sezen
- Department of Biology, Faculty of Science, Karadeniz Technical University, 61080, Trabzon, Turkey
| |
Collapse
|
25
|
Dultz G, Shimakami T, Schneider M, Murai K, Yamane D, Marion A, Zeitler TM, Stross C, Grimm C, Richter RM, Bäumer K, Yi M, Biondi RM, Zeuzem S, Tampé R, Antes I, Lange CM, Welsch C. Extended interaction networks with HCV protease NS3-4A substrates explain the lack of adaptive capability against protease inhibitors. J Biol Chem 2020; 295:13862-13874. [PMID: 32747444 PMCID: PMC7535904 DOI: 10.1074/jbc.ra120.013898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/26/2020] [Indexed: 12/20/2022] Open
Abstract
Inhibitors against the NS3-4A protease of hepatitis C virus (HCV) have proven to be useful drugs in the treatment of HCV infection. Although variants have been identified with mutations that confer resistance to these inhibitors, the mutations do not restore replicative fitness and no secondary mutations that rescue fitness have been found. To gain insight into the molecular mechanisms underlying the lack of fitness compensation, we screened known resistance mutations in infectious HCV cell culture with different genomic backgrounds. We observed that the Q41R mutation of NS3-4A efficiently rescues the replicative fitness in cell culture for virus variants containing mutations at NS3-Asp168 To understand how the Q41R mutation rescues activity, we performed protease activity assays complemented by molecular dynamics simulations, which showed that protease-peptide interactions far outside the targeted peptide cleavage sites mediate substrate recognition by NS3-4A and support protease cleavage kinetics. These interactions shed new light on the mechanisms by which NS3-4A cleaves its substrates, viral polyproteins and a prime cellular antiviral adaptor protein, the mitochondrial antiviral signaling protein MAVS. Peptide binding is mediated by an extended hydrogen-bond network in NS3-4A that was effectively optimized for protease-MAVS binding in Asp168 variants with rescued replicative fitness from NS3-Q41R. In the protease harboring NS3-Q41R, the N-terminal cleavage products of MAVS retained high affinity to the active site, rendering the protease susceptible for potential product inhibition. Our findings reveal delicately balanced protease-peptide interactions in viral replication and immune escape that likely restrict the protease adaptive capability and narrow the virus evolutionary space.
Collapse
Affiliation(s)
- Georg Dultz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Tetsuro Shimakami
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Markus Schneider
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Kazuhisa Murai
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Daisuke Yamane
- Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Antoine Marion
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Tobias M Zeitler
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Claudia Stross
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Christian Grimm
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Rebecca M Richter
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Katrin Bäumer
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - MinKyung Yi
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Ricardo M Biondi
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany; Biomedicine Research Institute of Buenos Aires - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany; University Center for Infectious Diseases, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter and Cluster of Excellence-Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany
| | - Iris Antes
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Life Sciences, Technical University Munich, Freising-Weihenstephan, Germany
| | - Christian M Lange
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Christoph Welsch
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt, Germany; University Center for Infectious Diseases, Goethe University Hospital Frankfurt, Frankfurt, Germany.
| |
Collapse
|
26
|
Cao X, Lu Y, Li J, Xia X, Gao Q, Gu W, Wang W, Meng Q. An ShK-domain serine protease of Eriocheir sinensis regulates the PO activity to resist Spiroplasma eriocheiris infection. Fish Shellfish Immunol 2020; 105:186-194. [PMID: 32615165 DOI: 10.1016/j.fsi.2020.06.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/17/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
A novel serine protease contains two ShK-domain was found from the Chinese mitten crab Eriocheir sinensis (EsShK-SP). The full-length EsShK-SP cDNA is 1927 bp and contains a 1260-bp open reading frame encoding a protein of 420 amino acids, including a signal peptide, two ShK domain, and Tryp-SPC domain. Quantitative real-time PCR showed that EsShK-SP was expressed mainly in the hemocytes, gills, intestine, and nerve, but weakly in heart, muscle, and hepatopancreas. After infected with Spiroplasma eriocheiris, the expression of EsShK-SP was significantly up-regulated from 1 d to 9 d. The Tryp-SPC domain was ligated with pGEX-4T-1 vector and prokaryotic expressed to obtain recombinant protein rSPC. When rSPC and S. eriocheiris stimulated the hemocytes of E. sinensis, the PO activity was significantly up-regulated. The subcellular localization revealed that recombinant EsShK-SP was mainly located in the cytoplasm of Drosophila S2 cells. Both absolute real-time PCR and confocal laser scanning microscope results showed that over-expression of EsShK-SP in S2 cells could decrease the copy number of S. eriocheiris. Meanwhile, the over-expression of EsShK-SP also increased the PO activity and cell viability of S2 cells. After EsShK-SP RNA interference using dsRNA, the expression levels of proPO and activity of PO decreased significantly from 48 h to 96 h. The knockdown of EsShK-SP by RNAi resulted in the copy number of S. eriocheiris in the EsShK-SP silenced group was significantly increased compared to the control groups during S. eriocheiris infection. Meanwhile, the survival rate of crabs decreased in the EsShK-SP-dsRNA group. The above results indicated that EsShK-SP plays an important immune role during E. sinensis against S. eriocheiris through regulation of the proPO system.
Collapse
Affiliation(s)
- Xiaohui Cao
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences & College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Yinyue Lu
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences & College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Jiyun Li
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences & College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Xiaoli Xia
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences & College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Qi Gao
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences & College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Wei Gu
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences & College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China; Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Wen Wang
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences & College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China.
| | - Qingguo Meng
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences & College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China; Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China.
| |
Collapse
|
27
|
Yue X, Sun XY, Liu F, Hu CX, Bai Y, Da Yang Q, Liu RD, Zhang X, Cui J, Wang ZQ. Molecular characterization of a Trichinella spiralis serine proteinase. Vet Res 2020; 51:125. [PMID: 32988413 PMCID: PMC7520982 DOI: 10.1186/s13567-020-00847-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
The aim of this study was to investigate the biological characteristics and functions of a Trichinella spiralis serine proteinase (TsSerp) during larval invasion and development in the host. The full-length TsSerp cDNA sequence was cloned and expressed in Escherichia coli BL21. The results of RT-PCR, IFA and western blotting analyses showed that TsSerp was a secretory protein that was highly expressed at the T. spiralis intestinal infective larva and muscle larva stages and primarily located at the cuticle, stichosome and intrauterine embryos of the parasite. rTsSerp promoted the larval invasion of intestinal epithelial cells (IECs) and the enteric mucosa, whereas an anti-rTsSerp antibody impeded larval invasion; the promotion and obstruction roles were dose-dependently related to rTsSerp and the anti-rTsSerp antibodies, respectively. Vaccination of mice with rTsSerp elicited a remarkable humoral immune response (high levels of serum IgG, IgG1/IgG2a, IgE and IgM), and it also triggered both systemic (spleen) and local intestinal mucosal mesenteric lymph node (MLN) cellular immune responses, as demonstrated by a significant elevation in Th1 cytokines (IFN-γ) and Th2 cytokines (IL-4) after the spleen and MLN cells from vaccinated mice were stimulated with rTsSerp. Anti-TsSerp antibodies participated in the killing and destruction of newborn larvae via ADCC. The mice vaccinated with rTsSerp exhibited a 48.7% reduction in intestinal adult worms and a 52.5% reduction in muscle larvae. These results indicated that TsSerp participates in T. spiralis invasion and development in the host and might be considered a potential candidate target antigen to develop oral polyvalent preventive vaccines against Trichinella infection.
Collapse
Affiliation(s)
- Xin Yue
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, China
| | - Xiang Yuan Sun
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, China
| | - Fang Liu
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, China
| | - Chen Xi Hu
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, China
| | - Ying Bai
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, China
| | - Qi Da Yang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, China
| | - Ruo Dan Liu
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, China
| | - Xi Zhang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, China
| | - Jing Cui
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, China.
| | - Zhong Quan Wang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, China.
| |
Collapse
|
28
|
Faucher F, Bennett JM, Bogyo M, Lovell S. Strategies for Tuning the Selectivity of Chemical Probes that Target Serine Hydrolases. Cell Chem Biol 2020; 27:937-952. [PMID: 32726586 PMCID: PMC7484133 DOI: 10.1016/j.chembiol.2020.07.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 02/08/2023]
Abstract
Serine hydrolases comprise a large family of enzymes that have diverse roles in key cellular processes, such as lipid metabolism, cell signaling, and regulation of post-translation modifications of proteins. They are also therapeutic targets for multiple human pathologies, including viral infection, diabetes, hypertension, and Alzheimer disease; however, few have well-defined substrates and biological functions. Activity-based probes (ABPs) have been used as effective tools to both profile activity and screen for selective inhibitors of serine hydrolases. One broad-spectrum ABP containing a fluorophosphonate electrophile has been used extensively to advance our understanding of diverse serine hydrolases. Due to the success of this single reagent, several robust chemistries have been developed to further diversify and tune the selectivity of ABPs used to target serine hydrolases. In this review, we highlight approaches to identify selective serine hydrolase ABPs and suggest new synthetic methodologies that could be applied to further advance probe development.
Collapse
Affiliation(s)
- Franco Faucher
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - John M Bennett
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
29
|
Ma L, Chen F, Wang W, Xu L, Lu ZQ. Identification of two clip domain serine proteases involved in the pea aphid's defense against bacterial and fungal infection. Insect Sci 2020; 27:735-744. [PMID: 30916875 DOI: 10.1111/1744-7917.12673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/01/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
Phenoloxidases (POs) are required for the pea aphid's defense against bacterial and fungal infection. Prophenoloxidases (PPOs) are proteolytically converted to its active form PO through a clip domain serine protease cascade. In this study, we identified five clip domain serine proteases in the pea aphids. The messenger RNA levels of two of them, Ap_SPLP and Ap_VP, were upregulated by Gram-positive bacterium Staphylococcus aureus and fungus Beauveria bassiana infections. Double-stranded RNA-based expression knockdown of these two genes resulted in reduced PO activity of the aphid hemolymph, higher loads of S. aureus and B. bassiana in the aphids, and lower survival rates of the aphids after infections. Our data suggest that Ap_SPLP and Ap_VP are involved in PPO activation pathway in the pea aphid.
Collapse
Affiliation(s)
- Li Ma
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Feng Chen
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Wen Wang
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Lu Xu
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhi-Qiang Lu
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
30
|
Singh N, Decroly E, Khatib AM, Villoutreix BO. Structure-based drug repositioning over the human TMPRSS2 protease domain: search for chemical probes able to repress SARS-CoV-2 Spike protein cleavages. Eur J Pharm Sci 2020; 153:105495. [PMID: 32730844 PMCID: PMC7384984 DOI: 10.1016/j.ejps.2020.105495] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/16/2020] [Accepted: 07/27/2020] [Indexed: 12/28/2022]
Abstract
In December 2019, a new coronavirus was identified in the Hubei province of central china and named SARS-CoV-2. This new virus induces COVID-19, a severe respiratory disease with high death rate. A putative target to interfere with the virus is the host transmembrane serine protease family member II (TMPRSS2). This enzyme is critical for the entry of coronaviruses into human cells by cleaving and activating the spike protein (S) of SARS-CoV-2. Repositioning approved, investigational and experimental drugs on the serine protease domain of TMPRSS2 could thus be valuable. There is no experimental structure for TMPRSS2 but it is possible to develop quality structural models for the serine protease domain using comparative modeling strategies as such domains are highly structurally conserved. Beside the TMPRSS2 catalytic site, we predicted on our structural models a main exosite that could be important for the binding of protein partners and/or substrates. To block the catalytic site or the exosite of TMPRSS2 we used structure-based virtual screening computations and two different collections of approved, investigational and experimental drugs. We propose a list of 156 molecules that could bind to the catalytic site and 100 compounds that may interact with the exosite. These small molecules should now be tested in vitro to gain novel insights over the roles of TMPRSS2 or as starting point for the development of second generation analogs.
Collapse
Affiliation(s)
- Natesh Singh
- Univ. Lille, INSERM, Institut Pasteur de Lille, U1177, F-59000 Lille, France
| | | | - Abdel-Majid Khatib
- Univ. Bordeaux, Allée Geoffroy St Hilaire, 33615 Pessac, France
- INSERM, LAMC, UMR 1029, Allée Geoffroy St Hilaire, 33615 Pessac, France
- Corresponding authors.
| | - Bruno O. Villoutreix
- Univ. Lille, INSERM, Institut Pasteur de Lille, U1177, F-59000 Lille, France
- Corresponding authors.
| |
Collapse
|
31
|
Li SW, Wright M, Healey JF, Hutchinson JM, O’Rourke S, Mesa KA, Lollar P, Berman PW. Gene editing in CHO cells to prevent proteolysis and enhance glycosylation: Production of HIV envelope proteins as vaccine immunogens. PLoS One 2020; 15:e0233866. [PMID: 32470085 PMCID: PMC7259603 DOI: 10.1371/journal.pone.0233866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/13/2020] [Indexed: 01/12/2023] Open
Abstract
Several candidate HIV subunit vaccines based on recombinant envelope (Env) glycoproteins have been advanced into human clinical trials. To facilitate biopharmaceutical production, it is necessary to produce these in CHO (Chinese Hamster Ovary) cells, the cellular substrate used for the manufacturing of most recombinant protein therapeutics. However, previous studies have shown that when recombinant Env proteins from clade B viruses, the major subtype represented in North America, Europe, and other parts of the world, are expressed in CHO cells, they are proteolyzed and lack important glycan-dependent epitopes present on virions. Previously, we identified C1s, a serine protease in the complement pathway, as the endogenous CHO protease responsible for the cleavage of clade B laboratory isolates of -recombinant gp120s (rgp120s) expressed in stable CHO-S cell lines. In this paper, we describe the development of two novel CHOK1 cell lines with the C1s gene inactivated by gene editing, that are suitable for the production of any protein susceptible to C1s proteolysis. One cell line, C1s-/- CHOK1 2.E7, contains a deletion in the C1s gene. The other cell line, C1s-/- MGAT1- CHOK1 1.A1, contains a deletion in both the C1s gene and the MGAT1 gene, which limits glycosylation to mannose-5 or earlier intermediates in the N-linked glycosylation pathway. In addition, we compare the substrate specificity of C1s with thrombin on the cleavage of both rgp120 and human Factor VIII, two recombinant proteins known to undergo unintended proteolysis (clipping) when expressed in CHO cells. Finally, we demonstrate the utility and practicality of the C1s-/- MGAT1- CHOK1 1.A1 cell line for the expression of clinical isolates of clade B Envs from rare individuals that possess broadly neutralizing antibodies and are able to control virus replication without anti-retroviral drugs (elite neutralizer/controller phenotypes). The Envs represent unique HIV vaccine immunogens suitable for further immunogenicity and efficacy studies.
Collapse
Affiliation(s)
- Sophia W. Li
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Meredith Wright
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - John F. Healey
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Jennie M. Hutchinson
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Sara O’Rourke
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Kathryn A. Mesa
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Pete Lollar
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Phillip W. Berman
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| |
Collapse
|
32
|
Latinović Z, Leonardi A, Koh CY, Kini RM, Trampuš Bakija A, Pungerčar J, Križaj I. The Procoagulant Snake Venom Serine Protease Potentially Having a Dual, Blood Coagulation Factor V and X-Activating Activity. Toxins (Basel) 2020; 12:toxins12060358. [PMID: 32485989 PMCID: PMC7354534 DOI: 10.3390/toxins12060358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 02/06/2023] Open
Abstract
A procoagulant snake venom serine protease was isolated from the venom of the nose-horned viper (Vipera ammodytes ammodytes). This 34 kDa glycoprotein, termed VaaSP-VX, possesses five kDa N-linked carbohydrates. Amino acid sequencing showed VaaSP-VX to be a chymotrypsin-like serine protease. Structurally, it is highly homologous to VaaSP-6 from the same venom and to nikobin from the venom of Vipera nikolskii, neither of which have known functions. VaaSP-VX does not affect platelets. The specific proteolysis of blood coagulation factors X and V by VaaSP-VX suggests that its blood-coagulation-inducing effect is due to its ability to activate these two blood coagulation factors, which following activation, combine to form the prothrombinase complex. VaaSP-VX may thus represent the first example of a serine protease with such a dual activity, which makes it a highly suitable candidate to replace diluted Russell’s viper venom in lupus anticoagulant testing, thus achieving greater reliability of the analysis. As a blood-coagulation-promoting substance that is resistant to serpin inhibition, VaaSP-VX is also interesting from the therapeutic point of view for treating patients suffering from hemophilia.
Collapse
Affiliation(s)
- Zorica Latinović
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; (Z.L.); (A.L.); (J.P.)
- Jožef Stefan International Postgraduate School, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Adrijana Leonardi
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; (Z.L.); (A.L.); (J.P.)
| | - Cho Yeow Koh
- Protein Science Laboratory, Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; (C.Y.K.); (R.M.K.)
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore 119228, Singapore
| | - R. Manjunatha Kini
- Protein Science Laboratory, Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; (C.Y.K.); (R.M.K.)
| | - Alenka Trampuš Bakija
- Division of Pediatrics, University Medical Center, Bohoričeva 20, SI-1000 Ljubljana, Slovenia;
| | - Jože Pungerčar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; (Z.L.); (A.L.); (J.P.)
| | - Igor Križaj
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; (Z.L.); (A.L.); (J.P.)
- Correspondence:
| |
Collapse
|
33
|
Labelle-Dumais C, Pyatla G, Paylakhi S, Tolman NG, Hameed S, Seymens Y, Dang E, Mandal AK, Senthil S, Khanna RC, Kabra M, Kaur I, John SWM, Chakrabarti S, Nair KS. Loss of PRSS56 function leads to ocular angle defects and increased susceptibility to high intraocular pressure. Dis Model Mech 2020; 13:dmm042853. [PMID: 32152063 PMCID: PMC7272341 DOI: 10.1242/dmm.042853] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/26/2020] [Indexed: 12/31/2022] Open
Abstract
Glaucoma is a leading cause of blindness, affecting up to 70 million people worldwide. High intraocular pressure (IOP) is a major risk factor for glaucoma. It is well established that inefficient aqueous humor (AqH) outflow resulting from structural or functional alterations in ocular drainage tissues causes high IOP, but the genes and pathways involved are poorly understood. We previously demonstrated that mutations in the gene encoding the serine protease PRSS56 induces ocular angle closure and high IOP in mice and identified reduced ocular axial length as a potential contributing factor. Here, we show that Prss56-/- mice also exhibit an abnormal iridocorneal angle configuration characterized by a posterior shift of ocular drainage structures relative to the ciliary body and iris. Notably, we show that retina-derived PRSS56 is required between postnatal days 13 and 18 for proper iridocorneal configuration and that abnormal positioning of the ocular drainage tissues is not dependent on ocular size reduction in Prss56-/- mice. Furthermore, we demonstrate that the genetic context modulates the severity of IOP elevation in Prss56 mutant mice and describe a progressive degeneration of ocular drainage tissues that likely contributes to the exacerbation of the high IOP phenotype observed on the C3H/HeJ genetic background. Finally, we identify five rare PRSS56 variants associated with human primary congenital glaucoma, a condition characterized by abnormal development of the ocular drainage structures. Collectively, our findings point to a role for PRSS56 in the development and maintenance of ocular drainage tissues and IOP homeostasis, and provide new insights into glaucoma pathogenesis.
Collapse
Affiliation(s)
| | - Goutham Pyatla
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad 500034, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | | | - Nicholas G Tolman
- Howard Hughes Medical Institute, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Syed Hameed
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad 500034, India
| | - Yusef Seymens
- Department of Ophthalmology, University of California, San Francisco, CA 94143, USA
| | - Eric Dang
- Department of Ophthalmology, University of California, San Francisco, CA 94143, USA
| | - Anil K Mandal
- Jasti V. Ramanamma Children's Eye Care Centre, L V Prasad Eye Institute, Hyderabad 500034, India
| | - Sirisha Senthil
- Jasti V. Ramanamma Children's Eye Care Centre, L V Prasad Eye Institute, Hyderabad 500034, India
| | - Rohit C Khanna
- Gullapalli Pratibha Rao International Centre for Advancement of Rural Eye Care, L V Prasad Eye Institute, Hyderabad 500034, India
| | - Meha Kabra
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad 500034, India
| | - Inderjeet Kaur
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad 500034, India
| | - Simon W M John
- Howard Hughes Medical Institute, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | - K Saidas Nair
- Department of Ophthalmology, University of California, San Francisco, CA 94143, USA
- Department of Anatomy, University of California, San Francisco, CA 94143, USA
| |
Collapse
|
34
|
Neumann C, Slagboom J, Somsen GW, Vonk F, Casewell NR, Cardoso CL, Kool J. Development of a generic high-throughput screening assay for profiling snake venom protease activity after high-resolution chromatographic fractionation. Toxicon 2020; 178:61-68. [PMID: 32112787 DOI: 10.1016/j.toxicon.2020.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/22/2020] [Accepted: 02/11/2020] [Indexed: 11/21/2022]
Abstract
Snakebites cause upwards of 1.8 million envenomings, 138,000 deaths and 500,000 cases of long term morbidity each year. Viper snake venoms (family Viperidae) generally contain a high proportion of proteases which can cause devastating effects such as hemorrhage, coagulopathy, edema, necrosis, and severe pain, in envenomed victims. In this study, analytical techniques were combined with enzymatic assays to develop a novel method for the detection of snake venom protease activity by using rhodamine-110-peptide substrate. In the so called at-line nanofractionation set up, crude venoms were first separated with reversed phase liquid chromatography, after which fractions were collected onto 384-well plates. Protease activity assays were then performed in the 384-well plates and bioassay chromatograms were constructed revealing protease activity. Parallel obtained UV absorbance, MS and proteomics data from a previous study facilitated toxin identification. The application of the rhodamine-110-peptide substrate assay showed significantly greater sensitivity compared to prior assays using casein-FITC as the substrate. Moreover, cross referencing UV and MS data and resulted in the detection of a number of tentative proteases suspected to exhibit protease activity, including snake venom serine proteases from Calloselasma rhodostoma and Daboia russelli venom and a snake venom metalloproteinase from the venom of Echis ocellatus. Our data demonstrate that his methodology can be a useful tool for selectively identifying snake venom proteases, and can be applied to provide a better understanding of protease-induced pathologies and the development of novel therapeutics for treating snakebite.
Collapse
Affiliation(s)
- Coleen Neumann
- Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Julien Slagboom
- Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Freek Vonk
- Naturalis Biodiversity Center, 2333 CR, Leiden, the Netherlands
| | - Nicholas R Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Carmen L Cardoso
- Departamento de Química, Grupo de Cromatografia de Bioafinidade e Produtos Naturais - Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto - Universidade de São Paulo, Brazil
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
| |
Collapse
|
35
|
Vanuopadath M, Shaji SK, Raveendran D, Nair BG, Nair SS. Delineating the venom toxin arsenal of Malabar pit viper (Trimeresurus malabaricus) from the Western Ghats of India and evaluating its immunological cross-reactivity and in vitro cytotoxicity. Int J Biol Macromol 2020; 148:1029-1045. [PMID: 31982532 DOI: 10.1016/j.ijbiomac.2020.01.226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023]
Abstract
The venom protein components of Malabar pit viper (Trimeresurus malabaricus) were identified by combining SDS-PAGE and ion-exchange chromatography pre-fractionation techniques with LC-MS/MS incorporating Novor and PEAKS-assisted de novo sequencing strategies. Total 97 proteins that belong to 16 protein families such as L-amino acid oxidase, metalloprotease, serine protease, phospholipase A2, 5'-nucleotidase, C-type lectins/snaclecs and disintegrin were recognized from the venom of a single exemplar species. Of the 97 proteins, eighteen were identified through de novo approaches. Immunological cross-reactivity assessed through ELISA and western blot indicate that the Indian antivenoms binds less effectively to Malabar pit viper venom components compared to that of Russell's viper venom. The in vitro cell viability assays suggest that compared to the normal cells, MPV venom induces concentration dependent cell death in various cancer cells. Moreover, crude venom resulted in chromatin condensation and apoptotic bodies implying the induction of apoptosis. Taken together, the present study enabled in dissecting the venom proteome of Trimeresurus malabaricus and revealed the immuno-cross-reactivity profiles of commercially available Indian polyvalent antivenoms that, in turn, is expected to provide valuable insights on the need in improving antivenom preparations against its bite.
Collapse
Affiliation(s)
| | | | - Dileepkumar Raveendran
- Indriyam Biologics Pvt. Ltd., SCTIMST-TIMed, BMT Wing-Poojappura, Thiruvananthapuram 695 012, Kerala, India
| | | | | |
Collapse
|
36
|
Bun JS, Slack MD, Schemenauer DE, Johnson RJ. Comparative analysis of the human serine hydrolase OVCA2 to the model serine hydrolase homolog FSH1 from S. cerevisiae. PLoS One 2020; 15:e0230166. [PMID: 32182256 PMCID: PMC7077851 DOI: 10.1371/journal.pone.0230166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/20/2020] [Indexed: 11/22/2022] Open
Abstract
Over 100 metabolic serine hydrolases are present in humans with confirmed functions in metabolism, immune response, and neurotransmission. Among potentially clinically-relevant but uncharacterized human serine hydrolases is OVCA2, a serine hydrolase that has been linked with a variety of cancer-related processes. Herein, we developed a heterologous expression system for OVCA2 and determined the comprehensive substrate specificity of OVCA2 against two ester substrate libraries. Based on this analysis, OVCA2 was confirmed as a serine hydrolase with a strong preference for long-chain alkyl ester substrates (>10-carbons) and high selectivity against a variety of short, branched, and substituted esters. Substitutional analysis was used to identify the catalytic residues of OVCA2 with a Ser117-His206-Asp179 classic catalytic triad. Comparison of the substrate specificity of OVCA2 to the model homologue FSH1 from Saccharomyces cerevisiae illustrated the tighter substrate selectivity of OVCA2, but their overlapping substrate preference for extended straight-chain alkyl esters. Conformation of the overlapping biochemical properties of OVCA2 and FSH1 was used to model structural information about OVCA2. Together our analysis provides detailed substrate specificity information about a previously, uncharacterized human serine hydrolase and begins to define the biological properties of OVCA2.
Collapse
Affiliation(s)
- Jessica S. Bun
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - Michael D. Slack
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - Daniel E. Schemenauer
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - R. Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
- * E-mail:
| |
Collapse
|
37
|
Timm J, Kosovrasti K, Henes M, Leidner F, Hou S, Ali A, Kurt-Yilmaz N, Schiffer CA. Molecular and Structural Mechanism of Pan-Genotypic HCV NS3/4A Protease Inhibition by Glecaprevir. ACS Chem Biol 2020; 15:342-352. [PMID: 31868341 PMCID: PMC7747061 DOI: 10.1021/acschembio.9b00675] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus, causative agent of chronic viral hepatitis, infects 71 million people worldwide and is divided into seven genotypes and multiple subtypes with sequence identities between 68 to 82%. While older generation direct-acting antivirals had varying effectiveness against different genotypes, the newest NS3/4A protease inhibitors including glecaprevir (GLE) have pan-genotypic activity. The structural basis for pan-genotypic inhibition and effects of polymorphisms on inhibitor potency were not well-known due to lack of crystal structures of GLE-bound NS3/4A or genotypes other than 1. In this study, we determined the crystal structures of NS3/4A from genotypes 1a, 3a, 4a, and 5a in complex with GLE. Comparison with the highly similar grazoprevir indicated the mechanism of GLE's drastic improvement in potency. We found that, while GLE is highly potent against wild-type NS3/4A of all genotypes, specific resistance-associated substitutions (RASs) confer orders of magnitude loss in inhibition. Our crystal structures reveal molecular mechanisms behind pan-genotypic activity of GLE, including potency loss due to RASs at D168. Our structures permit for the first time analysis of changes due to polymorphisms among genotypes, providing insights into design principles that can aid future drug development and potentially can be extended to other proteins.
Collapse
Affiliation(s)
- Jennifer Timm
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shurong Hou
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nese Kurt-Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| |
Collapse
|
38
|
Siritapetawee J, Teamtisong K, Limphirat W, Charoenwattanasatien R, Attarataya J, Mothong N. Identification and characterization of a protease (EuRP-61) from Euphorbia resinifera latex. Int J Biol Macromol 2020; 145:998-1007. [PMID: 31678105 DOI: 10.1016/j.ijbiomac.2019.09.190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/21/2019] [Accepted: 09/21/2019] [Indexed: 01/02/2023]
Abstract
A serine protease designated as EuRP-61 was purified from Euphorbia resinifera latex. The N-terminal sequence of 15 amino acids of EuRP-61 supported the conclusion that the enzyme was a serine protease because its amino acid sequence had homology (between 50 and 70% identities) with the subtilisin-like proteases of other plants. EuRP-61 had a molecular weight estimated at 61 kDa analyzed by MALDI-TOF MS. The enzyme could cleave human fibrinogen with optimal conditions at pH 5.0 and 45 °C. The enzyme had a broad range of pH stability from 1 to 14 and tolerance to denaturation up to a temperature of approximately 65-66 °C. EuRP-61 hydrolyzed fibrinogen with a Michaelis constant (Km) of 4.95 ± 0.1 μM; a maximal velocity (Vmax) of 578.1 ± 11.81 ng min-1; and a catalytic efficiency (Vmax/Km) of 116.8 ± 1 ng μM-1 min-1. EuRP-61was crystallized under the condition of sodium iodide (0.2 M), Bis-Tris propane (0.1 M, pH 8.5) and PEG3350 (20%) by the sitting-drop method. The crystal belonged to space group P212121, with unit cell dimension a = 109.91, b = 67.38 and c = 199.45 Å and diffracted X-ray to 2.53 Å resolution. The crystal structure of EuRP-61 will be explored further by special phase solving techniques.
Collapse
Affiliation(s)
- Jaruwan Siritapetawee
- Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Wanwisa Limphirat
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand
| | | | - Jakrada Attarataya
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand
| | - Narumol Mothong
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand
| |
Collapse
|
39
|
Collier AM, Nemtsova Y, Kuber N, Banach-Petrosky W, Modak A, Sleat DE, Nanda V, Lobel P. Lysosomal protein thermal stability does not correlate with cellular half-life: global observations and a case study of tripeptidyl-peptidase 1. Biochem J 2020; 477:727-745. [PMID: 31957806 PMCID: PMC8442665 DOI: 10.1042/bcj20190874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/16/2022]
Abstract
Late-infantile neuronal ceroid lipofuscinosis (LINCL) is a neurodegenerative lysosomal storage disorder caused by mutations in the gene encoding the protease tripeptidyl-peptidase 1 (TPP1). Progression of LINCL can be slowed or halted by enzyme replacement therapy, where recombinant human TPP1 is administered to patients. In this study, we utilized protein engineering techniques to increase the stability of recombinant TPP1 with the rationale that this may lengthen its lysosomal half-life, potentially increasing the potency of the therapeutic protein. Utilizing multiple structure-based methods that have been shown to increase the stability of other proteins, we have generated and evaluated over 70 TPP1 variants. The most effective mutation, R465G, increased the melting temperature of TPP1 from 55.6°C to 64.4°C and increased its enzymatic half-life at 60°C from 5.4 min to 21.9 min. However, the intracellular half-life of R465G and all other variants tested in cultured LINCL patient-derived lymphoblasts was similar to that of WT TPP1. These results provide structure/function insights into TPP1 and indicate that improving in vitro thermal stability alone is insufficient to generate TPP1 variants with improved physiological stability. This conclusion is supported by a proteome-wide analysis that indicates that lysosomal proteins have higher melting temperatures but also higher turnover rates than proteins of other organelles. These results have implications for similar efforts where protein engineering approaches, which are frequently evaluated in vitro, may be considered for improving the physiological properties of proteins, particularly those that function in the lysosomal environment.
Collapse
Affiliation(s)
- Aaron M. Collier
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - Yuliya Nemtsova
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - Narendra Kuber
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | | | - Anurag Modak
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
| | - David E. Sleat
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Rutgers
University, Piscataway, NJ 08854
- Department of Biochemistry and Molecular Biology, Rutgers
University, Piscataway, NJ 08854
| |
Collapse
|
40
|
Paulchamy R, Sreeramulu B, Karuppiah H, Arumugam G, Sundaram J. A serine protease-associated lectin in the cytolytic system of blowfly (Chrysomya megacephala) larvae: Evidence and characterization. Arch Insect Biochem Physiol 2020; 103:e21623. [PMID: 31579962 DOI: 10.1002/arch.21623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/28/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Cytolytic activity against invading microorganisms is one of the innate forms of immunity in invertebrates. A serine protease-associated sialic acid-specific cytolytic lectin was purified using glutaraldehyde-fixed ox erythrocytes from the larval extract of blowfly (Chrysomya megacephala). The purified lectin lysed vertebrate erythrocytes with effective haemolysis of ox red blood cells (RBCs) in an isotonic medium. The degree of haemolytic (HL) activity of the purified cytolytic lectin depended on its concentration, pH, temperature, and calcium ions. It was sensitive to ethylenediaminetetraacetic acid. The native molecular mass of the C-type lectin was 260 ± 26 kDa, comprising four different polypeptide subunits of 75 kDa (pI ~8), 69 kDa (pI ~7.0), 61 kDa (pI ~5.3), and 55 kDa (pI ~4.6). The association between the C-type lectin and serine protease was confirmed by MALDI-TOF-MS analysis that revealed its homology in the same spectral peak as well as the proteases and phenylmethylsulphonyl fluoride inhibition of HL activity. Haemolysis inhibition by N-acetylneuraminic acid and other sugars revealed the properties of the lectin. The purified lectin distorted the integrity of ox RBCs and Paenalcaligenes hermetiae. This in vitro study documents the presence of a cytolytic system in blowfly (C. megacephala) larvae for the clearance of invading microbial pathogens in their feeding niche.
Collapse
Affiliation(s)
- Ramaraj Paulchamy
- Department of Zoology, University of Madras, Chennai, Tamil Nadu, India
| | | | - Hilda Karuppiah
- Department of Zoology, University of Madras, Chennai, Tamil Nadu, India
| | - Ganesh Arumugam
- Department of Zoology, University of Madras, Chennai, Tamil Nadu, India
| | | |
Collapse
|
41
|
Sharma C, Salem GEM, Sharma N, Gautam P, Singh R. Thrombolytic Potential of Novel Thiol-Dependent Fibrinolytic Protease from Bacillus cereus RSA1. Biomolecules 2019; 10:E3. [PMID: 31861284 PMCID: PMC7022875 DOI: 10.3390/biom10010003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/06/2019] [Accepted: 12/12/2019] [Indexed: 01/12/2023] Open
Abstract
The present study demonstrates the production and thrombolytic potential of a novel thermostable thiol-dependent fibrinolytic protease by Bacillus cereus RSA1. Statistical optimization of different parameters was accomplished with Plackett-Burman design and validated further by central composite design with 30.75 U/mL protease production. Precipitation and chromatographic approaches resulted in 33.11% recovery with 2.32-fold purification. The molecular weight of fibrinolytic protease was 40 KDa and it exhibited a broad temperature and pH stability range of 20-80 °C and pH 5-10 with utmost activity at 50 °C and pH 8, respectively. The protease retained its fibrinolytic activity in organic solvents and enhanced the activity in solutions with divalent cations (Mn2+, Zn2+, and Cu2+). The enzyme kinetics revealed Km and Vmax values of 1.093 mg/mL and 52.39 µg/mL/min, respectively, indicating higher affinity of fibrinolytic activity towards fibrin. Also, complete inhibition of fibrinolytic activity with DFP and a 2-fold increase with DTT and β-mercaptoethanol indicates its thiol-dependent serine protease nature. MALDI-TOF analysis showed 56% amino acid sequence homology with Subtilisin NAT OS = Bacillus subtilis subsp. natto. The fibrinolysis activity was compared with a commercial thrombolytic agent for its therapeutic applicability, and fibrinolytic protease was found highly significant with absolute blood clot dissolution within 4 h in in vitro conditions. The isolated fibrinolytic protease of Bacillus cereus RSA1 is novel and different from other known fibrinolytic proteases with high stability and efficacy, which might have wide medicinal and industrial application as a thrombolytic agent and in blood stain removal, respectively.
Collapse
Affiliation(s)
- Chhavi Sharma
- Amity Institute of Microbial Biotechnology, Amity University Uttar Pradesh, Noida 201313, India; (C.S.)
| | - Gad Elsayed Mohamed Salem
- Amity Institute of Microbial Biotechnology, Amity University Uttar Pradesh, Noida 201313, India; (C.S.)
- National Organization for Drug Control and Research, 51 Wezaret El-Zeraa st., Giza 12618, Egypt
| | - Neha Sharma
- Amity Institute of Microbial Biotechnology, Amity University Uttar Pradesh, Noida 201313, India; (C.S.)
| | - Prerna Gautam
- Amity Institute of Microbial Biotechnology, Amity University Uttar Pradesh, Noida 201313, India; (C.S.)
| | - Rajni Singh
- Amity Institute of Microbial Biotechnology, Amity University Uttar Pradesh, Noida 201313, India; (C.S.)
| |
Collapse
|
42
|
Kraml J, Kamenik AS, Waibl F, Schauperl M, Liedl KR. Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces. J Chem Theory Comput 2019; 15:5872-5882. [PMID: 31589427 PMCID: PMC7032847 DOI: 10.1021/acs.jctc.9b00742] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 12/27/2022]
Abstract
Solvation and hydrophobicity play a key role in a variety of biological mechanisms. In substrate binding, but also in structure-based drug design, the thermodynamic properties of water molecules surrounding a given protein are of high interest. One of the main algorithms devised in recent years to quantify thermodynamic properties of water is the grid inhomogeneous solvation theory (GIST), which calculates these features on a grid surrounding the protein. Despite the inherent advantages of GIST, the computational demand is a major drawback, as calculations for larger systems can take days or even weeks. Here, we present a GPU accelerated version of the GIST algorithm, which facilitates efficient estimates of solvation free energy even of large biomolecular interfaces. Furthermore, we show that GIST can be used as a reliable tool to evaluate protein surface hydrophobicity. We apply the approach on a set of nine different proteases calculating localized solvation free energies on the surface of the binding interfaces as a measure of their hydrophobicity. We find a compelling agreement with the hydrophobicity of their substrates, i.e., peptides, binding into the binding cleft, and thus our approach provides a reliable description of hydrophobicity characteristics of these biological interfaces.
Collapse
Affiliation(s)
- Johannes Kraml
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innsbruck 6020, Austria
| | - Anna S. Kamenik
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innsbruck 6020, Austria
| | - Franz Waibl
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innsbruck 6020, Austria
| | - Michael Schauperl
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92039-0736, United States
| | - Klaus R. Liedl
- Institute
of General, Inorganic and Theoretical Chemistry and Center for Molecular
Biosciences Innsbruck (CMBI), University
of Innsbruck, Innsbruck 6020, Austria
| |
Collapse
|
43
|
Peres-da-Silva A, Antunes D, Quintanilha Torres AL, Caffarena ER, Lampe E. Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease. Viruses 2019; 11:v11080691. [PMID: 31366046 PMCID: PMC6723822 DOI: 10.3390/v11080691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/04/2019] [Accepted: 06/13/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus genotype 1a (HCV-1a) comprises clades I and II. The Q80K polymorphism is found predominantly in clade I but rarely in clade II. Here, we investigated whether natural polymorphisms in HCV-1a clade II entailed structural protein changes when occurrence of the Q80K variant was simulated. Based on HCV-1a clade I and II protein sequences, the structure of the HCV-1a Q80K mutant NS3-4A was obtained by comparative modeling. Its physicochemical properties were studied by molecular dynamics simulations and network analysis. Results demonstrate that, in the presence of the K80 variant, clade II protease polymorphisms A91 and S/G174 led to variations in hydrogen bond occupancies. Structural analyses revealed differences in (i) flexibility of the H57 catalytic residue on the NS3 protease and (ii) correlations between amino acids on the NS3 protease and the NS4A cofactor. The latter indicated possible destabilization of interactions, resulting in increased separation of these proteins. The present findings describe how the relationships between different HCV-1a NS3 protease amino acid residues could affect the appearance of viral variants and the existence of distinct genetic barriers to HCV-1a isolates.
Collapse
Affiliation(s)
- Allan Peres-da-Silva
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil.
| | - Deborah Antunes
- Programa de Computação Científica, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
| | - André Luiz Quintanilha Torres
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
- Laboratório de Bioinformática, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro/UFRJ, Rio de Janeiro, RJ 21941-909, Brazil
| | - Ernesto Raul Caffarena
- Programa de Computação Científica, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
| | - Elisabeth Lampe
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
| |
Collapse
|
44
|
Omrane Benmrad M, Mechri S, Zaraî Jaouadi N, Ben Elhoul M, Rekik H, Sayadi S, Bejar S, Kechaou N, Jaouadi B. Purification and biochemical characterization of a novel thermostable protease from the oyster mushroom Pleurotus sajor-caju strain CTM10057 with industrial interest. BMC Biotechnol 2019; 19:43. [PMID: 31262286 PMCID: PMC6604391 DOI: 10.1186/s12896-019-0536-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 06/17/2019] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Proteases are hydrolytic enzymes that catalyze peptide linkage cleavage reactions at the level of proteins and peptides with different degrees of specificity. This group draws the attention of industry. More than one protease in three is a serine protease. Classically, they are active at neutral to alkaline pH. The serine proteases are researched for industrial uses, especially detergents. They are the most commercially available enzyme group in the world market. Overall, fungi produced extracellular proteases, easily separated from mycelium by filtration. RESULTS A new basidiomycete fungus CTM10057, a hyperproducer of a novel protease (10,500 U/mL), was identified as Pleurotus sajor-caju (oyster mushroom). The enzyme, called SPPS, was purified to homogeneity by heat-treatment (80 °C for 20 min) followed by ammonium sulfate precipitation (35-55%)-dialysis, then UNO Q-6 FPLC ion-exchange chromatography and finally HPLC-ZORBAX PSM 300 HPSEC gel filtration chromatography, and submitted to biochemical characterization assays. The molecular mass was estimated to be 65 kDa by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Native-PAGE, casein-zymography, and size exclusion by HPLC. A high homology with mushroom proteases was displayed by the first 26 amino-acid residues of the NH2-terminal aminoacid sequence. Phenylmethanesulfonyl fluoride (PMSF) and diiodopropyl fluorophosphates (DFP) strongly inhibit SPPS, revealing that it is a member of the serine-proteases family. The pH and temperature optima were 9.5 and 70 °C, respectively. Interestingly, SPPS possesses the most elevated hydrolysis level and catalytic efficiency in comparison with SPTC, Flavourzyme® 500 L, and Thermolysin type X proteases. More remarkably, a high tolerance towards organic solvent tolerance was exhibited by SPPS, together with considerable detergent stability compared to the commercial proteases Thermolysin type X and Flavourzyme® 500 L, respectively. CONCLUSIONS This proves the excellent proprieties characterizing SPPS, making it a potential candidate for industrial applications especially detergent formulations.
Collapse
Affiliation(s)
- Maroua Omrane Benmrad
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Sondes Mechri
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Nadia Zaraî Jaouadi
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
- Biotech ECOZYM Start-up, Business Incubator, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Mouna Ben Elhoul
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
- Biotech ECOZYM Start-up, Business Incubator, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Hatem Rekik
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
- Biotech ECOZYM Start-up, Business Incubator, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Sami Sayadi
- Laboratory of Environmental Bioprocesses (LEBP), LMI COSYS-Med, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Samir Bejar
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
- Biotech ECOZYM Start-up, Business Incubator, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Nabil Kechaou
- Research Group of Agro-Food Processing Engineering (GP2A), Laboratory of Applied Fluid Mechanics, Process Engineering and Environment, National School of Engineers of Sfax (ENIS), University of Sfax, Road of Soukra Km 4, P.O. Box 1173, 3038, Sfax, Tunisia
| | - Bassem Jaouadi
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia.
- Biotech ECOZYM Start-up, Business Incubator, Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, 3018, Sfax, Tunisia.
| |
Collapse
|
45
|
Liu H, Liu Y, Song C, Ning J, Cui Z. Functional characterization of two clip-domain serine proteases in the swimming crab Portunus trituberculatus. Fish Shellfish Immunol 2019; 89:98-107. [PMID: 30851452 DOI: 10.1016/j.fsi.2018.12.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/17/2018] [Accepted: 12/23/2018] [Indexed: 06/09/2023]
Abstract
Clip domain serine proteases (cSPs), a family of multifunctional proteins, play a crucial role in innate immune system. Here, we report the functional characterization of two clip domain serine proteases (PtcSP1 and PtcSP3) from the swimming crab Portunus trituberculatus. The recombinant N-terminal clip domains and the C-terminal SP-like domains of PtcSP1 and PtcSP3 were expressed in Escherichia coli system, and assayed for various biological functions: protease activity, antimicrobial activity, bacterial clearance and microbial-binding activity. The recombinant SP-like domains of PtcSP1 and PtcSP3 exhibited trypsin-like protease activity, while their recombinant clip domains showed strong antibacterial activity and could bind to bacteria and yeast, suggesting the potential roles of PtcSP1 and PtcSP3 in immune defense and pattern recognition. Unlike PtcSP3, PtcSP1 revealed the opsonic activity as shown by a higher bacterial clearance rate of Vibrio alginolyticus coated with the combination of the recombinant clip domain and SP-like domain of PtcSP1 as compared with V. alginolyticus only. Knockdown of PtcSP1 or PtcSP3 by RNA interference resulted in a significant decrease of total phenoloxidase (PO) activity in crab, suggesting that PtcSP1 and PtcSP3 are involved in the proPO system. In addition, suppression of PtcSP1 or PtcSP3 changed the expression of PtALFs and complement-like components. All these findings suggest that PtcSP1 and PtcSP3 are multifunctional immune molecules and perform different protective functions in crab defense.
Collapse
Affiliation(s)
- Hourong Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chengwen Song
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Junhao Ning
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; School of Marine Science, Ningbo University, Zhejiang, Ningbo, 315211, China
| | - Zhaoxia Cui
- School of Marine Science, Ningbo University, Zhejiang, Ningbo, 315211, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| |
Collapse
|
46
|
Abstract
Identifying the viability of protein targets is one of the preliminary steps of drug discovery. Determining the ability of a protein to bind drugs in order to modulate its function, termed the druggability, requires a non-trivial amount of time and resources. Inability to properly measure druggability has accounted for a significant portion of failures in drug discovery. This problem is only further exacerbated by the large sample space of proteins involved in human diseases. With these barriers, the druggability space within the human proteome remains unexplored and has made it difficult to develop drugs for numerous diseases. Hence, we present a new feature developed in eFindSite that employs supervised machine learning to predict the druggability of a given protein. Benchmarking calculations against the Non-Redundant data set of Druggable and Less Druggable binding sites demonstrate that an AUC for druggability prediction with eFindSite is as high as 0.88. With eFindSite, we elucidated the human druggability space to be 10,191 proteins. Considering the disease space from the Open Targets Platform and excluding already known targets from the predicted data set reveal 2731 potentially novel therapeutic targets. eFindSite is freely available as a stand-alone software at https://github.com/michal-brylinski/efindsite .
Collapse
Affiliation(s)
- Omar Kana
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
- Center for Computation & Technology, Louisiana State University, Baton Rouge, LA, 70803, USA.
| |
Collapse
|
47
|
Doncheva NT, Domingues FS, McGivern DR, Shimakami T, Zeuzem S, Lengauer T, Lange CM, Albrecht M, Welsch C. Near-Neighbor Interactions in the NS3-4A Protease of HCV Impact Replicative Fitness of Drug-Resistant Viral Variants. J Mol Biol 2019; 431:2354-2368. [PMID: 31051172 DOI: 10.1016/j.jmb.2019.04.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/10/2019] [Accepted: 04/23/2019] [Indexed: 12/24/2022]
Abstract
A variety of amino acid substitutions in the NS3-4A protease of the hepatitis C virus lead to protease inhibitor (PI) resistance. Many of these significantly impair the replication fitness of the resistant variants in a genotype- and subtype-dependent manner, a critical factor in determining the probability with which resistant variants will persist. However, the underlying molecular mechanisms are unknown. Here, we present a novel residue-interaction network approach to determine how near-neighbor interactions of PI resistance mutations in NS3-4A can impact protease functional sites dependent on their genomic background. We constructed subtype-specific consensus residue networks for subtypes 1a and 1b from protease structure ensembles combined with biological properties of protein residues and evolutionary amino acid conservation. By applying local and global network topology analysis and visual exploration, we characterize PI resistance-associated sites and outline differences in near-neighbor interactions. We find local residue-interaction patterns and features at protease functional sites that are subtype specific. The noncovalent bonding patterns indicate higher fitness costs conferred by PI resistance mutations in a subtype 1b genomic background and explain the prevalence of Q80K and R155K in subtype 1a. Based on local residue interactions, we predict a subtype-specific role for the protease residue NS3-Q80 in molecular mechanisms related to the assembly of infectious virus particles that is supported by experimental data on the capacity of Q80K variants to replicate and produce infectious virus in subtype 1a and 1b cell culture.
Collapse
Affiliation(s)
- Nadezhda T Doncheva
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany; Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | | | - David R McGivern
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tetsuro Shimakami
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt a.M., Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Christian M Lange
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt a.M., Germany
| | - Mario Albrecht
- Institute for Knowledge Discovery, Graz University of Technology, Graz, Austria
| | - Christoph Welsch
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany; Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt a.M., Germany.
| |
Collapse
|
48
|
Nutho B, Mulholland AJ, Rungrotmongkol T. Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate. J Phys Chem B 2019; 123:2889-2903. [PMID: 30845796 DOI: 10.1021/acs.jpcb.9b02157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zika virus (ZIKV) is mainly transmitted to humans by Aedes species mosquitoes and is associated with serious pathological disorders including microcephaly in newborns and Guillain-Barré syndrome in adults. Currently, there is no vaccine or anti-ZIKV drug available for preventing or controlling ZIKV infection. An attractive drug target for ZIKV treatment is a two-compartment (NS2B/NS3) serine protease that processes viral polyprotein during infection. Here, conventional molecular dynamics simulations of the ZIKV protease in complex with peptide substrate (TGKRS) sequence at the C-terminus of NS2B show that the substrate is in the active conformation for the cleavage reaction by ZIKV protease. Hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling simulations (PM6/ff14SB) of acylation results reveal that proton transfer from S135 to H51 and nucleophilic attack on the substrate by S135 are concerted. The rate-limiting step involves the formation of a tetrahedral intermediate. In addition, the single-point energy QM/MM calculations, precisely at the level of coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), were performed to correct the potential energy profiles for the first step of the acylation process. The average computed activation barrier at this level of theory is 16.3 kcal mol-1. Therefore, the computational approaches presented here are helpful for further designing of NS2B/NS3 inhibitors based on transition-state analogues.
Collapse
Affiliation(s)
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
| | | |
Collapse
|
49
|
Abstract
Many plant viruses express their proteins through a polyprotein strategy, requiring the acquisition of protease domains to regulate the release of functional mature proteins and/or intermediate polyproteins. Positive-strand RNA viruses constitute the vast majority of plant viruses and they are diverse in their genomic organization and protein expression strategies. Until recently, proteases encoded by positive-strand RNA viruses were described as belonging to two categories: (1) chymotrypsin-like cysteine and serine proteases and (2) papain-like cysteine protease. However, the functional characterization of plant virus cysteine and serine proteases has highlighted their diversity in terms of biological activities, cleavage site specificities, regulatory mechanisms, and three-dimensional structures. The recent discovery of a plant picorna-like virus glutamic protease with possible structural similarities with fungal and bacterial glutamic proteases also revealed new unexpected sources of protease domains. We discuss the variety of plant positive-strand RNA virus protease domains. We also highlight possible evolution scenarios of these viral proteases, including evidence for the exchange of protease domains amongst unrelated viruses.
Collapse
Affiliation(s)
- Krin S Mann
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada.
| | - Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada.
| |
Collapse
|
50
|
Wei Z, Sun W, Tran NT, Gong Y, Ma H, Zheng H, Zhang Y, Li S. Two novel serine proteases from Scylla paramamosain involved in the synthesis of anti-lipopolysaccharide factors and activation of prophenoloxidase system. Fish Shellfish Immunol 2019; 84:322-332. [PMID: 30300737 DOI: 10.1016/j.fsi.2018.10.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/01/2018] [Accepted: 10/05/2018] [Indexed: 06/08/2023]
Abstract
Serine proteases (SPs) are important in various immune responses, including prophenoloxidase (proPO) activation, antimicrobial peptides (AMPs) synthesis, and hemolymph coagulation in invertebrates. In this study, SP3 and SP5 of mud crab (Scylla paramamosain) were studied. SP3 and SP5 were expressed in all examined tissues (mainly in hemocytes), and are associated with the immune responses of mud crab to Vibrio parahemolyticus and Staphylococcus aureus, as well as interacted with TRAF6, and are involved in the activation of anti-lipopolysaccharide factors (ALFs) probably through the TLR/NF-κB pathway. Depletion of SP3 inhibited the expression of ALF1, ALF2, ALF3, and ALF6, while knockdown of SP5 significantly decreased ALF5, and ALF6. Furthermore, both SP5 and TRAF6 regulated the PO activity in the hemolymph of mud crab. Overexpression assay showed that both SP3 and SP5 could enhance the promoter activities of ALFs in mud crab. Taken together, the results of this study indicate that SP3 and SP5 might play important roles in the immune system of mud crab against pathogen invasion.
Collapse
Affiliation(s)
- Zibo Wei
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Wanwei Sun
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China
| | - Ngoc Tuan Tran
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Yi Gong
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China; Marine Biology Institute, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
| |
Collapse
|