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Montero L, Okraine YV, Orlowski J, Matzkin S, Scarponi I, Miranda MV, Nusblat A, Gottifredi V, Alonso LG. Conserved cysteine-switches for redox sensing operate in the cyclin-dependent kinase inhibitor p21(CIP/KIP) protein family. Free Radic Biol Med 2024; 224:494-505. [PMID: 39277119 DOI: 10.1016/j.freeradbiomed.2024.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 09/10/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
The cell cycle is a tightly regulated, dynamic process controlled by multiple checkpoints. When the prevention of cell cycle progression is needed, key effectors such as members of the p21 (CIP/KIP) inhibit cyclin-dependent kinases (CDKs). It is accepted that p21 does not sense DNA damage and that stress signals affect p21 indirectly. A plethora of DNA damaging events activate the tumor suppressor p53, which in turn transcriptionally activates p21, steeply changing its levels to reach CDK inhibition. The levels of p21 are also controlled by phosphorylation and ubiquitination events, which are relevant as they modulate p21 activity, localization, and stability. Intriguingly, here we report the first evidence of the direct control of p21 cell proliferation inhibition by DNA damaging signals. Specifically, we have identified a redox regulating mechanism that controls p21 capacity to reduce cell proliferation. Using the human p21 protein, we identified two cysteine-switches that independently regulate its cyclin-binding and linker (LH) modules respectively. Additionally, we provide a mechanistic explanation of how reactive cysteines embedded in unstructured regions of intrinsically disordered proteins respond to ROS without the guidance of protein structure, contributing to a vastly unexplored area of research. Cellular experiments utilizing p21KID mutants that disrupt disulfide-based switches demonstrate their impact on the capacity of p21 to inhibit cell cycle progression, thus highlighting the functional relevance of our findings. Furthermore, our investigation reveals that reactive cysteine residues are highly conserved across the Kinase Inhibitory Domain (KID) sequences of p21 proteins from higher eukaryotes, and the p27 and p57 human paralogs. We propose that the presence of conserved regulatory cysteines within the KIDs of p21 family members from multiple taxa provides those proteins with the capability for directly sensing ROS, enabling the direct regulation of cyclin kinase activity by ROS levels.
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Affiliation(s)
- Luciano Montero
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Juan Orlowski
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Shadia Matzkin
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ignacio Scarponi
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Victoria Miranda
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandro Nusblat
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Leonardo G Alonso
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina; Fundación Instituto Leloir, IIB-BA Conicet, Buenos Aires, Argentina.
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He J, Li T, Cheng C, Li N, Gao P, Lei D, Liang R, Ding X. The polymorphism analysis and therapy vaccine target epitopes screening of HPV-35 E6 E7 among the threaten α-9 HPV in Sichuan area. Virol J 2024; 21:213. [PMID: 39252044 PMCID: PMC11384679 DOI: 10.1186/s12985-024-02357-3] [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: 12/23/2023] [Accepted: 04/02/2024] [Indexed: 09/11/2024] Open
Abstract
High-risk human papilloma virus (HR-HPV) persistent infection is closely associated with the development of cervical cancer and squamous intraepithelial lesion (SIL).The α-9 HPVs, which is predominantly composed of HR-HPV types, account for 75% of HR-HPV infection in Sichuan. The oncoproteins E6 and E7 of HPV play a crucial role in tumor initiation and progression. Notably, HPV-35 is the only HR-HPV type within the α-9 genus that is not included in the nine-valent HPV prophylactic vaccine. Cervical cell samples obtained from Sichuan were collected for HPV detection and genotyping. Among the 406 HPV-positive samples, 31 HPV-35 were detected, 24 HPV-35 E6 and 26 E7 were successfully amplified and sequenced, five nucleotide mutations in E6 and three in E7 were detected, T232C, T434G of E6 (W78R, I145R) and C67T, G84T of E7 (H23Y, L28F) were non-synonymy mutation. PAML 4.8 server was used to detect positive selection sites of HPV-35 E6, E7, and E6 is W78R. Phyre2 were used to predict and analyze protein structures, W78R made influences on protein structure. IEDB were used to screen epitopes vaccine target for HPV-35 affection therapy, and 5 HPV-35 E6 and 3 HPV-35 E7 most potential epitopes were obtained, the most potential peptides for therapy vaccine design were 79-91YRYSVYGETLEKQ, 45-60FACYDLCIVREGQPY, 124-135RFHNIGGRWTGR of E6; 3-19GEITTLQDYVLDLEPEA, 38-47TIDGPAGQAK, 70-88VQSTHIDIRKLEDLLMGTF of E7 and W78R mainly decreased the epitopes affinity.Conclusions Amino acid substitution in the positive selection sites of HPV-35 E6 and E7 genes have been found to influence protein structure and to decrease the overall affinity of antigen epitopes. This observation aligns with the evolutionary significance of positive selection site, which may confer advantages to the virus by making infected cells more challenging for the immune system to detect, thereby enhancing HPV's adaptability to the host environment. The polymorphism analysis of HPV-35 E6, E7 contributes to the enrichment of α-9 HPV data in Sichuan China, which is instrumental in improving the effectiveness of clinical detection. Furthermore, these findings provide a relevant theoretical foundation for the prevention and treatment of HPV-related diseases.
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Affiliation(s)
- Jiaoyu He
- Chengdu Second People's Hospital, Chengdu, Sichuan, 610021, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- Chongqing Nanchuan biotechnology research institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
| | - Tianjun Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- Chongqing Nanchuan biotechnology research institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Chunlan Cheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- Department of Laboratory Medicine, Sichuan Provincial Maternity and Child Health Care Hospital. The Affiliated Women's and children's Hospital of Chengdu Medical College, Chengdu, China
| | - Ning Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Peng Gao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Dan Lei
- Chengdu Second People's Hospital, Chengdu, Sichuan, 610021, China
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- Chongqing Nanchuan biotechnology research institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
| | - Rong Liang
- Department of Ultrasound, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, China
| | - Xianping Ding
- Chengdu Second People's Hospital, Chengdu, Sichuan, 610021, China.
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
- Chongqing Nanchuan biotechnology research institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China.
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Yu M, Wu S, Wang S, Cui C, Lu Y, Sun Z. Polymorphism of E6 and E7 Genes in Human Papillomavirus Types 31 and 33 in Northeast China. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:9338294. [PMID: 36950084 PMCID: PMC10027458 DOI: 10.1155/2023/9338294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/04/2023] [Accepted: 01/30/2023] [Indexed: 03/14/2023]
Abstract
Persistent infection with human papillomavirus (HPV) types 31 and 33 is an important causative factor for cervical cancer. The E6/E7 genes are key oncogenes involved in the immortalization and transformation of human epithelial cells. Genetic polymorphism may lead to differences in the virus' carcinogenic potential, the immune reaction of the host, and the potencies of vaccines. Few studies on HPV31/33 E6/E7 genetic polymorphism have been carried out. To study the genetic polymorphism of HPV31 and HPV33 E6/E7 genes in northeast China, these genes (HPV31 E6/E7, n = 151; HPV33 E6/E7, n = 136) were sequenced and compared to reference sequences (J04353.1, M12732.1) using BioEdit. Phylogenetic trees were constructed by the neighbor-joining method using MegaX. The diversity of the secondary structure was estimated using the PSIPred server. The positively selected sites were analyzed using PAML4.9. The major histocompatibility complex (MHC) class I and MHCII epitopes were predicted using the ProPred-I server and ProPredserver. B-cell epitopes were predicted using the ABCpred server. In the 151 HPV31E6 sequences, 25 (25/450) single-nucleotide mutations were found, 14 of which were synonymous mutations and 11 were nonsynonymous. In the 151 HPV31E7 sequences, 8 (8/297) nucleotide mutations were found, 3 of which were synonymous mutations and 5 were nonsynonymous. In the 136 HPV33E6 sequences, 17 (17/450) nucleotide mutations were observed, 7 of which were synonymous mutations and 10 were nonsynonymous. C14T/G (T5I/S) was a triallelic mutation. Finally, in the 136 HPV33E7 sequences, 9 (9/294) nucleotide mutations were observed, 3 of which were synonymous mutations and 6 were nonsynonymous. C134T/A (A45V/E) and C278G/A (T93S/N) were triallelic mutations. Lineage A was the most common lineage in both HPV31 and HPV33. In all of the sequences, we only identified one positively selected site, HPV33 E6 (K93N). Most nonsynonymous mutations were localized at sites belonging to MHC and/or B-cell predicted epitopes. Data obtained in this study should contribute to the development and application of detection probes, targeted drugs, and vaccines.
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Affiliation(s)
- Miao Yu
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Si Wu
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shuang Wang
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Changwan Cui
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yiping Lu
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhengrong Sun
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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He J, Li Q, Hu C, Peng J, Ma S, Song Z, Liu Y, Cui Y, Deng J, Wei X, Ding X. Human papillomavirus 68 prevalence and genetic variability based on E6/E7 genes in Sichuan. Virology 2021; 567:15-25. [PMID: 34942562 DOI: 10.1016/j.virol.2021.11.015] [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: 05/23/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 11/28/2022]
Abstract
HPV68 is a common HR-HPV, its persistent infection is closely related with the occurrence of cervical cancer. In this study, 2939 (27.60%, 2939/10650) positive samples were detected, and 174 (5.92%, 174/2939) were HPV68. 150 HPV68 E6-E7 were successful sequenced, 4 non-synonymous mutations were detected in E6, and E7 were 12. N133S non-synonymous mutations of HPV 68 E6 and C67G, T68 A/M of HPV68 E7 are E6, E7 positive selection sites, they all located in the key domains and major motifs of E6/E7 protein, the above amino-acid substitutions changed the protein structure, disturbed the interaction with other protein or cellular factors and make a difference in epitopes affinity, may affect the pathogenicity and adaptability of HPV68 to the environment. The enrichment of HPV68 data is of great significance for understanding the inherent geographical and biological differences of HPV68 in China.
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Affiliation(s)
- Jiaoyu He
- College of Phamaceutical Sciences , Southwest University, Chongqing, 400000, PR China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Chongqing Nanchuan Biotechnology Research Institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, PR China; Xindu District People's Hospital of Chengdu, Department of Medical Laboratory, PR China.
| | - Qiufu Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Chongqing Nanchuan Biotechnology Research Institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, PR China.
| | - Changhua Hu
- College of Phamaceutical Sciences , Southwest University, Chongqing, 400000, PR China.
| | - Jianying Peng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Chongqing Nanchuan Biotechnology Research Institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, PR China.
| | - Shiyu Ma
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Chongqing Nanchuan Biotechnology Research Institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, PR China.
| | - Zhilin Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Chongqing Nanchuan Biotechnology Research Institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, PR China.
| | - Yiran Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Chongqing Nanchuan Biotechnology Research Institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, PR China.
| | - Yanru Cui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Chongqing Nanchuan Biotechnology Research Institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, PR China.
| | - Junhang Deng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Chongqing Nanchuan Biotechnology Research Institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, PR China.
| | - Xia Wei
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Chongqing Nanchuan Biotechnology Research Institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, PR China.
| | - Xianping Ding
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, PR China; Chongqing Nanchuan Biotechnology Research Institute, Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, PR China.
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Sanami S, Azadegan-Dehkordi F, Rafieian-Kopaei M, Salehi M, Ghasemi-Dehnoo M, Mahooti M, Alizadeh M, Bagheri N. Design of a multi-epitope vaccine against cervical cancer using immunoinformatics approaches. Sci Rep 2021; 11:12397. [PMID: 34117331 PMCID: PMC8196015 DOI: 10.1038/s41598-021-91997-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/03/2021] [Indexed: 02/05/2023] Open
Abstract
Cervical cancer, caused by human papillomavirus (HPV), is the fourth most common type of cancer among women worldwide. While HPV prophylactic vaccines are available, they have no therapeutic effects and do not clear up existing infections. This study aims to design a therapeutic vaccine against cervical cancer using reverse vaccinology. In this study, the E6 and E7 oncoproteins from HPV16 were chosen as the target antigens for epitope prediction. Cytotoxic T lymphocytes (CTL) and helper T lymphocytes (HTL) epitopes were predicted, and the best epitopes were selected based on antigenicity, allergenicity, and toxicity. The final vaccine construct was composed of the selected epitopes, along with the appropriate adjuvant and linkers. The multi-epitope vaccine was evaluated in terms of physicochemical properties, antigenicity, and allergenicity. The tertiary structure of the vaccine construct was predicted. Furthermore, several analyses were also carried out, including molecular docking, molecular dynamics (MD) simulation, and in silico cloning of the vaccine construct. The results showed that the final proposed vaccine could be considered an effective therapeutic vaccine for HPV; however, in vitro and in vivo experiments are required to validate the efficacy of this vaccine candidate.
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Affiliation(s)
- Samira Sanami
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Fatemeh Azadegan-Dehkordi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mahmoud Rafieian-Kopaei
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Majid Salehi
- Department of Tissue Engineering, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Maryam Ghasemi-Dehnoo
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mehran Mahooti
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Morteza Alizadeh
- Department of Tissue Engineering, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran.
| | - Nader Bagheri
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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Chen Z, Li Q, Huang J, Li J, Yang F, Min X, Chen Z. E6 and E7 gene polymorphisms in human papillomavirus Type-6 identified in Southwest China. Virol J 2019; 16:114. [PMID: 31511025 PMCID: PMC6740006 DOI: 10.1186/s12985-019-1221-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human papillomavirus type-6 (HPV6) is the major etiological agent of anogenital warts both men and women. The present study aimed to characterize the genetic diversity among HPV6 in Southwest China, and to investigate the origin of, selective pressure experienced by, and impact of the resultantly identified genetic variants on the HPV6 secondary structure. METHODS Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by Molecular Evolutionary Genetics Analysis version 6.0. The diversity of secondary structure was analyzed by PSIPred software. The selection pressures acting on the E6/E7 genes were estimated by Phylogenetic Analyses by Maximum Likelihood version 4.8 software. RESULTS HPV6 was the most prevalent low risk HPV type in southwest China. In total, 143 E6 and E7 gene sequences of HPV6 isolated from patients were sequenced and compared to GenBank HPV6 reference sequence X00203. The results of these analyses revealed that both the HPV6 E6 and E7 were highly conserved within the analyzed patient samples, and comprised only 3 types of variant sequence, respectively. Furthermore, the analysis of HPV6 E6 and E7 sequences revealed seven/five single-nucleotide mutations, two/four and five/one of which were non-synonymous and synonymous, respectively. The phylogenetic analyses of the E6 and E7 sequences indicated that they belonged to sub-lineage A1 and sub-lineage B1, whereas the selective pressure analyses showed that only the E7 mutation sites 4R, 34E, and 52F were positive selection. CONCLUSIONS HPV6 (detection rate = 13.10%) was very prevalent in southwest China, both the HPV6 E6 and E7 sequences were highly conserved within the analyzed patient samples in southwest China, indicating that the low risk HPV6 can adapt to the environment well without much evolution.
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Affiliation(s)
- Zuyi Chen
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, Sichuan, People's Republic of China
| | - Qiongyao Li
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, Sichuan, People's Republic of China.,Department of Information Technology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Jian Huang
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Jin Li
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Feng Yang
- Department of Information Technology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Xun Min
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China.
| | - Zehui Chen
- Department of Laboratory medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
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He J, Yang Y, Chen Z, Liu Y, Bao S, Zhao Y, Ding X. Identification of variants and therapeutic epitopes in HPV-33/HPV-58 E6 and E7 in Southwest China. Virol J 2019; 16:72. [PMID: 31138240 PMCID: PMC6537359 DOI: 10.1186/s12985-019-1168-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/22/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Human papillomavirus (HPV) E6 and E7 oncoproteins play a crucial role in HPV-related diseases, such as cervical cancer, and can be used as ideal targets for therapeutic vaccines. Human leukocyte antigen (HLA) participates in the immune response to block HPV infection and invasion by its target/recognition function. HPV-33 and HPV-58 are highly prevalent among Chinese women. Therefore, it is of great significance to study the E6 and E7 region-specific gene polymorphisms of HPV-33 and HPV-58 in Southwest China and to identify ideal epitopes for vaccine design. Both HPV-33 and HPV-58 belong to α-9 genus HPV and are highly homologous, so their correlations are included in our research. METHODS To study the E6 and E7 variations and polymorphisms of HPV-33 and HPV-58 in Southwest China, we collected samples, extracted and sequenced DNA, and identified variants. Nucleotide sequences were translated into amino acids by Mega 6.0 software. The physical/chemical properties, amino acid-conserved sequences and secondary structure of protein sequences were analysed by the Protparam server, ConSurf server and PSIPRED software. The T and B cell epitopes of the E6/E7 reference and variant sequences in HPV-33 and HPV-58 were predicted by the Immune Epitope Database (IEDB) analysis server and the ABCpred server, respectively. RESULTS Five and seven optimal HLA-I restricted T cell epitopes were selected from HPV-33 and HPV-58 E6, respectively, and these optimal epitopes are mainly located in 41-58EVYDFAFADLTVVYREGN of HPV-33 E6 and 40-60SEVYDFVFADLRIVYRDGNPF of HPV-58 E6. Six optimal HLA-I-restricted T cell epitopes were selected from HPV-33 and HPV-58 E7, and these epitopes are mainly located in 77-90RTIQQLLMGTVNIV of HPV-33 E7 and 78-91RTLQQLLMGTCTIV of HPV-58 E7. CONCLUSIONS HPV-33/HPV-58 E6/E7 gene polymorphisms and T/B cell epitopes of their reference and variant sequences were studied, and candidate epitopes were selected by bioinformatics techniques for therapeutic vaccine design for people in Southwest China. This study was the first to investigate the correlation of epitopes between HPV-33 and HPV-58. After experimental validation, these selected epitopes will be employed to induce a wide range of immune responses in heterogeneous HLA populations.
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Affiliation(s)
- Jiaoyu He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China.,Chongqing Innovation Academy of Characteristic Bioindustry Technology, Chongqing, People's Republic of China
| | - Yasi Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China.,Chongqing Innovation Academy of Characteristic Bioindustry Technology, Chongqing, People's Republic of China
| | - Zuyi Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China.,Chongqing Innovation Academy of Characteristic Bioindustry Technology, Chongqing, People's Republic of China
| | - Yang Liu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Shanfei Bao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China.,Chongqing Innovation Academy of Characteristic Bioindustry Technology, Chongqing, People's Republic of China
| | - Yun Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Xianping Ding
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China. .,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China. .,Chongqing Innovation Academy of Characteristic Bioindustry Technology, Chongqing, People's Republic of China.
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Alvarez-Paggi D, Lorenzo JR, Camporeale G, Montero L, Sánchez IE, de Prat Gay G, Alonso LG. Topology Dictates Evolution of Regulatory Cysteines in a Family of Viral Oncoproteins. Mol Biol Evol 2019; 36:1521-1532. [DOI: 10.1093/molbev/msz085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Juan Ramiro Lorenzo
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Buenos Aires, Argentina
| | - Gabriela Camporeale
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Luciano Montero
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Ignacio E Sánchez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Buenos Aires, Argentina
| | - Gonzalo de Prat Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Leonardo G Alonso
- Instituto de Nanobiotecnología (NANOBIOTEC), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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9
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Chen X, Mims J, Huang X, Singh N, Motea E, Planchon SM, Beg M, Tsang AW, Porosnicu M, Kemp ML, Boothman DA, Furdui CM. Modulators of Redox Metabolism in Head and Neck Cancer. Antioxid Redox Signal 2018; 29:1660-1690. [PMID: 29113454 PMCID: PMC6207163 DOI: 10.1089/ars.2017.7423] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/04/2017] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE Head and neck squamous cell cancer (HNSCC) is a complex disease characterized by high genetic and metabolic heterogeneity. Radiation therapy (RT) alone or combined with systemic chemotherapy is widely used for treatment of HNSCC as definitive treatment or as adjuvant treatment after surgery. Antibodies against epidermal growth factor receptor are used in definitive or palliative treatment. Recent Advances: Emerging targeted therapies against other proteins of interest as well as programmed cell death protein 1 and programmed death-ligand 1 immunotherapies are being explored in clinical trials. CRITICAL ISSUES The disease heterogeneity, invasiveness, and resistance to standard of care RT or chemoradiation therapy continue to constitute significant roadblocks for treatment and patients' quality of life (QOL) despite improvements in treatment modality and the emergence of new therapies over the past two decades. FUTURE DIRECTIONS As reviewed here, alterations in redox metabolism occur at all stages of HNSCC management, providing opportunities for improved prevention, early detection, response to therapies, and QOL. Bioinformatics and computational systems biology approaches are key to integrate redox effects with multiomics data from cells and clinical specimens and to identify redox modifiers or modifiable target proteins to achieve improved clinical outcomes. Antioxid. Redox Signal.
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Affiliation(s)
- Xiaofei Chen
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Jade Mims
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Xiumei Huang
- Departments of Pharmacology, Radiation Oncology, and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Naveen Singh
- Departments of Pharmacology, Radiation Oncology, and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Edward Motea
- Departments of Pharmacology, Radiation Oncology, and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | | | - Muhammad Beg
- Department of Internal Medicine, Division of Hematology-Oncology, UT Southwestern Medical Center, Dallas, Texas
| | - Allen W. Tsang
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Mercedes Porosnicu
- Department of Internal Medicine, Section of Hematology and Oncology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Melissa L. Kemp
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - David A. Boothman
- Departments of Pharmacology, Radiation Oncology, and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas
| | - Cristina M. Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
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10
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Glavina J, Román EA, Espada R, de Prat-Gay G, Chemes LB, Sánchez IE. Interplay between sequence, structure and linear motifs in the adenovirus E1A hub protein. Virology 2018; 525:117-131. [PMID: 30265888 DOI: 10.1016/j.virol.2018.08.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 01/04/2023]
Abstract
E1A is the main transforming protein in mastadenoviruses. This work uses bioinformatics to extrapolate experimental knowledge from Human adenovirus serotype 5 and 12 E1A proteins to all known serotypes. A conserved domain architecture with a high degree of intrinsic disorder acts as a scaffold for multiple linear motifs with variable occurrence mediating the interaction with over fifty host proteins. While linear motifs contribute strongly to sequence conservation within intrinsically disordered E1A regions, motif repertoires can deviate significantly from those found in prototypical serotypes. Close to one hundred predicted residue-residue contacts suggest the presence of stable structure in the CR3 domain and of specific conformational ensembles involving both short- and long-range intramolecular interactions. Our computational results suggest that E1A sequence conservation and co-evolution reflect the evolutionary pressure to maintain a mainly disordered, yet non-random conformation harboring a high number of binding motifs that mediate viral hijacking of the cell machinery.
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Affiliation(s)
- Juliana Glavina
- Universidad de Buenos Aires. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas. Buenos Aires, Argentina
| | - Ernesto A Román
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Rocío Espada
- Universidad de Buenos Aires. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas. Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Lucía B Chemes
- Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIB-INTECH, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina; Departamento de Fisiología y Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Ignacio E Sánchez
- Universidad de Buenos Aires. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas. Buenos Aires, Argentina.
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11
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Cruz-Gregorio A, Manzo-Merino J, Lizano M. Cellular redox, cancer and human papillomavirus. Virus Res 2018; 246:35-45. [DOI: 10.1016/j.virusres.2018.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 01/10/2018] [Accepted: 01/10/2018] [Indexed: 12/28/2022]
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12
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Structural Insights in Multifunctional Papillomavirus Oncoproteins. Viruses 2018; 10:v10010037. [PMID: 29342959 PMCID: PMC5795450 DOI: 10.3390/v10010037] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 02/08/2023] Open
Abstract
Since their discovery in the mid-eighties, the main papillomavirus oncoproteins E6 and E7 have been recalcitrant to high-resolution structure analysis. However, in the last decade a wealth of three-dimensional information has been gained on both proteins whether free or complexed to host target proteins. Here, we first summarize the diverse activities of these small multifunctional oncoproteins. Next, we review the available structural data and the new insights they provide about the evolution of E6 and E7, their multiple interactions and their functional variability across human papillomavirus (HPV) species.
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13
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Borkosky SS, Camporeale G, Chemes LB, Risso M, Noval MG, Sánchez IE, Alonso LG, de Prat Gay G. Hidden Structural Codes in Protein Intrinsic Disorder. Biochemistry 2017; 56:5560-5569. [PMID: 28952717 DOI: 10.1021/acs.biochem.7b00721] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and β-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.
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Affiliation(s)
- Silvia S Borkosky
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Gabriela Camporeale
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Marikena Risso
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - María Gabriela Noval
- Department of Microbiology, New York University , Alexandria Center for Life Sciences, New York, New York 10016, United States
| | - Ignacio E Sánchez
- Protein Physiology Laboratory, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Universidad de Buenos Aires , Buenos Aires, Argentina
| | - Leonardo G Alonso
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Gonzalo de Prat Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
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14
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Chen Z, Jing Y, Wen Q, Ding X, Wang T, Mu X, Chenzhang Y, Cao M. E6 and E7 Gene Polymorphisms in Human Papillomavirus Types-58 and 33 Identified in Southwest China. PLoS One 2017; 12:e0171140. [PMID: 28141822 PMCID: PMC5283733 DOI: 10.1371/journal.pone.0171140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/16/2017] [Indexed: 11/18/2022] Open
Abstract
Cancer of the cervix is associated with infection by certain types of human papillomavirus (HPV). The gene variants differ in immune responses and oncogenic potential. The E6 and E7 proteins encoded by high-risk HPV play a key role in cellular transformation. HPV-33 and HPV-58 types are highly prevalent among Chinese women. To study the gene intratypic variations, polymorphisms and positive selections of HPV-33 and HPV-58 E6/E7 in southwest China, HPV-33 (E6, E7: n = 216) and HPV-58 (E6, E7: n = 405) E6 and E7 genes were sequenced and compared to others submitted to GenBank. Phylogenetic trees were constructed by Maximum-likelihood and the Kimura 2-parameters methods by MEGA 6 (Molecular Evolutionary Genetics Analysis version 6.0). The diversity of secondary structure was analyzed by PSIPred software. The selection pressures acting on the E6/E7 genes were estimated by PAML 4.8 (Phylogenetic Analyses by Maximun Likelihood version4.8) software. The positive sites of HPV-33 and HPV-58 E6/E7 were contrasted by ClustalX 2.1. Among 216 HPV-33 E6 sequences, 8 single nucleotide mutations were observed with 6/8 non-synonymous and 2/8 synonymous mutations. The 216 HPV-33 E7 sequences showed 3 single nucleotide mutations that were non-synonymous. The 405 HPV-58 E6 sequences revealed 8 single nucleotide mutations with 4/8 non-synonymous and 4/8 synonymous mutations. Among 405 HPV-58 E7 sequences, 13 single nucleotide mutations were observed with 10/13 non-synonymous mutations and 3/13 synonymous mutations. The selective pressure analysis showed that all HPV-33 and 4/6 HPV-58 E6/E7 major non-synonymous mutations were sites of positive selection. All variations were observed in sites belonging to major histocompatibility complex and/or B-cell predicted epitopes. K93N and R145 (I/N) were observed in both HPV-33 and HPV-58 E6.
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Affiliation(s)
- Zuyi Chen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Yaling Jing
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Qiang Wen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Xianping Ding
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
- * E-mail:
| | - Tao Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Xuemei Mu
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Yuwei Chenzhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
| | - Man Cao
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
- Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China
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15
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Camporeale G, Lorenzo JR, Thomas MG, Salvatierra E, Borkosky SS, Risso MG, Sánchez IE, de Prat Gay G, Alonso LG. Degenerate cysteine patterns mediate two redox sensing mechanisms in the papillomavirus E7 oncoprotein. Redox Biol 2016; 11:38-50. [PMID: 27863297 PMCID: PMC5278158 DOI: 10.1016/j.redox.2016.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/13/2016] [Accepted: 10/16/2016] [Indexed: 01/06/2023] Open
Abstract
Infection with oncogenic human papillomavirus induces deregulation of cellular redox homeostasis. Virus replication and papillomavirus-induced cell transformation require persistent expression of viral oncoproteins E7 and E6 that must retain their functionality in a persistent oxidative environment. Here, we dissected the molecular mechanisms by which E7 oncoprotein can sense and manage the potentially harmful oxidative environment of the papillomavirus-infected cell. The carboxy terminal domain of E7 protein from most of the 79 papillomavirus viral types of alpha genus, which encloses all the tumorigenic viral types, is a cysteine rich domain that contains two classes of cysteines: strictly conserved low reactive Zn+2 binding and degenerate reactive cysteine residues that can sense reactive oxygen species (ROS). Based on experimental data obtained from E7 proteins from the prototypical viral types 16, 18 and 11, we identified a couple of low pKa nucleophilic cysteines that can form a disulfide bridge upon the exposure to ROS and regulate the cytoplasm to nucleus transport. From sequence analysis and phylogenetic reconstruction of redox sensing states we propose that reactive cysteine acquisition through evolution leads to three separate E7s protein families that differ in the ROS sensing mechanism: non ROS-sensitive E7s; ROS-sensitive E7s using only a single or multiple reactive cysteine sensing mechanisms and ROS-sensitive E7s using a reactive-resolutive cysteine couple sensing mechanism. Transforming protein ROS-sensing. Reactive cysteine acquisition through evolution. Redox-switching mechanism. Papillomavirus-induced cancers.
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Affiliation(s)
- Gabriela Camporeale
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Juan R Lorenzo
- ULB-Neuroscience Institute, Universite Libre de Bruxelles, Bruxelles, Belgium
| | - Maria G Thomas
- RNA Cell Biology Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Edgardo Salvatierra
- Laboratory of Molecular and Cellular Therapy, Fundación Instituto Leloir-CONICET and IIBBA-CONICET, Buenos Aires, Argentina
| | - Silvia S Borkosky
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Marikena G Risso
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Ignacio E Sánchez
- Protein Physiology Laboratory, Universidad de Buenos Aires, CONICET, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
| | - Gonzalo de Prat Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina.
| | - Leonardo G Alonso
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina.
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16
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Songock WK, Kim SM, Bodily JM. The human papillomavirus E7 oncoprotein as a regulator of transcription. Virus Res 2016; 231:56-75. [PMID: 27818212 DOI: 10.1016/j.virusres.2016.10.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 12/12/2022]
Abstract
High-risk human papillomaviruses (HPVs) encode oncoproteins which manipulate gene expression patterns in the host keratinocytes to facilitate viral replication, regulate viral transcription, and promote immune evasion and persistence. In some cases, oncoprotein-induced changes in host cell behavior can cause progression to cancer, but a complete picture of the functions of the viral oncoproteins in the productive HPV life cycle remains elusive. E7 is the HPV-encoded factor most responsible for maintaining cell cycle competence in differentiating keratinocytes. Through interactions with dozens of host factors, E7 has an enormous impact on host gene expression patterns. In this review, we will examine the role of E7 specifically as a regulator of transcription. We will discuss mechanisms of regulation of cell cycle-related genes by E7 as well as genes involved in immune regulation, growth factor signaling, DNA damage responses, microRNAs, and others pathways. We will also discuss some unanswered questions about how transcriptional regulation by E7 impacts the biology of HPV in both benign and malignant conditions.
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Affiliation(s)
- William K Songock
- Department of Microbiology and Immunology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Seong-Man Kim
- Department of Microbiology and Immunology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Jason M Bodily
- Department of Microbiology and Immunology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA.
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17
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DeForte S, Reddy KD, Uversky VN. Quarterly intrinsic disorder digest (January-February-March, 2014). INTRINSICALLY DISORDERED PROTEINS 2016; 4:e1153395. [PMID: 28232896 DOI: 10.1080/21690707.2016.1153395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This is the 5th issue of the Digested Disorder series that represents a reader's digest of the scientific literature on intrinsically disordered proteins. We continue to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the first quarter of 2014; i.e., during the period of January, February, and March of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida , Tampa, FL, USA
| | - Krishna D Reddy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida , Tampa, FL, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Biology Department, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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18
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Foppoli C, De Marco F, Cini C, Perluigi M. Redox control of viral carcinogenesis: The human papillomavirus paradigm. Biochim Biophys Acta Gen Subj 2014; 1850:1622-32. [PMID: 25534611 DOI: 10.1016/j.bbagen.2014.12.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/11/2014] [Accepted: 12/13/2014] [Indexed: 01/01/2023]
Abstract
BACKGROUND Cervical cancer is the second most common neoplastic disease among women worldwide. The initiating event of such cancer is the infection with certain types of human papillomavirus (HPV), a very common condition in the general population. However, the majority of HPV infections is subclinical and transitory and is resolved spontaneously. Intriguingly, viral oncogene expression, although necessary, is not per se sufficient to promote cervical cancer and other factors are involved in the progression of infected cells to the full neoplastic phenotype. In this perspective it has been suggested that the redox balance and the oxidative stress (OS) may represent interesting and under-explored candidates as promoting factors in HPV-initiated carcinogenesis. SCOPE OF THE REVIEW The current review discusses the possible interplay between the viral mechanisms modulating cell homeostasis and redox sensitive mechanisms. Experimental data and indirect evidences are presented on the activity of viral dependent functions on i) the regulation of enzymes and compounds involved in OS; ii) the protection from oxidation of detoxifying/antiapoptotic enzymes and redox-sensitive transcription factors; iii) the suppression of apoptosis; and iv) the modulation of host microRNAs regulating genes associated with antioxidant defense. MAJOR CONCLUSIONS The resulting tangled scenario suggests that viral hosting cells adapt their metabolisms in order to support their growth and survival in the increasingly oxidant micro-environment associated with HPV tumor initiation and progression. GENERAL SIGNIFICANCE HPV can modulate the host cell redox homeostasis in order to favor infection and possibly tumor transformation. This article is part of a Special Issue entitled Redox regulation of differentiation and de-differentiation.
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Affiliation(s)
- Cesira Foppoli
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Federico De Marco
- Laboratory of Virology, Regina Elena National Cancer Institute, Rome, Italy
| | - Chiara Cini
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - M Perluigi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.
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