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Yang X, Cheng A, Wang M, Jia R, Sun K, Pan K, Yang Q, Wu Y, Zhu D, Chen S, Liu M, Zhao XX, Chen X. Structures and Corresponding Functions of Five Types of Picornaviral 2A Proteins. Front Microbiol 2017; 8:1373. [PMID: 28785248 PMCID: PMC5519566 DOI: 10.3389/fmicb.2017.01373] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 07/06/2017] [Indexed: 11/27/2022] Open
Abstract
Among the few non-structural proteins encoded by the picornaviral genome, the 2A protein is particularly special, irrespective of structure or function. During the evolution of the Picornaviridae family, the 2A protein has been highly non-conserved. We believe that the 2A protein in this family can be classified into at least five distinct types according to previous studies. These five types are (A) chymotrypsin-like 2A, (B) Parechovirus-like 2A, (C) hepatitis-A-virus-like 2A, (D) Aphthovirus-like 2A, and (E) 2A sequence of the genus Cardiovirus. We carried out a phylogenetic analysis and found that there was almost no homology between each type. Subsequently, we aligned the sequences within each type and found that the functional motifs in each type are highly conserved. These different motifs perform different functions. Therefore, in this review, we introduce the structures and functions of these five types of 2As separately. Based on the structures and functions, we provide suggestions to combat picornaviruses. The complexity and diversity of the 2A protein has caused great difficulties in functional and antiviral research. In this review, researchers can find useful information on the 2A protein and thus conduct improved antiviral research.
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Affiliation(s)
- Xiaoyao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Kunfeng Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Kangcheng Pan
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Xin-Xin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
| | - Xiaoyue Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural UniversityChengdu, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural UniversityChengdu, China
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Schünemann K, Connelly S, Kowalczyk R, Sperry J, Wilson IA, Fraser JD, Brimble MA. A simple solid phase, peptide-based fluorescent assay for the efficient and universal screening of HRV 3C protease inhibitors. Bioorg Med Chem Lett 2012; 22:5018-24. [PMID: 22763202 DOI: 10.1016/j.bmcl.2012.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/06/2012] [Indexed: 11/30/2022]
Abstract
With over a 100 different serotypes, the human rhinovirus (HRV) is the major aetiological agent for the common cold, for which only symptomatic treatment is available. HRV maturation and replication is entirely dependent on the activity of a virally encoded 3C protease that represents an attractive target for the development of therapeutics to treat the common cold. Although a variety of small molecules and peptidomimetics have been found to inhibit HRV 3C protease, no universally compatible assay exists to reliably quantify the activity of the enzyme in vitro. Herein we report the development of a universal and robust solid phase peptide assay that utilizes the full HRV-14 3C protease recognition sequence and the release of 5(6)-carboxyfluorescein to sensitively quantify protease activity. This novel assay overcomes several limitations of existing assays allowing for the simple and efficient analysis of HRV-14 3C protease activity facilitating both high-throughput screening and the accurate kinetic study of HRV-14 3C protease inhibitors.
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Affiliation(s)
- Katrin Schünemann
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
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Ettinger A, Ostroff R, Rhihanek M, Dragovich PS, Zalman LS, Patick AK, Prins TJ, Fuhrman SA, Brown EL, Worland ST, Polisky B. An optical thin film assay incorporating rhinovirus protease inhibitors as detector reagents. Antiviral Res 2004; 61:153-9. [PMID: 15168795 DOI: 10.1016/j.antiviral.2003.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2003] [Accepted: 09/09/2003] [Indexed: 11/30/2022]
Abstract
Human rhinoviruses (HRV) are the main cause of the common cold. Viral replication utilizes the activity of the HRV3C protease (3CP) enzyme [Antimicrob. Agents Chemother. 43 (1999) 2444; Antimicrob. Agents Chemother. 44 (2000) 1236]. Therefore, 3CP is an attractive target for antiviral drug development, and a new class of orally bioavailable irreversible 3CP inhibitors has been designed [J. Med. Chem. 45 (2002) 1607]. We have used related inhibitors to develop a rapid test for rhinovirus. The optical immuno assay (OIA) thin film detection technology utilizes an optically coated silicon surface to convert specific molecular binding events into visual color changes by altering the reflective properties of light through molecular thin films. The purpose of this study was to develop a rapid assay for the determination of 3CP combining the Thermo Electron Bio Star OIA technology and the newly designed inhibitor compounds. The advantage of this assay was in its approach, in which therapeutic and diagnostic targets are the same thus allowing patients with detected rhinoviruses to receive optimal treatment. Three different biotinylated inhibitor compounds were synthesized. The length of the spacer between the inhibitor and biotin core was 5, 10, and 15 atoms. These compounds were incorporated into the OIA format for the HRV assay development. A rapid (20 min) OIA test was developed using a 15 atom spacer biotinylated inhibitor (4). Forty different HRV serotypes were studied and thirty three serotypes of these 40 were detected (80%).
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Affiliation(s)
- Anna Ettinger
- Thermo Electron Corp., 331 South 104th Street, Louisville, CO 80027, USA.
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Abstract
Human rhinoviruses (HRV) represent the single most important causative agent of the common cold. The HRV genome encodes an RNA-dependent RNA polymerase (RdRp) designated 3D polymerase that is required for replication of the HRV RNA genome. We have expressed and purified recombinant HRV-16 3D polymerase to near homogeneity from Escherichia coli transformed with an expression plasmid containing the full-length 460 amino acid HRV-16 3D sequence with a methionine at the N-terminus and a glycine-serine linker followed by a 6-histidine affinity tag at the C-terminus. The purified recombinant protein has rifampicin-resistant activity in a poly(A)-dependent poly(U) polymerase assay while corresponding fractions similarly purified from E. coli transformed with an expression plasmid without the HRV-16 3D sequence showed no activity. The optimal conditions for temperature, pH, divalent cations Mg(2+) and Mn(2+), and KCl were determined. The recombinant protein has RNA polymerase activity on homopolymeric templates poly(A) and poly(C) and heteropolymeric RNA templates primed with either RNA or DNA oligonucleotide primers or self-primed by a copy-back mechanism. A unique, secondary structureless heteropolymeric RNA template that is an efficient substrate was developed to facilitate kinetic characterizations of the enzyme. In the presence of Mg(2+), the enzyme displayed strong base and sugar specificity. However, when Mg(2+) was replaced by Mn(2+) specificity for ribonucleotides was lost, utilization of deoxynucleotides became possible and primer-independent activity was observed on the poly(C) template. Zn(2+) was found to inhibit HRV-16 3D polymerase with an IC(50) as low as 0.6 microM by a mechanism distinct from the magnesium ion stimulation. The activity of this 6His-tagged HRV-16 3D polymerase was compared with that of a recombinant HRV-16 3D polymerase expressed without the 6His-tag and was found to be identical. The availability of recombinant rhinovirus RdRp in a purified form will facilitate the structure-function analysis of this enzyme as well as the identification of specific inhibitors to the rhinovirus 3D polymerase that have therapeutic value in the treatment of the common cold.
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Affiliation(s)
- Magdeleine Hung
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA
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Steininger C, Aberle SW, Popow-Kraupp T. Early detection of acute rhinovirus infections by a rapid reverse transcription-PCR assay. J Clin Microbiol 2001; 39:129-33. [PMID: 11136760 PMCID: PMC87691 DOI: 10.1128/jcm.39.1.129-133.2001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The development of a rhinovirus (RV)-RNA-specific reverse transcription (RT)-PCR assay is complicated by the close homology between the RV and enterovirus (EV) genomes in the highly conserved 5'-noncoding region, which is chosen for primer design in most RT-PCR assays. We have developed a sensitive, rapid, and RV-specific nested RT-PCR assay and have used it to test nasopharyngeal aspirates from 556 patients presenting with acute respiratory tract infections. RV RNA was detected by nested RT-PCR not only in all of 52 samples that were RV positive by virus isolation methods but also in 124 of 367 samples that were negative by virus isolation methods and enzyme-linked immunosorbent assay (ELISA). In addition, in 23 of 137 samples that were positive for a different respiratory virus by virus isolation and/or ELISA, RV RNA was detected by RT-PCR. EVs, adenoviruses, respiratory syncytial viruses, coronaviruses, and influenza and parainfluenza viruses, including clinical isolates as well as stock viruses, were not amplified in our RV-specific RT-PCR assay, indicating that this assay was highly specific. The processing time was less than 2 days for the RT-PCR, as opposed to up to 2 weeks for virus isolation. These results indicate that nested RT-PCR is more sensitive than conventional methods for the detection of RV in patients experiencing acute respiratory tract infections and represents the only reliable tool for the early laboratory diagnosis of RV infections. This is especially important in light of new opportunities for therapy currently being developed.
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Affiliation(s)
- C Steininger
- Institute of Virology, University of Vienna, A-1095 Vienna, Austria
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Abstract
Billions of people are infected with respiratory viruses annually. Infants and young children, the elderly, immunocompromised individuals and those debilitated by other diseases or nutritional deficiencies are most at risk for serious disease. There are few vaccines available for use against these viruses, and even where there are (influenza, measles and adenovirus), infections remain common. The continued prevalence of respiratory virus infections has lead to renewed efforts to find safe agents effective against the most medically important respiratory viruses: influenza, respiratory syncytial, parainfluenza, measles, rhino- and adenovirus. Copyright 1999 Harcourt Publishers Ltd.
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Affiliation(s)
- Philip R. Wyde
- Department of Microbiology, Immunology, Baylor College of Medicine, Houston, TX, USA
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