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Rabaan AA, Al Fares MA, Almaghaslah M, Alpakistany T, Al Kaabi NA, Alshamrani SA, Alshehri AA, Almazni IA, Saif A, Hakami AR, Khamis F, Alfaresi M, Alsalem Z, Alsoliabi ZA, Al Amri KAS, Hassoueh AK, Mohapatra RK, Arteaga-Livias K, Alissa M. Application of CRISPR-Cas System to Mitigate Superbug Infections. Microorganisms 2023; 11:2404. [PMID: 37894063 PMCID: PMC10609045 DOI: 10.3390/microorganisms11102404] [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: 08/08/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
Multidrug resistance in bacterial strains known as superbugs is estimated to cause fatal infections worldwide. Migration and urbanization have resulted in overcrowding and inadequate sanitation, contributing to a high risk of superbug infections within and between different communities. The CRISPR-Cas system, mainly type II, has been projected as a robust tool to precisely edit drug-resistant bacterial genomes to combat antibiotic-resistant bacterial strains effectively. To entirely opt for its potential, advanced development in the CRISPR-Cas system is needed to reduce toxicity and promote efficacy in gene-editing applications. This might involve base-editing techniques used to produce point mutations. These methods employ designed Cas9 variations, such as the adenine base editor (ABE) and the cytidine base editor (CBE), to directly edit single base pairs without causing DSBs. The CBE and ABE could change a target base pair into a different one (for example, G-C to A-T or C-G to A-T). In this review, we addressed the limitations of the CRISPR/Cas system and explored strategies for circumventing these limitations by applying diverse base-editing techniques. Furthermore, we also discussed recent research showcasing the ability of base editors to eliminate drug-resistant microbes.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Mona A Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia
| | - Manar Almaghaslah
- Infectious Disease Division, Department of Internal Medicine, Dammam Medical Complex, Dammam 32245, Saudi Arabia
| | - Tariq Alpakistany
- Bacteriology Department, Public Health Laboratory, Taif 26521, Saudi Arabia
| | - Nawal A Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Saleh A Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ibrahim Abdullah Almazni
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Ahmed Saif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62223, Saudi Arabia
| | - Abdulrahim R Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62223, Saudi Arabia
| | - Faryal Khamis
- Infection Diseases Unit, Department of Internal Medicine, Royal Hospital, Muscat 1331, Oman
| | - Mubarak Alfaresi
- Department of Pathology and Laboratory Medicine, Zayed Military Hospital, Abu Dhabi 3740, United Arab Emirates
- Department of Pathology, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates
| | - Zainab Alsalem
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | | | - Amal K Hassoueh
- Pharmacy Department, King Saud Medical City, Riyadh 7790, Saudi Arabia
| | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, India
| | - Kovy Arteaga-Livias
- Escuela de Medicina-Filial Ica, Universidad Privada San Juan Bautista, Ica 11000, Peru
- Escuela de Medicina, Universidad Nacional Hermilio Valdizán, Huanuco 10000, Peru
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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2
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Ali A, Zafar MM, Farooq Z, Ahmed SR, Ijaz A, Anwar Z, Abbas H, Tariq MS, Tariq H, Mustafa M, Bajwa MH, Shaukat F, Razzaq A, Maozhi R. Breakthrough in CRISPR/Cas system: Current and future directions and challenges. Biotechnol J 2023; 18:e2200642. [PMID: 37166088 DOI: 10.1002/biot.202200642] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023]
Abstract
Targeted genome editing (GE) technology has brought a significant revolution in fictional genomic research and given hope to plant scientists to develop desirable varieties. This technology involves inducing site-specific DNA perturbations that can be repaired through DNA repair pathways. GE products currently include CRISPR-associated nuclease DNA breaks, prime editors generated DNA flaps, single nucleotide-modifications, transposases, and recombinases. The discovery of double-strand breaks, site-specific nucleases (SSNs), and repair mechanisms paved the way for targeted GE, and the first-generation GE tools, ZFNs and TALENs, were successfully utilized in plant GE. However, CRISPR-Cas has now become the preferred tool for GE due to its speed, reliability, and cost-effectiveness. Plant functional genomics has benefited significantly from the widespread use of CRISPR technology for advancements and developments. This review highlights the progress made in CRISPR technology, including multiplex editing, base editing (BE), and prime editing (PE), as well as the challenges and potential delivery mechanisms.
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Affiliation(s)
- Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | | | - Zunaira Farooq
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Aqsa Ijaz
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Zunaira Anwar
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Huma Abbas
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Sayyam Tariq
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Hala Tariq
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Mahwish Mustafa
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | | | - Fiza Shaukat
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Abdul Razzaq
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Ren Maozhi
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Institute of, Urban Agriculture, Chinese Academy of Agriculture Science, Chengdu, China
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3
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Qian Y, Gong Y, Zou X, Liu Y, Chen Y, Wang R, Dai Z, Tasiheng Y, Lin X, Wang X, Luo G, Yu X, Cheng H, Liu C. Aberrant APOBEC3C expression induces characteristic genomic instability in pancreatic ductal adenocarcinoma. Oncogenesis 2022; 11:35. [PMID: 35750693 PMCID: PMC9232547 DOI: 10.1038/s41389-022-00411-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 11/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a well-known lethal and heterogeneous disease. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) is an important mutagenic driver that has seldom been investigated in PDAC. Therefore, this study investigated the significance of APOBEC3C in PDAC. First, cytosine deamination-associated mutation signatures were identified in the PDAC cohorts from TCGA and Fudan University Shanghai Cancer Center (FUSCC) datasets, and C > X-enriched kataegis regions were identified in the FUSCC cohort (12 to 27 counts per sample). Patients were stratified according to APOBEC3C expression, and high APOBEC3C expression was found to correlate with a higher motif enrichment score of 5’-CC-3’ and an elevated kataegis count within PCSK5 and NES genes. Second, we compared APOBEC expression in PDAC and normal pancreatic tissues and found that APOBEC3C was substantially upregulated in PDAC. APOBEC3C-overexpressing cell lines were generated to substantiate the effects of APOBEC3C on PDAC genome, including alterations in single-nucleotide variant (SNV) classes (higher proportion of C > T conversions) and the formation of kataegis regions (newly occurring kataegis regions detected in ACHE and MUC6 genes). Three different PDAC cohorts (FUSCC, TCGA, and QCMG) were analysed to evaluate the prognostic value of APOBEC3C, and APOBEC3C overexpression predicted shorter survival. Finally, the APOBEC3C overexpression correalted with the PDAC tumour microenvironment (TME) remodelling, APOBEC3C expression was associated with the invasion of CD4 + T lymphocytes and CD8 + T lymphocytes (cytotoxic T lymphocytes, CTLs), indicating enhanced immune activity and validating the practicality of APOBEC3C for guiding immunotherapy.
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Affiliation(s)
- Yunzhen Qian
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Yitao Gong
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Xuan Zou
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Yu Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Yusheng Chen
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Ruijie Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Zhengjie Dai
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Yesiboli Tasiheng
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Xuan Lin
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Xu Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Guopei Luo
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China.,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China.,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China. .,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China. .,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China.
| | - He Cheng
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China. .,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China. .,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China.
| | - Chen Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China. .,Department of Oncology, Shanghai Medical College, Fudan University, 200032, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, 200032, Shanghai, China. .,Pancreatic Cancer Institute, Fudan University, 200032, Shanghai, China.
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4
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Ni L, Li C, Li Y. Correlation of APOBEC3G expression with liver function indexes of patients with chronic hepatitis B and comparison in chronic hepatitis B, liver cirrhosis and liver cancer. Oncol Lett 2020; 19:2562-2567. [PMID: 32194760 DOI: 10.3892/ol.2020.11257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/05/2019] [Indexed: 01/23/2023] Open
Abstract
Correlation of APOBEC3G expression with liver function indexes of patients with chronic hepatitis B and its expression in chronic hepatitis B, liver cirrhosis and liver cancer were investigated to evaluated the significance of APOBEC3G. Fifty-eight patients with chronic hepatitis B were selected, including 20 cases of chronic hepatitis B, 19 cases of liver cirrhosis and 19 cases of liver cancer. Liver function indexes were detected and analyzed, and messenger ribonucleic acid (mRNA) and protein expression levels of APOBEC3G in liver tissues were detected via reverse transcription-polymerase chain reaction (RT-PCR), western blotting and immunohistochemistry, followed by correlation analysis. Certain liver function indexes had significant differences among the three groups of patients (P<0.05). Results of RT-PCR, Western blotting and immunohistochemistry confirmed that the content of APOBEC3G in liver tissues was the highest in patients with chronic hepatitis B, slightly lower in patients with liver cirrhosis and the lowest in patients with liver cancer. The content of APOBEC3G mRNA in liver tissues had a certain correlation with the content of alanine aminotransferase (ALT) (r2 =0.34, P<0.05). Other liver function indexes had no significant correlations with APOBEC3G (P>0.05). APOBEC3G expression has a certain correlation with some liver function indexes of patients with chronic hepatitis B. There are significant differences in the expression level of APOBEC3G in patients with hepatitis, liver cirrhosis and liver cancer.
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Affiliation(s)
- Lina Ni
- Department of Blood Transfusion, Weihai Central Hospital, Wendeng, Weihai, Shandong 264400, P.R. China
| | - Chuanbao Li
- Department of Hepatobiliary Surgery, Weihai Central Hospital, Wendeng, Weihai, Shandong 264400, P.R. China
| | - Yingbo Li
- Department of Blood Transfusion, Weihai Central Hospital, Wendeng, Weihai, Shandong 264400, P.R. China
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5
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Mishra R, Joshi RK, Zhao K. Base editing in crops: current advances, limitations and future implications. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:20-31. [PMID: 31365173 PMCID: PMC6920333 DOI: 10.1111/pbi.13225] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/23/2019] [Accepted: 07/29/2019] [Indexed: 05/19/2023]
Abstract
Targeted mutagenesis via genome-editing technologies holds great promise in developing improved crop varieties to meet future demands. Point mutations or single nucleotide polymorphisms often determine important agronomic traits of crops. Genome-editing-based single-base changes could generate elite trait variants in crop plants which help in accelerating crop improvement. Among the genome-editing technologies, base editing has emerged as a novel and efficient genome-editing approach which enables direct and irreversible conversion of one target base into another in a programmable manner. A base editor is a fusion of catalytically inactive CRISPR-Cas9 domain (Cas9 variants) and cytosine or adenosine deaminase domain that introduces desired point mutations in the target region enabling precise editing of genomes. In the present review, we have summarized the development of different base-editing platforms. Then, we have focussed on the current advances and the potential applications of this precise technology in crop improvement. The review also sheds light on the limitations associated with this technology. Finally, the future perspectives of this emerging technology towards crop improvement have been highlighted.
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Affiliation(s)
- Rukmini Mishra
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop ScienceChinese Academy of Agriculture Sciences (CAAS)BeijingChina
| | - Raj Kumar Joshi
- Department of BiotechnologyRama Devi Women's UniversityBhubaneswarOdishaIndia
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop ScienceChinese Academy of Agriculture Sciences (CAAS)BeijingChina
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6
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Arazoe T, Kondo A, Nishida K. Targeted Nucleotide Editing Technologies for Microbial Metabolic Engineering. Biotechnol J 2018; 13:e1700596. [PMID: 29862665 DOI: 10.1002/biot.201700596] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/15/2018] [Indexed: 12/31/2022]
Abstract
Since the emergence of programmable RNA-guided nucleases based on clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems, genome editing technologies have become a simplified and versatile tool for genome editing in various organisms and cell types. Although genome editing enables efficient genome manipulations, such as gene disruptions, gene knockins, and chromosomal translocations via DNA double-strand break (DSB) repair in eukaryotes, DSBs induced by the CRISPR/Cas system are lethal or severely toxic to many microorganisms. Therefore, in many prokaryotes, including industrially useful microbes, the CRISPR/Cas system is often used as a negative selection component in combination with recombineering or other related strategies. Novel and revolutionary technologies have been recently developed to re-write targeted nucleotides (C:G to T:A and A:T to G:C) without DSBs and donor DNA templates. These technologies rely on the recruitment of deaminases at specific target loci using the nuclease-deficient CRISPR/Cas system. Here, the authors review and compare CRISPR-based genome editing, current base editing platforms and their spectra. The authors discuss how these technologies can be applied in various aspects of microbial metabolic engineering to overcome barriers to cellular regulation in prokaryotes.
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Affiliation(s)
- Takayuki Arazoe
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Keiji Nishida
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
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7
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Eid A, Alshareef S, Mahfouz MM. CRISPR base editors: genome editing without double-stranded breaks. Biochem J 2018. [PMID: 29891532 DOI: 10.1042/bcj2017079.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 adaptive immunity system has been harnessed for genome editing applications across eukaryotic species, but major drawbacks, such as the inefficiency of precise base editing and off-target activities, remain. A catalytically inactive Cas9 variant (dead Cas9, dCas9) has been fused to diverse functional domains for targeting genetic and epigenetic modifications, including base editing, to specific DNA sequences. As base editing does not require the generation of double-strand breaks, dCas9 and Cas9 nickase have been used to target deaminase domains to edit specific loci. Adenine and cytidine deaminases convert their respective nucleotides into other DNA bases, thereby offering many possibilities for DNA editing. Such base-editing enzymes hold great promise for applications in basic biology, trait development in crops, and treatment of genetic diseases. Here, we discuss recent advances in precise gene editing using different platforms as well as their potential applications in basic biology and biotechnology.
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Affiliation(s)
- Ayman Eid
- Laboratory for Genome Engineering, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sahar Alshareef
- Laboratory for Genome Engineering, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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8
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CRISPR base editors: genome editing without double-stranded breaks. Biochem J 2018; 475:1955-1964. [PMID: 29891532 PMCID: PMC5995079 DOI: 10.1042/bcj20170793] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 05/12/2018] [Accepted: 05/15/2018] [Indexed: 12/26/2022]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 adaptive immunity system has been harnessed for genome editing applications across eukaryotic species, but major drawbacks, such as the inefficiency of precise base editing and off-target activities, remain. A catalytically inactive Cas9 variant (dead Cas9, dCas9) has been fused to diverse functional domains for targeting genetic and epigenetic modifications, including base editing, to specific DNA sequences. As base editing does not require the generation of double-strand breaks, dCas9 and Cas9 nickase have been used to target deaminase domains to edit specific loci. Adenine and cytidine deaminases convert their respective nucleotides into other DNA bases, thereby offering many possibilities for DNA editing. Such base-editing enzymes hold great promise for applications in basic biology, trait development in crops, and treatment of genetic diseases. Here, we discuss recent advances in precise gene editing using different platforms as well as their potential applications in basic biology and biotechnology.
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9
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Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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10
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Hess GT, Tycko J, Yao D, Bassik MC. Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes. Mol Cell 2017; 68:26-43. [PMID: 28985508 PMCID: PMC5997582 DOI: 10.1016/j.molcel.2017.09.029] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022]
Abstract
The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology.
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Affiliation(s)
- Gaelen T Hess
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Josh Tycko
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - David Yao
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics and Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, CA, USA.
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11
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Schmidt T, Leha A, Salinas-Riester G. Treatment of prostate cancer cells with S-adenosylmethionine leads to genome-wide alterations in transcription profiles. Gene 2016; 595:161-167. [PMID: 27688072 DOI: 10.1016/j.gene.2016.09.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/22/2016] [Indexed: 12/26/2022]
Abstract
The hypomethylation of DNA may support tumor progression; however, the mechanism underlying this relationship is not clear. Several studies have demonstrated that the in vitro application of the methyl donor S-adenosylmethionine (SAM) leads to promoter remethylation and the downregulation of proto-oncogene expression in cancer cells. It is not clear if this represents a general mechanism of SAM or is limited to selected genes. We examined this problem using new bisulfite sequencing and transcriptomic technologies. Treatment with SAM caused the downregulation of proliferation, migration, and invasion of prostate cancer (PC-3) cells. RNA sequencing revealed the genome-wide downregulation of genes involved in proliferation, migration, invasion, and angiogenesis. Real-time PCR of a subset of the genes confirmed these results. Reduced representation bisulfite sequencing (RRBS) displayed only minor differential methylation between treated cells and controls. In summary, we confirmed the anti-proliferative and anti-invasive effects of SAM. Additionally, we observed anti-migratory effects and downregulation of genes, especially those related to cancerogenesis. For some of the related genes, this is the first reported evidence of an association with prostate cancer. However, genome-wide modifications in methylation profiles were not observed by RRBS; thus, they are obviously not a major cause of alteration in transcription profiles and anti-cancer effects.
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Affiliation(s)
- Thomas Schmidt
- Institute of Anatomy and Clinical Morphology, University of Witten/Herdecke, 58448 Witten, Germany.
| | - Andreas Leha
- Department of Medical Statistics, University Medical Center, Goettingen, 37073 Goettingen, Germany
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Pham P, Afif SA, Shimoda M, Maeda K, Sakaguchi N, Pedersen LC, Goodman MF. Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification. DNA Repair (Amst) 2016; 43:48-56. [PMID: 27258794 DOI: 10.1016/j.dnarep.2016.05.029] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 05/10/2016] [Indexed: 12/18/2022]
Abstract
Activation-induced deoxycytidine deaminase (AID) initiates somatic hypermutation (SHM) and class-switch recombination (CSR) by deaminating C→U during transcription of Ig-variable (V) and Ig-switch (S) region DNA, which is essential to produce high-affinity antibodies. Here we report the crystal structure of a soluble human AID variant at 2.8Å resolution that favors targeting WRC motifs (W=A/T, R=A/G) in vitro, and executes Ig V SHM in Ramos B-cells. A specificity loop extending away from the active site to accommodate two purine bases next to C, differs significantly in sequence, length, and conformation from APOBEC proteins Apo3A and Apo3G, which strongly favor pyrimidines at -1 and -2 positions. Individual amino acid contributions to specificity and processivity were measured in relation to a proposed ssDNA binding cleft. This study provides a structural basis for residue contributions to DNA scanning properties unique to AID, and for disease mutations in human HIGM-2 syndrome.
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Affiliation(s)
- Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States
| | - Samir A Afif
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States
| | - Mayuko Shimoda
- Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan; Laboratory of Host Defence, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan
| | - Kazuhiko Maeda
- Laboratory of Host Defence, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan
| | - Nobuo Sakaguchi
- World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, 565-0871, Japan; Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, United States
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, United States; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, United States.
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Valera MS, de Armas-Rillo L, Barroso-González J, Ziglio S, Batisse J, Dubois N, Marrero-Hernández S, Borel S, García-Expósito L, Biard-Piechaczyk M, Paillart JC, Valenzuela-Fernández A. The HDAC6/APOBEC3G complex regulates HIV-1 infectiveness by inducing Vif autophagic degradation. Retrovirology 2015; 12:53. [PMID: 26105074 PMCID: PMC4479245 DOI: 10.1186/s12977-015-0181-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 06/10/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) has evolved a complex strategy to overcome the immune barriers it encounters throughout an organism thanks to its viral infectivity factor (Vif), a key protein for HIV-1 infectivity and in vivo pathogenesis. Vif interacts with and promotes "apolipoprotein B mRNA-editing enzyme-catalytic, polypeptide-like 3G" (A3G) ubiquitination and subsequent degradation by the proteasome, thus eluding A3G restriction activity against HIV-1. RESULTS We found that cellular histone deacetylase 6 (HDAC6) directly interacts with A3G through its C-terminal BUZ domain (residues 841-1,215) to undergo a cellular co-distribution along microtubules and cytoplasm. The HDAC6/A3G complex occurs in the absence or presence of Vif, competes for Vif-mediated A3G degradation, and accounts for A3G steady-state expression level. In fact, HDAC6 directly interacts with and promotes Vif autophagic clearance, thanks to its C-terminal BUZ domain, a process requiring the deacetylase activity of HDAC6. HDAC6 degrades Vif without affecting the core binding factor β (CBF-β), a Vif-associated partner reported to be key for Vif- mediated A3G degradation. Thus HDAC6 antagonizes the proviral activity of Vif/CBF-β-associated complex by targeting Vif and stabilizing A3G. Finally, in cells producing virions, we observed a clear-cut correlation between the ability of HDAC6 to degrade Vif and to restore A3G expression, suggesting that HDAC6 controls the amount of Vif incorporated into nascent virions and the ability of HIV-1 particles of being infectious. This effect seems independent on the presence of A3G inside virions and on viral tropism. CONCLUSIONS Our study identifies for the first time a new cellular complex, HDAC6/A3G, involved in the autophagic degradation of Vif, and suggests that HDAC6 represents a new antiviral factor capable of controlling HIV-1 infectiveness by counteracting Vif and its functions.
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Affiliation(s)
- María-Soledad Valera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Laura de Armas-Rillo
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Jonathan Barroso-González
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Serena Ziglio
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Julien Batisse
- Architecture et Réactivité de l'ARN, CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France.
| | - Noé Dubois
- Architecture et Réactivité de l'ARN, CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France.
| | - Sara Marrero-Hernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Sophie Borel
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS) UMR5236 CNRS UMSF, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Laura García-Expósito
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
| | - Martine Biard-Piechaczyk
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS) UMR5236 CNRS UMSF, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Jean-Christophe Paillart
- Architecture et Réactivité de l'ARN, CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 15 rue René Descartes, 67084, Strasbourg, France.
| | - Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, La Laguna, Tenerife, Spain.
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Bęczkowski PM, Hughes J, Biek R, Litster A, Willett BJ, Hosie MJ. Feline immunodeficiency virus (FIV) env recombinants are common in natural infections. Retrovirology 2014; 11:80. [PMID: 25699660 PMCID: PMC4180853 DOI: 10.1186/s12977-014-0080-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/01/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recombination is a common feature of retroviral biology and one of the most important factors responsible for generating viral diversity at both the intra-host and the population levels. However, relatively little is known about rates and molecular processes of recombination for retroviruses other than HIV, including important model viruses such as feline immunodeficiency virus (FIV). RESULTS We investigated recombination in complete FIV env gene sequences (n = 355) isolated from 43 naturally infected cats. We demonstrated that recombination is abundant in natural FIV infection, with over 41% of the cats being infected with viruses containing recombinant env genes. In addition, we identified shared recombination breakpoints; the most significant hotspot occurred between the leader/signal fragment and the remainder of env. CONCLUSIONS Our results have identified the leader/signal fragment of env as an important site for recombination and highlight potential limitations of the current phylogenetic classification of FIV based on partial env sequences. Furthermore, the presence of abundant recombinant FIV in the USA poses a significant challenge for commercial diagnostic tests and should inform the development of the next generation of FIV vaccines.
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Jones PH, Mehta HV, Okeoma CM. A novel role for APOBEC3: susceptibility to sexual transmission of murine acquired immunodeficiency virus (mAIDS) is aggravated in APOBEC3 deficient mice. Retrovirology 2012; 9:50. [PMID: 22691411 PMCID: PMC3418182 DOI: 10.1186/1742-4690-9-50] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/16/2012] [Indexed: 01/28/2023] Open
Abstract
Background APOBEC3 proteins are host factors that restrict infection by retroviruses like HIV, MMTV, and MLV and are variably expressed in hematopoietic and non-hematopoietic cells, such as macrophages, lymphocytes, dendritic, and epithelia cells. Previously, we showed that APOBEC3 expressed in mammary epithelia cells function to limit milk-borne transmission of the beta-retrovirus, mouse mammary tumor virus. In this present study, we used APOBEC3 knockout mice and their wild type counterpart to query the role of APOBEC3 in sexual transmission of LP-BM5 MLV – the etiological agent of murine AIDs (mAIDs). Results We show that mouse APOBEC3 is expressed in murine genital tract tissues and gametes and that genital tract tissue of APOBEC3-deficient mice are more susceptible to infection by LP-BM5 virus. APOBEC3 expressed in genital tract tissues most likely plays a role in decreasing virus transmission via the sexual route, since mice deficient in APOBEC3 gene have higher genitalia and seminal plasma virus load and sexually transmit the virus more efficiently to their partners compared to APOBEC3+ mice. Moreover, we show that female mice sexually infected with LP-BM5 virus transmit the virus to their off-spring in APOBEC3-dependent manner. Conclusion Our data indicate that genital tissue intrinsic APOBEC3 restricts genital tract infection and limits sexual transmission of LP-BM5 virus.
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Affiliation(s)
- Philip H Jones
- Department of Microbiology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242-1109, USA
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16
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Wang Y, Whittall T, Rahman D, Bunnik EM, Vaughan R, Schøller J, Bergmeier LA, Montefiori D, Singh M, Schuitemaker H, Lehner T. The role of innate APOBEC3G and adaptive AID immune responses in HLA-HIV/SIV immunized SHIV infected macaques. PLoS One 2012; 7:e34433. [PMID: 22514633 PMCID: PMC3326050 DOI: 10.1371/journal.pone.0034433] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 02/28/2012] [Indexed: 01/27/2023] Open
Abstract
The AID/APOBEC family (activation induced deaminase/apolipoprotein B mRNA editing cytokine deaminase) in B cells play important roles in adaptive and innate immunity. Whereas APOBEC3G has been studied in CD4+ T cells and myeloid cells its functional potential in B cells has received little attention. AID combines two critical functions of antibodies, class switching and affinity maturation and may serve as a functional surrogate of protection. These functions were studied following systemic immunization of rhesus macaques with recombinant HLA constructs, linked with HIV and SIV antigens and HSP70 to dextran. The results showed significant upregulation of AID in CD20+ B cells, APOBEC 3G in CD27+ memory B cells and CD4+ effector memory T cells. After immunization the upregulated APOBEC 3G and AID were directly correlated in B cells (p<0.0001). Following challenge with SHIV SF162.P4 the viral load was inversely correlated with AID in B cells and APOBEC 3G in B and T cells, suggesting that both deaminases may have protective functions. Investigation of major interactions between DC, T cells and B cells showed significant increase in membrane associated IL-15 in DC and CD40L in CD4+ T cells. IL-15 binds the IL-15 receptor complex in CD4+ T and B cells, which may reactivate the DC, T and B cell interactions. The overall results are consistent with AID inhibiting pre-entry SHIV by eliciting IgG and IgA antibodies, whereas APOBEC 3G may contribute to the post-entry control of SHIV replication and cellular spread.
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Affiliation(s)
- Yufei Wang
- Mucosal Immunology Unit, King's College London, Guy's Hospital, London, United Kingdom
| | - Trevor Whittall
- Mucosal Immunology Unit, King's College London, Guy's Hospital, London, United Kingdom
| | - Durdana Rahman
- Mucosal Immunology Unit, King's College London, Guy's Hospital, London, United Kingdom
| | | | - Robert Vaughan
- Department of Tissue Typing, King's College London, Guy's Hospital, London, United Kingdom
| | | | - Lesley A. Bergmeier
- Queen Mary, University of London, Barts and The London Schools of Medicine and Dentistry, Centre for Clinical and Diagnostic Oral Sciences, London, United Kingdom
| | - David Montefiori
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | | | | | - Thomas Lehner
- Mucosal Immunology Unit, King's College London, Guy's Hospital, London, United Kingdom
- * E-mail:
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Expression analysis of LEDGF/p75, APOBEC3G, TRIM5alpha, and tetherin in a Senegalese cohort of HIV-1-exposed seronegative individuals. PLoS One 2012; 7:e33934. [PMID: 22479480 PMCID: PMC3313979 DOI: 10.1371/journal.pone.0033934] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/23/2012] [Indexed: 11/19/2022] Open
Abstract
Background HIV-1 replication depends on a delicate balance between cellular co-factors and antiviral restriction factors. Lens epithelium-derived growth factor (LEDGF/p75) benefits HIV, whereas apolipoprotein B mRNA-editing catalytic polypeptide-like 3G (APOBEC3G), tripartite motif 5alpha (TRIM5α), and tetherin exert anti-HIV activity. Expression levels of these proteins possibly contribute to HIV-1 resistance in HIV-1-exposed populations. Methodology/Principal Findings We used real-time PCR and flow cytometry to study mRNA and protein levels respectively in PBMC and PBMC subsets. We observed significantly reduced LEDGF/p75 protein levels in CD4+ lymphocytes of HIV-1-exposed seronegative subjects relative to healthy controls, whereas we found no differences in APOBEC3G, TRIM5α, or tetherin expression. Untreated HIV-1-infected patients generally expressed higher mRNA and protein levels than healthy controls. Increased tetherin levels, in particular, correlated with markers of disease progression: directly with the viral load and T cell activation and inversely with the CD4 count. Conclusions/Significance Our data suggest that reduced LEDGF/p75 levels may play a role in resistance to HIV-1 infection, while increased tetherin levels could be a marker of advanced HIV disease. Host factors that influence HIV-1 infection and disease could be important targets for new antiviral therapies.
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Direct evidence that RNA inhibits APOBEC3G ssDNA cytidine deaminase activity. Biochem Biophys Res Commun 2011; 412:612-7. [PMID: 21856286 DOI: 10.1016/j.bbrc.2011.08.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 08/04/2011] [Indexed: 11/20/2022]
Abstract
APOBEC3G (A3G) is a deoxycytidine deaminase active on ssDNA substrates. In HIV infected cells A3G interacted with reverse transcription complexes where its activity as a deoxycytidine deaminase led to mutation of the viral genome. A3G not only bound ssDNA, but it also had an intrinsic ability to bind RNA. In many cell types that can support HIV replication, A3G ssDNA deaminase activity was suppressed and the enzyme resided in high molecular mass, ribonucleoprotein complexes associated with cytoplasmic P-bodies and stress granules. Using a defined in vitro system, we show that RNA alone was sufficient to suppress A3G deaminase activity and did so in an RNA concentration-dependent manner. RNAs of diverse sequences and as short as 25nt were effective inhibitors. Native PAGE analyses showed that RNA formed ribonucleoprotein complexes with A3G and in so doing prevented ssDNA substrates from binding to A3G. The data provided direct evidence that A3G binding to cellular RNAs constituted a substantial impediment to the enzyme's ability to interact with ssDNA.
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Mous K, Jennes W, De Roo A, Pintelon I, Kestens L, Van Ostade X. Intracellular detection of differential APOBEC3G, TRIM5alpha, and LEDGF/p75 protein expression in peripheral blood by flow cytometry. J Immunol Methods 2011; 372:52-64. [PMID: 21784078 DOI: 10.1016/j.jim.2011.06.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 06/24/2011] [Accepted: 06/24/2011] [Indexed: 01/07/2023]
Abstract
Expression studies on specific host proteins predominantly use quantitative PCR and western blotting assays. In this study, we optimized a flow cytometry-based assay to study intracellular expression levels of three important host proteins involved in HIV-1 replication: apolipoprotein B mRNA-editing catalytic polypeptide-like 3G (APOBEC3G), tripartite motif 5alpha (TRIM5α), and lens epithelium-derived growth factor (LEDGF/p75). An indirect intracellular staining (ICS) method was optimized using antibodies designed for other applications like enzyme-linked immunosorbent assay (ELISA), confocal imaging, and western blotting. The median fluorescence intensity (MFI) value--a measure for the protein expression level--increased upon higher antibody concentration and longer incubation time, and was reduced following preincubation with recombinant proteins. Staining of stably transfected or knock-down cell lines supported the method's specificity. Moreover, confocal microscopy analysis of peripheral blood mononuclear cells (PBMC), when stained according to the ICS method, confirmed the localization of APOBEC3G and TRIM5α in the cytoplasm, and of LEDGF/p75 in the nucleus. Also, stimulation with mitogen, interferon-alpha, or interferon-beta resulted in detectable, albeit weak, increases in intracellular expression of APOBEC3G and TRIM5α. After optimization, the method was applied to healthy control and HIV-1 infected subjects. For all subjects studied, the memory subset of CD4+ T cells showed significantly higher expression levels of APOBEC3G, TRIM5α, and LEDGF/p75, while the CD16+ subset of monocytes was characterized by higher expression levels of LEDGF/p75. In addition, we observed that therapy-naïve HIV-1 patients tended to have lower expression levels of APOBEC3G and TRIM5α than HIV-1 negative controls. In summary, our data provide proof-of-principle for the detection of specific host factors at the level of a single cell, which may prove useful for our further understanding of their role in virus-host interactions.
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Affiliation(s)
- Kim Mous
- Laboratory for Proteinscience, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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Bernacchi S, Mercenne G, Tournaire C, Marquet R, Paillart JC. Importance of the proline-rich multimerization domain on the oligomerization and nucleic acid binding properties of HIV-1 Vif. Nucleic Acids Res 2010; 39:2404-15. [PMID: 21076154 PMCID: PMC3064812 DOI: 10.1093/nar/gkq979] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The HIV-1 viral infectivity factor (Vif) is required for productive infection of non-permissive cells, including most natural HIV-1 targets, where it counteracts the antiviral activities of the cellular cytosine deaminases APOBEC-3G (A3G) and A3F. Vif is a multimeric protein and the conserved proline-rich domain 161PPLP164 regulating Vif oligomerization is crucial for its function and viral infectivity. Here, we expressed and purified wild-type Vif and a mutant protein in which alanines were substituted for the proline residues of the 161PPLP164 domain. Using dynamic light scattering, circular dichroism and fluorescence spectroscopy, we established the impact of these mutations on Vif oligomerization, secondary structure content and nucleic acids binding properties. In vitro, wild-type Vif formed oligomers of five to nine proteins, while Vif AALA formed dimers and/or trimers. Up to 40% of the unbound wild-type Vif protein appeared to be unfolded, but binding to the HIV-1 TAR apical loop promoted formation of β-sheets. Interestingly, alanine substitutions did not significantly affect the secondary structure of Vif, but they diminished its binding affinity and specificity for nucleic acids. Dynamic light scattering showed that Vif oligomerization, and interaction with folding-promoting nucleic acids, favor formation of high molecular mass complexes. These properties could be important for Vif functions involving RNAs.
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Affiliation(s)
- Serena Bernacchi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France
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21
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The remarkable frequency of human immunodeficiency virus type 1 genetic recombination. Microbiol Mol Biol Rev 2009; 73:451-80, Table of Contents. [PMID: 19721086 DOI: 10.1128/mmbr.00012-09] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The genetic diversity of human immunodeficiency virus type 1 (HIV-1) results from a combination of point mutations and genetic recombination, and rates of both processes are unusually high. This review focuses on the mechanisms and outcomes of HIV-1 genetic recombination and on the parameters that make recombination so remarkably frequent. Experimental work has demonstrated that the process that leads to recombination--a copy choice mechanism involving the migration of reverse transcriptase between viral RNA templates--occurs several times on average during every round of HIV-1 DNA synthesis. Key biological factors that lead to high recombination rates for all retroviruses are the recombination-prone nature of their reverse transcription machinery and their pseudodiploid RNA genomes. However, HIV-1 genes recombine even more frequently than do those of many other retroviruses. This reflects the way in which HIV-1 selects genomic RNAs for coencapsidation as well as cell-to-cell transmission properties that lead to unusually frequent associations between distinct viral genotypes. HIV-1 faces strong and changeable selective conditions during replication within patients. The mode of HIV-1 persistence as integrated proviruses and strong selection for defective proviruses in vivo provide conditions for archiving alleles, which can be resuscitated years after initial provirus establishment. Recombination can facilitate drug resistance and may allow superinfecting HIV-1 strains to evade preexisting immune responses, thus adding to challenges in vaccine development. These properties converge to provide HIV-1 with the means, motive, and opportunity to recombine its genetic material at an unprecedented high rate and to allow genetic recombination to serve as one of the highest barriers to HIV-1 eradication.
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Li Q, Smith AJ, Schacker TW, Carlis JV, Duan L, Reilly CS, Haase AT. Microarray analysis of lymphatic tissue reveals stage-specific, gene expression signatures in HIV-1 infection. THE JOURNAL OF IMMUNOLOGY 2009; 183:1975-82. [PMID: 19596987 DOI: 10.4049/jimmunol.0803222] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Untreated HIV-1 infection progresses through acute and asymptomatic stages to AIDS. Although each of the three stages has well-known clinical, virologic, and immunologic characteristics, much less is known of the molecular mechanisms underlying each stage. In this study, we report lymphatic tissue microarray analyses, revealing for the first time stage-specific patterns of gene expression during HIV-1 infection. We show that although there is a common set of key genes with altered expression throughout all stages, each stage has a unique gene expression signature. The acute stage is most notably characterized by increased expression of hundreds of genes involved in immune activation, innate immune defenses (e.g., RIG-1, MDA-5, TLR7 and TLR8, PKR, APOBEC3B, 3F, 3G), adaptive immunity, and in the proapoptotic Fas-Fas ligand pathway. Yet, quite strikingly, the expression of nearly all acute stage genes return to baseline levels in the asymptomatic stage, accompanying partial control of infection. This transition from acute to asymptomatic stage is tied to increased expression of a diverse array of immunosuppressive genes (e.g., CLEC12B, ILT4, galectin-3, CD160, BCMA, FGL2, LAG3, GPNMB). In the AIDS stage, decreased expression of numerous genes involved in T cell signaling identifies genes contributing to T cell dysfunction. These common and stage-specific gene expression signatures identify potential molecular mechanisms underlying the host response and the slow, natural course of HIV-1 infection.
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Affiliation(s)
- Qingsheng Li
- Department of Microbiology, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
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23
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Wu L, Wu X, Zhu B, Cao X. Identification and functional characterization of a novel cytidine deaminase in a gastropod abalone, Haliotis diversicolor supertexta. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2009; 33:709-717. [PMID: 19150626 DOI: 10.1016/j.dci.2008.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 12/18/2008] [Accepted: 12/18/2008] [Indexed: 05/27/2023]
Abstract
Cytidine deaminase (CDA, also designated CDD) is a zinc-dependent enzyme involved in the pyrimidine salvage pathways and becoming very important in anticancer and antiviral therapy. Here we report the identification and characterization of a CDA homologue in abalone, which we named ab-CDA. The analysis of the amino acids sequence revealed that the ab-CDA shares conserved signature motifs and belongs to homotetrameric class of CDA family. Real-time PCR analysis indicated that the ab-CDA was ubiquitously expressed in various tissues of abalone and relatively higher expressed in hemocyte. Significant up-regulation of ab-CDA was also observed after LPS or Poly I: C challenge. The biological activity of ab-CDA was identified by spectrophotometry analysis and the intracellular localization displayed that ab-CDA was largely concentrated in the cytoplasm and partially in the nuclei. These results strongly suggest that ab-CDA is a CDA homologue and it is involved in the immune response of gastropod abalone.
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Affiliation(s)
- Liuji Wu
- Laboratory of Marine Life Science and Technology, College of Animal Sciences, Zhejiang University, 268 Kaixuan Road, Hangzhou, PR China
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Induction of APOBEC3 in vivo causes increased restriction of retrovirus infection. J Virol 2009; 83:3486-95. [PMID: 19153238 DOI: 10.1128/jvi.02347-08] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
APOBEC3 proteins are important cellular factors that restrict infection by a number of viruses, including human immunodeficiency virus type 1 (HIV-1). Previously, we found that the mouse APOBEC3 (mA3) restricts infection by mouse mammary tumor virus (MMTV) in its natural host. Dendritic cells (DCs) are the first in vivo targets of MMTV infection. In this study, we demonstrate that mA3 expressed in target cells restricts MMTV infection in DCs ex vivo and in vivo. By comparing infection of DCs from mA3(+/+) and mA3(-/-) mice with one-hit viruses, we show that mA3 expression in target cells blocked MMTV infection at a postentry step and acted together with virion-packaged mA3 to inhibit infection. Similar results were obtained upon infection of mouse DCs with HIV-1 cores pseudotyped with vesicular stomatitis virus G protein. In addition, treatment of cells or mice with lipopolysaccharide (LPS) caused increased levels of mA3 expression and rendered them resistant to MMTV infection. Alpha interferon treatment had a similar effect. This LPS-induced resistance to infection was seen only in mA3(+/+) mice and not in mA3(-/-) mice, arguing that mA3 is the major anti-MMTV restriction factor that is induced upon DC maturation. Thus, increasing the levels of this intrinsic antiretroviral factor in vivo can lead to increased levels of restriction because of higher levels of both cell-intrinsic as well as virion-packaged APOBEC3.
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Asparuhova MB, Barde I, Trono D, Schranz K, Schümperli D. Development and characterization of a triple combination gene therapy vector inhibiting HIV-1 multiplication. J Gene Med 2008; 10:1059-70. [PMID: 18642399 DOI: 10.1002/jgm.1238] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND RNA-based approaches are promising for long-term gene therapy against HIV-1. They can target virtually any step of the viral replication cycle. It is also possible to combine anti-HIV-1 transgenes targeting different facets of HIV replication to compensate for limitations of any individual construct, maximizing efficacy and decreasing chances of escape mutations. We have previously developed two strategies to inhibit HIV-1 multiplication. One was a short hairpin RNA targeting the host factor cyclophilin A implicated in HIV-1 replication. Additionally, an antisense derivative of U7 small nuclear RNA was designed to induce the skipping of the HIV-1 Tat and Rev internal exons. RESULTS In the present study, we have established an additional tRNAval promoter-driven shRNA against the coding sequence of viral infectivity factor. When human T-cell lines or primary CD4+ T cells are transduced with a triple lentiviral vector encoding these three therapeutic RNAs, HIV-1 multiplication is very efficiently suppressed. Moreover, all three therapeutic RNAs exhibit antiviral effects at early stages of the viral replication cycle (i.e. prior to viral cDNA integration or gene expression). CONCLUSIONS These findings make this triple lentiviral vector an attractive candidate for a gene therapy against HIV/AIDS.
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Mouse APOBEC3 restricts friend leukemia virus infection and pathogenesis in vivo. J Virol 2008; 82:10998-1008. [PMID: 18786991 DOI: 10.1128/jvi.01311-08] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several members of the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like complex 3 (APOBEC3) family in primates act as potent inhibitors of retroviral replication. However, lentiviruses have evolved mechanisms to specifically evade host APOBEC3. Likewise, murine leukemia viruses (MuLV) exclude mouse APOBEC3 from the virions and cleave virion-incorporated APOBEC3. Although the betaretrovirus mouse mammary tumor virus has been shown to be susceptible to mouse APOBEC3, it is not known if APOBEC3 has a physiological role in restricting more widely distributed and long-coevolved mouse gammaretroviruses. The pathogenicity of Friend MuLV (F-MuLV) is influenced by several host genes: some directly restrict the cell entry or integration of the virus, while others influence the host immune responses. Among the latter, the Rfv3 gene has been mapped to chromosome 15 in the vicinity of the APOBEC3 locus. Here we have shown that polymorphisms at the mouse APOBEC3 locus indeed influence F-MuLV replication and pathogenesis: the APOBEC3 alleles of F-MuLV-resistant C57BL/6 and -susceptible BALB/c mice differ in their sequences and expression levels in the hematopoietic tissues and in their abilities to restrict F-MuLV replication both in vitro and in vivo. Furthermore, upon infection with the pathogenic Friend virus complex, (BALB/c x C57BL/6)F(1) mice displayed an exacerbated erythroid cell proliferation when the mice carried a targeted disruption of the C57BL/6-derived APOBEC3 allele. These results indicate, for the first time, that mouse APOBEC3 is a physiologically functioning restriction factor to mouse gammaretroviruses.
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Knoepfel SA, Salisch NC, Huelsmann PM, Rauch P, Walter H, Metzner KJ. Comparison of G-to-A mutation frequencies induced by APOBEC3 proteins in H9 cells and peripheral blood mononuclear cells in the context of impaired processivities of drug-resistant human immunodeficiency virus type 1 reverse transcriptase variants. J Virol 2008; 82:6536-45. [PMID: 18448538 PMCID: PMC2447050 DOI: 10.1128/jvi.00554-08] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Accepted: 04/16/2008] [Indexed: 11/20/2022] Open
Abstract
APOBEC3 proteins can inhibit human immunodeficiency virus type 1 (HIV-1) replication by inducing G-to-A mutations in newly synthesized viral DNA. However, HIV-1 is able to overcome the antiretroviral activity of some of those enzymes by the viral protein Vif. We investigated the impact of different processivities of HIV-1 reverse transcriptases (RT) on the frequencies of G-to-A mutations introduced by APOBEC3 proteins. Wild-type RT or the M184V, M184I, and K65R+M184V RT variants, which are increasingly impaired in their processivities, were used in the context of a vif-deficient molecular HIV-1 clone to infect H9 cells and peripheral blood mononuclear cells (PBMCs). After two rounds of infection, a part of the HIV-1 env gene was amplified, cloned, and sequenced. The M184V mutation led to G-to-A mutation frequencies that were similar to those of the wild-type RT in H9 cells and PBMCs. The frequencies of G-to-A mutations were increased after infection with the M184I virus variant. This effect was augmented when using the K65R+M184V virus variant (P < 0.001). Overall, the G-to-A mutation frequencies were lower in PBMCs than in H9 cells. Remarkably, 38% +/- 18% (mean +/- standard deviation) of the env clones derived from PBMCs did not harbor any G-to-A mutation. This was rarely observed in H9 cells (3% +/- 3%). Our data imply that the frequency of G-to-A mutations induced by APOBEC3 proteins can be influenced by the processivities of HIV-1 RT variants. The high number of nonmutated clones derived from PBMCs leads to several hypotheses, including that additional antiretroviral mechanisms of APOBEC3 proteins other than their deamination activity might be involved in the inhibition of vif-deficient viruses.
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Affiliation(s)
- Stefanie Andrea Knoepfel
- University of Erlangen-Nuremberg, Institute of Clinical and Molecular Virology, Schlossgarten 4, 91054 Erlangen, Germany
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Insulin-like growth factor II mRNA binding protein 1 associates with Gag protein of human immunodeficiency virus type 1, and its overexpression affects virus assembly. J Virol 2008; 82:5683-92. [PMID: 18385235 DOI: 10.1128/jvi.00189-08] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The assembly of human immunodeficiency virus type 1 (HIV-1) particles is driven by viral Gag protein. This function of Gag not only benefits from its self-multimerization property but also depends on its interaction with a number of cellular factors such as TSG101 and ALIX/AIP1 that promote virus budding and release from cell surfaces. However, interaction with Gag also allows some cellular factors such as APOBEC3G and Trim5alpha to access viral replication machinery and block viral replication. In this study, we report a new HIV-1 Gag-binding factor named insulin-like growth factor II mRNA binding protein 1 (IMP1). Gag-IMP1 interaction requires the second zinc finger of the nucleocapsid (NC) domain of Gag and the KH3 and KH4 domains of IMP1. A fourfold reduction of HIV-1 infectivity was seen with overexpression of the wild-type IMP1 and its mutant that is able to interact with Gag but not with overexpression of IMP1 mutants exhibiting Gag-binding deficiency. The decreased viral infectivity was further shown as a result of diminished viral RNA packaging, abrogated Gag processing on the cellular membranes, and impeded maturation of virus particles. Together, these results demonstrate that IMP1 interacts with HIV-1 Gag protein and is able to block the formation of infectious HIV-1 particles.
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Votteler J, Schubert U. Ubiquitin ligases as therapeutic targets in HIV-1 infection. Expert Opin Ther Targets 2008; 12:131-43. [PMID: 18208363 DOI: 10.1517/14728222.12.2.131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Introduction of highly active antiretroviral therapy has led to a profound reduction in human immunodeficiency virus (HIV) related mortality; although, the complete eradication of the virus from infected individuals has never been achieved. In addition, due to the high mutation and evolution rate, drug-resistant viruses are continuously emerging. OBJECTIVE Genetically more stable cellular pathways represent attractive targets for innovative antiviral strategies, especially the ubiquitin proteasome system, which regulates various steps in the HIV replication cycle. METHODS This review focuses on certain interactions of HIV and E3 ligases as a major player in the ubiquitin proteasome system. RESULTS/CONCLUSION Due to the importance in HIV replication, and together with the high substrate specificity, E3 ligases can be considered as bona fide targets to interfere with HIV infection.
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Affiliation(s)
- Jörg Votteler
- University of Erlangen-Nuremberg, Institute of Clinical and Molecular Virology, Schlossgarten 4, 91054 Erlangen, Germany.
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Browne EP, Littman DR. Species-specific restriction of apobec3-mediated hypermutation. J Virol 2008; 82:1305-13. [PMID: 18032489 PMCID: PMC2224457 DOI: 10.1128/jvi.01371-07] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2007] [Accepted: 11/08/2007] [Indexed: 11/20/2022] Open
Abstract
Apobec proteins are a family of cellular cytidine deaminases, among which several members have been shown to have potent antiviral properties. This antiviral activity is associated with the ability to cause hypermutation of retroviral cDNA. However, recent research has indicated that Apobec proteins are also able to inhibit retroviruses by other mechanisms that are independent of their deaminase activity. We have compared the antiviral activities of human and murine Apobec3 (A3) proteins, and we have found that, consistent with previous reports, human immunodeficiency virus (HIV) is able to resist human A3G but is sensitive to murine A3, whereas murine leukemia virus (MLV) is relatively resistant to murine A3 (mA3) but sensitive to human A3G. In contrast to previous studies, we observed that mA3 is packaged efficiently into MLV particles. The C-terminal cytidine deaminase domain (CDD2) is required for packaging of mA3 into MLV particles, and packaging did not depend on the MLV viral RNA. However, mA3 packed into MLV particles failed to cause hypermutation of viral DNA, indicating that its deaminase activity is blocked or inhibited. hA3G also caused significantly less hypermutation of MLV than of HIV DNA. Both mA3 and the splice variant mA3Delta5 exhibited some residual antiviral activity against MLV and caused a reduction in the ability of MLV particles to generate reverse transcription products. These results suggest that MLV has evolved specific mechanisms to block the ability of Apobec proteins to mediate deaminase-dependent hypermutation.
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Affiliation(s)
- Edward P Browne
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, 540 First Ave., Second Floor, New York, NY 10016, USA
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The DNA deaminase activity of human APOBEC3G is required for Ty1, MusD, and human immunodeficiency virus type 1 restriction. J Virol 2008; 82:2652-60. [PMID: 18184715 DOI: 10.1128/jvi.02391-07] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human APOBEC3G and several other APOBEC3 proteins have been shown to inhibit the replication of a variety of retrotransposons and retroviruses. All of these enzymes can deaminate cytosines within single-strand DNA, but the overall importance of this conserved activity in retroelement restriction has been questioned by reports of deaminase-independent mechanisms. Here, three distinct retroelements, a yeast retrotransposon, Ty1, a murine endogenous retrovirus, MusD, and a lentivirus, human immunodeficiency virus type 1 (HIV-1), were used to evaluate the relative contributions of deaminase-dependent and -independent mechanisms. Although human APOBEC3G can restrict the replication of all three of these retroelements, APOBEC3G lacking the catalytic glutamate (E259Q) was clearly defective. This phenotype was particularly clear in experiments with low levels of APOBEC3G expression. In contrast, purposeful overexpression of APOBEC3G-E259Q was able to cause modest to severe reductions in the replication of Ty1, MusD, and HIV-1(DeltaVif). The importance of these observations was highlighted by data showing that CEM-SS T-cell lines expressing near-physiologic levels of APOBEC3G-E259Q failed to inhibit the replication of HIV-1(DeltaVif), whereas similar levels of wild-type APOBEC3G fully suppressed virus infectivity. Despite the requirement for DNA deamination, uracil DNA glycosylase did not modulate APOBEC3G-dependent restriction of Ty1 or HIV-1(DeltaVif), further supporting prior studies indicating that the major uracil excision repair system of cells is not involved. In conclusion, the absolute requirement for the catalytic glutamate of APOBEC3G in Ty1, MusD, and HIV-1 restriction strongly indicates that DNA cytosine deamination is an essential part of the mechanism.
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Abstract
OBJECTIVE IL-27 is a novel anti-HIV cytokine that inhibits HIV-1 replication in both CD4 T cells and monocyte-derived macrophages (MDM) as IFN-alpha does. To elucidate the mechanism of the antiviral activity, we compared the activity and the gene expression profile of IL-27-treated cells with that of IFN-alpha-treated cells. METHODS CD4 T cells and monocytes were isolated from peripheral blood mononuclear cells of healthy donors. CD4 T cells were stimulated with phytohemagglutinin, and MDM were induced from monocytes using macrophage-colony stimulating factor. HIV-1 replication was monitored by p24 antigen capture assay. The gene expression profiles were analysed using DNA microarray analysis. The increase in the expression of IFN-inducible genes (IFIG) was confirmed by the Quantigene plex assay. RESULTS Both cytokines preferentially inhibited HIV-1 replication in MDM compared with CD4 T cells. Quantitative real time polymerase chain reaction, enzyme-linked immunosorbent assay and neutralization assay using anti-IFN indicated that IFN-alpha, IFN-beta and IFN-gamma had no significant impact on IL-27-mediated HIV inhibition. DNA microarray analysis illustrated that IFN-alpha induced 33 and 18 IFIG in MDM and CD4 T cells, respectively. IL-27 induced 28 IFIG in MDM and five IFIG in CD4 T cells. The quantitative assay confirmed that IL-27 activated genes of RNA-dependent kinase, oligoadenylate synthetase, myxovirus protein, and apolipoprotein B messenger RNA-editing enzyme-catalytic polypeptide-like 3G. CONCLUSION IL-27 differentially regulates the gene expression between CD4 T cells and MDM. IL-27 significantly induces antiviral genes in MDM as does IFN-alpha, suggesting that IL-27 inhibits HIV replication in MDM via mechanism(s) similar to that of IFN-alpha.
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Role of APOBEC3G/F-mediated hypermutation in the control of human immunodeficiency virus type 1 in elite suppressors. J Virol 2007; 82:3125-30. [PMID: 18077705 DOI: 10.1128/jvi.01533-07] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While many studies show that the APOBEC3 family of cytidine deaminases can inhibit human immunodeficiency virus type 1 (HIV-1) replication, the clinical significance of this host defense mechanism is unclear. Elite suppressors are HIV-1-infected individuals who maintain viral loads below 50 copies/ml without antiretroviral therapy. To determine the role of APOBEC3G/F proteins in the control of viremia in these patients, we used a novel assay to measure the frequency of hypermutated proviral genomes. In most elite suppressors, the frequency was not significantly different than that observed in patients on highly active antiretroviral therapy. Thus, enhanced APOBEC3 activity alone cannot explain the ability of elite suppressors to control viremia.
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Aguiar RS, Lovsin N, Tanuri A, Peterlin BM. Vpr.A3A chimera inhibits HIV replication. J Biol Chem 2007; 283:2518-25. [PMID: 18057006 DOI: 10.1074/jbc.m706436200] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Several APOBEC3 proteins (A3F and A3G), that are cytidine deaminases restrict human immunodeficiency virus (HIV) replication in the absence of the viral infectivity factor (Vif) protein. However, Vif leads to their degradation and counteracts their effects. Another member, A3A, restricts some retrotransposons and another virus but not HIV. We reasoned that this failure was due to the lack of appropriate targeting. Thus, we fused A3A to another viral protein, Vpr, which binds p6 in Gag and is incorporated into viral cores. Indeed, the Vpr.A3A chimera but not A3A was found abundantly in the viral core. It also restricted potently the replication of HIV and simian immunodeficiency virus in the presence and absence of Vif. Because we identified a high frequency of G to A mutations in viral cDNAs, this antiviral activity was mediated by DNA editing. Interestingly, our fusion protein did not restrict murine leukemia virus, which does not incorporate Vpr. Thus, by targeting appropriately a potent single domain cytidine deaminase, we rendered HIV and simian immunodeficiency virus restriction resistant to Vif.
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Affiliation(s)
- Renato S Aguiar
- Department of Medicine, Microbiology, and Immunology, University of California at San Francisco, 533 Parnassus Avenue, San Francisco, CA 94143-0703, USA
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Miller JH, Presnyak V, Smith HC. The dimerization domain of HIV-1 viral infectivity factor Vif is required to block virion incorporation of APOBEC3G. Retrovirology 2007; 4:81. [PMID: 18036235 PMCID: PMC2222665 DOI: 10.1186/1742-4690-4-81] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 11/24/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The HIV-1 accessory protein known as viral infectivity factor or Vif binds to the host defence factor human APOBEC3G (hA3G) and prevents its assembly with viral particles and mediates its elimination through ubiquitination and degradation by the proteosomal pathway. In the absence of Vif, hA3G becomes incorporated within viral particles. During the post entry phase of infection, hA3G attenuates viral replication by binding to the viral RNA genome and deaminating deoxycytidines to form deoxyuridines within single stranded DNA regions of the replicated viral genome. Vif dimerization has been reported to be essential for viral infectivity but the mechanistic requirement for Vif multimerization is unknown. RESULTS We demonstrate that a peptide antagonist of Vif dimerization fused to the cell transduction domain of HIV TAT suppresses live HIV-1 infectivity. We show rapid cellular uptake of the peptide and cytoplasmic distribution. Robust suppression of viral infectivity was dependent on the expression of Vif and hA3G. Disruption of Vif multimerization resulted in the production of virions with markedly increased hA3G content and reduced infectivity. CONCLUSION The role of Vif multimerization in viral infectivity of nonpermissive cells has been validated with an antagonist of Vif dimerization. An important part of the mechanism for this antiretroviral effect is that blocking Vif dimerization enables hA3G incorporation within virions. We propose that Vif multimers are required to interact with hA3G to exclude it from viral particles during their assembly. Blocking Vif dimerization is an effective means of sustaining hA3G antiretroviral activity in HIV-1 infected cells. Vif dimerization is therefore a validated target for therapeutic HIV-1/AIDS drug development.
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Affiliation(s)
- James H Miller
- OyaGen, Inc, 601 Elmwood Ave,, Rochester, NY 14642, USA.
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Thielen BK, Klein KC, Walker LW, Rieck M, Buckner JH, Tomblingson GW, Lingappa JR. T cells contain an RNase-insensitive inhibitor of APOBEC3G deaminase activity. PLoS Pathog 2007; 3:1320-34. [PMID: 17892323 PMCID: PMC1993843 DOI: 10.1371/journal.ppat.0030135] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Accepted: 07/27/2007] [Indexed: 12/22/2022] Open
Abstract
The deoxycytidine deaminase APOBEC3G (A3G) is expressed in human T cells and inhibits HIV-1 replication. When transfected into A3G-deficient epithelial cell lines, A3G induces catastrophic hypermutation by deaminating the HIV-1 genome. Interestingly, studies suggest that endogenous A3G in T cells induces less hypermutation than would be expected. However, to date, the specific deaminase activity of endogenous A3G in human CD4+ T cells has not been examined directly. Here, we compared deaminase activity of endogenous and exogenous A3G in various human cell lines using a standard assay and a novel, quantitative, high-throughput assay. Exogenous A3G in epithelial cell lysates displayed deaminase activity only following RNase treatment, as expected given that A3G is known to form an enzymatically inactive RNA-containing complex. Surprisingly, comparable amounts of endogenous A3G from T cell lines or from resting or activated primary CD4+ T cells exhibited minimal deaminase activity, despite RNase treatment. Specific deaminase activity of endogenous A3G in H9, CEM, and other T cell lines was up to 36-fold lower than specific activity of exogenous A3G in epithelial-derived cell lines. Furthermore, RNase-treated T cell lysates conferred a dose-dependent inhibition to epithelial cell lysates expressing enzymatically active A3G. These studies suggest that T cells, unlike epithelial-derived cell lines, express an unidentified RNase-resistant factor that inhibits A3G deaminase activity. This factor could be responsible for reduced levels of hypermutation in T cells, and its identification and blockade could offer a means for increasing antiretroviral intrinsic immunity of T cells. APOBEC3G (A3G) is an antiviral enzyme that is expressed in human T cells and macrophages, which are the cell types infected by HIV. Early in the HIV life cycle, the HIV RNA genome is reverse transcribed into DNA. A3G can modify this DNA enzymatically, leading to high rates of mutation such that the virus can no longer replicate. To date, most studies of A3G's enzymatic activity have utilized cell lines (293T and HeLa) that can be transfected to express A3G but do not express it endogenously. A report of unexpectedly low levels of mutation in viral DNA from HIV-infected human T cells led us to investigate regulation of A3G enzymatic activity in T cells. We developed a high-throughput assay to compare the enzymatic activity of endogenous A3G in T cells versus transfected (exogenous) A3G. Surprisingly, enzymatic activity of A3G from human T cell lines and primary T cells was very low relative to A3G from transfected cells, even when corrected for A3G protein amount. Moreover, T cell lysates inhibited enzymatic activity of exogenously expressed A3G. These data suggest that enzymatic activity of endogenous A3G in human T cells is inhibited by an uncharacterized mechanism that may protect the host from this DNA mutator and could have important implications for A3G antiviral activity in vivo.
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Affiliation(s)
- Beth K Thielen
- Department of Pathobiology, University of Washington, Seattle, Washington, United States of America
| | - Kevin C Klein
- Department of Pathobiology, University of Washington, Seattle, Washington, United States of America
| | - Lorne W Walker
- Department of Pathobiology, University of Washington, Seattle, Washington, United States of America
| | - Mary Rieck
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Jane H Buckner
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Garrett W Tomblingson
- Department of Pathobiology, University of Washington, Seattle, Washington, United States of America
| | - Jaisri R Lingappa
- Department of Pathobiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- * To whom correspondence should be addressed. E-mail:
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Abstract
The majority of current anti-HIV drugs target the viral reverse transcriptase or protease enzymes. However, enfuvirtide and maraviroc are drugs that have been US FDA approved recently and which function by inhibiting virus cell binding and entry which normally occurs through the interaction of the viral envelope protein with its cellular coreceptor. As HIV-1 utilizes many cellular cofactors during its replication cycle, there are a number of other protein–protein interactions that can serve as targets for anti-HIV drug development. In this review article we discuss the general method used to identify anti-HIV drugs that function through targeting protein–protein interactions. We also discuss the currently known cellular cofactors that may serve as targets in future drugs screens.
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Affiliation(s)
- Andrew P Rice
- Baylor College of Medicine, Department of Molecular Virology & Microbiology, Houston, TX 77030, USA
| | - Richard E Sutton
- Baylor College of Medicine, Department of Molecular Virology & Microbiology, Houston, TX 77030, USA
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Human immunodeficiency virus type 1 Vif functionally interacts with diverse APOBEC3 cytidine deaminases and moves with them between cytoplasmic sites of mRNA metabolism. J Virol 2007; 82:987-98. [PMID: 17977970 DOI: 10.1128/jvi.01078-07] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vif(IIIB), which has been a standard model for the viral infectivity factor of human immunodeficiency virus type 1 (HIV-1), binds the cytidine deaminase APOBEC3G (A3G) and induces its degradation, thereby precluding its lethal incorporation into assembling virions. Additionally, Vif(IIIB) less efficiently degrades A3F, another potent anti-HIV-1 cytidine deaminase. Although the APOBEC3 paralogs A3A, A3B, and A3C have weaker anti-HIV-1 activities and are only partially degraded by Vif(IIIB), we found that Vif(IIIB) induces their emigration from the nucleus to the cytosol and thereby causes net increases in the cytosolic concentrations and anti-HIV-1 activities of A3A and A3B. In contrast, some other Vifs, exemplified by Vif(HXB2) and Vif(ELI-1), much more efficiently degrade and thereby neutralize all APOBEC3s. Studies focused mainly on A3F imply that it occurs associated with mRNA-PABP1 in translationally active polysomes and to a lesser extent in mRNA processing bodies (P-bodies). A3F appears to stabilize the P-bodies with which it is associated. A correspondingly small proportion of Vif(IIIB) also localizes in P-bodies in an A3F-dependent manner. Stress causes A3A, A3B, A3C, and A3F to colocalize efficiently with Vif(IIIB) and mRNA-PABP1 complexes in stress granules in a manner that is prevented by cycloheximide, an inhibitor of translational elongation. Coimmunoprecipitation studies suggest that Vifs from different HIV-1 isolates associate with all tested APOBEC3s. Thus, Vifs interact closely with structurally diverse APOBEC3s, with effects on their subcellular localization, degradation rates, and antiviral activities. Cytosolic APOBEC3-Vif complexes are predominantly bound to mRNAs that dynamically move between translationally active and storage or processing pools.
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40
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Jónsson SR, LaRue RS, Stenglein MD, Fahrenkrug SC, Andrésdóttir V, Harris RS. The restriction of zoonotic PERV transmission by human APOBEC3G. PLoS One 2007; 2:e893. [PMID: 17849022 PMCID: PMC1963317 DOI: 10.1371/journal.pone.0000893] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Accepted: 08/13/2007] [Indexed: 01/27/2023] Open
Abstract
The human APOBEC3G protein is an innate anti-viral factor that can dominantly inhibit the replication of some endogenous and exogenous retroviruses. The prospects of purposefully harnessing such an anti-viral defense are under investigation. Here, long-term co-culture experiments were used to show that porcine endogenous retrovirus (PERV) transmission from pig to human cells is reduced to nearly undetectable levels by expressing human APOBEC3G in virus-producing pig kidney cells. Inhibition occurred by a deamination-independent mechanism, likely after particle production but before the virus could immortalize by integration into human genomic DNA. PERV inhibition did not require the DNA cytosine deaminase activity of APOBEC3G and, correspondingly, APOBEC3G-attributable hypermutations were not detected. In contrast, over-expression of the sole endogenous APOBEC3 protein of pigs failed to interfere significantly with PERV transmission. Together, these data constitute the first proof-of-principle demonstration that APOBEC3 proteins can be used to fortify the innate anti-viral defenses of cells to prevent the zoonotic transmission of an endogenous retrovirus. These studies suggest that human APOBEC3G-transgenic pigs will provide safer, PERV-less xenotransplantation resources and that analogous cross-species APOBEC3-dependent restriction strategies may be useful for thwarting other endogenous as well as exogenous retrovirus infections.
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Affiliation(s)
- Stefán R. Jónsson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Experimental Pathology, University of Iceland, Reykjavík, Iceland
| | - Rebecca S. LaRue
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Mark D. Stenglein
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Scott C. Fahrenkrug
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Animal Sciences, University of Minnesota, St. Paul, Minnesota, United States of America
| | | | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Arnold and Mabel Beckman Center for Transposon Research, University of Minnesota, Minneapolis, Minnesota, United States of America
- * To whom correspondence should be addressed. E-mail:
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Suh HS, Zhao ML, Rivieccio M, Choi S, Connolly E, Zhao Y, Takikawa O, Brosnan CF, Lee SC. Astrocyte indoleamine 2,3-dioxygenase is induced by the TLR3 ligand poly(I:C): mechanism of induction and role in antiviral response. J Virol 2007; 81:9838-50. [PMID: 17626075 PMCID: PMC2045380 DOI: 10.1128/jvi.00792-07] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Indoleamine 2,3-dioxygenase (IDO) is the first and rate-limiting enzyme in the kynurenine pathway of tryptophan catabolism and has been implicated in neurotoxicity and suppression of the antiviral T-cell response in HIV encephalitis (HIVE). Here we show that the Toll-like receptor 3 (TLR3) ligand poly(I:C) (PIC) induces the expression of IDO in human astrocytes. PIC was less potent than gamma interferon (IFN-gamma) but more potent than IFN-beta in inducing IDO. PIC induction of IDO was mediated in part by IFN-beta but not IFN-gamma, and both NF-kappaB and interferon regulatory factor 3 (IRF3) were required. PIC also upregulated TLR3, thereby augmenting the primary (IFN-beta) and secondary (IDO and viperin) response genes upon subsequent stimulation with PIC. In HIVE, the transcripts for TLR3, IFN-beta, IDO, and viperin were increased and IDO immunoreactivity was detected in reactive astrocytes as well as macrophages and microglia. PIC caused suppression of intracellular replication of human immunodeficiency virus pseudotyped with vesicular stomatitis virus G protein and human cytomegalovirus in a manner dependent on IRF3 and IDO. The involvement of IDO was demonstrated by partial but significant reversal of the PIC-mediated antiviral effect by IDO RNA interference and/or tryptophan supplementation. Importantly, the cytokine interleukin-1 abolished IFN-gamma-induced IDO enzyme activity in a nitric oxide-dependent manner without suppressing protein expression. Our results demonstrate that IDO is an innate antiviral protein induced by double-stranded RNA and suggest a therapeutic utility for PIC in human viral infections. They also show that IDO activity can be dissociated from protein expression, indicating that the local central nervous system cytokine and nitric oxide environment determines IDO function.
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MESH Headings
- Astrocytes/enzymology
- Astrocytes/immunology
- Astrocytes/virology
- Cells, Cultured
- Cytokines/immunology
- Cytokines/pharmacology
- Cytomegalovirus/genetics
- Cytomegalovirus/immunology
- Cytomegalovirus Infections/enzymology
- Cytomegalovirus Infections/genetics
- Cytomegalovirus Infections/immunology
- Encephalitis, Viral/enzymology
- Encephalitis, Viral/genetics
- Encephalitis, Viral/immunology
- Gene Expression Regulation, Enzymologic/drug effects
- Gene Expression Regulation, Enzymologic/genetics
- Gene Expression Regulation, Enzymologic/immunology
- HIV Infections/enzymology
- HIV Infections/genetics
- HIV Infections/immunology
- HIV-1/genetics
- HIV-1/immunology
- Humans
- Indoleamine-Pyrrole 2,3,-Dioxygenase/biosynthesis
- Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics
- Indoleamine-Pyrrole 2,3,-Dioxygenase/immunology
- Interferon Inducers/pharmacology
- Interferon Regulatory Factor-3/immunology
- Interferon Regulatory Factor-3/metabolism
- Kynurenine/genetics
- Kynurenine/immunology
- Kynurenine/metabolism
- Ligands
- Macrophages/enzymology
- Macrophages/immunology
- Macrophages/virology
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/immunology
- Membrane Glycoproteins/metabolism
- Microglia/enzymology
- Microglia/immunology
- Microglia/virology
- NF-kappa B/immunology
- NF-kappa B/metabolism
- Nitric Oxide/immunology
- Nitric Oxide/metabolism
- Oxidoreductases Acting on CH-CH Group Donors
- Poly I-C/pharmacology
- Proteins/immunology
- Proteins/metabolism
- Toll-Like Receptor 3/agonists
- Toll-Like Receptor 3/immunology
- Toll-Like Receptor 3/metabolism
- Tryptophan/immunology
- Tryptophan/metabolism
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/immunology
- Viral Envelope Proteins/metabolism
- Virus Replication/drug effects
- Virus Replication/genetics
- Virus Replication/immunology
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Affiliation(s)
- Hyeon-Sook Suh
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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Domingo E, Gomez J. Quasispecies and its impact on viral hepatitis. Virus Res 2007; 127:131-50. [PMID: 17349710 PMCID: PMC7125676 DOI: 10.1016/j.virusres.2007.02.001] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Revised: 01/11/2007] [Accepted: 02/03/2007] [Indexed: 12/17/2022]
Abstract
Quasispecies dynamics mediates adaptability of RNA viruses through a number of mechanisms reviewed in the present article, with emphasis on the medical implications for the hepatitis viruses. We discuss replicative and non-replicative molecular mechanisms of genome variation, modulating effects of mutant spectra, and several modes of viral evolution that can affect viral pathogenesis. Relevant evolutionary events include the generation of minority virus variants with altered functional properties, and alterations of mutant spectrum complexity that can affect disease progression or response to treatment. The widespread occurrence of resistance to antiviral drugs encourages new strategies to control hepatic viral disease such as combination therapies and lethal mutagenesis. In particular, ribavirin may be exerting in some cases its antiviral activity with participation of its mutagenic action. Despite many unanswered questions, here we document that quasispecies dynamics has provided an interpretation of the adaptability of the hepatitis viruses, with features conceptually similar to those observed with other RNA viruses, a reflection of the common underlying Darwinian principles.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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Prochnow C, Bransteitter R, Klein MG, Goodman MF, Chen XS. The APOBEC-2 crystal structure and functional implications for the deaminase AID. Nature 2007; 445:447-51. [PMID: 17187054 DOI: 10.1038/nature05492] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Accepted: 11/28/2006] [Indexed: 12/22/2022]
Abstract
APOBEC-2 (APO2) belongs to the family of apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) polypeptides, which deaminates mRNA and single-stranded DNA. Different APOBEC members use the same deamination activity to achieve diverse human biological functions. Deamination by an APOBEC protein called activation-induced cytidine deaminase (AID) is critical for generating high-affinity antibodies, and deamination by APOBEC-3 proteins can inhibit retrotransposons and the replication of retroviruses such as human immunodeficiency virus and hepatitis B virus. Here we report the crystal structure of APO2. APO2 forms a rod-shaped tetramer that differs markedly from the square-shaped tetramer of the free nucleotide cytidine deaminase, with which APOBEC proteins share considerable sequence homology. In APO2, two long alpha-helices of a monomer structure prevent the formation of a square-shaped tetramer and facilitate formation of the rod-shaped tetramer via head-to-head interactions of two APO2 dimers. Extensive sequence homology among APOBEC family members allows us to test APO2 structure-based predictions using AID. We show that AID deamination activity is impaired by mutations predicted to interfere with oligomerization and substrate access. The structure suggests how mutations in patients with hyper-IgM-2 syndrome inactivate AID, resulting in defective antibody maturation.
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Affiliation(s)
- Courtney Prochnow
- Molecular and Computational Biology, University of Southern California Los Angeles, California 90089, USA
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Abstract
More than a decade has passed since the discovery that the peptidyl prolyl isomerase cyclophilin A (CypA) specifically binds to a proline-rich sequence in HIV-1 capsid (CA) and is thereby incorporated into viral particles. Since then, a variety of possible functions of CypA in the HIV-1 replication cycle have been intensively investigated, but the biological function of this interaction remains to be determined. The binding of CypA to CA increases HIV-1 infectivity in human cells, but promotes an anti-HIV-1 restriction activity in cells from nonhuman primates. Numerous studies have been undertaken to understand the paradoxical effects of CypA and, along with the parallel discovery of the restriction factor tripartite motif 5α, our understanding of how CypA modulates HIV-1 infectivity has now been changed completely. However, 13 years after its discovery, the biological function of the specific interaction between HIV-1 CA and CypA is still not fully understood. Even though much insight has been provided to date, many questions remain unanswered.
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Affiliation(s)
- Jörg Votteler
- Institute for Clinical & Molecular Virology, University of Erlangen-Nürnberg, Schlossgarten 4, 91054 Erlangen, Germany
| | - Victor Wray
- Helmholtz Centre for Infection Research, Department of Structural Biology Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Ulrich Schubert
- Institute for Clinical & Molecular Virology, University of Erlangen-Nürnberg, Schlossgarten 4, 91054 Erlangen, Germany
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Fujimuro M, Hayward SD, Yokosawa H. Molecular piracy: manipulation of the ubiquitin system by Kaposi's sarcoma-associated herpesvirus. Rev Med Virol 2007; 17:405-22. [PMID: 17688306 DOI: 10.1002/rmv.549] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Ubiquitination, one of several post-translational protein modifications, plays a key role in the regulation of cellular events, including protein degradation, signal transduction, endocytosis, protein trafficking, apoptosis and immune responses. Ubiquitin attachment at the lysine residue of cellular factors acts as a signal for endocytosis and rapid degradation by the 26S proteasome. It has recently been observed that viruses, especially oncogenic herpesviruses, utilise molecular piracy by encoding their own proteins to interfere with regulation of cell signalling. Kaposi's sarcoma- associated herpesvirus (KSHV) manipulates the ubiquitin system to facilitate cell proliferation, anti-apoptosis and evasion from immunity. In this review, we will describe the strategies used by KSHV at distinct stages of the viral life-cycle to control the ubiquitin system and promote oncogenesis and viral persistence.
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Affiliation(s)
- Masahiro Fujimuro
- Faculty of Pharmaceutical Sciences, Department of Biochemistry, Hokkaido University, Kita-ku, Sapporo, Japan.
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