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Bhattacharya K, Chanu NR, Jha SK, Khanal P, Paudel KR. In silico design and evaluation of a multiepitope vaccine targeting the nucleoprotein of Puumala orthohantavirus. Proteins 2024. [PMID: 38742930 DOI: 10.1002/prot.26703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/19/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
The Puumala orthohantavirus is present in the body of the bank vole (Myodes glareolus). Humans infected with this virus may develop hemorrhagic fever accompanying renal syndrome. In addition, the infection may further lead to the failure of an immune system completely. The present study aimed to propose a possible vaccine by employing bioinformatics techniques to identify B and T-cell antigens. The best multi-epitope of potential immunogenicity was generated by combining epitopes. Additionally, the linkers EAAAK, AAY, and GPGPG were utilized in order to link the epitopes successfully. Further, C-ImmSim was used to perform in silico immunological simulations upon the vaccine. For the purpose of conducting expression tests in Escherichia coli, the chimeric protein construct was cloned using Snapgene into the pET-9c vector. The designed vaccine showed adequate results, evidenced by the global population coverage and favorable immune response. The developed vaccine was found to be highly effective and to have excellent population coverage in a number of computer-based assessments. This work is fully dependent on the development of nucleoprotein-based vaccines, which would constitute a significant step forward if our findings were used in developing a global vaccination to combat the Puumala virus.
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Affiliation(s)
- Kunal Bhattacharya
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, Assam, India
- Royal School of Pharmacy, The Assam Royal Global University, Guwahati, Assam, India
| | - Nongmaithem Randhoni Chanu
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, Assam, India
- Faculty of Pharmaceutical Science, Assam Downtown University, Guwahati, Assam, India
| | - Saurav Kumar Jha
- Department of Biological Sciences and Bioengineering (BSBE), Indian Institute of Technology, Kanpur, Uttar Pradesh, India
| | - Pukar Khanal
- Department of Pharmacology and Toxicology, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, India
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, New South Wales, Australia
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Qiu C, Halterman D, Zhang H, Liu Z. Multifunctionality of AsCFEM6 and AsCFEM12 effectors from the potato early blight pathogen Alternaria solani. Int J Biol Macromol 2024; 257:128575. [PMID: 38048930 DOI: 10.1016/j.ijbiomac.2023.128575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/31/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Plant pathogens secrete fungal-specific common in several fungal extracellular membrane (CFEM) effectors to manipulate host immunity and contribute to their virulence. Little is known about effectors and their functions in Alternaria solani, the necrotrophic fungal pathogen causing potato early blight. To identify candidate CFEM effector genes, we mined A. solani genome databases. This led to the identification of 12 genes encoding CFEM proteins (termed AsCFEM1-AsCFEM12) and 6 of them were confirmed to be putative secreted effectors. In planta expression revealed that AsCFEM6 and AsCFEM12 have elicitor function that triggers plant defense response including cell death in different botanical families. Targeted gene disruption of AsCFEM6 and AsCFEM12 resulted in a change in spore development, significant reduction of virulence on potato and eggplant susceptible cultivars, increased resistance to fungicide stress, variation in iron acquisition and utilization, and the involvement in 1,8-dihydroxynaphthalene (DHN) melanin biosynthesis pathway. Using maximum likelihood method, we found that positive selection likely caused the polymorphism within AsCFEM6 and AsCFEM12 homologs in different Alternaria spp. Site-directed mutagenesis analysis indicated that positive selection sites within their CFEM domains are required for cell death induction in Nicotiana benthamiana and are critical for response to abiotic stress in yeast. These results demonstrate that AsCFEM effectors possess additional functions beyond their roles in host plant immune response and pathogen virulence.
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Affiliation(s)
- Chaodong Qiu
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Dennis Halterman
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
| | - Huajian Zhang
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Hefei 230036, China.
| | - Zhenyu Liu
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Hefei 230036, China.
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3
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Sen P, Roy Acharyya S, Arora A, Ghosh SS. An in-silico approach to understand the potential role of Wnt inhibitory factor-1 (WIF-1) in the inhibition of the Wnt signalling pathway. J Biomol Struct Dyn 2024; 42:326-345. [PMID: 36995086 DOI: 10.1080/07391102.2023.2192810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/12/2023] [Indexed: 03/31/2023]
Abstract
WIF1 (Wnt inhibitory factor 1) is a potent tumour suppressor gene which is epigenetically silenced in numerous malignancies. The associations of WIF1 protein with the Wnt pathway molecules have not been fully explored, despite their involvement in the downregulation of several malignancies. In the present study, a computational approach encompassing the expression, gene ontology analysis and pathway analysis is employed to obtain an insight into the role of the WIF1 protein. Moreover, the interaction of the WIF1 domain with the Wnt pathway molecules was carried out to ascertain the tumour-suppressive role of the domain, along with the determination of their plausible interactions. Initially, the protein-protein interaction network analysis endowed us with the Wnt ligands (such as Wnt1, Wnt3a, Wnt4, Wnt5a, Wnt8a and Wnt9a), along with the Frizzled receptors (Fzd1 and Fzd2) and the low-density lipoprotein complex (Lrp5/6) as the foremost interactors of the protein. Further, the expression analysis of the aforementioned genes and proteins was determined using The Cancer Genome Atlas to comprehend the significance of the signalling molecules in the major cancer subtypes. Moreover, the associations of the aforementioned macromolecular entities with the WIF1 domain were explored using the molecular docking studies, whereas the dynamics and stability of the assemblage were investigated using 100 ns molecular dynamics simulations. Therefore, providing us insights into the plausible roles of WIF1 in inhibiting the Wnt pathways in various malignancies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Plaboni Sen
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Suchandra Roy Acharyya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Arisha Arora
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Siddhartha Sankar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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4
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Shahab M, Aiman S, Alshammari A, Alasmari AF, Alharbi M, Khan A, Wei DQ, Zheng G. Immunoinformatics-based potential multi-peptide vaccine designing against Jamestown Canyon Virus (JCV) capable of eliciting cellular and humoral immune responses. Int J Biol Macromol 2023; 253:126678. [PMID: 37666399 DOI: 10.1016/j.ijbiomac.2023.126678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/21/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Jamestown Canyon virus (JCV) is a deadly viral infection transmitted by various mosquito species. This mosquito-borne virus belongs to Bunyaviridae family, posing a high public health threat in the in tropical regions of the United States causing encephalitis in humans. Common symptoms of JCV include fever, headache, stiff neck, photophobia, nausea, vomiting, and seizures. Despite the availability of resources, there is currently no vaccine or drug available to combat JCV. The purpose of this study was to develop an epitope-based vaccine using immunoinformatics approaches. The vaccine aimed to be secure, efficient, bio-compatible, and capable of stimulating both innate and adaptive immune responses. In this study, the protein sequence of JCV was obtained from the NCBI database. Various bioinformatics methods, including toxicity evaluation, antigenicity testing, conservancy analysis, and allergenicity assessment were utilized to identify the most promising epitopes. Suitable linkers and adjuvant sequences were used in the design of vaccine construct. 50s ribosomal protein sequence was used as an adjuvant at the N-terminus of the construct. A total of 5 CTL, 5 HTL, and 5 linear B cell epitopes were selected based on non-allergenicity, immunological potential, and antigenicity scores to design a highly immunogenic multi-peptide vaccine construct. Strong interactions between the proposed vaccine and human immune receptors, i.e., TLR-2 and TLR-4, were revealed in a docking study using ClusPro software, suggesting their possible relevance in the immunological response to the vaccine. Immunological and physicochemical properties assessment ensured that the proposed vaccine demonstrated high immunogenicity, solubility and thermostability. Molecular dynamics simulations confirmed the strong binding affinities, as well as dynamic and structural stability of the proposed vaccine. Immune simulation suggest that the vaccine has the potential to effectively stimulate cellular and humoral immune responses to combat JCV infection. Experimental and clinical assays are required to validate the results of this study.
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Affiliation(s)
- Muhammad Shahab
- State key laboratories of chemical Resources Engineering Beijing University of chemical technology, Beijing 100029, China
| | - Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia
| | - Abbas Khan
- Deparment of Biostatistics and Bioinformatics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China; School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia.
| | - Dong-Qing Wei
- Deparment of Biostatistics and Bioinformatics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Guojun Zheng
- State key laboratories of chemical Resources Engineering Beijing University of chemical technology, Beijing 100029, China.
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Tan Q, Li R, Liu L, Wang D, Dai XF, Song LM, Zhang DD, Kong ZQ, Klosterman SJ, Usami T, Subbarao KV, Liang WX, Chen JY. Functional Characterization of Verticillium dahliae Race 3-Specific Gene VdR3e in Virulence and Elicitation of Plant Immune Responses. Microbiol Spectr 2023; 11:e0108323. [PMID: 37378525 PMCID: PMC10434166 DOI: 10.1128/spectrum.01083-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Verticillium dahliae is a soilborne fungal pathogen that causes disease on many economically important crops. Based on the resistance or susceptibility of differential cultivars in tomato, isolates of V. dahliae are divided into three races. Avirulence (avr) genes within the genomes of the three races have also been identified. However, the functional role of the avr gene in race 3 isolates of V. dahliae has not been characterized. In this study, bioinformatics analysis showed that VdR3e, a cysteine-rich secreted protein encoded by the gene characterizing race 3 in V. dahliae, was likely obtained by horizontal gene transfer from the fungal genus Bipolaris. We demonstrate that VdR3e causes cell death by triggering multiple defense responses. In addition, VdR3e localized at the periphery of the plant cell and triggered immunity depending on its subcellular localization and the cell membrane receptor BAK1. Furthermore, VdR3e is a virulence factor and shows differential pathogenicity in race 3-resistant and -susceptible hosts. These results suggest that VdR3e is a virulence factor that can also interact with BAK1 as a pathogen-associated molecular pattern (PAMP) to trigger immune responses. IMPORTANCE Based on the gene-for-gene model, research on the function of avirulence genes and resistance genes has had an unparalleled impact on breeding for resistance in most crops against individual pathogens. The soilborne fungal pathogen, Verticillium dahliae, is a major pathogen on many economically important crops. Currently, avr genes of the three races in V. dahliae have been identified, but the function of avr gene representing race 3 has not been described. We investigated the characteristics of VdR3e-mediated immunity and demonstrated that VdR3e acts as a PAMP to activate a variety of plant defense responses and induce plant cell death. We also demonstrated that the role of VdR3e in pathogenicity was host dependent. This is the first study to describe the immune and virulence functions of the avr gene from race 3 in V. dahliae, and we provide support for the identification of genes mediating resistance against race 3.
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Affiliation(s)
- Qian Tan
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, People’s Republic of China
| | - Lei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Dan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, People’s Republic of China
| | - Li-Min Song
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Zhi-Qiang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Steve J. Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, California, USA
| | - Toshiyuki Usami
- Graduate School of Horticulture, Chiba University, Matsudo City, Japan
| | - Krishna V. Subbarao
- Department of Plant Pathology, University of California—Davis, c/o U.S. Agricultural Research Station, Salinas, California, USA
| | - Wen-Xing Liang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, People’s Republic of China
| | - Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, People’s Republic of China
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6
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Wang J, Wang D, Ji X, Wang J, Klosterman SJ, Dai X, Chen J, Subbarao KV, Hao X, Zhang D. The Verticillium dahliae Small Cysteine-Rich Protein VdSCP23 Manipulates Host Immunity. Int J Mol Sci 2023; 24:ijms24119403. [PMID: 37298354 DOI: 10.3390/ijms24119403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/12/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Verticillium wilt caused by Verticillium dahliae is a notorious soil-borne fungal disease and seriously threatens the yield of economic crops worldwide. During host infection, V. dahliae secretes many effectors that manipulate host immunity, among which small cysteine-rich proteins (SCPs) play an important role. However, the exact roles of many SCPs from V. dahliae are unknown and varied. In this study, we show that the small cysteine-rich protein VdSCP23 inhibits cell necrosis in Nicotiana benthamiana leaves, as well as the reactive oxygen species (ROS) burst, electrolyte leakage and the expression of defense-related genes. VdSCP23 is mainly localized in the plant cell plasma membrane and nucleus, but its inhibition of immune responses was independent of its nuclear localization. Site-directed mutagenesis and peptide truncation showed that the inhibition function of VdSCP23 was independent of cysteine residues but was dependent on the N-glycosylation sites and the integrity of VdSCP23 protein structure. Deletion of VdSCP23 did not affect the growth and development of mycelia or conidial production in V. dahliae. Unexpectedly, VdSCP23 deletion strains still maintained their virulence for N. benthamiana, Gossypium hirsutum and Arabidopsis thaliana seedlings. This study demonstrates an important role for VdSCP23 in the inhibition of plant immune responses; however, it is not required for normal growth or virulence in V. dahliae.
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Affiliation(s)
- Jie Wang
- College of Plant Protection, Shanxi Agricultural University, Taigu, Jinzhong 030801, China
| | - Dan Wang
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaobin Ji
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jun Wang
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Steven J Klosterman
- Crop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905, USA
| | - Xiaofeng Dai
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Jieyin Chen
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Krishna V Subbarao
- Crop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905, USA
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA 93905, USA
| | - Xiaojuan Hao
- College of Plant Protection, Shanxi Agricultural University, Taigu, Jinzhong 030801, China
| | - Dandan Zhang
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
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Liu F, Liu A, Zhu Z, Wang Y, Ye H. Crustacean female sex hormone: More than a female phenotypes-related hormone in a protandric simultaneous hermaphroditism shrimp. Int J Biol Macromol 2023; 238:124181. [PMID: 36965556 DOI: 10.1016/j.ijbiomac.2023.124181] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/13/2023] [Accepted: 03/22/2023] [Indexed: 03/27/2023]
Abstract
Crustacean female sex hormone (CFSH) is believed to regulate the development of female-related phenotypes in crustaceans. However, its role in gonadal development has been understudied. This study identified a CFSH gene, Lvit-CFSH1b, in the peppermint shrimp Lysmata vittata, a protandric simultaneous hermaphroditism (PSH) species. Lvit-CFSH1b is only expressed in the eyestalk ganglion. qRT-PCR showed that the expression level of Lvit-CFSH1b significantly increased with the gonad development from stage I to III (male phase) and decreased at stage IV (euhermaphrodite phase). Gene knockdown of Lvit-CFSH1b resulted in retardation of female phenotypes and stimulated the development of male phenotypes. At the same time, ovarian development was inhibited, and spermatogenesis was promoted. In addition, injection of rCFSH1b increased ovarian expression of vitellogenin (Lvit-Vg) and hepatopancreas expression of vitellogenin receptor (Lvit-VgR), while suppressing the expressions of insulin-like androgenic gland hormones (Lvit-IAG1 and Lvit-IAG2) in androgenic glands. The addition of rCFSH1b induced the in vitro expression of Lvit-Vg in ovarian and Lvit-VgR in hepatopancreas explants. In conclusion, this study provides convincing evidence that CFSH expedites the feminization process and impedes masculinization by inhibiting IAG in hermaphroditic crustaceans.
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Affiliation(s)
- Fang Liu
- Fisheries College, Jimei University, Xiamen 361021, People's Republic of China
| | - An Liu
- Fisheries College, Jimei University, Xiamen 361021, People's Republic of China
| | - Zhihuang Zhu
- Fisheries Research Institute of Fujian, Xiamen 361013, People's Republic of China
| | - Yilei Wang
- Fisheries College, Jimei University, Xiamen 361021, People's Republic of China.
| | - Haihui Ye
- Fisheries College, Jimei University, Xiamen 361021, People's Republic of China.
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Gao M, Günther S. HyperCys: A Structure- and Sequence-Based Predictor of Hyper-Reactive Druggable Cysteines. Int J Mol Sci 2023; 24:ijms24065960. [PMID: 36983037 PMCID: PMC10054327 DOI: 10.3390/ijms24065960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The cysteine side chain has a free thiol group, making it the amino acid residue most often covalently modified by small molecules possessing weakly electrophilic warheads, thereby prolonging on-target residence time and reducing the risk of idiosyncratic drug toxicity. However, not all cysteines are equally reactive or accessible. Hence, to identify targetable cysteines, we propose a novel ensemble stacked machine learning (ML) model to predict hyper-reactive druggable cysteines, named HyperCys. First, the pocket, conservation, structural and energy profiles, and physicochemical properties of (non)covalently bound cysteines were collected from both protein sequences and 3D structures of protein-ligand complexes. Then, we established the HyperCys ensemble stacked model by integrating six different ML models, including K-nearest neighbors, support vector machine, light gradient boost machine, multi-layer perceptron classifier, random forest, and the meta-classifier model logistic regression. Finally, based on the hyper-reactive cysteines' classification accuracy and other metrics, the results for different feature group combinations were compared. The results show that the accuracy, F1 score, recall score, and ROC AUC values of HyperCys are 0.784, 0.754, 0.742, and 0.824, respectively, after performing 10-fold CV with the best window size. Compared to traditional ML models with only sequenced-based features or only 3D structural features, HyperCys is more accurate at predicting hyper-reactive druggable cysteines. It is anticipated that HyperCys will be an effective tool for discovering new potential reactive cysteines in a wide range of nucleophilic proteins and will provide an important contribution to the design of targeted covalent inhibitors with high potency and selectivity.
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Affiliation(s)
- Mingjie Gao
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, 79104 Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, 79104 Freiburg, Germany
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Srila W, Min TT, Sumphanapai T, Rangnoi K, Berkmen M, Yamabhai M. Production and applications of fluorobody from redox-engineered Escherichia coli. Appl Microbiol Biotechnol 2023; 107:1959-1970. [PMID: 36729226 PMCID: PMC10050041 DOI: 10.1007/s00253-023-12395-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 02/03/2023]
Abstract
Efficient selection and production of antibody fragments in microbial systems remain to be a challenging process. To optimize microbial production of single-chain variable fragments (scFvs), we have chosen five model targets, 1) a hapten, Zearalenone (ZEN) mycotoxin, along with infectious agents 2) rabies virus, 3) Propionibacterium acnes, 4) Pseudomonas aeruginosa, and a cancer cell 5) acute myeloid leukemia cell line (HL-60). The scFv binders were affinity selected from a non-immunized human phage display scFv antibody library and genetically fused to the N-terminus of emerald green fluorescent protein (EmGFP). The scFv-EmGFP fusion constructs were subcloned into an expression vector, under the control of T7 promoter, C-terminally tagged with hexa-histidine and expressed in different Escherichia coli (E. coli) hosts. This enabled the detection of cells that expressed the correct scFv-EmGFP fusion, termed fluorobody, via bright fluorescent signal in the cytoplasm. Among the three E. coli hosts tested, an engineered E. coli B strain called SHuffle B that promotes disulfide bond formation in the cytoplasm appeared to be the most appropriate host. The recombinant fluorobodies were well expressed (2-8 mg/L), possessed the fluorescence property of EmGFP, and retained the ability to bind to their cognate targets. Their specific bindings were demonstrated by ELISA, fluorescence-linked immunosorbent assay (FLISA), flow cytometry, and fluorescent microscope imaging. The fluorobody expression platform in this study could be further adopted as a one-step immunostaining technique based on scFv, isolated from phage display library to numerous desired targets. KEY POINTS: • E. coli SHuffle express T7 is a suitable expression host for scFv-EmGFP (fluorobody) • Only the clones harboring scFv-EmGFP plasmid will show bright fluorescent signal • This platform can be used to produce fluorobodies for numerous purposes.
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Affiliation(s)
- Witsanu Srila
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Thae Thae Min
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Thitima Sumphanapai
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Kuntalee Rangnoi
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | | | - Montarop Yamabhai
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
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10
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Hasenahuer MA, Sanchis-Juan A, Laskowski RA, Baker JA, Stephenson JD, Orengo CA, Raymond FL, Thornton JM. Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins. J Mol Biol 2023; 435:167892. [PMID: 36410474 PMCID: PMC9875310 DOI: 10.1016/j.jmb.2022.167892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/08/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
Constrained Coding Regions (CCRs) in the human genome have been derived from DNA sequencing data of large cohorts of healthy control populations, available in the Genome Aggregation Database (gnomAD) [1]. They identify regions depleted of protein-changing variants and thus identify segments of the genome that have been constrained during human evolution. By mapping these DNA-defined regions from genomic coordinates onto the corresponding protein positions and combining this information with protein annotations, we have explored the distribution of CCRs and compared their co-occurrence with different protein functional features, previously annotated at the amino acid level in public databases. As expected, our results reveal that functional amino acids involved in interactions with DNA/RNA, protein-protein contacts and catalytic sites are the protein features most likely to be highly constrained for variation in the control population. More surprisingly, we also found that linear motifs, linear interacting peptides (LIPs), disorder-order transitions upon binding with other protein partners and liquid-liquid phase separating (LLPS) regions are also strongly associated with high constraint for variability. We also compared intra-species constraints in the human CCRs with inter-species conservation and functional residues to explore how such CCRs may contribute to the analysis of protein variants. As has been previously observed, CCRs are only weakly correlated with conservation, suggesting that intraspecies constraints complement interspecies conservation and can provide more information to interpret variant effects.
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Affiliation(s)
- Marcia A. Hasenahuer
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK,Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK,Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK,Corresponding author at: European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK. @MarHasenahuer
| | - Alba Sanchis-Juan
- Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge CB2 0XY, UK,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Roman A. Laskowski
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - James A. Baker
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - James D. Stephenson
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Christine A. Orengo
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - F. Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Janet M. Thornton
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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Mohan Kumar R, Anantapur R, Peter A, H V C. Computational investigation of phytoalexins as potential antiviral RAP-1 and RAP-2 (Replication Associated Proteins) inhibitor for the management of cucumber mosaic virus (CMV): a molecular modeling, in silico docking and MM-GBSA study. J Biomol Struct Dyn 2022; 40:12165-12183. [PMID: 34463218 DOI: 10.1080/07391102.2021.1968500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Replication Associated Proteins (RAP-1 and RAP-2) encoded by CMV ORF 1a and ORF 2a are required for the different stages of the viral replication cycle; being multi-functional, they are good inhibitory targets for anti-CMV compounds. As a new perspective for sustainable crop improvement, we investigated the natural plant-based antimicrobial phytoalexins for their anti-CMV potential. Here, we modeled and predicted the functional domains of RAP-1 and RAP-2, docked with a ligand library comprising 128 phytoalexins reported with broad-spectrum activity, determined their binding energies (BEs), molecular interactions, and inhibition constant (Ki), and compared with the reference plant antiviral compounds ribavirin, ningnanmycin, and benzothiadiazole (BTH). Further, the change in Gibb's free energy of binding (ΔG) and the per residue contribution of the selected top-scored ligand molecules was assessed by the prime MM-GBSA approach. Our results revealed RAP-1 as a discontinuous two-domain and RAP-2 as a multi-domain protein. The compounds glyceollidin (9.8 kcal/mol) and moracin D (7.8 kcal/mol) topped the list for RAP-1 and RAP-2 protein targets respectively and also, the lead molecules had energetically more favorable and comparative ΔG values than the top-scored plant antiviral agent ningnanmycin. The evaluation of in vitro toxicity and agrochemical-like properties showed the least toxicity of these anti-CMV compounds. Taken together, our results provide new insights in understanding the inhibitory effects of phytoalexins towards the RAP proteins and could be employed as new promising anti-CMV candidate compounds for their application in agriculture as biopesticides to combat the CMV disease incidence.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Roshni Mohan Kumar
- Department of Plant Biotechnology, GKVK, University of Agricultural Sciences, Bengaluru, India
| | - Ramachandra Anantapur
- Department of Plant Biotechnology, GKVK, University of Agricultural Sciences, Bengaluru, India
| | - Anitha Peter
- Department of Plant Biotechnology, GKVK, University of Agricultural Sciences, Bengaluru, India
| | - Chaitra H V
- Department of Plant Biotechnology, GKVK, University of Agricultural Sciences, Bengaluru, India
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Duarte PL, Andrade FRN, Sousa ARDO, Andrade AL, de Vasconcelos MA, Teixeira EH, Nagano CS, Sampaio AH, Carneiro RF. A fibrinogen-related Lectin from Echinometra lucunter represents a new FReP family in Echinodermata phylum. FISH & SHELLFISH IMMUNOLOGY 2022; 131:150-159. [PMID: 36216229 DOI: 10.1016/j.fsi.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Fibrinogen-related proteins (FREPs) have been identified in several animals. They are involved in the body's defense, acting as mediators of phagocytosis. Ficolins and intelectins are some of the most studied Fibrinogen-related Domain (FReD)-containing lectins. In this work, we have isolated a singular FReD-containing lectin, which cannot be classified as ficolin or intelectin. ELL (Echinometra lucunter lectin) was isolated from coelomic plasma by affinity chromatography on xanthan gum. Primary structure was determined by tandem mass spectrometry. Moreover, antimicrobial activity of ELL was evaluated against planktonic cells and biofilm of Escherichia coli, Staphylococcus aureus and S. epidermidis. ELL showed hemagglutinating activity in Ca2+ presence, which was inhibited by glycoprotein mucin and thyroglobulin. Complete amino acid sequence consisted of 229 residues, including a FReD in the N-terminal. Searches for similarity found that ELL was very close to putative proteins from Strongylocentrotus purpuratus. ELL showed moderate similarity with uncharacterized sea stars proteins and protochordate intelectins. ELL was able to inhibit the planktonic growth of the Gram-positive bacteria and significantly reduce the biofilm formation of all bacteria tested. In conclusion, we identified a new type of FReP-containing lectin with some structural and functional conservation towards intelectins.
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Affiliation(s)
- Philippe Lima Duarte
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Francisco Regivânio Nascimento Andrade
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Andressa Rocha de Oliveira Sousa
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Alexandre Lopes Andrade
- Laboratório Integrado de Biomoléculas - LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, 60430-160, Fortaleza, Ceará, Brazil
| | - Mayron Alves de Vasconcelos
- Laboratório Integrado de Biomoléculas - LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, 60430-160, Fortaleza, Ceará, Brazil; Laboratorio de Quimica de Proteínas e Produtos Naturais - LABQUIMP, Universidade do Estado de Minas Gerais, Unidade Divinópolis, 35501-170, Divinópolis, Minas Gerais, Brazil
| | - Edson Holanda Teixeira
- Laboratório Integrado de Biomoléculas - LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, 60430-160, Fortaleza, Ceará, Brazil
| | - Celso Shiniti Nagano
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Alexandre Holanda Sampaio
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil
| | - Rômulo Farias Carneiro
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, 60440-970, Fortaleza, Ceará, Brazil.
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Akter S, Shahab M, Sarkar MMH, Hayat C, Banu TA, Goswami B, Jahan I, Osman E, Uzzaman MS, Habib MA, Shaikh AA, Khan MS. Immunoinformatics approach to epitope-based vaccine design against the SARS-CoV-2 in Bangladeshi patients. J Genet Eng Biotechnol 2022; 20:136. [PMID: 36125645 PMCID: PMC9487853 DOI: 10.1186/s43141-022-00410-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/25/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic which has brought a great challenge to public health. After the first emergence of novel coronavirus SARS-CoV-2 in the city of Wuhan, China, in December 2019. As of March 2020, SARS-CoV-2 was first reported in Bangladesh and since then the country has experienced a steady rise in infections, resulting in 13,355,191 cases and 29,024 deaths as of 27 February 2022. Bioinformatics techniques are used to predict B cell and T cell epitopes from the new SARS-CoV-2 spike glycoprotein in order to build a unique multiple epitope vaccine. The immunogenicity, antigenicity scores, and toxicity of these epitopes were evaluated and chosen based on their capacity to elicit an immune response. RESULT The best multi-epitope of the possible immunogenic property was created by combining epitopes. EAAAK, AAY, and GPGPG linkers were used to connect the epitopes. In several computer-based immune response analyses, this vaccine design was found to be efficient, as well as having high population coverage. CONCLUSION This research is entirely reliant on the development of epitope-based vaccines, and these in silico findings would represent a major step forward in the development of a vaccine that might eradicate SARS-CoV-2 in Bangladeshi patients.
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Affiliation(s)
- Shahina Akter
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | | | - Chandni Hayat
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul Wali Khan University, Mardan, Pakistan
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Eshrar Osman
- SciTech Consulting and Solutions, Dhaka, Bangladesh
| | | | - Md Ahashan Habib
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Aftab Ali Shaikh
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Salim Khan
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka, Bangladesh.
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Chen HD, Yu CC, Yang IH, Hung CC, Kuo MC, Tarng DC, Chang JM, Hwang DY. UMOD Mutations in Chronic Kidney Disease in Taiwan. Biomedicines 2022; 10:biomedicines10092265. [PMID: 36140366 PMCID: PMC9496136 DOI: 10.3390/biomedicines10092265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/21/2022] Open
Abstract
UMOD is the first identified and the most commonly mutated gene that causes autosomal dominant tubulointerstitial kidney disease (ADTKD). Recent studies have shown that ADTKD-UMOD is a relatively common cause of chronic kidney disease (CKD). However, the status of ADTKD-UMOD in Taiwan remains unknown. In this study, we identified three heterozygous UMOD missense variants, c.121T > C (p.Cys41Arg), c.179G > A (p.Gly60Asp), and c.817G > T (p.Val273Phe), in a total of 221 selected CKD families (1.36%). Two of these missense variants, p.Cys41Arg and p.Gly60Asp, have not been reported previously. In vitro studies showed that both uromodulin variants have defects in cell membrane trafficking and excretion to the culture medium. The structure model predicted altered disulfide bond formation in both variants, but only p.Gly60Asp was predicted to cause protein destabilization. Our findings extend the mutation spectrum and indicate that the ADTKD-UMOD contributed to a small but significant cause of CKD in the Taiwanese population.
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Affiliation(s)
- Huan-Da Chen
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
| | - Chih-Chuan Yu
- National Institute of Cancer Research, National Health Research Institutes, Tainan 70456, Taiwan
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
| | - I-Hsiao Yang
- Department of Medical Imaging, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
| | - Chi-Chih Hung
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
| | - Mei-Chuan Kuo
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
| | - Der-Cherng Tarng
- Institutes of Physiology and Clinical Medicine, Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, National Yang-Ming Chiao-Tung University, Taipei 112201, Taiwan
| | - Jer-Ming Chang
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
- Correspondence: (J.-M.C.); (D.-Y.H.); Tel.: +886-7-3121101 (ext. 7901) (J.-M.C.); +886-6-7000123 (ext. 65163) (D.-Y.H.)
| | - Daw-Yang Hwang
- National Institute of Cancer Research, National Health Research Institutes, Tainan 70456, Taiwan
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
- Center for Biomarkers and Biotech Drugs, Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
- Correspondence: (J.-M.C.); (D.-Y.H.); Tel.: +886-7-3121101 (ext. 7901) (J.-M.C.); +886-6-7000123 (ext. 65163) (D.-Y.H.)
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Ting TY, Baharin A, Ramzi AB, Ng CL, Goh HH. Neprosin belongs to a new family of glutamic peptidase based on in silico evidence. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:23-35. [PMID: 35537348 DOI: 10.1016/j.plaphy.2022.04.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/29/2022] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
Neprosin was first discovered in the insectivorous tropical pitcher plants of Nepenthes species as a novel protease with prolyl endopeptidase (PEP) activity. Neprosin has two uncharacterized domains of neprosin activation peptide and neprosin. A previous study has shown neprosin activity in hydrolyzing proline-rich gliadin, a gluten component that triggers celiac disease. In this study, we performed in silico structure-function analysis to investigate the catalytic mechanism of neprosin. Neprosin sequences lack the catalytic triad and motifs of PEP family S9. Protein structures of neprosins from Nepenthes × ventrata (NvNpr) and N. rafflesiana (NrNpr1) were generated by ab initio methods and comparatively assessed to obtain high-quality models. Structural alignment of models to experimental structures in the Protein Data Bank (PDB) found a high structural similarity to glutamic peptidases. Further investigations reveal other resemblances to the glutamic peptidases with low optimum pH that activates the enzyme via autoproteolysis for maturation. Two highly conserved glutamic acid residues, which are stable according to the molecular dynamics simulation, can be found at the active site of the substrate cleft. Protein docking demonstrated that mature neprosins bind well with potent antigen αI-gliadin at the putative active site. Taken together, neprosins represent a new glutamic peptidase family, with a putative catalytic dyad of two glutamic acids. This study illustrates a hypothetical enzymatic mechanism of the neprosin family and demonstrates the useful application of an accurate ab initio protein structure prediction in the structure-function study of a novel protein family.
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Affiliation(s)
- Tiew-Yik Ting
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor, Malaysia
| | - Anis Baharin
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor, Malaysia
| | - Ahmad Bazli Ramzi
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor, Malaysia
| | - Chyan-Leong Ng
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor, Malaysia.
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Anisimova OK, Shchennikova AV, Kochieva EZ, Filyushin MA. Identification of Monodehydroascorbate Reductase (MDHAR) Genes in Garlic (Allium sativum L.) and Their Role in the Response to Fusarium proliferatum Infection. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422070031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Expression of the K74 Killer Toxin from Saccharomyces paradoxus Is Modulated by the Toxin-Encoding M74 Double-Stranded RNA 5' Untranslated Terminal Region. Appl Environ Microbiol 2022; 88:e0203021. [PMID: 35389250 DOI: 10.1128/aem.02030-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yeast killer toxins are widely distributed in nature, conferring a competitive advantage to the producer yeasts over nonkiller ones when nutrients are scarce. Most of these toxins are encoded on double-stranded RNAs (dsRNAs) generically called M. L-A members of the viral family Totiviridae act as helper viruses to maintain M, providing the virion proteins that separately encapsidate and replicate L-A and M genomes. M genomes are organized in three regions, a 5' region coding the preprotoxin, followed by an internal poly(A) stretch and a 3' noncoding region. In this work, we report the characterization of K74 toxin encoded on M74 dsRNA from Saccharomyces paradoxus Q74.4. In M74, there is a 5' upstream sequence of 141 nucleotides (nt), which contains regulatory signals for internal translation of the preprotoxin open reading frame (ORF) at the second AUG codon. The first AUG close to the 5' end is not functional. For K74 analysis, M74 viruses were first introduced into laboratory strains of Saccharomyces cerevisiae. We show here that the mature toxin is an α/β heterodimer linked by disulfide bonds. Though the toxin (or preprotoxin) confers immunity to the carrier, cells with increased K74 loads have a sick phenotype that may lead to cell death. Thus, a fine-tuning of K74 production by the upstream regulatory sequence is essential for the host cell to benefit from the toxin it produces and, at the same time, to safely avoid damage by an excess of toxin. IMPORTANCE Killer yeasts produce toxins to which they are immune by mechanisms not well understood. This self-immunity, however, is compromised in certain strains, which secrete an excess of toxin, leading to sick cells or suicidal phenotypes. Thus, a fine-tuning of toxin production has to be achieved to reach a balance between the beneficial effect of toxin production and the stress imposed on the host metabolism. K74 toxin from S. paradoxus is very active against Saccharomyces uvarum, among other yeasts, but an excess of toxin production is deleterious for the host. Here, we report that the presence of a 5' 141-nt upstream sequence downregulates K74 toxin precursor translation, decreasing toxin levels 3- to 5-fold. Thus, this is a special case of translation regulation performed by sequences on the M74 genome itself, which have been presumably incorporated into the viral RNA during evolution for that purpose.
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Box ICH, Matthews BJ, Marshall KE. Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates. J Exp Biol 2022; 225:274373. [PMID: 35258616 DOI: 10.1242/jeb.243409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/20/2021] [Indexed: 12/21/2022]
Abstract
Ice-binding proteins (IBPs) have evolved independently in multiple taxonomic groups to improve their survival at sub-zero temperatures. Intertidal invertebrates in temperate and polar regions frequently encounter sub-zero temperatures, yet there is little information on IBPs in these organisms. We hypothesized that there are far more IBPs than are currently known and that the occurrence of freezing in the intertidal zone selects for these proteins. We compiled a list of genome-sequenced invertebrates across multiple habitats and a list of known IBP sequences and used BLAST to identify a wide array of putative IBPs in those invertebrates. We found that the probability of an invertebrate species having an IBP was significantly greater in intertidal species than in those primarily found in open ocean or freshwater habitats. These intertidal IBPs had high sequence similarity to fish and tick antifreeze glycoproteins and fish type II antifreeze proteins. Previously established classifiers based on machine learning techniques further predicted ice-binding activity in the majority of our newly identified putative IBPs. We investigated the potential evolutionary origin of one putative IBP from the hard-shelled mussel Mytilus coruscus and suggest that it arose through gene duplication and neofunctionalization. We show that IBPs likely readily evolve in response to freezing risk and that there is an array of uncharacterized IBPs, and highlight the need for broader laboratory-based surveys of the diversity of ice-binding activity across diverse taxonomic and ecological groups.
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Affiliation(s)
- Isaiah C H Box
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
| | - Benjamin J Matthews
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
| | - Katie E Marshall
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, CanadaV6T 1Z4
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19
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Echinococcus granulosus cyclophilin: Immunoinformatics analysis to provide insights into the biochemical properties and immunogenic epitopes. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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20
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Dutta SK, Sengupta S, Tripathi A. In silico and in vitro evaluation of silibinin: a promising anti-Chikungunya agent. In Vitro Cell Dev Biol Anim 2022; 58:255-267. [PMID: 35381943 DOI: 10.1007/s11626-022-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Chikungunya virus (CHIKV) infection and subsequent high patient morbidity is a global threat. The present study aimed to identify the potent antiviral agent against Chikungunya virus, with minimum in vitro cytotoxicity. CHIKV nsP4 3D structure was determined using the I-TASSER server followed by its refinement and pocket determination. Furthermore, high-throughput molecular docking was employed to identify candidate CHIKV nsP4 inhibitors in a library containing 214 compounds. The top ranked compound was evaluated further with various assays, including cytotoxicity, antiviral activity, time of drug addition, viral entry attachment, and microneutralization assays. High-throughput computational screening indicated silibinin to have the best interaction with CHIKV nsP4 protein, immature and mature glycoproteins with highest negative free binding energy, - 5.24 to - 5.86 kcal/mol, and the lowest inhibitory constant, 50.47 to 143.2 µM. Further in vitro analysis demonstrated silibinin could exhibit statistically significant (p < 0.05) dose-dependent anti-CHIKV activity within 12.5-100-µM concentrations with CC50 as 50.90 µM. In total, 50 µM silibinin interfered with both CHIKV attachment (75%) and entry (82%) to Vero cells. Time of addition assay revealed silibinin interfered with late phase of the CHIKV replication cycle. Microneutralization assay revealed that silibinin could inhibit clearing of 50% Vero cell monolayer caused by CHIKV-induced CPE at a minimum dose of 25 µM. These data indicated silibinin to be a promising candidate drug against CHIKV infection.
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Affiliation(s)
- Sudip Kumar Dutta
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, C.R. Avenue, Kolkata, 700073, West Bengal, India
| | - Siddhartha Sengupta
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, C.R. Avenue, Kolkata, 700073, West Bengal, India
| | - Anusri Tripathi
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, C.R. Avenue, Kolkata, 700073, West Bengal, India.
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Bui TKN, Mawatari K, Emoto T, Fukushima S, Shimohata T, Uebanso T, Akutagawa M, Kinouchi Y, Takahashi A. UV-LED irradiation reduces the infectivity of herpes simplex virus type 1 by targeting different viral components depending on the peak wavelength. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 228:112410. [PMID: 35193038 DOI: 10.1016/j.jphotobiol.2022.112410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/11/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Herpes simplex virus type 1 (HSV-1) is an enveloped virus that mainly infects humans. Given its high global prevalence, disinfection is critical for reducing the risk of infection. Ultraviolet-light-emitting diodes (UV-LEDs) are eco-friendly irradiating modules with different peak wavelengths, but the molecules degraded by UV-LED irradiation have not been clarified. To identify the target viral molecules of UV-LEDs, we exposed HSV-1 suspensions to UV-LED irradiation at wavelengths of 260-, 280-, 310-, and 365-nm and measured viral DNA, protein, and lipid damage and infectivity in host cells. All UV-LEDs substantially reduced by inhibiting host cell transcription, but 260- and 280-nm UV-LEDs had significantly stronger virucidal efficiency than 310- and 365-nm UV-LEDs. Meanwhile, 260- and 280-nm UV-LEDs induced the formation of viral DNA photoproducts and the degradation of viral proteins and some phosphoglycerolipid species. Unlike 260- and 280-nm UV-LEDs, 310- and 365-nm UV-LEDs decreased the viral protein levels, but they did not drastically change the levels of viral DNA photoproducts and lipophilic metabolites. These results suggest that UV-LEDs reduce the infectivity of HSV-1 by targeting different viral molecules based on the peak wavelength. These findings could facilitate the optimization of UV-LED irradiation for viral inactivation.
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Affiliation(s)
- Thi Kim Ngan Bui
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Kuramoto-cho 3-18-15, Tokushima City, Tokushima 770-8503, Japan
| | - Kazuaki Mawatari
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Kuramoto-cho 3-18-15, Tokushima City, Tokushima 770-8503, Japan.
| | - Takahiro Emoto
- Graduate School of Science and Technology, Tokushima University, Minamijyousanjima-cho 2-1, Tokushima City, Tokushima 770-8506, Japan
| | - Shiho Fukushima
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Kuramoto-cho 3-18-15, Tokushima City, Tokushima 770-8503, Japan
| | - Takaaki Shimohata
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Kuramoto-cho 3-18-15, Tokushima City, Tokushima 770-8503, Japan; Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama, Fukui 917-0003, Japan
| | - Takashi Uebanso
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Kuramoto-cho 3-18-15, Tokushima City, Tokushima 770-8503, Japan
| | - Masatake Akutagawa
- Graduate School of Science and Technology, Tokushima University, Minamijyousanjima-cho 2-1, Tokushima City, Tokushima 770-8506, Japan
| | - Yohsuke Kinouchi
- Graduate School of Science and Technology, Tokushima University, Minamijyousanjima-cho 2-1, Tokushima City, Tokushima 770-8506, Japan
| | - Akira Takahashi
- Department of Preventive Environment and Nutrition, Institute of Biomedical Sciences, Tokushima University Graduate School, Kuramoto-cho 3-18-15, Tokushima City, Tokushima 770-8503, Japan
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22
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Verticillium dahliae CFEM proteins manipulate host immunity and differentially contribute to virulence. BMC Biol 2022; 20:55. [PMID: 35197059 PMCID: PMC8867779 DOI: 10.1186/s12915-022-01254-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/15/2022] [Indexed: 02/06/2023] Open
Abstract
Background Verticillium dahliae is a fungal pathogen that causes a vascular wilt on many economically important crops. Common fungal extracellular membrane (CFEM) domain proteins including secreted types have been implicated in virulence, but their roles in this pathogen are still unknown. Results Nine secreted small cysteine-rich proteins (VdSCPs) with CFEM domains were identified by bioinformatic analyses and their differential suppression of host immune responses were evaluated. Two of these proteins, VdSCP76 and VdSCP77, localized to the plant plasma membrane owing to their signal peptides and mediated broad-spectrum suppression of all immune responses induced by typical effectors. Deletion of either VdSCP76 or VdSCP77 significantly reduced the virulence of V. dahliae on cotton. Furthermore, VdSCP76 and VdSCP77 suppressed host immunity through the potential iron binding site conserved in CFEM family members, characterized by an aspartic acid residue in seven VdSCPs (Asp-type) in contrast with an asparagine residue (Asn-type) in VdSCP76 and VdSCP77. V. dahliae isolates carrying the Asn-type CFEM members were more virulent on cotton than those carrying the Asp-type. Conclusions In the iron-insufficient xylem, V. dahliae is likely to employ the Asp-type CFEM members to chelate iron, and Asn-type CFEM members to suppress immunity, for successful colonization and propagation in host plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01254-x.
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Wang L, Xue C, Owens G, Chen Z. Artificial intelligence modeling and molecular docking to analyze the laccase delignification process of rice straw by Comamonas testosteroni FJ17. BIORESOURCE TECHNOLOGY 2022; 345:126565. [PMID: 34921918 DOI: 10.1016/j.biortech.2021.126565] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
The laccase enzymatic characteristics and delignification processes of rice straw by Comamonas testosteroni FJ17 were investigated. Artificial intelligence modeling and molecular docking revealed the specific functional properties involved in the interaction between laccase and lignin compounds with a maximum laccase activity of 2016.7 U L-1 at 24 h. Scanning electron microscopy and X-ray diffractometer analysis confirmed that laccase caused fractures and holes on the surface of rice straw, where crystallinity decrease from 45.3 to 39.9%, and lignin content decreased from 19.0 to 10.3%. Gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry analysis showed that the main delignification process for laccase was via β-o-4 and α-aryl ether cleavage, which generated several small molecular products. The laccase gene was cloned and bioinformatics analysis presented 317 amino acids with a predicted molecular weight of 33.13 kDa. Finally, laccase protein was found to have low binding energies with all lignin compounds tested, and lignin compounds were oxidized by laccase through hydrogen-bonding interactions with the amino acid residues.
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Affiliation(s)
- Lijie Wang
- School of Environmental Science and Engineering, Fujian Normal University, Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, Fujian Province, PR China
| | - Chao Xue
- School of Environmental Science and Engineering, Fujian Normal University, Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, Fujian Province, PR China.
| | - Gary Owens
- Environmental Contaminants Group, Future Industries Institute, University of South Australian, Mawson Lakes, SA 5095, Australia
| | - Zuliang Chen
- School of Environmental Science and Engineering, Fujian Normal University, Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, Fujian Province, PR China
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24
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Richards JK, Kariyawasam GK, Seneviratne S, Wyatt NA, Xu SS, Liu Z, Faris JD, Friesen TL. A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat. THE NEW PHYTOLOGIST 2022; 233:427-442. [PMID: 34227112 PMCID: PMC9292537 DOI: 10.1111/nph.17601] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/27/2021] [Indexed: 05/21/2023]
Abstract
Parastagonospora nodorum is a fungal pathogen of wheat. As a necrotrophic specialist, it deploys effector proteins that target dominant host susceptibility genes to elicit programmed cell death (PCD). Here we identify and functionally validate the effector targeting the host susceptibility genes Snn2, Snn6 and Snn7. We utilized whole-genome sequencing, association mapping, gene-disrupted mutants, gain-of-function transformants, virulence assays, bioinformatics and quantitative PCR to characterize these interactions. A single proteinaceous effector, SnTox267, targeted Snn2, Snn6 and Snn7 to trigger PCD. Snn2 and Snn6 functioned cooperatively to trigger PCD in a light-dependent pathway, whereas Snn7-mediated PCD functioned in a light-independent pathway. Isolates harboring 20 SnTox267 protein isoforms quantitatively varied in virulence. The diversity and distribution of isoforms varied between populations, indicating adaptation to local selection pressures. SnTox267 deletion resulted in the upregulation of effector genes SnToxA, SnTox1 and SnTox3. We validated a novel effector operating in an inverse-gene-for-gene manner to target three genetically distinct host susceptibility genes and elicit PCD. The discovery of the complementary gene action of Snn2 and Snn6 indicates their potential function in a guard or decoy model. Additionally, differences in light dependency in the elicited pathways and upregulation of unlinked effectors sheds new light onto a complex fungal necrotroph-host interaction.
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Affiliation(s)
- Jonathan K. Richards
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLA70803USA
| | | | | | - Nathan A. Wyatt
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Steven S. Xu
- Department of Plant SciencesNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Zhaohui Liu
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
| | - Justin D. Faris
- Department of Plant SciencesNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Timothy L. Friesen
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
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25
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Serine carboxypeptidases from the carnivorous plant Nepenthes mirabilis: Partial characterization and heterologous expression. Int J Biol Macromol 2021; 198:77-86. [PMID: 34963626 DOI: 10.1016/j.ijbiomac.2021.12.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022]
Abstract
This study aimed to partially characterize the three main serine carboxypeptidases (SCP3, SCP20, and SCP47) from Nepenthes mirabilis. Furthermore, one peptidase (SCP3) was chosen for further heterologous expression in Escherichia coli Shuffle®T7. SCP3 also was characterized in terms of its allergenic potential using bioinformatics tools. SCP3, SCP20, and SCP47 showed very similar 3D structures and mechanistic features to other plant serine peptidases belonging to clan SC and family S10. Although SCP3 was obtained in its soluble form, using 1% ethanol during induction with 0.5 mM IPTG at 16 °C for 18 h, it did not show proteolytic activity by zymography or in vitro analysis. SCP3 presented a few allergenic peptides and several cleavage sites for digestive enzymes. This work describes additional features of these enzymes, opening new perspectives for further studies for characterization and analysis of heterologous expression, as well as their potential biotechnological applications.
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26
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Radin I, Kost L, Gey U, Steinebrunner I, Rödel G. The mitochondrial copper chaperone COX11 has an additional role in cellular redox homeostasis. PLoS One 2021; 16:e0261465. [PMID: 34919594 PMCID: PMC8682889 DOI: 10.1371/journal.pone.0261465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 12/02/2021] [Indexed: 01/15/2023] Open
Abstract
Mitochondria are sites of cellular respiration, which is accompanied by the generation of dangerous reactive oxygen species (ROS). Cells have multiple mechanisms to mitigate the dangers of ROS. Here we investigate the involvement of the COX complex assembly chaperone COX11 (cytochrome c oxidase 11) in cellular redox homeostasis, using homologs from the flowering plant Arabidopsis thaliana (AtCOX11) and yeast Saccharomyces cerevisiae (ScCOX11). We found that AtCOX11 is upregulated in Arabidopsis seedlings in response to various oxidative stresses, suggesting a defensive role. In line with this, the overexpression of either AtCOX11 or ScCOX11 reduced ROS levels in yeast cells exposed to the oxidative stressor paraquat. Under normal growth conditions, both Arabidopsis and yeast COX11 overexpressing cells had the same ROS levels as the corresponding WT. In contrast, the COX11 knock-down and knock-out in Arabidopsis and yeast, respectively, significantly reduced ROS levels. In yeast cells, the ScCOX11 appears to be functionally redundant with superoxide dismutase 1 (ScSOD1), a superoxide detoxifying enzyme. The ΔSccox11ΔScsod1 mutants had dramatically reduced growth on paraquat, compared with the WT or single mutants. This growth retardation does not seem to be linked to the status of the COX complex and cellular respiration. Overexpression of putatively soluble COX11 variants substantially improved the resistance of yeast cells to the ROS inducer menadione. This shows that COX11 proteins can provide antioxidative protection likely independently from their COX assembly function. The conserved Cys219 (in AtCOX11) and Cys208 (in ScCOX11) are important for this function. Altogether, these results suggest that COX11 homologs, in addition to participating in COX complex assembly, have a distinct and evolutionary conserved role in protecting cells during heightened oxidative stress.
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Affiliation(s)
- Ivan Radin
- Institute for Genetics, Technische Universität Dresden, Dresden, Germany
- * E-mail: (IR); (UG); (GR)
| | - Luise Kost
- Institute for Genetics, Technische Universität Dresden, Dresden, Germany
| | - Uta Gey
- Institute for Genetics, Technische Universität Dresden, Dresden, Germany
- * E-mail: (IR); (UG); (GR)
| | | | - Gerhard Rödel
- Institute for Genetics, Technische Universität Dresden, Dresden, Germany
- * E-mail: (IR); (UG); (GR)
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27
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Hasanshahi Z, Hashempour A, Ghasabi F, Moayedi J, Musavi Z, Dehghani B, Sharafi H, Joulaei H. First report on molecular docking analysis and drug resistance substitutions to approved HCV NS5A and NS5B inhibitors amongst Iranian patients. BMC Gastroenterol 2021; 21:443. [PMID: 34819046 PMCID: PMC8612383 DOI: 10.1186/s12876-021-01988-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 10/22/2021] [Indexed: 12/13/2022] Open
Abstract
Background NS5A and NS5B proteins of hepatitis C virus (HCV) are the main targets of compounds that directly inhibit HCV infections. However, the emergence of resistance-associated substitutions (RASs) may cause substantial reductions in susceptibility to inhibitors. Methods Viral load and genotyping were determined in eighty-seven naïve HCV-infected patients, and the amplified NS5A and NS5B regions were sequenced by Sanger sequencing. In addition, physicochemical properties, structural features, immune epitopes, and inhibitors-protein interactions of sequences were analyzed using several bioinformatics tools. Results Several amino acid residue changes were found in NS5A and NS5B proteins; however, we did not find any mutations related to resistance to the treatment in NS5B. Different phosphorylation and few glycosylation sites were assessed. Disulfide bonds were identified in both proteins that had a significant effect on the function and structure of HCV proteins. Applying reliable software to predict B-cell epitopes, 3 and 5 regions were found for NS5A and NS5B, respectively, representing a considerable potential to induce the humoral immune system. Docking analysis determined amino acids involved in the interaction of inhibitors and mentioned proteins may not decrease the drug efficiency. Conclusions Strong interactions between inhibitors, NS5A and NS5B proteins and the lack of efficient drug resistance mutations in the analyzed sequences may confirm the remarkable ability of NS5A and NS5B inhibitors to control HCV infection amongst Iranian patients. The results of bioinformatics analysis could unveil all features of both proteins, which can be beneficial for further investigations on HCV drug resistance and designing novel vaccines. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-021-01988-y.
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Affiliation(s)
- Zahra Hasanshahi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ava Hashempour
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Farzane Ghasabi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Javad Moayedi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Musavi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Behzad Dehghani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Heidar Sharafi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Middle East Liver Diseases (MELD) Center, Tehran, Iran
| | - Hassan Joulaei
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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28
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Belkahia H, Ben Abdallah M, Andolsi R, Selmi R, Zamiti S, Kratou M, Mhadhbi M, Darghouth MA, Messadi L, Ben Said M. Screening and Analysis of Anaplasma marginale Tunisian Isolates Reveal the Diversity of lipA Phylogeographic Marker and the Conservation of OmpA Protein Vaccine Candidate. Front Vet Sci 2021; 8:731200. [PMID: 34746278 PMCID: PMC8566978 DOI: 10.3389/fvets.2021.731200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/16/2021] [Indexed: 01/18/2023] Open
Abstract
Bovine anaplasmosis caused by Anaplasma marginale is a disease responsible for serious animal health problems and great economic losses all over the world. Thereby, the identification of A. marginale isolates from various bioclimatic areas in each country, the phylogeographic analysis of these isolates based on the most informative markers, and the evaluation of the most promising candidate antigens are crucial steps in developing effective vaccines against a wide range of A. marginale strains. In order to contribute to this challenge, a total of 791 bovine samples from various bioclimatic areas of Tunisia were tested for the occurrence of A. marginale DNA through msp4 gene fragment amplification. Phylogeographic analysis was performed by using lipA and sucB gene analyses, and the genetic relationship with previously characterized A. marginale isolates and strains was analyzed by applying similarity comparison and phylogenetic analysis. To evaluate the conservation of OmpA protein vaccine candidate, almost complete ompA nucleotide sequences were also obtained from Tunisian isolates, and various bioinformatics software were used in order to analyze the physicochemical properties and the secondary and tertiary structures of their deduced proteins and to predict their immunodominant epitopes of B and T cells. A. marginale DNA was detected in 19 bovine samples (2.4%). Risk factor analysis shows that cattle derived from subhumid bioclimatic area were more infected than those that originated from other areas. The analysis of lipA phylogeographic marker indicated a higher diversity of Tunisian A. marginale isolates compared with other available worldwide isolates and strains. Molecular, phylogenetic, and immuno-informatics analyses of the vaccine candidate OmpA protein demonstrated that this antigen and its predicted immunodominant epitopes of B and T cells appear to be highly conserved between Tunisian isolates and compared with isolates from other countries, suggesting that the minimal intraspecific modifications will not affect the potential cross-protective capacity of humoral and cell-mediated immune responses against multiple A. marginale worldwide strains.
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Affiliation(s)
- Hanène Belkahia
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Meriem Ben Abdallah
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Rihab Andolsi
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Rachid Selmi
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia.,Ministère de la Défense Nationale, Direction Générale de la Santé Militaire, Service Vétérinaire, Tunis, Tunisia
| | - Sayed Zamiti
- Service de Parasitologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Myriam Kratou
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Moez Mhadhbi
- Service de Parasitologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Mohamed Aziz Darghouth
- Service de Parasitologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Lilia Messadi
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia
| | - Mourad Ben Said
- Service de Microbiologie et Immunologie, Ecole Nationale de Médecine Vétérinaire, University of Manouba, Sidi Thabet, Tunisia.,Département des Sciences Fondamentales, Institut Supérieur de Biotechnologie de Sidi Thabet, University of Manouba, Sidi Thabet, Tunisia
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A Monoallelic Variant in REST Is Associated with Non-Syndromic Autosomal Dominant Hearing Impairment in a South African Family. Genes (Basel) 2021; 12:genes12111765. [PMID: 34828371 PMCID: PMC8618167 DOI: 10.3390/genes12111765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 01/03/2023] Open
Abstract
Hearing impairment (HI) is a sensory disorder with a prevalence of 0.0055 live births in South Africa. DNA samples from a South African family presenting with progressive, autosomal dominant non-syndromic HI were subjected to whole-exome sequencing, and a novel monoallelic variant in REST [c.1244GC; p.(C415S)], was identified as the putative causative variant. The co-segregation of the variant was confirmed with Sanger Sequencing. The variant is absent from databases, 103 healthy South African controls, and 52 South African probands with isolated HI. In silico analysis indicates that the p.C415S variant in REST substitutes a conserved cysteine and results in changes to the surrounding secondary structure and the disulphide bonds, culminating in alteration of the tertiary structure of REST. Localization studies using ectopically expressed GFP-tagged Wild type (WT) and mutant REST in HEK-293 cells show that WT REST localizes exclusively to the nucleus; however, the mutant protein localizes throughout the cell. Additionally, mutant REST has an impaired ability to repress its known target AF1q. The data demonstrates that the identified mutation compromises the function of REST and support its implication in HI. This study is the second report, worldwide, to implicate REST in HI and suggests that it should be included in diagnostic HI panels.
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30
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Amador VC, dos Santos-Silva CA, Vilela LMB, Oliveira-Lima M, de Santana Rêgo M, Roldan-Filho RS, de Oliveira-Silva RL, Lemos AB, de Oliveira WD, Ferreira-Neto JRC, Crovella S, Benko-Iseppon AM. Lipid Transfer Proteins (LTPs)-Structure, Diversity and Roles beyond Antimicrobial Activity. Antibiotics (Basel) 2021; 10:1281. [PMID: 34827219 PMCID: PMC8615156 DOI: 10.3390/antibiotics10111281] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 01/21/2023] Open
Abstract
Lipid transfer proteins (LTPs) are among the most promising plant-exclusive antimicrobial peptides (AMPs). They figure among the most challenging AMPs from the point of view of their structural diversity, functions and biotechnological applications. This review presents a current picture of the LTP research, addressing not only their structural, evolutionary and further predicted functional aspects. Traditionally, LTPs have been identified by their direct isolation by biochemical techniques, whereas omics data and bioinformatics deserve special attention for their potential to bring new insights. In this context, new possible functions have been identified revealing that LTPs are actually multipurpose, with many additional predicted roles. Despite some challenges due to the toxicity and allergenicity of LTPs, a systematic review and search in patent databases, indicate promising perspectives for the biotechnological use of LTPs in human health and also plant defense.
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Affiliation(s)
- Vinícius Costa Amador
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Carlos André dos Santos-Silva
- Department of Advanced Diagnostics, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, 34100 Trieste, Italy;
| | - Lívia Maria Batista Vilela
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Marx Oliveira-Lima
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Mireli de Santana Rêgo
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Ricardo Salas Roldan-Filho
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Roberta Lane de Oliveira-Silva
- General Microbiology Laboratory, Agricultural Science Campus, Universidade Federal do Vale do São Francisco, Petrolina 56300-990, Brazil;
| | - Ayug Bezerra Lemos
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Wilson Dias de Oliveira
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - José Ribamar Costa Ferreira-Neto
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Sérgio Crovella
- Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, Doha 1883, Qatar;
| | - Ana Maria Benko-Iseppon
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
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McDermott H, Robinson HK, Caswell R, Gowda H, Offiah A, Naik S. Robinow syndrome in an extremely preterm infant: Novel homozygous ROR2 variant detected by rapid exome sequencing. Am J Med Genet A 2021; 188:298-303. [PMID: 34558814 DOI: 10.1002/ajmg.a.62499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/13/2021] [Accepted: 08/21/2021] [Indexed: 11/08/2022]
Abstract
An extremely preterm infant presented with clinical and radiological features of Robinow syndrome including butterfly vertebrae, posterior rib fusion, brachydactyly, nail hypoplasia, and retromicrognathia resulting in difficult endotracheal intubation in the intensive care setting. Rapid trio exome sequencing detected a novel homozygous likely pathogenic missense variant in the ROR2 gene, NM_004560.3:c.950A>G, p.(Tyr317Cys), for which both parents were heterozygous carriers. In-silico protein modeling predicted a deleterious effect on the function of the protein. We report an extreme premature infant with novel homozygous likely pathogenic variant in the ROR2 gene consistent with autosomal recessive Robinow syndrome. This case expands the phenotypic and genotypic spectrum of this disorder and highlights the benefit of performing rapid exome sequencing early during evaluation to aid in patient management and providing accurate genetic counseling to families.
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Affiliation(s)
- Helen McDermott
- Clinical Genetics Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Hannah K Robinson
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Richard Caswell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Harsha Gowda
- Birmingham Heartlands Neonatal Unit, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Amaka Offiah
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Swati Naik
- Clinical Genetics Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
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Kim JE, Son SH, Oh SS, Kim SC, Lee JY. Pairing of orthogonal chaperones with a cytochrome P450 enhances terpene synthesis in Saccharomyces cerevisiae. Biotechnol J 2021; 17:e2000452. [PMID: 34269523 DOI: 10.1002/biot.202000452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/24/2021] [Accepted: 07/12/2021] [Indexed: 12/16/2022]
Abstract
The supply of terpenes is often limited by their low extraction yield from natural resources, such as plants. Thus, microbial biosynthesis has emerged as an attractive platform for the production of terpenes. Many strategies have been applied to engineer microbes to improve terpene production capabilities; however, functional expression of heterologous proteins such as cytochrome P450 enzymes (P450s) in microbes is a major obstacle. This study reports the successful pairing of cognate chaperones and P450s for functional heterologous expression in Saccharomyces cerevisiae. This chaperone pairing was exploited to facilitate the functional assembly of the protopanaxadiol (PPD) biosynthesis pathway, which consists of a P450 oxygenase and a P450 reductase redox partner originating from Panax ginseng and Arabidopsis thaliana, respectively. We identified several chaperones required for protein folding in P. ginseng and A. thaliana and evaluated the impact of the coexpression of the corresponding chaperones on the synthesis and activity of PPD biosynthesis enzymes. Expression of a chaperone from P. ginseng (PgCPR5), a cognate of PPD biosynthesis enzymes, significantly increased PPD production by more than 2.5-fold compared with that in the corresponding control strain. Thus, pairing of chaperones with heterologous enzymes provides an effective strategy for the construction of challenging biosynthesis pathways in yeast.
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Affiliation(s)
- Jae-Eung Kim
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea
| | - So-Hee Son
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea.,Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Ju Young Lee
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea
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Naveed M, Tehreem S, Arshad S, Bukhari SA, Shabbir MA, Essa R, Ali N, Zaib S, Khan A, Al-Harrasi A, Khan I. Design of a novel multiple epitope-based vaccine: An immunoinformatics approach to combat SARS-CoV-2 strains. J Infect Public Health 2021; 14:938-946. [PMID: 34119848 PMCID: PMC8093003 DOI: 10.1016/j.jiph.2021.04.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Since the SARS-CoV-2 outbreak in December 2019 in Wuhan, China, the virus has infected more than 153 million individuals across the world due to its human-to-human transmission. The USA is the most affected country having more than 32-million cases till date. Sudden high fever, pneumonia and organ failure have been observed in infected individuals. OBJECTIVES In the current situation of emerging viral disease, there is no specific vaccine, or any therapeutics available for SARS-CoV-2, thus there is a dire need to design a potential vaccine to combat the virus by developing immunity in the population. The purpose of present study was to develop a potential vaccine by targeting B and T-cell epitopes using bioinformatics approaches. METHODS B- and T-cell epitopes are predicted from novel M protein-SARS-CoV-2 for the development of a unique multiple epitope vaccine by applying bioinformatics approaches. These epitopes were analyzed and selected for their immunogenicity, antigenicity scores, and toxicity in correspondence to their ability to trigger immune response. In combination to epitopes, best multi-epitope of potential immunogenic property was constructed. The epitopes were joined using EAAAK, AAY and GPGPG linkers. RESULTS The constructed vaccine showed good results of worldwide population coverage and promising immune response. This constructed vaccine was subjected to in-silico immune simulations by C-ImmSim. Chimeric protein construct was cloned into PET28a (+) vector for expression study in Escherichia coli using snapgene. CONCLUSION This vaccine design proved effective in various computer-based immune response analysis as well as showed good population coverage. This study is solely dependent on developing M protein-based vaccine, and these in silico findings would be a breakthrough in the development of an effective vaccine to eradicate SARS-CoV-2 globally.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan.
| | - Sana Tehreem
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Sundas Arshad
- Faculty of Science, Technology and Medicine, University of Luxembourg, Luxembourg
| | - Syeda Aniqa Bukhari
- Research Center for Modeling and Simulation, National University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Ramsha Essa
- Center of Excellence in Molecular Biology (CEMB), Punjab University, Lahore, Pakistan
| | - Nouman Ali
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Sumera Zaib
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, P.O Box 33, Postal Code 616, Birkat Al Mauz, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, P.O Box 33, Postal Code 616, Birkat Al Mauz, Nizwa, Oman.
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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ING2 tumor suppressive protein translocates into mitochondria and is involved in cellular metabolism homeostasis. Oncogene 2021; 40:4111-4123. [PMID: 34017078 DOI: 10.1038/s41388-021-01832-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 04/25/2021] [Accepted: 05/05/2021] [Indexed: 02/04/2023]
Abstract
ING2 (Inhibitor of Growth 2) is a tumor suppressor gene that has been implicated in critical biological functions (cell-cycle regulation, replicative senescence, DNA repair and DNA replication), most of which are recognized hallmarks of tumorigenesis occurring in the cell nucleus. As its close homolog ING1 has been recently observed in the mitochondrial compartment, we hypothesized that ING2 could also translocate into the mitochondria and be involved in new biological functions. In the present study, we demonstrate that ING2 is imported in the inner mitochondrial fraction in a redox-sensitive manner in human cells and that this mechanism is modulated by 14-3-3η protein expression. Remarkably, ING2 is necessary to maintain mitochondrial ultrastructure integrity without interfering with mitochondrial networks or polarization. We observed an interaction between ING2 and mtDNA under basal conditions. This interaction appears to be mediated by TFAM, a critical regulator of mtDNA integrity. The loss of mitochondrial ING2 does not impair mtDNA repair, replication or transcription but leads to a decrease in mitochondrial ROS production, suggesting a detrimental impact on OXPHOS activity. We finally show using multiple models that ING2 is involved in mitochondrial respiration and that its loss confers a protection against mitochondrial respiratory chain inhibition in vitro. Consequently, we propose a new tumor suppressor role for ING2 protein in the mitochondria as a metabolic shift gatekeeper during tumorigenesis.
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Functionally confirmed compound heterozygous ADAM17 missense loss-of-function variants cause neonatal inflammatory skin and bowel disease 1. Sci Rep 2021; 11:9552. [PMID: 33953303 PMCID: PMC8100128 DOI: 10.1038/s41598-021-89063-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/13/2021] [Indexed: 12/13/2022] Open
Abstract
A disintegrin and metalloprotease 17 (ADAM17) is the major sheddase that processes more than 80 substrates, including tumour necrosis factor-α (TNFα). The homozygous genetic deficiency of ADAM17 causing a complete loss of ADAM17 expression was reported to be linked to neonatal inflammatory skin and bowel disease 1 (NISBD1). Here we report for the first time, a family with NISBD1 caused by functionally confirmed compound heterozygous missense variants of ADAM17, namely c.1699T>C (p.Cys567Arg) and c.1799G>A (p.Cys600Tyr). Both variants were detected in two siblings with clinical features of NISBD1, such as erythroderma with exudate in whole body, recurrent skin infection and sepsis and prolonged diarrhoea. In a cell-based assay using Adam10/17 double-knockout mouse embryonic fibroblasts (Adam10/17−/− mEFs) exogenously expressing each of these mutants, phorbol 12-myristate 13-acetate-stimulated shedding was strongly reduced compared with wild-type ADAM17. Thus, in vitro functional assays demonstrated that both missense variants cause the loss-of-function of ADAM17, resulting in the development of NISBD1. Our study further expands the spectrum of genetic pathology underlying ADAM17 in NISBD1 and establishes functional assay systems for its missense variants.
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36
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Stable Display of Artificially Long Foreign Antigens on Chimeric Bamboo mosaic virus Particles. Viruses 2021; 13:v13040572. [PMID: 33805417 PMCID: PMC8067224 DOI: 10.3390/v13040572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022] Open
Abstract
Plant viruses can be genetically modified to generate chimeric virus particles (CVPs) carrying heterologous peptides fused on the surface of coat protein (CP) subunits as vaccine candidates. However, some factors may be especially significant in determining the properties of chimeras. In this study, peptides from various sources and of various lengths were inserted into the Bamboo mosaic virus-based (BaMV) vector CP N-terminus to examine the chimeras infecting and accumulating in plants. Interestingly, it was found that the two different strains Foot-and-mouth disease virus (FMDV) VP1 antigens with flexible linker peptides (77 or 82 amino acids) were directly expressed on the BaMV CP, and the chimeric particles self-assembled and continued to express FMDV antigens. The chimeric CP, when directly fused with a large foreign protein (117 amino acids), can self-fold into incomplete virus particles or disks. The physicochemical properties of heterologus peptides N-terminus, complex strand structures of heterologus peptides C-terminus and different flexible linker peptides, can affect the chimera accumulation. Based on these findings, using plant virus-based chimeras to express foreign proteins can increase their length limitations, and engineered plant-made CVP-based vaccines have increasing potential for further development as novel vaccines.
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Mishra A, Kabir MWU, Hoque MT. diSBPred: A machine learning based approach for disulfide bond prediction. Comput Biol Chem 2021; 91:107436. [PMID: 33550156 DOI: 10.1016/j.compbiolchem.2021.107436] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/28/2020] [Accepted: 01/10/2021] [Indexed: 12/25/2022]
Abstract
The protein disulfide bond is a covalent bond that forms during post-translational modification by the oxidation of a pair of cysteines. In protein, the disulfide bond is the most frequent covalent link between amino acids after the peptide bond. It plays a significant role in three-dimensional (3D) ab initio protein structure prediction (aiPSP), stabilizing protein conformation, post-translational modification, and protein folding. In aiPSP, the location of disulfide bonds can strongly reduce the conformational space searching by imposing geometrical constraints. Existing experimental techniques for the determination of disulfide bonds are time-consuming and expensive. Thus, developing sequence-based computational methods for disulfide bond prediction becomes indispensable. This study proposed a stacking-based machine learning approach for disulfide bond prediction (diSBPred). Various useful sequence and structure-based features are extracted for effective training, including conservation profile, residue solvent accessibility, torsion angle flexibility, disorder probability, a sequential distance between cysteines, and more. The prediction of disulfide bonds is carried out in two stages: first, individual cysteines are predicted as either bonding or non-bonding; second, the cysteine-pairs are predicted as either bonding or non-bonding by including the results from cysteine bonding prediction as a feature. The examination of the relevance of the features employed in this study and the features utilized in the existing nearest neighbor algorithm (NNA) method shows that the features used in this study improve about 7.39 % in jackknife validation balanced accuracy. Moreover, for individual cysteine bonding prediction and cysteine-pair bonding prediction, diSBPred provides a 10-fold cross-validation balanced accuracy of 82.29 % and 94.20 %, respectively. Altogether, our predictor achieves an improvement of 43.25 % based on balanced accuracy compared to the existing NNA based approach. Thus, diSBPred can be utilized to annotate the cysteine bonding residues of protein sequences whose structures are unknown as well as improve the accuracy of the aiPSP method, which can further aid in experimental studies of the disulfide bond and structure determination.
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Affiliation(s)
- Avdesh Mishra
- Department of Electrical Engineering and Computer Science, Texas A&M University-Kingsville, Kingsville, TX, USA
| | - Md Wasi Ul Kabir
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA
| | - Md Tamjidul Hoque
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA.
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Chen Z, Ruan P, Wang L, Nie X, Ma X, Tan Y. T and B cell Epitope analysis of SARS-CoV-2 S protein based on immunoinformatics and experimental research. J Cell Mol Med 2020; 25:1274-1289. [PMID: 33325143 PMCID: PMC7812294 DOI: 10.1111/jcmm.16200] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/22/2020] [Accepted: 11/28/2020] [Indexed: 12/13/2022] Open
Abstract
COVID-19 caused by SARS-CoV-2 is pandemic with a severe morbidity and mortality rate across the world. Despite the race for effective vaccine and drug against further expansion and fatality rate of this novel coronavirus, there is still lack of effective antiviral therapy. To this effect, we deemed it necessary to identify potential B and T cell epitopes from the envelope S protein. This can be used as potential targets to develop anti-SARS-CoV-2 vaccine preparations. In this study, we used immunoinformatics to identify conservative B and T cell epitopes for S proteins of SARS-CoV-2, which might play roles in the initiation of SARS-CoV-2 infection. We identified the B cell and T cell peptide epitopes of S protein and their antigenicity, as well as the interaction between the peptide epitopes and human leucocyte antigen (HLA). Among the B cell epitopes, 'EILDITPCSFGGVS' has the highest score of antigenicity and great immunogenicity. In T cell epitopes, MHC-I peptide 'KIADYNYKL' and MHC-II peptide 'LEILDITPC' were identified as high antigens. Besides, docking analysis showed that the predicted peptide 'KIADYNYKL' was closely bound to the HLA-A*0201. The results of molecular dynamics simulation through GROMACS software showed that 'HLA-A*0201~peptide' complex was very stable. And the peptide we selected could induce the T cell response similar to that of SARS-CoV-2 infection. Moreover, the predicted peptides were highly conserved in different isolates from different countries. The antigenic epitopes presumed in this study were effective new vaccine targets to prevent SARS-CoV-2 infection.
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Affiliation(s)
- Ziwei Chen
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China.,Department of Clinical Laboratory, Third Xiangya Hospital, Central South University, Changsha, China.,Department of NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Pinglang Ruan
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Lili Wang
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Xinmin Nie
- Department of Clinical Laboratory, Third Xiangya Hospital, Central South University, Changsha, China
| | - Xuejun Ma
- Department of NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yurong Tan
- Department of Medical Microbiology, Xiangya School of Medicine, Central South University, Changsha, China
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Nikoloudakis N, Pappi P, Markakis EA, Charova SN, Fanourakis D, Paschalidis K, Delis C, Tzortzakakis EA, Tsaniklidis G. Structural Diversity and Highly Specific Host-Pathogen Transcriptional Regulation of Defensin Genes Is Revealed in Tomato. Int J Mol Sci 2020; 21:ijms21249380. [PMID: 33317090 PMCID: PMC7764197 DOI: 10.3390/ijms21249380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 01/17/2023] Open
Abstract
Defensins are small and rather ubiquitous cysteine-rich anti-microbial peptides. These proteins may act against pathogenic microorganisms either directly (by binding and disrupting membranes) or indirectly (as signaling molecules that participate in the organization of the cellular defense). Even though defensins are widespread across eukaryotes, still, extensive nucleotide and amino acid dissimilarities hamper the elucidation of their response to stimuli and mode of function. In the current study, we screened the Solanum lycopersicum genome for the identification of defensin genes, predicted the relating protein structures, and further studied their transcriptional responses to biotic (Verticillium dahliae, Meloidogyne javanica, Cucumber Mosaic Virus, and Potato Virus Y infections) and abiotic (cold stress) stimuli. Tomato defensin sequences were classified into two groups (C8 and C12). Our data indicate that the transcription of defensin coding genes primarily depends on the specific pathogen recognition patterns of V. dahliae and M. javanica. The immunodetection of plant defensin 1 protein was achieved only in the roots of plants inoculated with V. dahliae. In contrast, the almost null effects of viral infections and cold stress, and the failure to substantially induce the gene transcription suggest that these factors are probably not primarily targeted by the tomato defensin network.
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Affiliation(s)
- Nikolaos Nikoloudakis
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus
- Correspondence: (N.N.); (G.T.)
| | - Polyxeni Pappi
- Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization ELGO-DIMITRA, Mesa Katsabas, 71307 Heraklion, Crete, Greece; (P.P.); (E.A.M.); (E.A.T.)
| | - Emmanouil A. Markakis
- Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization ELGO-DIMITRA, Mesa Katsabas, 71307 Heraklion, Crete, Greece; (P.P.); (E.A.M.); (E.A.T.)
| | - Spyridoula N. Charova
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), 70013 Heraklion, Crete, Greece;
- Department of Biology, University of Crete, 70013 Heraklion, Crete, Greece
| | - Dimitrios Fanourakis
- Giannakakis SA, Export Fruits and Vegetables, 70200 Tympaki, Crete, Greece;
- School of Agricultural Sciences, Hellenic Mediterranean University, Estavromenos, 71004 Heraklion, Crete, Greece;
| | - Konstantinos Paschalidis
- School of Agricultural Sciences, Hellenic Mediterranean University, Estavromenos, 71004 Heraklion, Crete, Greece;
| | - Costas Delis
- Department of Agricultural Technology, School of Agricultural Technology and Food Technology and Nutrition, University of Peloponnese, 24100 Antikalamos, Kalamata, Greece;
| | - Emmanuel A. Tzortzakakis
- Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization ELGO-DIMITRA, Mesa Katsabas, 71307 Heraklion, Crete, Greece; (P.P.); (E.A.M.); (E.A.T.)
| | - Georgios Tsaniklidis
- Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization ELGO-DIMITRA, Mesa Katsabas, 71307 Heraklion, Crete, Greece; (P.P.); (E.A.M.); (E.A.T.)
- Correspondence: (N.N.); (G.T.)
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Al-Azzam S, Ding Y, Liu J, Pandya P, Ting JP, Afshar S. Peptides to combat viral infectious diseases. Peptides 2020; 134:170402. [PMID: 32889022 PMCID: PMC7462603 DOI: 10.1016/j.peptides.2020.170402] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
Viral infectious diseases have resulted in millions of deaths throughout history and have created a significant public healthcare burden. Tremendous efforts have been placed by the scientific communities, health officials and government organizations to detect, treat, and prevent viral infection. However, the complicated life cycle and rapid genetic mutations of viruses demand continuous development of novel medicines with high efficacy and safety profiles. Peptides provide a promising outlook as a tool to combat the spread and re-emergence of viral infection. This article provides an overview of five viral infectious diseases with high global prevalence: influenza, chronic hepatitis B, acquired immunodeficiency syndrome, severe acute respiratory syndrome, and coronavirus disease 2019. The current and potential peptide-based therapies, vaccines, and diagnostics for each disease are discussed.
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Affiliation(s)
- Shams Al-Azzam
- Professional Scientific Services, Eurofins Lancaster Laboratories, Lancaster, PA, 17605, USA
| | - Yun Ding
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Jinsha Liu
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Priyanka Pandya
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Joey Paolo Ting
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Sepideh Afshar
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA.
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Genes Identification, Molecular Docking and Dynamics Simulation Analysis of Laccases from Amylostereum areolatum Provides Molecular Basis of Laccase Bound to Lignin. Int J Mol Sci 2020; 21:ijms21228845. [PMID: 33266512 PMCID: PMC7700495 DOI: 10.3390/ijms21228845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 11/17/2022] Open
Abstract
An obligate mutualistic relationship exists between the fungus Amylostereum areolatum and woodwasp Sirex noctilio. The fungus digests lignin in the host pine, providing essential nutrients for the growing woodwasp larvae. However, the functional properties of this symbiosis are poorly described. In this study, we identified, cloned, and characterized 14 laccase genes from A. areolatum. These genes encoded proteins of 508 to 529 amino acids and contained three typical copper-oxidase domains, necessary to confer laccase activity. Besides, we performed molecular docking and dynamics simulation of the laccase proteins in complex with lignin compounds (monomers, dimers, trimers, and tetramers). AaLac2, AaLac3, AaLac6, AaLac8, and AaLac10 were found that had low binding energies with all lignin model compounds tested and three of them could maintain stability when binding to these compounds. Among these complexes, amino acid residues ALA, GLN, LEU, PHE, PRO, and SER were commonly present. Our study reveals the molecular basis of A. areolatum laccases interacting with lignin, which is essential for understanding how the fungus provides nutrients to S. noctilio. These findings might also provide guidance for the control of S. noctilio by informing the design of enzyme mutants that could reduce the efficiency of lignin degradation.
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Carriero MM, Henrique-Silva F, Meira CM, Gato IMQ, Caetano AR, Lobo FP, Alves AL, Varela ES, Maia AAM. Molecular characterization and gene expression analysis of the pro-inflammatory cytokines IL-1β and IL-8 in the South American fish Piaractus mesopotamicus challenged with Aeromonas dhakensis. Genet Mol Biol 2020; 43:e20200006. [PMID: 33174977 PMCID: PMC7687281 DOI: 10.1590/1678-4685-gmb-2020-0006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/06/2020] [Indexed: 11/24/2022] Open
Abstract
In the present study, the complete characterization of cDNA and genomic sequences of IL-1β and IL-8, as well as the expression profile of these genes in the South American fish pacu (Piaractus mesopotamicus) is provided. The full-length pmIL-1β cDNA was composed of 1208 nucleotides that would produce a precursor peptide with 273 amino acid residues. A putative caspase-1 cleavage site, similar to what is found in mammalian IL-1β, was identified producing a mature peptide with a theoretical molecular weight of 17.21 kDa. The pmIL-8 cDNA sequence consisted of 1019 nucleotides which encoded a 95-amino acid protein with a theoretical molecular weight of 10.43 kDa that showed all typical CXC chemokine features, including a 20-residue signal peptide and four conserved cysteine residues. Constitutive mRNA expression was detected for both genes in the liver, head kidney, gill, intestine, skin and spleen. After a bacterial challenge, up-regulation was detected for both pmIL-1β and pmIL-8 in the spleen and head kidney at 12 h post-infection. At 24 h post-infection there was a decrease in the expression of both genes, with pmIL-8 showing a significant down-regulation in the liver and head kidney when compared to the control groups.
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Affiliation(s)
- Mateus Maldonado Carriero
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
| | - Flavio Henrique-Silva
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Caroline Munhoz Meira
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
| | - Igor Mateus Queiroz Gato
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
| | - Alexandre Rodrigues Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Empresa Brasileira de Pesquisa Agropecuária, Brasília, DF, Brazil
| | - Francisco Pereira Lobo
- Embrapa Informática na Agricultura, Empresa Brasileira de Pesquisa Agropecuária, Campinas, SP, Brazil
| | - Anderson Luis Alves
- Embrapa Pesca e Aquicultura, Empresa Brasileira de Pesquisa Agropecuária, Palmas, TO, Brazil
| | - Eduardo Sousa Varela
- Embrapa Pesca e Aquicultura, Empresa Brasileira de Pesquisa Agropecuária, Palmas, TO, Brazil
| | - Antonio Augusto Mendes Maia
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Pirassununga, SP, Brazil
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Garcia EJ, Liao PC, Tan G, Vevea JD, Sing CN, Tsang CA, McCaffery JM, Boldogh IR, Pon LA. Membrane dynamics and protein targets of lipid droplet microautophagy during ER stress-induced proteostasis in the budding yeast, Saccharomyces cerevisiae. Autophagy 2020. [PMID: 33021864 DOI: 10.1080/15548627.2020.1826691.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022] Open
Abstract
Our previous studies reveal a mechanism for lipid droplet (LD)-mediated proteostasis in the endoplasmic reticulum (ER) whereby unfolded proteins that accumulate in the ER in response to lipid imbalance-induced ER stress are removed by LDs and degraded by microlipophagy (µLP), autophagosome-independent LD uptake into the vacuole (the yeast lysosome). Here, we show that dithiothreitol- or tunicamycin-induced ER stress also induces µLP and identify an unexpected role for vacuolar membrane dynamics in this process. All stressors studied induce vacuolar fragmentation prior to µLP. Moreover, during µLP, fragmented vacuoles fuse to form cup-shaped structures that encapsulate and ultimately take up LDs. Our studies also indicate that proteins of the endosome sorting complexes required for transport (ESCRT) are upregulated, required for µLP, and recruited to LDs, vacuolar membranes, and sites of vacuolar membrane scission during µLP. We identify possible target proteins for LD-mediated ER proteostasis. Our live-cell imaging studies reveal that one potential target (Nup159) localizes to punctate structures that colocalizes with LDs 1) during movement from ER membranes to the cytosol, 2) during microautophagic uptake into vacuoles, and 3) within the vacuolar lumen. Finally, we find that mutations that inhibit LD biogenesis, homotypic vacuolar membrane fusion or ESCRT function inhibit stress-induced autophagy of Nup159 and other ER proteins. Thus, we have obtained the first direct evidence that LDs and µLP can mediate ER stress-induced ER proteostasis, and identified direct roles for ESCRT and vacuolar membrane fusion in that process.
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Affiliation(s)
- Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Gary Tan
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jason D Vevea
- HHMI and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA
| | - Cierra N Sing
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Istvan R Boldogh
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
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Garcia EJ, Liao PC, Tan G, Vevea JD, Sing CN, Tsang CA, McCaffery JM, Boldogh IR, Pon LA. Membrane dynamics and protein targets of lipid droplet microautophagy during ER stress-induced proteostasis in the budding yeast, Saccharomyces cerevisiae. Autophagy 2020; 17:2363-2383. [PMID: 33021864 PMCID: PMC8496710 DOI: 10.1080/15548627.2020.1826691] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Our previous studies reveal a mechanism for lipid droplet (LD)-mediated proteostasis in the endoplasmic reticulum (ER) whereby unfolded proteins that accumulate in the ER in response to lipid imbalance-induced ER stress are removed by LDs and degraded by microlipophagy (µLP), autophagosome-independent LD uptake into the vacuole (the yeast lysosome). Here, we show that dithiothreitol- or tunicamycin-induced ER stress also induces µLP and identify an unexpected role for vacuolar membrane dynamics in this process. All stressors studied induce vacuolar fragmentation prior to µLP. Moreover, during µLP, fragmented vacuoles fuse to form cup-shaped structures that encapsulate and ultimately take up LDs. Our studies also indicate that proteins of the endosome sorting complexes required for transport (ESCRT) are upregulated, required for µLP, and recruited to LDs, vacuolar membranes, and sites of vacuolar membrane scission during µLP. We identify possible target proteins for LD-mediated ER proteostasis. Our live-cell imaging studies reveal that one potential target (Nup159) localizes to punctate structures that colocalizes with LDs 1) during movement from ER membranes to the cytosol, 2) during microautophagic uptake into vacuoles, and 3) within the vacuolar lumen. Finally, we find that mutations that inhibit LD biogenesis, homotypic vacuolar membrane fusion or ESCRT function inhibit stress-induced autophagy of Nup159 and other ER proteins. Thus, we have obtained the first direct evidence that LDs and µLP can mediate ER stress-induced ER proteostasis, and identified direct roles for ESCRT and vacuolar membrane fusion in that process.
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Affiliation(s)
- Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Gary Tan
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jason D Vevea
- HHMI and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA
| | - Cierra N Sing
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Istvan R Boldogh
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
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Adegbaju MS, Morenikeji OB, Borrego EJ, Hudson AO, Thomas BN. Differential Evolution of α-Glucan Water Dikinase (GWD) in Plants. PLANTS 2020; 9:plants9091101. [PMID: 32867090 PMCID: PMC7569903 DOI: 10.3390/plants9091101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/13/2020] [Accepted: 08/22/2020] [Indexed: 11/16/2022]
Abstract
The alpha-glucan water dikinase (GWD) enzyme catalyzes starch phosphorylation, an integral step in transitory starch degradation. The high phosphate content in stored starch has great industrial value, due to its physio–chemical properties making it more versatile, although the phosphate content of stored starch varies depending on the botanical source. In this study, we used various computational approaches to gain insights into the evolution of the GWD protein in 48 plant species with possible roles in enzyme function and alteration of phosphate content in their stored starch. Our analyses identified deleterious mutations, particularly in the highly conserved 5 aromatic amino acid residues in the dual tandem carbohydrate binding modules (CBM-45) of GWD protein in C. zofingiensis, G. hirsutum, A. protothecoides, P. miliaceum, and C. reinhardtii. These findings will inform experimental designs for simultaneous repression of genes coding for GWD and the predicted interacting proteins to elucidate the role this enzyme plays in starch degradation. Our results reveal significant diversity in the evolution of GWD enzyme across plant species, which may be evolutionarily advantageous according to the varying needs for phosphorylated stored starch between plants and environments.
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Affiliation(s)
- Muyiwa S. Adegbaju
- Institute for Plant Biotechnology, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - Olanrewaju B. Morenikeji
- Department of Biomedical Sciences, College of Health Science and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA;
- Department of Biology, Hamilton College, Clinton, NY 14623, USA
| | - Eli J. Borrego
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA; (E.J.B.); (A.O.H.)
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA; (E.J.B.); (A.O.H.)
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, College of Health Science and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA;
- Correspondence: ; Tel.: +1-(585)-475-6382; Fax: +1-(585)-475-5809
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Ullah A, Masood R. The Sequence and Three-Dimensional Structure Characterization of Snake Venom Phospholipases B. Front Mol Biosci 2020; 7:175. [PMID: 32850964 PMCID: PMC7419708 DOI: 10.3389/fmolb.2020.00175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/06/2020] [Indexed: 11/23/2022] Open
Abstract
Snake venom phospholipases B (SVPLBs) are the least studied enzymes. They constitute about 1% of Bothrops crude venoms, however, in other snake venoms, it is present in less than 1%. These enzymes are considered the most potent hemolytic agent in the venom. Currently, no structural information is available about these enzymes from snake venom. To better understand its three-dimensional structure and mechanisms of envenomation, the current work describes the first model-based structure report of this enzyme from Bothrops moojeni venom named as B. moojeni phospholipase B (PLB_Bm). The structure model of PLB_Bm was generated using model building software like I-TESSER, MODELLER 9v19, and Swiss-Model. The build PLB_Bm model was validated using validation tools (PROCHECK, ERRAT, and Verif3D). The analysis of the PLB_Bm modeled structure indicates that it contains 491 amino acid residues that form a well-defined four-layer αββα sandwich core and has a typical fold of the N-terminal nucleophile aminohydrolase (Ntn-hydrolase). The overall structure of PLB_Bm contains 18 β-strands and 17 α-helices with many connecting loops. The structure divides into two chains (A and B) after maturation. The A chain is smaller and contains 207 amino acid residues, whereas the B chain is larger and contains 266 amino acid residues. The sequence and structural comparison among homologous snake venom, bacterial, and mammals PLBs indicate that differences in the length and sequence composition may confer variable substrate specificity to these enzymes. Moreover, the surface charge distribution, average volume, and depth of the active site cavity also vary in these enzymes. The present work will provide more information about the structure-function relationship and mechanism of action of these enzymes in snakebite envenomation.
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Affiliation(s)
- Anwar Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Rehana Masood
- Department of Biochemistry, Shaheed Benazir Bhutto Women University Peshawar, Peshawar, Pakistan
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Khodadad N, Seyedian SS, Moattari A, Biparva Haghighi S, Pirmoradi R, Abbasi S, Makvandi M. In silico functional and structural characterization of hepatitis B virus PreS/S-gene in Iranian patients infected with chronic hepatitis B virus genotype D. Heliyon 2020; 6:e04332. [PMID: 32695898 PMCID: PMC7365991 DOI: 10.1016/j.heliyon.2020.e04332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/23/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
Objective Chronic hepatitis B (CHB) virus infection is the most prevalent chronic liver disease and has become a serious threat to human health. In this study, we attempted to specify and predict several properties including physicochemical, mutation sites, B-cell epitopes, phosphorylation sites, N-link, O-link glycosylation sites, and protein structures of S protein isolated from Ahvaz. Materials and methods Initially, hepatitis B virus DNA (HBV DNA) was extracted from five sera samples of untreated chronic hepatitis B patients. The full-length HBV genomes were amplified and then cloned in pTZ57 R/T vector. The full sequences of HBV were registered in the GenBank with accessions numbers (MK355500), (MK355501) and (MK693107-9). PROTSCALE, Expasy's ProtParam, immuneepitope, ABCpred, BcePred, Bepipred, Algpred, VaxiJen, SCRATCH, DiANNA, plus a number of online analytical processing tools were used to analyse and predict the preS/S gene of genotype D sequences. The present study is the first analytical research on samples obtained from Ahvaz. Results We found major hydrophilic region (MHR) mutations at "a" determining region that included K122R, N131T, F134Y, P142L, and T126N mutations. Moreover, Ahvaz sequences revealed four sites (4, 112, 166, and 309) in the preS/S gene for N-glycosylation that could possibly be a potential target for anti-HBV therapy. Conclusion In the present study, mutations were identified at positions T113S and N131T within the MHR region of S protein; these mutations can potentially decrease the effect of hepatitis B vaccination in vaccine recipients.
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Affiliation(s)
- Nastaran Khodadad
- Infectious and Tropical Disease Research Center, Health Research Institute, and Department of Virology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Saeed Seyedian
- Alimentary Tract Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Somayeh Biparva Haghighi
- Department of General Courses, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Roya Pirmoradi
- Infectious and Tropical Disease Research Center, Health Research Institute, and Department of Virology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Manoochehr Makvandi
- Infectious and Tropical Disease Research Center, Health Research Institute, and Department of Virology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Hashempour T, Dehghani B, Musavi Z, Moayedi J, Hasanshahi Z, Sarvari J, Hosseini SY, Hosseini E, Moeini M, Merat S. Impact of IL28 Genotypes and Modeling the Interactions of HCV Core Protein on Treatment of Hepatitis C. Interdiscip Sci 2020; 12:424-437. [PMID: 32656614 DOI: 10.1007/s12539-020-00382-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 05/02/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Mutations in the core CVR region of hepatitis C virus (HCV) and polymorphisms of interleukin 28B (IL28B) are associated with progression toward liver disease and in response to therapy. In addition, interactions of the core protein with some cell interactors can be related to HCV liver damage. AIM This study aimed to evaluate the effect of core mutations as well as IL28B polymorphism on clinical features, sustained virological response (SVR) in 1a and 3a HCV genotypes amongst Iranian HCV infected patients, and the impact of mutations on core protein properties, antigenic properties, and interactions with HCV inhibitors, using several bioinformatics tools. METHODS Seventy-nine Iranian patients infected with HCV genotypes 1a and 3a and diagnosed with chronic active hepatitis were examined. Plasma viral RNA was used to amplify and sequence the HCV Core gene; also, HCV viral load, molecular genotyping, and the liver enzymes were determined for all samples. The sequencing results were analyzed by several reliable bioinformatics tools to determine the physicochemical properties, B cell epitopes, post-modification changes, and secondary/tertiary structures; and evaluate the interactions with 4 drugs by docking method. RESULT There were some substitutions in core CVR related to ALT and AST enzymes that can lead to HCV advanced liver disease. The most prevalent mutation for 3a genotypes was a substitution in aa 162 (I to V) while we did not find any mutation in 1a responder group. Polymorphism of the rs8099917 showed that the majority of patients had TG heterozygous and carried CT genotype at the rs12979860. Analysis indicated several phosphorylation sits for core protein as well as two important disulfide bonds. Immunogenic prediction showed that core protein can strongly induce the immune system. Interaction analysis, using the docking method revealed two potential interactors (Vitronectin and SETD2). CONCLUSION Generally, mutations in all core CVR regions in all patients showed a relationship between such substitutions and higher liver enzymes that can result in advanced liver disease progression in HCV infected patients. Furthermore, immunoinformatics analysis determined the possible immunodominant regions to be considered in HCV vaccine designs. Furthermore, no association between SVR and IL28B polymorphism was shown. In silico analysis determined modification sites, structures, B-cell epitopes of core protein and interactions with several interactors can lead to persistent HCV infection in the cell and the progress of liver diseases.
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Affiliation(s)
- Tayebeh Hashempour
- Clinical Microbiology Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Behzad Dehghani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Musavi
- Clinical Microbiology Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Javad Moayedi
- Clinical Microbiology Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hasanshahi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jamal Sarvari
- Bacteriology and Virology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Younes Hosseini
- Bacteriology and Virology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ebrahim Hosseini
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Maryam Moeini
- Gastroenterology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shahin Merat
- Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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Mapes NJ, Rodriguez C, Chowriappa P, Dua S. Local Similarity Matrix for Cysteine Disulfide Connectivity Prediction from Protein Sequences. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1276-1289. [PMID: 30640622 DOI: 10.1109/tcbb.2019.2892441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Accurately predicting three dimensional protein structures from sequences would present us with targets for drugs via molecular dynamics that would treat cancer, viral infections, and neurological diseases. These treatments would have a far reaching impact to our economy, quality of life, and society. The goal of this research was to build a data mining framework to predict cysteine connectivity in proteins from the sequence and oxidation state of cysteines. Accurately predicting the cysteine bonding configuration improves the TM-Score, a quantitative measurement of protein structure prediction accuracy. We provided state of the art Qp and Qc on the PDBCYS and IVD-54 Datasets. Furthermore, we have produced a Local Similarity Matrix that compares favorably to the default PSSMs generated from PSI-Blast in a statistically significant way. Our Qp for SP39, PDBCYS, and IVD-54 were 90.6, 80.6, and 68.5, respectively.
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50
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Lin L, Ting S, Yufei H, Wendong L, Yubo F, Jing Z. Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2. Virus Res 2020; 288:198082. [PMID: 32621841 PMCID: PMC7328648 DOI: 10.1016/j.virusres.2020.198082] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/16/2022]
Abstract
Linear B-cell epitopes in RBD of S protein predicted against SARS-CoV-2. Discontinuous B-cell epitopes from S protein predicted against SARS-CoV-2. T-cell epitopes from S, M and N protein predicted against SARS-CoV-2.
The outbreak of the 2019 novel coronavirus (SARS-CoV-2) has infected millions of people with a large number of deaths across the globe. The existing therapies are limited in dealing with SARS-CoV-2 due to the sudden appearance of the virus. Therefore, vaccines and antiviral medicines are in desperate need. We took immune-informatics approaches to identify B- and T-cell epitopes for surface glycoprotein (S), membrane glycoprotein (M) and nucleocapsid protein (N) of SARS-CoV-2, followed by estimating their antigenicity and interactions with the human leukocyte antigen (HLA) alleles. Allergenicity, toxicity, physiochemical properties analysis and stability were examined to confirm the specificity and selectivity of the epitope candidates. We identified a total of five B cell epitopes in RBD of S protein, seven MHC class-I, and 18 MHC class-II binding T-cell epitopes from S, M and N protein which showed non-allergenic, non-toxic and highly antigenic features and non-mutated in 55,179 SARS-CoV-2 virus strains until June 25, 2020. The epitopes identified here can be a potentially good candidate repertoire for vaccine development.
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Affiliation(s)
- Li Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China; School of Biological Science and Medical Engineering, Beihang University, Beijing China
| | - Sun Ting
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China; School of Biological Science and Medical Engineering, Beihang University, Beijing China
| | - He Yufei
- School of Biological Science and Medical Engineering, Beihang University, Beijing China
| | - Li Wendong
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China; School of Biological Science and Medical Engineering, Beihang University, Beijing China
| | - Fan Yubo
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China; School of Biological Science and Medical Engineering, Beihang University, Beijing China.
| | - Zhang Jing
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China.
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